Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session N00: Poster Session II (11am- 2pm CST)Poster Undergrad Friendly
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Room: McCormick Place Exhibit Hall F1 |
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N00.00001: POLYMER PHYSICS
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N00.00002: The elasticity of single flexible polymers using AFM based nanorheology vikhyaat ahlawat The force versus extension curves generated by single molecule technique like AFM curves have been routinely used to describe the entropic elasticity of single polymer chains. These curves are typically modelled with an entropic worm-like chain model to estimate persistence length, a measure of local bending flexibility of chain. However, its estimated value is anomaly low and inconsistent when measured with AFM in high force regime than with other techniques like Magnetic Tweezers in low force regime. To understand this, we performed AFM based experiments on Polyethylene glycol (PEG) polymer by oscillating the AFM cantilever probe externally through excitation of fixed frequency provided to it. We show that a proper quantification of elastic response measured locally and directly by oscillatory rheology technique deviates significantly from conventional force-extension curves. The persistence length obtained by WLC modelling of stiffness-extension data matches well with magnetic tweezers experiments. In addition, polystyrene chain in poor solvent show no deviation in elastic response between oscillatory technique and coventional constant velocity pulling experiments. However, such deviation was observed for polystyrene in good solvent. We attribute this to hydrophobic interaction between monomer units of polystyrene in water. |
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N00.00003: Improving Label-Free Nanoparticle Detection Accuracy in Interferometric Scattering Microscopy (iSCAT) Images Using a Mask R-CNN Machine Learning Framework Michael J Boyle, Russell J Composto, Yale E. Goldman Interferometric Scattering Microscopy (iSCAT) has emerged as powerful technique for imaging nano-sized objects (i.e. proteins, nanoparticles, and viruses) with excellent spatiotemporal resolution without fluorescent labels. However, contrast in iSCAT is based on scattering, and image processing is required to gain meaningful information from experiments. The most essential step in processing, image segmentation, is complicated by strong scattering from features in the background of samples and remains a challenge. We improve upon traditional segmentation algorithms used in iSCAT processing by leveraging the power of instance image segmentation with machine learning using the Mask RCNN architecture. In a novel approach, we create a training dataset by superimposing point spread functions on background images from experiments collected on our iSCAT instrument. We then use transfer learning to train a Mask RCNN network to detect nanoparticles, reducing the time and resources needed for training. Improved performance is demonstrated via processing of a model nanoparticle adsorption experiment. Our processing workflow is not specific to iSCAT imaging, and we anticipate this methodology will improve image analysis in microscopy and single particle tracking research areas in general. |
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N00.00004: Computational reverse-engineering analysis for scattering experiments (CREASE) on thermoresponsive assembly of methylcellulose in aqueous solutions Zijie Wu, Arthi Jayaraman Past studies have shown that methylcellulose (MC) assembles into fibrils in aqueous solutions, with consistent average fibril diameters with varying MC molecular weight and concentration. However, the molecular mechanism of the assembly and the packing of individual MC chains within the fibrils remain unclear. In this study, we use a newly developed coarse-grained model of MC and molecular dynamics simulations to understand the molecular mechanism of assembly and MC chain packing in the fibrils. Taking small angle X-ray scattering (SAXS) profiles for MC solutions obtained experimentally by Bates, Lodge and coworkers [Macromolecules, 2018, 51, 7767-7775] as input to our recently developed machine learning enhanced computational reverse engineering method for scattering analysis (CREASE) [ACS Polymers Au, doi.org/10.1021/acspolymersau.1c00015] we determine the fibrils’ dimensions (length, diameter, flexibility, dispersity) and chain packing within the fibrils. Our computational work provides insight into the intriguing self-assembly of MC into fibrils and gels, and generally, fibrillar network formation in solutions of semiflexible polymers. |
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N00.00005: BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks Fabian Berressem, Arash Nikoubashman Neural networks (NNs) are employed to predict equations of state from a given isotropic pair potential using the virial expansion of the pressure. The NNs are trained with data from molecular dynamics simulations of monoatomic gases and liquids, sampled in the NVT ensemble at various densities. We find that the NNs provide much more accurate results compared to the analytic low-density limit estimate of the second virial coefficient and the Carnahan–Starling equation of state for hard sphere liquids. Furthermore, we design and train NNs for computing (effective) pair potentials from radial pair distribution functions, g(r), a task that is often performed for inverse design and coarse-graining. Providing the NNs with additional information on the forces greatly improves the accuracy of the predictions since more correlations are taken into account; the predicted potentials become smoother, are significantly closer to the target potentials, and are more transferable as a result. |
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N00.00006: Identification of conformer defects associated with tacticity in polymers using Terahertz spectroscopy Nilanjan Mitra Control of tacticity (stereochemistry) is important for controlling polymer properties. Numerous synthetic protocols are used to manipulate polymer stereoregularity. However, still these conformer defects cannot be completely controlled and expensive NMR methods are used to determine the molecular structure of the resultant material. Terahertz spectroscopy (probing the range of 0-400 cm-1 wavenumbers) can be used to identify these defects. A DFT simulation has been done to demonstrate the changes in spectra with presence of racemo and meso dyads in polypropylene molecule. |
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N00.00007: Boson peak of self-healable polymers: terahertz time-domain spectroscopy and low-temperature specific heat measurement Shin Nakagawa, Yuta Fujisawa, Takuzo Aida, Suguru Kitani, Hitoshi Kawaji, Yohei Yamamoto, Tatsuya Mori We investigated the vibrational density of states (VDOS) of self-healable polymers in the terahertz region by terahertz time-domain spectroscopy and low-temperature specific heat measurement. The VDOS determined from the low temperature specific heat measurements showed the boson peak (BP) at about 0.6 THz. The BP in the absorption coefficient (α(ν)) also appeared in α/ν2 plot. Regarding the determinant of the BP frequency of the system of self-healable polymers, it is located between hydrogen-bonded glasses and van der Waals glasses. |
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N00.00008: Relating fractional free volume to physical aging: A study of tunability and molecular weight dependence of physical aging behavior of polystyrene and poly(methyl methacrylate) films Tong Wang, Tong Wei, Xiaobo Lin, John M Torkelson Ellipsometry is used to investigate the physical aging behavior of bulk polystyrene (PS) and poly(methyl methacrylate) (PMMA) films supported on silicon over a relatively large range of molecular weight (MW) and aging quench depth. Here, the aging quench depth is defined as the difference between aging temperature and the glass transition temperature. At shallow quench depth, for both PS and PMMA, ultralow MW films show higher aging rates compared to high MW films. However, at deep quench depth, there is no significant MW dependence of aging rate for PMMA whereas low MW PS shows a lower aging rate compared to high MW PS. The difference of aging behavior in deep and shallow quench depth may be attributed to the interplay of polymer chain mobility and thermodynamic driving force. In the shallow quench depth, we observe correlated MW dependence of fractional free volume and physical aging rate based on which we demonstrate that the physical aging rate of PS can be tuned to be significantly higher by incorporating flexible chain ends. |
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N00.00009: Physical Aging Behavior of Hydroxypropyl Methylcellulose Acetate Succinate via Enthalpy Recovery Studies Yejoon Seo, Rodney Priestley Amorphous solid dispersions (ASDs) utilize the kinetic stability of the amorphous state to stabilize drug molecules within a glassy polymer matrix. Naturally, ASDs are subject to thermodynamic instability that manifests as phase separation between the drug and polymer. The complex relationship between ASD drug stability and physical aging is critical to ASD design and performance but remains understudied. This study investigates the physical aging behavior of hydroxypropyl methylcellulose acetate succinate (HPMCAS). When aged well-below the glass transition temperature (Tg) and upon re-heating, HPMCAS does not access the α-relaxation mechanism and completely devitrifies before Tg. This behavior supports the existence of an alternate equilibrium mechanism that is accessible well-below Tg. Furthermore, the aging rates of HPMCAS near Tg and well-below Tg are calculated and exhibit minor but notable differences, implying that physical aging readily continues even at aging temperatures 80°C below Tg and aging times up to 600 minutes. |
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N00.00010: Predicting the Phase Behavior of Ternary Polymer Solutions Consisting of Two Polymers in a Common Solvent Using Autonomous Experimentation and Machine Learning Boris Rasin, Jeffrey G Ethier, Maneesh K Gupta, Richard A Vaia Knowledge of the phase behavior of multi-component polymer solutions is essential for many technologies, ranging from efficient synthesis to formulation of inks for additive manufacturing. Although the phase behavior has been extensively studied experimentally and theoretically, accurate prediction remains elusive. Recently, machine learning was shown to successfully predict upper, lower, and closed binary polymer solution behavior using previously published co-existence data. Here, we combine automated experimentation and machine learning to expand prediction to the phase behavior of ternary polymer solutions. AI algorithms are used to guide subsequent experiments based on past data to efficiently develop polymer 1-polymer 2-solvent ternary co-existence curves. The resulting data is combined with previously published results, and used to train a machine learning model (e.g. neural network) for generalized prediction of ternary polymer 1-polymer 2-solvent systems. |
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N00.00011: The relaxation dynamics of single flow-stretched polymers in semidilute to concentrated solutions. Neha Tyagi, Binny J Cherayil Recent experiments on the return to equilibrium of solutions of entangled polymers stretched by extensional flows [Zhou and Schroeder, Phys. Rev. Lett 120, 267801 (2018)] have highlighted the possible role of the tube model’s two-step mechanism in the process of chain relaxation. In this paper, motivated by these findings, we use a generalized Langevin equation (GLE) to study the time evolution, under linear mixed flow, of the linear dimensions of a single finitely extensible Rouse polymer in a solution of other polymers. Approximating the memory function of the GLE, which contains the details of the interactions of the Rouse polymer with its surroundings, by a power law defined by two parameters, we show that the decay of the chain’s fractional extension in the steady-state can be expressed in terms of a linear combination of Mittag-Leffler and generalized Mittag-Leffler functions. For the special cases of elongational flow and steady shear flow, and after adjustment of the parameters in the memory function, our calculated decay curves provide satisfactory fits to the experimental decay curves from the Zhou-Schroeder work and earlier work by Teixeira et al. [Macromolecules 40, 2461, (2007)]. The non-exponential character of the Mittag-Leffler functions, and the consequent absence of characteristic decay constants, suggest that melt relaxation may proceed by a sequence of steps with an essentially continuous, rather than discrete, spectrum of timescales. |
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N00.00012: Extensional rheology, pinching dynamics, and processability of polymer solutions Carina Martinez, Vivek Sharma The processability of polymer solutions is determined by the shear and extensional rheology response, pinching dynamics, and interfacial properties. Particularly, dispensing, and liquid transfer to substrates by dripping, jetting, spraying, or coating flows involve capillarity-driven pinching of liquid necks with strong extensional flows. However, due to a lack of suitable techniques, the extensional rheology response of polymeric complex fluids with low viscosity and low elasticity that are industrially relevant in a vast variety of formulations has not been characterized in adequate detail. In this study, we examine how pinching and interfacial dynamics and the shear and extensional rheological response of polymer solutions are modified by the addition of ionic surfactants and particles or additional interactions. We utilize dripping-onto-substrate rheometry protocols and show that shear and extensional rheology responses display contrasting concentration-dependent variation. We elucidate the effect of multiple interactions on the pinching dynamics and extensional rheology response, and we discuss the implications for dispensing of macromolecular complex fluids. |
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N00.00013: A Scaling Tool for Quantifying Properties of Polymer Solutions Ryan Sayko, Michael Jacobs, Andrey V Dobrynin We have developed a scaling approach that provides the groundwork for obtaining interaction parameters, Kuhn length and the packing number for polymer solutions. Notably, we utilize an approach based on the relationship between the solution correlation length ξ=lgν/B and the number of repeat units per correlation blob g for polymers with repeat unit projection length l. The coefficient B and exponent ν are determined by the solvent quality for the polymer backbone. The values of the B-parameters are extracted from plateaus of normalized specific viscosity as a function of repeat unit concentration in different solution regimes and applied to measurements of specific viscosity, diffusion coefficient, osmotic pressure, and relaxation time to represent them as functions of the number of correlation blobs per chain. From this data, both the Rouse and entangled regimes are highlighted and used to obtain the chain packing number Pe, completing the set of parameters {B,Pe} that uniquely identifies the properties of a polymer/solvent pair. This method is implemented to characterize the statics and dynamics of synthetic polymers, polysaccharides, and charged polymers in organic and aqueous solutions and ionic liquids. |
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N00.00014: Mechanics of model semiflexible conjugated-polymer glasses Robert S Hoy, Kai Nan, Joseph Fox D Dietz Conjugated polymers have attracted great interest recently owing to their potential use in flexible electronic circuits, including bio-implantable devices. These semiflexible polymers possess an entanglement-mesh-scale structure that is dramatically different than that of their flexible counterparts; specifically, their entangled strands are approximately one Kuhn segment (rather than >> 1 Kuhn segments) long. This difference must necessarily lead to qualitatively different mechanical properties, but since these polymers have been synthesized only recently, their mechanics have been little explored. Preparing samples suitable for mechanics experiments remains challenging, and hence much can be learned from simulations of these systems. We present the results of molecular dynamics studies of semiflexible polymers' glassy-state mechanics under a wide range of deformation protocols, for a wide range of temperatures. Our results show that although these glasses are likely to be brittle, they may be less brittle than one might expect based on traditional theories of glassy-polymer mechanics such as Kramer's expression for the craze extension ratio. |
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N00.00015: Flexible-Spacer Embedded Polymer Donors Afford Superior Blend Miscibility for High-Performance and Mechanically-Robust Organic Solar Cells Jin-Woo Lee, Dahyun Jeong, Dong Jun Kim, Taek-Soo Kim, Bumjoon J Kim Developing organic solar cells (OSCs) with high photovoltaic performance and mechanical robustness is one of the most urgent tasks to ensure their operational reliability in wearable devices. However, it remains challenging to enhance their mechanical properties without compromising the electrical properties of high-performance active materials. Here, we develop a series of polymer donors (PDs), with which highly efficient OSCs having remarkable mechanical reliability are demonstrated. By interposing a controlled amount of 1,10-di(thiophen-2-yl)decane flexible spacer (FS) into a PM6 backbone, we are able to significantly enhance the intermixing of the new PDs with a small molecule acceptor (Y7), affording sufficient pathways for efficient charge percolation and mechanical stress dissipation. As a result, OSCs based on the PD containing 5 mol% FS units and Y7 exhibit a high power conversion efficiency (PCE) of 17% with a crack onset strain (COS) of 12% and a cohesive fracture energy (Gc) of 2.1 J m−2, significantly outperforming reference PM6-based devices (PCE = 15%, COS = 2% and Gc = 1.0 J m−2). |
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N00.00016: Design of n-type Radical Polymers and Their Utilization as Solid-State Conductors Zihao Liang, Bryan W Boudouris Radical polymers are receiving increasing attention due to their ability to transport charge in solid state. However, the radical polymer conductors evaluated to date have been almost exclusively based on (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO); thus, macromolecules bearing preferentially-reduced (i.e., n-type) radicals have received little attention. Herein, phenoxy-based, n-type radical polymers featuring ethylene oxide-based and siloxane-based backbones are developed. Their singly occupied molecular orbital energy level is around 4.7 eV removed from vacuum. Moreover, the spin-spin interaction among the intra-chain radical groups was quantified using electron paramagnetic resonance (EPR) spectroscopy. In addition, the glass transition temperatures for these polymers are below room temperature due to their flexible macromolecular backbones. Furthermore, the solid-state conductivity values of thin films of these radical polymers reach values up to 0.01 S m-1, demonstrating the potential of these materials as future solid-state conductors. In this way, we have determined the fundamental physics that dictates transport in nonconjugated, n-type radical polymers and help to establish the solid-state conducting performance for an emerging class of n-type radical polymers. |
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N00.00017: Elucidating Magnetic and Spintronic Effects in Open-shell Macromolecules Hamas U Tahir, Brett M Savoie, Bryan W Boudouris Open-shell macromolecules are an emerging class of materials, and they have the potential to be implemented in a variety of organic electronic applications.The presence of unpaired electrons endows these materials with properties, such as extremely long spin relaxation times, which are difficult to achieve with common organic semiconductors. In addition to exhibiting weak spin-orbit coupling, these polymers are paramagnetic in nature. This added functionality make these materials suitable for spintronics applications as radicals retain their magnetic moment in solid state electronic devices, thus enabling facile coupling with an external magnetic field. However, the utilization of open-shell macromolecules that could favor spin polarization and spin conservation during transport have never been investigated. Here, we establish the paramagnetic behavior of these molecules at room temperature. We also observe that, at temperatures < 10 K, these materials exhibit weak antiferromagnetic coupling. Additionally, spin transport performance (i.e., giant negative magnetoresistance (i.e., on the order of –100%) of these systems has been demonstrated. These spin-related results suggest that open-shell macromolecules are remarkably potential materials for spintronic applications. |
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N00.00018: Magnetic and Electronic Properties of aDendritic 3-Armed Nonconjugated Open-Shell Macromolecule Hyunki Yeo, Siddhartha Akkiraju, Ying Tan, Hamas U Tahir, Neil R Dilley, Brett M Savoie, Bryan W Boudouris Nonconjugated radical polymers (i.e., macromolecules with aliphatic backbones possessing stable open-shell sites on their pendant groups) have arisen as an intriguing complement to π-conjugated polymers in organic electronic applications, due to their low optical density and easy-tunable structure. Moreover, conjugated dendritic macromolecules have shown significant promise in terms of their response under magnetic fields; however, the molecular design of nonconjugated radical polymers has focused on linear polymers. Therefore, we have synthesized a 3-armed nonconjugated radical macromolecule through a single step reaction and evaluated the electronic and magnetic behavior in both experimental and computational approach. The conductivity value of this macromolecule is on par with many previous linear radical polymers. Additionally, this macromolecule showed shifting magnetic behavior from paramagnetic (300 K) to antiferromagnetic (5 K) at low temperatures due to local ordering. Computational predictions support tighter packing of nitroxides groups for higher-generation dendrimers, which promotes enhanced spin interactions. Thus, this dendritic radical macromolecule affords a promising, high-performance system for the next generation of dendrimers of this type. |
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N00.00019: The behavior analysis of the mixture of two oppositely charged polyelectrolytes with the help of a macroscopic mechanical system Arkadii Arinshtein, Viatcheslav Soukhanov, Eyal Zussman To realize the idea of imitation modelling proposed by us recently, a mechanical system consisting of identical quantity of two types springs (20 ones of each type) having different elasticities and equilibrium lengths, was fabricated. To mimic a polymer network, all springs should be connected in such a manner that a quadrangular lattice will formed, in doing so each node of this lattice should contain two springs of each type. As a result of such restriction, the springs of one type form chains at any allowable spring distribution, and these chains can be considered as "polymer macromolecules". Each random system configuration generated by computer, was assembled inside of metallic frame and photographed with further analysis with the help of the computer program including pattern recognition, image analysis. As a result, the system parameters (energy and order parameter) were calculated and collected for 256 generated configurations, differed by system orientational ordering when more springs of the one type are orientated along one direction (for example, along x-axis), whereas the orientation along other direction (along y-axis) is preferable for the other type springs. The statistical analysis of obtained data allows one to derive the dependence of the system energy vs. spatial distribution of the system springs (more exactly, their orientational ordering). Using the obtained dependence, the statistical weight of each system state characterized by energy and orientation ordering, can be calculated (more exactly, the state portion corresponding to a narrow range of the above system parameters). Thereafter the system entropy as well as the free energy can be introduced, and the minimum of last corresponds to the system equilibrium state. The above examining allows one to verify experimentally the outcomes of theoretical model analyzing the self-ordering in a 2D two-component system modelling the behavior of a mixture of two oppositely charged polyelectrolytes. |
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N00.00020: The phase behavior and rheological properties of natural polyelectrolyte complexes with salt addition Santanu Kundu, Anandavalli Varadarajan, Logan T Kearney, Amit K Naskar Oppositely charged polyelectrolytes can form polyelectrolyte complexes (PECs) due to the electrostatic interactions. The structure and properties of PECs can be tuned by varying the salt concentration, as the addition of salt can facilitate the associative phase separation. In this work, PECs are prepared from two biopolymers, positively charged chitosan and negatively charged alginate. Without any salt addition, the water content of the complex phase was >95%. The addition of salt led to a decrease in the complex phase's water content with increasing shear-modulus. However, at a very high salt concentration, the shear-modulus of the complex phase decreased. In the non-linear regime, the shear modulus decreased with the increase of strain amplitude. The non-linear rheological behavior of the salt-doped PECs was further investigated using large amplitude oscillatory shear experiments. The compositions of the PECs were determined as a function of salt concentration, and the results indicate the preferential partitioning of salt into the complex phase. Small-angle X-ray scattering was used to understand the structure of the salt-doped systems. This study provides insights into the tunability of PECs properties necessary for developing functional materials from natural polyelectrolytes. |
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N00.00021: Entanglements and Dynamics of Polyelectrolytes in Concentrated Solutions and Complexes Yuan Tian, Ryan Sayko, Heyi Liang, Andrey V Dobrynin We performed coarse-grained molecular dynamics simulations of polyelectrolyte solutions and mixtures of oppositely charged chains with different degrees of polymerization. Analysis of the simulation results for the mean-square displacement of the monomers belonging to the central part of the chain and the chains’ centers of mass shows that the chains’ dynamics is a combination of constraint release and chain reptation in the confining tube. The constraint release appears to play a dominant role in mixtures of positively and negatively charged chains with intermediate and low degrees of polymerization. The degree of polymerization between entanglements Ne of the tube and super tube in systems of charged chains scales with solution concentration as Ne~ρ-2 and has corresponding packing number Pe = 18.45+/−0.93. This is qualitatively different from the behavior of similar composition mixtures of neutral chains where in addition to the Ne~ρ-2 scaling dependence, the degree of polymerization between entanglements for the super tube demonstrates a Ne~ρ-4/3 concentration dependence with corresponding packing number Pe = 6.64+/−0.19. |
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N00.00022: Salt partitioning in fully charged polyelectrolyte solutions: bulk thermodynamics and RPA Junhan Cho, Xinyue Zhang, Mingge Zhao The formation of complex coacervates and salt partitioning for polyelectrolyte solutions are investigated through bulk thermodynamic and random-phase approximation (RPA) analyses. Our model system consists of fully charged hard sphere polyanions, counterions, uncharged components along with added hard sphere salt. A molecular equation of state is first formulated for those systems based on liquid state theory. Then, RPA analysis is performed via the Gaussian thread approach by taking the equation of state as effective local interactions and adding nonlocal interactions from long-ranged Coulomb potential. It is shown that the bulk thermodynamic calculation predicts salt partitioning between complex coacervate and supernatant phases in agreement with experiments, where the classical Voorn-Overbeek theory fails due to the absence of excluded volume and chain connectivity. We additionally probe the condition for microphase separation by using RPA. The effects of osmotic pressure on salt partitioning phenomena are also considered through both methods. |
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N00.00023: Phase behaviors of a binary blend of weakly charged polyanions and polycations without salt Junhan Cho, Mingge Zhao, Xinyue Zhang A Landau free energy density is obtained for a salt-free binary blend of weakly charged polyanions and polycations in order to investigate their phase behaviors. The free energy functional is first formulated through the combination of the Gaussian thread approach and a molecular equation of state based on liquid state theory. The series expansion of the free energy functional in constituent density fluctuations up to quartic order yields the desired Landau free energy density. It is shown that long-ranged Coulomb interactions between charged monomers make the blend microphase separate. Various situations are covered for the blend at selected charged monomer fractions with disparity in self dispersion interaction and chain sizes. The effective second-order vertex coefficient is used to probe blend stability. The critical behavior and equilibrium phase diagram containing classical nanostructures for the blend are considered in the mean-field picture. In addition, we discuss the effects of osmotic pressure on the phase boundaries of the blend. Thermo and baroresponsive properties of the blend are also to be investigated. |
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N00.00024: AC-electrospinning Complex Nanofibers from Inorganic Nanocolloid -Polymer Complex Coacervates in Aqueous Media JAMUNA K VAISHNAV, Ali Hatami, Yingxi Elaine Zhu
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N00.00025: Interplaying Ion Transport and Structure of Polymerized Ionic Liquids Javad Jeddi, Jukka Niskanen, Benoît H. Lessard, Joshua R.Sangoro In this study, correlation between nanoscale organization and ion transport of 1,2,3-triazole based polymerized ionic liquids (PILs) was investigated using wide-angle X-ray scattering (WAXS) and broadband dielectric spectroscopy (BDS). The dc ionic conductivity of PILs was correlated with the glass temperature transition (Tg) in which the low Tg system exhibited higher dc conductivity. A comparison of the WAXS and BDS results indicates mobile ion volume and chemical structure of the pendant groups controlled structural heterogeneity and ion conduction of the studied PILs. The normalized heterogeneity length extracted from X-ray scattering spectra is considered as a criterion for the structural packing. For the polycation samples, larger TFSI–mobile ion results in a higher packed structure than small Cl–anion, and polyanion (PVBSO3C4MIm) samples. The estimation of the characteristic ion diffusion lengths from the activation energies of the dc conductivity below Tg measured by BDS is quantitatively correlated to the ion-ion correlation lengths and structural heterogeneity obtained from nanostructure analysis using WAXS. This suggests that increasing the spatial heterogeneity of the PILs lead to a reduction in activation energy barriers of long-range ion motions. These results highlight the role of spatial heterogeneity in designing efficient polymerized ionic liquids. |
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N00.00026: Influence of polarizability on the ion transport mechanism of polymeric ionic liquid Zidan Zhang, Dachey Lin, Everett S Zofchak, Jakub Krajniak, Venkatraghavan Ganesan In the current study, we compared the prediction of three different implementations of force field, namely, the original full partial charge system, the scaled partial charge system and the Drude oscillator polarizable force field on the structural and dynamic properties of poly(1-butyl-3-methyl-imidazolium hexafluorophosphate) by atomistic simulations. We found that both the scaled and the polarizable force field models are comparable in prediction of structural and dynamic properties, although the scaled charge model artificially lowers the first-neighbor peak of the radial distribution function and therefore leads to a slight reduction in density. The full charge model is not suitable for prediction of the dynamic properties, but it could reproduce the structural properties. With the refined analysis method for the ion hopping mechanism, we found that all three methods could produce very similar conclusions, namely that the mobile anion is naturally associated with three cations from two distinct polymer chains, and the fraction of inter- and intra-molecular hopping events are comparable. |
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N00.00027: Effects of LiCl and water on thermal properties of polyzwitterions John Thomas, Yajnaseni Biswas, Ayse Asatekin, Peggy Cebe The thermal and structural properties of five polyzwitterion (PZI) and salt (LiCl) complexes were measured using thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and temperature modulated DSC, and Fourier transform inferred (FTIR) spectroscopy. Poly(sulfobetaine methacrylate), PSBMA, poly(sulfobetaine acrylate), PSBA, poly(ethyl sulfobetaine methacrylate), PESBMA, poly(ethyl sulfobetaine acrylate), PESBA, and poly(sulfobetaine methacylamide), PSBMAm, were synthesized with variations in the sidechain and backbone. Complexes are cast from solution containing LiCl in amounts ranging from 0.06 to 1.65 mol%. The total and reversing heat capacity (cp) and glass transition temperatures (Tg) are measured using DSC and TMDSC. A standard drying treatment in DSC is applied to ensure no surface or molecularly bound water. We use TGA to quantify the initial bound water content and develop an expression for the change in mass as a function of temperature. Addition of LiCl interrupts the intra- and inter-molecular crosslinking formed by the zwitterionic moieties resulting in a decrease in Tg and an increase in the heat capacity increment at Tg. FTIR confirms the interruption of the crosslinks through an increase in the asymmetric stretching of the S=O side chain group. |
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N00.00028: Probing the physical origin of the anti-biofouling performance of synthetic polyzwitterions Carlos Medina Jimenez, Angelika Neitzel, Guilhem De Hoe, Matthew V Tirrell Zwitterionic polymers have been widely promoted as effective antifouling agents due to the often-observed resilience of surfaces modified with zwitterionic moieties to the adhesion of proteins and microbial organisms. Nevertheless, a deep understanding of the relationship between zwitterion structure and fundamental properties, such as the degree of hydration or solubility, remains lacking. This project entails a systematic study of the interactions between zwitterionic polymers and surrounding water molecules, as conveyed by the chain dimensions of polyzwitterions in aqueous environments. By extracting and contrasting the effective solvent quality of polyzwitterions with different side chain chemistries, a clear relationship between zwitterion structure and solvent interactions will be established. Following comparison with observations from foulant adhesion studies will elucidate the connection between surface hydration and foulant repulsion, allowing for better design of anti-biofouling materials. |
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N00.00029: Molecular Dynamics Study of Polystyrene Sulfonate in Dilute Solutions: from Ionomers to Polyelectrolytes Jailyn Johnson, Supun S Mohottalalage, Gary S Grest, Dvora Perahia Ionizable polymers are often cast into membranes from solutions, where solutions structure determines the membrane morphology and function in their many applications. These polymers associate in solutions forming a rich variety of assemblies from random aggregates to well defined micelles, depending on the specific polymer chemistries and topology. Association takes place at very low concentrations, making the conformation of isolated molecules a critical factor in the understanding of the assembly process. With the working hypothesis that one could drive the micellar structure in solution through tuning the electrostatic interactions, the current study probes the conformation and dynamics of polystyrene sulfonate in dilute solutions of different dielectric constants using atomistic molecular dynamic simulations. Polystyrene sulfonate with 100 monomers and sulfonation levels from 0 to 95% was studied in implicit solvents with dielectric constants of 7.8, 30, 78, that correspond to that of THF, alcohols and water respectively. The evolution of the structure of the polymer as the polymer transitions from a non-ionic polymer to ionomers and to polyelectrolytes, as the dielectric constant is varied will be presented and compared to the conformations in explicit solvents. |
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N00.00030: Ion transport properties in salt-doped polymer electrolytes Eiko Ino, Rachel A Segalman, Shuyi Xie Polymer electrolytes with high lithium-ion conductivity provide a route toward improved safety and performance of lithium-ion batteries. For instance, conventional Li salt-doped poly(ethylene oxide) (PEO) shows high conductivity while it suffers from a lower lithium-ion contribution to the conductivity (the lithium transport number, t+). Single-ion conductors (SICs) in which the anions are immobilized by tethering to the polymer backbone have a high lithium transport number while the conductivity is relatively low since lithium is the only mobile ion and strongly interacts with tethered anion. Here, we report polymer electrolytes by mixing bis(trifluoromethane sulfonyl)imides tethered polyacrylate(PA) with a high content of Li bis(trifluoromethane sulfonyl)imide (LiTFSI) salt. As a SIC, PA itself shows low conductivity but is capable of solubilizing very high quantities of salt (LiTFSI). As a result, LiTFSI-doped PA shows comparable or higher ionic conductivity than the industry benchmark PEO. In addition, the LiTFSI-doped PA shows a high transport number ( t+ > 0.5), indicating that the system is promising as a polymer electrolyte. |
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N00.00031: Effects of Homopolymer Additives on Ion Transport and Conductivity in Model Salt-Doped Block Copolymers Yuanhao Zhang, Mengdi Fan, Lisa M Hall Salt-doped block copolymers (BCP) are promising solid electrolytes because of their ionic conductivity and mechanical strength brought by the combination of two distinct polymer microphases. Recent study has shown that the presence of relatively high molecular weight (MW) homopolymer (of the same type as the conductive phase) creates a relatively homopolymer-rich region within the conducting phase and leads to a higher overall ion conductivity. We use coarse-grained molecular dynamics simulations to understand the correlation between distribution of each component and the local transport of ions. The like-like interactions and masses of the nonconducting block monomers are increased to reflect their higher glass transition temperature. We analyze the distribution of homopolymers and ions as a function of homopolymer additive MW and concentration. We also calculate the distribution of ion drift velocity and conductivity for these systems and show that the dynamic behavior of ions depends on their location within the conductive domain. |
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N00.00032: Solution rheology of polyelectrolytes in organic media Anish Gulati, Carlos G Lopez The solution rheology of polyelectrolytes has been widely studied in aqueous media. Studies in non-aqueous media are less common, in part because of the limited solubility of polyelectrolytes in organic solvents. Here we study the solution behaviour of the tetrabutylammonium salt of carboxymethyl cellulose (TBACMC) in over 20 different solvents. The TBA ions increase the solubility of CMC in linear alcohols, diols etc. compared to more common counterions such as sodium or potassium. |
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N00.00033: Enhanced ion transport by tuning intra-domain structure and dynamics in nanostructured block polymer electrolytes Priyanka M Ketkar, Nicholas F Pietra, Andrew G Korovich, Kuan-Hsuan Shen, Mengdi Fan, Lisa M Hall, Louis A Madsen, Thomas H Epps Nanostructured block polymer (BP) electrolytes with modified ion/monomer segment distributions have demonstrated the potential to boost the performance and safety in lithium-ion batteries by enabling intra-domain structures that are challenging to realize in conventional BPs. We synthesize BPs with gradient monomer segment composition profiles between the homogeneous blocks (i.e., tapered BPs) to tune the abovementioned distributions. Through a combination of reflectometry experiments and coarse-grained molecular dynamics simulations that include strong ion solvation effects, we identify that the addition of a tapered region increases transport by reducing chain stretching and conducting segment/ion content near the confining interface. To further elucidate the connection between intra-domain structure and local mobility, we create a quantitative framework and validate it through nuclear magnetic resonance spectroscopy studies on solid electrolyte samples. In addition to segmental mixing, chain stretching, and confinement effects, the dynamical heterogeneity within a monomer segment (e.g., along a side chain) also influences local mobility significantly. This link between local and global dynamics can facilitate the design of next-generation electrolytes. |
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N00.00034: Accelerated Discovery of Optimal Ion Transport Characteristics in Nanoparticle-Based Electrolytes Using Convolutional Neural Networks Sanket R Kadulkar, Michael P Howard, Thomas M Truskett, Venkatraghavan Ganesan Spatial arrangement of spherical nanoparticles in nanocomposite materials can significantly influence the macroscopic behavior. However, iterative probing of all the possible nanoparticle configurations for their corresponding macroscopic properties to identify the optimal configurations is often intractable even using computer simulations. To overcome such challenges, in this work, we highlight the capability of Convolutional Neural Networks (CNNs) to serve as machine learning-based surrogate models to establish quantitative structure−property linkage in composites with monodisperse spherical particles. This is specifically demonstrated using a CNN model to quantitatively link the diffusivity of ions to the spatial arrangement of the nanoparticles in nanoparticle-based electrolytes, and its success in identifying configurations exhibiting optimal diffusivities on combining with a metaheuristic topology optimization algorithm. We also discuss the use of data-driven approaches such as Principal Component Analysis to elucidate the correlations between the simple physical descriptors of the microstructure topology and the resulting property, thus providing a physical rationale for the observed optimal configurations. |
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N00.00035: Polyelectrolyte Complex-Interpenetrating Polymer Networks Hydrogels Defu Li, Tobias Göckler, Samanvaya Srivastava Polyelectrolyte complex (PEC) hydrogels are three-dimensional polymer networks comprising oppositely charged ABA triblock polyelectrolytes with the electrostatically assembled domains composed of highly dense oppositely charged blocks serving as netpoints. PEC hydrogels self-assemble rapidly, are stimuli-responsiveness, and possess self-healing attributes, enabling potential applications in drug delivery, 3-D bioprinting, and wet adhesion technologies. However, the application-specific requirements demand a precise tunability of hierarchical structures and mechanical properties. To enhance the tunability of structure and properties of PEC hydrogels, we have developed a strategy to fabricate polyelectrolyte complex-interpenetrating polymer network (PEC-IPN) hydrogels, comprising a PEC network and a covalent network. We will demonstrate the generality of the approach by discussing hydrogels consisting of four different photocurable precursors - 4-arm poly (ethylene glycol) acrylate, poly (ethylene glycol) diacrylate, gelatin methacryloyl, and acrylamide - individually interpenetrated with the PEC networks to form a series of PEC-IPN hydrogels. All these hydrogels not only maintain diverse microstructures but also exhibit superior mechanical properties regardless of their distinct polymer shapes, polymer origin, molecular weights, crosslinking density, and crosslinking mechanisms, indicating a universal approach to engineer PEC-IPN hydrogels. We envision the versatility of our approach to broaden the application of PEC-based self-assembled materials in diverse biomedical research fields. |
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N00.00036: Swelling and Deformation of Polyelectrolyte Gels in Salt Solutions Zilu Wang, Michael Jacobs, Andrey V Dobrynin Polyelectrolyte (PE) gels consist of crosslinked polyelectrolyte chains and are featured by their incredible capability of water absorption which is found can be greatly affected by the salt content in the solution environment. In order to quantify this effect, we performed coarse-grained molecular dynamics simulations of swelling and deformation of the thick film-like polyelectrolyte networks immersed in a salt solution. We study the swelling ability and shear modulus of PE gels made of linear chain and brush-like network strands and compare their behavior at different salt concentrations, fraction of the charged monomers per network strand, degree of polymerization between crosslinks and network preparation conditions. As expected, the gel swelling decreases with increasing salt concentration and decreasing the fraction of ionized groups per network strand while it increases with increasing the degree of polymerization between crosslinks. The gel mechanical properties in linear and nonlinear deformation regimes were obtained from simulations of the uniaxial deformation of the gels. These simulations have shown that there is a salt redistribution upon gel deformation with salt partition coefficient α= Csalt,gel/ Csalt increasing as gel deformation increases. |
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N00.00037: Vanadium Ion Dynamics of Ionomer-Nanoparticle Hybrid Membranes Xueting Wang, Eric M Davis, Madhusudan Tyagi, Mayura Silva, Stephen Creager Creager, Apoorva Balwani Herein, the dynamics of water and hydrated vanadium ions in Nafion–NP membranes was investigated via quasi-elastic neutron scattering (QENS), specially, high-flux backscattering. The broadening of the energy spectra was attributed to the incoherent scattering from hydrogen atoms – both protons and water molecules in the vanadyl ion hydration sphere. These quasi-elastic events were deconvoluted from the scattering data through peak fitting in Data Analysis and Visualization Environment. Vanadium ion dynamics were measured for Nafion–NP membranes prepared through both a sol-gel condensation and solution casting process. The silica nanoparticle (SiNP) loading in these membranes was varied from 0 mass% to 10 mass%. The q-dependent peak shape parameters and elastic incoherent structure factors were extracted from analysis of the data using a jump diffusion within a sphere model. A delta function and a lorentzian function were applied in the fitting to extract information for both jump diffusion and local motion. By comparing the ion dynamics from these two types of ionomer nanocomposite membranes, the impact of SiNPs on the ion transport in these nanocomposites was better explained, providing deeper insight into the decreased vanadium ion crossover observed for these membranes. |
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N00.00038: Structural analysis of ethylene ionomers containing two types of metal ions Shunsuke Murayama, Go Matsuba Polymers with a small amount of ionic groups introduced into a hydrophobic polymer are called as ionomers. In particular, ethylene-based ionomers with polyethylene as the main chain have high toughness and transparency. These polymers are used for packaging films and sporting goods. |
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N00.00039: Effects of Chain Architecture on the Gel Modulus of Graft Polymer Networks Michael Jacobs, Andrey V Dobrynin Polymer networks whose strands are made of graft polymers have been shown to possess mechanical properties similar to biological tissues and the ability to swell to larger volumes than their linear chain counterparts. We use a combination of theoretical analysis and molecular dynamics simulations to elucidate the effect of graft polymer architecture on the swelling ratio, Q, and the modulus of the swollen gel, Ggel(Q), and its relationship with the modulus of the dry network, Gdr. Our analysis indicates that for networks made of comb-like strands with with few grafted side chains the gel modulus scales as Ggel(Q)=Gdr/Qα, with exponent α≈0.56 in a good solvent and 1/3 in a θ-solvent. For networks with bottlebrush-like strands, however, we find that the additional chain thickness and rigidity introduced by the swelling of the densely grafted side chains require a significant correction, due to the strong concentration dependence of the effective Kuhn length of the bottlebrush strands. The resulting relationship between chain architecture, swelling ratio, and gel modulus is summarized in a universal equation relating the normalized modulus QαGgel(Q)/Gdr as a function of the strand architecture and effective Kuhn length. |
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N00.00040: Swelling Behavior of Organogels Containing Two Unique Block Copolymers Ridwana Bashar, Kenneth P Mineart Organogels based on styrenic block copolymers are good candidates for many applications including transdermal drug delivery since their transport and mechanical properties can be easily tuned through formulation changes. Understanding the swelling behavior of such organogels is helpful in relating formulation changes to gels’ microscopic structure. In this work, the equilibrium swelling ratios of two series of styrenic block copolymer gels are investigated. The first series consists of a triblock copolymer (triblock1: 248 kg/mole, ƒPS=0.297), a diblock copolymer (136 kg/mole, ƒPS=0.334) and mineral oil (MO). The second series consists of two different triblock copolymers (triblock1 and triblock2: 76 kg/mole, ƒPS=0.658) and MO. In each series, triblock1 is fixed at three levels (10, 20, and 30 wt%) while the diblock, or triblock2, is varied from 0 wt% to 30 wt%. For a fixed amount of triblock1, it is observed that an increase in diblock (Series 1) amount leads to increased swelling until a total copolymer concentration of 35 wt% whereas swelling monotonically decreases with increasing triblock2 (Series 2) concentration. The cause of these trends will be discussed. |
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N00.00041: The Role of Gel Mesh and Particle Size in Predicting Nanoparticle Diffusion in Hydrogel Nanocomposites Paige Moncure, Jennifer E Laaser, Zoe C Simon, Jill E Millstone The diffusion of poly(ethylene glycol) methyl ether thiol (PEGSH) capped gold nanoparticles (NPs) was measured in polyacrylamide gels of various crosslinking densities. The molecular weight of the PEGSH capping ligand and the crosslinking density of the gel were both varied, yielding particles with hydrodynamic diameters between 7 and 21 nm and gels with theoretical mesh sizes of approximately 16 to 44 nm. While we expected the diffusion constants of the NPs to depend on their core:ligand ratios, since high molecular weight ligands are expected to yield more compressible particles, our measurements revealed that the diffusion instead resulted primarily from changes in the overall hydrodynamic diameter. Across all particles and gels, we found that the diffusion was best predicted by the confinement ratio calculated from the diameter of the particle and an estimate of the gel mesh size obtained from the elastic blob model. These results suggest that this model is the effective pore size that the particles "see" as they diffuse through the gel. This work brings new insights into the mechanisms by which NPs move through polymer gels, and will inform development of hydrogel nanocomposites for applications such as of drug delivery in heterogenous, viscoelastic biological materials. |
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N00.00042: Coherent States Field Theory for Supramolecular Miktoarm Star Polymer Networks Dan Sun, Daniel L Vigil, Kris T Delaney, Glenn H Fredrickson The conformational asymmetry of ABn mitoarm star polymers results in deflected phase boundaries that favor discrete A domains and non-conventional (Frank-Kasper) spherical packings. The stabilization of discrete A domains to extreme volume fractions offers potential for unique property combinations in dry and wet networks that utilize the ABn motif. In this study, we explore the use of miktoarm stars as supramolecular building blocks to form reversible dry networks that retain the unique morphologies of non-reactive polymers, but with thermally tunable mechanical properties. To study such systems, we apply the coherent states (CS) field-theoretic representation in tandem with a mean-field approximation. The CS framework is highly advantaged over the conventional “auxiliary field” (AF) representation because it eliminates the need for explicit enumeration of all reaction products. We show how the phase behavior is influenced by the placement of reactive groups, their binding strength, and their self vs. hetero-complementary character. In particular, the relative stability of Frank-Kasper phases was explored and compared with non-reactive miktoarm stars. |
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N00.00043: Static Light Scattering measurements on Microgels Below and Above Volume Phase Transition. Kiril A Streletzky, Andrew L Scherer, Patrick Herron, Samantha C Tietjen Polymeric microgels were synthesized from a polysaccharide at various crosslinker concentrations. Dynamic Light Scattering on these microgels revealed crosslinker-concentration-dependent dynamics below and above their volume phase transition. A proper multi-concentration Static Light Scattering (SLS) with direct dn/dc measurements, Zimm/Berry analysis, and form factor analysis was used to study particle’s structure, molecular weight, and interactions under various conditions. While at low crosslinker concentrations microgel dn/dc was largely in agreement with the dn/dc value for the parent polymer, at high crosslinker dn/dc showed a significant increase with increase of crosslinker concentration and temperature. Microgel scattering form factors were also found to depend on crosslinker concentration changing from shapes consistent with more spherical to less spherical shapes with the increase of the crosslinker. The overall light scattering analysis shows that the crosslinker concentration affects the apparent density and structure of microgels and could be related to non-uniform crosslinker distribution in microgels at higher crosslinker concentrations. The argument for a future higher resolution probing of microgel internal structure with small angle scattering methods will also be made. |
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N00.00044: Super-stretchable Elastomer from Cross-linked Ring Polymers Thomas C O’Connor, Gary S Grest, Ting Ge Stretchability of polymeric materials is critical to many applications such as stretchable electronics and soft robotics, and yet the stretchability of conventional cross-linked linear polymers is often limited by the entanglements between polymers. We show using molecular dynamics simulations that cross-linked ring polymers are significantly more stretchable. Compared to cross-linked linear polymers, the degree of entanglements between ring polymers is much reduced. As a result, the stretchability of cross-linked ring polymers is determined by the maximum extension of polymer sections between cross-links, rather than the maximum extension of entanglement strands as in cross-linked linear polymers. Additionally, the more compact conformation of ring polymers before deformation also contributes to the increase in the stretchability. |
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N00.00045: Effect of Sticker Clustering on Dynamics of Associative Polymer Networks Ameya Rao, Irina Mahmad Rasid, Jorge Ramirez, Niels Holten-Andersen, Bradley D Olsen Recent studies of associative networks have explored chain architectures with stickers clustered in groups along the chain, enhancing strength and toughness. Here, we provide microscopic insight into the effect of sticker clustering in associative networks by combining experiment and coarse-grained modeling, comparing networks with stickers randomly distributed along the chain versus stickers clustered on the chain ends. Small-angle neutron scattering of a model hydrogel based on metal-coordinate bonds shows an increase in large-scale density fluctuations in networks with clustered stickers, which correlates with slower stress relaxation due to the cooperative effect of multiple bonds. However, sticker clustering results in faster self-diffusion of the network-forming chains, despite the slower relaxation. Brownian dynamics simulations demonstrate key changes to the network topology caused by the clustered stickers, particularly an enhancement in loop defects, which increase the rate of chain hopping and overall self-diffusivity on large length scales. These studies highlight the strong effects of sticker clustering on the structure and dynamics of associative networks on different length scales, providing handles for design. |
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N00.00046: Investigating the Effect of Network Architecture and Topography in tuning Vitrimer Behavior through Coarse-Grained Molecular Dynamics Simulations Shalini Jayaraman Rukmani, Jan-Michael Y Carrillo, Loukas Petridis, Aditya Savara Vitrimers are dynamically cross-linked polymers that undergo associative bond exchange at high temperatures (above the topological transition temperature, Tv) allowing material reprocessability, while retaining the mechanical strength of thermosets. Optimal design of vitrimers with the desired operating temperature window for reprocessability can be achieved by tuning Tv. Our vitrimer architecture consists of linear polymer chains and star cross-linkers modeled by Lennard-Jones beads. A combined molecular dynamics (MD)/Monte Carlo (MC) approach is used to model associative bond exchange with Arrhenius type temperature (T) dependence. We investigate the effect of vitrimer architecture and topography on shifting Tv by varying chemical building blocks: length of polymer chain beads (Nw,p = 5, 10, 20, and 40), number of arms per cross-linker (f=3, 4), and activation energy barrier for bond exchange (Ea,BE = 40, 53, 60, 67, and 74 kJ/mol). Tv is predicted through shear viscosity (h) calculations from Non-Equilibrium MD simulations. From the h -T curves, we observe that an increasing Ea,BE produces a pronounced shift in the vitreous region to higher temperatures and increases the width of the vitreous region in comparison to f, while varying Nw,p does not produce any noticeable trends. Hence, an increased energy barrier to swapping and increased stiffness of the network (f=4) can be used to tune the vitreous region. The trends obtained from viscosity curves and the underlying molecular mechanisms provide insight for optimizing design of experiments to obtain vitrimer behavior at service temperatures. |
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N00.00047: Mechanics of Triblock Copolymer & Dual Triblock Copolymer Gels Matthew Vallely, Kenneth P Mineart The goal of this project is to compare the mechanical behavior of triblock copolymer and dual triblock copolymer gels with the slip-tube network (STN) theory. These gels are used in a variety of different applications ranging from model surgery and ballistics gels to bike seat cushions. The triblock copolymer gels we study are composed of styrenic ABA triblock copolymers, such as SEBS, and aliphatic mineral oil. Dual triblock copolymer gels are similar, but contain two unique styrenic ABA triblock copolymers. The copolymers in gels form a physically-crosslinked network which explains their mechanical robustness. To characterize the mechanical behavior of these gels, we perform quasi-static tensile tests. The results of which are nonlinear, elastic stress-extension curves. We fit this data using the slip-tube network model that yields the crosslinked network and chain entanglement modulus contributions. These modulus contributions allow us to understand and quantitatively interpret trends in stress-extension curves as functions of our formulation parameters (copolymer concentration, block fractions, and molecular weight). Comparison of experimental modulus contributions with their theoretical expectation further provides an updated understanding of gels' microstructure. |
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N00.00048: Tuning enthalpic and entropic interactions in blends of block copolymer and polymeric additives Karthika Madathil, Bishal Upadhyay, Michael Kilbey, Gila E Stein Block copolymer thermoplastic elastomers (TPE) are used for a wide range of applications including adhesives, footwear and automobile parts. However, durability of these materials is challenged by creep and stress relaxation behavior. Blending TPEs with miscible polymeric additives is a simple potential strategy to tailor their mechanical properties. In this work, we conduct a systematic study on the effects of interaction-tuned additives on the structure and mechanics of poly(styrene-b-ethylene butadiene-b-styrene) (SEBS), a widely used TPE. The additive used are linear poly(methyl methacrylate-co-cyclohexyl methacrylate). The enthalpic interaction between the additive and the polystyrene blocks is controlled by the mole fraction of cyclohexyl methacrylate, and the entropic interactions are tuned by the relative molecular weights. Blend structures are analyzed using small angle X-ray scattering, which shows that short chain additives that are miscible with polystyrene are distributed throughout the domain. These blends showed increased modulus and creep resistance in proportion to the strength of the favorable interaction (as captured by χ). This study provides a framework to manipulate the nanoscale structure and bulk mechanical properties of TPEs. |
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N00.00049: Energy Storage and Release of Polydimethylsiloxane Comb and Bottlebrush Network Polymers Carolyn Du, Halie Kim, Mark Ilton Nature has beaten humanity at creating high energy-loading and energy-releasing systems. Through Latch Mediated Spring Actuated systems, such as the mantis shrimp punch or trap jaw ant mandible snap, natural systems achieve much higher mass to energy release ratios at much faster release rates than what we are currently capable of creating. One possible source of this incredible energy performance could be the material properties of biological tissues. Most types of materials show an inverse linear relationship between Young's modulus (E) and stretch (λ), but biological materials can break away from that "Golden Rule". Our goal is to recreate the nonlinear relationship between E and λ with polydimethylsiloxane (PDMS) polymers, aiming to achieve similar energy release rates as biological tissues like chitin and tendon. We can create PDMS comb polymers with different material properties by varying the amounts and proportions of side chains and crosslinks within the polymer network structures. We explore the relationship between energy storage and release by examining both the material properties and the loading/unloading rates of our polymers through mechanical testing. |
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N00.00050: Effect of Hydrogen Bonding on Relaxation Time of Polymers for Ballistic Impact Resistance Katherine M Evans, Kanae Ito, Ajay Krishnamurthy, Edwin P Chan, Joseph M Dennis, Daniel B Knorr Jr., Kevin A Masser, Timothy W Sirk, Christopher Soles The toughness of some polymers such as polycarbonate (PC) and poly(dicyclopentadiene) has led to their use in ballistic impact resistance applications. However, the origin of this toughness and how it relates to the structure and dynamics of the polymer is still not well-understood. Previously quasielastic neutron scattering (QENS) experiments on a series of PCs were carried out to investigate the molecular dynamic origin of toughness. It was found that the activation of a (1 to 3 ps) relaxation process in QENS is critical for realizing the toughness in these PCs. In this presentation we extend these QENS experiments to a series of copolymers of 5-ethylidene-2-norbornene (ENB) and 5-methanol-2-norbornene (NBOH). The NBOH concentration was systematically varied to determine the effect of hydrogen bonding on relaxation times and toughness. These studies show that as hydrogen bonding increases the elasticity of the system increases and slows down this quasielastic relaxation process that was critical for toughness in the PCs by a factor of five, from approximately 0.6 ps to 3 ps. This is accompanied by a suppression in the amplitude of the quasielastic peak, indicating number of atom participating in the relaxation also decreases. We show that toughness of these materials, quantified in terms of the critical stress intensity factor (K1C), is strongly coupled with these relaxations; K1C decreases as the amplitude of the relaxation process decreases and the time scale of the relaxation processes slows down. This confirms our previous finding in PCs that relaxation processes on the time scale of a ps are critical for dissipating energy and realizing toughness in polymer glasses. |
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N00.00051: Mechanoresponsive Molecules to Visualize the Stress Field in the Matrix of a Single Fiber Reinforced Polymer Composite Nazmul Haque, Jared A Gohl, Chelsea S Davis Stress accumulation in the matrix during fracture of fiber-reinforced composite materials is a critical phenomenon that substantially impacts the composite's overall performance. However, the instantaneous nature of the fracture event makes it very difficult to obtain experimental data of the damaged region. Moreover, there is a lack of experimental tools for sensing and quantifying real-time stress distribution within the matrix during fracture. Therefore, a molecular force probe (mechanophore) was employed within the polymer matrix (polydimethylsiloxane) for visualizing the stress field distribution during fracture. The spiropyran mechanophore transitions from a fluorescent inactive state to an active state (merocyanine) via isomerization under the application of force and strain. To simplify the composite model, one single glass fiber was used with the matrix for their single fiber fragmentation test (SFFT). SFFT demonstrates the fundamental failure modes prevalent in traditional fiber-reinforced composites during uniaxial tensile testing along the fiber direction. At the interface, the tensile load transfer from matrix to fiber via shear stress causing fiber fragmentation. Confocal microscopy was used to visualize mechanophore activation and quantifying the fluorescence intensity. As in previous work, the fluorescence intensity was correlated to hydrostatic stress distribution in the matrix. Uniaxial tensile test of dogbone samples showed conical stress fields in the matrix around fragmented fiber. The results indicated that these mechanoresponsive molecules could be a promising tool for visualizing real-time stress distribution and designing high-performance composites. |
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N00.00052: Linear Viscoelastic Properties of Polybutadiene Melts and Nanocomposites through Multiscale Simulations Alireza Foroozani Behbahani, Patrycja Polinska, Craig Burkhart, Manolis Doxastakis, Vagelis Harmandaris Predicting the viscoelastic response of polymers is important in relation to a variety of applications of polymers. Due to the broad ranges of time-scales and length-scales that are involved in the dynamics of long polymer chains, the computational prediction of the viscoelastic properties of polymers is challenging and a multiscale simulation methodology is needed. Here we present the results of atomistic and coarse grained simulations for the linear viscoelastic properties of bulk melts of polybutadiene (PB) and the results of atomistic simulations for the viscoleastic properties of PB/Silica nanocomposites. For coarse-grained (CG) simulations, we use a moderately CG model that preserves the chemical identity of the PB chain and the entanglement effects. The CG model has been derived by matching local structural distributions of the CG model to those of the atomistic model through iterative Boltzmann inversion. We focus on the calculation of shear- stress relaxation modulus from the autocorrelation function of shear stresses. Furthermore, the characteristic times of segmental and terminal dynamics that are extracted from shear-stress relaxation modulus are compared to the direct indicators of segmental and chain relaxation times that are measured from the simulation trajectory. |
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N00.00053: Structural Morphology and Dynamical Confinement in PIB/β-alanine Graft Copolymer Nanocomposites Aarushi Srivastava, Logan Benninghoff, Antonio Faraone, John Meyerhofer, Li Jia, Mark D Foster Polymer chains when grafted to nanoparticles at high grafting densities are stretched more near the nanoparticle interface. Such strong stretching can lead to chain confinement close to the nanoparticle/polymer interface. Further from this interface, stretching decreases. This phenomena were studied in three different Polyisobutylene (PIB) graft copolymer rubbers. The grafts on the PIB backbones contain β-alanine trimers which self-assemble into crystalline nanodomain. By tailoring the chemistry of the grafts, the nanodomain length in one rubber was shortened by about 10 times, relative to the others. The effects of molecular design on domain self-assembly were quantified using small angle neutron scattering (SANS). The effects on chain dynamics close to the domain interfaces in swollen rubber was probed using neutron spin echo (NSE). SANS showed that these systems adopted a core shell morphology with varying extents of the region over which chain stretching occurs. NSE results showed that in the system designed to have the most highly stretched chains, confinement effects were seen over the widest range of length scales. The strongest dynamical confinement in the swollen state was observed at lengths of the order of the mean distance between nanodomains. |
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N00.00054: Spectroscopic Investigations on Polyethylene Oxide and Their Nanocomposites Mircea Chipara, Karen Martirosyan, Karen Lozano, Dorina M Chipara, Nicholas Dimakis, Victoria Padilla, Alexandro Trevino, Mataz Alcoutlabi, Carlos Delgado Polyethylene oxide-based nanocomposites were obtained by loading the polymeric matrix with fullerene, using the solution path. Various morphologies were obtained by using different solvents, and concentrations of C60. Raman investigations were performed using a Renishaw inVia spectrometer, operating at 785 nm. FTIR spectroscopy data were obtained by using a Bruker Hyperion Confocal Microscope. These studies were focused on the molecular basis of elasticity, analyzing in detail the effect of the nanofiller on the position and width of main lines. Complementary data were obtained by X-ray diffraction, using a Bruker Discovery 8 system. The line width was analyzed within HW approach to deconvolute between the effect of stress/strain and the size of crystallites. Molecular dynamics simulations were used to analyze experimental data. EPR measurements using a Bruker Elexsys operating in the X-band provided complementary information regarding C60 and their interactions. The effect of polymer morphology and of the loading by C60 on phase transitions was investigated by Differential Scanning Calorimetry. Thermogravimetric analysis was used to assess the thermal stability of these nanocomposites. An unusually strong increase in thermal stability was observed. |
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N00.00055: Disentangelment in Polymer/POSS Nanocomposite Blends Walter W Young, Reika Katsumata In the melt state of nanocomposites, rheological behavior is dictated by complex and often non-intuitive interactions between components. Many nanocomposites with relatively large and hard fillers show rheological jamming, which prevents terminal flow on long timescales and makes processing these advanced materials challenging. In contrast, polymers loaded with a much smaller filler, polyhedral oligomeric silsesquioxane (POSS), readily exhibit terminal flow on timescales comparable to neat polymers. Furthermore, the phenomenon of polymer disentanglement at high POSS loadings has been widely reported, but a molecular perspective of this phenomenon is elusive. Here, we study these disentanglement effects in the model poly(2-vinylpyridine) (P2VP)/octa(aminophenyl) silsesquioxane (OAPS) nanocomposite system. In this presentation, we discuss the effects of OAPS loading and P2VP molecular weight on the disentanglement to elucidate a detailed picture of the molecular-level processes taking place. We anticipate that an understanding of disentanglement mechanisms will prove vital for precisely tailoring and predicting the rheological behavior of complex materials used in fields such as additive manufacturing, where both high performance and facile processing are essential. |
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N00.00056: Using Time-of-Flight Secondary Ion Mass Spectrometry to Study Surface Wetting of Nanoparticles in Polymer Nanocomposites Aria C Zhang, Shawn M Maguire, Michael J Boyle, Jamie Ford, Kohji Ohno, Russell J Composto Polymer nanocomposites (PNCs), a combination of inorganic and organic fillers in polymer matrices, are of considerable interest because of their versatile properties. Specifically, the wetting behavior of nanoparticles (NPs) can enhance surface properties, such as wettability, friction, and durability. In our work, we utilize time-of-flight secondary ion mass spectrometry (ToF-SIMS) to investigate the wetting of poly(methyl methacrylate) grafted silica nanoparticles (PMMA-NPs) in a poly(styrene-ran-acrylonitrile) (SAN) matrix. To useToF-SIMS, experimental parameters such as incident beam energy and current as well as charge compensation are optimized to maximize secondary ion yields and minimize sample damage. From ToF-SIMS depth profiles, the PMMA-NP surface excesses (Z*) are measured as a function of annealing time, allowing for the determination of the mutual diffusion coefficient. By varying the molecular weights of PMMA grafted chains and film thicknesses, we study how diffusion of PMMA-NPs in SAN depends on NP sizes and PNC film thicknesses, respectively, aiming to elucidate a morphology map for the PNC system. The results allow for greater control over NP dispersions and PNC morphologies, which are crucial in tailoring PNC properties. |
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N00.00057: A New Direction of Polymer Nanocomposite: Polymer Infiltrated Scaffold Metals Weiwei Kong, Yueli Chen, Shawn Maguire, Connor Bilchak, Jamie Ford, Alexander Ng, Eric Detsi, Zahra Fakhraai, Russell J Composto Polymer composites have been widely studied because of their outstanding properties. Typically, polymer nanocomposites (PNC) are fabricated by adding inorganic nanofillers to a polymer matrix. In this work, a high-filler PNC is created by infiltrating polystyrene (PS) or poly(2-vinylpyridine) (P2VP) into a nanoporous gold scaffold exhibiting a bicontinuous structure and nanoscale pores. Infiltration occurs through capillary forces by heating PS (P2VP) above its glass transition temperature. PS and P2VP, having different affinities to the gold scaffold, exhibit different segmental dynamics inside the confined pores as measured through Tg. The more attractive P2VP shows a 20°C increase in Tg while PS shows only a 6°C increase at a comparable molecular weight. The effect of molecular weight on infiltration kinetics is presented with P2VP exhibiting longer infiltration time compared to PS having a similar molecular weight. The interconnected structure of these composites could facilitate high ion (electron) conductivity, thus enabling enhanced performance for batteries and flexible electronics. |
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N00.00058: Nanoparticle Patterning in Polymer Composite Fibers with Forced Assembly Process Kenan Song Research in nanoparticle-filled polymer composites has evolved over the years in terms of the structure-property relationship. From homogeneous dispersion to an interconnected 3D framework, the ability to pattern nanoparticles during a continuous, scalable fabrication process is essential for various functionalities. In this work, a combination of the forced assembly process and the dry-jet-wet spinning process is developed for generating a series of alternating layered structures. A 100 µm thick fiber consists of alternating polyacrylonitrile (PAN)/carbon nanotube (CNT), PAN/voids, or PAN/boron nitride (BN) layers with minimum layer thickness down to 170 nm. Two materials are extruded through a 3D printed nozzle for layer multiplication during the forced assembly process, followed by coagulation and post-treatments. Through engineering, the alternating layer patterns, mechanical and thermal properties are significantly enhanced compared to composites with homogeneously dispersed nanofillers. |
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N00.00059: A Simulation Study of Entropic and Enthalpic Effects on Local Dispersed Morphologies of Carbon-based Nanofillers in Thermoplastic Polyurethane Matrix Sunsheng Zhu, Shaghayegh Khani, Joao M Maia Carbon-based nanofillers (CNs) are widely applied to improve the engineering properties of polymer materials. The dispersion of CNs dominates the uniformity of micro-structures which is crucial to the enhancement of macroscopic properties. Herein, a simulation technique of modified Dissipative Particle Dynamics (DPD) is employed to study the effects of chemistry, interactions, and geometric structures on the locally dispersed morphologies of CNs in the Thermoplastic Polyurethane (TPU) matrix. Our findings indicate that 2-D nanosheets of CNs with a stacked initial morphology can be locally dispersed in the TPU matrix with long hard blocks at equilibrium, while they remain stable in the vicinity of short blocks. Through tuning the oxidation degree, it can be inverted to dispersed morphologies. It's observed that CNs are separated by the insertion of TPU hard blocks and repelled further in strongly aggregated hard blocks. Furthermore, the effects of dispersed initial morphologies and varied geometric structures of CNs on the finial morphological dispersions are studied giving rise to enthalpic stability. Our studies theoretically explain the entropic and enthalpic effects on the local dispersion of CNs and can be the guideline for evaluating the properties of TPU-CNs nanocomposites. |
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N00.00060: Reinforcement of Polyolefins with Polymer-Grafted Cellulose Nanocrystals Diana Cousins To improve their strength, toughness, and other mechanical properties, we have reinforced polyolefins using polyethylene-grafted cellulose nanocrystals. As the most widely used plastics, polyolefins such as polyethylene and polypropylene are extremely diverse. Various structures and molecular weights span a large range of mechanical properties. In order to reinforce polyolefins with a versatile and sustainably-sourced material, we have synthesized polyethylene-grafted cellulose nanocrystals (PE-g-CNC). CNCs are rod-like particles with excellent stiffness and strength, with previously proven potential to reinforce polymers. Asymmetric nanoparticles with high aspect ratio have significant potential for mechanical reinforcement, as demonstrated by clay-platelet dispersed nanocomposites in literature. With surface energy similar to that of polyethylene, these polymer-grafted nanoparticles can be more easily dispersed in polyethylene and similar nonpolar systems. AFM sand X-ray scattering studies revealed the details of CNC structure, dispersion and crystallization aspects of the functionalized polyethylene, while mechanical reinforcement of the films through addition of polyethylene-grafted CNCs was quantified through tensile testing. Ultimately, we will systematically examine the correlation between the molecular parameters of the asymmetric nanoparticles and polyolefins, and the associated macroscopic properties that emerge in such systems. |
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N00.00061: Mechanisms of Shock Dissipation in Semicrystalline Polyethylene John P Mikhail, Gregory C Rutledge This work analyzes various mechanisms for the dissipation of shock wave energy in a realistic, atomically detailed model of semicrystalline polyethylene (SCPE), for the purpose of understanding how this material can be applied in protective armor for people and equipment. The mechanisms considered for shocks 10 GPa and less are structural and vibrational in manner. Systems are studied using equilibrium molecular dynamics with a Hugoniostat to simulate application of the shock wave. To determine the extent of structural dissipation, order parameters and configuration time series are collected during the course of the shock simulations at different pressures and crystallinity fractions. Vibrational data are analyzed by computing density of states spectra pre- and post-shock. We conclude that the major mechanisms responsible for the shock energy dissipation of SCPE are plastic deformation and amorphization of the systems, manifested as changes in material gradients and order parameters, as well as changes to the crystalline structure via chain slip and reshaping of the unit cell. |
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N00.00062: Remarks on the deformation of semicrystalline polymers: double yielding, crystal relaxation, and beyond Masoud Razavi, Shi-Qing Wang Improvement of the mechanical properties of existing semicrystalline polymers (SCPs) or synthesis of new SCPs with enhanced mechanical performance requires a molecular-level understanding of the deformation in these polymers. In this respect, we design experiments to provide better insights into the deformation of SCPs. Apparent decoupling of yielding of amorphous and crystalline phases will be shown for the first time [1], as a generic behavior of deformation of SCPs. We will show that crystal mobility (αc relaxation) is not the only criteria to have an ultra-drawable SCP. This will be supported by a counter-example of PLLA, uncommon rate dependency of drawability in this polymer, and ultra-deformability of SCPs in compression. It will be indicated that crystal relaxation not only controls the later stages of deformation but can also affect small strain behavior of SCPs e.g., yield stress. Discussions will be continued with the classification of SCPs based on drawability and a simple estimation for the chain pullout force from a single crystal. |
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N00.00063: Raman and Infrared Study of Polar Crystals in Poly(vinylidene fluoride) Electrospun Fibers and Films Anuja S Jayasekara, Peggy Cebe Poly (vinylidene fluoride), PVDF, is a semi-crystalline polymorphic polymer with three stable crystalline forms. Its α crystalline phase is the most thermodynamically stable crystalline form with TGTḠ chain conformation. The polar β-crystallographic phase of PVDF with TTTT chain conformation is often used in fabricating piezoelectric and pyroelectric materials. α-phase PVDF films were prepared by compression molding PVDF powder at 200ºC and γ-phase films were prepared from solutions using dimethylacetamide. Fibers were formed by electrospinning, which is known to produce dominantly β-phase crystals. The crystalline fractions in different PVDF samples were controlled by applying various heat treatments to the films and changing electrospinning parameters in fiber preparation. Raman and Fourier-transform infrared spectra of PVDF samples were analyzed to determine specific precursors for each crystalline phase. Variations in the α-, β-, and γ-phase crystalline fractions were then determined from this analysis. |
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N00.00064: Development of rigid amorphous fraction in bulk samples and confined films of semi-crystalline syndiotactic polystyrene: Studies by differential scanning calorimetry and ellipsometry Boran Chen, John M Torkelson We investigated rigid amorphous fraction (RAF) in cold-crystallized, semi-crystalline syndiotactic polystyrene (sPS) as a function of crystallinity or crystalline fraction (CF). Characterization was by differential scanning calorimetry (DSC) for bulk samples with CF as high as 50% and ellipsometry for thin, confined films with CF as low as 1%. While DSC is commonly used to study RAF and its relationship to CF in bulk, semi-crystalline polymers, we developed for the first time a simple ellipsometry-based methodology for quantitative determination of CF and RAF in semi-crystalline films. Combining the results from bulk samples and thin films, with increasing CF during cold-crystallization we find that RAF in sPS increases from ~4% at 1% CF to ~16% at 10-25% CF and then decreases with increasing CF, achieving a RAF value of ~7% at the limiting CF of 50%. Importantly, there is a monotonic reduction in specific RAF, i.e., the ratio of RAF to CF, from 4.2 to 0.1 as CF increases from 1% to 50%, indicative of an increasing crystal perfection and extent of decoupling of amorphous and crystalline regions with cold-crystallization. We also observed a major dependence of maximum CF on film thickness, supporting a strong effect of near-nanoscale confinement on crystallization in sPS films. |
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N00.00065: Layer-by-layer crystallization from surface-induced nematic layers: a new mechanism of secondary nucleation revealed by molecular dynamic simulations Yanan Gong, Wenlin Zhang, Ronald G Larson Molecular dynamic simulations were conducted to study the surface nucleation of n-pentacontane (C50) near the surface of a crystal slab of stretched periodic chains. Order parameters identifying nematic and crystalline order showed that, even above the melting point of C50, a nematic layer with thickness around 0.9 nm (equivalent to about two layers of crystal) is induced on the crystal slab surface and grew as two-dimensional patches instead of stem-by-stem. When quenched below the melting point, the nematic layer transforms into a crystalline phase, following a classical nucleation theory in two dimensions, similar to that developed by Bourque and coworkers (Macromolecules, 2016, 49(9), 3619–3629). As the new crystalline layer approaches completion, a new nematic over-layer forms, which then, in turn, propagates the crystalline front another step forward. These novel results suggest a new mechanism of secondary nucleation of oligomers and polymers. |
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N00.00066: Polyolefin Co-Crystal Alloys: Mobile and Fixed Crystals Navin K Kafle, Toshikazu Miyoshi Co-crystallization of most semicrystalline polymers, especially polyolefins consisting of hydrocarbons is challenging due to difficulty of parallel packing in the same crystal. In this work, we report polymer co-crystallization of mobile and fixed polyolefin crystals using syndiotactic- (s) and atactic–(a) hydrogenated poly(norbornene) (hPNB)s, which are conformationally similar but dynamically dissimilar in the crystalline regions created by controlling stereoregularity in hPNB. Interestingly, these novel polyolefin co-crystals vary crystallinity (Φc) of 50-80% , long period (L) of 22 - 80 nm and melting temperature (Tm) of 135 -145 °C by simply changing compositions. |
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N00.00067: Roles of Conformational Flexibility in the Crystallization of Stereoirregular Polymers Toshikazu Miyoshi, Navin Kafle Stereoregularity significantly influences the crystallization, mechanical, and thermal properties of polymers. In this work, we investigate crystallization behaviors and molecular dynamics of atactic (a)-, isotactic (i)-, and syndiotactic (s)-hydrogenated poly(norbornene) (hPNB)s by using small-angle X-ray scattering and solid-state (ss) NMR. a-hPNB exhibits a much higher crystallinity (Φc) (82%) and long period (L) (80 nm) than i- and s-hPNB (50–55% and 17–21 nm). Moreover, in the s-hPNB crystalline region, chain dynamics is not thermally activated up to the melting temperature (Tm), while in the crystalline regions of i- and a-hPNB, small amplitude motions occur in a slow dynamic regime of 10–2–102 s. The molecular dynamics follows Arrhenius behavior in a-hPNB up to the crystal–crystal transition temperature (Tcc), while these dynamics are surprisingly saturated in i-hPNB under these conditions. Temperature dependence of the molecular dynamics leads to different crystal–crystal transitions between i- and a-hPNBs: i-hPNB changes the trans conformation to the gauche one due to the localized bond rotations where chain dynamics is restricted, whereas a-hPNB keeps a nearly trans conformation and conducts fast chain dynamics due to the amplified C–C bond rotations in the high-temperature phase. Such fast chain dynamics leads to unique crystallization behaviors of hPNB, specifically in the atactic configuration due to configurational disorder coupled with conformational flexibility. |
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N00.00068: Effect of Grafting Density on Molecular Bottlebrush Crystallization Behavior Jeffrey T Wilk, Michael Kelly, Bin Zhao, Christopher Y Li Tethered polymer chains, or polymer brushes, have widely been studied for their novel physical behavior and for their myriad of applications. In this presentation, we utilize a bottlebrush as a model system to study chain crystallization under confinement. A series of bottlebrush samples composed of a Poly(2-hydroxyethyl methacrylate) backbone with poly(ethylene oxide) (PEO) side chains was fabricated at different grafting densities. Both isothermal and non-isothermal crystallization studies were conducted to reveal the side chain grafting density effect on the sidechain packing and overall structure of the bottlebrush. Additionally, the retention of chain orientation within the melt state at elevated temperature was examined through a thermal fractionalization method and grafting density-dependent memory effects were discovered. This work suggests an architecture-based dependence on the nucleation and crystallization behavior in molecular bottlebrushes. |
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N00.00069: Functionalization of C=C bonds in Polycyclooctene: Progress in a Two-Step Approach to Polyolefin Valorization Eli J Fastow, Weihao Zhu, Marisa Kozlowski, Karen I Winey Polyolefins comprise a majority of plastic waste generated globally, and much of it ends up occupying landfills or polluting the environment as a result of low recycling rates. Here, we propose a two-step approach to chemical recycling of polyolefins by dehydrogenating to create C=C bonds in the backbone and then attaching functional groups via these bonds. In this study, we report hydrocarboxylation with cobalt-based catalysts of polycyclooctene (PCOE), a polymer used to model dehydrogenated polyethylene. An optimization study enabled the development of high-yield reaction conditions to add carboxylic acid functionalities to PCOE, as confirmed with infra-red and nuclear magnetic resonance spectroscopy. This reaction avoids deleterious crosslinking side-reactions and uses catalysts based on earth abundant metals. We compared the physical properties of these functionalized PCOEs to poly(ethylene-co-acrylic acid), a valuable material in the packaging industry, using contact angle and lap joint shear tests. Thus, we report progress in developing a reaction to functionalize dehydrogenated polyolefins, the second step of our proposed two-step approach to chemical recycling of polyolefins. |
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N00.00070: Upcycling LDPE to Dynamic Covalent LDPE Networks: Improved Mechanical Properties and High-Temperature Creep Resistance from Free-Radical Grafting of Dialkylamino Disulfide Bonds Logan Fenimore, Boran Chen, John M Torkelson Current methods for recycling spent polyolefins like low-density polyethylene (LDPE) most commonly result in their eventual downcycling to lower value products via thermal-mechanical degradation that occurs during extrusion. Recently, potential solutions have involved enriching waste plastics with dynamic covalent bonds, thereby enhancing mechanical properties through the introduction of crosslinks at use temperatures while maintaining the reprocessability that is characteristic of the original thermoplastic materials. For the first time, LDPE was upcycled to dynamically crosslinked LDPE networks by way of melt-state, free-radical graft copolymerization to incorporate dialkylamino disulfide bonds capable of dissociative reversible pathways at high temperature. These dynamic LDPE networks exhibit improved mechanical properties over a wide range of temperatures relative to LDPE as well as full recovery of crosslink density and associated properties with successive compression molding cycles at mild conditions. In addition, elevated-temperature viscous creep deformation is suppressed over long periods of time in the dynamic LDPE networks relative to LDPE. |
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N00.00071: Synthesis of a Recyclable Epoxy and its Thermomechanical Behavior During Depolymerization Samantha Lindholm, Brandon T McReynolds, Kavon Mojtabai, John D McCoy, Sanchari Chowdhury, Youngmin Lee
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N00.00072: Monomer Recovery from and Recycling of Biobased Polyhydroxyurethanes Marcus LaPorte, John M Torkelson, Yixuan Chen Past studies have demonstrated the recyclability of polyhydroxyurethane (PHU) networks exploiting available dynamic chemistries, reverse cyclic carbonate aminolysis and transcarbamoylation. These polymers are not infinitely recyclable as they undergo small levels of thermal degradation during each melt-state reprocessing step, eventually altering their desirable mechanical properties. To mitigate these drawbacks and provide further recycling options, monomer-like compounds were recovered from PHU via base-catalyzed solvolysis with methanol. These monomer-like compounds can be repolymerized into virgin PHU by transcarbamoylation or used separately as a bifunctional methyl carbamate and bifunctional vicinal diol for upcycling via synthesis of other step-growth polymers. Purification of solvolysis products can be achieved by boronate affinity chromatography, which selectively binds the vicinal diol product to the 4-vinylphenylboronic acid – styrene copolymer stationary phase. |
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N00.00073: Chemical Recycling of Isocyanate-Based and Non-Isocyanate, Bio-Based Polythiourethane Vitrimers Nicholas Mielke, Yixuan Chen, John M Torkelson Polythiourethane (PTU) networks are part of a growing class of materials known as vitrimers which possess the ability to be physically recycled by melt-state reprocessing despite possessing crosslinks. The implications these materials have on increased sustainability of thermosets, in addition to growing research demonstrating promising material properties, means that PTUs have the potential to begin replacing polyurethanes in a variety of applications. However, with the increasing turnover rate of new technologies and materials, methods to recycle the polymer into an entirely new material is needed. For this reason, finding ways to return the polymer to monomers and repolymerize them into new materials is an important subject of research. Here, we examine PTU depolymerization under alcohol solvolysis and explore ways to repolymerize the products of those reactions. Through proton NMR, results have shown promise in recovering monomer-like materials that have been successfully used for repolymerization, and DSC results demonstrate recovery of the polymer's original properties thus demonstrating the efficacy and sustainability potential of PTU vitrimers. |
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N00.00074: Reprocessable Catalyst-Free Polymethacrylate Networks Containing Dynamic Hindered Urea Bonds and Exhibiting Full Recovery of Cross-Link Density after Recycling. Mohammed A Bin Rusayyis, John M Torkelson Conventional cross-linked polymers cannot be reprocessed due to the presence of permanent covalent cross-links, preventing reuse and recycling. Covalent adaptable networks (CANs) employ dynamic covalent bonds that undergo dynamic reactions under external stimulus, allowing recyclability of these network materials. Hindered urea chemistry is one of the recently discovered dissociative dynamic chemistries. While hindered urea bonds have traditionally been exploited in the synthesis of step-growth type CANs, the use of hindered urea bonds in the synthesis of addition-type dynamic networks has only been narrowly explored. Here, we present a simple, fast method to synthesize a hindered-urea-based dynamic cross-linker that can undergo a free radical polymerization with vinyl-type monomers or polymers to form reprocessable CANs. Using this cross-linker, we developed dynamic catalyst-free polymethacrylate networks that can be (re)processed multiple times and exhibit full recovery of cross-link density after three recycling steps. Unlike other dissociative dynamic polymer networks, polymethacrylate networks containing dissociative dynamic hindered urea bonds do not flow and maintain their network nature even at high temperature (T>300 °C). |
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N00.00075: Non-food biobased, isocyanate-free linear and network polyhydroxyuthane and polythiourethane: Recyclability with cross-link density recovery and excellent elevated-temperature creep resistance Yixuan Chen, Boran Chen, Nicholas Mielke, John M Torkelson While major efforts have been made to improve the renewability of linear and network non-isocyanate polyurethane (NIPU) and polythiourethane (NIPTU), no previous study has exploited non-food biobased precursors to synthesize NIPUs or NIPTUs. Here, we employ several non-food biobased monomers, including four cyclic carbonates, two cyclic thiocarbonates, and three amines, and employed different combinations of them to prepare a variety of NIPUs and NIPTUs with segmented linear or network structures. For segmented linear non-food biobased NIPUs, we demonstrate that different non-food biobased cyclic carbonates provide for excellent tunability of properties and behavior, e.g., noise damping, crystallizability, and nanophase separation. For network non-food biobased NIPU and NIPTU, we demonstrate their robustness and reprocessability, including full recovery of crosslink density after three melt-state recycling steps. In particular, NIPTU exhibit promising tensile performance and excellent high-temperature creep resistance, which has never before been reported. |
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N00.00076: Tuning the Elevated-Temperature Creep Resistance of Reprocessable Polythiourethane Networks through Latent Catalysis and Stoichiometric Variations Nathan S Purwanto, Logan Fenimore, Mohammed A Bin Rusayyis, John M Torkelson The relatively rapid reaction of thiol and isocyanate groups results in thiourethane moieties and provides a route to synthesize both linear and network polythiourethanes (PTUs). PTU networks parallel the mechanical properties of conventional polyurethane (PU) networks and may be reprocessed with appropriate catalysis under mild conditions through both associative exchange and dissociative reversible dynamic mechanisms. Unfortunately, as conventionally made at stoichiometric balance, PTU networks exhibit poor elevated-temperature (T) creep resistance. Here, latent catalysis through the use of a thermally latent, protonated 1,8-diazabicyclo(5.4.0)undec-7-ene (DBUH+) complexed with tetraphenylborate (BPh4-) anion (DBUH·BPh4) catalyst as well as stoichiometric variations during synthesis were employed to produce PTU networks that fully recover their crosslink density and associated properties after successive compression molding cycles. Additionally, our PTU networks exhibited excellent creep resistance at high T, indicating that thermal latent catalysis and stoichiometric variations may be used to tune the rheological and dynamic mechanisms responsible for elevated-T creep behavior, a phenomenon detrimental to the mechanical performance of PU-like networks. |
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N00.00077: Thermomechanical Characterization of Recyclable Diels-Alder Epoxies with TiN Nanoparticle Loading Brandon T McReynolds, John D McCoy, Samantha Lindholm, Youngmin Lee, Kavon Mojtabai, Sanchari Chowdhury Typically, epoxy products are non-recyclable and difficult to remove. Recyclable epoxies were crosslinked by a Diels-Alder (DA) reaction between maleimide and furan functional group containing adducts (synthesized from polyetheramines and epoxide precursors). Epoxy variants studied include different architectures (4-arms or 6-arms) and different stoichiometric ratios of furan to maleimide. Titanium nitride (TiN) nanoparticles with significant visible light absorption were added for local, instant triggering of the rDA reaction by a high-intensity light source. Epoxies showed calorimetric glass transition temperatures in the range 0 to 30°C depending on molecular composition. High-temperature (~120°C) endothermic peaks corresponding to the rDA reaction were observed. In addition to the low temperature glassy phase, rheometry detected a rubbery plateau at moderate temperature followed by a rapid decrease in modulus indicative of liquid behavior. This high temperature (above ~140°C) decrease is a consequence of the rDA reaction depolymerizing the network. Lowering the temperature regenerates the network with a return of glassy and rubbery plateaus upon reheating. The incorporated TiN filler (<1wt%) slightly increased the modulus of the epoxies and permits localized heating. |
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N00.00078: Joule-heating-induced Multi-stage Reconfiguration in Dynamic Polymer Nanocomposites with Low Percolation Threshold Zhen Sang, Qing Zhou, Kartik K Rajagopalan, Edwin L Thomas, Frank Gardea, Svetlana A Sukhishvili Diels-Alder-based polymers (DAP) possess the distinctive ability to transition from a solid to a liquid phase when thermally stimulated. In addition, DAPs have the capability of solid-state plasticity. While DAPs provide a new approach to self-healing, actuation, and additive manufacturing, their respective nanocomposites are an area of research currently lacking attention. Herein, we report DAP/branched carbon nanotubes (b-CNTs) nanocomposites with an extremely low percolation threshold of electrical conductivity and Joule-heating-induced spatiotemporal controlled shape reconfigurability. The unique behavior of solid to low viscosity fluid transitioning allows the liquified DAP to effectively wet and infiltrate b-CNTs, leading to unprecedented fine dispersion. The dispersion of the fillers is further stabilized and maintained by chemical bonding between DAP and filler and by the rapid “click” behavior of the DAP upon cooling, which serves to “lock” the dispersion in place. These nanocomposites can self-heal and be 3D printed to strongly interbonded multi-material constructs with mismatched properties. By selectively activating different parts of the hybrid constructs, spatiotemporal control of shape reconfiguration was achieved via Joule-heating-induced network plasticity. |
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N00.00079: Upper Critical Solution Temperature Behavior of Linear and Star Polymers Aliaksei Aliakseyeu, Raman Hlushko, Svetlana A Sukhishvili This study explores the effect of molecular architecture (linear vs. star) on the upper critical solution temperature (UCST) behavior of ureido-modified polymers in solution. To that end, a series of linear and star poly(2-ureidoethyl methacrylate) (PUEM) polymers with the number of arms 2, 4, 6, and 8 were synthesized and studied. Our preliminary data showed that an increase in the number of arms of polymers with matched molecular weights leads to elevation of the transition temperature. This is likely due to a higher density of units and more extensive hydrogen-bonding between ureido-modified groups in the star polymers. In addition, we explored the effect of a hydrogen-bonded competitor on the UCST transition. Dimethyl sulfoxide (DMSO) – a hydrogen-bonded competitor – was demonstrated to efficiently control UCST transition for polymers with both molecular architectures by competing with polymer intramolecular hydrogen bonding. This work provides fundamental insight into the phase behavior of temperature-responsive star polymers which are potentially useful for controlled delivery applications. |
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N00.00080: Relaxation Spectra of Polymer Associated and Bulk Solvent in Poly(N-isopropylacrylamide) Water / Methanol Solutions Eric Rende, Bart-Jan Niebuur, Wiebke Lohstroh, Christine Papadakis, Alfons Schulte The hydration behavior of the responsive polymer Poly(N-isopropylacrylamide) (PNIPAM) provides a driving force in its demixing transition, and it is crucial for a molecular understanding of the co-nonsolvency effect of PNIPAM, i.e. the depression of the cloud point in water-methanol mixtures. We present an analysis of quasi-elastic neutron scattering (QENS) measurements1,2 of 25 wt % PNIPAM in water / methanol solvents across the demixing transition in terms of susceptibility spectra which allows for a clear separation of the various relaxation processes in the dynamic structure factor. Through contrast variation by employing deuterated solvent components the contributions from water and methanol can be distinguished. In addition to the bulk solvent processes the susceptibility spectra show two slower relaxation processes that are attributed to polymer associated water and methanol. Across the transition bound solvent is released which influences the effective bulk solvent composition. |
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N00.00081: Reversible Shape- and Color- Changing Block Copolymer Particles Driven by Photoisomerizable Surfactant Jinwoo Kim Polymer particles that switch their shape and color in response to light are of great interest to develop programmable smart materials. Herein, we report block copolymer (BCP) particles with reversible shapes and colors, activated by irradiation with UV and visible lights. This shape transformation of the BCP particles is achieved by a spiropyran-based surfactant (SP-DTAB) that changes its amphiphilicity upon photoisomerization. Under UV light (365 nm) irradiation, the hydrophilic ring-opened merocyanine form of SP-DTAB surfactant affords the formation of spherical, onion-like BCP particles. In contrast, when exposed to visible light, surfactants with the ring-closed form yields prolate or oblate BCP ellipsoids with axially stacked nanostructures. Importantly, the change in BCP particle morphology between spheres and ellipsoids is reversible over multiple UV and visible light irradiation cycles. In addition, the shape- and color-switchable BCP particles are integrated to form a composite hydrogel, demonstrating their potential as high-resolution displays with reversible patterning capabilities. |
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N00.00082: Photo-induced Block Copolymer Transitions in Ionic Liquids Claire L Seitzinger, Timothy P Lodge Photo-stimuli are widely used to induce changes in polymer systems, from crosslinking to curing. However, the ability to influence the phase behavior of a block copolymer with light remains underexplored. Our group has previously shown that the order-disorder transition (OD) of poly(methyl methacrylate)-b-poly(benzyl methacrylate) in imidazolium-based ionic liquids, a lower critical ordering transition behavior system, can be controlled with light by incorporating an azobenzene-based monomer into the poly(benzyl methacrylate) block. Our studies also demonstrated the ability to tune the OD by changing the solvent quality through the alkyl chain length on the ionic liquid cation. To explore this behavior further, we use small-angle X-ray scattering to identify the ordered states formed by the system and UV-irradiated small-amplitude oscillatory shear rheology (UV-SAOS) to observe the photo-response. The UV-SAOS involves a lower plate attachment to our rheometer where a light source can be guided into a channel and reflected on a mirror up through a quartz lower plate onto the sample. This allows for the sample to be irradiated in operando. We will discuss how the phase behavior of this system is influenced by varying the ratio of responsive to inert block in the polymer, as well as the relative azobenzene monomer content in the responsive block. |
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N00.00083: Stimuli-responsive Polymers for Pulsatile Release Reihaneh Jamshidi In this study, stimuli-responsive polymers have been utilized for generating pulsatile drug release systems. Pulse-release is more common in multi-unit systems, in which a programmable lag time between different dose/drug is essential. The lag time varies from hours to months depending on the disease state and drug types. The burst release after a certain lag time in the pulsatile system is commonly achieved by one of these approaches: rupturing (swelling/ osmotic pressure), degradation (hydrolysis/ enzyme), and changed permeability of the coating membrane. In this study, the release time of the implant is controlled by the thickness of the encapsulation layer, which consists of 5 % wt solution of gelatin, 1.5 % wt of sucrose, 1.5 % wt of glycerol, and 0.5 % wt of Poly(vinyl alcohol) (PVA) in DI water, dried at ambient condition for 24 hr. The lag time was controlled by a coating layer on the encapsulation. Samples designed to have 4-6 days lag time, were prepared by soaking the encapsulation in 0.5% glutaraldehyde (GA) aqueous solutions for 10 min to crosslink, and then soaked into a 20 % wt poly(lactic acid)(PLA) in methylene chloride 3 times, 30 sec each. Samples designed to have a 20-40 hr lag time were only soaked in PLA one time for 30 sec. The PLA-coated encapsulant was then put into 5 mL PBS buffer to test the drug release profile. PBS was replaced every 2 hr for samples for hour-range lag time, and 12 hr for day-range lag time. UV-vis spectroscopy was performed to characterize the release behavior. |
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N00.00084: Characterizing the full distribution of polypeptoid end-to-end distances via combined simulation and experiment Audra J DeStefano, Sally Jiao, Scott Shell, Songi Han, Rachel A Segalman Secondary and higher order structure as encoded in monomer sequence is critical to the function of proteins. Attainment of similar structural control in synthetic polymers offers the potential to access materials with unique properties driven by precisely-controlled structural ensembles, but remains largely out of reach due to a lack of understanding of how to control chain shape with polymer sequence, particularly in non-biological polymers. Sequence-controlled polypeptoids serve as a bridge between synthetic and biological polymers, and thus provide tremendous opportunity to develop design rules for programming primary sequence to modulate chain shape. This work demonstrates that polypeptoid conformational landscapes can be precisely probed via Double Electron Electron Resonance (DEER) spectroscopy and advanced molecular dynamics simulations, and moreover, that such synergistic experimental-computational studies elucidate the effects of polymer sequence and chemistry on conformational ensembles. Rather than obtaining an average end-to-end distance, this novel combined approach probes the full distribution of end-to-end distances and thus provides nuanced insights to structural changes that are often inaccessible by more traditional polymer characterization methods. Our results suggest that such a combined experimental-computational approach, leveraging the synthetic flexibility of the polypeptoid platform, can inform more general design rules for engineering sequence-specific polymers. |
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N00.00085: Self-assembled nanotube via control over polypeptoid helix Kai-Chieh Yang, Ronnie Garcia, Robert Murphy, Audra J DeStefano, Rong-Ming Ho, Craig J Hawker, Rachel A Segalman Chirality effect plays a crucial role in life science by underpinning the formation of chiral structures across all length scales, which further manifests itself in material properties, but is notoriously difficult to leverage in synthetic systems. Here, bioinspired polypeptoids-poly(N-substituted glycines) incorporating a chiral center on the backbone were designed and synthesized to understand the effect of chirality on self-assembly in bioinspired peptidomimics devoid of hydrogen bonding. As demonstrated in this study, polypeptoid helices display sergeants-and-soldiers behaviour to give chiral amplification. In addition, the rotational strength of polypeptoid helix was tuned by the numbers of chiral centers incorporated on the backbone. Stable helical conformational as examined by electron circular dichroism (ECD) and vibrational circular dichroism (VCD) results in strong inter-chain interactions, giving rise to self-assembled nanotube in good solvent as driven by orientational packing. |
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N00.00086: Protein-ligand binding in a temperature gradient Jutta Luettmer-Strathmann Many of the biological functions of proteins are closely associated with their ability to bind ligands. Since binding state and conformation of a protein affect its response to a temperature gradient, they may be probed with thermophoresis. In recent years, thermophoretic techniques to investigate biomolecular interactions, quantify ligand binding, and probe conformational changes have become established. To develop a better understanding of the mechanisms underlying the thermophoretic behavior of proteins and ligands, we employ a simple, off-lattice model for a protein and ligand in explicit solvent. To investigate the partitioning of the particles in a temperature gradient, we perform Wang-Landau type simulations in a divided simulation box and construct the density of states over a two-dimensional state space. This method gives us access to the entropy and energy of the divided system and allows us to estimate the configurational contribution to the Soret coefficient. For dilute solutions of hydrophobic proteins, we find that a hard-sphere solvent model captures important aspects of protein-ligand interactions and allows us to relate the binding energy to the change in Soret coefficient upon ligand binding. |
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N00.00087: 1D and 2D nanostructure formation via click conjugation of coiled-coil peptide bundlemer building blocks Weiran Xie, Rui Guo, Christopher J Kloxin, Jeffery G Saven, Darrin J Pochan Alpha-helical peptides that themselves assemble into coiled-coil bundles, or bundlemers, are being explored as a versatile building block to construct well-defined nanostructures. Computational designed 29 amino acids peptides self-assemble into monodisperse, homotetrameric coiled coils that are antiparallel in the water. With the tunable bundlemer surface groups and peptide termini, covalent 'click' conjugation reactive groups can be precisely presented for desired inter-bundlemer covalent interaction. Building blocks have been linked together to construct a 1D physical-covalent hybrid supramolecular polymer as previously shown. Herein we report our novel design of peptide bundlemer with click functional group presented from the side of the coiled-coil bundle. Novel ladder-like 1D peptide nanostructures are targeted by clicking the end-functionalized bundlemers with the new body-functionalized peptide bundlemer. In addition, we have also shown the capability to extend this 1D ladder-like peptide nanostructure to a 2D peptide sheet by controlling the surface functional groups on the coiled-coil peptide bundlemers. |
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N00.00088: Sequence-Encoded Supramolecular Assembly of Peptide Amphiphiles Qinsi Xiong, Chuang Li We used all-atom molecular dynamics calculations to elucidate the origin of the twisting that occurs in self-assembled peptide amphiphile (PA) ribbons. By changing the sequence length of VE repeats that are found to form twisted ribbons, we have connected the twisting to β-sheet formation in combination with hydrogen bonds between the strands. The right-handed twisted β-sheets are found to stack along the growth direction in a left-handed manner, which leads to a left-handed twisted ribbon. Furthermore, a chirality change from left-handed to right-handed twisted ribbons can be observed by introducing GRGD, which implies that GLY and protonated ARG do not have a bias toward right-handed twisted β-sheets. We also report the molecular design of supramolecular-covalent hybrid materials by incorporating PAs with various morphologies into photoactive covalent polymers. Supramolecular fibrous morphologies were found to play a more significant role in providing mechanical reinforcement and enhanced photoactuation. MD simulations indicate that the supramolecular fiber effectively facilitates the transport of trapped water molecules by functioning as a channel and therefore enhancing the actuation of the hybrid system. These are crucial for the precise design of chiral and hybrid materials. |
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N00.00089: Self-assembly of computationally designed peptide coiled-coil bundles Zihan Zhang, Jacquelyn Blum, Jeffery G Saven, Christopher J Kloxin, Darrin J Pochan 30 amino-acid peptides were computationally designed to assemble into homotetrameric coiled-coil bundles in a parallel arrangement. The N-termini of peptides were modified by cysteine or a non-natural maleimide functional group, respectively. Parallel coiled-coil bundles were linked together by thiol-Michael ‘click’ conjugation reaction to form bundle chains. Because all four N-termini of the constituent peptides are displayed from the same bundle end, only dimer bundle chains are possible by design making monodisperse chains a possibility when linking them together in an end-to-end fashion. The difference between the designed parallel peptide arrangement and undesired antiparallel bundle structure can be proved by Förster resonance energy transfer (FRET) experiments. The distance between the FRET pair on the two kinds of bundles is different, which leads to different fluorescence intensities. Small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS) are used to characterize the size and shape of chains. The liquid crystal behavior of parallel bundles will be studied under polarized optical microscopy. |
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N00.00090: Lattice solution assembly of coiled coil 'bundlemer' peptides in aqueous solutions Amanda L McCahill, Darrin J Pochan, Christopher J Kloxin, Jeffery G Saven Bundlemers are homotetrameric, antiparallel coiled coils in aqueous solution. The constituent peptide molecules are computationally designed and have great design flexibility with respect to sequence modifications and side chain functionality. During solid phase peptide synthesis, protecting groups are utilized on the functional side chains of amino acids to prevent side reactions. Alloc, or allyloxycarbonyl, is used as a common protecting group on the side chain of lysine in order to protect the primary amine. In this work, alloc groups are kept in the final, assembling peptides to be used as crosslinking points due to the carbon-carbon double bond on the alloc. The placement of these alloc groups on the periphery of bundlemer particles results in unique lattice-like structure self-assembly in solution. The effect of peptide net charge and solution pH on the assembly will be described. Transmission electron microscopy (TEM) and small angle x-ray scattering (SAXS) was used to characterize this assembly behavior. |
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N00.00091: Characterizing the Interactions Between Synthetic Random Heteropolymers with Molecular Dynamics Priya Ganesh, Shayna Hilburg, Ting Xu, Alfredo Alexander-Katz Synthetic random heteropolymers (RHPs) are amphiphilic, globular macromolecules that provide insight into protein behavior. While RHPs are inspired by proteins, the RHPs considered here are simpler systems composed of methacrylate-based building blocks without deterministic sequence-to-structure correlations. We use atomistic molecular dynamics simulations to show how sequence composition and surface chemistry impact the energetics and dynamics of inter-RHP interactions in water, including interaction time, solvent accessibility, and interface compositions. Our results show that although hydrophobic surface content is an important factor in the initiation of RHP dimerization, intermolecular contacts are not limited to hydrophobic regions. We also found that the dynamics of RHP remodeling in multi-chain assemblies are similar to those in single-chains on simulation timescales. Finally, we contextualize our results using methodologies for more widely-studied protein-protein interactions. |
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N00.00092: How to correctly simulate local chromosome organization with minimal computing effort: lessons from crumpled polymer physics. Amith Zafal Abdulla, Cedric Vaillant, Daniel Jost Gene regulation is highly dependent on the multi-scale 3D organization of chromosomes. In higher eukaryotes, biochemical modifications of the chromatin -epigenomic marks, modulate DNA accessibility thus transcription. Recent experimental evidence suggested that 1D epigenomic information, 3D genome folding and the formation of nuclear spatial compartments are coupled, but the mechanisms driving this coupling remain elusive. In my work, I employ polymer physics simulations to address this question. Often, biologically, genes or regions of interest are much smaller compared to the full length of a chromosome. Since (1) simulating long polymers (a full chromosome) for a biologically-relevant-long time period (hours) requires a lot of computing effort and that (2) the physics of long, topologically-constraint, aka crumpled, polymers differs from standard polymer theory, we address the theoretical question of what is the minimal genomic region around a locus of interest that one should simulate to effectively capture the correct dynamical and structural properties of this locus. We show that this minimal size depends on the overall epigenomic context and of the entanglement properties of the long polymer. We then show how our model can be contextualized to specific biological systems. |
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N00.00093: Molecular simulations of DNA-binding proteins dissociating from a self-avoiding bacterial chromosome. Aykut Erbas, Zafer Kosar, Ali G Attar By using extensive coarse-grained molecular simulations, we model the unbinding of specific and nonspecific dimeric DNA-binding proteins from a high-molecular-weight circular DNA molecule in a cylindrical structure mimicking the cellular confinement of a bacterial chromosome. Our simulations show that a concentration-dependent dissociation phenomenon, referred to as facilitated dissociation, can occur at physiological protein concentrations. When tens of micromolar protein concentrations (e.g., peaks levels of Fis protein in nutrient-rich conditions) are emulated, proteins significantly change the chromosome structure by forming dense protein clusters bridging specific sites or juxtaposing remote DNA segments. These structures, depending on the proteins’ binding specificity, either increase or decrease the protein off-rates (i.e., the inverse residence time of the protein on DNA). Overall, our results indicate that the cellular-concentration level of a structural DNA-binding protein is intermingled with the genome architecture and DNA-residence times, thereby providing a basis for understanding the complex effects of dynamic protein-DNA interactions on gene regulation. |
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N00.00094: An Efficient Method for Chitin Processing Using Phosphoric Acid: Oligomers, Nanocrystals, and High Polymers Xin Zhang, Yimin Mao, Natalie L Schwab, Robert M Briber Chitin is the second most abundant biopolymer on Earth behind cellulose. It is an important component in the shells of shrimp and crabs, the cell walls of fungi, etc. Chitin processing has remained challenging due to its poor solubility in common solvents, which greatly limits its utilization. We report using phosphoric acid as a versatile medium for chitin processing. With a precise control of the kinetics of two competitive processes, namely physical dissolution and acid hydrolysis, three types of products can be produced from chitin: water-soluble oligomers, nanowhiskers, and high molecular weight polymers. Properties of these products, which include the degree of deacetylation, surface charge, molecular weight and polydispersity, etc., were characterized. Potential applications of these materials in areas such as agriculture, food science, and polymer engineering are discussed. |
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N00.00095: Macromolecular Engineering of Spinnability Cheryl L Slykas, Carina Martinez, Jorgo Merchiers, Masab Bokhari, Naveen Reddy, Vivek Sharma Spinnability refers to a heuristic property associated with the possibility of making fibers using polymer solutions and melts. The long-standing challenge for fiber engineering is to correlate spinnability to macromolecular concentration and molecular weight, solvent properties like viscosity, surface tension, and volatility, and processing conditions. In this contribution, we explore spinnability of various polymer solutions using centrifugal force spinning, and seek a better understanding of how shear and extensional rheology response and polymer or solvent choice influence fiber morphology, properties, and applications. |
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N00.00096: Electrospun, non-woven, nano-fibrous novel Poly(vinyl Alcohol) membranes functionalized with L-Arginine for virus capture Salma Ly The development of pretreatment membranes have led to multiple advancements in water and air filtration systems. Previous studies have tested the porous structure, tensile strength, and physicochemical properties by introducing different ligands to the backbone of a polymer. Electrospinning a membrane can lead to improvement in reproducible samples, and accuracy in pore size.One derivative of these membranes can serve as an antiviral layer in a mask rendering more accurate results with eco-friendly materials, reusability, and increased screening accuracy in viral droplets. The enhanced electronegative properties of the mat are supported by previous experiments to attract and capture viruses of multiple varieties.This electronegative property will have increased longevity compared to previously produced masks due to the electrospinning process. The nano-fibrous electrospun polyvinyl(alcohol) mat can then be functionalized with L-arginine to increase the charged guanidinium groups in the membrane. These charged groups will then improve ionic conductivity, thermal and chemical stability. The interchangeable steps of crosslinking and quaternizing the PVA come after electrospinning the solution of ligand and polymer. Crosslinking the membrane will enhance the overall tensile strength and mechanical properties.The Quaternization fabricates an anion-exchange and enhances hydrophilicity. The different concentration ratios of L-arginine to the PVA, and the variety cross linking reagents were tested with a carbon capture apparatus which supported evidence of functionalized L-arginine. The chemical shifts in H-NMR supported a physical incorporation of the L-Arginine to the surface of the polymer. However, there is no evidence of esterification that will support a chemical bonding to the surface. However, virus capture apparutus testing resulted in 100% virus capture on the control supporting improved porous structure for the PVA mat encouraging further testing. |
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N00.00097: Modeling Adsorption and Transport Properties of Gases in Amorphous Polymers Micah L Welsch, Brian B Laird Developing greener and more cost-effective polymer membranes for gas separation is of major interest within the industry of gas purification, in particular with regard to H2 separation. In this work, molecular modeling was used to aid experimental efforts to optimize furan-based and fluorinated polymer membranes for high H2 permeance selectivity. Preliminary findings for furan-based membranes showed potential for advancing this goal but further investigation yielded insufficient permeance selectivity of H2 over N2. Present findings show that fluorinated membranes are also a promising medium for gas separation with much higher selectivities for H2 observed. To guide a detailed understanding of this behavior a molecular-level approach has been applied with both Monte Carlo and molecular dynamics simulation. Permeability is comprised of the product of solubility and diffusivity, both of which are highly accessible computationally. Gibbs-Ensemble Monte Carlo was used to calculate gas solubility and allowed for the determination of preferred adsorption sites within the polymer systems. Molecular dynamics simulation was then used to calculate rates of gas diffusion with each polymer studied. Fluorinated polymers of interest also possessed differing tacticities whose unique structures were examined in hopes that they may offer an additional degree of freedom for polymer optimization. Gaining an understanding of these processes on a molecular level will help guide the optimization of polymer structures and conditions needed to develop efficient separation membranes. |
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N00.00098: Shape-selective filtration using lamellar block copolymer based slit membranes Maninderjeet Singh, Edward Armijo, Alamgir Karim The growing need for highly efficient water purification and bioseparations necessitates innovations in ultra-filtration membranes. Block copolymer (BCP) membranes have emerged as a promising player for efficient ultra-filtration due to their uniform pore sizes and sharp cut-offs. Most of the work in BCP membranes has focused on using cylindrical pores. In this work, we have developed novel slit-based membranes using lamellar block copolymers. The lamellar BCPs are vertically oriented in one step film casting process by tuning the solvent evaporation rates with additives. The vertically oriented BCPs are converted to slit membranes using a wet etching process. The pore sizes of these slit-based membranes are measured using surface characterization and filtration cut-off experiments. We demonstrate the enhanced separation of 1-D nanomaterials as compared to the 0-D nanomaterials using these slit-based membranes, which is facilitated by the shape similarity of 1-D nanomaterials with the nano-slits. Such membranes possess the potential for shape-selective filtration of biomaterials such as proteins, viruses, and pharmaceutical drugs and open avenues for shape-selective filtration across a spectrum of applications. |
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N00.00099: Autonomous exploration of non-equilibrium block copolymer assembly Masafumi Fukuto, Sebastian T Russell, Suwon Bae, Kevin Yager Artificial intelligence and machine-learning methods hold enormous promise for accelerating the discovery of new materials. Autonomous experimentation (AE) leverages machine learning for decision-making within an experimental loop, allowing more efficient exploration of large and complex parameter spaces. However, several challenges remain in deploying these exciting approaches to realistic experimental problems. Here, we apply these methods to exploration of the multidimensional material and processing parameter spaces associated with non-equilibrium self-assembly of block copolymer (BCP) thin films, using AE to guide the execution of both small-angle x-ray scattering (SAXS) measurements, and molecular dynamics simulations of these materials. The experimental AE loop couples data acquisition, real-time data analytics, and a decision-making algorithm based on Gaussian Process modeling. The resultant multi-dimensional dataset is clustered using semi-supervised K-means in order to generate a catalog of structurally unique motifs. Molecular dynamics simulations elucidated the impacts of processing and material parameters on the diffusion of constituent BCP chains and the structural development of target nonequilibrium morphologies. Overall, this coordinated exploration enabled discovery of new non-native BCP architectures. |
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N00.00100: Symmetric Diblock Copolymers in Cylindrical Confinement: A Way to Chiral Morphologies? Ludwig Schneider, Daniel Vega, Georg Lichtenberg, Marcus Mueller We investigate the confinement-induced formation and stability of helix morphologies in lamella-forming AB diblock copolymers via large-scale, particle-based, SCMF simulations. Such helix structures are rarely observed in bulk or thin films. |
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N00.00101: Combining Particle-Based Simulations and Machine Learning to Understand Defect Kinetics in Thin Films of Symmetric Diblock Copolymers Ludwig Schneider, Juan De Pablo The self-assembly of soft matter provides a practical and scalable route towards production of nanostructured materials, with minimal need for direct intervention at nanoscopic length scales. |
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N00.00102: Interface-induced ordering in lamellar block copolymer electrolytes Jonathan P Coote, Joshua Sangoro, Gila E Stein Lamellar block polymers base on polymer ionic liquids (PILs) show promise as electrolytes in electrochemical devices but often exhibit structural anisotropy that depresses through-film ionic conductivity. We propose that one source of structural anisotropy in these systems is short-range stacking of lamellae adjacent to the electrodes due to preferential adsorption of one block at this surface. This point is demonstrated with lamellar diblock copolymers of polystyrene (PS) and a polymer ionic liquid (PIL). Grazing-incidence X-ray scattering (GISAXS) from thin films reveals lamellae stacked normal to the plane of the film, with no evidence of isotropic lamellar order, while transmission small-angle X-ray scattering (SAXS) in 50-100 μm films detects randomly oriented lamellar grains. The ionic conductivity of 100 μm PS-PIL films was found to be approximately 20x higher in the in-plane direction than the through-plane direction, consistent with a mixed structure consisting of highly oriented lamellae at the electrode surfaces and randomly oriented lamellae throughout the interior. To reduce the tendency to form highly-oriented interfacial structures, the electrodes can be coated with random copolymers that screen preferential interactions. |
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N00.00103: Control of nanostructures in multi-components polymer brushes TAEYI KIM, Luis A Padilla, Vikram Thapar, Su-Mi Hur In addition to switching surfaces, multicomponent polymer brushes have the ability to modify their surface with microphase-separated various nanoscale structures similar to block copolymer thin film. While there have been numerous theoretical and numerical efforts to predict the phase behavior of polymer brushes, comprehensive understandings on the roles of numerous system variables on morphology formation are limited. Here, we study microphase separations of block copolymer brushes and mixed polymer brushes using a coarse-grained simulation model with a generalized Hamiltonian, which allows the system to have a topologically unconstrained free surface. The effects on major system variables, including molecular composition, grafting density, segregation strength, surface affinity, chain stiffness, and solvent quality on morphologies in brushes, are investigated within a single simulation framework. We summarize our findings in phase diagrams and provide a discussion about the underlying phenomena dictating the behavior of polymer brushes. |
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N00.00104: Effective Interface Control of Block Copolymer Thin Films using the Air-Water Interfacial Layer of Short-Chain Block Copolymers Seong Eun Kim, Dong Hyup Kim, So Youn Kim Self-assembly of block copolymer (BCP) thin films is of interest in nanoscience due to their potential to be employed in nanopatterning. For BCP nanopatterning, the vertical orientation of BCP is lithographically useful, which is only realized when the energy of the substrate and interface is neutral for both blocks. |
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N00.00105: Modeling Polymerization-Induced Self-Stratifying Coatings Hyeonmin Jeong, Charles E Sing Multilayer coatings have various applications such as car paint, self-healing, and anti-fouling surfaces, where it is useful to have multiple layers with complementary functions. However, multilayer coatings involve many processing steps, increasing cost and the possibility of interfacial failures. Self-stratifying coatings are excellent candidates to address these issues, by relying on the assembly (i.e. stratification) of a singly-applied coating that minimizes cost while preventing interfacial failures. Our goal is to develop a computational model to understand the fundamental processes underlying the behavior of self-stratifying coatings, thereby predicting the physical forces driving stratification and facilitating the chemical design of new coatings. We present the simulation model developed to study phase separation in binary mixtures where components undergo a polymerization reaction, a relevant model system for understanding polymerization-induced self-stratification. We use a combination of field theoretic simulations and numerical evaluation of Cahn-Hilliard theory, along with models of reaction kinetic models, to understand the interplay of polymerization and phase separation dynamics in self-stratifying systems. |
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N00.00106: Wetting Transparency of Ultrathin Polymer Films Reika Katsumata, Evon Petek, Zachary Ahmad Recent advancements in chemical vapor deposition, surface-initiated polymerization, and others provide fine-tuning of polymeric coatings below 10 nm-thick, which becomes comparable to the length scales of molecular interactions. In these ultrathin coatings, surface wettability can be influenced by its underlayer as if it is “transparent” in terms of wettability: so-called wetting transparency. While wetting transparency has been extensively studied for graphene, little work has been done with polymeric materials, perhaps because of the structural heterogeneity of polymers. Herein, we study a model bilayer system of thin, crosslinked polymer films of poly(methyl methacrylate) and polystyrene (PS) to prevent undesired interphase diffusion or dewetting. We aim to decouple surface energy contributions from long-range van der Waals (vdW) forces and short-range hydrogen bonding interactions by performing contact angle measurements with hydrophilic (water) and hydrophobic (diiodomethane) test liquids. The thickness dependence of these contact angles will determine a critical film thickness for wetting transparency associated with short and long-range interactions. In preliminary calculations derived from existing theories of vdW potential and the Lifshitz theory, we find that the contact angle of PS films shows thickness dependence when films are smaller than ~5 nm due to vdW forces from underlying substrates. This prediction cannot explain previous experimental work, which shows that the water contact angle on a PS film/silicon oxide substrate starts to deviate from its bulk value at thickness ~ 100 nm. In this poster, we will discuss a hypothesis to describe the mismatch between theory and experiments. |
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N00.00107: Observing Thermal Motion for Isolated Poly(tert-butyl methacrylate) Chains on Solid Surfaces Masayuki KAWANO, Yuma Morimitsu, Yukari Oda, Daisuke Kawaguchi, Keiji Tanaka A better understanding of the hierarchical dynamics of polymers on a solid surface is of pivotal importance for improving the material designs of polymer nanocomposites. Here, we examined the thermal molecular motion of isolated poly(tert-butyl methacrylate) (PtBMA) chains on solid surfaces based on atomic force microscopy. While the center-of-mass diffusion of chains was not clearly observed on the hydrophobic hydrogen-passivated silicon substrate, it was on the hydrophilic hydroxy-terminated silicon substrate. The diffusion coefficient for chains on the hydrophilic substrate was (1.35 ± 0.08) x 10-14 cm2•s-1. The mobility difference of PtBMA chains on the two substrates might be explained in terms of the presence or absence of adsorbed water molecules in addition to the interaction with the substrate. |
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N00.00108: Nanostructure of Atmospheric Plasma Polymerized Films Measured by X-ray Reflectivity Brenna Rossi, Cagatay Yilmazoglu, Mark D Foster Plasma polymerization is a facile method of depositing robust films on a wide variety of substrates without the volatile organic solvents associated with conventional coatings. Films plasma polymerized in vacuum have been widely studied, but deposition using atmospheric plasma polymerization is less cumbersome. However, while the nanoscale structure of films deposited in vacuum has been studied some, little is known of the nanoscale structure of the films deposited in the more complex atmospheric conditions. X-ray reflectivity measurements reveal that films deposited using hexamethyldisiloxane (HMDSO) precursor often have depth profiles of scattering length density (SLD) consisting of a center ("bulk") region where the SLD is uniform with depth, a 4-8 nm thick transition region at the substrate and a 3-10 nm thick layer with distinct structure next to air. Deposition rate and SLD in the film center change with plasma power, but these characteristics are also sensitive to changes in ambient humidity. At higher humidity deposition rate and film interior SLD are less sensitive to power level. |
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N00.00109: Effect of polymerization kinetics in photopolymerization-induced phase separation for polyether in photo-curable monomers in film geometry Yeongsik Kim, Younghan Song, Lauren Zakrzewski, Chang Y Ryu, Chulsung Bae Photopolymerization-induced phase separation is triggered by the polymerization to convert the low molecular weight monomers into polymer networks, and it would serve as a useful strategy for fabricating 3D printed porous structures in stereolithography. Polyether as phase separation additives has an incompatibility with photo-curable (meth)acrylate monomer system and removable properties using alcohol to create porous polymer networks. We have compared the difference in the morphological development of polymerization-induced phase separation with different types of additive polymer. Real-time optical turbidity measurements have been carried out to measure UV light transmittance for the in-situ monitoring of the photopolymerization induced phase separation under the continuous UV irradiation. Optical and electron microscopy tools have been utilized to investigate the morphology for the photopolymerization-induced phase separation confined in film geometry. |
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N00.00110: Effect of Photo-Polymerization and Phase Separation Kinetics on the Structure-Property Relationship of 3D Printing Resins Using PPG Lauren A Zakrzewski The physical properties of 3D printed porous materials can be tailored via photo-polymerization-induced phase separation. The competition between photo-polymerization kinetics and phase separation can be studied through use of a multiscale method to show the extent of phase separation and its overall effect on the material once 3D printed. A main characterization method of phase separation is a UV transmittance experiment performed using a custom-built light transmission apparatus. Additional characterizations have been performed to get information on the photo-polymerization kinetics and morphology of the polymer films such as real time-fourier transform infrared spectroscopy, polarized optical microscopy, and scanning electron microscopy. Compression testing and tensile testing have been used to characterize the mechanical properties of the molded material. Polypropylene glycol (PPG) is used as a polymer additive. PPG-containing resins show a drastic increase in turbidity upon photo-polymerization. By altering the composition and molecular weight of PPG additive used, the extent of phase separation and therefore the mechanical properties of the material can be tuned. |
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N00.00111: Effect of Compatibilizers on the Structure and Dynamics at Polymer Blend Interfaces Shoumik Saha, Dilip Gersappe Polymer blends, which provide improved rheological and mechanical properties, are difficult to mix and leads to high energy interfaces between the components. This results in significant mechanical weakness but can be mediated by using compatibilizers. Here, we use molecular dynamics simulations to determine the effect of different types of compatibilizers on the interfacial behavior between two types of identical polymer chains. We investigate the effects of three types of copolymers (diblock, random and alternating) and compare its effect to inorganic sheet-like compatibilizers. Our results indicate that sheet-like fillers that have equal affinity to either polymer in a binary blend can produce a larger reduction of interfacial tension when compared to copolymers at equal volume fractions. We also show that sheet fillers reduce slip, thus providing for improved stress transfer across the interface, leading to a stronger blend. However, the localization of sheet fillers at the interface can be a possible limiting factor. Thus, we attempted to bracket the limits of sheet filler behavior by either allowing them to maximally localize at the interface or where the segregation at interface is kinetically limited. This step is highly dependent on sample preparation. |
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N00.00112: SOFT MATTER PHYSICS
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N00.00113: Tracer dynamics in a concentrated colloidal system Jimpaul Samukcham Tracer dynamics of a concentrated colloidal system is studied using the Dissipative Particle Dynamics (DPD) simulation model. The particle softness is varied and the dynamics is studied near the transition temperature of the fluid. The Tracer-Tracer (TT) softness parameter is fixed for the whole simulation. And the Fluid-Fluid (FF) softness parameter along with the Fluid-Tracer (FT) softness parameter are made to vary. The MSDs of tracers are studied for the different combinations of the FF and the FT softness parameters. |
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N00.00114: Controlling and Patterning Polyelectrolyte Liquid Droplets with Electric Field Aman Agrawal, Matthew V Tirrell, Jack F Douglas, Alamgir Karim Control and manipulation of colloidal 'particles' using external electric fields have been of much interest for their potential uses in many applications, including drug delivery. Much of this work has focused on solid particles, with less emphasis on liquid droplets, due to the ease of manufacturing those materials. From a materials point of view, a surfactant stabilized oil droplet in water could serve this purpose. However, it is a non-trivial task to encapsulate biomolecules in an oil phase. To over this challenge, we have made a water-in-water emulsion of a phase-separated polyelectrolyte blend and stabilized the liquid droplets against coalescence. These droplet can serve as field responsive bio-capsules. The capsules are electrostatically charged, and can be simply manipulated using a 9V battery. We found that the droplets exhibit controlled mobility under the E-field in a 2D plane. Moreover, due to the high polarizability of polyelectrolytes, these polyelectrolyte capsules can be patterned into parallel, pearl-like chains - typical of an electrorheological fluid of conventionally solid particles - albeit at orders of magnitude lower E-field strengths. As a demonstration, we encapsulated and transported protein molecules of various kinds in these field-driven capsules. |
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N00.00115: Encoding Bespoke Textures in Block Copolymers Using Magnetic Fields Yvonne Zagzag Liquid-crystalline block copolymers (LCBCPs) self-assemble into microphase-separated structures that are magnetically anisotropic. As such, orientational order in these systems can be prescribed using a magnetic field whereby the resulting texture is governed by the balance between magnetostatics, elasticity, and interfacial block interactions. On this basis, we can program carefully designed textures (methodical arrangements of mesophase grain orientation) in these systems using patterned magnetic fields. To direct the self-assembly of the LCBCP, ferromagnetic materials are used in the presence of a weak background field to create predetermined field patterns. These fields alter the nematic director of the mesogenic material. As such, the system adopts the field-imposed structure during the microphase separation process of the diblock. We anticipate that coupling thermomechanical, thermochromic, and optical properties of LCBCPs to bespoke texture design will enable a new paradigm for geometric actuation in soft materials. This development of stimuli-responsive material, will lay a groundwork for the invention of materials with tunable properties for industries like soft-robotics, smart-wearables, and photonics. |
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N00.00116: Confinement induced relaxations and phase behavior of a nanoconfined columnar ionic liquid crystal Mohamed A Kolmangadi, Andreas Schoenhals Liquid crystalline mesophases in nanoconfinement exhibit intriguing phase transition behaviors and relaxation dynamics. We investigate the molecular dynamics and electrical conductivity of a linear-shaped guanidinium-based ionic liquid crystal (ILC) confined in self-ordered nanoporous alumina oxide templates of pore diameter 180nm down to 25nm by employing broadband dielectric spectroscopy (BDS) and calorimetry. Calorimetric investigation reveals a complete suppression of the columnar – isotropic transition, while the plastic crystalline – columnar transition temperature decrease with decreasing pore size. Two relaxation modes similar to the bulk sample, the γ, and α1 relaxation, are observed in the plastic crystalline phase, and a new fast relaxation mode, the α3 relaxation process emerges in the columnar phase, which is absent for the bulk sample. The γ relaxation is assigned to the localized fluctuations while the α1 is due to the segmental dynamics of the alkyl chains. Further possible interpretations for the α3 process are discussed. For the bulk ILC, a jump of 4 orders of magnitude in the absolute values of DC conductivity occurs at the transition from the plastic crystalline to hexagonal columnar phase, while for the confined ILC, this transition is smooth. |
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N00.00117: Structural Color Production in Melanin-based Disordered Colloidal Nanoparticle Assemblies in Spherical Confinement Christian M Heil, Anvay A Patil, Ali Dhinojwala, Arthi Jayaraman Melanin is a ubiquitous natural pigment that exhibits broadband absorption and high refractive index. Despite its widespread use in structural color production, how the absorbing material melanin affects the generated color is unknown. Using a combined molecular dynamics and finite-difference time-domain computational approach, we investigate structural color generation in one-component melanin nanoparticle-based supraballs as well as binary mixtures of melanin and silica (non-absorbing) nanoparticle-based supraballs. We validate our approach by demonstrating that experimentally produced one-component melanin and one-component silica supraballs produce reflectance profiles similar to the computational analogues. We isolate the influence of melanin's absorption, packing fraction, and nanoparticle size dispersity on color generation in one-component melanin supraballs in our optical simulations. We also extend our computational approach to study how nanoparticle stratification and degree of interparticle mixing/demixing of melanin and silica nanoparticles affect optical properties. These results provide design principles for synthesizing melanin-based systems to control color, saturation, and lightness factor for applications as pigments for cosmetics, paints, and food coloring. |
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N00.00118: Regulation of Elastic instability from non-Brownian Suspension Sijie Sun, Nan Xue, Stefano Aime, Howard A Stone, Gareth H McKinley, David A Weitz Viscoelastic fluid flows distinctly from the Newtionian liquid. When the shear rate is high, the flow elasticity cannot be relaxed. And secondary flows will emerge. This phenomenon is named elastic instability. In this experimental work, we combined different rheoflow visualization techniques to investigate the influence of finite volume fraction non-Brownian suspension on the elastic instability of visco-elastic shear flow. We found that, in the visco-elastic flow, suspension assembles to large ordered structures, even under a volume fraction far lower than the random close pack. Further, such structures will regulate the secondary flow, which suppresses higher-order modes of the secondary flow. This research highlights the connections between suspension structures and the elastic instabilities of a viscoelastic flow. It also provides a new method to phase separate particles from the liquid. |
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N00.00119: Modeling Dynamic Swelling of Polymer-Based Artificial Muscles Shefik D Bowen, Daniel T Hallinan Polymer-based artificial muscles could potentially replace traditional motors and actuators in applications where weight and flexibility are important, such as soft robotics, active prosthetics, and microfluidics. Material chemistry and muscle geometry are important parameters that impact device performance, e.g. strain, strain rate, lifetime, achievable work, and efficiency. Modeling the rate and degree of swelling of polymer fibers is an essential part of developing materials and designing muscles that perform as desired. This study is motivated by the possibility of significant actuation from twisted and coiled polymer fibers that rely on radial swelling to produce reversible work. An analytical thermodynamic expression (based on Flory-Huggins Theory) was combined with a numerical transport model in order to simulate transient swelling of a polymeric network driven by diffusion and migration. The numerical model evaluates the impact of polymer swelling on transport in polymers directly by locally accounting for the length increase of discrete elements due to solvent presence, which cannot be done analytically. The combined model of transient radial swelling of polymer fibers can be used for parametric studies or analysis of experimental data. This study will aid efforts to identify the best material candidates for practical use as artificial muscle fibers and will help evaluate the geometry needed to achieve device requirements. |
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N00.00120: Non-linear interactions between muscle and scaffold in biohybrid robots M Taher Saif, Onur Aydin Bio hybrid robots use living muscles for actuation. These muscles are formed in situ by dispensing a liquid mixture of myoblasts and extra cellular matrix (ECM) on the robot scaffold. The cells compact the ECM after curing, apply a static force on the scaffold and differentiate to myotubes. This differentiation process depends on the force that the cells generate and the amount of self-stretch they experience. The evolution kinetics of the muscle results from a complex cross talk between the cells and the scaffold deformation history. If the scaffold is too compliant then the cells cannot generate the force and the differentiation is hampered. If the scaffold is too stiff, then excessive cell force may cause them slide with respect to each other limiting myotube formation. The detailed nature of this cross talk is yet to be resolved. Here, we propose a robot scaffold that serves as a non-linear spring – stiff during early phase of differentiation but soft as differentiation proceeds. This allows the cells to generate sufficient force and self-stretch during the formation of myotubes, but large deformation of the scaffold with small increase of muscle force during actuation of the robot. The principle is applied on a biohybrid swimmer robot as a proof of principle. |
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N00.00121: Assur graphs and marginally jammed packings Jose M Ortiz, Xiaoming Mao, Ethan M Stanifer Jammed packings of soft frictionless spheres are important example systems for the study of granular media and glasses. Here we make an observation about the graph theory attributes of the contact network. It is known that at the unjamming point the contact network is isostatic. We argue that the unjamming point is not only isostatic but minimally isostatic meaning that the network does not possess any proper isostatic subgraphs. Minimally isostatic graphs are also known as Assur graphs. It had been previously observed that isostatic packing derived networks become globally floppy when any bond is removed and globally over-constrained when some bond is added. This is a hallmark property of Assur graphs. Furthermore, we argue that minimal isostaticity may be a necessary consequence of having a repulsive interaction and the first order like nature of the unjamming transition. |
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N00.00122: A soft robotic fluidic transmission system Maziar Arfaee, Johannes B Overvelde, Jolanda Kluin Soft pneumatic actuators are powerful, relatively easy to control, and becoming popular due to their embodied intelligence. Studies have shown that geometrical design and material properties can affect their behavior significantly. Here we introduce a soft fluidic transmission system that is inspired by pouch motors. By developing these structures, we are interested in pumping higher flows at lower pressures by actuating the system at lower flows and higher pressures. In other words, we would like to achieve a flow transmission ratio higher than one. we started by investigating the effect of geometries and material elasticity on pouch motors functionality to optimize their design. We designed and conducted mechanical tests on different groups of the pouch motors with different geometries and material properties to characterize them. We have also developed analytical models to simulate and predict the behavior of the system, which we are currently validating using experimental samples fabricated from a range of different materials. Ultimately, we are interested in determining if we can control the behavior of soft actuators using higher pressures and lower flows generated, e.g., by hydraulic pumps or chemical reactions, to potentially decrease the size of the control system. |
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N00.00123: Orbital magnetism of an active particle in viscoelastic suspension Muhammed Muhsin A, MAMATA SAHOO, Arnab Saha We consider an active (self-propelling) particle in a viscoelastic fluid. The particle is charged and constrained to move in a two-dimensional harmonic trap. Its dynamics is coupled to a constant magnetic field applied perpendicular to its plane of motion via Lorentz force. Due to the finite activity, the generalized fluctuation- dissipation relation (GFDR) breaks down, driving the system away from equilibrium. While breaking GFDR, we have shown that the system can have finite classical orbital magnetism only when the dynamics of the system contains finite inertia. The orbital magnetic moment has been calculated exactly. Remarkably, we find that when the elastic dissipation timescale of the medium is larger (smaller) than the persistence timescale of the self-propelling particle, it is diamagnetic (paramagnetic). Therefore, for a given strength of the magnetic field, the system undergoes a transition from diamagnetic to paramagnetic state (and vice versa) simply by tuning the timescales of underlying physical processes, such as active fluctuations and viscoelastic dissipation. Interestingly, we also find that the magnetic moment, which vanishes at equilibrium, behaves nonmonotonically with respect to increasing persistence of self-propulsion, which drives the system out of equilibrium. |
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N00.00124: Rupture of stochastic networks: relation between structural parameters and network strength and toughness Catalin Picu, Shengguang Jin, Sai S Deogekar Network materials are encountered broadly in the engineering and natural worlds. These materials have a molecular or fiber network as their main structural component. The integrity of network materials is critical in many applications. Therefore, it is of interest to determine ways to control their strength and toughness. In this work we investigate the relation between structural parameters of the network, its architecture and its strength and toughness. We report the dependence of the strength on network density, crosslink density, and fiber properties. We also investigate the toughness of networks without pre-existing defects as a function of the same set of structural parameters. We observe and characterize the intermittent dynamics of rupture in stochastic networks and relate it to similar processes in other materials with stochastic structure. Numerical results are compared with equivalent experimental data. |
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N00.00125: Large change of thermal conductivity induced by temperature and light in azobenzene-based mesophases Noa Varela-Dominguez, Carlos Lopez-Bueno, Alejandro Lopez-Moreno, Gustavo Rama, Maria Gimenez-Lopez, Francisco Rivadulla Achieving an efficient management of heat is of paramount importance in a wide range of applications. Thus, one of the biggest challenges in materials science is to develop functional materials allowing an active control over thermal conductivity. |
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N00.00126: Colloidal suspensions down an incline plane: at the crossroad between granular and glassy rheology. Alice Billon, Yoel Forterre, Olivier Pouliquen, Olivier Dauchot Suspensions composed of large, respectively small, enough particles flow according to granular, respectively glassy, rheology. In practice, many colloidal suspensions sit right at the crossover between these two regimes, where a comprehensive description of the suspension rheology is still lacking. |
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N00.00127: Dynamics of SeSPs in a sea of sheared disks Ollie Yakimow, Jack Ryan, Scott V Franklin We study the motion of superellipse sector particles (SeSPs), two-dimensional curved particles that parameterize corner sharpness, aspect ratio, and opening aperture. Some shapes that SeSPs encompass include discs, rods, convex "stars", and C- and U-shaped concave particles. In our study, a small number of SeSPs (with 180° openings and an annular shape) are surrounded by a monolayer of monodisperse hard disks in a 360° annular-planar shear cell that allows for arbitrarily large simple shear. The number of SeSPs is kept small (to minimize SeSP-SeSP interactions), all particles are tracked with video analysis, and we analyze the translational and rotational mean-squared displacements of all particles. To analyze how SeSPs impact the structure and motion of the background disks, we examine radial density and bond orientation distribution functions and nonaffine motions. We compare these quantities for disks near and far from SeSPs and, when SeSPs approach one another, their rate of approach and relative orientation. |
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N00.00128: Assembly of Janus Nanoparticles on Lipid Vesicles yu zhu, yu zhu, Eric J Spangler, Mohamed Laradji Janus nanoparticles (JNPs), which integrates two different components into one structure to promote different functions, have a wide range of potential application, and have thus been the subject of many studies during the past few years. Here, we investigate the adhesion modes of two spherical JNPs on and inside lipid vesicles through large scale molecular dynamics simulations of a coarse-grained implicit-solvent model. Compared to isotropic spherical nanoparticles, the wrapping of JNPs by the membrane is mainly controlled by their degree of Janusity and their diameter. A detailed phase diagram of the NPs arrangement on the vesicle is obtained from molecular dynamics simulations of coarse-grained implicit-solvent model in conjunction with the Weighted Histogram Analysis Method. In the case where the JNPs are inside the vesicle, they prefer to be apart at specific preferred locations relative to each other, regardless of the degree of Janusity. In the case where the JNPs are outside the vesicle, and for low degrees of Janusity, the JNPs again prefer to be apart from each other at specific locations. However, for relatively high values of the degree of Janusity, the JNPs dimerize. Overall, our results agree with those of Bahrami and Weikl [Nano Lett. 18, 1259 (2018)], which are based on a Monte Carlo Monte Carlo energy minimization of a dynamically triangulated vesicle. Interesting, however, the deformations caused by the JNPs on the vesicle are not always symmetric, when they adhere to the exterior. |
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N00.00129: Characteristics of Respiratory Microdroplet Nuclei on Common Substrates Zhenyu J Zhang, Alexandros Kosmidis-Papadimitriou, Shaojun Qi, Ophelie Squillace, Nicole Rosik, Mark Bale, Peter Fryer To evaluate the role of surface in the transmission of respiratory virus, in particularly SARS-CoV-2, microdroplets of artificial saliva (approximate diameter 10 μm) were generated using an advanced inkjet printing technology to replicate the aerosol droplets, and were subsequently deposited to five different types of substrates (glass, stainless steel, polytetrafluoroethylene (PTFE), stainless steel, acrylonitrile butadiene styrene (ABS), and melamine) that are commonly in contact with human. The droplets were found to evaporate within a short timeframe (less than 3 seconds), which is consistent with previous reports. Both fluorescence microscopy and atomic force microscopy were used to characterise the droplet nuclei formed. We found that droplets of 10 μm diameter (or less) would form a solid nuclei on a surface, independent of the surface characteristics, which clarifies the antiviral surface strategies towards small droplets. It is worth noting that the interfacial energy has a significant influence on the characteristics of the resulting nuclei: droplets of artificial saliva would spread on substrates of high surface free energy (SFE) before forming a nuclei, but result in a nuclei of minimal dimension on substrates of low SFE. Nanomechanical measurements confirm that the nuclei possess similar surface adhesion (~20 nN) and Young's modulus (~4 MPa), supporting a core-shell structure of the droplet nuclei, which could have a critical impact on the surface viability of viruses. We would like to highlight that the interfacial details of proteinaceous droplet is much more complex than that of pure solvent, which is affected by the characteristics of the solid substrates. |
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N00.00130: Single-Molecule Studies of Confined Branched Polymers Louis Wang, Danielle J Mai Densely branched polymers such as lubricin and mucin play a crucial role in controlling biolubrication behavior. Biolubrication occurs at interfaces, which can be modeled as confined environments. Understanding the behavior of branched polymers at the single-molecule level is critical to understanding their behavior at the ensemble level. In this study, we investigate topologically complex polymers placed in confined environments by observing changes in the diffusivity of branched polymers in 1D slit-like confinement. We demonstrate the synthesis of branched DNA polymers by enzymatic replication of linear precursors and biochemical coupling of DNA branches onto DNA backbones. We fabricate nanofluidic devices with high-aspect-ratio nanochannels using wet etch lithography on borosilicate glass substrates. We observe the single-molecule behavior of branched polymers inside nanochannels using 2-color fluorescence optical microscopy with different fluorophores coupled to the polymer backbone and branches to distinguish sub-molecular mechanisms. Understanding of molecular- scale contributions to biolubrication will enable the design of novel materials to treat lubrication-deficient diseases. |
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N00.00131: Measuring capillary wave fluctuations and droplet coalescence in colloidal fluids with light sheet microscopy Ruilin You, Ryan McGorty We measure capillary wave fluctuations, droplet coalescence, and dripping in a colloidal fluid system by using a custom-built single objective light sheet microscope (SOLS). We acquire volumetric imaging data at several volumes per second with submicron resolution. We show that we can use SOLS to detect capillary fluctuations at the interface of coexisting colloidal fluids. We measure submicron fluctuations and capillary velocities on the order of 0.1 micron per second. We additionally measure the width of the growing bridge that connects a coalescing droplet to the continuous phase. Our SOLS system allows us to acquire fast optically sectioned images for volumetric data collection without needing to move the objective lens. Rather, the focal plane and sheet of excitation light are swept across the sample using a scanning mirror. This method provides fast 3D imaging with minimal mechanical perturbation to the sample. |
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N00.00132: Kinetic ratchet effect and counter-equilibrium transportation in narrow channels. Chase N Slowey, Zhiyue Lu Nonequilibrium transportation of particles through a crowded space (such as porous media or narrow channels) significantly differs from free space. Salient examples are dynamical phase transitions in various exclusive process models and the selective transportation of ions through ion channels. Using a simple model for multi-site channels capable of transporting two species of particles, we identify a counterintuitive kinetic ratchet effect. The channel is found to operate in two modes, a dud mode and a ratchet mode. In contrast to the dud mode, where both species relax into thermal equilibrium, the ratchet mode allows one species to force the other into a counter-equilibrium flow against its gradient. We also find that the kinetic ratchet effect provides a general theoretical framework to explain the selective transportation of particles via passive channels. Finally, the kinetic ratchet effect also provides a generic optimal design principle for selective transportation via narrow channels without sacrificing the rate of transportation. |
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N00.00133: Enhanced frustration and forbidden zones in a system of two mutually entangled SeSPs Hyo Sun Park, Scott V Franklin, Ted A Brzinski We present the results of a molecular dynamics-based study of a pair of entangled, Brownian Superellipse sector particles (SeSPs) to study the dynamics that arise from mutual entanglement as particle shape is systematically varied. SeSPs comprise a class of particle shapes with continuous variation of angularity, convexity, and aspect ratio. Previous work has investigated the space of allowable configurations in a system of two hard-particle SeSPs, revealing distinct classes of entangled and mutually-entangled configurations. This preliminary work suggests that transitions between the classes of entanglement become frustrated by a topological change in the configuration space as the particle shape is varied from open to closed. We explore the possible existence of a glasslike phase transition related to the topological change observed in the pairwise configuration space for SeSPs. |
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N00.00134: On the formation of channels in Escherichia coli colonies and the implications of bacteriophage infection Rory Claydon
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N00.00135: Topological and Protein-Functionalised DNA hydrogels Giorgia Palombo The Watson-Crick base pairing make DNA an ideal building block for smart biomaterials. Recently there has been an increasing effort to design and characterise hydrogels made by DNA nanostars. In spite of this, their functionalisation using proteins or enzymes has been overlooked so far. |
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N00.00136: Investigating the role of cohesin in chromatin organization and transcriptional activity Cleis Battaglia The three-dimensional organization of DNA chromatin within the nucleus has been long shown to be highly interconnected with gene expression and crucial for the correct functioning of the cell. It has been observed that cohesin plays a key role in organizing the genome by extruding loops that stop at convergent occupied CTCF binding sites. However, the effect of cohesion on the transcriptional regulatory network of the cell has not yet been completely understood [1]. |
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N00.00137: Particle propulsion at the isotropic-nematic interface Noe d Atzin, Gustavo Perez, Antonio Tavera-Vazquez, Danai montalvan, Juan De Pablo, Vinothan N Manoharan Using continuum framework based on Landau-de Gennes theory, we simulate a particle in nematic phase near at the transition temperature and we show that the external force in the particle at the isotropic-nematic transition is no zero and generate a self-mobility in the particle to the isotropic phase. |
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N00.00138: Adhesion Directed Capillary Origami Timothy J Twohig, Andrew B Croll Capillary forces are often used to provide the force needed to create simple origami structures from thin films. Until recently, the adhesive component of these systems has been largely avoided or ignored, resulting in structures which are not stable after the drop disappears. This work explores the relations between a film and a substrate specifically focusing on what allows a film to be peeled from a patterned substrate by a capillary drop and what would allow structures to become fixed in place. We use the results to demonstrate how to guide peel fronts along specific paths with patterned substrates and how a “racquet” bend – a fold that is held in place due to adhesion rather than plasticity -- can be used to fix structures in place. The results of this work allow the demonstration of complex, multi-step structures permanent structures created with capillary drops. |
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N00.00139: Modelling the Dynamic Self Assembly of DNA Nanostructures Using a Switchable Forcefield Coarse Grained Model Marcello DeLuca, Gaurav Arya DNA nanotechnology leverages DNA's canonical binding rules and geometry to use it as a building material for nanoscale devices and sensors. While fundamentally simple, the self-assembly process of DNA nanostructures is still poorly understood. Many experimental and computational efforts have sought to better understand DNA origami folding, but the small length scale of individual events and long timescale over which folding occurs have acted as barriers. We have developed a new coarse grained model which uses a switchable forcefield to reasonably capture the mechanical behavior of single stranded DNA, double stranded DNA, motifs like crossovers, and transition events like hybridization, at a coarseness level of 8 nucleotides per particle; this enables simulation of DNA at timescales sufficient to capture the self-assembly of full-sized 15 kilobase DNA origami. We simulated the self-assembly of some common DNA Origami structures and studied the kinetics of self assembly. Our current results indicate the existence of a previously undocumented folding mechanism whereby origami exhibit early compaction followed by a significant reduction in the rate constant of staple binding until the completion of folding. |
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N00.00140: Study of the depletant concentration on the rheology of concentrated nanoemulsions Zahra Abbasian Chaleshtari, Hamed Salimi-kenari, Reza Foudazi Nanoemulsions are metastable colloidal dispersions with a wide range of applications in food, cosmetic, and pharmaceutical industries due to their unique structural properties. Gelation in nanoemulsions can effectively be used to expand their applications as rheology modifiers and to design highly structured porous materials. In this research, we study the colloidal gelation of concentrated nanoemulsion with the oil volume fraction of 50% and 60% in the presence of depletant molecules. The rheological properties of the concentrated nanoemulsions are studied at different concentration of polyethylene glycol diacrylate (PEGDA) as the depletant. The gelation behavior and the structure-flow relationship of nanoemulsions are examined through flow curve and oscillatory shear measurements. Due to the probable presence of polymer-surfactant complexation at the interface and in order to achieve a comprehensive knowledge of PEGDA effect on nanoemulsion behavior, the interfacial properties of different systems are also studied over time. These results offer a foundation for controlling the properties of colloidal systems and nanoemulsion-templated porous materials. |
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N00.00141: Sheared gels form vorticity-aligned flocs depending on the shape of connected colloidal clusters Ryle R Rel, Dennis J Terwilliger, Ryan McGorty We investigate the rheology, structure, and flow-induced patterning of colloidal gels composed of thermosensitive poly(N-isopropylacrylamide) (pNIPAM) microgel particles. We mix these particles with a polymer to induce a depletion attraction. At room temperature, these mixtures phase separate into coexisting fluid phases. At slightly higher temperatures, these mixtures form a gel due to the increased hydrophobicity of the colloidal microgel particles. By applying shear to our samples while in the fluid-fluid demixed state, we can deform the colloid-rich domains. By then increasing the temperature, these colloid-rich domains connect together to form a sample-spanning gel. We observe the flow-induced patterns that form when we continue shearing this gel and it yields. We find that the patterns depend on how deformed, by flow, the colloid-rich domains were prior to gelation. For a range of shear rates applied to the sample while in the fluid-fluid demixed state, when the sample transitions to the gel state and is sheared we observe vorticity-aligned log-like flocs which roll between the parallel plates of our geometry. Our data suggests that the morphology of the colloidal clusters, which is dependent on the shear rate applied while in the fluid-fluid demixed state, is an important factor in determining whether or not vorticity-aligned flocs form. This work may offer routes for tuning the strength and structure of colloidal gels. |
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N00.00142: Collective behaviors of fire ant rafts and black soldier fly larvae under external flows Hungtang Ko, David L Hu, Daniel I Goldman Animal collectives must adapt to changing environments in order to survive. In this poster, we present two case studies for probing collective behavior under external fluid flows. Fire ant rafts elongate and deform in water currents. Collectives of black soldier fly larvae loosen and become more porous as they are subjected to the airflow in fluidized beds. In both cases, we find that the behaviors of these collectives are strikingly different from traditional soft materials placed under the same conditions. We present experiments and simulations of these active materials and conclude that the active movement of the constituents is crucial to the response of the collectives. |
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N00.00143: Shear cessation in the pre-yielding and post-yielding of jammed suspensions H. A Vinutha, Emanuela del Gado, Vishwas V. Vasisht, Gavin J Donley A range of soft materials, for example, foams, emulsions & grains, begin to flow beyond some threshold value of external deformation. This transition from solid-like to liquid-like deformation behavior is known as yielding. Here, we simulate the steady shear startup of a non-Brownian jammed suspension, whose flow curve is described by the Herschel-Bulkley form. The transient behavior of our dense soft solids shows a stress overshoot followed by a steady shear plateau. We perform an iterative series of flow cessation simulations as the strain increases to probe the progression of yielding. We study the time-dependent recovery of the solid-like character in these granular materials by separating the role of the shear rate prior to flow cessation and the jammed structure. |
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N00.00144: Simulation of emergent macroscopic structure based on experimental nanoscale potentials Ugochukwu O Okoli, Greg Beaucage, Kabir Rishi, Eric Jankowski Inks and paints are made of pigment dispersions stabilized by surfactants. These pigments are comprised of nanoscale, ramified primary particles. ~3nm elemental crystals clustered into 5 to 8 nm 3D primary particles which further form aggregates of about 10 to 100 nm. Aggregates can form 3D agglomerates or form space-filling networks the latter of which advantageously scatter light and present uniform dispersion. The rate of drying and the film thickness control structural emergence as the concentration increases. Thick films display 3D agglomerates, which are not desirous in applications. For drying in micron thick films, a dual hierarchical network forms which are composed of clusters of aggregates that form micron size networks that are optimal for light scattering. It is desirable to predictably control this multi-hierarchical emergent structure. The interaction potentials of the pigment structural levels are determined experimentally using USAXS, SAXS, and WAXS. These potentials are employed in a Monte-Carlo simulation to model the interplay between the thermodynamic driving force for multi hierarchical structural emergence and transport kinetics. Observed agglomeration and network formation can be recreated using as input the surfactant characteristics. |
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N00.00145: Evolution of the Shape and Surrounding Stress-Strain of an Oil Droplet Embedded in a Drying Colloidal Suspension Zhiyu Jiang, Megan T Valentine, Anard Jagota, H Daniel Ou-Yang During drying, colloidal dispersions undergo solidification where particles pack in the drying front and rearrange themselves to release stress. An immiscible liquid droplet embedded in the packed colloids was thought to be a potentially useful probe to map the stress distribution. To understand how the droplet deform in compacting colloids, we designed experiments that used time-lapse confocal microscopy to measure the movement and deformation of an oil droplet when colloids transited from a uniform suspension to compaction during uniaxial drying in a microfluidic channel. Fluorescent tracer particles in the colloids were used to map the displacement fields from which the stress-strain fields were obtained in the areas surrounding the oil droplet. We observed that an initially spherical oil droplet slowed relative to the surrounding fluid, suggesting diffusiophoresis of the droplet in the concentration gradient of the colloidal particles. As time progressed, the concentration of the colloidal particles grew, and the droplet was deformed by the hydrostatic pressure gradient. The distortion of the oil droplet showed that the elastic modulus of the nearby colloidal particles increased and overcame the surface tension of the oil droplet. At long times, when the colloidal particles were near closed packing, the shape of the oil droplet lost front-back symmetry – with higher curvature in the more packed front. The curvature of the droplet was found to be due to the hydrostatic pressure gradient rather than the colloidal osmotic pressure gradient which was in the direction opposite to that of the hydrostatic pressure gradient. Video images, analysis of the droplet slowing down due to diffusiophoresis, time evolution of the shape of an oil droplet and the stress-strain field surrounding droplet will be presented at the talk. |
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N00.00146: Temperature dependent relative mass density measurement of a highly polar liquid crystal compound having multiple ferroelectric nematic phases. Md Sakhawat Hossain, Rony Saha, Pawan Nepal, Chenrun Feng, James T. Gleeson, Samuel Sprunt, Robert J. Twieg, Antal Jákli The relative mass density measurement can represent both the polarity and the efficient molecular packing of a particular liquid crystal material. We studied the temperature dependence of the relative mass density of a new highly polar ferroelectric nematic compound, 4-nitrophenyl 4-[(2,4-dimethoxylbenzoyl) oxy]-2-fluorobenzoate (RT11001) that was found to have 3 different ferroelectric nematic phases (arXiv:2104.06520). A section of the 50 rectangular capillary was filled with the material and studied by polarized optical microscopy (POM) images for the better definition of the meniscus position. The temperature dependence of the relative mass density reveals the N-NF1 and NF1-NF2 transitions seen by differential scanning calorimetry (DSC) but does not show any jump through the NF2-NF3 phase transitions. These results can be understood in view of recent x-ray scattering results (Multiple ferroelectric nematic phases of a highly polar liquid crystal compound, submitted to Journal of Materials Chemistry C - TC-ART-08-2021-003587). |
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N00.00147: Influence of Pins on The Jamming Transition of a Sheared Athermal System Katharina Vollmayr-Lee, AKM Sadman Mahmud, Michael J Bolish, Amy L Graves, Cacey S Bester, Brian Utter We use molecular dynamics simulations to study a two-dimensional athermal, bidisperse system with purely repulsive harmonic interactions. Via the motion of rough top and bottom walls consisting of frozen particles, we shear the system. Energy is dissipated via interactions FD= -b (rij/rij .vij) rij/ri . The system furthermore has non-moving “pins”. The size ratio of pins:small:large is 0.004:1:1.4 and pins are located on a square lattice. We show preliminary results for pressure and shear stress as function of packing fraction. We find that in agreement with previous work on the non-sheared system, the jamming transition decreases with increasing number of pins. |
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N00.00148: Tuning lipid composition to explore the monolayer collapse phase diagram Anna Gaffney, Kathleen Cao, Angelo Rosario Carotenuto, Nhung Nguyen, David R Owen, Massimiliano Fraldi, Luca Deseri, Ka Yee C Lee, Luka Pocivavsek Langmuir monolayers provide a controlled system to study the multiscale geometry and mechanical states of lipid monolayers at an air/water interface under compression. At high lipid packing density and high surface pressure, the monolayers collapse and can be observed to undergo wrinkling, folding, crumpling, shear banding, or vesiculation. Recent work has begun to establish a general lipid monolayer collapse phase diagram, where the collapse mechanism can be altered through tuning characteristics such as lipid composition and temperature. This poster will present ongoing work in exploring uncharted regions of this phase diagram. We combine fluorescence imaging and atomic force microscopy to study the micro- and nano-scale structures to probe the mechanical properties of lipid monolayers near and during collapse at compositions of varying in-plane rigidity. We focus on the phenomenon of shear banding and the conditions necessary to produce such morphology and utilize finite element analysis to simulate collapse based on experimental data. |
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N00.00149: Collective dynamics and conical structure of particles levitated by thermophoretic force Callum L Welsh, Cheng Chin We study the dynamics of two to many particles levitating in a thermophoretic trap. Establishing the potential against gravity, we confined many 10 micron-scale polyethylene and ceramic particles in a thermal cell at air pressures of 1-10 Torr. We find that for more than 100 particles, the particles form an irrotational vortex line despite the air being far from the Rayleigh-Bénard convection regime. We find that the circulation of the vortices increases when more particles are levitated, which suggests that the dynamics are collective in nature. Furthermore, we find that the particles in these vortices settle into a "hollow cone" structure. We present a discussion of possible causes for these novel unexplained phenomena. A better understanding of these phenomena will not only improve our understanding of thermophoretic dynamics, but also offer a new path to simulate the aggregation dynamics of particles in micrograviation environments. |
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N00.00150: Measures of entanglement in systems employing Periodic Boundary Conditions Eleni Panagiotou We introduce a definition for the Jones polynomial of open or |
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N00.00151: Active matter thermodynamics: Powering an E. coli engine with help from field theory Connor Roberts Active matter particles convert energy from their environment into mechanical work, such as self-propulsion. A well-studied example of self-propulsion is ‘run-and-tumble’ motion performed by E. coli. When many run-and-tumble particles are brought together they exhibit behaviour like a gas. This run-and-tumble gas differs from everyday gases in many ways. Most significantly, it is a non-equilibrium system, a property that could allow us to devise machines, such as an autonomous E. coli engine, that are impossible to construct from everyday gases. |
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N00.00152: Dynamic wetting phenomena and contact angle hysteresis on polymer brushes and gels Lukas Hauer, Doris Vollmer Droplet mobility on surfaces is obtained by polymeric coatings, like gels or brushes. Both types hold some amount of un-crosslinked or un-grafted polymer (‘free’) chains which are mobile within the coating. In the presence of droplets, these free chains accumulate around the three-phase contact line, leading to contact lubrication and wetting ridge formation. When droplets move over the surface, the wetting ridge moves accordingly, yielding visco- and poroelastic responses of the surface. The coupling between surface response, free chain reorganization, and the sliding droplet is key to understanding liquid repellency. However, investigations are hampered by the large-scale separation of free chains (nanometer), surface (micrometer), and droplet (millimeter). Here, we utilize confocal laser scanning microscopy and interferometry to directly visualize the wetting ridge during droplet motion. Those methods let us distinguish between phases and enable optical resolutions below a micron. A novel optical force sensor let us measure the evolving friction forces between droplets and surface which occur in the order of micro Newton. We show that friction forces scale with velocity and contact lubrication. The presented techniques give new methods to directly determine the coating rheology of soft surfaces. |
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N00.00153: Reverse Janssen effect in narrow granular columns Shivam Mahajan Janssen showed that the pressure of silos filled with grains matches the hydrostatic one for small filling heights but then saturates as the weight of the grains is supported by the lateral container wall through wall/grain frictional forces. Via a combined experimental and numerical investigation, we demonstrate a reverse Janssen effect whereby the pressure at the bottom exceeds the hydrostatic one. We show that this effect results from the emergence of compressive frictional forces, discuss the dependence on the various control parameters involved, and introduce a model accounting for our observations. |
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N00.00154: Motility and morphodynamics of confined cells Ido Lavi, Nicolas Meunier, Raphael Voituriez, Jaume Casademunt We present a minimal hydrodynamic model of polarization, migration, and deformation of a biological cell confined between two parallel surfaces. In our model [1], the cell cytoplasm is likened to a viscous droplet that is driven out of equilibrium by an active cytsokeleton force. This force acts on the cell membrane and is modulated locally by an internal diffusive solute. While fairly simple and analytically tractable, this two-dimensional sharp-interface model predicts a range of compelling cell-like behaviors. A linear stability analysis reveals that solute activity first destabilizes a global polarization-translation mode, prompting motility through spontaneous symmetry breaking. At higher activity, the system crosses a series of Hopf bifurcations leading to coupled oscillations of droplet shape and solute concentration profiles. At the nonlinear level, we find traveling-wave solutions associated with unique polarized shapes that resemble experimental observations. Altogether, this model offers an analytical paradigm of active deformable systems in which viscous hydrodynamics are coupled to diffusive force transducers. |
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N00.00155: A multiphase theory for transient osmotic swelling of chemically responsive hydrogels Chinmay Katke, Peter A Korevaar, Joanna Aizenberg, C. Nadir Kaplan The osmotic pressure due to a concentration difference of identical solute molecules across a semi-permeable membrane can be determined by van't Hoff's formula for chemical potential equilibration when the number of solute molecules remain constant on both sides of the membrane. This condition can be inherently relaxed at the interface between an aqueous supernatant domain and a chemically responsive hydrogel, when a chemical stimulus freed from inside the gel slowly diffuses into the supernatant while creating a dynamic osmotic pressure balanced by the poroelastic diffusion of water into the gel. We introduce a continuum poroelastic theory for the dynamic build-up and relaxation of osmotic pressure due to an interplay between copper cations as osmosis-driving agents and acid in a polyacrylic acid hydrogel thin film. Our theory relates the non-equilibrium osmotic pressure to the vertical gradients of the solute concentration across the interface. The theory quantitatively captures the osmosis induced swelling and contraction of the gel film, in agreement with experiments. |
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N00.00156: From sea slugs to robots: Computation, discrete geometry, and soft mechanics in non-Euclidean elasticity Kenneth Yamamoto, Toby Shearman, Erik Struckmeyer, John Gemmer, Shankar Venkataramani The intricate, self-similar wrinkles along the edges of growing leaves, blooming flowers, torn plastic sheets, and frilly sea slugs are striking manifestations of the extreme mechanics of hyperbolic elastic sheets. These complex and exquisite patterns are governed by interacting non-smooth geometric defects in the material. Characterizing and analyzing these defects uncover insights into elastic behavior and properties underlying the morphogenesis of leaves and flowers, the biomechanics of sea slugs, and how one might design and actuate soft robots. We have developed novel and powerful techniques based on discrete differential geometry for modeling these defects to predict the mechanics and dynamics of thin hyperbolic bodies and enable new biomimetic technologies. |
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N00.00157: Understanding the structure of surfactants at the water/oil interface Dan Ye, Thomas C Fitzgibbons, Jingwei Fan, John K Riley, Wanglin Yu APEs (alkyl phenol ethoxylates) are versatile and cost-effective surfactants widely used in a variety of consumer and industrial applications, including detergent and cleaners, agrochemical, and emulsion polymerization. The historic annual market size of NPE (nonylphenol ethoxylate) surfactants is over 1 billion pounds worldwide. NPE surfactants and their breakdown products, notably nonylphenol, however, can harm aquatic animals and plants and are resistant to natural degradation. The environmental and health risks have triggered restrictions of APE use in many applications. Great effort has been devoted to identifying and developing alternative surfactants to replace APEs. Despite the great progress and success, it is challenging to match the high performance of NPEs with alternative surfactants in some applications. The objective of this study is to gain more fundamental understanding on the unique performance of NPE surfactants in stabilizing emulsions. We prepare stable swollen micelles by solubilizing oil into NPE micelles. Then we use dynamic light scattering (DLS) and small angle X-ray scattering (SAXS) to study the molecular structure of nonylphenol ethoxylate surfactants at the water/oil interface. The high-brilliance X-ray beamlines enable detailed structural modeling of high-quality data from the micelle solutions. The insights on the interfacial structure from this work will help us understand how the NPE structure translates into interfacial properties such as interfacial tension, critical micelle concentration and emulsion stability. |
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N00.00158: X-ray imaging for respiratory droplet deposition on face masks Marta Alves Moreira Gonçalves, Byung Mook Weon Upon coughing or sneezing, the expelled respiratory droplets from an infected individual contain a virus load that inevitably contacts several surfaces, such as face masks, representing the main route of disease transmission. Since the early COVID-19 global outbreak, health organizations and governmental disease control task forces urged the population to use face masks as a prevention measure. Understanding the multilayered porous materials that constitute face masks and the dynamics between evaporation and absorption of respiratory droplets becomes crucial to assess the risk of disease transmission if not carefully handled. In the present study, virus-sized nanoparticles were suspended in artificial saliva. After the surrogate respiratory droplet evaporation on the face mask, the final deposit was observed using X-ray imaging. Consequently, X-ray imaging enabled a thorough analysis of facial masks' complex morphology. A physical model is proposed to explain the droplet evaporation, absorption, and the final viral deposit formation from the experimental data. The result can contribute to improve prevention measurements for respiratory diseases. |
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N00.00159: 2D Deployable Nanostructures from DNA Jong Hyun Choi, Ruixin Li Deployable structures preserve their overall shapes during expansion and contraction. Their structural transformation shows auxetic behaviors, and thus exhibits negative Poisson's ratio. Such topological behaviors originate from their unique geometries. For example, the Hoberman sphere, a popular children’s toy, is formed by rods with flexible scissor-like linkages. In this work, we demonstrate a deployable nanostructure via DNA self-assembly. We constructed a simplified 2D version of Hoberman sphere from DNA, and characterized its dynamic reconfigurations and negative Poisson's ratio. The topology includes six triangles of wireframe DNA origami in two layers, forming a trefoil knot. The DNA structure can switch between open and closed states by sliding the triangles against each other via introduction of DNA oligos. This work provides insights on the topological assembly and reconfiguration of nanoscale DNA architectures. |
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N00.00160: Uniform, crack-free colloidal deposition with surface wettability adjusting Hyo Eun Kim, Byung Mook Weon Deposition of colloidal nanoink is a useful method for inkjet printing. Typically, evaporation on micropillar array leads droplet to be pinned and makes final deposition pattern to have various polygonal shape which has strength for industrial application. But those micropatterns additionally make surface to have hydrophobic properties and keep height difference between center and edge of deposition pattern until the end of evaporation. This non-uniform height induces physical instability and eventually makes deposited film destruction. Thus, we have used plasma treatment to control the chemical characteristic and induce spreading force beyond micropillars. We finally intend to improve the uniformity of binary colloidal deposition with crack-free pattern. |
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N00.00161: An Analysis of the Thermal Transition Behavior of P666,14 NTF2 Around the Liquid-liquid Transition Benworth B Hansen Recent research has suggested that various ionic liquids (ILs) may exhibit signs of liquid-liquid transitions (LLT) at temperatures around the glass transition. Because the presence of an LLT in any liquid would have large implications on our understanding of the potential behavior of all liquids, overwhelming evidence is needed to support such a claim. |
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N00.00162: Investigating human chromosome organization by whole-genome simulations Matheus Mello, Antonio Oliveira Junior, Vinicius Contessoto, Jose N Onuchic In recent years, both theoreticians and experimentalists have dedicated significant effort to studying chromosome organization and its relation to gene expression and regulation. Many experimental procedures were designed, such as Hi-C, to capture the dynamic information of chromosome structure. Several theoretical models were then proposed to try to understand the principles underlying chromosome compartmentalization. In this work, we use the Open-MiChroM software to simulate the whole genome of GM12878 human cells at 50 kbp resolution. At this scale, 121,504 beads are necessary to model all 46 chromosomes, creating challenges of convergence and proper sampling of the ensemble of structures due to the size of the system. To address this, we performed analysis on the chromosome contacts and the correlation between states during the simulation, estimating the necessary number of replicas and sampling interval to perform the computations. The whole-genome simulations provide insights into inter-chromosome interactions and the relative distribution of chromosomes within the nucleus. Additionally, they also allow further investigation of the dynamics of phase separation of A/B compartments over time. |
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N00.00163: Effect of Cosurfactant on the Properties of Polymerized High Internal Phase Emulsions (PolyHIPEs) Muchu Zhou, Reza Foudazi High internal phase emulsions (HIPEs) are obtained when the internal phase volume fraction exceeds 74%. HIPEs can be used as templates to produce highly porous polymers through the polymerization of monomers in the external phase, which is known as polymerized high internal phase emulsions (polyHIPEs). The properties of polyHIPEs significantly depend on the properties of the primary HIPEs, which are affected by the interfacial properties. Surfactants play an important role in improving the stability of HIPEs owing to the reduction of interfacial tension. A cosurfactant can be used to reduce the droplet size of emulsions. However, cosurfactants can also reduce the stability of polyHIPEs. In the present work, different cosurfactants are employed to prepare the polyHIPEs. Our results reveal that the morphology of polyHIPEs changes by applying different cosurfactants or by varying their concentration. In addition, our study suggests that interfacial elasticity influences the formation of interconnections between pores. |
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N00.00164: Electroresponsive Ionic Liquid Crystal Elastomers Chenrun Feng, Antal I Jakli, Chathuranga Prageeth H Rajapaksha We will describe the preparation, physical properties and electric bending actuation of a new class of active materials - ionic liquid crystal elastomers (iLCEs). It is demonstrated that iLCEs can be actuated by low frequency AC or DC voltages of less than 1 V. The bending strains of the not optimized first iLCEs are already comparable to the well-developed ionic electroactive polymers (iEAPs). Additionally, iLCEs exhibit several novel and superior features, such as the alignment that increases the performance of actuation, the possibility of pre-programed actuation pattern at the level of cross-linking process, and dual (thermal and electric) actuations in hybrid samples. Since liquid crystal elastomers are also sensitive to magnetic fields, and can also be light sensitive, iLCEs have far-reaching potentials toward multi-responsive actuations that may have so far unmatched properties in soft robotics, sensing and biomedical applications. |
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N00.00165: Probing 2D Phase Separation in Mixed Silica and Gold Nanoparticle Assemblies Zachary Fink, Paul Y Kim, Maged Abdelsamie, Carolin Sutter-Fella, David Hoagland, Thomas P Russell While much attention has been directed toward interfaces decorated with functional, uniform NPs, less effort has focused on mixed NP assemblies that have the potential to prepare well-defined heterogeneous surfaces and 2D phase separated morphologies. We capitalize on nanoparticle surfactant (NPS) assembly at a liquid-liquid interface to increase NP binding energy and provide a platform to probe highly packed layers of mixed silica and gold NPSs by UV-Vis reflection spectroscopy. As predicted by the Mie theory, the plasmon excitation energy depends not only on the properties of individual gold NPs but also on the number of NPs in the ensemble, their relative location, and interparticle distances. Silica prevents significant ordering of the gold NPs into larger structures. By tuning the size, number, and adsorption rate of each NP species in the assembly, we can control the morphology of the jammed assembly using the rate of 2D phase separation. The maximum reflection intensity and corresponding wavelength reveal structural correlations of the gold NP clusters. This method can be used to understand and control the molecular and nanoscopic factors that govern the phase separation in two dimensions. |
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N00.00166: Vine Robot Actuated with Silicone Fused Chevron Fabric Tube With Diameter Less Than a Millimeter Orkesh Nurbolat A vine robot is a single chamber phneumatic actuator that is made up of thin plastic flim. |
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N00.00167: Mechanics of Bi-Chiral Mechanical Metamaterials: Design, Modelling and Experiments Tiantian Li, Yaning Li A family of bi-chiral mechanical metamaterials with both regular and random handedness distribution patterns are designed. The mechanical properties of them are explored via systematic finite element simulations. The effects of handedness distributions, handedness ratio, and domain size and length aspect ratios are investigated. Furthermore, the anisotropic properties of bi-chiral mechanical metamaterials are studied. Specimens with various material orientations are fabricated via 3D printing. Mechanical experiments are performed to measure the effective mechanical properties in the corresponding material orientations. Experimental results show bi-chiral mechanical metamaterial has strong anisotropic behavior in stiffness, Poisson's ratio and coupling coefficients which agrees well with FE simulations. To further predict these anisotropic properties, micropolar continuum theory are used and micropolar parameters are obtained from FE simulations. The influences of these parameters on the anisotropy are systematically quantified. Finally, the effect of handedness, hinge rigidity, lattice topology and lattice tessellation on the anisotropic properties are studied. The results provide design guidelines for bi-chiral mechanical metamaterials with enhanced mechanical performance and widely tuned mechanical properties for broad engineering and biomedical applications. |
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N00.00168: Rheology of High Internal Phase Emulsions (HIPEs) with Different Interdroplet Interactions Muchu Zhou, Reza Foudazi The volume fraction of the dispersed phase exceeds 74% in high internal phase emulsions (HIPEs). The HIPEs have applications in many fields, such as cosmetics, foods, and the production of porous polymers. The HIPEs have solid-like rheological behavior. However, the HIPEs stabilized by different surfactants behave differently under shearing due to the difference in the interdroplet interactions, inducing adhesive and non-adhesive droplets. In addition, the effect of droplet size on the rheological properties of adhesive and non-adhesive HIPEs has not comprehensively been investigated yet. Therefore, in the present work, the effect of droplet size on the dynamic moduli and yield stress of HIPEs with different interdroplet interactions are investigated. Moreover, we investigate the large amplitude oscillatory shear (LAOS) behavior of HIPEs with different interdroplet interactions. |
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N00.00169: Deployable Surfaces Featuring Bistable Auxetics Kirigami Tian Chen, Tran Hoang Ngoc Tran, Nadine Saab, Jacob Griese Ancient motifs have inspired families of kirigami surface structures that are mechanically bistable under tension. In-plane mechanics of periodic tessellations have been investigated in literature. In this work, we aim to understand the effect of aperiodic tessellation and the resulting out-of-plane transformation due to geometric frustration. We show that when such unit cells are uniaxially stretched, the Poisson's ratio of is -1 throughout. By parametrically varying the unit cell geometry, we are able to bistably transform unit cells with a theoretical maximum scale factor of 2. Such expansion can be captured by conformal maps, which locally preserve angles and shapes, but not size or curvature. Indeed, the Gaussian curvature of a surface is proportional to the Laplacian of the conformal scale factor. If we specify a target 3D shape, we can obtain a scalar field of scale factors required to flatten it. By discretizing the shape and tessellate spatially varying unit cells based on the scale factors, we demonstrate families of unit cells that can all stably deploy into 3D shape at various length scales. Lastly, by abstracting the in-plane deformation, we propose a continuum model to capture the deployment process as well as the mechanical characteristics when deployed. |
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N00.00170: Explosive Spontaneous Emulsification Xuefei Wu, Robert Streubel, Gautam Bordia, Ahmad K Omar, Jaffar Hasnain, Phillip Geissler, Han Xue, jianjun wang, Thomas P Russell We investigated the spontaneous emulsification characteristics of an aqueous containing carboxy-functionalized Fe3O4 paramagnetic nanoparticles emersed in a toluene solution of triamine-modified polystyrene (PS-triNH2), a cationic surfactant. The NPs and surfactants interact at the interface between the fluid to form nanoparticle surfactants, NPSs, reducing the interfacial tension (IFT). With increasing areal density of NPSs, the IFT decreases to a point where a spontaneous emulsification occurs, with microdroplets spontaneously forming at the interface. In the presence of an external magnetic field induced dipolar interparticle interactions trap the droplet in an oversaturated state. Upon removal of the magnetic field, an explosive relaxation towards equilibrium is observed via a plume of ferromagnetic liquid microdroplets that are jettisoned from the surface of the parent drop. The ability to externally trigger or suppress spontaneous emulsification, through this highly efficient energy conversion mechanism, introduces a unique energy storage system. |
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N00.00171: Continuum theory for carpets of model cilia Sebastian Fuerthauer, Anup V Kanale, Feng Ling, Hanliang Guo, Eva Kanso In biology, fluid transport often emerges from the coordinated activity of |
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N00.00172: Diffusion and sedimentation in colloidal suspensions using multiparticle collision dynamics with a discrete particle model. Yashraj M Wani, Grace Kovakas, Arash Nikoubashman, Michael P Howard We study self-diffusion and sedimentation in colloidal suspensions of nearly-hard spheres using the multiparticle collision dynamics simulation method for the solvent with a discrete mesh model for the colloidal particles (MD+MPCD). We cover colloid volume fractions from 0.01 to 0.40 and compare the MD+MPCD simulations to Brownian dynamics simulations with free-draining hydrodynamics (BD) as well as pairwise far-field hydrodynamics described using the Rotne--Prager--Yamakawa mobility tensor (BD+RPY). The dynamics in MD+MPCD suggest that the colloidal particles are only partially coupled to the solvent at short times. However, the long-time self-diffusion coefficient in MD+MPCD is comparable to that in BD and BD+RPY, and the sedimentation coefficient in MD+MPCD is in good agreement with that in BD+RPY, suggesting that MD+MPCD gives a reasonable description of the hydrodynamic interactions in colloidal suspensions. The discrete-particle MD+MPCD approach is convenient and readily extended to more complex shapes, and we determine the long-time self-diffusion coefficient in suspensions of nearly-hard cubes to demonstrate its generality. |
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N00.00173: Effects of crowding and confinement on the transport and localization of DNA Steven Dang, Mehdi Shafiei Aporvari, Juexin Marfai, Kara Coursey, Ryan McGorty, Rae M Anderson Two hallmarks of the intracellular environment are crowding and confinement. Macromolecular crowding within cells induces depletion interactions that can lead to anomalous transport, clustering, and sequestration of macromolecules such as DNA. Confinement by the lipid membrane of cells further dictates macromolecular dynamics and localization. Here, we investigate the transport of DNA molecules through crowded and confined environments, using dextran polymers as crowders and using lipids to encapsulate DNA and dextran in cell-sized droplets. By varying the dextran concentration and lipid composition we can control the degree of crowding and the properties of the confining boundary. We use differential dynamic microscopy (DDM) and spatial image autocorrelation analysis to quantify DNA diffusion rates and organization within the droplets, and the dependence of these properties on dextran concentration as well as droplet size and stiffness. Our results shed light on the effects on the coupled effects of crowding and confinement on biomacromolecular transport in cells. |
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N00.00174: Membrane viscosity effects on the dynamics of vesicles Petia Vlahovska, Rony Granek, Hammad Faizi, Rumiana Dimova Lipid bilayers are the main structural component of cell membranes. The nanometrically thin bilayer behaves as a two-dimensional fluid and its shear viscosity controls the transport of embedded biomolecules and membrane deformations. In this study, we investigate the effect of membrane viscosity on dynamics of giant vesicles (closed membrane sacs). We show that membrane viscosity affects the thermally-driven shape fluctuations, especially the low-wavenumber modes. We develop a theoretical model based on the Seifert-Langer formulation and we apply it to analyze the time-correlations of the shape modes. The surface viscosity effect on the dynamic structure factor of membranes will also be discussed. |
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N00.00175: Time-Dependent Electrical Conductivity of Liquid Crystal Cells David Webb, Yuriy Garbovskiy Liquid crystal devices are becoming increasingly ubiquitous. As a rule, the tunability of such devices is achieved by applying an electric field. This field reorients liquid crystals and changes their physical properties. Ions, typically present in liquid crystals in minute quantities, can alter the reorientation of liquid crystals through the well-known screening effect thus altering the overall performance of liquid crystal devices. To mitigate negative side effects caused by ions in liquid crystals, better understanding of ionic phenomena in liquid crystals is needed. Information about ions in liquid crystals can be obtained by measuring their direct current (DC) electrical conductivity. Electrical measurements of liquid crystals are very non-trivial because they can be affected by numerous factors. A very important factor, often overlooked in existing literature, involves interactions between ions and substrates of a liquid crystal cell. In this talk we present an analysis of how such interactions make DC electrical conductivity of liquid crystal cells time dependent. |
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N00.00176: A Generic Explanation of the Mechanism of Co-solvency Xiangyu Zhang, Jing Zong, Dong Meng Mixed solvents are extensively utilized in solution processing of polymers. In solvent mixtures, polymers are often observed to exhibit highly non-trivial behaviors. One example is co-solvency --- polymers that collapse in two different poor solvents become soluble in their mixtures. Explanations based on chemistry-specific arguments are less than satisfactory in carving out a clear physical picture of this intriguing phenomena. In this study, we conduct theorical calculations and computer simulations based on a generic polymer solution model in order to offer a clear account of the driving mechanism of co-solvency. We show that co-solvency results from the composite nature of polymer-solvent interactions, made up of the van der Waals type interactions and associations such as hydrogen bonding. Competition of the two effects gives rise to collapsed conformation when polymers are mixed with each solvent individually. In binary solvent mixtures, cross competitions among the four factors can lead to a swollen polymer conformation at suitable solvent compositions. Implications of the predicted collapse-swelling-collapse transition on the bulk solution phase behavior is further explored using the generic model. The obtained phase diagram compares well with existing experiment data. |
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N00.00177: Can one detect intermediate denaturation states of DNA sequences by following the equilibrium open-close dynamic fluctuations of a single base-pair? Rony Granek, Keerti Chauhan, Amit R Singh, Sanjay Kumar Melting of DNA sequences may occur through a few major intermediate states, whose influence has been suggested previously on the melting curve, while their effect on the kinetics has not been explored thoroughly. Here we chose a simple DNA sequence, forming a hairpin in its native (zipped) state, and study it using molecular dynamic (MD) simulations, and a model integrating the Gaussian network model with bond-binding energies -- the Gaussian binding energy (GBE) model. We reveal two major partial denaturation states, a bubble state, and a partial unzipping state. We show how these two states can influence the closing-opening base-pair dynamics as probed by a tagged bond auto-correlation function (ACF). We argue that the latter is measured by fluorescence correlation microscopy (FCS) experiments in which one base of the pair is linked to a fluorescent dye while the complementary base is linked to a quencher, as was performed by Altan-Bonnet et al. [Phys. Rev. Lett. 90, 138101 (2003)]. We find that tagging certain base pairs at temperatures around the melting temperature results in a multi-step relaxation of the ACF, while tagging other base pairs leads to an effectively single-step relaxation, albeit non-exponential. Only the latter type of relaxation has been observed experimentally so far, and we suggest which of the other base pairs should be tagged in order to observe multi-step relaxation. We demonstrate that this behavior can be observed with other sequences, and argue that the GBE can reliably predict these dynamics for very long sequences, including those used to construct DNA origami, where MD simulations are very limited by computer resources. |
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N00.00178: Temperature dependent soft wetting of polymer melts Krishnaroop Chaudhuri, Jonathan Pham Wetting studies on soft surfaces, though prolific, have been mostly limited to equilibrium cases at room temperature, often on crosslinked elastomers. In this work, we investigate the transient wetting characteristics of a polymer melt (poly n-butyl methacrylate) at temperatures much higher than its glass-transition. When a glycerol drop is placed on the polymer melt surface, an out-of-plane wetting ridge forms at the three-phase contact line. We use stylus profilometry to measure the height and the profile of the wetting ridge for different temperatures and times of contact between the drop and the melt. The wetting ridge growth rate is dependent on the system temperature and the time scale of the experiment. Using oscillatory rheology, scaling laws are developed to predict the time-dependent growth of the wetting ridge. We demonstrate that for a range of temperatures, both Rouse and reptation kinetics affect the rate of ridge growth over different timescales. Moreover, the shape profile of the wetting ridge is dictated by the time-dependent complex modulus, which is a departure from the constant shear modulus values often used for soft elastomers. However, the shape profile can be predicted by a simple consideration of the complex modulus within the context of current models. |
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N00.00179: Rigidity dictates spontaneous helix formation of thermoresponsive colloidal chains in poor solvent Bipul Biswas, Guruswamy Kumaraswamy, Debarshi Mitra, Apratim Chatterji, Fayis KP, Suresh Bhat The formation of helical motifs typically requires specific directional interactions. Here, we demonstrate that isotropic interparticle attraction can drive self-assembly of colloidal chains into thermo-reversible helices, for chains with critical backbone rigidity. We prepare thermoresponsive colloidal chains by crosslinking PNIPAM microgel-coated polystyrene colloids "monomers", aligned in an AC electric field. We control the chain rigidity by varying crosslinking time. Above the LCST of PNIPAM, there is an effective attraction between monomers so that the colloidal chains are in a bad solvent. On heating, the chains decrease in size. For rigid chains, the decrease is modest and is not accompanied by a change in shape. Much less rigid chains form relatively compact structures, resulting in a large increase in the local monomer density. Remarkably, chains with intermediate rigidity spontaneously assemble into helical structures. The chain helicity increases with temperature and plateaus above the collapse transition temperature of the microgel particles. Our minimal simulation model suggests that a purely mechanical instability for semiflexible filaments can drive helix formation, without the need to invoke directional interactions. |
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N00.00180: Multi-scale simulations characterize the influence of H4K16 modifications on nucleosome dynamics Yiheng Wu, Aria E Coraor, Riccardo Alessandri, Juan De Pablo Post-translational modifications (PTM) on histones play a critical role in regulating gene expression and are closely correlated with disease. One kind of PTM, H4K16 acetylation, has been shown to weaken inter-nucleosomal interactions and make chromatin more accessible. Specifically, H4K16 acetylation has been demonstrated to weaken the interaction between residue lysine in H4 and the acidic patch in H2A by charge neutralization. Recently, propionylation (Pr) and butyrylation (Bu) of the same residue have been shown to couple metabolism with chromatin restructuring, but the mechanisms still remain unknown. In this work, we combine our coarse-grained DNA model and chromatin model in silico to elucidate the effect of PTM on dynamics of a 12 nucleosome array. To match the predictions from coarse-grained DNA and protein model, we re-parametrize the inter-nucleosome interactions of our chromatin model. Then replica exchange simulations are run to provide efficient sampling on dynamics of the 12 nucleosome array. We also provide avenues for future validation of our results by predicting experimental FRET efficiency distributions. Moreover, our analysis on chromatin accessibility and tetra-nucleosome motifs paves the way to further understanding of PTMs’ effects on chromatin dynamics. |
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N00.00181: Circular DNA exhibits non-monotonic changes in diffusivity during active topological conversion Natalie Crist
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N00.00182: Quantitative Modeling of Behavior of Water in Hydrophobic Confinement Sumit Sharma A macroscopic thermodynamics-based theory that can quantitatively describe the behavior of water confined between hydrophobic solutes has so far remained elusive. In this work, we have determined free energy profiles of water confined between two nanometer-sized surfaces of varying hydrophobicity using molecular simulations, and have estimated thermodynamic properties such as contact angle, line tension and size of the critical vapor tube from independent simulations. We show that inclusion of line tension is important for a quantitative match between thermodynamic theory and experimental results. The free energy barrier to evaporation scales as a quadratic function of the confinement gap, and the radius of the critical vapor tube scales linearly with the confinement gap. We also demonstrate that macroscopic theory that includes the line-tension term is able to quantitatively match the entire free energy profile associated with the formation of a vapor-tube inside the confined region for conditions when the vapor state is the most stable state. Overall, the conclusion is that the inclusion of line-tension in macroscopic theory is necessary to describe the behavior of water under nanoscale confinement between two hydrophobic solutes. |
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N00.00183: Thin Film Rheology via Focused Laser Spike Thermocapillary Dewetting Jonathan P Singer, Tianxing Ma, Alex Liu, Kyle Buznitsky, Yi Jin, Zahra Fakhraai Focused laser spike (FLaSk) dewetting employs the localized heat source of a focused laser to create thermocapillary-induced trench-ridge morphologies. By using a universal heating substrate to create a material-independent thermal profile coupled with optical microscopy, we have studied the dewetted ridge feature for several distinct glassy thin films. The evolution of the ridge's radius over time can be modeled using stretched exponential functions to derive a maximum dewetted radius and a characteristic decay time. The characteristic decay time shows a super-Arrhenius behavior resembling viscosity change during the glass transition process. The extracted activation energies are independent of thickness and show direct correlation with molecular weight and entanglement. Further, an effective viscosity of TC dewetting may be defined that correlates with previous theoretical and experimental results. The extracted values appear to also capture additional ordering mechanisms, as indicated by the abnormally high activation energy and resultant FLaSk viscosity of the molecular glass N,N′-Bis(3-methylphenyl)-N,N′-diphenylbenzidine. In this way, we have demonstrated that FLaSk rheology can be a useful tool to probe difficult to investigate regimes of thin film fluid mechanics that can be developed through more systematic study. |
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N00.00184: Identifying Defect-Induced Trion in Monolayer WS2 Riya Sebait Unusually high exciton binding energies (BEs), as much as ∼1 eV in monolayer transition-metal dichalcoge-nides, provide opportunities for exploring exotic and stable excitonic many-body effects. These include many-body neutral excitons, trions, biexcitons, and defect-induced excitons at room temperature, rarely realized in bulk materials. Never-theless, the defect-induced trions correlated with charge screening have never been observed, and the corresponding BEs remain unknown. Here we report defect-induced A-trions and B-trions in monolayer tungsten disulfide (WS2) viacarrier screening engineering with photogenerated carrier modulation, external doping, and substrate scattering. Defect-induced trions strongly couple with inherent SiO2 hole traps under high photocarrier densities and become more prominent in rhenium-doped WS2. The absence of defect-induced trion peaks was confirmed using a trap-free hexagonal boron nitride substrate, regardless of power density. Moreover, many-body excitonic charge states and their BEs were compared via carrier screening engineering at room temperature. The highest BE was observed in the defect-induced A-trion state (∼214 meV), comparably higher than the trion (209 meV) and neutral exciton (174 meV), and further tuned by external photoinduced carrier density control. This investigation allows us to demonstrate defect-induced trion BE localization via spatial BE mapping in the monolayer WS2 midflake regions distinctive from theflake edges. |
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N00.00185: Mirau interferometry of fluid interfaces deformed by colloids under the influence of external fields Peter J Beltramo, Samuel Trevenen There exists a challenge in measuring how changes to the interfacial deformation around particles and three-phase contact angle modify particle pinning properties in situ as external curvature and electromagnetic fields are applied. Here we describe a modified technique based on phase-shifted Mirau interferometry to determine the relative height of the fluid interface surrounding interfacially pinned colloids while applying external fields. The resolution of this technique is ±44 nm laterally in the plane of the interface and ±4 nm along the height axis, and corrections for in-plane motion of the particle and remnant far-field interfacial curvature are implemented. The measured topography of the surface is used in conjunction with the particle geometry to identify the contact line where the two fluids meet the particle. We apply this technique to quantify the contact angle (θc) and maximal interfacial deformation (∆umax) of pinned ellipsoids in order to understand how changing particle characteristics and external field conditions modify interparticle capillary interactions. We find that electric fields increase θc but do not alter ∆umax, indicating that the height of the particle at the interface changes upon application. Ongoing work is applying this technique to additional interfacial systems, including biphasic ellipsoidal particles, and external field characteristics. |
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N00.00186: Colloidal depletion gel elasticity arises from the packing of locally glassy clusters Eric M Furst, James Swan, Lilian C Hsiao, Michael Solomon In colloidal gels, attractive interactions among suspended particles drive a thermodynamic instability that promotes aggregation, arresting in a space spanning network structure possessing elasticity and a yield stress. As the attractive strength between particles increases, the gel elastic modulus increases. Surprisingly, this change cannot be accounted for by the immediate increase in bond stiffness between particles and clusters derived from the depletion interaction energy. Instead, the quantitative agreement between integrated experimental, computational, and graph theoretic approaches are used to understand the arrested state and the origins of the gel elastic response. The micro-structural source of elasticity is identified by the l-balanced graph partition of the gels into minimally interconnected clusters that act as rigid, load bearing units. The number density of cluster-cluster connections grows with increasing attraction, and explains the emergence of elasticity in the network through the classic Cauchy-Born theory. Clusters are amorphous and iso-static; the internal cluster particle density maps onto the known attractive glass line of sticky colloids at low attraction strengths and extends this line to higher strengths and lower particle volume fractions. |
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N00.00187: Phase transitions in magnetic rods driven by dynamic magnetic fields Chase A Brisbois, Monica Olvera De La Cruz Magnetic fields can remotely, and precisely, drive magnetic matter into far-from-equilibrium states. We use molecular dynamics to study phase transitions in stiff filaments composed of superparamagnetic colloids in precessing magnetic fields. By controlling the magnetic torque that drives filament precession, we observe transitions from paranematic to smectic states. Furthermore, the inter-filament magnetic coupling directly affects the local alignment of the filaments, producing disordered to hexagonal order transitions. These results show how time-dependent magnetic fields can navigate the phase space of dense solutions of magnetic colloidal structures. |
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N00.00188: Diffusion in a realistic simulated model for the stratum corneum Peter D Olmsted, Oleh Tovkach, Gustavo S Luengo, Fabien Leonforte, Ann Detroyer The outermost layer of mammalian skin, called the stratum corneum (SC), constitutes a self-healing barrier against moisture loss and ingress of foreign substances. The SC comprises flat ``bricks'' (50-100 micron wide and 1 micron thick corneocytes largely filled with keratins) held together by a ``mortar'' of 6-10 layers of lipids (100 nm thick). The corneocytes are hydrophilic, while the lipid matrix is hydrophobic. The ability and way of a chemical to pass the SC is a key point for risk assessment and development of cosmetics. |
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N00.00189: Topological data analysis of the stress state of granular packings. Ivan Tseytlin, Alyx Patterson, Woodkensia Charles, Theodore Brzinski We apply topological data analysis to describe the multi-scale structure of the stress state of granular systems. Our approach differs from prior efforts by analyzing the interactions over all geometric length scales, instead of just at physical contact. We demonstrate this analysis on data from packings of photoelastic grains and molecular dynamics simulations of packings of bidisperse spheres in 2 and 3 dimensions. We observe nontrivial persistence in higher-dimension homology groups. We hypothesize these higher-dimensional features represent mechanically significant structures which cannot be identified in more conventional 'force chain'-inspired topological analyses. |
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N00.00190: Linking dynamics and structure in highly asymmetric ionic liquids Mariana Farias-Anguiano, Ernesto Carlos Cortes Morales, Jonathan K Whitmer, Pedro E Ramirez-Gonzalez In this work, we explore an idealized theoretical model for the transport of ions within highly asymmetric ionic liquid mixtures. A primitive model (PM)-inspired system serves as a representative for asymmetric ionic materials (such as liquid crystalline salts) which quench to form disordered, partially-arrested phases. Self-Consistent Generalized Langevin Equation (SCGLE) Theory is applied to understand the connection between the size ratio of charge-matched salts and their average mobility. Within this model, we identify novel glassy states where one of the two charged species (either the macro-cation or the micro-anion) are arrested, while the other retains mobility. We discuss how this result is useful in the development of novel single-ion conducting phases in ionic liquid-based materials. |
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N00.00191: Computational Modeling of White Matter with Axon Connectivity Xincheng Wang In the brain, white matter is embedded with innumerable axon tracts that provide connectivity and functionality. It has recently become evident that many neurological disorders and diseases are related to abnormal white matter connectivity. However, the fundamental understanding of axon tracts physical influence on the brain tissue is still superficial. To address this issue, we built a computational model to explicitly simulate axon tracts throughout the process of cortical folding. We believe the axon tension could serve as a slight perturbation, triggering global surface instability in the subcritical state. Our preliminary results support our hypothesis, showing that axon tension plays a vital role during the cortical folding process. In the future, we aim to fuse the computational model with experimental data from diffusion MRI. Our ultimate goal is to integrate a high-fidelity white matter simulation platform for helping the diagnosis and treatment of neurological disabilities. |
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N00.00192: Anomalous Small Angle X-ray Scattering Study of Counterion Distribution around Macroion and Biopolyelectrolytes Jiahui Chen, Mrinal Bera, Tianbo Liu The counterion condensed around marcoion is important for their solution behavior. While other techniques can hardly achieve, anomalous small angle X-ray scattering (ASAXS) can deterimine numbers and spatial distribution of counterions around the macroion. {Mo132}, a negetively charged sphere of ~3 nm diameter, was used as a model of macroions to be investigated by ASAXS. The result shows: 1. Extra Rb+ can neutralize most of negative charges and induce coagulation of {Mo132}. 2. Extra Sr2+ can effectively screen the electrostatic interaction between {Mo132} but cannot induce coagulation. Contrary to DLVO or Debye-Huckel theory, Sr2+ only loosely associate with macroion. While the Coulomb force dominate the interactions between macroions and counterions in most cases, the energy penalty of break the hydration shell of the divalent cation (Sr2+) upon counterion-macroion association is important, which caused this abnormal counterion association behavior. Counterion distribution around several other soft and rigid charged polysaccharides were also studied. |
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N00.00193: Robotic models of swimming bacteria Bruce E Rodenborn, Asha Ari, Alexandra Boardman, Tanner May The swimming of microorganisms is typically studied using biological experiments and/or numerical simulations. However, numerical simulations of microorganisms are often not compared to precise measurements because of the difficulty of making microscopic measurements of forces and torques in biological experiments, which are typically ∼ 10 μm. Instead, our research group uses robotic models that are about 10 cm in size and match the Reynolds number of swimming microorganisms by using highly viscous silicone oil that is 100,000X more viscous than water. We can then measure the forces and torques more easily and scale the results from our dynamically similar experiments to biologically relevant sizes. We have used our experiments to calibrate the method images for regularized Stokeslets and found excellent agreement between our data for both cylinders and helices. Our results also have confirmed the theory of Jeffrey and Onishi (1981) for the torque on a cylinder near a plane wall, as reported in Shindell et al., Fluids (2021). |
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N00.00194: Building a macroscopic, low Reynolds number three-link swimmer Bruce E Rodenborn, Zaid Ahmed, RJ Smith One of the simplest robots that can swim at low Reynolds number is Purcell’s three-link swimmer, which consists of three hinged links in a chain. The work of Hatton and Choset (IEEE Trans. Robot, 2013) provides a theoretical framework to predict the displacement and rotation of such a swimmer, but assumes the robot links are slender. They use a phase space of the two joint angles and a 3-D map known as a height function derived from the Navier-Stokes equations to determine the motion of the swimmer. However, to our knowledge, no one has tested this theory experimentally, which is the goal of our study. We are building a macroscopic three link robotic swimmer that will swim in highly viscous silicone oil so the Reynolds number is small. We will compare the motion of our robot to that predicted using the theoretical height function. We will also determine the height function for our robot empirically (Hatton et al., PRL 2013) to understand the error introduced by our robot not being a truly slender body. We will also be able to systematically change the aspect ratio and length of the swimmer using 3-D printed body parts to understand the how the performance of the swimmer is affected by body shape. |
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N00.00195: Chromosome Modeling on Downsampled Hi-C Maps Enhances Compartmentalization Signal Antonio B Oliveira Jr, Vinicius Contessoto, Jose N Onuchic The human genome is organized within a nucleus where chromosomes fold into an ensemble of different conformations. Chromosome conformation capture techniques such as Hi-C provide information about the genome architecture by creating a 2D heatmap. Initially, Hi-C maps experiments were performed in human interphase cell lines. Recently, efforts were expanded to several different organisms, cell lines, tissues, and cell cycle phases where obtaining high-quality maps is challenging. Poor sampled Hi-C maps present high sparse matrices where compartments located far from the main diagonal are difficult to observe. Aided by recently developed models for chromatin folding and structure, we develop a framework to enhance the compartments' information far from the diagonal observed in experimental sparse matrices. The simulations were performed using the Open-MiChroM platform aided by new trained parameters into the Minimal Chromatin Model (MiChroM) energy function. The simulations optimized on a downsampled experimental map (10% of the original data) allow the prediction of a similar contact frequency to the complete (100%) experimental Hi-C. The modeling results open a discussion on how simulations and modeling can increase the statistics and help fill in some Hi-C regions not captured by poor sampling experiments. Open-MiChroM simulations allow us to explore the 3D genome organization of different organisms, cell lines, and cell phases that often do not produce a high-quality Hi-C map. |
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N00.00196: Exploiting Geometrical Frustration in Multistable Soft Robots Part 2: Finite-State Mechanologic Andres F Arrieta, Juan C Osorio-Pinzon, Harith Morgan Mechanologic and information processing in elastic metamaterials has focused on realizations of Boolean logic following a von Neumann architecture. This implies the separation of memory and computation and the use of mechanical binary logic as the fundamental operation for information processing. Recently, hierarchical multistable metasheets have been shown to display collocated memory and computation capabilities. Concretely, such multistable metastructures use energy minimization into an encoded stable state as the fundamental operation for computation. We extend this principle to realize embodied finite-state mechanologic in multistable soft robots, whose kinematic configuration depends on a sequence of state transitions. We show that constructive deformation of parts of the robot leads to particular kinematic finite states. These finite states can be designed as desired robotic configurations, for example, for adopting different manipulation poses. Our results demonstrate finite-state mechanologic in soft multistable robotics, thus departing from von-Neumann architectures and binary logic for mechanical computation. |
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N00.00197: Linking Hi-C and Spectroscopic Single-molecule Socalization Microscopy (sSMLM) Experiments through Molecular Simulation and Machine Learning Aria E Coraor, Juan De Pablo Super-resolution optical microscopy techniques such as spectroscopic single-molecule localization microscopy (sSMLM) have shown great potential to enable structural analysis of chromatin across the genome with nanometer-scale resolution and time-domain information. However, progress remains to be made in analysis techniques which allow the results of such microscopy methods to be compared with complementary non-microscopic techniques such as Hi-C, Chip-seq, and ATAC-seq. In this work, we introduce analytical formulas for a descriptive quantity, the epigenetic molar contact ratio, which characterizes the ‘plaid pattern’ detectable in Hi-C maps, and which we show can be calculated directly from both Hi-C data and the results of well-established sSMLM techniques. We validate this technique by comparison to a ground-truth polymer model, both determining the performance of this model and identifying the biological systems in which we expect this technique to be more or less accurate. We also demonstrate the ability to quantitatively reconstruct the Hi-C map of a polymer by performing this analysis on in silico-generated sSMLM images. Our analysis demonstrates the potential for advanced analytical techniques to predict complex parameters from individual sSMLM images in single cells. |
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N00.00198: The common and the exotic: exceptional topology in ordinary soft matter Tsvi Tlusty We will discuss how hydrodynamics induces non-Hermitian topological phenomena in ordinary, passive soft matter. This is demonstrated by subjecting a two-dimensional elastic lattice to a low-Reynolds viscous flow. The interplay of hydrodynamics and elasticity splits Dirac cones into bulk Fermi arcs, pairing exceptional points with opposite half-integer topological charges. The bulk Fermi arc is a generic hallmark of the system exhibited in all lattice and flow symmetries. An analytic model and simulations explain how the emergent singularities shape the spectral bands and give rise to a web of van Hove singularity lines in the density of states. The present findings suggest that non-Hermitian physics can be explored in a broad class of ordinary soft matter, living and artificial alike, opening avenues for topology-based technology in this regime. Possible experimental realizations will be examined. |
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N00.00199: Analysis of Langmuir trough synthetic lung surfactant monolayers exposed to e-cigarette additives Jocelyn Ochoa, Alauna Wheeler, Rayner Hernandez Perez, Linda S Hirst The use of electronic cigarettes (e-cigarettes) has widely increased; in 2019, about 10.9 million people reported to use e-cigarettes. The flavoring additives have been associated with the increase of e-cigarette usage. Interestingly, some of these flavoring chemicals are known to be toxic and have been associated with lung illnesses such a popcorn lung. Also, while the flavoring chemicals may meet the safety levels for ingestion, the inhalation levels have not been determined. This shows that investigation of the impact that e-cigarettes have in our health is important since they might not be as safe as advertised and unfortunately, not many studies have been reported. |
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N00.00200: Time-dependent rheology of enzymatically-active composites of DNA and dextran Juexin Marfai, Pawan Khanal, Philip D Neill, Davide Michieletto, Ryan McGorty, Rae M Anderson Polymer topology has been shown to play a principal role in the rheology and miscibility of polymer composites. At the same time, active materials, which undergo bulk rheological changes driven by macromolecular rearrangement and restructuring, are the topic of intense investigation. Here, we design polymer composites comprising entangled ring DNA and dextran polymers, and measure the dependence of rheological properties on the ratio of the two polymers. To push the composites out of equilibrium we incorporate enzymes that convert DNA rings to linear fragments and measure the time-dependent rheological properties of the 'topologically-active' DNA-dextran composites during enzymatic activity. The bulk linear viscoelastic moduli that we measure show that composites undergo shear thickening and thinning over time, with the timescale and magnitude of the rheological changes dependent on the DNA:dextran ratio. Our system combines the tunability and versatility of polymer composites with the power of topologically-distinct DNA and enzymatic reactions to create topologically-active polymeric fluids that can be used for diverse applications from drug delivery, to filtration to infrastructure repair. |
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N00.00201: Colloid levitation and Quincke electrorotation in confinement Zhanwen Wang, Michael J Miksis The Quincke effect is an electrohydrodynamic instability which gives rise to a torque on a dielectric particle in a uniform DC electric field. If a colloid is initially resting on the electrode, it rolls with steady velocity, and the collective dynamics of these Quincke rollers has been subject to a great interest since the pioneering work of Bricard et al, Nature (2013). However, Pradillo et al, Soft Matter (2019) found another regime, where the colloid initially lifts off the bottom electrode and levitates in the space between the electrodes. The lift force is puzzling because the interaction between a charge-neutral sphere and an electrode is always attractive. In this study we theoretically investigate the origin of the repulsive force. We calculate the electrostatic force between a sphere and one or two planar electrodes. Furthermore, we investigate the dynamics of the Quincke rotor in the hovering state and compare it to the dynamics in free space. |
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N00.00202: Dynamics of Spin Glasses James N MACLAURIN This project contributes new equations for understanding the dynamics of mean-field spin glass systems. It focusses on the Sherrington-Kirkpatrick spin glass system: with both discrete `hard' spins, and a soft-spin spherical model. This system involves pairwise all-to-all interaction, where the strength of the interaction scales as N^{-1/2} multiplied by a centered Gaussian variable of unit variance. It is widely considered a paradigm for glassy dynamics, in both condensed matter physics and data science. The dynamics is initiated from a deep quench (random initial conditions). |
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N00.00203: Influence of Surfactants, Polymers and Proteins on Foam Film Drainage Chenxian Xu, Lena Hassan, Chrystian Ochoa, Patrycja Kotwis, Vivek Sharma Foams can be described as colloidal dispersions containing large gas cells separated by thin liquid films, whose junctions are called Plateau borders. Drainage of individual ultrathin foam films (thickness < 100 nm) into Plateau borders is governed by the interplay of capillarity, disjoining pressure, viscosity, and interfacial rheology. It is well-established that confinement-induced structuring and layering of supramolecular structures like micelles, liquid crystals, colloidal particles, or polyelectrolytes within foam films results in drainage via stratification. Only few examples show the possibility of stratification in foam films containing polymers or proteins. In this contribution, we visualize and analyze drainage in foam formulated with surfactants, proteins, polymers and their mixtures, and describe the specific connection to foam stability and applications in diverse areas in foods, cosmetics, environmental remediation, oil recovery, and healthcare. |
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N00.00204: Sculpting vesicles with active particles:Less is more Hanumantha Rao Vutukuri Biological cells are able to generate intricate structures and respond to external stimuli, sculpting their membrane from within. In this talk, we present a simplified biomimetic experimental model system in order to address the question how the lipid/cell membrane responds to highly localized point forces from inside, such as those exerted by the cytoskeleton. In our experimental model system, the cell membrane is mimicked by giant unilamellar vesicles of lipid bilayers, and the local internal forces are generated by enclosing self-propelled particles [1]. We demonstrate that the propulsion forces of individual self-propelled particles, as small as ~ 0.1 pN, are sufficient to induce dramatic vesicle shapes and lead to active membrane fluctuations. Microscopic visualization is revealing, strikingly, the formation of tethered, dendric-like structures at low volume fractions and low tensions, whereas more global deformations of the vesicle shape are observed for increasing particle loadings. Moreover, the analysis of the mechanical properties of the membrane by shape fluctuation spectra shows a strong deviation from the Helfrich model elucidating the specific role of active non-equilibrium processes. Our state diagram predicts the conditions under which local internal forces generate various membrane morphologies. Strikingly-Less is more! Our study shows how the interplay of local active forces, membrane elasticity and viscosity can give rise to a plethora of novel vesicle shapes, which do not exist in equilibrium systems. |
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N00.00205: Interfacial and rheological properties of milk proteins and derivatives Lena Hassan, Karthika Suresh, Chenxian Xu, Vivek Sharma, Karim Al Zahabi Milk is an emulsion, a type of colloidal suspension,primarily composed of fat droplets dispersed in water, with proteins present at the oil -water interface and in bulk. Understanding the interfacial and rheological behavior of bovine milk proteins is critical for developing alternative plant-based milks. In this study, we analyze the shear and extensional rheological properties of two major protein groups found in milk, caseins and whey, alongside a milk protein derivative: sodium caseinate (NaCas). We examine the adsorption kinetics of these proteins and analyze the thin film drainage to elucidate the influence of protein concentration and type on foam and emulsion stabilty and rheology. |
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N00.00206: Unmodified Clay Nanosheets at the Air-Water Interface Jon Otto Fossum, Paulo Henrique O Michels Brito, Antonio Malfati-Gasperini, Lina Mayr, Ximena Puentes-Martinez, Rômulo P Tenório, Daniel R Wagner, Kenneth D Knudsen, Koiti Araki, Rafael G Oliveira, Josef Breu, Leide P Cavalcanti Clay nanolayers are 2D soft materials, such as graphene oxide layers. Clay nanolayers are of great general interest, in particular, because of their use as Pickering emulsion stabilizers and their ability to provide colloidosome capsules. Many reports show that clays could only adhere at oil-water or air-saline-water interfaces in the aggregated state. However, here we demonstrated that unmodified clay nanolayers can be located at air-deionized-water interfaces. In the present work, we use a clay nanolayer made by a synthetic Fluorohectorite with a very high aspect ratio, superior quality in homogeneity and charge distribution. We studied clay nanosheet organization at the air-water interface by combining different experimental methods: Langmuir film studies show insignificant surface tension when the clay particles are at the surface, whereas Grazing Incidence X-ray Off Specular Scattering (GIXOS) confirmed the presence of unmodified and functionalized clay nanosheets at the air-water interface, and Brewster Angle Microscopy (BAM) demonstrated a dynamic equilibrium between unmodified clay nanolayers on the air-liquid interface and the subphase. |
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N00.00207: Arrangement of Spherical Nanoparticles inside Nanoscale Liposomes Kumar Pandey The understanding of the interaction between nanoparticles (NPs) and lipid membranes is important to the development of safe and effective nanomaterials for a wide array of technological and biomedical applications. The adhesion of aspherical NP on a lipid membrane leads to its wrapping by the membrane and its deformations. This in turn leads to effective forces between the NPs and, in some instances, to their self-assembly on the membrane. Here,we present results based on coarse-grained molecular dynamics simulations of an implicit solvent model in conjunction with the Weighted Histogram Analysis Method, of the arrangement of two spherical NPs, with uniform surfaces, inside nanoscale liposomes. In contrast to the case where the NPs adhere to the exterior surface of liposomes1, we found that NPs that adhere to the interior surface of liposomes pefer configurations in which they are always apart from each other. |
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N00.00208: Data Driven Modelling of Chromosome Architecture at Nucleosome Resolution Soren C Kyhl, Juan De Pablo The three-dimensional organization of chromatin has been recognized to play a major role in pathways of gene regulation and disease. Increasing evidence indicates that features of the three-dimensional structure control the physical readout of genetic information and may ultimately establish programs of gene expression. Advances in experimental probes of chromatin organization (Hi-C) provide unprecedented insight into pairwise contact frequencies, but the complete configuration of chromatin in three-dimensions is not furnished by these methods. Computational models have been advanced to predict chromatin structures consistent with these experiments, but have thus-far been limited to a resolution no finer than the resolution of state-of-the-art Hi-C experiments (~5 kbp). However, models of this type are unable to investigate the structure inerior to individual genes which are crucial to regulatory pathways. In this poster, we present a model for chromosome architecture at nucleosome resolution, using maximum entropy methods to recapitulate experimental Hi-C contact maps. We explore how models at this resolution can connect length scales from nucleosome interactions all the way to whole-chromosome organization. We expect that models of this resolution are necessary to investigate important features of epigenetic regulation that require information at the sub-gene scale. |
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N00.00209: Biosynthetic Chiral Nematic Soft Materials with Enhanced Adhesion: Luminescent Adhesives with Universal Adhesions on Hydrophobic and Hydrophilic Surfaces Minkyu Kim, Kellina J Pierce, Daria Bukharina, Dhriti Nepal, Timothy J Bunning, Vladimir V Tsukruk We present two strategies to achieve excellent adhesive materials based on chiral nematic cellulose nanocrystals (CNC). In the first strategy, we demonstrate crack-free soft monolithic chiral nematic films using the capillary confinement where the increased cohesion is obtained by tailoring hydrogen bonding. To obtain the long-range ordered CNC during a confined drying, we utilized tunicate-inspired hydroxyl group-rich 3,4,5-trihydroxyphenethylamine hydrochloride (TOPA) for hydrogen-bonding. Similarly, physical crosslinking of CNC and polyethylene glycol (PEG) enabled releasing internal stresses at the inner capillary surface. Cross-sectional scanning electron microscopy images revealed that symmetry-breaking occurred with film dried in the capillary tube: transition from the horizontally organized left-handed chiral nematic structure over the wide capillary tube surface to a vertically organized left-handed chiral nematic structure inside of capillary. Overall, we demonstrate a minimal amount of TOPA, 3 wt.%, in the CNC/TOPA/PEG composite enables crack-free monolithic films through enhanced cohesion and adhesion, which improved the mechanical performances, achieved tunable optical bandgap, and enhanced the circular polarization. In the second strategy, chiral nematic CNC and polyelectrolyte complexes enabled universal adhesive properties, including strong adhesion on both hydrophobic and hydrophilic substrates. Furthermore, dynamic and strong photoluminescence with highly asymmetric circularly polarized luminescent is achieved by rare earth europium doping without compromising adhesive strength and original iridescent color. Thus, the unique properties of luminescent soft bio-adhesives with universal adhesion, amplified and switchable photoluminescence, and large and dynamic circularly polarized luminescence can be employed for optical encoding, bio-optical memory, and wearable stickers on human clothes, skins, and gadgets. |
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N00.00210: Experimental analysis of deep eutectic solvents to derive fundamental correlations between local parent species properties and bulk material properties utilizing differential scanning calorimetry Kaylie Glynn, Joshua Sangoro Deep eutectic solvents (DESs) are a newer class of solvents with the potential to substitute for conventional organic solvents used in a wide variety of chemical processing applications, including separations, syntheses, and red-ox flow electrochemical cell units, among others. These solvents offer benefits over traditional organic solvents such as lower health hazards, lower environmental impacts, higher sustainability, ease of preparation, and the ability to meet very specific design specifications. The appeal of DESs is their ability to serve as designer solvents. However, there is a lack of predictive models which accurately characterize the thermophysical properties of the mixtures. This work focuses on developing a fundamental understanding of how local structures of parent species may be used to predict and correlate to bulk material properties of corresponding mixtures. Experimental data has been collected for binary DES mixtures of choline halide salts with ethylene glycol, glycerol, and urea using differential scanning calorimetry. Applications of constant-ratio DSC testing has been utilized to assess trends in glass transition temperature as a function of heating a cooling rate, in efforts to determine true transition temperatures. Coupling of experimental data and ideal solution theory has provided insights to begin developing predictive models for deep eutectic solvent design. |
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N00.00211: STATISTICAL AND NONLINEAR PHYSICS
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N00.00212: Non-ergodic Brownian oscillator Alex Plyukhin We consider an open (Brownian) classical harmonic oscillator |
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N00.00213: Temporal Network Characteristics for Bio-Inspired Networks Nicholas S DiBrita, Khouloud Eledlebi, Hanno Hildmann, Lucas Culley, A. F. Isakovic Bio-inspired algorithms offer a heuristic approach to optimizing complex systems, and have become increasingly important within a variety of technical domains. In prior work, we developed a hybrid Genetic-Algorithm-Voronoi approach to create adaptive networks that optimize coverage within noisy, obstacle-rich finite spaces [1]. Performance of these networks was then categorized in terms of application-driven measures, like Percent Area Coverage and Cumulative Distance Traveled. In more recent work [2], we approached the analysis of these swarm-like networks using a Temporal Network Graph (TNG) framework, where networks are allowed to be changing over time to model dynamical changes in the network structure. This allowed us to utilize a variety of network-centric measures in a time-dependent matter, giving new insight into how these adaptive networks evolve in a variety of environmental conditions. Specifically, we used an edge-centric representation of the network, and tracked how eigenvector centrality and regularity changed over the course of network deployment. It is shown that the distribution of edge lengths undergoes a phase transition like behavior, and our cross-correlation analysis of time traces shows similar results. |
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N00.00214: Self-organization of oscillation in an epidemic model for COVID-19 Takashi Odagaki On the basis of a compartment model, the infection curve is investigated when the net rate of change λ=(dI/dt)/I of the number of infected individuals ?? is given by an ellipse (??/??0 )2+[(??−??0 )/Δ]2=1 in the λ−?? plane which is supported in [??ℓ,??ℎ] where ??ℎ=??0+Δ, ??ℓ=??0−Δ. With a≡(??ℎ−??ℓ)/(??ℎ+??ℓ )=Δ/??0 , it is rigorously shown that (1) when a<1 or ??ℓ>0, oscillation of the infection curve is self-organized and the period ?? of the oscillation is given by T??0=??(??ℎ−??ℓ)/(??ℎ??ℓ)1/2, (2) when a=1 or ??ℓ=0, the infection curve shows a critical behavior where it decays obeying a power law function with exponent −2 in the long time limit after a peak, and (3) when a>1 or ??ℓ<0, the infection curve decays exponentially in the long time limit after a peak and the relaxation time τ is given by τ??0=(??ℎ−??ℓ)/2(−??ℎ??ℓ)1/2. The present result indicates that the pandemic can be controlled by a measure which keeps ??ℓ<0. |
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N00.00215: Abstract Withdrawn
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N00.00216: Active matter under control Luke K Davis, Étienne Fodor Active matter consumes fuel in order to sustain individual motion. This gives rise to interesting collective effects, such as motility induced phase separation, a hallmark of active matter. Currently, we lack a physical framework that predicts the best protocol for driving active systems between different states in a way that optimizes the dissipated energy. Indeed, existing equilibrium thermodynamics is an inadequate foundation to build a framework of control for active systems due to the constant consumption of fuel. Here, we derive and implement a nonequilibrium stochastic thermodynamic framework, using nonlinear response theory, to optimally control active systems. |
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N00.00217: High-speed soliton ejection generated from the scattering of bright solitons by modulated reflectionless potential wells Laila Al Sakkaf We investigate numerically and theoretically the conditions leading to soliton ejection stimulated through the scattering of bright solitons by modulated reflectionless potential wells. Such potential wells allow for the possibility of controlled ejection of solitons with significantly high speeds. At the outset, we describe the scattering setup and characterize the soliton ejection in terms of the different parameters of the system. Then, we formulate a theoretical model revealing the underlying physics of soliton ejection. The model is based on energy and norm exchange between the incident soliton and a stable trapped mode corresponding to an exact solution of the governing nonlinear Schrödinger equation. Remarkably, stationary solitons can lead to high-speed soliton ejection where part of the nonlinear interaction energy transforms to translational kinetic energy of the ejected soliton. Our investigation shows that soliton ejection always occurs whenever the incident soliton norm is greater than that of the trapped mode whereas their energy is almost the same. Once the incident soliton is trapped, the excess in norm turns to an ejected soliton in addition to a small amount of radiation that share translational kinetic energy. We found that higher ejection speeds are obtained with multi-node trapped modes that have higher binding energy. Simultaneous two-soliton ejection has been also induced by two solitons scattering with the potential from both of its sides. An ejection speed almost twice as that of single soliton ejection was obtained. Ejection outcome and ejection speed turn out to be sensitive to the relative phase between the two incoming solitons, which suggests a tool for soliton phase interferometry. |
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N00.00218: Density-dependent behavior of self-propelled particles at the air-water interface Alistair Dumaup, Farbod Movagharnemati, Nicholas Brubaker, Wylie W Ahmed
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N00.00219: Collective Motion of Intermediate-Scale Active Matter Farbod Movagharnemati, Alistair Dumaup, Nicholas Brubaker, Wylie W Ahmed Active matter is often studied at either the microscopic scale where thermal noise strongly contributes and inertial effects can be ignored (e.g. janus particles) or at larger macro scales where inertial effects dominate and noise is negligible (e.g. flocking animals). We study an intermediate scale macroscopic system with active agents at the centimeter scale, which experience effects of both noise and inertia. Our active agents are self-propelled motorized particles that crawl on a dry surface (hexbugs). They exhibit quasi-Brownian motion with inertial persistence, and interact with each other and the container walls exclusively via collisions. We use techniques from statistical mechanics to characterize the collective motion of our agents and explore changes in dynamics as a function of particle density. We find that increasing density causes a shift from: (1) ballistic to diffusive motion, and (2) uniform to random-like motion in the vortex order parameter. |
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N00.00220: Power production from anisotropic fluctuations Olga Movilla Miangolarra, Tryphon T Georgiou Power production from anisotropic fluctuations: The Brownian gyrator represents the most basic thermodynamic system from which one can extract work by tapping simul- taneously into two heat baths with different temperatures. Specifically, it consists of an overdamped system with two coupled degrees of freedom in an anisotropic temperature field. Whereas the hallmark of the gyrator is a nonequilibrium steady-state curl-carrying probability current, we explore the coupling of this natural gyrating motion with a periodic actuation potential for the purpose of producing power. We show that path-lengths traversed in the manifold of thermodynamic states, measured in a suitable Riemannian metric, represent dissipative losses, while area integrals of a work-density quantify work being extracted. Thus, the maximal amount of work that can be extracted relates to an isoperimetric problem, trading off area against length of an encircling path. We derive an isoperimetric inequality that provides a universal bound on the efficiency of all cyclic operating protocols, and a bound on how fast a closed path can be traversed before it becomes impossible to extract positive work. The analysis presented provides guiding principles for building autonomous engines that extract work from anistropic fluctuations. |
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N00.00221: Data-driven effective model shows a liquid-like deep learning Wenxuan Zou The geometric structure of an optimization landscape is argued to be fundamentally important to support the success of deep neural network learning. A direct computation of the landscape beyond two layers is hard. Therefore, to capture the global view of the landscape, an interpretable model of the network-parameter (or weight) space must be established. However, the model is lacking so far. Furthermore, it remains unknown what the landscape looks like for deep networks of binary synapses, which plays a key role in robust and energy efficient neuromorphic computation. Here, we propose a statistical mechanics framework by directly building a least structured model of the high-dimensional weight space, considering realistic structured data, stochastic gradient descent training, and the computational depth of neural networks. We also consider whether the number of network parameters outnumbers the number of supplied training data, namely, over- or under-parametrization. Our least structured model reveals that the weight spaces of the under-parametrization and over-parameterization cases belong to the same class, in the sense that these weight spaces are well-connected without any hierarchical clustering structure. In contrast, the shallow-network has a broken weight space, characterized by a discontinuous phase transition, thereby clarifying the benefit of depth in deep learning from the angle of high dimensional geometry. Our effective model also reveals that inside a deep network, there exists a liquid-like central part of the architecture in the sense that the weights in this part behave as randomly as possible, providing algorithmic implications. Our data-driven model thus provides a statistical mechanics insight about why deep learning is unreasonably effective in terms of the high-dimensional weight space, and how deep networks are different from shallow ones. |
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N00.00222: Second Law of Thermnodynamics for Active Heat Engines Arya Datta Cyclic heat engines have been a major motivation for the emergence of thermodynamics. In the last decade, cyclic heat engines that have large fluctuations and operate at finite time were studied within the more modern framework of stochastic thermodynamics. The second law for such heat engines is the standard second law of thermodynamics, which states that the efficiency of the heat engine cannot be larger than the Carnot efficiency. The concept of active cyclic heat engines for a system in the presence of hidden dissipative degrees of freedom, also known as a nonequilibrium or active reservoir, has also been studied in theory and experiment. Such active engines show rather interesting behavior such as an "efficiency" larger than the Carnot bound. They are also likely to play an important role in future developments, given the ubiquitous presence of active mediums. However, a general second law for cyclic active heat engines was still lacking. Here we obtain a second law for active heat engines. Two main features of our second law are: it does not involve the energy dissipation of the hidden degrees of freedom, which is typically much larger than the extracted work, and it is expressed in terms of quantities that can be measured directly from the observable degrees of freedom. Besides heat and work our second law contains an information-theoretic term, which constitute an extra resource that active heat engines can explore to extract work. |
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N00.00223: Associative memory model with arbitrary Hebbian length Zijian Jiang, Haiping Huang, jianwen zhou, Tianqi Hou, Ziming Chen, K.Y. Michael Wong Our brains build connections within events, i.e. associative memory. Specifically, the brain can establish correlation between temporal sequential events by conversion the correlation into the spatial-structured synapses, which is related to the function of learning and the feeling of time passing. However, The correlation conversion can happens in a wide integration window, whose influence on the correlation conversion remains elusive. |
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N00.00224: A physics perspective to understand credit assignment Chan Li, Haiping Huang, Wenxuan Zou Deep learning has been playing a seminal role in a variety of fields, while the Achilles heel of it lies in the black-box property hidden behind it, i.e., it is still unknown how the learning coordinates a huge number of parameters to achieve decision making. To explain hierarchical credit assignment, we propose a mean-field learning model by assuming that an ensemble of sub-networks, rather than a single network, is trained in a supervised scenario. The model works well and we identify three kinds of weights: VIP(important), UIP(unimportant), and other connections allowing for a broad distribution of their values, which provides insights toward understanding the macroscopic behavior of deep learning through distinct roles of synaptic weights. Then, we extend this model to learn the harder temporal credit assignment framed in the recurrent neural networks, which are widely used in processing complex temporal sequences. We successfully reveal important connections determining the overall performance of the network and produce an ensemble of candidate networks. Our method links network statistics, distinct functions of computational layers and neural selectivity, and can be used as a general and promising tool to understand credit assignment in networks with various architectures. |
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N00.00225: Modeling the El Niño Southern Oscillation with Neural Differential Equations Ludovico T Giorgini, Soon Hoe Lim, Woosok Moon, John S Wettlaufer El Niño Southern Oscillation (ENSO) is the largest inter-annual variability phenomenon in the tropical Pacific and its influence goes beyond tropics to higher latitudes via atmospheric and oceanic teleconnections; therefore, it has a significant impact on global climate predictions. |
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N00.00226: Critical synchronization dynamics on power-grids Shengfeng Deng, Geza Odor, Balint Hartmann, Lilla Barancsuk Power-grids are among the largest man-made complex systems, staying in the synchronization state of billions of nodes. Formerly power-law tailed cascade size distributions have been found by outage statistics and DC models. The spread of renewable resources poses unprecedented pressure on system stability. Here we show how this can be modeled by Kuramoto-like synchronization models, which describe the real power flow in AC systems. The combination of swing equations with line threshold failures allows us to describe the dynamical avalanche-like blackout failures in different HV power-grid networks. In particular, we compare the stability and blackout statistics for the US and the EU HV networks, taking into account the feedback effects. We show that nonuniversal power-law size and duration distributions emerge below the first-order transitions of the Kuramoto model, thus we see an example for hybrid transition known in other branches of physics. |
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N00.00227: Opinion Formation Model on Random Graphs for Financial Markets Mateus Francisco B Granha, Andre L M. Vilela, H E Stanley We investigate the financial market dynamics by proposing a heterogeneous agent-based opinion formation model. In this work, we classify the individuals in a financial market by their trader strategy, namely noise traders and fundamentalists. The local majority drives the market exchanging behavior of noise traders, whereas the global minority of the network influences the fundamentalist agents. We represent the individuals as nodes in an Erdös-Rényi random graph and, at a given time, they assume one of two opinion states, +1 or -1, regarding buying or selling an asset. Our model presents such fundamental qualitative and quantitative real-world market features as the distribution of logarithmic returns with fat-tails, clustered volatility, and long-term correlation of returns. We use Student's t distributions to fit the histograms of logarithmic returns, showing the gradual shift from a leptokurtic to a mesokurtic regime, depending on the fraction of fundamentalist agents. We also investigate the distribution of logarithmic returns of several real-world financial indices. |
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N00.00228: A Nonlinear Dynamical Analysis of History Dependence in Granular Media William C Buchholtz, Edward J Banigan, David A Egolf Researchers have observed that key properties of granular materials, including the density at which systems jam, depend on the details of their history, such as the compression rate or the initial compression density. In this work, we employ the tools of nonlinear dynamics, particularly Lyapunov exponents and vectors, to provide new insights on history dependence in two-dimensional systems of soft disks. We characterize how the Lyapunov spectra differ when systems are prepared using various protocols, focusing especially on the transition from chaotic to non-chaotic behavior. Further, using Lyapunov vectors, we quantify how the shapes and sizes of the most important dynamical modes are affected by the preparation protocol. |
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N00.00229: De-tangling the Strength of the Rhinoceros Horn Krishma Singal, Andrew Schulz, Thomas C Day, Joseph Mendelson, Jennifer Mickleberg, Peter Yunker, David L Hu The rhino population has dropped over 50% in the last 50 years due to poaching for their strong and durable horns. But where does this strength and durability come from? Unlike other animal horns, rhino horns do not have a bony core; instead, they are made completely out of keratin, the same material comprising nails, feathers and hair. The material properties of the horn thus arise solely from the arrangement of its keratin fibers. In this experimental study, we analyze the structure, orientation, and function the fibers play in this strength. We hypothesize that the structural integrity is built through entangled and intertwined fibers. Entangled and intertwined structures increase material strength evident by a nonlinear stress-strain relationship. We characterize the effects of the keratin’s structural impact by performing mechanical, histochemical, and microscopy tests on a preserved Black rhinoceros (Diceros bicornis) horn. Through these tests, we have developed a “map” of the morphology and compositional differences of orientation and structure throughout the horn. Understanding the complete inner fiber structure will help build a rhino horn mimic to flood the black market with and thereby help reduce poaching. |
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N00.00230: Influence of Cooperative Agents on the Dynamics and Social Entropy production of the Majority-vote Model Igor G Oliveira, Andre L M. Vilela, H E Stanley We investigate the cooperative behavior phenomena in social networks using anisotropic effects on the majority-vote model with noise. In our formulation, a given individual selects an opinion equal to the majority of its neighbors with probability 1 - μq and the opposite with probability μq. The parameter q is called the system noise and acts as a social temperature promoting the social disorder, whereas μ stands for the cooperative behavior intensity, stimulating collective agreement. In our numerical investigations, we set a fraction f of collaborative agents to have noise sensibility 0 < μ < 1, while the complementary fraction 1 - f follows the standard majority-vote dynamics, i. e., μ = 1. We perform Monte Carlo simulations and the mean-field analysis to estimate the critical noise parameter qc(μ, f) on regular lattices and obtain the phase diagram of the model. We conclude that the critical social temperature is an increasing function of the anisotropic fraction f for different cooperative phenomena intensity μ. We also estimate the critical exponents β/ν, γ/ν, and 1/ν, and find that the presence of the cooperative agents does not affect the Ising universality class of the model. |
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N00.00231: Unveiling classes of self-organization across complex multiscale stochastic systems through a generalized theory of interactions Santiago Núñez-Corrales, Eric Jakobsson Complex multiscale stochastic systems (CMSS), are systems composed of many objects and processes that interact with each other in non-trivial manners (i.e. interdependent), whose structure and behavior can be described at several nested, coupled scales by different principles and laws. Yet, these remain causally connected and their spatio-temporal evolution and interactions are inherently stochastic, leading to complementarity relations with non-zero statistical uncertainty. CMSS show overall consistency with fundamental physical laws such as conservation of energy and irreversible thermodynamics. Understanding the principles behind self-organization across these systems constitutes a major milestone toward addressing grand challenges in science and society. |
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N00.00232: Angular frequency of rotating spiral waves in a chemical reaction-diffusion system Melita F Wiles, Niklas Manz Rotating spiral waves have been observed in various excitable physical, chemical, and biological reaction-diffusion systems. Most of the theoretical and experimental studies of two-dimensional excitable systems were done in planar geometries. However, in nature, many excitation waves occur on curved surfaces, e.g., the heart, the visual cortex, or the retina. In the framework of kinematic approach it has been shown, that the spiral wave's angular frequency depends on the curvature of the system itself. The chemical Belousov-Zhabotinsky reaction can be used as a model system to investigate the propagation dynamics of these spirals. We use quasi-two-dimensional hemispherical shells with various curvatures to determine experimentally the curvature dependence of the spiral's rotational frequency. |
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N00.00233: A Stochastic Thermodynamics-based Network Architecture (ThN) for Machine Learning Sadasivan Shankar, Vishnu Shankar We have developed a new network architecture based on the principles of stochastic thermodynamics for machine learning. The architecture has been developed based on the principles of thermodynamics in which energy and entropy represented by the attributes. As these are both extrinsic properties, they are essentially determined by the specific problem for which machine learning is applied to. The challenges in the formulation have been in the representation of the intrinsic complexity and the presence of disparate length and time scales. However, given the combinatorial nature of many problems, this architecture has a unique advantage of being able to evolve dynamically in non-equilibrium dynamic mode and also learn in equilibrium conditions. The dynamics of the network and its stochastic nature provides additional advantages for application of this formalism to both chemical and biological systems. We will also be presenting the comparisons of the Thermodynamic network (ThN) with more conventional Deep neural Networks. |
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N00.00234: Lattice model of active matter Viktor Skultety, Matthew J Metson, Richard Blythe Active systems -- collections of self-propelling particles with mutual interactions -- have been the subject of much research in recent years. This is because they often exhibit novel properties such as collective motion, or motility induced phase separation, which are absent in their passive counterparts. |
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N00.00235: Classical and quantum random-walk centrality measures in multilayer networks Lucas Boettcher, Mason A Porter Multilayer network analysis is a useful approach for studying the structural properties of entities with diverse, multitudinous relations. Classifying the importance of nodes and node-layer tuples is an important aspect of the study of multilayer networks. To do this, it is common to calculate various centrality measures, which allow one to rank nodes and node-layers according to a variety of structural features. In this paper, we formulate occupation, PageRank, betweenness, and closeness centralities in terms of node-occupation properties of different types of continuous-time classical and quantum random walks on multilayer networks. We apply our framework to a variety of synthetic and real-world multilayer networks, and we identify marked differences between classical and quantum centrality measures. Our computations also give insights into the correlations between certain random-walk-based and geodesic-path-based centralities. |
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N00.00236: Time crystal dynamics in a weakly modulated stochastic time delayed system Cristina Masoller, Jordi Tiana Time crystal oscillations in interacting, periodically driven many-particle systems are highly regular oscillations that persist for long periods of time, are robust to perturbations, and whose frequency differs from the frequency of the driving signal. Making use of underlying similarities of spatially-extended systems and time-delayed systems (TDSs), we present an experimental demonstration of time-crystal-like behavior in a stochastic, weakly modulated TDS. We consider a semiconductor laser near threshold with delayed feedback, whose output intensity shows abrupt spikes at irregular times. When the laser current is driven with a small-amplitude periodic signal we show that the interaction of delayed feedback and modulation can generate long-range regularity in the timing of the spikes, which lock to the modulation and, despite the presence of noise, remain in phase over thousands of modulation cycles. With pulsed modulation we find harmonic and subharmonic locking, while with sinusoidal modulation, we find only subharmonic locking, which is a characteristic feature of time-crystal behavior. |
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N00.00237: Understanding stochastic resonance and hysteresis in climate considering state-dependent fluctuations Moupriya Das, Holger Kantz We consider two aspects in climatic science where bistability between the two stable states of the systems is observed. One is the transition between the glacial and the interglacial phase in Earth's glacial cycle. Another is the thermohaline circulation in the North Atlantic ocean. It is possible to model both of these phenomena by the overdamped dynamics of a Brownian particle in a double-well potential subject to periodic forcing. For the former, the two wells correspond to two different climates and the periodic forcing is sufficiently weak so that no transition can occur between the two states without noise. Whereas in case of the latter, the two states represent two different conditions of the flow and the strength of the periodic forcing is high enough to cause hysteresis in the system. We suggest that the short-term fluctuations related to weather, in both of these two cases, depend on the present climatic state of the system. This leads to the introduction of the state-dependent diffusion coefficients in the dynamics because the diffusion coefficient takes into account the strength of the fluctuations. We show that this consideration produces important features in the dynamics which agree with the real observations for both the glacial cycles and thermohaline flow. |
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N00.00238: Self-Supervised Learning of Generative Spin-Glasses with Normalizing Flows Gavin S Hartnett, Masoud Mohseni We develop generative spin-glass models that can be used to represent multi-scale phenomena in physics and computer science. These systems are parametrized in terms of Normalizing Flows, a class of deep neural network-based generative models. Normalizing Flows are designed to operate on continuous variables, whereas our focus is on discretely-valued spin systems. Therefore, we first provide a continuous formulation of spin-glasses and convert the discrete Boltzmann distributions into physically equivalent continuous distributions. We then machine learn generative models of these systems in a self-supervised fashion wherein the training data is derived from the system itself. Within this self-supervised framework, we explore two alternative methods for training the normalizing flow. The first approach minimizes the standard or forward Kullback-Leibler (KL) divergence and is able to capture key physical characteristics of the spin-glass phase, including a non-trivial overlap order parameter and ultrametricity. In contrast, an alternative approach based on minimizing the reverse KL divergence, where the order of the arguments is reversed relative to the forward case, could suffer from mode collapse and fail to capture these properties. We also consider hybrid approaches designed to overcome the mode collapse problem while still retaining the efficient data generation aspect of the reverse KL minimization approach. |
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N00.00239: High-throughput binding pose refinement through induced-fit ligand docking Darren J Hsu, Jens Glaser Virtual ligand screening has become a fundamental step in the drug candidate discovery process. As the ligand libraries grow to billions of compounds, a workflow tailored for such a data-rich regime is required. We present the development of a high-throughput ligand pose refinement workflow, using the SARS-CoV-2 main protease active site as an example. The workflow takes in coarsely-docked ligand poses and parametrizes them for atomistic simulations with a semi-flexible, truncated protein core. We evaluate the effect of different protein core assemblies, solvation models, and integration protocols on numerical stability and success rate of the refinement. Finally, we discuss the workflow in the context of a drug discovery pipeline. |
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N00.00240: Uniform rotation and multi-period oscillation in the Malkus-Lorenz waterwheel George H Rutherford, Russell F Roberts, Minani Alexis The Malkus-Lorenz waterwheel is a simple mechanical system whose equations of motion reduce to the Lorenz equations under simplifying assumptions. Our apparatus has 36 acrylic cylinders around the periphery of a wheel with a 9 in (0.229 m) radius. The wheel's shaft is held by two air bushings and a flat air bearing to support the axial force. An aluminum ring around the periphery of the wheel passes between the poles of variable gap magnets, producing a frictional torque approximately proportional to the angular velocity. The wheel's angular position is measured with a non-contact, two-axis Hall sensor, and phase space variables are obtained by differentiation via fast Fourier transformation. The wheel can exhibit all three types of motion seen in the Lorenz equations: uniform rotation, periodic reversals, and chaotic reversals. The first two types of motion, although conceptually simplest, nevertheless reveal intriguing details about the wheel and its dynamics. Minor variations in the uniform rotation can yield information about imperfections in the wheel's construction and departures from ideal behavior caused by the use of discrete cells to contain the water in the wheel. We also see within the periodic region bands of mostly period-3 motion that occur outside the chaotic region when using the brake strength as the bifurcation parameter. We also present progress toward computer simulations to model both types of motion in a more realistic manner than the usual simplifying assumptions. |
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N00.00241: Topology-Driven Dynamical Arrest in Polymer Knots Anna Lappala, Hyo Jung Park, L Mahadevan Knots are entangled structures that cannot be untangled without a cut. Topological stability of knots is one of the many examples of their important properties that can be used in information storage and transfer. Knot dynamics is important for understanding general principles of entanglement as knots provide an isolated system where tangles are highly controlled and easily manipulated. To unravel the dynamics of these entangled topological objects, the first step is to identify the dominant motions that are uniquely guided by knot structure and its complexity. We identify and classify motions into three main groups– orthogonal, aligned, and mixed motions, that often act in unison, orchestrating the complex dynamics of knots. The balance between these motions is what creates an identifiable signature for every knot. As knot complexity increases, the carefully orchestrated dynamics is gradually silenced, eventually reaching a state of topologically driven dynamical arrest. Together, these findings demonstrate a link between topology and dynamics presenting applications to nanoscale materials. |
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N00.00242: BIOLOGICAL PHYSICS
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N00.00243: An autism spectrum disorder-related risk gene impacts gut tissue mechanics and the gut microbiome in Drosophila melanogaster Eliza Morris, Mikkel H Jensen, Jeffery Cavanaugh, Prince Yadav, Nguyên Henry Võ, Chloe Welch, Aliyah Penn, Kimberly Mulligan The bacteria in the human gastrointestinal (GI) tract, the so-called gut microbiome, have co-evolved with the host to form a symbiotic relationship and is an essential component of human health and healthy development. A growing body of research has revealed an intricate reciprocal relationship between neuronal development and the gut microbiota, in which changes in neuronal development affects the gut microbiota and vice versa. However, the role of the biophysical properties of the gut in this so-called gut-brain axis is poorly understood. Here, we employ a Drosophila melanogaster fly model carrying a mutation in the autism spectrum disorder-related risk gene chromatin helicase DNA-binding 8/kismet (CHD8/kis, or “kis” for short). We found that kis mutant flies exhibit changes in their gut mechanics, gut microbiome and organism behavior compared to wild-type flies. Interestingly, our mechanics measurements revealed changes in the mechanics of the kis mutant fly gut, both in terms of the strain stiffening behavior and overall elasticity. Our results support the idea that gut tissue mechanics may play a role in the gut-brain axis paradigm, and future work will further explore any reciprocal relationship between gut mechanics, the microbiome, and neuronal development. |
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N00.00244: Double-edged role of resource competition in gene expression noise and control Xiaojun Tian, Hanah Goetz, Austin Stone, Rong Zhang, Ying-Cheng Lai Despite extensive investigation demonstrating that resource competition can significantly alter the circuits' deterministic behaviors, a fundamental issue is how resource competition contributes to the gene expression noise and how the noise can be controlled. Utilizing a two-gene circuit as a prototypical system, we uncover a surprising double-edged role of resource competition in gene expression noise: the competition decreases noise through a resource constraint but generates its own type of noise which we name as ``resource competitive noise.'' Utilization of orthogonal resources enables retaining the noise reduction conferred by resource constraint while removing the added resource competitive noise. We further compare three types of negative feedback controllers: negatively competitive regulation (NCR), local, and global controllers. Both local and NCR controllers with mRNA-mediated inhibition are efficacious at reducing noise, with NCR controllers demonstrating a superior noise-reduction capability. Combining negative feedback controllers with orthogonal resources can improve the local controllers. This work provides deep insights into the origin of stochasticity in gene circuits with resource competition and guidance for developing effective noise control strategies. |
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N00.00245: Coating Bio-hybrid Pearls by Atomic Layer Deposition Oujie Kevin Tong, Lisa R Wang, Yifei Jenny Jin, Wei Wu Pearls are essentially a hybrid material of bio-organic and inorganic with micro-and nanostructured composition. The beautiful luster of a natural pearl is explained by nano-optics and the layered structure of the material. Pearls degrade under high temperature and low and high humidity environments and are susceptible to surface scratch without surface protection and chemicals such as weak acids. As a result, pearls require good handling, caring, and protection during wearing and storage. Currently, during the process of producing pearls jewelry, pearls are rubbed with a thin layer of wax or lacquer or organic coating to achieve such protections. However, due to pearls’ complicated surface structures, the coating is not able to cover or conform well enough with all the exposed surfaces or interfaces. As a result, such a coating process is not optimal. In this work, Atomic Layer Deposition (ALD) is used to coat a conformal coating of Al2O3. ALD offers a high conformality which conforms to structures with an even a 100:1 aspect ratio and down to atomic precision. Such coatings can be very conformal to the nanostructured surface of pearls and are also very robust and durable. Meanwhile, we can also utilize such coatings to introduce additional functionality such as adding color and certain optical functions. Our work showed that ALD coated surfaces of pearls significantly reduce surface roughness while improving the durability of pearls. |
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N00.00246: Towards understanding the influence of stochastic fluctuations on pattern formation in the Notch signaling pathway Madeline Galbraith, Federico Bocci, Jose N Onuchic Notch signaling is an evolutionary conserved pathway involved in many cellular processes including spatiotemporal pattern formation in tissues. It is also well known that noise is important in biological process, but how stochastic fluctuations influence pattern formation in the Notch pathway is still relatively unexplored. We focus on two common types of noise – white and shot – in multicellular systems to show optimal noise promotes a more ordered pattern. The results suggest that an intermediate range of noise perturbs the system, causing cells to "flip" to the correct state. Further, the fluctuations seem to allow the system to explore many configurations before settling into the most ordered pattern that is accessible. |
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N00.00247: Transiently increased intercommunity regulation characterizes concerted cell phenotypic transition Jianhua Xing, Weikang Wang, Dante Poe, Ke Ni Phenotype transition takes place in many biological processes such as differentiation and reprogramming. A fundamental question is how cells coordinate switching of expressions of clusters of genes. To address the question, we integrated dynamical systems theories and single cell big data analyses into analyzing scRNA-seq data. Mathematical modeling based on dynamical systems theories has been extensively used in modeling small regulatory networks, while scRNA-seq data analyses are typically statistics-based approaches with limited mechanistic insights on cellular dynamics. Through analyzing single cell RNA sequencing data in the framework of transition path theory, we studied how such a genome-wide expression program switching proceeds in three different cell transition processes. For each process we reconstructed a reaction coordinate describing the transition progression, and inferred the gene regulation network (GRN) along the reaction coordinate. Our study reveals a common principle on how cells coordinate reprograming their expression program during a transition process. In all three processes we observed common pattern that the effective number and strength of regulation between different communities increase first and then decrease. The change accompanies with similar change of the GRN frustration, defined as overall confliction between the regulation received by genes and their expression states, and GRN heterogeneity. While studies suggest that biological networks are modularized to contain perturbation effects locally, our analyses reveal a general principle that during a cell phenotypic transition intercommunity interactions increase to concertedly coordinate global gene expression reprogramming, and canalize to specific cell phenotype as Waddington visioned. |
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N00.00248: Temperature Sensitive Contact Analysis Directs Hyperactive Enzyme Design. Dan Burns Homologous mesostable and thermostable enzymes exhibit markedly different thermostabilty and activities as a result of their unique amino acid sequences. This is a necessary consequence of an organism’s metabolism and environmental pressures of which temperature is the most prominent. The mechanisms by which sequence specific interactions tune the activity of an enzyme to a particular temperature is of fundamental importance for understanding protein functional dynamics and has significant implications for the design and application of synthetic enzymes. To this end we recently designed hybrid thermophilic/mesophilic variants of the C domain of bacterial Enzyme I (EIC) with modulated activity by hybridizing the disordered catalytic loops of each wild type with the remainder of the other wild type’s C domain. In order to reveal the residue level interactions encoding enzymatic activities, we employed Hamiltonian Replica Exchange Molecular Dynamics (HREMD) to sample the conformational ensemble across temperature of the disordered catalytic loops of these 4 EIC homologs. Employing Principal Component Analysis (PCA), we extracted and ranked residues according to their contact frequencies’ temperature sensitivity. We hypothesize that these residues have the strongest effect in tuning the enzymes’ activities to their physiological temperatures. To test our hypothesis we assayed 3 mutant thermophile EIC enzymes with mutations based on these most temperature sensitive contacts. We found a minimal mutation set to the thermophilic homolog (inactive at low temperature) that increased its activity at low temperature substantially toward that of the hybrid homolog. These results suggest an efficient computational approach for designing hyperactive thermophilic enzymes and a novel analysis method for studying protein dynamics across temperature and identifying key dynamical features not otherwise apparent. |
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N00.00249: Root growth response to rigid obstacles. Manon Quiros, Evelyne Kolb, Marie-Béatrice Bogeat-Triboulot, Etienne Couturier In the current context of climate change and the ensuing hardening of the soil because of a predicted increase of drought events, studying the effect of soil mechanical resistance on growing roots takes a whole new significance and importance. Our research aims at studying the impact of mechanical stress on a primary root growing inside a soft homogeneous soil and encountering a single rigid obstacle such as a stone or a hard pan. |
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N00.00250: Molecular Implementations of Positive and Negative FeedbackInform Robustness in Biological Oscillator Motifs Chaitra Agrahar, Michael J Rust Biological oscillators like the cell cycle, the circadian sleep-wake cycle, etc. are vital to an organism's survival. Biochemical oscillator circuits are typically classified based on the net logic of the regulatory connections between interacting molecules. However, we show that the robustness response of biochemical oscillator motifs vary substantially based on the regulatory implementation of the logic of interactions encoded in the circuit topology. Nullcline analyses and linear stability arguments predict the robustness response of different mechanisms of a topology. Robust regulatory implementations not only enhance the probability of obtaining stable limit cycles over larger ranges of parameter variations, but also exhibit an increased resilience of oscillations to stochasticity. We further show that there are preferred regulatory implementations for particular biological functions, and that the most robust regulatory implementations of a topology are realized in naturally occurring oscillator systems where high phase coherence is desired. |
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N00.00251: On the Application of the Gell-Mann Classification Method in Ancient DNA (aDNA) Research V. Alexander Stefan The Gell-Mann method [1] [2] can be used in the ancient DNA[3] research, among other topics,[4] to predict the existence of aDNA not yet discovered (facilitating the classifications similar to Gell-Mann’s and Mendeleev’s in physics and chemistry, respectively). This, in turn, can facilitate the prediction of the most probable human migration trajectories, providing, in that way, new insights into the unfolding of the Homo sapiens sapiens race [1] Murray Gell-Mann, The Quark and the Jaguar-Adventures in the Simple and the Complex (W.H.Freeman, New York, 1994. [2] Murray Gell-Mann in, V. Stefan: Physics and Society-Essays in Honor of Victor Frederick Weisskopf by the International Community of Physicists (American Institute of Physics Press and Springer Verlag, New York, 1998); pp.109-121 [3] V. Alexander Stefan: APS March Meeting 2020, Abstract: M71.00360 [4] In Memory of Murray Gell-Mann by Vladislav Alexander (Sasha) Stefan: USPEKHI-PHYSICS: Uspekhi Fizicheskikh Nauk, Tom 189, No 9, September 2019. |
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N00.00252: The Biophysics Research-Education as the Vehicle in both National and Global Emergency Events, such as COVID-19 Pandemic V. Alexander Stefan It is argued that the Biophysics Research-Education projects, in addition to their focus on the national-global general public health, can also facilitate the efforts in emergency events, such as Covid-19 pandemic, via its scientific expertise; and also by their funding, equipment, personnel, etc. This would also augment the national-global stability. [1] [2] [1] V. F. WEISSKOPF CENTER for NATIONAL-SECURITY-PHYSICS and GLOBAL COOPERATION-Stefan University; You Tube video: https://www.youtube.com/watch?v=aVtOYuX816s Marshall Nicholas Rosenbluth Center for Controlled Thermonuclear Fusion Studies-Stefan University; You Tube video: https://www.youtube.com/watch?v=0iCMIAX3tjA [2] V. Stefan (Editor-Author) Physics and Society (AIP-Springer, 1998)—In Honor of V.F. Weisskopf; p.21., Weisskopf, the Director General of the CERN. |
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N00.00253: Exploring the functional conformational states and their transitions in ligand binding of SAM riboswitch Xizhu Zhao, Yanyan Xue, Yu Liu, Liang Hong Conformational transition of SAM riboswitch plays an important role in its specifically binding with S-adenosyl-L-methionine (SAM) and the regulation of downstream gene expression. Recent studies using X-ray crystallography have reported holo state of the riboswitch RNA that corresponded to regulation off. To investigate the dynamics in conformational transition, we marked multiple sets of donor and acceptor dyes on different stems of the RNA in single molecule Forster Resonance Energy Transfer (smFRET) experiments under different buffer conditions. By modeling smFRET trajectories with Hidden Markov Model (HMM), we identified multiple conformational states. Further analysis of transition kinetics, such as Transition Density Plot and dwell time statistics, was applied to explore the transitions between these states and the underlying microscopic mechanism. |
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N00.00254: Outlier detection identifies stable intra-chromosomal interactions over tens of million base pairs apart Jingyu Zhang, Weikang Wang, Yaxuan Yang, Yong Lu, Harinder Singh, Simon C Watkins, Jianhua Xing A fundamental question in the regulation of mammalian genome expression patterns is how three-dimensional chromosome structures are coupled to dynamic transcriptional activity of specific genes. Our previous computational analyses of RNA-seq and Hi-C data revealed that functionally related genes that were coregulated by common transcription factors tended to be physically close (Zhang et al., PLoS Comp Biol, 15, e1006786 (2019)). Some genes well separated by their genomic distance along a chromosome were nevertheless in physical proximity in the context of three-dimensional chromosome structure. We developed an outlier detection procedure, and identified the existence of well-reserved long-range chromome-interaction structures (> 20 Mb) from hi-C data. To further verify these structures and examine whether they are transient or stable, we performed live-cell imaging of selected genomic loci labeled with the CRISPR-dCas9 system in human 293 T and A549 cells. We observed a pair of loci separated over 80 Mb to form a stable assembly that fluctuated together during hours of observations. Cells showed heterogeneity in the number of such assembled higher order structures. We hypothesize that this structural juxtapositioning may coordinate gene regulation through mechanisms like phase separation to create specific local chromosome environments (Zhang et al. Phys Rev. Lett., 112, 068101 (2014)), or canalize chromosome configuration space for cell type specification. |
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N00.00255: Ecological Oscillators in Small-World Networks Davi Arrais Nobre, Alan Hastings, Shadi Esmaeili-Wellman, Jonathan L Machta, Karen Abbott, Vahini Reddy Nareddy, Appilineni Kushal The synchronization of oscillations in space is a ubiquitous phenomenon in several fields, and long-range correlations can arise from short-range coupling. Previous work shows that two-cycle ecological oscillators on a regular lattice undergo a second-order phase transition that falls under the Ising universality class. However, real ecological systems are unlikely to be evenly connected, as in a square lattice. In this study, we investigate the dynamics of the oscillators on a small world network. It has been shown that, even for very small values of rewiring probability, p, Ising spins undergo a mean-field transition. We will present results for maps on small-world networks and compare their behavior to that of Ising models on similar networks. |
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N00.00256: Learning Biological Physics via Modeling and Simulation: A Course for Science and Engineering Undergraduates Phil Nelson I'll describe an intermediate-level course on Physical Models of Living Systems embodied in a new edition of a textbook. The course is a response to rapidly growing interest among undergraduates in a broad range of science and engineering majors. Students acquire several research skills that are often not addressed in traditional undergraduate courses. The combination of experimental data, modeling, and physical reasoning used in this course represents a new mode of "how to learn" for many of my students. These basic skills are presented in the context of case studies from cell biology, including: |
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N00.00257: Wetting regulates autophagy of phase-separated compartments and the cytosol Jaime Agudo-Canalejo, Sebastian W Schultz, Haruka Chino, Simona M Migliano, Chieko Saito, Ikuko Koyama-Honda, Harald Stenmark, Andreas Brech, Alexander I May, Noboru Mizushima, Roland Knorr While the importance of compartmentalization of cellular material in droplet-like structures is increasingly recognized, the mechanisms of droplet removal are still poorly understood. Evidence suggests that droplets can be degraded by autophagy, a degradation system in which membrane sheets bend to isolate portions of the cytoplasm within double-membrane vesicles known as autophagosomes. Here, we examine how autophagosomes sequester droplets that contain the protein p62 in living cells, and also demonstrate that autophagosome-like vesicles form at the surface of protein-free droplets through partial wetting in an in-vitro system. Using a minimal physical model, we show that droplet surface tension supports the formation of membrane sheets, in a manner robust to variations in the droplet-membrane interaction strength. Furthermore, we uncover a switching mechanism that allows droplets to act either as autophagy targets, or as liquid assembly platforms for the formation of cytosol-degrading autophagosomes. All in all, droplet-mediated autophagy belongs to a novel class of intracellular processes that are driven by elastocapillarity and highlight the importance of wetting in cytosolic organization. |
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N00.00258: Short-term plasticity regulates both divisive normalization and adaptive responses in Drosophila olfactory system Yuxuan Liu, Yuhai Tu, Qianyi Li, Chao Tang, Shanshan Qin In Drosophila, olfactory information received by olfactory receptor neurons (ORNs) is first processed by an incoherent feed forward neural circuit in the antennal lobe (AL) that consists of ORNs (input), inhibitory local neurons (LNs), and projection neurons (PNs). This "early" olfactory information processing has two important characteristics. First, response of a PN to its cognate ORN is normalized by the overall activity of other ORNs, a phenomenon termed "divisive normalization". Second, PNs respond strongly to the onset of ORN activities, but they adapt to prolonged or continuously varying inputs. Despite the importance of these characteristics for learning and memory, their underlying mechanisms are not fully understood. Here, we develop a circuit model for describing the ORN-LN-PN dynamics by including key neuron-neuron interactions such as short-term plasticity (STP) and presynaptic inhibition (PI). By fitting our model to experimental data quantitatively, we show that a strong STP balanced between short-term facilitation (STF) and short-term depression (STD) is responsible for the observed nonlinear divisive normalization in Drosophila. Our circuit model suggests that either STP or PI alone can lead to adaptive response. However, by comparing our model results with experimental data, we find that both STP and PI work together to achieve a strong and robust adaptive response. Our model not only helps reveal the mechanisms underlying two main characteristics of the early olfactory process, it can also be used to predict PN responses to arbitrary time-dependent signals and to infer microscopic properties of the circuit (such as the strengths of STF and STD) from the measured input-output relation. Our circuit model may be useful for understanding the role of STP in other sensory systems. |
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N00.00259: Intrinsic dynamics of SARS-CoV-2 spike proteins and structural changes using Principal Component and Anisotropic Network Model analysis Saravana Prakash Thirumuruganandham, Dayanara Lissette Yánez Arcos Several studies have revealed different conformations of SARS-CoV-2, which may obscure the study of significant structures. We have focused on the SARS-CoV-2 herringbone structure. 84 structures determined for these enzymes in the presence of various inhibitors, such as antibodies, nanostructures, and in unbound form allowed us to theorize a comprehensive comparative analysis of the conformational space accessed after ligand binding and its relationship to the intrinsic dynamics prior to ligand binding, as predicted by elastic lattice model analysis. We detailed the important zones of ligand coupling in the affinity energy measurements. Also, performed a detailed analysis of the SARS-CoV-2 spike protein's experimentally observed conformational changes upon binding to a variety of ligands, as well as those predicted by simple physics-based models based on the contact topology of its native fold. In both cases, the first major mode of structural change, PC1, observed in the experiments shows a correlation of 0.71 with a higher rank mode (ANM1-ANM2) intrinsically preferred by the unbound protein. The findings imply that basic but robust rules encoded in the protein structure play a prominent role in predefining ligand binding pathways, which could be useful in inhibitor development. |
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N00.00260: Cell shape formation through material heterogeneity in the plant cell wall Anja Geitmann, Amir J Bidhendi, Bara Altartouri Plant cells come in a kaleidoscopic variety of shapes that are intimately tied to their respective functions. The growth and shaping of plant cells involve the deformation of the cell envelope driven by the internal hydrostatic pressure. While the morphogenetic process is known to be influenced by cellulose microfibril reinforcements in the cell wall, a detailed understanding of the underlying mechanical principles is elusive. We discovered that in complex cell shapes, spatial heterogeneity in the cell wall mechanical properties is tightly controlled and relies on local enrichment in pectin and strategically deposited microfibrils. Through high resolution fluorescence imaging, we correlated the presence of these polysaccharides in space and time with morphogenetic events. The experimental observations confirm predictions made by a finite element modeling approach developed to simulate plant cell shaping. A computational model of the jigsaw puzzle shaped cell patterns in the leaf epidermis also revealed that symmetry breaking events in the cell morphogenetic process might be initiated through turgor-driven buckling events. The mechanical modeling approach has led to a multitude of predictions guiding experimentalists towards biological agents with morphogenetic roles. |
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N00.00261: Estimating the branching ratio in living neural networks Jonathan A Moncada Experimental evidence suggests the cortex operates near a critical point (Cocchi et al., 2017) where information processing functions are optimized. Proximity to this point is measured by the branching ratio, which is the average number of neurons activated by one active neuron. If this ratio is one, the network is critical. If the ratio is above one or below one, the network is supercritical or subcritical, respectively. A new method for measuring the branching ratio corrects for subsampling (Wilting and Priesemann, 2018), but produces some puzzling results. It reports patients with epilepsy have a branching ratio less than one (Hagemann, Wilting et al., 2020), when models predict a branching ratio greater than one (Hsu et al., 2008). We investigated this in simulations of neural networks using both a naïve method that just looks at the first two time steps of an avalanche, and the new method that corrects for subsampling. We found that under certain conditions both methods seem to fail. Thus, more accurate ways of estimating the branching ratio are needed; they will help us monitor seizures in epilepsy patients, when a drug treatment works, and when a patient returns to consciousness. |
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N00.00262: Fission mechanisms of cylindrical membrane tubes under tension Russell K Spencer, Marcus Mueller Membrane remodeling, such as fusion and fission, is involved in a variety of basic, cellular processes. This work investigates the mechanisms and pathways for the fission of phospholipid membranes, in particular double-membrane fission as it occurs in mitochondrial division. We employ self-consistent field theory and utilize the string method to find the Minimum Free Energy Path (MFEP) in order to determine the most likely pathway for the transition. Our results suggest that the free energy barrier to membrane fission, as well as the dominant pathway, can be controlled by the tension experienced by the membrane. At high tension, the inner tube partially collapses into a worm-like micelle, which then ruptures, resulting in two capped tubes. The outer membrane then follows similarly. This pathway is non-leaky, i.e. the solvent inside the inner membrane, between the membranes and outside the outer membrane never mix. At lower tension, the barrier to forming a worm-like micelle becomes prohibitive, and instead, the inner and outer membranes fuse. This pathway is leaky as pores form close to the fusion sites. We also investigate the role of a constricting protein, such as dynamin, on the fission mechanism and barrier. |
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N00.00263: Self-Assembly of Diphenylalanine Peptides on Graphene via Detailed Atomistic Simulations Anastassia Rissanou, Andriani Keliri, Maria Arnittali, Vagelis Harmandaris The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom Molecular Dynamics simulations. Two interfacial systems are studied, with different concentration of dipeptides and results are compared with an aqueous solution of FF at room temperature. Length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface. A hierarchical formation of FF structures is observed involving two sequential processes: first, a stabilized interfacial layer of dipeptides onto the graphene surface is formulated, followed by the development of a structure of self-aggregated dipeptides on top of this layer. The whole procedure is completed in almost 200ns, whereas self-assembly in the system without graphene is accomplished much faster; in less than 50ns cylindrical structures, signal of the macroscopic fibrilliar ones, are formed. Strong π – π* interactions between FF and the graphene lead to a parallel to the graphene layer orientation of the phenyl rings. Reduction in the number of hydrogen bonds between FF peptides is observed because of the graphene layer, since it disturbs their self-assembly propensity. |
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N00.00264: Fitness-valley crossing in the emergence of SARS-CoV-2 mutants Qihan Liu As for Oct 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 240 millions infections and about 5 millions deaths worldwide [1]. |
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N00.00265: Simulations suggest double sodium binding induces unexpected conformational changes in thrombin Freddie R Salsbury, Dizhou Wu Thrombin is a multifunctional Na+-activated protein. There is one Na+-binding site that has been the focus of the study of the thrombin. Previous work based on molecular dynamics (MD) simulations suggests that there are two Na+-binding sites in thrombin. This work also suggests that thrombin exhibits dynamic, aka generalized, allostery. These sites can be bound separately or simultaneously. In this study, we performed 12 independent 2μs all-atom MD simulations of wild-type (WT) thrombin and studied the different Na+binding modes. We used root-mean-square fluctuations to study how different binding events rigidify different regions. We also used correlation matrixes to suggest regions that may play a role in thrombin's allosteric response. Non-parametric clustering and principal component analyses are used to examine the conformations induced by different sodium binding modes. Based on these analyses, as well as SASA analysis, we suggest that the double binding mode might be an inactive mode. We also suggest that the kinetic scheme for Na+ binding to thrombin involves a multiple-step mechanism. |
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N00.00266: Molecular dynamics simulations as a tool for the study and structure-guided engineering of type III interferons William S Grubbe, Fabian Byléhn, Walter Alvarado, Juan L Mendoza, Juan De Pablo Type III interferons (IFNλ1-4) are proteins which combat viral infections and cancer and have naturally targeted activity due to tissue-specific receptor expression. However, their low activity relative to type I IFNs has limited their clinical use. Previous work used an engineered, high-affinity IFNλ3 (H11) to increase its antiviral and antiproliferative properties as well as solve the crystal structure of the ligand-receptor complex; however, the total differences in behavior between H11 and wild type IFNλs are unknown, and the activity of H11 is still lower than type I IFN. To better study and engineer IFNλs, we use molecular dynamics (MD) simulations to model the H11 and IFNλ3 complexes. Using trajectory and free energy data, we quantify differences in residue contact, strain, and fluctuation experienced by the protein complexes, reveal novel structural differences, and estimate the individual contributions of the residues to binding. These simulations reveal regions of the proteins that can be engineered to improve both complex stability and IFNλ activity. In combination with experimental techniques, future work using MD as a tool to study ligand-receptor complexes can expedite and improve approaches to solving crystal structures and develop more effective therapeutics. |
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N00.00267: A mathematical model of chemotactic endothelial cell migration in a porous extracellular matrix Josep Ferré Torres The formation of new vasculature from existing blood vessels, or angiogenesis, occurs as a multistep process driven by an extensive collection of pro- and anti-angiogenic factors. In this process, the extracellular matrix (ECM) plays a crucial role due to its structural function, the store of mediators, such as vascular endothelial growth factor (VEGF), and matrix-cell interactions. A standard approach to study angiogenesis is to explore the underlying cellular mechanisms focusing on endothelial cell (EC) motility regulated by chemotactic stimulus, ignoring mechanotactic stimuli. In cultured ECs, it is possible to easily analyze, separately, the concentration of growth factors, namely VEGF, and the structure of the culture substrate, mimicking ECM material. |
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N00.00268: Reconstituting the self-organization of a minimal kinase/phosphatase system in vitro Beatrice Ramm, Ting-Sung Hsieh, Vincent S Tagliabracci Lipid modifying kinases and phosphatases are crucial for signal transduction, cytoskeletal organization and membrane trafficking. Lipid distribution as well as kinase/phosphatase localization exhibit spatiotemporal dynamics in many instances, but the underlying mechanism and regulation as well as the impact on membrane properties and downstream effector proteins remain enigmatic. Recently, the Legionella pneumophila effector proteins MavQ and SidP, a phosphatidylinositol lipid kinase and phosphatase, respectively, have been shown to dynamically remodel ER membranes in the host cell. Here, we set out to reconstitute the self-organization of this minimal kinase/phosphatase system in vitro. Using supported lipid bilayers with phosphatidylinositol lipids we show that purified MavQ/SidP can self-organize into traveling surface waves in vitro. Interrogating the self-organization of this system in a controlled manner we aim to elucidate the underlying self-organization mechanism. |
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N00.00269: Learning a biologically plausible linear controller for nonlinear systems Parisa Karimi, Siavash Golkar, Johannes Friedrich, Dmitri Chklovskii Understanding how an animal's brain learns to execute proper movements is a major problem of interest in neuroscience. A prominent framework to solve this problem is Optimal Feedback Control (OFC). However, solving the OFC problem requires knowledge of the underlying dynamics as well as iterating a matrix Riccati equation. A biologically plausible learning mechanism is expected to 1) be able to perform online learning on the fly, and 2) have local synaptic plasticity rules. This work presents a model-free control approach for nonlinear dynamic systems that satisfies both these requirements. Specifically, the proposed approach employs policy gradient to learn a linear controller for the nonlinear dynamic system in kernel space and using local learning rules, without requiring any knowledge about the underlying dynamic of the system. |
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N00.00270: Recovery of Enzyme Structure and Activity Following Rehydration From Ionic Liquid Pei-Yin Lee, Onkar Singh Long-term preservation of proteins at room temperature continues to be a major challenge. Towards using ionic liquids (ILs) to address this challenge, here we present a combination of experiments and simulations to investigate changes in lysozyme upon rehydration from IL mixtures using two imidazolium-based ILs. Circular dichroism spectroscopy confirms that lysozyme maintains its secondary structure upon rehydration, even after 295 days. Increasing the IL concentration decreases the activity of lysozyme and is ultimately quenched at sufficiently high IL concentrations, but the rehydration of lysozyme from high IL concentrations completely restores its activity. From simulations we observe kinetic trapping of active site by EMIM+, which leads to possible competitive inhibition and results in the diminish of lysozyme activity. Upon rehydration, fast leaving of EMIM+ is observed and the availability of active site is restored. In addition, suppression of structure fluctuations is also observed when in high IL concentrations, which also explains the decrease of activity. The return of native protein structure and activity indicates that after rehydration lysozyme returns to its original state. Our results also suggest a simple route to protein recovery following extended storage. |
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N00.00271: Stochastic acquisition of the gut microbiome in Drosophila melanogaster Eric Jones, Jean M Carlson, David A Sivak, Will Ludington Observational studies reveal substantial variability in microbiome composition across individuals. While some of this variability can be explained by external factors like environmental, dietary, and genetic differences between individuals, here we show that the process of microbiome assembly is inherently stochastic for the model organism Drosophila melanogaster. Individuals are constantly exposed to microbial organisms that may or may not colonize their gut microbiome, and this contributes a baseline level of microbiome variability even among organisms that are identically reared, housed, and fed. In germ-free flies fed known combinations of bacterial species, we find that some species colonize more frequently than others even when fed identically. Incorporating context-dependent interactions substantially improves our ability to explain the observed variability in colonization outcomes. Stochastic, context-dependent microbiome assembly underlies clinical therapies like fecal microbiota transplantation and probiotic administration, and is relevant for the design of synthetic fecal transplants and dosing regimes. |
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N00.00272: Hierarchy of brain oscillations emerge from recurrent error correction Trevor McPherson, Alexander P Kuczala, Tatyana O Sharpee Neuronal processing in the brain occurs rhythmically across a set of discrete frequency bands, spanning almost two orders of magnitude. The origin of these rhythms remains a matter of debate, as well as why activity appears to be organized in canonical bands. Here we demonstrate that the relative distribution of frequency bands emerge from the dynamics of recurrent neural networks (RNNs) performing error correction. These networks achieve best performance when processing pulsed inputs with noise levels proportional to those observed in cortical networks. In this optimal regime, the performance timescale is T0 ≈ 2.14 ∗ τ , where τ denotes the integration time constant for network nodes. A minimal timescale T0 can be obtained for recurrent networks composed of individual neurons. Longer timescales Tn are sequentially derived when the outputs of individual RNNs become the nodes of a higher order recurrent network of their own, where Tn = T0 ∗ (T0 /τ)(n - 1). We show that this pattern of timescales reproduces the canonical oscillatory bands seen in neural data. The intrinsic timescale T0 can be reduced by increasing the gain of individual nodes. This could allow neuromodulatory or attentional gain mechanisms to modulate the processing speed of salient signals. Successful error correction can be achieved in small networks with several neurons, with no substantial benefit of using larger networks. These results describe a mechanism through which the empirically observed discrete set of frequency bands can emerge through hierarchically organized RNNs. |
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N00.00273: Computable early Caenorhabditis elegans embryo with a phase field model Guoye Guan Morphogenesis is a precise and robust dynamic process during metazoan embryogenesis, consisting of both cell proliferation and cell migration. Despite the fact that much is known about specific regulations at molecular level, how cell proliferation and migration together drive the morphogenesis at cellular and organismic levels is not well understood. Using Caenorhabditis elegans as the model animal, we present a phase field model to compute early embryonic morphogenesis within a confined eggshell. With physical information about cell division obtained from three-dimensional time-lapse cellular imaging experiments, the model can precisely reproduce the early morphogenesis process as seen in vivo, including time evolution of location and morphology of each cell. Furthermore, the model can be used to reveal key cell-cell attractions critical to the development of C. elegans embryo. Our work demonstrates how genetic programming and physical forces collaborate to drive morphogenesis and provides a predictive model to decipher the underlying mechanism. |
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N00.00274: Quantification of Weak Protein-Protein Interaction from Mobility Based Assay. Amandeep Sekhon, Alon Grossman, Gil Rahamim Intermolecular interactions play an essential role in the function of cellular systems. These interactions are mainly composed of strong and weak interactions. In comparison to the strong interaction, weak protein-protein interactions (PPIs) are the order of thermal energy. Such weak PPIs are critical in understanding the rapid response of cellular systems, disordered protein interactions, and liquid-liquid phase separation, to name a few. Many conventional experimental techniques characterize PPIs very precisely, but those are focused either on strong PPIs or limited to low-throughput manner. We report on our recently developed method to quantify the weak PPIs in a high-throughput manner. Using video-microscopy, we measure the diffusion/mobility of colloids grafted with proteins over surfaces grafted with a different set of proteins. We show that such mobility assay is susceptible to minor alteration in PPIs up to a single amino acid mutation between intrinsically disordered peptides. |
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N00.00275: A synaptic novelty signal to switch hippocampal attractor networks from generalization to discrimination Massimiliano Trippa, Ruy Gómez-Ocádiz, Lorenzo Posani, Simona Cocco, Rémi Monasson, Christoph Schmidt-Hieber Episodic memory formation and recall are complementary processes that put conflicting requirements on neuronal computations, as the reliable retrieval of familiar representations, supported by robust attractor properties in hippocampal circuits, opposes the formation of new neuronal assemblies for the storage of novel episodic memories. To address this problem, we studied the activity of dentate gyrus granule cells in mice exploring familiar and novel environments. A consistent transient depolarization in these cells was found when mice are exposed to a novel environment for the first time. We show through a computational neural network model how this novelty signal can drive the downstream attractor networks from a familiar representation to a new state, not supported by strong synaptic inputs, thereby favoring the switch from memory retrieval to encoding. We then show that the introduction of Hebbian learning in the model is essential not only to consolidate the representation but also to reinstate network activity in the new neural state during subsequent explorations of the novel environment, winning the competition against the already consolidated attractors associated to familiar environments, even in the absence of additional inputs from the granule cells population. |
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N00.00276: Unravelling the biomechanical interactions controlling growth and posture in plant stems Viraj Alimchandani, Anne-Lise Routier While the genetic control of plant development is well studied, the underlying physical basis behind plant growth remains largely unknown. At the cellular level, the fundamental link between mechanical forces and cell expansion is not fully understood and is still a matter of debate. At the level of tissues and organs, the interactions between cells and their geometric complexity make it difficult to predict the very nature of the physical forces acting locally, and to understand how they affect plant growth. Using the sunflower (H. annuus) as a model species, we aim to elucidate how plant anatomy, which determines the spatial arrangement of cells in organs, affects mechanical interactions between cells. Our primary mechanical testing techniques include microindentations, cellular force microscopy (CFM), extensometry, and osmotic treatments. Combining these with epi-fluorescent microscopy, we are able to obtain live 3D images of the effects of our mechanical tests at the cellular scale. Analysing our data with MorphoGraphX will allow us to extract the growth and geometry of each individual cell, giving us the direct effects of physical constraints with unprecedented accuracy. |
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N00.00277: Mpipi: a transferable coarse-grained model for biomolecular phase-separation with near-quantitative accuracy. Anne Aguirre, Jerelle A Joseph, Aleks Reinhardt, Rosana Collepardo-Guevara, Pin Yu Chew, Kieran O Russel, Jorge R Espinosa, Adiran Garaizar The formation of biomolecular condensates via liquid-liquid phase separation is one of the chief mechanisms used by cells for spatiotemporal organisation. Importantly, biomolecular phase separation has been directly linked to many biological functions such as heterochromatin organization and transcription, DNA repair and ribonucleoprotein formation, as well as dysfunction, via the formation of in terms of pathological aggregates. |
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N00.00278: Local biofilm architecture shapes, and is shaped by, cooperative resistance in an opportunistic bacterial pathogen Keanu A Guardiola Flores Recent work suggests that antibiotic resistance can be an emergent property of microbial communities that depends on interactions between cells. For example, cells producing a drug-degrading enzyme can offer protection to non-producing cells at length scales of millimeters or more, even when the enzyme remains attached to the producing cell. Here we investigate how different biophysical parameters affect the length scales of cooperative resistance in E. faecalis, an opportunistic pathogen. While dynamics at the colony level suggest global coupling between resistant and sensitive cells, experiments at the single-cell level identify spatial signatures of cooperative resistance on length scales of just a few microns. These length scales are surprisingly sensitive to slight changes in biophysical parameters—such as the activity of the enzymes—a finding that can be traced to strong synergistic effects that arise between multiple resistant cells. Our results suggest that the spread of resistance is not merely a result of global selection pressures but instead depends critically on the variable length scales of cooperation—and the resulting spatial distribution of cells—within a community. |
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N00.00279: Cellular Compartmentalisation and Receptor Promiscuity as a strategy for accuracy and robustness in Positional Inference during Morphogenesis Krishnan S Iyer Precise spatial patterning of cell fate during morphogenesis requires accurate inference of cellular position. In making such inferences from morphogen profiles, cells must contend with inherent stochasticity in morphogen production, transport, sensing and signalling. Using multiple signalling mechanisms in development as motivation, we show how cells may utilise multiple tiers of processing (compartmentalisation) and parallel branches (multiple receptor types), together with feedback control, to bring about fidelity in morphogenetic decoding of their positions within a developing tissue. By simultaneously deploying specific and nonspecific receptors, cells achieve a more robust inference. This distributed information processing at the scale of the cell highlights how local cell autonomous control facilitates global tissue scale design. |
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N00.00280: Examining the interplay between face mask usage, asymptomatic transmission, and social distancing on the spread of COVID19 Benjamin A Catching, Sara Capponi, Ming T Ye, Raul Andino, Simone Bianco From the beginning of the COVID-19 pandemic, alongside the enormous humanitarian and medical effort, the scientific community came together to achieve as much information as possible about the virus and to identify control strategies for the infection. The result was the rapid development of several highly effective vaccines, some of them already adopted. Since the distribution of vaccines is currently underway and is heterogeneous among all countries, it remains still essential to understand the most efficacious measures to control the spread of the virus. By using an agent-based model we examine the efficacy of wearing face masks in combination with practicing social distancing. We explicitly consider a heterogeneous population of asymptomatic individuals and realistic values of face masks protection against viral transmission. Our simulations show that high compliance in social distancing is necessary to curb the spread of the infection and that wearing face masks provides the highest protection even if only a small population fraction are simultaneously practicing social distance. Finally, even if a large population fraction is asymptomatic, face mask effectiveness in controlling the viral spread is not reduced. In conclusion, our simulations demonstrate that the synergistic use of face masks and social distancing is the most effective intervention strategy for the infection. |
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N00.00281: Fundamental Cell Behavior Emerges from Whole Cell Simulations of a Minimal Cell by Integrating Experiment and Theory Zane R Thornburg, David M Bianchi, Troy A Brier, Benjamin R Gilbert, Andras Cook, Kim Wise, Clyde Hutchison, John I Glass, Zaida Luthey-Schulten An overarching goal of molecular biology is to explain the basic processes of life in terms of the laws of physics and chemistry. Just as physics had studied the hydrogen atom as its simplest system to understand more complex atoms and molecules, a simplest, minimal cell would be the ideal platform to study the fundamental behavior of cellular life and expand the principles to more complex cells. JCVI-syn3A is a genetically minimal cell consisting of 493 genes, 452 of which code for proteins, on a singular 543 kbp circular chromosome. The cell cannot be described by a simple small set of equations like the hydrogen atom, but it can be simulated as a whole-cell model of all the chemical reactions inside the cell. Whole-cell modeling requires the combination of multiple simulation methods with results of many experimental techniques to inform dynamics and cell architecture. We constructed a whole-cell kinetic model of Syn3A including the complete metabolic network, cell growth, and genetic information processing reactions for DNA replication initiation and elongation, transcription of all 493 genes, and translation and degradation of all 452 mRNA. Parameters were obtained from kinetic parameter databases such as BRENDA. A spatial model of Syn3A used cell architecture constructed from cryo-electron tomograms. From the mRNA diffusion and degradation reactions occurring at membrane-bound degradosomes, we predict the distribution of mRNA half-lives. A well-stirred version of the model simulated for complete cell cycles includes multiple DNA replication initiation and elongation events per cell cycle, which agrees with qPCR experiments and was observed to help maintain homeostasis in metabolism. These novel simulations track the exact time-dependent ATP use of each reaction in the simulation. |
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N00.00282: Anomalous DNA unwinding dynamics in mismatched DNA uncovered with laser temperature-jump spectroscopy and implicated in DNA damage sensing Saroj Baral, Sagnik Chakraborty, Debamita Paul, Jung-Hyun Min, Anjum Ansari Altered DNA dynamics at lesion sites are implicated in how DNA-repair proteins sense damage amid genomic DNA. We examined DNA dynamics in the context of damage recognition by NER protein XPC (yeast ortholog Rad4). Fluorescence lifetime studies on DNA with cytosine-analog FRET pair on either side of 3-bp mismatches – recognized by Rad4 as specific substrates in vitro – unveiled major deviations from B-DNA for high-specificity Rad4 substrates, even in the absence of Rad4.1 With laser T-jump, we revealed the unwinding dynamics of these DNA. Specific, mismatched DNA showed large-amplitude kinetics over multiple timescales, including “missing amplitudes” outside our T-jump time-window – a fast (<20 μs) phase with 70-80% amplitude and an additional slower (>100 ms) phase appearing above ∼35 °C, which disappeared with Rad4 bound. We suggest that the <20-μs DNA fluctuations engage the protein at a “faulty” site and that the >100-ms kinetics reflect a propensity for specific DNA to adopt severely distorted conformations preferred by Rad4, albeit with high free energy barriers. Rad4, once engaged, lowers the barrier for full DNA distortions to form the recognition complex. These studies provide compelling evidence for unusual DNA dynamics at damaged sites that Rad4 can sense. |
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N00.00283: The Molecular Mechanisms underlying the Translational Control by a Prion-like RNA-binding Protein, CPEB3, in dendritic spines Xinyu Gu, Nicholas P Schafer, Carlos Bueno, Wei Lu, Peter G Wolynes Synaptic plasticity, specifically the structural change of dendritic spines is essential for maintaining long-term memory. Local synthesis of synaptic proteins provides the molecular basis for the structural change of synapses, in response to input signals. CPEB3, a functional prion that binds RNA, has been proposed as a synaptic tag to regulate local translation of target mRNAs in spines. Cellular experiments have shown that soluble CPEB3 monomers repress translation, whereas in contrast CPEB3 aggregates activate the translation of its target mRNAs. However, how this bi-directional translational control is realized and regulated remains unclear. We proposed a mathematical model to show that the vectorial nature of translation, coupled with the polarized structure of mRNA/CPEB3 assemblies determines the direction and significance of the translational control. We also built a structural dynamics model for how CPEB3 binding to SUMO2, a small ubiquitin-like modifier protein, can regulate the translational control in response to stimulation signal. |
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N00.00284: Revealing condensation affinities of multivalent protein residues through atomistic simulation of model peptide mixtures. William Brown Bio-molecular condensation of proteins has emerged as a key mechanism underlying the formation of membraneless cellular bodies. The thermodynamic driving force of condensation is often rationalized from the perspective of polymeric liquid-liquid phase separation and classical mean-field theories. However, the environment of biomolecular condensates often deviates from the mean-field picture and requires a more detailed microscopic model of intra and inter-residue interactions within condensates. In this work, we set up model peptide mixtures, which allows one to quantify the affinity of different residue-base pairs under various external and internal conditions, including salt, stoichiometry, density, and temperature. |
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N00.00285: Revealing condensation affinities of nucleic bases through atomistic simulation of model RNA-peptide mixtures. Christopher J Gayvert Bio-molecular condensation of proteins and nucleic acids has emerged as a key mechanism underlying the formation of membraneless cellular bodies. The thermodynamic driving force of condensation is often rationalized from the perspective of polymeric liquid-liquid phase separation and classical mean-field theories. However, the environment of bio-molecular condensates often deviates from the mean-field picture and requires a more detailed microscopic model of amino acid-nucleic base interactions within condensates. In this work, we set up model peptide nucleo-base mixtures, which allows one to quantify the affinity of different residue-base pairs under various external and internal conditions, including salt, stoichiometry, density, and temperature. |
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N00.00286: Impact of reactive environment on phase separation of proteins and RNAs in a minimalist model of nucleoplasm Rabia Laghmach, Davit Potoyan The phase separation concept has recently emerged as the principal mechanism driving the formation of biomolecular condensates. These condensates are membraneless organelles assembled from a mixture of proteins and RNAs components such as ribonucleoprotein granules and other nuclear bodies. The transience and environmental sensitivity of biomolecular condensation are strongly suggestive of kinetic gene-regulatory control of phase separation. To better understand how kinetic aspects controlling biomolecular phase-separation, we have constructed a minimalist model of the reactive nucleoplasm to study liquid-liquid phase separation in ternary protein-RNA-nucleoplasm coupled to non-equilibrium and spatially dependent gene expression. We find a broad range of kinetic regimes through an extensive set of simulations where the interplay of phase separation and reactive timescales can generate heterogeneous multi-modal gene expression patterns. Furthermore, the significance of this finding is that heterogeneity of gene expression is linked directly with the heterogeneity of length scales in phase-separated condensates. |
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N00.00287: Mechanism of translocation by Bacteriophage T7 Helicase gp4 using AWSEM-Suite Shikai Jin In the process of DNA replication, the efficient unwinding of the duplex parental DNA is mediated by DNA helicases. Helicases are chemo-mechanic motors that use the energy of ATP hydrolysis to translocate unidirectionally along with DNA. Helicase gp4 from bacteriophage T7 is a model system for studying helicase in DNA replication. However, how ATP hydrolysis drives the conformational changes and the unidirectional translocation remains elusive. Here, molecular dynamics simulations using coarse-grained protein model AWSEM-Suite and DNA model 3SPN2 were applied to explore the global energy landscape of the helicase gp4 translocation along ssDNA. |
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N00.00288: Molecular-scale mechanical properties of calcium-responsive proteins Alana P Gudinas, Marina P Chang, Danielle J Mai Chemically responsive proteins are responsible for many biological processes, but the molecular-scale mechanics of ion-driven protein folding remain elusive. Repeats-in-Toxin (RTX) proteins are calcium-responsive, undergoing conformational changes from random coils to folded beta-roll structures upon binding to calcium ions. We have generated fusion proteins containing RTX domains that replicate the calcium-responsive behavior of naturally occurring RTX proteins. Using atomic force microscopy (AFM), we demonstrate single-molecule force spectroscopy (SMFS) of RTX and model fusion proteins. Proteins were genetically modified for SMFS to have terminal thiol and amine groups for molecular tethering between the AFM tip and substrate. We characterize the mechanical response of tethered RTX proteins in both their disordered calcium-free state and folded calcium-bound state, and we compare AFM force–extension curves to the worm-like chain model. Understanding the molecular-scale mechanical behavior of RTX proteins will enable the development of tunable biomaterials and other chemically responsive proteins. |
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N00.00289: Robots as Avatars of Evolution Under Stress Trung V Phan, Gao Wang, Shengkai Li, Jin Wang, Yan Peng, Daniel I Goldman, Simon A Levin, Kenneth J Pienta, Sarah Amend Experimental robo-biological physics can bring new insights into biological evolution. We present a development of hybrid analog/digital autonomous robots with mutable diploid dominant/recessive 6-byte genomes which exhibit pleiotropy because of multi-phenotype control by discrete genes. The robots are capable of death, rebirth and breeding. We map the quasi-steady state surviving local density of the robots onto a multi-dimensional abstract ``survival landscape''. We show it is generally necessary for robot survival on an externally and self-modified resource landscape to require the exchange of genes between the robots in addition to mutations, and we show via measurement of the Shannon genetic entropy that high genomic diversity and pleiotropy is essential for survival in a time and space stochastic environment. We propose that diploid gene robots with pleiotropy can act as avatars of diploid mammalian cells for novel programs of administration of drugs, and that a stochastic time and drug chemotherapy course would target cancer cells more effectively. |
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N00.00290: Seed banks alter the rate and direction of molecular evolution of Bacillus subtilis William R Shoemaker, Evgeniya Polezhaeva, Kenzie B Givens, Jay T Lennon Nature is rarely static. Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which in turn alters evolution at the population scale. Many organisms respond to such fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e., a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. We find that the ability to enter a dormant state increases the accumulation of genetic diversity over time and alters the trajectory of mutations, findings that are recapitulated using simulations based on a simple mathematical model. Remarkably, the removal of a seed bank also altered the direction of molecular evolution across the genome, suggesting that the presence of a life-history strategy can alter the evolutionary trajectory of a population in addition to its rate. |
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N00.00291: Hydrodynamic Black Holes, Bacterial Entropy Generation and Emergent Inverted Populations Robert H Austin, Trung V Phan, Domenic Ferreris, Julia Bos, Paul M Chaikin, Buming Guo, Stephano Martiniani We have created an a microfluidic environment where there is "gravity" (funnels that pump bacteria that are motile) into an "event horizon" (a streamline in a hydrodynamic flow field which sweeps the bacteria away) in analogy to black holes - regions of space- time where gravity is so strong that there is an event horizon. We use a form of Shannon entropy to compute the local entropy generation of a bacterial population in the area around our hydrodynamic black hole. We show that at a critical cell density the bacterial population density collectively inverts itself radially and moves against the funnel gravity field, avoiding crossing the hydrodynamic event horizon. |
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N00.00292: SARS-CoV-2 and its variants detection by palladium nano-thin-film impedance-based biosensor Yen chen Chen, Sheng-Yu Huang, Chia-Yu Chang, Yi-Xuan Huang, Chia-Ching Chang SARS-CoV-2 is identified at the end of 2019. This is a highly contagious, and global spreading virus. Furthermore, a lot of variants of this virus have been identified in different areas. Unfortunately, the spreading of these variants, especially the delta variant, is much faster than that of wildtype. Some breakthrough infections are also observed in the fully vaccinated people. Therefore, a rapid, sensitive and accurate sensing platform for the detection of SARS CoV-2 is important for better controlling the spread of this newly emerging infectious disease. In this study we have synthesized and refolded these key proteins, spike protein receptor binding domain (spike RBD) and angiotensin converting enzyme II (ACE2), into functional forms by over-critical refolding process. The ACE2 which can directly immobilize on the palladium nano thin film (Pd-NTF) via Pd-thiol linkage. The functionalized Pd-NTF can be used as electrode probe of electrochemical impedance spectrometer to analyze the interaction between ACE2 and wildtype or mutants spike RBD. We found that the delta variant has higher affinity than wildtype. This biosensing system can be used not only in viruses detection but also anti-virus infection drugs screen. |
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N00.00293: Memory capacity of large structured neural networks Chung-Yueh Lin, Tatyana O Sharpee, Alexander P Kuczala Neural networks have a large capacity for retaining information about input signals. Previous studies have demonstrated that networks need to be primarily feedforward to maximize information recall. However, only small networks were considered. Here, we use mean-field methods to characterize information storage in large networks composed of a small number of blocks, with the possibility of recurrent connections within and between blocks. We find that the optimal network structure undergoes sharp phase transitions with increasing average connection strength. These transitions involve the redistribution of neurons between sub-populations as well as the connections within and between sub-populations. It is typically advantageous to construct a network with a small input-recipient population and a larger downstream population. Regarding recurrent interactions within sub-populations, these have to be set either at the optimal level that maximizes the performance of this sub-population on its own or absent altogether. We also find that, contrary to the results for small networks, feedback connections between sub-populations can increase memory capacity. However, this is observed only in networks larger than a certain critical size, which can be as small as several hundred neurons, depending on the allowed degree of imbalance in the size of sub-populations. These results highlight previously under-appreciated functions of feedback and recurrent connections in neural circuits. |
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N00.00294: Cancer progression as a learning process Aseel Shomar Drug resistance and metastasis - the major complications in cancer - both entail adaptation of cancer cells to stress, whether a drug or a lethal new environment. Intriguingly, these adaptive processes share similar features that cannot be explained by a pure Darwinian scheme, including dormancy, increased heterogeneity, and stress-induced plasticity. We propose that learning theory offers a framework to explain these features and may shed light on these two intricate processes. In this framework, learning is performed at the single cell level, by stress-driven exploratory trial-and-error. Such a process is not contingent on pre-existing pathways but on a search in the high-dimensional space of phenotypic states, for one that diminishes the stress. We identify biological mechanisms that may support this search, and point to specific analogies with learning theories. At the population level, we view the tissue as a network of exploring agents that communicate and restrain cancer formation in health. In this view, disease results from the breakdown of homeostasis between cellular exploratory drive and tissue homeostasis. |
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N00.00295: Anti-SARS-Cov-2 infection drugs and neutralizing antibody screening by palladium nano-thin-film electrode-based biosensor Yi Xuan Huang, Lik-Voon Kiew, Chia-Hsing Cheng, Chia-Yu Chang, Yen-Chen Chen, Chia-Ching Chang Outbreak of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has infected more than 240 million people and caused nearly five million death. In order to alleviate the symptoms of viral infections and severe illness, drugs/functional peptides to suppressed the virus infection are highly desired. A rapid and sensitive anti-viral infection drugs screening sensing system has been developed by mimicking the SARS-CoV-2 enters the cell model. Four potential leads have been identified, such as perindoprilat and ramiprilat, which can reduce virus infection 67% and 72%, respectively by palladium nano-thin-film electrode-based biosensor (Pd-NTF biosensor) within 21 mins and at low analyte concentration and small volume (0.1 μg/mL and ~1 μL, estimated total analyte consumption < 4 pg). Furthermore, the titer of neutralizing antibody can be analyzed and the effective titer is as high as 19500. |
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N00.00296: Dynamics of Chromosome Organization During the Cell Cycle of a Minimal Bacterial Cell Benjamin R Gilbert, Zane R Thornburg, Vinson Lam, Fatema-Zahra M Rashid, John I Glass, Elizabeth Villa, Remus T Dame, Zaida Luthey-Schulten
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N00.00297: Individuals' timings of decision-making and group performance Mariko Ito The timing of an individual making a decision depends on the amount of information he/she has. Kurvers et al. showed that informative individuals tend to answer earlier than the others in group decision-making by an experiment, which assumed that each individual in a group can give his/her answer at any timing for a binary choice problem [1]. My interest is whether the pattern observed in individuals' decision timings is associated with the number of individuals who gave the correct answer, called group performance. |
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N00.00298: The topology of the native state and protein folding rates Eleni Panagiotou Characterizing the global conformation of proteins rigorously and separating secondary structure effects from topological effects is a challenge. New developments in Applied Knot Theory allow to characterize the topological characteristics of proteins (knotted or not). By analyzing a small set of two-state and multi-state proteins with no knots or slipknots, our results show that 95.4\% of the analyzed proteins have non-trivial topological characteristics, as reflected by the second Vassiliev measure, and that the logarithm of the experimental protein folding rate depends on both the local geometry and the topology of the protein's native state. |
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N00.00299: Spontaneous polarization and locomotion of an active particle with surface-mobile enzymes Marco De Corato, Ignacio Pagonabarraga, Loai Abdelmohsen, Samuel Sánchez, Marino Arroyo We examine a mechanism of locomotion of active particles whose surface is uniformly coated with mobile enzymes. The enzymes catalyze a reaction that drives phoretic flows but their homogeneous distribution forbids locomotion by symmetry. We find that the ability of the enzymes to migrate over the surface combined with self-phoresis can lead to a spontaneous symmetry-breaking instability whereby the homogeneous distribution of enzymes polarizes and the particle propels. The instability is driven by the advection of enzymes by the phoretic flows and occurs above a critical Péclet number. The transition to polarized motile states occurs via supercritical or subcritical pitchfork bifurcations, the latter of which enables hysteresis and coexistence of uniform and polarized states. |
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N00.00300: How do organelles move? Sheda Ben Nejma Organelles are extremely important components of the cell. Each one of them carries vital functions. Among many other functions, mitochondria produce ATP, the energy currency inside the cell, constitute signaling pathways, carry calcium ions… Lipid droplets act like reservoirs for neutral lipids and regulate lipid metabolism. |
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N00.00301: Understanding the Helical Stability of Charged Peptides Nitin K Singh, Mithun Radhakrishna, Manish Agarwal α-helices play an essential role in the tertiary and quaternary folding of a protein and are vital for protein functioning. Helical peptides have found their applications in membrane transport, vaccine development, and therapeutics. Their application is limited because of the reduced solubility of the hydrophobic residue helices and the low stability of the helices with charged amino acids in the aqueous solution. This study aims to bridge this gap by designing water-soluble helical peptides by controlling the charge density and the amino acid sequence. In this study, we used leucine (hydrophobic) and lysine (charged) amino acid residues to design proteins with considerably higher stability than fully charged polypeptides. Results from Molecular Dynamics Simulations show that charge density plays a central role in tuning the helical stability. At a fixed charge density, the sequence pattern has a minor influence. We believe this study could help the scientific community involved in the de novo design of protein sequences. |
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N00.00302: The Importance of Experimental Controls: Evidence that Task-Dependent Invariances Define Functional Specialization in Cortical Hierarchy Laura E Brandt The recent surge in collaboration between neuro/cognitive scientists and machine learning researchers has generated a large body of work that uses artificial neural nets (ANNs) to model brain function. This work is often focused on strong positive correlations between the output of an ANN layer and observed activations in a brain region in response to a sensory stimulus. But the absence of adequate controls often limits our ability to conclude that mechanisms in the brain are similar to those in the ANN (or any other statistical pattern analyzer). Data and tools like those publicly available at BrainScore.org can be used to provide controls in the form of alternative models that yield similar correlations with functional brain data. Interestingly, these BrainScore comparisons show that models with widely-varying architectures can score similarly well. We argue that rather than suggesting architectural analogies between ANN and brain, activity correlation emerges inevitably in any hierarchical network trained for a given task, based on the invariances required to perform that task. Furthermore, neuron specialization will occur in multi-task ANNs, as determined by the invariances required for each task. |
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N00.00303: Investigation of the Law of Volume Constancy in Cortical Laminae Jack Consolini Decades of research has shown that the cortex contains gyral folds (peaks) which are thicker than the sulcal folds (valleys). This observation led early 1900s scientists to propose that these thickness differences made gyri and sulci functionally distinct regions. However, an anatomist showed that the the layers within the cortex (cortical lamina) maintained their relative volume and neuron composition throughout the curved sections, suggesting that curvature alone is not an indicator of function (Bok 1929 DOI: 10.1007/BF02864437). In this study, we investigated the validity of this "Law of Volume Constancy" in our computational model of cortical folding, including simulations of heterogeneous cortical growth (Wang et al. 2021, DOI: 10.1007/s10237-020-01400-w). To do so, we calculated the average difference in relative laminar volume and thickness between gyral and sulcal folds in both Bok's original analysis and our simulations. The folding simulations maintained their volume within approximately the same error (+/- 3%) as Bok's analysis. However, we determined that the volume preservation was likely a result of the prescribed initial volume and identical initial laminar thickness, thus highlighting the limitations of current soft-tissue growth models in accurately replicating natural growth patterns. |
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N00.00304: Single molecule multi-color multi-pair FRET microscopy Sayan Mondal, Jonathan Jeffet, Ben Ambrose, Tim Craggs, Yuval Ebenstein Single molecule Förster resonance energy transfer (smFRET) microscopy is an important tool to understand function of biomolecules by measuring their structural dynamics at nanometer length scale. However, to monitor more than one distances at once, simultaneous multi-pair FRET measurement is challenging due to the spectral bandwidth required for the donor and acceptor fluorophores. We have recently developed Continuously Controlled Spectral resolution (CoCoS) microscopy by integrating a pair of coaxially rotating amici prisms in front of the camera in a standard epi-fluorescence microscope. We show that CoCoS microscopy allows us to perform smFRET experiments on DNA molecules to simultaneously register multiple distinguishable FRET signals, and with a five-fold larger field of view compared to traditional dual-channel TIRF optics. These multicolor experiments are possible owing to the unique feature of CoCoS to simultaneously register several emission channels without compromising throughput. Using the herein described multi-color multi-pair smFRET, we would be able to simultaneously monitor multiple distances in large bio-molecular assemblies in order to decipher their structural dynamics. |
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N00.00305: Coarse-Grained Modeling of Coronavirus Spike Proteins and ACE2 Receptors. Timothy Leong, Chandhana Voleti We developed coarse-grained models of spike proteins in SARS-CoV-2 coronavirus and angiotensin-converting enzyme 2 (ACE2) receptor proteins to study the endocytosis of a whole coronavirus under physiologically relevant spatial and temporal scales. We first conducted all-atom explicit-solvent molecular dynamics simulations of the recently characterized structures of spike and ACE2 proteins. We then established coarsegrained models using the shape-based coarse-graining approach based on the protein crystal structures and extracted the force field parameters from the all-atom simulation trajectories. To further analyze the coarse-grained models, we carried out normal mode analysis of the coarse-grained models to refine the force field parameters by matching the fluctuations of the internal coordinates with the original all-atom simulations. Finally, we demonstrated the capability of these coarse-grained models by simulating the endocytosis of a whole coronavirus through the host cell membrane. We embedded the coarse-grained models of spikes on the surface of the virus envelope and anchored ACE2 receptors on the host cell membrane, which is modeled using a one-particle-thick lipid bilayer model. The coarse-grained simulations show the spike proteins adopt bent configurations due to their unique flexibility during their interaction with the ACE2 receptors, which makes it easier for them to attach to the host cell membrane than rigid spikes. |
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N00.00306: A mathematical model of chemotactic endothelial cell migration in a fibrin-based hydrogel extracellular matrix Josep Ferré Torres The formation of new vasculature from existing blood vessels, or angiogenesis, occurs as a multistep process driven by an extensive collection of pro- and anti-angiogenic factors. In this process, the extracellular matrix (ECM) plays a crucial role due to its structural function, the store of mediators, such as vascular endothelial growth factor (VEGF), and matrix-cell interactions. The scenario of the remodelling of the ECM and matrix-cell interactions during angiogenesis is intricate. A standard approach to study angiogenesis is to explore the underlying cellular mechanisms focusing on endothelial cell (EC) motility regulated by chemotactic stimulus, ignoring mechanotactic stimuli. In cultured ECs, it is possible to easily analyze, separately, the concentration of growth factors, namely VEGF, and the structure of the culture substrate, mimicking ECM material. |
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N00.00307: Mechanical Energy Needed for Cyclizing a DNA Origami Rectangle Jong Hyun Choi, Ruixin Li DNA nanotechnology has emerged as a versatile bottom-up approach to construct complex nanoscale architectures from programmable DNA self-assembly. For example, a DNA origami structure is composed of double-stranded DNA helices and crossovers that connect neighboring folded scaffold segments. To ensure the structural integrity and programmed functions, it is important to understand the mechanical aspects of the self-assembled structures. In this work, we used a DNA origami rectangle as a model system to study the structural deformability and related mechanics. We performed molecular dynamics (MD) simulations based on a coarse-grained model on oxDNA, an open-source software. We computed mechanical energy needed to cyclize the origami rectangle, and compared the results with experiment and theory. We found that the initial curvature is overcome gradually from initial to the last stage of cyclization and that the energy associated with cyclization matches with the experimental and theoretical results. This work offers detailed insights into DNA mechanics and deformability, which could be useful for studying energy driven process on self-assembled nanostructures. |
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N00.00308: Oscillatory instabilities in active mechanical networks Neelima Sharma, Madhusudhan Venkadesan Active mechanical networks represent systems across domains and length scales, from actin meshes in cells to limbs in animals and robots. The stability of these networks is governed by an interplay between actuation, constraints, external forces, and viscoelastic properties of the network. Unlike passive systems, active systems under constraints are subject to loads that arise from internal actuation. If the combination of forces due to the external loads, constraints, and viscoelasticity fails to restore the original configuration after a perturbation, the system is unstable. Using a structural stability analysis of a general active mechanical network subject to Pfaffian constraints, we show that a network with circulation-free stiffness, damping, and feedback can only destabilize by static buckling when subject to holonomic constraints. In contrast, the same mechanical network with non-holonomic constraints can exhibit either static buckling or flutter instability. We provide bounds on the system's viscoelasticity and show how feedback can stabilize active networks under different types of constraints. |
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N00.00309: Time as the supervisor: Unsupervised learning of classification of natural auditory stimuli via Slow Feature Analysis Ron W DiTullio, Chetan K Parthiban, Eugenio Piasini, Vijay Balasubramanian, Yale Cohen A fundamental goal of sensory systems is to extract sensory information from the environment and convert it into perceptual representations. As the brain cannot simply transduce and represent all of the information present in the environment, sensory systems must select features of the stimuli to encode. |
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N00.00310: Lipid Membranes Cushioned by Polymer Brushes: A Coarse-Grained Molecular Dynamics Study Mohamed Laradji, Jeremy V Walker Solid-supported lipid bilayers (SLBs) are commonly used as biomimetic membranes for understanding the physico-chemical properties of biomembranes and membrane-bound proteins. The thin aqueous layer between the bilayer and the substrate, with typical thickness varying between 0.5 and 3 nm, makes SLBs not suitable for studying transmembrane proteins with protruding domains. The closeness of the lipid bilayer to the substrate also hidners out-of-plane deformations of the bilayer, which are necessary for many biological processes. Polymer-cushioned lipid bilayers are attractive alternative systems for biomembranes in cell-mimicking environments. Here, we present a numerical study, based on coarse-grained molecular dynamics simulations of an implicit-solvent model, of lipid membranes that are cushioned by polymer brushes. Our investigation over a wide range of polymer-lipid interactions, polymer chain lengths and polymer grafting densities, shows that the polymer brush has a strong effect on the elastic properties of the lipid membrane. In particular, we found that attractive interactions between the polymer chains and the lipid head groups lead to a decrease of the tension of the membrane and an increase of the membrane's bending modulus. These effects are amplified with increasing the chain length or grafting density. |
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N00.00311: DNA Programmable Protocell Aggregation Behavior Jong Hyun Choi, Yancheng Du Synthetic systems mimicking biological cells with simplified structures and functions are known as protocells. Various cell behaviors have been demonstrated with such model systems. Cell aggregation is an important function involved in cell viability, differentiation, and migration. Here, we propose a synthetic model system to study the cell interactions and signaling process in cell aggregation. We developed engineered lipid vesicles as a structural model for protocells with DNA strands attached on the surface. Two kinds of DNA-decorated vesicles were used in the experiments. Giant unilamellar vesicles (GUVs) were integrated with transmembrane channels made of DNA origami for recognizing and processing intercellular signals. Small unilamellar vesicles (SUVs) were modified with DNA strands responding to the DNA signals. Our experiments showed successful aggregation and dissociation between SUVs and GUVs upon introduction of proper DNA signals. We demonstrated that the DNA signals can be recognized by the GUVs and processed by the encapsulated enzymes to perform programmed aggregation behavior. The DNA programmable protocells have the potential as model systems for studying intricate cell signaling and cell-to-cell communication. |
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N00.00312: Radiofrequency Heating of Gold Nanoparticles: Frequency and Size Study Ghanem H Alatteili Traditional cancer therapies such as chemotherapy and radiation are difficult for patients in terms of pain, effectiveness, and cost. To overcome these obstacles, doctors and researchers have been shifting towards hyperthermia applications. Heating of gold nanomaterials using electromagnetic radiation, particularly in the radiofrequency region, is highly desirable as this would be non-invasive and cost-effective. However, there has been a great deal of debate among researchers as to whether gold nanoparticles heat when exposed to radiofrequency (RF) fields and, if they do, this heating is limited to particles less than 10 nm in diameter. In this work, we show that a variety of sizes of gold nanoparticles (AuNPs), including 20 and 30 nm particles, heat when exposed to megahertz range of RF fields. We experimentally demonstrate that AuNPs exhibit significant heating rates in the frequency range of 10 to 15 MHz. This work demonstrates that heating of gold solutions is not necessarily limited to size or frequency but depends more on the concentration of gold present and the size of the electric field applied. With this insight, we can continue to explore gold nanoparticles as candidates for RF hyperthermia applications. |
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N00.00313: Relaxation of a natural microbial ecosystem to a metabolic steady state Oshani Fernando, Alexander P Petroff Ecosystems persist over geological time scales as organisms with complimentary metabolisms mediate nutrient cycles . The dynamics by which these cycles form and are stabilized remain poorly understood. Here we investigate the dynamics by which a natural microbial community, extracted from salt marsh sediment and containing oxygen consuming and oxygen producing microbes, relaxes to a metabolic steady state in a quasi-two-dimensional chamber. Filtered pore water continuously flows through the chamber, refreshing it at a rate of 0.8 1/hr. We measure the two dimensional distribution of oxygen at five minute intervals for several days, and infer the instantaneous rates of oxygen production and consumption. Preliminary results show that the metabolic activity of oxygen-producing and oxygen-consuming microbes relaxes to a steady state along a low dimensional trajectory. In future work, we will regularly extract DNA from the effluent to characterize the community dynamics both in the initial convergence to steady state and in the following days. |
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N00.00314: A Mesoscopic Model for the Condensation of Intrinsically Disordered Proteins Theodore S Yang Proteins containing intrinsically disordered regions (IDRs) often mediate the formation of phase-separated biomolecular condensates involved in cellular signaling, epigenetic inheritance, and disease pathology. Mechanistically, these protein condensates are thought to be important for physical sequestration, membrane selectivity, and control of biochemical microenvironments. However, assessing the physical validity of these functions requires an understanding of both the detailed microstructure and particle hydrodynamics within these compartments. Here, we develop a method for generating multiscale coarse-grained models for the condensation of proteins containing both ordered and disordered regions. Using Langevin Dynamics simulations, we study how electrostatic and entropic forces combine to control time-dependent liquid, gel, and solid transitions. Furthermore, we probe the physical mechanisms for the reversibility of protein condensates under changes in temperature, pH, and ionic strength. From this physical framework, we ask if size exclusion plays a role in how protein condensates achieve selectivity. We leverage Voronoi diagrams to understand size-specific tracer migration within protein condensates which undergo gelation. |
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N00.00315: Ultraviolet-Assisted Direct Ink Writing of Biodegradable Tissue Scaffold for Pelvic Floor Prolapse (POP) Kenan Song Pelvic floor prolapse (POP) is a disorder bothering a growing number of women. A sedentary lifestyle and longer life expectancy are increasing the risk of this dysfunction. Re-classifying the current polypropylene mesh as a high-risk device by FDA is announcing the urgent need for new biocompatible materials for reconstructive surgeries. As a biocompatible polymer, polyvinyl alcohol (PVA) was functionalized to adapt to direct ink writing. The thiol-norbornene UV-initiated reaction was the key to the sol-gel transition during the printing, where the rheology properties changed rapidly to maintain the printed geometry. Rapid prototyping can adjust the morphology and the pore size of the scaffolds to benefit tissue growth. The biocompatibility was proven by the cell proliferation test, which can potentially change the immune response compared to traditional materials. Moreover, post-printing treatment further increased the crosslink density of the scaffold so that a proper degradation rate was obtained. Consequently, mechanical support would be valid during the neotissue growth, and removal surgery is unnecessary. This research offers a new solution to POP by applying a more bioactive material and sheds light on personalized medicine with additive manufacturing. |
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N00.00316: Dynamics of cooperative antibiotic resistance at mesoscopic scales Marlis Denk-Lobnig, Keanu A Guardiola Flores, Kevin Wood Communal behaviors are an important aspect of life across different scales. Understanding how interactions at the level of individual units (e.g., cells) relate to population-level dynamics is often non-trivial and, at times, the behavior at different scales can even appear mutually incompatible. For example, interactions between drug-sensitive and drug-resistant bacteria can lead to cooperative resistance on length scales many times the size of a single colony; by contrast, at the single-cell level, experiments and simple reaction-diffusion models suggest these effects are localized to only a few cell lengths. Here we combine quantitative imaging experiments in microfluidic chambers with simple mathematical models to investigate cooperative resistance on “mesoscopic” length scales where multi-cellular clusters can be approximately described as continuous tissues. By quantitatively interrogating the tissue-level dynamics of these communities, our work highlights how synergistic effects of spatially localized, resistance-rich cell clusters modulate the effective range—and the corresponding tissue-level dynamics—of cooperative resistance across scales. |
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N00.00317: How spiders actively modulate web-vibration sensing for prey localization Hsin-Yi Hung, Abel Corver, Andrew Gordus Organisms flexibly adjust postures and movements to acquire information from environments based on real-time sensory feedback. Despite the ubiquity of vibrational sensation in animals, less is known about how behavioral dynamics modulate vibratory sensory information. |
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N00.00318: Searching for Quantum in Biological Ion Channels Ying-Ying Lu, Andrei Tretiakov, Vanessa Scheller Transmembrane ion channels are proteins that allow ions to travel in and out of a cell. Normal operation of ion channels is essential for cellular well-being, and its disruption can lead to neurological disorders and cancer proliferation. Yet, the operation of ion channels and some of their fundamental properties are not well understood at the nanoscale. Of particular interest are the effects arising from the interactions with the nowadays ubiquitous external electromagnetic fields. We are working towards combining state-of-the-art electrophysiology with synchronized electromagnetic field excitation (of different strengths, frequencies, and directions) in order to perform a systematic study of these light-biomatter interactions -- from static fields to optical frequencies. Our ultimate goal is to investigate length- and timescales in which quantum effects are expected to play a significant role on ion channel properties, and develop tools that will allow us not only to study these effects, but also to control the ion channel performance via quantum degrees of freedom. |
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N00.00319: 2'-deoxyguanosine riboswitch motion regulated by ligand and magnesium Erdong Ding Riboswitch, often found in bacteria, is a family of untranslated message RNA regions located at 5' end. Acting like a switch, it regulates the transcription or translation process, and thus metabolism, by binding to certain metabolite. As an example, the 2'-deoxyguanosine (dG) riboswitch is able to bind the 2'-deoxyguanosine molecule. When the binding is formed, the transcription process is terminated (OFF state), however, when there is no ligand binding, the riboswitch takes a conformation change during RNA elongation, hence enabling the process (ON state). So, it is important to understand how the ligand-binding (aptamer) region of the riboswitch works and how the ligand affect it. Since RNA is negatively charged, cations, especially magnesiums, also play a very important role in stablizing RNA molecule. In this work, we used all atom simulation to study how ligand and magnesium affect the motion of the aptamer region of 2' dG ribowitch and how we relate RNA motion from simulaiton to the result from selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiment, which measures RNA backbone flexibility. |
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N00.00320: Cell-wise Stress-Strain Relation in 2D Polygonal Tessellation Systems Ran Li, Hao Lin, Seyedsajad Moazzeni, Liping Liu Randomized polygonal tessellations are frequently observed as nature’s preferred geometric pattern and engineering platform. Mechanical aspects such as constitutive relations and elasticity have been the topics of extensive study in the past decades in various contexts such as foams and more recently, in confluent biological tissues. In this work we present a theory for the cell-level stress-strain relationship. Both analytical derivation and numerical simulation indicate a consistent stress-strain relation across different energy models. An analytical expression for cell-wise shear modulus is derived, validated numerically, and compared with prior work in the foam literature. This result finds broad applicability in tessellated structures at mechanical equilibria. |
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N00.00321: Emergent Ecological Phenomena in Evolving and Migrating Populations Casey Barkan, Shenshen Wang Evolution is a ubiquitous feature of systems of interacting organisms. However, ecological models that neglect evolution often provide an adequate description of systems composed of distinct species. Even in cases where only one species is considered, evolutionary dynamics can lead to the emergence of multiple strains that interact in ways resembling distinct species. For example, a recent study of gut microbiota showed that several strains of a single species coexist and obey simple ecological laws. A theoretical understanding of how and when ecological laws emerge from evolutionary dynamics may be critical for understanding such systems. We study a model of an evolving population that migrates through a spatially heterogeneous environment. We give precise criteria for when distinct strains emerge, and we analyze how they interact. We show that extinction of strains corresponds to a phase transition characterized by slow relaxation to steady state. This slow relaxation may provide a signal to detect impending extinction. Our results may apply to a variety of systems including human microbiomes, antibodies undergoing affinity maturation, and bacteria acquiring antibiotic resistance. |
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N00.00322: Role of protein-mRNA droplet formation in regulation of meiotic exit in yeast Sima Setayeshgar, Renyu Wang, Soni Lacefield Liquid-liquid phase separated condensates consisting of key molecules together with other proteins or RNA ensure the execution of a variety of cellular regulatory processes in a spatially and temporally controlled manner. The dynamic assembly, disassembly and clearance of amyloid-like aggregates of the translational repressor Rim4 in yeast has been shown to be essential for progression through meiotic divisions [Wang et al., Dev. Cell (2020)]. These aggregates sequester and prevent translation of mRNAs critical for exit from meiosis II. Multisite phosphorylation of Rim4 triggers disassembly of aggregates followed by autophagy of monomeric or oligomeric units, releasing mRNAs and enabling translation. We have developed a model informed by experiments for the meiosis II exit regulatory module. We present analytical and numerical results for the stochastic dynamics of the model that explore the role of Rim4-mRNA droplet formation in regulating noise and fidelity of exit. |
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N00.00323: Driving biomolecular droplets through polymer meshes Divya Kota, Huan-Xiang Zhou Biomolecular condensates are commonly thought as being formed through phase separation from a dilute bulk phase. However, inside cells, biomolecular condensates reside in crowded environments or dense polymer meshes (e.g., cytoskeleton or nucleoskeleton plus chromatin). To characterize the effects of such dense polymer meshes, here we used optical tweezers to trap and drive biomolecular droplets through the meshes formed by a synthetic polymer, Ficoll70. The movement of solid polystyrene beads requires the displacement of Ficoll70 chains and thus encounters the full viscous resistance. By contrast, due to their liquid nature, biomolecular droplets can transiently deform when passing through polymer meshes, and thus experiences reduced viscous resistance. When the polymer meshes are dense (as found at 200 g/L Ficoll), polystyrene beads, but not biomolecular droplets, are elastically coupled to the meshes. The liquid nature biomolecular droplets thus enable them to easily migrate through dense polymer meshes, which in turn may facilitate their cellular functions. |
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N00.00324: Light Scattering Study of Eye Lens Beta Crystallin Proteins in Solution Malcolm F LaRose, Timothy R McNutt, George M Thurston We perform light scattering on bovine beta-high crystallin, an important protein component of the mammalian eye lens. We compare light scattering results to simplified models for the free energy of mixing of beta crystallins with water. Our static light scattering data are well-represented by a hard convex body equation of state (1) having a dimensionless non-sphericity coefficient of close to 3, compatible with a prolate spheroid, among other shapes, and a weight-average molecular weight of close to 5 x 10^5 grams/mole. We also present our quasielastic light scattering results, and compare our results with other recent investigations of beta-high crystallin (2). |
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N00.00325: Balance of osmotic pressures determines the volume of the cell nucleus Dan Deviri, Samuel A Safran The volume of the cell nucleus varies across cell-types and species, and is commonly thought to be determined by the size of the genome and degree of chromatin compaction. However, this notion has been challenged over the years by multiple experimental evidence. Here, we consider the physical condition of mechanical force balance as a determining condition of the nuclear volume and use quantitative, order-of-magnitude analysis to estimate the forces from different sources of nuclear and cellular pressure. Our estimates suggest that the dominant pressure within the nucleus and cytoplasm originates from the osmotic pressure of proteins and RNA molecules that are localized to the nucleus or cytoplasm by out of-equilibrium, active nucleocytoplasmic transport rather than from chromatin or its associated ions. This motivates us to formulate a physical model for the ratio of the cell and nuclear volumes in which osmotic pressures of localized proteins determine the relative volumes. In accordance with unexplained observations that are century-old, our model predicts that the ratio of the cell and nuclear volumes is a constant, robust to a wide variety of biochemical and biophysical manipulations, and is changed only if gene expression or nucleocytoplasmic transport are modulated. |
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N00.00326: Investigating mathematical properties of non-equilibrium signatures in biological information processing systems Sabina J Haque, Ugur Cetiner, Jeremy Gunawardena Detecting nonequilibrium behavior in biological information processing systems poses a technical challenge in experimental and theoretical contexts. To address this difficulty, several mathematical signatures of broken detailed balance in Markovian systems have been suggested. While these signatures identify the presence of energy expenditure, little is known about how they relate to underlying thermodynamic forces. Here we use a graph-theoretic approach to Markov processes to probe the relationship between force and the Steinberg signature, which detects nonequilibrium behavior through the inequality of forward and reverse higher-order autocorrelation functions. We have developed software to calculate the Steinberg signature from arbitrary graphs. We find that when a Markovian system is perturbed progressively from equilibrium and its force increases from zero, the Steinberg signature reaches its maximum at an intermediate value of force before decaying asymptotically, potentially to zero. This non-monotonic relationship shows the Steinberg signature's limitations as a tool for detecting energy expenditure. Characterizing the mathematical behavior of such signatures may elucidate new properties of nonequilibrium systems to be tested experimentally in real biological contexts. |
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N00.00327: Self-organized flows in phase-synchronizing active fluids Brato Chakrabarti, Sebastian Fürthauer, Michael J Shelley Active particles, such as motor proteins and motile micro-organisms, convert chemical energy from a reservoir to do mechanical work in their environment. We are interested in cases where this energy conversion process involves a periodic duty cycle, such as a cyclic swimming stroke or a periodic stepping of a motor, and can be mapped onto a phase variable. We study the hydrodynamics of a suspension of such particles. For an orientationally aligned suspension of active particles, a stability analysis predicts that both the phase-ordered and disordered states are unstable. Nonlinear simulations of such aligned suspensions reveal the formation of chimera states. The phase dynamics can further trigger alignment instabilities that are unique to these systems and are absent in classical active fluids with time-periodic force dipoles. We find that in channels, a combination of the alignment and phase instability allows these active particles to self-organize and generate unidirectional pumping. |
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N00.00328: Extracellular matrix geometry regulates T cell migration mode Alexia Caillier, Patrick W Oakes Most of what we know about cell migration stems from studies using mesenchymal cells on stiff substrates. Immune cells, however, use a different mode of migration known as amoeboid migration which allows them to move significantly faster, with less adhesion, through more complex environments. Immune cells are one of the few cells in the body that are naturally exposed to a wide variety of microenvironments. Previous reports have established that immune cells are able to migrate in the absence of integrins, the protein at the foundation of adhesions. Other reports have suggested, however, that adhesion plays a normal role in regulating immune cell migration in tissue. We therefore hypothesize that immune cells can adapt their migration from adhesion independent to adhesion dependent in response to their environment. To test our hypothesis, we have constructed a variety of ways to confine immune cells and measure both their ability to migrate and the forces they generate in this process. We find that the forces are several orders of magnitude smaller than those measured in mesenchymal cells like fibroblasts and take on a different distribution. Our results provide important insights into the mechanical processes underlying this alternative form of migration. |
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N00.00329: Mechanical Basis for Epithelialization Christian Cammarota, Nicole Dawney, Mimi Jüng, Dan Bergstralh Epithelial tissues are comprised of sheets of cells that must establish and maintain proper architecture to function. The role cell mechanics in architecture development has been difficult to study in vivo since tissue development is predicated on the existence of cell-cell contacts. Our work addresses the question of how physical constraints such as the cellular density of a tissue, cell stiffness, and cell-cell or cell-substrate connections affect the development of a polarized tissue architecture. We made a 2D computational model of cells in a plane perpendicular to the tissue plane and found that a spatial constraint holding the cells in close proximity is required for cells to develop cell-cell borders. The model also predicts that cell-cell borders form in reduced adhesion simulations. These results were validated in culture using Madin Darby Canine Kidney cells. Our work suggests that cell density is the primary factor in cell-cell border development and that cell-cell adhesion is subordinate. We are currently working to address the question of how cell density affects the regulation of epithelial architecture. |
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N00.00330: Inheritance of broadcast enzymes enables high dispersal of chitin-associated marine bacteria Ghita Guessous, Terence T Hwa Insoluble in water, chitin, one of the most abundant biopolymers, sinks through the ocean and sediments as small particles termed ‘marine snow’. The biodegradation of these particles is central to the global carbon and nitrogen cycles. We studied the degradation of chitin by a marine bacterium of the Vibrio species. We found that two co-existing, exponentially growing sub-populations emerged: a minority attached to the particles and a dispersed planktonic majority. We demonstrated that while planktonic cells could not replicate, their increase was due to the detachment of the replicating cells resident on the particles. Proteomic analysis showed that chitin degrading enzymes were “broadcast” extra-cellularly by the entire population and accumulated on the particles. The resident minority thus “inherited” these enzymes, which enabled its fast replication, sustaining the overall growth of the population. This “inheritance” effect allows the level of chitinase synthesis to dictate the population growth rate, irrespective of the number of attached cells and thus of the dispersal rate. It provides a novel mechanism through which small growing colonies can be maintained on particles while the majority of the population is shed. Evolutionary rationales favoring the eager dispersal of cells from their sole nutrient source will be discussed. |
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N00.00331: Laser light painting of exhaled droplets: imaging with accessible, lower-power lasers Timothy Suzuki, Sean Ives, Arian Dovald, Blake Laing The spatial distribution of exhaled droplets produced during speech, singing, and playing wind and brass instruments is characterized and compared. Rather than using a stationary laser with a flat-and-wide profile, droplets are imaged in a long exposure during which a narrow laser beam is scanned vertically across the field of view with a technique we think of as "light painting". The advantage of this method is that the same illumination can be obtained with a lower-power laser (such as a class IIIb or less). |
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N00.00332: Single molecule imaging reveals actin-dependent diffusive states of IQGAP1 molecules in Jurkat T cells Mohamad Eftekharjoo Cytoskeletal elements of T cells such as actin and microtubules are known to regulate T cell function. The Ras GTPase-activating-like protein, IQGAP1 has been known to directly bind F-actin and serves as a scaffold for multiple microtubule and actin regulators. In T cells, IQGAP1 is recruited to the immune synapse where it serves as a negative regulator of signaling. A key step in understanding how IQGAP1 functions is to precisely define its mobility and the kinetics of its interactions with actin filaments and microtubules. We used single molecule imaging of IQGAP1 to track its accumulation and dynamics during the early stages of T cell activation. Using perturbation expectation-maximization (pEM), a machine learning based method, we characterized IQGAP1 trajectories into distinct diffusive states. Using pharmacological inhibitions and genetic perturbations, we determine the links between actin polymerization, microtubule dynamics and IQGAP1 mobility. Our results indicate that actin polymerization regulates single molecule dynamics of IQGAP1 and provide information about the timescale of actin-IQGAP1 interactions. Overall, our work sheds light on the mechanisms underlying IQGAP1 accumulation at the immune synapse and its coordination of signaling and cytoskeletal dynamics. |
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N00.00333: Molecular catch-bonds as a route to mechanical memory in active gels Carlos S Floyd, Aaron Dinner, Suriyanarayanan Vaikuntanathan Active gels like the cytoskeleton are non-equilibrium polymeric systems which display many fascinating behaviors. These include contractility, dissipative self-organization, and, the focus of our talk, mechanical memory. The ability for the gel to store a memory of its stress history through its orientation and chemical concentration fields should, in a cellular context, endow the gel with greater ability to produce contractile force in a tailored and useful manner. We hypothesize that molecular catch-bonds, which are unbinding reactions with rates that decrease as the tension applied to the bound molecule increases, should constitute a mechanochemical feedback that allows for enhanced mechanical memory in active gels. To explore this possibility, we developed hydrodynamical simulations of an active gel which, in a novel theoretical treatment, includes molecular catch-bonds. The simulations account for non-equilibrium stresses, reaction-advection-diffusion dynamics of molecular motors with catch-bond kinetics, and viscoelasticity that locally depends on the underlying filament orientations. We will describe applications of this numerical approach to characterize the conditions and relevant timescales associated with catch-bond induced mechanical memory in active gels. |
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N00.00334: Instability of bilayered systems under surface pressure: The effect of cerebrospinal fluid on cortical folding Fatemeh Jafarabadi Buckling instability is a common phenomenon in many biological and engineering layered structures. Once the compressive strain in a layered material reaches a critical value, the system becomes unstable, and it forms different patterns, such as wrinkles, folds, and creases. However, instability analysis is primarily conducted for zero-stress boundary conditions and in the absence of surface pressure. Here, we focused on the brain as a bilayer and aimed to study the influence of cerebrospinal fluid (CSF) pressure on its gyrification process. We present a nonlinear finite element solution for instability of a 3D bilayer under surface pressure, which consists of two inhomogeneous, incompressible layers (gray and white matter). We analyzed the effect of surface pressure on the critical strain and buckling criteria over a range of stiffness ratios, from 1.5 to 4, and normalized pressures, from 0.2 to 3. We also investigated thickness variations between gyral hills and sulcal valleys in relation to the CSF pressure. Our results suggested that adding pressure decreases the system's stability, especially in low stiffness contrasts with softer films. |
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N00.00335: Bayesian Image Analysis to Quantify the Perturbation of Cell Membrane by Exogenous AC Electric Field Sanjana Mukherjee, J. Shepard Bryan IV, Minxi Hu, Steve Presse, Quan Qing We recently showed that an exogenous electric field (EF) can electrostatically perturb membrane protein initiated intracellular signaling pathways. But, the molecular mechanism of EF modulation of enzymatic activities at the cell membrane is unclear. Here we try to quantify the overall coupling strength between EF and cell membrane by identifying dynamic membrane shifts under different EF stimulations at millisecond time scale. Sequential cell images are taken under EF stimulation synchronized with the exposure. A Bayesian inference method is used to find the most likely position of the membrane using a Gaussian model of the intensity profile across the membrane. Analysis was tested on simulated data and then applied on real cell images. Comparing results to a previously reported differential image analysis method, we showed that the Bayesian method has better signal-to-noise ratio beyond optical resolution of the images. We hope to develop this method into a framework for quantifying mechanical motions of cell membrane and study the correlation between different EF stimulations and cell response at a fast timescale, for quantification and modeling of the EF coupling of membrane and effect on enzymatic activities of membrane proteins. |
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N00.00336: Multifield modeling of brain development Shuolun Wang Brain development involves precisely orchestrated genetic, biochemical, and mechanical events. This work brings a new understanding of brain development by calibrating and validating a biomechanical model of neuronal migration to an innovative experimental approach for labeling and tracing neurons in the developing ferret in vivo. The proposed model builds upon previous work by de Rooij and Kuhl (2018), which introduced volume growth governed by cell density, with neuronal migration modeled as an advection-diffusion process. As a significant improvement, we define multiple cell types instead of a single cell density to capture more complex neuronal migration – younger neurons bypass their older counterparts to reside near the outer surface – in the experiments (Shinmyo et al., 2017). We numerically implement our model in Abaqus/Standard (2020) by writing user-defined element (UEL) subroutines. Our model is calibrated to experimental data using uteroelectroporation (IUE) in ferret brains to visualize and track cohorts of neurons born at different stages of embryonic development. The simulations with calibrated parameters qualitatively capture the cortical folding in ferret brains. |
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N00.00337: Erythro-PmBs: A Novel Polymyxin B Delivery System Using Antibody-Conjugated Hybrid Erythrocyte Liposomes Hannah Krivic, Sebastian Himbert, Ruthie Sun, Maikel C Rheinstadter As a result of the growing world-wide antibiotic resistance crisis, many currently existing antibiotics have become ineffective due to bacteria developing resistive mechanisms. There are a limited number of potent antibiotics successful at suppressing microbial growth, such as polymyxin B (PmB); however, they are deemed as a last resort due to their toxicity. We present a novel PmB delivery system constructed by conjugating hybrid erythrocyte liposomes with bacterial antibodies to combine a high loading efficiency with guided delivery. PmB encapsulation is enhanced by incorporating negatively charged lipids into the red blood cells' cytoplasmic membrane. Anti-E.coli antibodies are attached to the hybrid erythrocyte liposomes through DSPE-PEG malemeide linkers. We show that these Erythro-PmBs have a loading efficiency of 90%, and are effective in delivering PmB to E. coli, with values for the minimum inhibitory concentration (MIC) comparable to those of free PmB. MIC values for K. aerogenes were significantly increased beyond the resistant breakpoint, indicating that inclusion of the anti-E.coli antibodies enables the Erythro-PmBs to selectively deliver antibiotics to specific targets. This versatile platform can be used for different types of antibiotics and bacterial targets. |
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N00.00338: Towards a statistical physics of slender animal behaviour Jane Loveless, Greg J Stephens Slenderness is a common morphological trait shared by diverse animal species, including several commonly studied model organisms, in which individuals are much larger in one dimension than in the other two. This property can be exploited to describe a slender animal's mechanical configuration in terms of two scalar fields, measuring strain and curvature along the body axis. To build a statistical field theoretic description of slender animal movement, we choose to work within a "Riewe" theory space, in which driven and/or dissipative Langevin dynamics can be derived from a complex action functional containing higher- and fractional-order derivatives. In the spirit of effective field theory, we write down a generic action functional for the strain and curvature fields then follow through with a renormalisation procedure. This allows us to predict and explain the coarse-grained behavioural dynamics of slender animals that dominate at low frequencies and long wavelengths. |
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N00.00339: Influence of Charge Density and Patterning on the Conformations of FG Nups Pratyasha Bhardwaj, Mithun Radhakrishna The primary feature that distinguishes eukaryotes from prokaryotes is the presence of a nuclear envelope separating the cytoplasm from the nucleus. The Nuclear Pore Complex |
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N00.00340: Building Stimuli-Responsive Nanoparticle Assemblies In Polymer Matrix and Solutions Pothukuchi Rajesh Pavan, Mithun Radhakrishna Nanoparticle assemblies had drawn tremendous interest because of their potential applications in the fields of biomedicine, drug delivery, therapeutics, and cancer cell imaging. Building nanoparticle assemblies that are responsive to external stimuli offers great potential to tune a wide array of morphological transitions. Self-assembly of polymer grafted nanoparticles is responsive to external stimuli including polymer chain length, polymer concentration, salt concentration, pH, ionic strength of salt, and so on. In the present work, we used electrostatics to tune these stimuli-responsive transitions in solutions. Molecular dynamics simulations have been performed in the framework of the coarse grain model to study and understand the transitions in self-assembly. Transitions in self-assembly at different graft lengths and graft densities are reported. By varying the parameters including polymer and salt concentration, matrix length, and polymer weight, we are able to tune the transitions of self-assembled morphologies from rings to dispersed state, ordered crystal structures to smaller disordered aggregates. We believe that this model will act as a template in building stimuli-responsive systems which offer diverse applications in bio-imaging, targeting drug delivery, and sensing applications. |
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N00.00341: How network structure shapes dynamics and learning in recurrent neural networks Matthew Ding, Rainer Engelken Recent work is yielding connectivity data in a diversity of neural systems. However, it is an open problem how connectivity statistics shape network activity and trainability. In this work, we study the effects of partially symmetric and antisymmetric weight matrices, weight variance, and self-coupling on the dynamics and trainability of continuous-time recurrent neural networks (RNNs). We calculate the full Lyapunov spectrum, yielding estimates of attractor dimension and entropy rate. In networks with small weight variance, partial symmetry increases dimension and entropy rate. However, partial antisymmetry increases dimension and entropy rate in large weight variance networks because of a decreased fraction of nonlinear units in saturation. In networks with self-coupling, dimension and entropy rate increase with antisymmetry regardless of weight variance. To study the implications of connectivity in learning, we investigate how initial (anti)symmetry affects the training of RNNs with backpropagation to generate limit cycles and integrate multidimensional input. Partial antisymmetry leads to better final performance and faster learning in both tasks. Our work on RNN structure may provide insights on how connectivity shapes dynamics, learning, and function in biological networks. |
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N00.00342: Quantifying protein interactions in a living organism Aniket Ravan, Yann R Chemla, Martin Gruebele In recent years, experiments have shown that weak protein-protein interactions are influenced by enthalpic ('sticking') and entropic ('crowding') effects of their environment. The chaperoning activity of the molecular chaperone Hsp70 and its client Phosphoglycerate Kinase (PGK) lies in the realm of weak protein-protein interactions. In this work, we demonstrate a pipeline to study such protein-protein interactions in different tissues of live zebrafish larvae. Using meganuclease-mediated transformation, we induce mosaic bicistronic expression of fluorescently tagged HspA1A variant of Hsp70 and a low melting point mutant of yeast PGK. We subject anesthetized larvae to a heat shock to induce measurable chaperoning interactions in its transformed cells. Using fluorescence resonance energy transfer (FRET), we detect the onset of binding of the two proteins near the melting temperature of PGK in the larval myocytes. Our experiments at quantitatively comparing these interactions in different tissues of the larvae as well as comparing the chaperoning activity of Hsp70 and the constitutively expressed homolog, heat shock cognate protein Hsc70 (HSPA8). |
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N00.00343: Multiphase Organization Is a Second Phase Transition Within Multi-Component Biomolecular Condensates Konstantinos Mazarakos, Huan-Xiang Zhou Biomolecular condensates formed via phase separation are a very common occurrence in vivo and in vitro. When multiple components are present, condensates often demix to form multiple phases. Using a mean-field theoretical model and molecular simulations, we show that the multiphase organization is a second phase transition. Whereas the first phase transition that results in the separation of condensates from the bulk phase is driven by overall attraction among the macromolecular components, the second phase transition, leading to multiphase organization within condensates, is driven by disparity in strength between self and cross-species attraction. At a given strength of cross-species attraction, both of the phase transitions can be observed by decreasing temperature, leading first to phase separation and then to demixing of the condensates. These predictions are validated by molecular dynamics simulations of model binary mixtures. The binary mixtures comprise two types of Lennard-Jones particles or chains: D and R, with strengths of self-attraction εDD and εRR. At temperatures below the critical temperature for phase separation and strengths of cross-species attraction (εDR) above the mean of εDD and εRR, the components are homogeneously mixed in the condensates. When εDR is below the mean of εDD and εRR, condensates demix when temperatures are below a second critical value. The demixing leads to a variety of multiphase configurations, including core-shell, physical association, and droplet-inside-droplet. Calculation of interfacial tensions suggest that some of these configurations are metastable. Together, these results provide the missing physical underpinning for the multiphase organization of biomolecular condensates. |
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N00.00344: Framework for identifying 3d neural firing Dominika Lyzwa New optical tools allow imaging the firing of neurons, of a network of neurons, in 3d in real-time. To match this experimental advancement, comprehensive, robust algorithms need to be applied. We present an algorithm which enables identifying simultaneous, real-time detection of firing within a network. |
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N00.00345: Bursty RNA Velocity of Gene Programs for Trajectory Inference Frank Gao, Suriyanarayanan Vaikuntanathan, Samantha Riesenfeld Advances in single-cell RNA sequencing (scRNA-seq) allow collections of tens of thousands cells undergoing differentiation or experiencing external stimuli, revealing a detailed picture of stochasticity of gene expression. This permits trajectory inference (TI) which leverages variation in transcriptional profiles to assign an order of progression to cells, enabling a temporal interpretation of cell state. Traditional TI methods are data-driven and ignore the underlying biological processes so the directionality of developmental courses must be provided as inputs. While the standard RNA velocity method has provided additional insights, its moments-based coarse-grained setup has led to results that are contradictory to experiments. Here, we introduce a new RNA velocity model which accounts for transcriptional bursting and infers kinetic parameters using the joint distributions of counts. Furthermore, our model incorporates topic modeling, a popular method to explore gene programs, which helps delineate dynamical patterns of local gene programs not observed on the global scale. By disentangling the intertwining dynamics of genes, our method provides crucial mechanistic insights for cell fate commitments. |
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N00.00346: Characterizing Evolutionary and Physical Energy Landscapes of Evolving, Devolving, and Random Sequences Hana Jaafari, Nicholas P Schafer, Faruck Morcos, Peter G Wolynes Due to evolutionary constraints, protein sequences cooperatively fold into unique, energetically minimized three-dimensional structures in timescales as short as microseconds. The evolutionary importance of maintaining a stable protein structure can be quantified by the selection temperature. The selection temperature can be calculated using AWSEM, a coarse-grained free energy function, and DCA, a protein-specific information theoretic Hamiltonian. Expanding upon the list of previously studied proteins, we quantified selection temperatures of multiple proteins with a wide-array of biological functions. We found selection temperatures to be below physiological temperatures, indicating that folding energetics are an important evolutionary consideration. Furthermore, we incorporated temporal information by calculating the energetics of pseudogenes, devolved and randomly mutated protein-coding genes. We found that pseudogenes are more unstable than protein sequences, as a function of their degree of devolution. |
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N00.00347: Molecular dynamics simulations of droplet fusion reveals shear thinning Sahithya Sridharan Iyer, Konstantinos Mazarakos, Huan-Xiang Zhou Recent experiments have shown that biomolecular condensates are viscoelastic rather than purely viscous. One consequence, from both experimental and theoretical studies of shape dynamics, is that condensates exhibit shear thickening (or thinning), i.e., with effective viscosity higher (or lower) than the zero-shear viscosity. To gain deeper physical insight into the effects of viscoelasticity on condensate dynamics, here we carried out molecular dynamics simulations of droplet fusion. Droplets formed from phase separation of Lennard-Jones particles or chains were brought together to fuse. Particle droplets have fast shear relaxation, and their fusion speeds agree with the inverse of the viscocapillary ratio (zero-shear viscosity over interfacial tension). In contrast, chain droplets have slow shear relaxation, and their fusion speeds are faster than predicted by the viscocapillary model, thereby exhibiting shear thinning. The conformations of chains indeed show the telltale sign of shear thinning, with a tendency to align with the velocity field. We hope that these experimental and simulation studies together will compel the biomolecular condensate community to abandon the viscocapillary model and to finally think condensates as viscoelastic systems with all their complexities. |
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N00.00348: An epigenetic mechanism underlying melanoma cancer metastasis persistence Tianchi Chen, Eduardo Sontag, Herbert Levine, Muhammad Ali In this work, we build a computational dynamical system model to recapitulate a recent experimental finding of melanoma cancer metastasis persistence under the induction of the Notch pathway. We found that the regulatory feedback at the histone level could be a potential contributor to such persistence of the metastatic phenotype. Furthermore, we studied how different types of Notch ligand dynamics affect the underlying epigenetic states, thus leading to different cell fates. Furthermore, a 1D Duffing oscillator is used to theoretically understand the relationship between the phenotypic switching amplitude and switching frequency at the histone level. |
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N00.00349: Core-Shell Architecture for Engineered Biocompatible Quantum Nanoprobes Uri Zvi, Aidan Jones, Adam Weiss, Peter Maurer, Aaron Esser-Kahn Nitrogen-vacancy (NV) centers in nanodiamonds (NDs) have emerged as versatile qubit sensors capable of probing biophysical parameters not accessible by conventional techniques. Their applications range from probing fundamental cellular processes to novel diagnostic devices. Although powerful, applications have been limited by sensitivity and difficulties in targeting desired biological compartments. In this work, we present a core-shell architecture designed to address these challenges. We show that an engineered protective shell simultaneously increases the NV coherence properties while serving as a scaffold for biochemical modifications. Our approach is based on an initial encapsulation of the NDs with a high-quality SiO2 shell followed by silanization for subsequent surface functionalization. Single and double quantum relaxation measurements reveal prolonged longitudinal spin relaxation times, likely caused by a reduction in defect density associated with the diamond surface. Furthermore, in cell labeling assays, our engineered NDs allow us to efficiently target specific subcellular sites. |
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N00.00350: A unicellular walker controlled by a microtubule-based finite state machine Ben T Larson, Jack Garbus, Jordan B Pollack, Wallace F Marshall
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N00.00351: Irradiation of porphyrins modulate the structure of human serum albumin Abdullah Albalawi Recent research in our group has revealed that irradiating metal-free porphyrins binding to globular proteins can cause changes in the structure of the polypeptides under certain conditions. In this study we investigated the impact of irradiation of a series metal protoporphyrin on the structure of HSA at pH 7.0. UV-Vis absorption, fluorescence, fluorescence lifetime and circular dichroism of HSA with a series of metal PPIXs including Fe, Mg, Mn, Sn and Zn were measured. Spectra were recorded by using a spectrophotometer to observe bleaching of the PPIXs. Fluorescence and fluorescence lifetime were taking place to monitor the changes of Trp 214 in HSA. CD spectroscopy was carried out to estimate the change in the secondary structure of the protein. |
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N00.00352: CHEMICAL PHYSICS
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N00.00353: Investigation of Electronic, Optical and Thermoelectric Properties of Perovskite BaTMO3 (TM=Zr, Hf): First-Principles Calculations Said M Al Azar, Ibrahim Alzoubi, Ahmad Mousa, Emad Jaradat The structural, electronic, optical, and thermoelectric characteristics of crystalline oxides-perovskites BaTMO3 (TM=Zr or Hf) were investigated using the all-electron full-potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory (DFT). The GGA as parameterized in Perdew, Burke, and Ernzerhof (PBE-GGA) was employed to calculate exchange-correlation potential. Also, the modified Becke Johnson exchange potential approximation as parameterized by Tarn and Blaha (TB-mBJ) was used to improve the bandgap estimation. According to the researchers’ calculations, the two perovskites BaZrO3 and BaHfO3 show insulator behavior and have widely indirect band-gap energy (R-Γ) 4.42 (3.39) eV for BaZrO3 and 5.25 (3.69) eV for BaHfO3 from both approaches, TB-mBJ (PBE-GGA), respectively. The optical properties such as dielectric tensor, the refractive index, the absorption coefficient, and the electron loss function have been calculated and analyzed. The optical transitions mainly take place if an electron radiate from the initial state O-2p to the final state Hf-5d or to the Zr-4d in BaHfO3 or BaZrO3 case, respectively. Furthermore, the transport characteristics calculations based on semi-classical Boltzmann theory have been discussed. |
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N00.00354: Quantum Process Tomography of Light-Matter Interactions with a Polarization-entangled Biphoton Probe Ravyn Malatesta Quantum-light spectroscopy can yield higher spatio-temporal resolution and information inaccessible using its classical counterpart. Most current research on quantum-light spectroscopy uses entangled photon pairs (EPPs) as an analog for classical light. In contrast, our approach is to use quantum process tomography to treat the light-matter interaction fully quantum mechanically. By characterizing the density matrix of an entangled biphoton state in the polarization basis before and after interaction with a sample, we can measure the quantum mechanical operator associated with the light-matter interaction. With this technique we probe whether the correlated triplet-triplet pair intermediate in the singlet fission of TIPS-tetracene is an entangled state. |
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N00.00355: Compositional dependence of optical properties of praseodymium (Pr3+) ions in binary and ternary bismuth borate glasses Saisudha B Mallur, P. K. Babu We studied the compositional effects on Pr3+ absorption and fluorescence properties in binary bismuth borates and ternary bismuth boro-tellurite glasses. Addition of TeO2 can significantly affect the optical properties of Pr3+ ions doped in bismuth borate glasses. We used a modified Judd-Ofelt analysis to obtain the intensity parameters from the optical absorption spectra. With increase in bismuth oxide content, an increase in the covalency of the Pr-O bond in the binary glasses and a more pronounced variation in the ternary glasses is observed. Optical band gap decreases with increase in bismuth content in both binary and ternary glasses. Fluorescence spectra show peaks in the blue and red region characteristic of Pr3+ ions. We carried out a phonon side band analysis which suggests that the energy levels of Pr3+ responsible for the intense red emission are populated through a cross-relaxation mechanism instead of a multi-phonon decay process. The blue transition of Pr3+ shows significant enhancement for the stimulated emission cross-section in ternary system containing TeO2 compared to the binary system. Our glass samples also possess high spectroscopic quality factors compared to similar systems doped with Pr3+ ions which make them suitable for optical applications. |
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N00.00356: Accelerating ab-initio calculations using semiempirical methods. Zehao Zhou We report a general strategy to speedup the Time-Dependent Density Functional Theory (TDDFT) calculations of molecular response properties by leveraging semiempirical models. Instead of replacing expensive ab-initio methods with cheap semiempirical methods, we use the semiempirical methods to accelerate the ab-initio calculations. As an example, we use a semi-empirical preconditioner in the iterative Davidson algorithm to accelerate the TDDFT excitation energy calculation, acquiring a cost reduction of 37-70%. The crucial advantage of using the semi-empirical preconditioner is that the converged result is unchanged, so there is no tradeoff between accuracy and speedup. Moreover, the preconditioner can be further improved by tuning the empirical parameters that define the semiempirical model, leading to an additional cost reduction of 10 to 20%. A promising application of our work is non-adiabatic molecular dynamics, where significant cost reduction should be expected since excitation energies are computed millions of times. |
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N00.00357: Optically- and thermally-driven huge lattice orbital and spin angular momenta from spinning fullerenes Guoping Zhang, Yihua Bai, Thomas F George
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N00.00358: The rovibrational spectrum of neon trimer in a three–dimensional Faddeev approach Reda Ahnouch, Lavano D Sands, Mohammadreza Hadizadeh The three-dimensional (3D) form of Faddeev integral equations for three-body (3B) bound states with amplitudes depending on the Jacobi momentum vectors [1] are solved to calculate the rovibrational energy levels and wave functions of Neon trimer ground and excited states. The inputs for 3D Faddeev integral equation are the fully-off-shell transition matrix elements that are calculated from Ne-Ne interactions developed by Hellmann et al. [2]. The properties of Ne trimer ground and excited state wave functions are studied in detail. The stability and accuracy of our numerical solutions are tested by calculating the expectation value of the 3B Hamiltonian, indicating an excellent agreement with the energy eigenvalues. |
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N00.00359: Molecular Structure Optimization based on Quantum Dynamics ComputationMolecular Structure Optimization based on Quantum Dynamics Computation Hirotoshi Hirai We show the concept of the molecular structure optimization method based on quantum dynamics computations. There, the nuclei are treated as quantum mechanical particles so are the electrons, and the many-body wave function of the system is optimized by an imaginary time evolution method. We focus on the fact that the optimized many-body wave function has large stochastic amplitudes at the nuclei positions, and show that the optimized nuclei positions can be specified with a small number of observations. |
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N00.00360: Identification of the invariant manifolds of the LiCN molecule using Lagrangian descriptors Fabio Revuelta, Rosa M Benito, Florentino Borondo In this communication, we apply Lagrangian descriptors to study the invariant manifolds that emerge from the top of two barriers existing in the LiCN<->LiNC isomerization reaction. We demonstrate that the integration times must be large enough compared with the characteristic stability exponents of the periodic orbit under study. The invariant manifolds manifest as singularities in the Lagrangian descriptors. Furthermore, we develop an equivalent potential energy surface with 1 and 2 degrees of freedom, which reproduces with a great accuracy previous results. |
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N00.00361: On the anti-compensation effect? Nayeli Zuniga-Hansen, Andrew J Bevolo, Leo Silbert, M. Mercedes Calbi The kinetic compensation effect (KCE) refers to an observed systematic variation in the apparent magnitudes of the Arrhenius parameters, the energy of activation Ea, and the preexponential factor ν, as a response to perturbations. The extracted parameters tend to exhibit a strong positive linear correlation. This is attributed to enthalpic and entropic contributions changing in the same direction. However, when these contributions change in the opposite direction, a negative linear correlation is expected, the anti-compensation effect. |
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N00.00362: Towards uncontracted basis sets in Density Functional Theory Sherab Dolma, Kusal Khandal, Karma Dema, Mark R Pederson From the standpoint of quantum calculations, contracted Gaussian orbital basis sets have proven useful for very accurate Hartree-Fock, Density-Functional and high-level quantum solutions [1]. Still today there are times when inaccuracies in calculations are incorrectly attributed to a lack of polarization functions rather than strong ionicity effects. Further, it is recognized that greater accuracy could be achieved by removing the constraint of contracted orbitals. To this point, we have developed an automated approach to remove inaccuracies due to contracted orbitals. This work proceeds through the use of an advanced automated calculation for efficient optimization in which separate environmentally informed contractions are used for each and every atom in the molecule. The result is a machine generated code for basis optimization which is applicable to any type of molecular/atomic orbitals. We present results on diatomic molecules and the SF6 molecule and discuss strategies for deciding one whether to optimize on an iteration-by-iteration basis or at the end of each single-point calculation. |
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N00.00363: In-silico Screening of Inhibitors Targeting the SARS-CoV-2 Envelope Protein Md Lokman Hossen, Prabin Baral, Bernard S Gerstman, Prem P Chapagain The Envelope protein (E), one of the three membrane proteins in SARS-CoV-2, plays an important role in assembling the virus, mediating the budding process and finally releasing the progeny viruses into the host cells. Recently, Venkata et al crystalized the transmembrane domain of E (ETM) and proposed that it can kick Ca2+ ions out of the endoplasmic reticulum–Golgi intermediate compartment (ERGIC) and resulting host cell inflammasome activation, and therefore, is a potential drug target. In this research, we took 3800 FDA approved and investigational drugs and targeted the E protein to obtain the drug-protein complexes using molecular docking. The top 10 complexes were selected based on the docking score and embedded in the ERGIC membrane to relax with unconstrained Molecular Dynamics simulation for investigating their interactions and dynamics. The top-scoring and most stably bound compounds are proposed as potential candidates for drug repurposing. |
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N00.00364: Solvent effects on photodissociation of nCl (n=1,2) loss from PdCl42- by DFT calculation Aiko Anzai, Yuzuru Kurosaki, Morihisa Saeki, Azusa Muraoka Recently, Saeki et al. succeeded in measuring the concentration of 107Pd by precipitating Pd from spent fuel of a nuclear power plant using the laser induced particle formation method. According to reaction formula, ????????????−+????????????????+????→??????+????????????+????++??????− , PdCl42- can be irradiated with a 266 nm UV laser to reduce Pd2+ in aqueous EtOH solution, which has a charge transfer absorption band in the UV region, and neutralize Pd2+ to Pd0 [1]. |
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N00.00365: Quantum simulation of molecules in solution Davide Castaldo, Stefano Corni, Alain Delgado Quantum chemical calculations on quantum computers have mostly focused on molecules in gas-phase. In this work we extend the Variational Quantum Eigensolver to the simulation of molecules in solution. |
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N00.00366: Characterization of the electronic structure of the CpMePtMe3 complex for the development of a new generation of hydrosilation catalysts for silicon polymers Patrick Landry, Peter J Bonitatibus Jr., K.V. Lakshmi Hydrosilation is a common reaction employed for silicon polymer product synthesis and specifically paper release coatings (1). Currently, the industrial process requires a high heat curing processes and higher than desired loading of precious metal catalyst. There have been recent reports on photoreactive platinum catalysts that allow for UV or even visible light curing (2). It has been demonstrated that cyclopentadienyl platinum complexes have a higher photochemical activity than the commonly used Pt catalyst, Pt(acac)2 (1). In this study, we use density functional theory (DFT), optical and nuclear magnetic resonance (NMR) spectroscopy to determine the electronic structure of CpMePtMe3 catalyst. We use experimentally determined absorption maxima, NMR chemical shifts, and molecular orbital structure in conjunction with the excited state energies, charge density distribution, and NMR chemical shifts calculated by DFT methods to characterize the catalytic, photophysical, and chemical properties of the CpMePtMe3 catalyst. The goal is to understand the electronic structure of CpMePtMe3 in order to design related molecules with improved catalytic performance. |
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N00.00367: Minimization of Laplacian-level orbital-free exchange-correlation functionals Tun Sheng Tan, Samuel B Trickey Several Laplacian-level orbital-free kinetic energy density functionals (KEDFs) such as PerdewConstantin (PC) [1] and Cancio-Red (CR) [2, 3] have been used to de-orbitalize meta-GGA exchange-correlation XC functionals to yield SCAN-L [4] and R2SCANL-L [5]. Those XC functionals yield rather accurate results in the context of the conventional Kohn-Sham equation. Here we investigate the use of such XC functionals together with modern KEDFs for self-consistent solution of the orbital-free Kohn-Sham equation. We find that direct minimization of these Laplacian-level kinetic functionals induces huge fluctuations in the potential and discuss ways to mitigate the problem. |
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N00.00368: Characterizing the Bonding Motifs in X−(HOCl) complexes (X = Cl, Br, I) in the Gas Phase with Cryogenic Ion Vibrational Spectroscopy: Hydrogen vs. Halogen Bonding Santino Stropoli, Thien Khuu, Natalia Karimova, Mark A Boyer, Coire Gavin-Hanner, Sayoni Mitra, Anton L Lachowicz, Nan Yang, Robert B Gerber, Anne B McCoy, Mark A Johnson
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N00.00369: Approaches for the Computation of Magnetic Exchange Couplings. Lucas Aebersold, Juan E Peralta Computation of magnetic exchange coupling constants is important for a growing number of areas, including spintronics, magnetic memory storage, and novel molecular magnet design. Determining exchange coupling for high-nuclearity complexes is not possible experimentally, and thus, computational methods are needed to make predictions. The most widely used methods compute the differences in total energies of a set of magnetic configurations, but the cost and difficulty increase steeply as more centers are added. Thus, it is desirable to have a black-box method that involves only a single state. Therein, we present new developments to compute magnetic exchange couplings based on approximate perturbation theory using a local rotation of the magnetization direction. This method can be implemented as an efficient post-processing tool, requiring only a single electronic structure calculation, and allowing automation to compute a large number of high-nuclearity complexes. We further compare results to related approximate Green's function method, which offers similar efficiency. |
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N00.00370: Non-contact molecular manipulation based on Reinforcement Learning Ramsauer Bernhard, Grant J Simpson, Leonhard Grill, Oliver T Hofmann At the world’s first race of nanocars at the CEMES-CNRS, in France, participants had to direct a nanocar across a specific “racetrack” [1]. In order to control their nanocar, they have to pull it via an STM-tip, without being in direct contact with the nanocar. |
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N00.00371: Electronic structure and NMR spectra of sodium clusters in sodium ion batteries Ayane Suzaki, Azusa Muraoka, Koichi Yamashita In recent years, due to the resource and cost issues of lithium in lithium-ion batteries (LIB), there has been growing interest in resource-rich sodium-ion batteries (NIB) with equivalent electrode potential. Among them, NIBs that use Na metal oxide as the positive electrode and hard carbon (HC) as the negative electrode has attracted attention in particular. To develop a NIB with high capacity, high efficiency, long life, and acceptable safety, it is essential to elucidate the state of the sodium ion and the mechanism of charge and discharge on the electrode. The states of sodium electrochemically inserted in HC samples have been experimentally reported using solid 23Na-NMR [1].In this study, we use Na clusters in HC pores as a model and discuss the dependence of chemical shift on Na clusters, the dependence of 3s orbitals on electron density, and the effect of relativistic effects on chemical shift. DFT calculations were performed at the B3LYP/6-31G(d) level using Gaussian 16 and at the B3LYP/6-31G(d) level using ADF.As a result, the value of the chemical shielding depends on the interaction between Na size of clusters from NMR analysis, and the effect of relativistic effects must be taken into account. |
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N00.00372: Operando transient ATR-FTIR for probing plasmonic photoelectrocatalysis mechanisms Aaron H Rose, Nathan R Neale, Jao van de Lagemaat Selectively producing desired products is a key challenge in the CO2 reduction reaction. Recent experimental observations have shown greatly enhanced selectivity of CO:H2 as well as increased yield of hydrocarbons, when exciting plasmons at the catalyst-electrolyte interface. The mechanisms are so far unclear. We describe an experimental apparatus to tease out the plasmon’s role. |
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N00.00373: Investigation of ionization energies and photoelectron cross-section of semiconductor quantum dots beyond the electric dipole approximation Arindam Chakraborty, Shivangi Nangia, Nicole Spanedda This work presents a computation investigation of the photoionization process in a series of PbS and CdS quantum dots without making the dipole approximation in the light-matter interaction Hamiltonian. Photoionization of quantum dots provides important information about the occupied energy levels and can provide insight into their electronic and photochemical properties. Typically light-matter interaction in quantum dots is treated using electric-dipole approximation. However, going beyond the dipole approximation becomes critical for understanding interactions with high-energy photons. In this work, we have combined the 2nd-order electron-propagator method with the stochastic enumeration technique to construct a stochastic self-energy operator. The ionization energies were obtained from the self-consistent solution of the resulting Dyson equation. The photoionization cross-section was calculated in a mixed Gaussian-plane wave basis and was calculated using the fully complex response kernel. The calculation was performed for a series of PbS and CdS quantum dots and the results for the ionization energies, pole-strengths, and the photoelectron spectra in the X-ray and XUV region for these systems will be presented. Comparisons between the complex-response kernel and the dipole-approximation results will be discussed. The results from this study show the importance of non-dipolar effects for understanding light-matter interaction in semiconductor quantum dots. |
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N00.00374: Studying the driving force of photoelectrochemical reactions on semiconductor electrodes under strong coupling conditions James C Howard, Mark D Steger, Bryon W Larson, Jeffrey L Blackburn, Andrew J Ferguson, Aaron H Rose Strong exciton-polariton coupling hybridizes semiconductor and photon modes, splitting the energy levels of the system (Rabi splitting) and thus modifying the photonic, electronic, and chemical properties of the semiconductor. While there have been many demonstrations of using strong coupling to tune optical properties, there is very limited work showing tuning of chemical reactions in liquid electrolyte. In this work we show progress towards moving strong coupling studies into an aqueous electrochemical environment. Our photoelectrode consists of a plasmonic thin film metal coated with a layer of semiconducting carbon nanotubes (CNTs). The plasmon is tuned to overlap with the ground state S11 exciton of the CNTs, leading to strong coupling. We measure charge transfer photocurrent as a function of potential for different redox species to test the hypothesis that the overpotential is reduced under strong coupling conditions. As an open-polariton cavity system, our technique offers a way to study conventional photoelectrochemistry under strong coupling conditions, potentially opening the door to photonic control of chemical reactions. |
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N00.00375: Synthesis of ZnO and SnO2 nanoparticles comparing two different sol-gel methods. Flavio Manuel N Maldonado, Maria Argelia Lopez Luna, Juan Armando Flores de la Torre, Maria Jose Moran Reyes, Karla Arely Rodriguez Magdaleno Metal oxides semiconductors (MOSs) are binary compounds formed by oxygen and metals (SnO2, CuO, ZnO, NiO, Co3O4, TiO2) which have physical-chemical properties and they have been studied because of its application versatility. Tin dioxide and Zinc oxide have been capturing attention in last years by precursor accessibility and inexpensive synthesis process, furthermore an ample assortment of applications. There are several synthesis methods, but this work is focused on Sol-Gel method since providing higher homogeneity, purity, and quality for products. Material properties might be varied by using different solvents and complexing agents. Due to aforementioned background, our interest is synthesis of ZnO and SnO2 by two sol-gel methods each. First for ZnO, precursor ZnC4H6O4 was dissolved with water, then Triton X-100 added, stirred 3 hours, ammonia was added, product was washed, dried and calcinated at 700 oC. By other hand, ZnC4H6O4 was dissolved with water, stirred at 80 oC, pH adjusted to 10, product was dried, washed, dried and calcinated at 550 oC. For SnO2, SnCl4*2H2O was precursor, dissolved with ethanol and pH adjusted to 4, product was washed, dried and calcined at 650 oC. Another way was dissolving SnCl4*2H2O with water, ammonia was added, filtered, washed and later dissolved with acetic acid and ethylen glycol was added, solution was stirred, a gel was obtained, It was dried and calcinated to 350 oC. Four obtained powders were characterized by Raman spectrometry and XRD. For ZnO with XRD both cases were defined as wurzite phase but when ZnC4H6O4 was dissolved with water Raman shift shows a higher intensity. For SnO2 with XRD both cases were defined as tin oxide tetragonal phase but when SnCl4*2H2O was dissolved with ethanol Raman shift shows a higher intensity. Zinc oxide and tin oxide that show higher intensity can be deposited over SiO2 substrates to be used for photocatalysis, bacterial inhibitors, photovoltaics, electronic and biomedical applications. |
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N00.00376: Ultrafast chemical bond studies by X-Ray Spectroscopy Ana Martinez Gutierrez, Antonio Picón, Solène Oberli, Jesús González-Vázquez Among the most prominent ultrafast advances are the new capabilities of the X-ray Free Electron Lasers (XFELs). XFELs produce attosecond/femtosecond X-ray pulses providing a way to study ultrafast electronic processes in matter induced by X-ray photons [1,2]. A second XFEL pulse can be used in order to track the X-ray induced dynamics through X-ray Photoelectron Spectroscopy (XPS). When a core electron is removed from an atom or molecule it turns out into a core-hole state. Those core-hole states decay via Auger transitions. Every inner-shell ionization process is followed by an excitation in the valence resulting in additional states called satellite states. These states are close in energy to the main core-hole state, and it is expected that they have a high contribution in the XPS at the ultrafast regime. Our group collaborates in projects with experimental XFELs groups, providing theoretical support and developing numerical tools to simulate the dynamics of molecular systems. In particular, we have developed a semi-classical model that combines nuclear propagation with XPS calculations. The main objective of using this model is to study the dynamics of the electron together with the motion of the nucleus in molecules under the effect of XFEL pulses. So far, we are getting fairly accurate results for the carbon monoxide molecule and we hope to be able to extend our model to larger and complex systems. |
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N00.00377: Controlling Amorphous Silica Surface Roughness. Nuong P Nguyen Amorphous silica (a-SiO2) surfaces have found application in heterogeneous catalysts by grafting metals on the active sites of the functionalized surfaces. From a molecular modeling perspective, one challenge has been the creation of a-SiO2 slab models with a wide range of surface functionalization and roughness. In this work, we present a method, based on Capillary Fluctuation Theory (CFT), to create and functionalize a-SiO2 surfaces of controlled surface roughness using the ReaxFF potential, which is a classical reactive force field that allows bond forming, breaking and charge equilibration without the high cost of quantum mechanics methods. Currently, the most common method for generation of a-SiO2 surfaces with ReaxFF involves a “melt-quench-cleave” protocol in which a-SiO2 is equilibrated a high temperature (above Tg) followed by quenching to room temperature and cleaving with a flat plane, a procedure that yields artificially flat surfaces. In this study, we modify this method to generate surfaces of controlled roughness, as measured by the mean-squared displacement (MSD) of the surface atom positions from a flat plane. In this work, we generate a sample set of 2-d grid meshes in Fourier space from the CFT distribution corresponding to a specific surface stiffness. Inverse Fourier transforms of each k-space mesh yields a set of real-space surface meshes of controlled mean-squared displacement. These real-space surface meshes are then used to cleave the quenched silica bulk samples to create silica surfaces of controlled roughness. We show that this procedure yields a linear relationship between the input surface stiffness and the MSD of the surface, consistent with CFT. To create rough functionalized surfaces, the slabs are then exposed to ReaxFF water to allow for autofunctionalization of the surface with silanol groups followed by structural characterization of the slabs. |
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N00.00378: Quantitatively Accurate Theory to Predict Adsorbed Configurations of Surfactants on Metal Surfaces Sumit Sharma, Xueying Ko We have developed a theoretical model to predict adsorbed configurations of surfactant molecules on metal surfaces. Coarse-grained simulations of adsorption of surfactants show that our theoretical model is quantitatively accurate in predicting adsorbed configurations. We show that depending on the relative interaction strengths of the polar group and the alkyl tails with the metal surface, the surfactant molecules either adsorb by lying parallel to the surface to form stripes or adsorb perpendicular to the surface to form a monolayer. In the case of monolayer formation, our theory predicts that adsorbed surfactant molecules will undergo an orientational transition. This orientational transition is observed in our simulations and have also been reported in experiments. |
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N00.00379: Include Nuclear Quantum Effects in Classical Molecular Dynamics Zehua Chen, Xi Xu, Yang Yang The accurate inclusion of nuclear quantum effects remains a big challenge for large-scale molecular simulations. We present an alternative formulation for the equations of motions of classical molecular dynamics with nuclear quantum effects included. With this new formulation, molecular dynamics simulations can be performed on an effective energy surface obtained from constrained energy minimization with assigned quantum nuclear expectation positions. We test the new molecular dynamics approach on the Morse oscillator and protonated water clusters and get significantly improved dynamical properties as compared to conventional molecular dynamics and ring-polymer molecular dynamics. |
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N00.00380: Structure property relations in (As2Se3)x(GeTe4)100-x glasses Shweta Chahal Bulk (As2Se3)x(GeTe4)100-x glasses have been prepared over the entire composition range 0 ≤ x ≤ 100. In this tie-line, the average coordination number (Zav) of all the glasses is 2.40 at which the constraints acting on the network and the number of degrees of freedom are balanced. Glass transition (Tg) and non-reversing heat flow (ΔHnr) determined from DSC and MDSC measurements exhibit interesting variations with composition. Based on these variations the structural network can be divided into three regions: (I) 0 ≤ x ≤ 20 (II) 25 ≤ x ≤ 45 and (III) 50 ≤ x ≤ 100. Both Tg and ΔHnr show a decreasing trend in the region I and remain invariant in region II. In region III, Tg and ΔHnr show an increasing trend. From the Raman measurements, we infer that the network in region I is dominated by the GeTe4/2 tetrahedral units. The addition of As2Se3 initially depolymerizes the network due to which a decrease in Tg is observed in region I. The region II is dominated by the AsTe3/2 pyramidal units and Te-Te chains. In this region, the network starts polymerizing and at the same time there is a decrease in the mean bond energy. These two factors compete with each other and hence both Tg and ΔHnr remain invariant. The region III is rich with As2Se3 and the structural network is dominated by AsSe3/2 structural units. Both network connectivity and the mean bond energy go hand in hand in this region and there is an increase in the Tg and ΔHnr. For 25 ≤ x ≤ 45, ΔHnr almost vanishes indicating non aging of the glasses in region II. This study underlines the effects of chemical composition and the mean bond energy variations in a critically coordinated covalent network. |
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N00.00381: Dynamics of mixed quantum-classical wavefunctions Cesare Tronci Despite the widespread use of mixed quantum-classical (QC) methods in nonadiabatic dynamics, the formulation of a consistent QC coupling model continues to pose several challenges. The most accredited model, the QC Liouville equation, fails to recover Heisenberg's uncertainty principle and other proposals suffer from similar drawbacks. |
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N00.00382: Comparison between adsorption properties of pristine FePc and F16FePc on Rh(111) surface: DFT study Abdelkader Kara, mohamed el hafidi, meysoun jabrane, Moulay Youssef Elhafidi In this work, we compare the adsorption properties of FePc and F16FePc on Rh(111) in order to study the effect of fluorination on electronic properties of FePc molecule using density of functional theory calculations and taking into consideration the van der Waals interaction, optB88 functional specifically. The results show a symmetry reduction of the fourfold (C4) molecules due to the deformation along [1i0] axis in both molecules when deposited on Rh(111) surface. In addition, we noticed that the charge transfer, which has substrate – molecule direction, doubles when adsorbing F16FePc on Rh(111). This leads to the possibility to tune the charge transfer coming from Rh substrate for capacitor like applications. |
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N00.00383: DFT simulation of polymer(s) on graphene: Polymer conformation and adhesion energy considerations Jared K Averitt, Sajedeh Pourianejad, Olubunmi Ayodele, Tetyana Ignatova Many technological applications of graphene and graphene device fabrication often involve a polymer assisted transfer technique. Despite the simplicity and robustness of this process, graphene properties could be modulated by remaining polymer residues on graphene's surface. Many efforts have been made to address the polymer contamination problem by proper choice of polymer when interaction with graphene is reduced but still enough to use it as a sacrificial layer. Here, the role of polymer conformation and the surface energy of two polymers on graphene was determined by using DFT simulations. A quantitative analysis of the adhesion ability of a dimer of polymethyl methacrylate and angelica lactone dimer is performed by a comparison of their respective binding energies and adhesion energy per unit area to graphene. This area corrected binding energy allows the direct comparison of simulated results to experimental values of adhesion energy defined from contact angle measurements. |
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N00.00384: A comparative study of algorithms to find information entropy in equilibrium and non-equilibrium systems. Jerome P Delhommelle, Caroline Desgranges, Bappa Ghosh The second law of thermodynamics establishes the concept of entropy as an observable physical quantity. However, while the use of the statistical-mechanical definition of entropy is common for equilibrium systems, there is no well-established expression for non-equilibrium systems. In order to address this challenge, we look into a generalized definition of entropy from an information theory perspective. A few recent studies [1-2] have indicated the possibility of quantifying the information density and applying it to simple systems to understand them qualitatively as well as quantitatively. |
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N00.00385: Crafting Hydrogen Bond Networks for Ultrafast Proton Conduction in Confined Imidazole Systems Austin J Conte, Joshua Sangoro Proton conducting materials are of extreme interest to chemists, engineers, and physicists alike. Imidazole, a five-membered aromatic heterocycle with non-adjacent nitrogen atoms, is one of these potential proton conducting materials. |
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N00.00386: Machine Learned Entropy for Phase Transitions in Aromatic Compounds Jerome P Delhommelle, Nazim A Belabbaci, Caroline Desgranges Aromatic compounds are involved in many chemical processes, for instance, as solvents or combustion products, and have been increasingly used in organic photovoltaics [1]. Here we develop a machine learning (ML) model for entropy on the example of benzene, anthracene, phenanthrene and coronene. To this end, we generate a dataset for the training of the ML model by carrying out molecular dynamics simulations of the condensed phases for each compound. Building on results from prior work [2], we use all-toms force fields to model these molecules, and carry out an extensive sampling of the parameter (temperature, density) space to generate the dataset. The dataset is then used to train and validate a ML model for the rapid determination of entropy, and the exploration of phase transitions processes. |
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N00.00387: Gaussian process regression acceleration of calculations for determining the mechanism and rate of atomic rearrangements Hannes Jonsson Calculations of minimum energy paths and searches for saddle points on energy surfaces to characterize the mechanism of atomic rearrangements and estimate their rate can be accelerated using machine learning based on Gaussian process regresssion by reducing the number of energy and atomic force evaluations needed to reach convergence. While standard squared exponential covariance function can give good performance in some cases [1], problems can arise when configurations with large forces due to short distance between atoms are included in the data set. A greatly improved performance is obtained by using a non-stationary covariance function based on inverse distances between pairs of atoms [2]. Calculations using the nudged elastic band method for finding minimum energy paths and minimum mode following method for finding first order saddle points [3] are presented for various chemical reactions and structural transitions on solid surfaces. The use of Gaussian process regression can reduce the number of energy and force evaluations by an order of magnitude. |
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N00.00388: Abstract Withdrawn |
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