Session L60: Poster Session II

Effect of Hydroxyl Mobility on the Cure Kinetics of Diglycidyl Ether of Bisphenol A (DGEBA) Epoxy in the Presence of a Tertiary Amine

Previous work on curing a DGEBA epoxy with diethanolamine (DEA) has highlighted the complexity of the reaction. This involves a rapid secondary amine, adduct forming reaction followed by a slower anionic polymerization, crosslinking reaction. This second reaction is activated by the tertiary amine created in the adduct and is strongly influenced by the alcohol groups in the DEA. In the present study, dibutylamine (DBA) and octanol were employed instead of DEA. The octanol hydroxyls are more mobile than the DEA hydroxyls. The epoxide to amine ratio was kept constant while the hydroxyl concentration was varied by changing the amount of octanol added. A non-reactive alkane was used to control the reactive group concentrations in both the DEA and DBA mixtures. Isothermal cures are performed on an air cooled thermal activity monitor (TAMAir) for varying DBA/Octanol/alkane ratios and temperatures. Distinctive kinetic signatures are found for the different reactive mixtures.

Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc. for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.   

Mean free volume and self-diffusion coefficient of short polymer chains: Computer simulations and statistical mechanical theory

We report a comprehensive investigation on computing thermodynamics and diffusion coefficients of short linear and ring polymer chains using statistical mechanical theories and molecular dynamics (MD) simulations. The polymer chain lengths of five and ten are taken into account. We first compute the location of fluid phase envelope using the equilibrium MD simulations. Then the diffusion coefficients are computed via two different methods: 1-computing the mean squared displacement using MD simulation and 2- free volume theory method. We utilize the Generic van der Waals theory to compute the mean free volume and apply the results in the modified Cohen-Turnbull theory to obtain the diffusion constant and compare the results to the MD simulation outcomes. The virial minimization method is used to compute the effective site diameters and the results are applied as the repulsion-attraction splitting distance of the interaction potentials within the theory. We show that the logarithm of the mean free volume versus density is almost linear at densities above the critical point independent of the chain length. We analyzed the self diffusion coefficient results of the theory and computer simulations in detail.
  

Effect of Architecture on the Phase Behavior of PS-b-PLA Block Copolymer

Block copolymers (BCPs) are widely used in materials science due to their unique ability to self-assemble into various nanostructures. Recent advances in BCPs have focused on the development of new systems that can overcome the size limitation of traditional BCPs. Such efforts have been demonstrated with design and synthesis of new type of BCPs having high interaction parameter (χ). Although many previous studies have been mainly focused on linear BCPs, it was also suggested that nonlinear architecture such as star BCPs can further promote the phase segregation. Herein we synthesized well-defined miktoarm PS-b-PLA BCPs to compare the segregation behavior with linear PS-b-PLA BCPs having similar molecular weights and volume fraction. First, polylactide (PLA) was grown from our choice of core and then polystyrene (PS) was clicked onto the core-PLA star polymer, resulting in miktoarm PS-b-PLA BCPs. As a control sample, linear PS-b-PLA BCPs of similar volumetric ratio were synthesized. The samples were thermally annealed in thin film and bulk state, and characterized with SEM, TEM, and SAXS. The phase behaviors such as order-disorder transition and morphology was also compared with SCFT simulation.   

Microporosity in ladder polymers from coarse-grained molecular simulations

Solution-processable ladder polymer with stiff backbone is ideal for preparing membranes with intrinsic microporosity used for gas separation and sensing. Understanding the molecular factors affecting the pore size distribution is crucial for engineering the mechanical strength and selective permeability for specific gases. The trial-and-error approach is expensive and time-consuming, and is not feasible for screening a large number of molecular architectures. We developed a bead-stick model that properly captures the structure and backbone stiffness of ladder polymers and performed coarse-grained MD simulations to generate equilibrated configurations. The pore size distribution are obtained by Voronoi tessellation and by imposing a mesh and introducing distance criteria to tessellate the space. The histograms and their variations with molecular architecture and molecular weights are reported and compared to indirect evidence obtained from experimental gas separation studies.   

Influence of hydroxyl concentration on the cure kinetics of diglycidyl ether of bisphenol A (DGEBA) epoxy in the presence of a tertiary amine

DGEBA epoxy is reacted with hardener mixtures of diethanolamine (DEA, HN(CH₂CH₂OH)₂) and dibutylamine (DBA, HN(CH₂CH₂CH₂CH₃)₂). Both DEA and DBA have a single secondary amine that reacts rapidly with epoxide forming a non-crosslinked adduct at 70°C. The subsequent crosslinking reaction is slower, taking 24 hrs. at 70°C to near completion for the standard DGEBA/DEA mix. The mixtures studied keep the mole ratio of epoxide to amine constant at 4.8:1 and vary the epoxide to hydroxyl ratio from 2.4:1 for a hardener of pure DEA to nearly 1:0 for pure DBA. Proton transfer is expected to play a major role in the reaction at high hydroxyl concentrations (high DEA/DBA ratio). It is also expected that a high OH concentration will result in a high reaction rate while low OH concentration (low DEA/DBA ratio) will result in a negligible reaction rate. We show that these expectations are overly simplistic. At 70°C, the maximum reaction rate occurs at 25% DBA indicating an optimal hydroxyl concentration.   

Interaction between highly compressed brushes of hard-sphere chains

The behavior of compressed polymer brushes composed of hard-sphere chains are investiaged with the excluded volume interactions among the chain segments treated by using a classical density functional theory (DFT). For the brush-brush compressing systems, an obvious interpenetration zone can be observed. The extent of the interpenetration depends strongly on the grafting density. Furthermore, the repulsive force between the brush and wall or between the two brushes has been obtained as a function of the compression distance. Compared to the prediction of the analytic self-consistent field theory, such force increases more rapidly in the brush-wall compression with high polymer grafting densities or at higher compressions.   

Quadratic Electro-optic Measurements in Metal Nanoparticles within Glass: Effect of Particle-size and comparison with Iodine-doped Nonconjugated Conductive Polymers

Quadratic electro-optic effect in gold nanoparticles within glass has been measured for three different particle sizes, using field-induced birefringence at 633 nm wavelength. The measurements have been made using 4-cm long samples, with an ac field applied at 4 kHz, and with cross-polarized configuration. A quadratic dependence of the modulation on the applied field has been observed. Significant increases in the Kerr coefficient were observed for smaller particle sizes. Electroabsorption has also been measured. More detailed measurements are in progress. The particle-size dependence is consistent with the magnitudes of the exceptionally large Kerr coefficients reported for subnanometer-size metallic quantum dots created upon doping and charge-transfer involving the isolated double-bonds in nonconjugated conductive polymers.   

Prospects and Design Rules for Singlet Fission-Enhanced Visibly Transparent Organic Solar Cells

The quantum mechanical mechanism of singlet fission (SF), in which a singlet exciton rapidly decays to form two low-energy triplet states, has previously been demonstrated as a route to external quantum efficiencies above 100% in organic solar cells (OSCs). Unfortunately, this gain in short-circuit current is offset by a reduction in open-circuit voltage to accommodate efficient triplet dissociation at low-lying charge transfer states. Here, we implement a simple numerical model to assess the potential net effect of SF on the power conversion efficiency (PCE) of OSCs. In particular, we consider the application of SF to semi-transparent OSCs, which are of interest for use in solar windows and necessarily operate at low voltages to allow for visible light transmission. Under the assumptions of our model, the maximum PCE of a conventional (non-transparent) OSC exceeds that of the SF cell by > 1%. The SF cell competes more favorably with semi-transparent OSCs, suggesting that SF is best suited for devices in which power output is primarily limited by current generation, such as tandem solar cells.   

Design of Ethanol/Water-Processable Conjugated Polymers and Fullerene Derivatives for Eco-Friendly Processed Organic Transistors and Solar Cells

It is very urgent to develop new electroactive materials that can be processed with eco-friendly solvents, because aromatic solvents is a big obstacle to transferring lab-scale to industry-scale production. In this work, we design highly-crystalline conjugated polymers and fullerene derivatives that can be processed with ethanol/water solvents for producing organic field effect transistors (OFETs) and organic solar cells (OSCs). Oligoethylene glycol (OEG)-based polar non-ionic side chains were attached to high-performing p-type conjugated polymers and n-type fullerene cores to provide solubility in ethanol/water mixtures. The introduction of flexible OEG chains induced lower T_m and T_c of conjugated polymer, which can improve processability of polymer into crystalline thin film. High-performance eco-OFETs and -OSCs yielding a hole mobility of 2.3 × 10^-2 cm² V^-1 s^-1 and a power conversion efficiency of 1.4% were demonstrated using ethanol/water solvent, which surprisingly outperformed the devices processed using toxic processing solvent.   

Effects of Enhanced Spin Delocalization in Blatter’s Radical

Polymers and small molecules that bear open-shell, stable organic radical groups have proven to be quite beneficial in myriad organic electronic materials and device applications (e.g., magnetic systems and energy storage and energy conversion devices). The highly tunable optoelectronic properties of these materials, the potential for low-temperature processing, and the compatibility of these organic materials with flexible, mechanically-robust substrates distinguish radical polymers from their oft-used inorganic counterparts. However, because of their bourgeoning nature, many questions regarding the physics of their solid-state charge transfer mechanism still exist. To answer said questions we employed the 1,3-diphenyl-1,4-dihydro-1,2,4-triazin-4-yl radical (i.e., Blatter’s radical), which is a stable conjugated radical, in order to evaluate the charge transport mechanics in radical small molecules and macromolecules. Moreover, we characterized the impact of enhanced spin delocalization, facilitated through extended conjugation of the molecular architecture, in relation to charge transport physics. These results provide experimental insights into the mechanism of solid-state electrical conduction in radical-containing small molecules and polymers.
  

Diffusion-ordered NMR spectroscopy of conjugated polymers: a complementary method for determining polymer size

Size exclusion chromatography (SEC), the standard way to characterize the molecular weight (MW) and distribution of polymers, is less suited for characterizing conjugated polymers that strongly absorb at the detection wavelengths. We demonstrate diffusion-ordered NMR spectroscopy (DOSY) as a complementary method for characterizing the size and size distribution of conjugated polymers. Starting with four distinct batches of poly(3-hexyl thiophene), or P3HT, whose MW distributions had been fully characterized by a combination of SEC and NMR end-group analysis, we establish a power-law relationship between the weight-average MW and the diffusion coefficient measured through DOSY. Quantification of the distribution of diffusion coefficients with the power-law relationship yields MW distributions that are qualitatively similar to those extracted from SEC measurements. We extended this approach to characterizing poly[4-(4,4-dihexadecyl-4H- cyclopenta[1,2-b:5,4-b′]dithiophen-2-yl)-alt-[1,2,5]thiadiazolo- [3,4-c]pyridine], or PCDTPT, with absorption in the visible that precludes SEC characterization of its MW. Applying the same power law on the diffusion coefficients obtained by DOSY measurements has yielded P3HT-equivalent MW and MW distribution of PCDTPT.   

Comparative Study of Thermal Stability and Performance of All-Polymer, Fullerene−Polymer, and Ternary Blend Solar Cells Based on the Same Polymer Donor

We compared the thermal and morphological stability of all-polymer solar cells (all-PSCs) and fullerene-based PSCs (fullerene-PSCs) having the same polymer donor with comparable power conversion efficiencies (PCEs) of >6%. We observed that the performance of the fullerene-PSCs completely deteriorated after annealing for 5 h at 150 °C, whereas that of the all-PSCs remained stable even after annealing for 50 h at 150 °C. Pronounced phase separation was observed in the fullerene-PSCs at two different length scales. In stark contrast, almost no morphological changes in the all-PSCs were observed, likely due to the low diffusion kinetics of the polymer acceptors. Next, we evaluated the thermal stability of ternary blends composed of PBDTTTPD:polymer acceptor:fullerene acceptor with different fullerene contents to understand the role of polymer acceptor on the morphological changes. When fullerene contents <30 wt % of the acceptor mixture, fullerene was well-dispersed in the amorphous portion of the donor/acceptor polymer blend under thermal stress and led to thermally stable devices with a higher PCE (7.12%) than both all-PSCs and fullerene-PSCs.   

Vapor Doped Spiro-OMeTAD as a Model System for Disordered Charge Transport

Amorphous small molecule semiconductor films are widely used in organic light emitting displays and have promising applications in solar cells and thermoelectric devices. Dopants can be used to increase the electrical conductivity of molecular films. Understanding how the resulting conductivity depends on the concentration of dopants is complex because they simultaneously add carriers to and alter the structure of the host film.

To study charge transport in amorphous small molecule films, we electrically doped spiro-OMeTAD films with F₄TCNQ vapor, increasing their conductivity to 0.02 S/cm. Spiro-OMeTAD provides a unique model system for doping because UV-Vis spectra show the presence of two charge states of the molecule, spiro-OMeTAD⁺ and spiro-OMeTAD²⁺. Structural measurements showed that the dopant molecules were dispersed throughout the film and did not aggregate. To examine the transport mechanism at low and high doping levels, we measured the temperature-dependent conductivity and Seebeck coefficient of the films at varying dopant concentrations. The relationship between the thermopower and conductivity in this amorphous system will be discussed in relation to recent results on ordered polymers and molecular materials.   

Controlling the Mode of Operation in Polymeric Thermoelectrics Through Polymeric Ionic Liquid-gated Transistors

Studying the thermoelectric properties of organic semiconductors is an emerging way to understand interplay between ions and electrons, as it provides an independent measurement technique to ascertain transport properties. Conventional vapor- and solution-phase doping increase electrical conductivity (σ) by increasing carrier concentration (n), but morphological changes created by dopant infiltration complicates the interpretation of results. We have utilized a field-effect transistor geometry to control ion infiltration in a p-type semiconducting polymer via gating. Polymeric Ionic Liquids (PILs) are high-capacitance polymers containing tethered ionic liquid-like moieties. To study the effect of dopant infiltration on charge transport in the high carrier concentration regime, we employed a PIL as the gate dielectric, where the degree of infiltration is tuned by tethering either the anion or cation in the PIL. The transistor geometry allows for n, thermopower (S), and σ to be determined experimentally, offering a straightforward method to explore thermoelectric transport. Our studies demonstrate that gating with PILs offers a novel strategy to deconvolute charge transport and microstructure and guide development in these systems.   

Unexpected Effect of Small Nanoparticles: New Horizon for Polymer Nanocomposites

The addition of nanoscale fillers with strong attraction to polymers causes significant changes to the polymers’ dynamics and mechanical properties. The challenge of polymer nanocomposite (PNC) research is to understand the critical microscopic parameters (e.g. chain rigidity, molecular weight, nanoparticle geometry) that control the emergent macroscopic properties of PNCs. In this work, we investigated the effects of adding very small (~1.8nm) POSS nanoparticles to a polymer (P2VP) melt. We found unexpectedly large increases in Tg (~35K) and fragility for the POSS-PNCs compared to PNCs with conventional 10-50nm filler. Further, the POSS-PNCs had unexpectedly small thermodynamic and viscoelastic changes from the neat polymer. This potential for easy processing overcomes a major challenge for polymer nanocomposites’ use in practical applications. Combining these results with theoretical calculations, we ascribe these unusual behaviors to two unique properties of PNCs with small nanoparticles: (i) fast mobility of small nanoparticles, and (ii) relatively short chain – nanoparticle desorption time. These features that are not accessible in conventional PNCs provide a new frontier for property enhancement in polymer composite materials.
  

Stepwise Crystallization Kinetics of poly (ethylene terephthalate) Ultrathin Film studied by Fast Scanning Calorimetry

Under confinement, unique features of crystallization arise substantial investigations, among which the slowing down and accelerating crystallization are both reported. In order to characterize the crystallization kinetics of thin films of poly (ethylene terephthalate) (PET). We utilize fast scanning calorimetry (Flash DSC1™) to study the isothermal crystallization in a wide range of film thicknesses and temperatures. Nucleation at the free surface, which account for the stepwise crystallization behavior, dominate the overall crystallization at large undercooling. This is due to the fast transformation of disordered chains into crystals caused by the highly mobile surface layer. When crystallized at low undercooling, heterogeneous nucleation at the interface enhanced crystallization. Additional heterogeneities, which are introduced by the interface, considerably increase the amount of supercritical nuclei. These findings can be interpreted in terms of the undercooling vs half-crystallization time by a phase diagram, by which one can manipulate the crystallization under confinement through controlling the interface or temperature.   

The Role of Surface Diffusion in Stable Glass Formation

Physical vapor deposition (PVD) produces glasses with exceptional stability and unique properties (higher density, anisotropy etc.). The current understanding is that the free surface, with its enhanced dynamics compared to the bulk, allows access to these near-equilibrium configurations during PVD. To this end, surface diffusion measurements on molecular glasses have been performed and showed it to be enhanced and decoupled from bulk relaxation dynamics. In this study, we measure the surface diffusion of three structurally very similar organic molecular glasses below their glass transition temperature (T_g) using tobacco mosaic virus as a probe of their surface evolution. Vapor deposited glasses of these compounds are found to have very similar increase in density when deposited at 0.85Tg. However, in spite of their ability to form stable glasses,only one of these molecules shows enhanced surface diffusion below T_g, while others are found to have no surface diffusion within our ability to measure even at temperatures close to T_g (T_g - 4K). Our results suggest that lateral surface diffusion may not be a good indicator of the enhanced relaxation dynamics required to produce stable glasses and other types of measurements may be necessary.   

Laves Phases in Block Copolymer-Homopolymer Blends

Recently, new Frank-Kasper phases, e.g. C14 and C15 Laves phases, have been observed in specific conformation-asymmetric AB diblock copolymers via a special thermal process by expeiments. Surprisingly, the two Laves phases have been predicted to be stable in binary blends of conformtion-symmetric AB diblock copolymers by theory. In this presentation, we investigate the self-assembly of binary blends of conformtion-asymmetric AB-type block copolymer and A homopolymer, where the minority A-component forms the spherical domains, using the self-consistent field theory (SCFT). With three typical block copolymer systems, forming face-centered cubic, sigma and A15 phases, respectively, the addition of A-homopolymer leads to the formation of stable C14 and C15 phases. Our SCFT calculations reveals that the C14 and C15 phases are stabilized by the unequal contents of A-homopolymer among spherical domains that facilitate the formation of highly nonuniform sizes of domains. This work provides another simple facile way to fabricate the novel Frank-Kasper phases.   

From Melts of Graft Polymers to Supersoft and Hyperelastic Materials

We use scaling analysis and molecular dynamics simulations to study relationship between mechanical properties of graft polymer networks and their molecular architecture. The elastic response of such networks can be described by replacing the graft polymer strands with worm-like strands characterized by the effective Kuhn length b_k. Simulations of graft polymer melts show that b_k of graft polymers is controlled by the degree of polymerization of side chains n_sc and their grafting density 1/n_g to the backbone. These results are used to obtain the structural shear modulus G and strands extension ratio β in terms of the network architectural triplet [n_sc, n_g, n_x] (n_x is the degree of polymerization of the backbone between crosslinks). Simulations show that G of graft polymer networks could decrease with decreasing β. This behavior for linear chain networks known as a “golden rule” reflects that softer materials are more deformable, G∝β. However, graft polymer networks could break this rule showing an increase of G with decreasing β such as G∝β^-2. This can be achieved by changing n_g and keeping n_x and n_sc constant. This peculiar mechanical response of graft polymer networks agrees with experimental studies of PDMS graft polymer elastomers.   

Effect of Background Ions on the Morphological and Electrochemical Properties of Polyampholyte Hydrogels

Polyampholyte (PAm) hydrogels are a class of electroneutral physical gels, formed by inter and intra chain ionic cross-linking between counter charged functional groups, present on the polymer chains. Recently, PAm hydrogels have gained intensive attention because of their typical properties including high toughness, self healing and self adjustable adhesion. We have previously shown that PAm hydrogels show potential as gel electrolyte in electrochemical energy storage devices; in addition to its stretchable and self-healing properties, they displayed high ionic conductivity at low temperatures due to inhibited ice formation. When dialyzed in different electrolyte solutions, PAm hydrogels undergo structural changes due to the charge screening effect of foreign ionic species. Electrochemical properties were consequently affected. In this work, we have carried out a systematic study to understand the effect background ionic species- of varying charge, valency and size, on the chain conformation of PAm hydrogels. A combination of mechanical, morphological and electrochemical studies has revealed structure-property relations in the context of energy storage devices that can operate over a wide range of temperatures.   

Effect of dielectric inhomogeneity in aggregation of multiple charged Nanoparticles and Polyelectrolyte

We study the structural characteristics in a system of charged nanoparticles in an oppositely charged polyelectrolyte solution, and the effect of their low dielectric constant than the solvent. We have used a hybrid computational method of combined single chain in mean field theory and the solution of general Poisson-Boltzmann equation. Charged particles experience increased repulsion in case of inhomogeneous dielectric constant leading to less aggregation in the system. In the presence of oppositely charged polymers with low dielectric constant, the behavior becomes more complex and interesting due to the interplay of electrostatic and depletion effects. We study the effect of charge of the particle and polymers, volume fraction of particle and concentration of polymer on the aggregation properties in terms of radial distribution function and cluster distribution function.   

Structural Evolution and Phase Behaviors of Electrostatic Macromolecular Assemblies

Macromolecular assemblies that are driven by electrostatic interaction create an avenue for a broad range of biomedical applications including therapeutic delivery and tissue engineering. These aqueous solution micellar assemblies are able to sequester hydrophilic nucleic acid macromolecules and release them upon a stimulus applied. Further, increasing the polymer concentration above micelle overlap concentration leads to unique hierarchical structures, e.g. body-centered cubic, and hexagonally packed cylinders morphologies, that can be strategically exploited as transient hydrogel networks with tunable topology, rheology, and electrical conductivity. The structural evolution and phase transition of micellar electrostatic assemblies, however, remains elusive. Herein, we systematically employ small-angle X-ray scattering and neutron scattering to investigate the structural evolution of micellar electrostatic assemblies, and the large-scale phase behaviors of concentrated micelles evolving into hierarchical hydrogels. We compare the kinetics and ordering processes between micelles composed of carefully synthesized homo-, di-, and tri-block charged polymers. These findings will assist the rational design of electrostatic macromolecular assemblies for future applications.   

Thermal and Mechanical Responded PLGA Based Electrospun Fibers as Implants

With highly stretched chain configuration, slight functionalization of electrospun membranes could end up with specific responses, including ECM simulation, controlled drug release, shape conformation, selective cellular biology or bioactivity. Detailed investigation on PLGA fibrous membrane has been carried out for years in our group, and the entropy relaxation related to polymer component, molecular weight, blending homogeneity and manufacture parameter showed to be the essential reason on the change of sterization stability, aging process, swelling, biocompatibility and degradation properties. Through blending with amphiphilic polymer with lower Tg, lots of thermal and mechanical response behavior of the PLGA fibrous membrane could be induced and controlled. The kinetic process caused by the combination of several entropy relaxation modes became complicated while related temperature is near Tg. Longer wave length relaxation modes did not reach their final states because they became much more slower, and resulted in dispersed stress relaxation. These unique advantages benefit its biomedical application however create new obstacle in industrialization. The insight of understanding the entropy relaxation from a different angle could broaden its application.   

Response of Ionic co Polymers to Tuning Solution Dielectrics

Ionic cluster formation often drives assembly of ionizable co-polymers in solutions, where response to any stimuli is a balance of the behavior polymers with significantly different characteristics. Here, small angle neutron scattering (SANS) was used to follow the response of assemblies of a symmetric pentablock copolymer, that consists of a randomly sulfonated polystyrene (sPS) centers with sulfonation fractions varied from neutral to ionomer to the polyelectrolyte regime. This block is symmetrically tethered to polyethylene-r-propylene block, terminated by poly (t-butyl styrene). SANS measurements were carried out as the solvent polarity was manipulated through addition of propanol to cyclohexane, increasing the dielectric constant. We find that regardless of sulfonation fraction, the propanol penetrates and swells the ionic core, decreasing the cohesiveness of the ionic clusters. The polymers however remain assembled as the corona collapses with increasing propanol, but assemblies change their shape from spherical to elliptical. The assemblies that were initially formed by segregation of the ionic blocks are now held together by the collapse of the hydrophobic blocks.   

Nanoparticle dynamics near the volume-phase transition temperature of N-isopropylacrylamide gels

Nanoparticle (NP) probes were used to characterize the local structure of N-isopropylacrylamide (NIPAAm), a thermoresponsive hydrogel, using single particle tracking (SPT). Swelling ratio, and thus gel network confinement, was varied by tuning polymer and crosslinker concentration. Based on the swelling ratio, the volume-phase transition (VPT) was determined to be near 32 °C. In general, NPs were found to be localized by two barriers. A primary barrier with a localization region of approximately 100 nm was attributed to attractive interactions between the NIPAAm strands and the polyethylene glycol (PEG) brush grafted to the NP. As the polymer and crosslinker concentration were reduced, or temperature approached the VPT, NPs were able to escape the primary barrier and explore a larger secondary localization region (150-300 nm), ascribed to the confinement of the gel network. As temperature was raised above the VPT, however, the increase in confinement due to the collapse of the gel dominated, causing NPs to become localized to a single cage despite the higher temperature. This study of NP dynamics provides insight into controlling the release and loading of drugs in responsive hydrogel systems.   

Exploring Photo-Alignment of Liquid Crystals by Guest-Host Interactions: Toward Bulk-Mediated Photo-Alignment of Liquid Crystal Elastomers

Liquid crystal elastomers (LCEs) combine rubber elasticity with liquid crystal (LC) order. It is well-known that elastomers in which the LC constituents are aligned can experience significant reversible shape changes due to order-disorder transitions driven by stimuli (e.g. thermal energy or light). Well controlled LC alignment is a critical requirement for harnessing the desired response. Typically, alignment is achieved by command surfaces within a polymerization cell or by a two-step mechanical stretching and photo crosslinking technique. However, the mechanisms required for simultaneous alignment and polymerization of LCEs without enclosed cells or mechanical stretching, which would facilitate fabrication of complex 2D and 3D structures, are not well understood. In this work we investigate the alignment of low molecular weight liquid crystals by guest-host interactions with poly(vinyl cinnamate) dopants that have been cross-linked with polarized uv light. The LCs examined are similar in structure to the common LCE monomer RM257. We investigate and report on conditions required for in situ, bulk mediated alignment in preparation for simultaneous alignment and polymerization of thiol-acrylate based LCEs. Challenges and future steps will be discussed.   

Tuning dynamics of moisture responsive wrinkling surfaces

The wrinkle dynamics (such as reversibility and stability) of human skin are affected by the external stimuli, as well as the skin’s structure and mechanical properties. Inspired by these tunable responses, three types of moistureresponsive wrinkle dynamics are achieved, for the first time, through a single film–substrate system. These dynamics include: (1) completely reversible wrinkles formation; (2) irreversible wrinkles formation I: the initially formed wrinkles can be permanently erased and never reappear; and (3) irreversible wrinkles formation II: once the wrinkles form, they can no longer be erased. The key to success is to control the stiffness and thickness ratios of the film and the substrate, and tailor the crosslink degree/gradient of the film to allow for moisture-dependent changes of modulus and swelling degree. These unique responsive dynamics motivate the invention of a series of optical devices triggered by moisture, including anticounterfeit tabs, encryption devices, water indicators, light diffusors, and antiglare films. This study also paves the road for further understanding of the skin wrinkling dynamics and manipulation.   

Thin Films of Block Copolymer-Based Supramolecules with Feature Size Over 50 nm

Block copolymer-based supramolecular self-assembly offers a simple method to overcome issues with incommensurability, surface chemistry, and assembly kinetics to access nanostructures in thin films. Much work has been focused on creating nanostructures with periodicities between 10-50 nm. However, for some applications, including the interaction with visible light, larger periodicity features are necessary. Creating thin films with feature sizes larger than 100 nm, however, is challenging. Large MW nanocomposites have differing kinetic and thermodynamic considerations when compared to the low MW analogs. Thermodynamically, incorporation of particles does not have the same entropic penalty when the polymer chain length increases. Kinetically, the diffusions of nanoparticle and supramolecule may play a more critical role in determining the NP placement and NP packing within supramolecular microdomains. Here, we demonstrate that nanocomposites with controllable morphology can be created with a periodicity of up to ~100 nm. The size and loading of nanoparticles, as well as the solvent annealing condition, determines the final morphology as well as the periodicity, grain size, and packing of nanoparticles.
  

Photothermal heating as a strategy to align anisotropic metal nanoparticles within polymeric films

Thin polymer films containing aligned anisotropic metal nanoparticles are desirable for potential optical applications (e.g., polarizers and filters), as well as for fundamental research (e.g., micro-rheology). Experimentally, achieving alignment at dilute particle loading levels is challenging as reduced inter-particle coupling prevents self-organization or packing. Mechanical sample stretching (to several times its original length) or applications of a strong electric field during film casting are common approaches. However, both schemes result in polymeric systems that are fundamentally altered (with highly elongated chains) and thereby, limit the ability to probe the innate polymer dynamics. An alternative approach is to apply an electric field while simultaneously undergoing photothermal heating. In this case, application of light resonant with the surface plasmon of the nanoparticle results in localized heating, melting only the immediate surrounding polymer and enabling electric field driven reorientation. Because the environment within the small (< 1 μm) molten region is highly constrained and entangled, effects from fabrication on the polymer should be minimized.   

Multiscale characterization of polymer dynamics in carbon nanotube grafted fiber-reinforced polymer composites

Grafting carbon nanotubes (CNTs) onto microscale fiber surfaces has improved the mechanical, electrical and thermal properties of fiber-reinforced polymer composites. Using these multifunctional materials for commercial applications involves extensive understanding of their structure-property relationships. The current study attempts to understand the role of CNTs in affecting polymer dynamics and viscoelastic properties as a function of both time (10^-9 s to 10¹⁰ s) and length scale (nm to cm). Dynamic mechanical thermal analysis (DMTA) and elastic neutron scattering (ENS) experiments were conducted on plain epoxy, unidirectional glass fiber reinforced composite (FRP), and unidirectional glass fiber reinforced composite containing 1.35 mass % of multiwall CNTs (CNT-FRP). Master curves generated after time-temperature superposition (TTS) identify minor reinforcements in shear glassy modulus, reductions in the shear rubbery modulus and no major changes in the polymer glass transition temperature (T_g) due to CNT addition. The mean square displacement of the hydrogen atoms measured by ENS indicates that the polymer chain dynamics in the CNT-FRP is enhanced with respect to the FRP specimens near and above T_g.   

A Small Angle Scattering Study of Water-resistant All-Cellulose Nanocomposites

Cellulose nanofibers (CNF) are the basic structural elements of cellulosic materials; they show excellent mechanical properties due to their high crystallinity. Molecular cellulose solutions (MCS) with no apparent aggregation can be made using an ionic liquid and dimethyl sulfoxide (DMSO) binary solvent mixture. Solutions containing a minimum amount of ionic liquid can be made by maintaining a 3:1 molar ratio of ionic liquid to cellulose sugar units, with the remainder of the solvent mixture being DMSO. In this study, all-cellulose nanocomposites of CNF and regenerated cellulose from MSC have been fabricated by co-precipitation. CNF with average diameters of 2.5+/-0.5 nm and lengths of 300+/-100 nm were first dispersed in water, then transferred to DMSO by solvent exchange and subsequently mixed with MSC. Nanocomposites show higher water resistance compared to neat CNF films, similar to cellulose films regenerated from MSC. Atomic force microscopy shows even dispersion of CNF within the regenerated cellulose. Small angle neutron and x-ray scattering of these films show a prominent shoulder corresponding to a real-space size of 25 nm in the nanocomposites that is not present in films from neat CNF or MC. Mechanical properties of the nanocomposites will also be discussed.   

Hollow Polymer Microcapsule Embedded Transparent Film for Thermal Management

To safely accommodate global increases in population and per capita consumption, a significant need for immediate energy conservation has been emphasized. An effective way towards conserving energy is to improve the thermal insulation of building windows while maintaining a high visible transparency. To this end, in this poster, we describe a facile and scalable approach to manufacturing highly transparent, heat-insulating films. By incorporating hollow poly(methyl methacrylate) microcapsules into the transparent polymeric films, less thermally conductive air could be efficiently included into the matrix. Thus, the current approach can enhance the thermal barrier property of the films without a significant reduction in the optical transparency. The solid film possessing 30 wt% microcapsules, for example, exhibited a high visible light transmittance (~80%) and the thermal conductivity was reduced to 0.06 W/mK, corresponding to 46% of the capsule free film. To quantify and verify this result, theoretical models describing a heat transfer in hollow microsphere composite were used, which the model effort showed a good agreement with our experimental observations.   

Flexible h-BN Foam Sheets for Multifunctional Electronic Packaging Materials with Ultrahigh Thermostability

Miniaturization and integration of electronic devices has required for additional functions such as dissipation of emitting heat and thermal stability. However, phase or structural stability of existing electronic packaging materials is limited by viscoelastic behaviors of polymeric materials (i.e. low heat resistance and poor mechanical strength). Herein, we report a simple and efficient approach to prepare flexible and robust hexagonal boron nitride (h-BN) foam sheet, which exhibits low thermal interfacial resistance due to the formation of three-dimensional continuous networks at high h-BN filling fraction (up to ~80 wt.%). Furthermore, it shows a significant enhancement in thermal stability such as flammability and shrinkage at a high temperature. Combination of thermostability and mechanical strength based on the h-BN foam sheets provides novel opportunities for multifunctional thermal conductive materials in coating and films without severely compromising auxiliary characteristics such as mechanical strength and thermal stability.
  

Polymer Nanocomposite Inks for Smart Textiles in Wearable Bioelectronics

Wearable biosensors, which can monitor heart rate, wrist pulse, body temperature and sweat bio-information, provide unprecedented opportunities for personal portable devices with remote medicine practices. Printing technology is a promising method for fabricating wearable textiles since it allows arbitrary pattern designs with a simple process. However, the conductive ink printed atop of textile substrate is vulnerable to cracks and delamination under constant motion. Here, we developed a stretchable silver nano-ink which can permeate into the structure of commercialized polyurethane-based nano-textile. The stretchability of the polymer nanocomposite ink offers ability to conform to arbitrarily shaped objects. Adequate choice of solvent and additives enables deep permeation into the textile. The conductive fillers, serving as conductive bridges connected with silver flakes, allow stable connections during deformation. Finally, we fabricated a surface electromyogram device and a strain sensor are to demonstrate the nanocomposite ink’s potential to be used in wearable textiles for healthcare devices and smart garment.   

Filler mesh size from dynamic viscoelastic measurements and x-ray scattering

Nanoscale-filled elastomers display dramatically improved performance compared to unfilled elastomers. In addition to interfacial chemical affinity and specific surface area, the improvement in properties is intimately related to the structure of the nanofillers. At concentrations above the percolation threshold, filler properties are linked to an emergent structure that can be quantified on the simplest level by the filler network. The filler network displays a mesh-size, which is smaller than the filler aggregate size but larger than the primary particle diameter. Within these limits the mesh size scales with the filler concentration. The relationship between mesh size and concentration is linked to the details of the ramified filler aggregates in commercial elastomers. In this paper a model is proposed to link the dynamic response of filled elastomers and the filler mesh size as determined using X-ray scattering. The model is supported by the observed behavior. A predictive link between nanostructure and dynamic response of filled elastomers results.   

Nanoparticle motion and segmental mobility in polymer nanocomposites subjected to large shear

The effect of large deformation on mobility of nanoparticles and chain dynamics in attractive polymer nanocomposites were investigated using x-ray and neutron scattering techniques. Polymer segmental mobility, measured by QENS, reduced in presence of attractive, well-dispersed nanoparticles. After application of large deformation, the Rouse dynamics was further slowed down at high particle loadings (in strongly confined state) while no noticeable change was detected for light confinement. On a larger scale, the reptation tube diameter, measured by neutron spin echo, remained unaltered after shear, suggesting that the level of chain–chain entanglements was not significantly affected. The results suggest a shear induced de-bridging of nanoparticles via stronger adsorption of polymer on NPs with deformation. The changes at the nanoparticle-polymer interface also cause speeding up nanoparticles after shearing.   

Biomimetic Nanocoatings with Exceptional Mechanical, Barrier, and Flame Retardant Properties from Large Scale One-Step Co-assembly

Large-scale biomimetic organic/inorganic hybrid nanocoatings with a nacre-like microstructure were prepared via a facile co-assembly process. Different from conventional polymer nanocomposites, such nanocoatings contain a high concentration of nanosheets, which can be well aligned along the substrate surface. Moreover, the nanosheets and polymer matrix can be chemically co-crosslinked. As a result, the nanocoatings exhibit exceptional mechanical properties (high stiffness and strength), barrier properties (to both oxygen and water vapor), and flame retardancy, but meanwhile they are highly transparent (maintaining more than 85% of their original transmittance to visible light). The nanocoatings can be applied to various substrates and regular or irregular surfaces (e.g., films as well as foams). Because of their excellent performance and high versatility, such nanocoatings are expected to find widespread application.   

Multi-scale Simulations of Ion Transport in Polymeric Electrolytes

Optimizing ion transport properties in polymeric electrolytes is paramount to develop solid-state lithium-ion batteries for future electrical vehicles. To mitigate the material design process from a molecular structure and architecture perspective, we use a combination of theoretical analysis and multi-scale simulations incorporating atomistic and coarse-grained models to study the fundamentals of ion transport phenomena in polymeric systems. The configurations of PEO chains are analyzed in both melt state and concentrated LiTFSI/PEO solutions. The oxygen-oxygen correlations along the polymer backbone can be described by a single or double exponential function. We further develop a coarse-grained model based on the mapping of PEO macromolecules into ideal chains with an effective Kuhn length, in which ion hopping is captured by a dynamic bond formation/breaking scheme. This approach allows for bridging multiple time and length scales to investigate ion diffusion in polymeric systems with hierarchical molecular structures such as combs and bottlebrushes.
  

Local Dynamics and Transport Mechanisms in Polymerized Ionic Liquid Block-Copolymers

We present results from single-chain in mean field (SCMF) and atomistic molecular dynamics (MD) simulations of polymerized 1-butyl-3-vinylimidazolium-PF₆-co-polystyrene block-copolymer polymerized ionic liquids. We report equilibrium two-dimensional lamellar and one-dimensional cylindrical morphologies from SCMF, including electrostatic contributions to the free energy. Using reverse coarse-graining approaches, we overlay atomistic details onto these morphologies and extract diffusivities and relaxation dynamics using atomistic MD simulations. We report local structure, dynamics, and transport properties in the bulk and near the interface of each phase.   

Electrical Impedance of Single Ion-Conducting Polymer Networks

Ionic liquids (ILs) - low temperature molten salts composed only of ions- have been widely investigated as promising ion conductive materials for a variety of electrochemical applications. ILs, however, possess critical limitation due to the intrinsically low mechanical integrity of liquid materials. These drawbacks can be overcome by mixing them with macromolecules or directly polymerizing them, yielding ion-conducting solid or gel electrolytes. Such materials combine many of the attractive properties of ILs along with the flexibility and mechanical strength of polymers. In the present work, we have selectively polymerized one of the ionic moieties to provide single ion—either cation or anion— conducting gels based on 1-ethyl-3-methyl imidazolium (3-sulfopropyl) acrylate ([EMIM][SPA]) and [(1-acryloyloxy) propyl]-3-methyl imidazolium bis-(trifloromethylsulfonyl) imide ([AEBI][TFSI]) and used these single ion conducting networks for fabrication of soft ionic P/N diodes. Our studies shed light on the impedance behavior of single ion conducting networks and open new opportunities for the application of these soft ionic diodes.
  

Electron-Transfer Reaction in Ether- and Carbonate-based Solid Polymer Electrolytes at Electrochemical Interfaces

Battery interfaces are complicated by the presence of polymeric materials of various composition called a solid electrolyte interphase (SEI), which forms immediately and spontaneously through the electrodeposition of electrolytes. In this poster, we employ atomistic molecular dynamics simulations to address solvation properties and electron-transfer kinetics of electrochemical reactions in the SEI. We investigate model SEIs composed of linear homopolymers, including poly (ethylene oxide) (PEO), poly (ethylene carbonate) (PEC), and poly (vinylene carbonate) (pVC) at the interface with pristine polarizable electrodes.   

Effects of Cationic Pendant Groups on Ionic Conductivity for Anion Exchange Membranes: Structure−Conductivity Relationships

Anion exchange membranes(AEMs) have attracted increasing interests due to their various applications, especially for Fuel cells. Previous proton exchange membranes(PEMs), such as Nafions® have better conductivity than AEMs so far. However, technical limitations such as slow electrode kinetics, carbon monoxide (CO) poisoning of metal catalysts, high methanol crossover and high cost of Pt-based catalyst deterred further usages. AEMs have advantages to supplement its drawbacks. In this work, we synthesized PS-PAGE (polystyrene-b-poly allyl glycidyl ether) block copolymer as backbone by anionic polymerization. And then we obtain various AEMs with different ratio of cationic groups by post modification. We also control nanostructures such as domain spacing, morphology by differentiating the block ratio. Hydroxide conductivity is measured using AC impedance analyzer and small angle x-ray scattering is employed to study nanostructures. Systematically investigated structure-conductivity relationships provide a foundation for further researches on AEMs with better performance.
  

Tunable Solid Electrolytes Formed from a Double Helix Polyanion and a Dense Sea of Mobile Ions

Recently our group discovered a new class of solid electrolyte materials, formed from a rigid-rod polyanion and an ionic liquid. This material’s cohesion arises from a massively collective electrostatic network, in which each polymer rod connects to its neighbors via the superposition of thousands of weak ion-ion interactions. The high degree of correlation of electrostatic interactions provide a stiff matrix, while individual ions move as if they were in a liquid. Thus, this material relieves the usual strict tradeoff between ionic conductivity and modulus in organic electrolytes, demonstrating its potential to resolve limitations in battery technologies, as well as in other molecular separations applications. We will discuss our fundamental understanding of the double helical supramolecular structure for the sulfonated aramid polymer that forms the reinforcing fibers (of aspect ratio ~1000) in this “molecular ionic composite” (MIC). We will also discuss the next larger level of hierarchical structure, the electrostatic network, and new ideas and new data on even larger morphological heterogeneities. Finally, we will present progress on incorporating 0.5 to 4 M of Li⁺ or Na⁺ and testing these MICs in electrochemical cells.   

Morphology and ion transport in glassy polymerized ionic liquids

The impact of macromolecular structure on ion dynamics and morphology in ammonium and imidazolium based glassy polymerized ionic liquids are investigated using broadband dielectric spectroscopy and wide angle X-ray scattering (WAXS). A new approach is suggested to determine ionic mobility in a broad range spanning up to five orders of magnitude below the calorimetric glass transition temperaturesof polymerized ionic liquids is proposed, providing access to a regime of diffusivities that is inaccessible to many current experimental techniques. A quantitative agreement between the mean ion jump lengths from dielectric data and the ion-to-ion correlation lengths from WAXS is found. The ion mobility is found to be more sensitive to variation of the molecular structure compared to the effective number density of the mobile ions. These results showcase the subtle interplay between the molecular structure, morphology and ion dynamics in polymerized ionic liquids.   

Understanding ion transport in polymeric electrolytes via X-ray photon correlation spectroscopy

Polymer battery electrolytes are a safe alternative to flammable liquid organic electrolytes; however, they suffer from low ionic conductivity and key questions remain regarding the ion transport mechanisms across multiple length-scales. To better understand this transport and to obtain insights that may lead to better electrolytes, we measured the length-scale-dependent structural dynamics of polymer diffusion related ion transport in LiTFSI (Li bis(trifluoromethylsulphonyl)imide)/PEO (poly(ethylene oxide)) using small angle X-ray photon correlation spectroscopy (XPCS). Arrhenius relationships of the obtained decorrelation times with respect to temperature closely match the Arrhenius value for ionic conductivity reported in literature [1]. This indicates a close connection between polymer self-diffusion and ion conductivity in such materials. We also present recent results on operando experiments, in which we track, under external bias, the motion of the ion front through the polymer matrix and are able to measure the ions’ velocity via heterodyne mixing.

[1] Gorecki et al., Phys.: Condens. Matter 1995, 7, 6823.   

Effect of High Polarity on Ionic Transport in High Dielectric Constant Polyether-Based Electrolytes

The ionic conductivities of polymer electrolytes are intrinsically related to the host material properties. In many polymer electrolytes, it has been shown that the host segmental dynamics is the primary controlling factor in lithium ion transport. However, prior studies of poly(glycidyl ether)-based polymer electrolytes have revealed that the host polymer polarity may also be a strongly influencing factor for ionic conductivity. This influence is mediated through competitive association of negatively charged polymer moieties and anions to lithium ions. As the polarity increases, the negatively charged moieties “win” this competition, thus leading to decreased ionic association. In this work, we seek to extend these findings to novel, highly polar polyethers. We hypothesize that increasing the host polymer polarity will indeed decrease ionic association. However, we anticipate increases in polymer-polymer and -ion interaction strength, which will considerably slow segmental dynamics. Using molecular dynamics, we seek to elucidate ionic transport mechanisms and the relative importance of host polarity and segmental dynamics to changes in ionic conductivity.   

Printed Active Liquids

We present printed, all-liquid, water/oil and water/water systems. Our constructs are structured by the assembly of nanoparticles and polymers at the liquid-liquid interface. The insoluble layers that these assemblies form have significant, highly tunable shear moduli (order 0.1-10 N/m) that can be used to structure liquid-liquid systems into a wealth of shapes. We cover the materials used to generate these threads, namely polyelectrolytes, nanoparticles and, nanoparticle surfactants. Finally, we discuss the encapsulation of active and living systems in the printed constructs, most notably colonies of Geobacter Sulferreducens and dispersions of active tubulin filaments that are rendered motile by ATP-consuming molecular motors. Of particular interest is the effect of the soft confining walls of the tubules on both the coherence of the motion of the tubulin filaments, as well as the deformation modes of the printed structures due to the motion of the active rods.   

Soft Robotic Manipulation and Locomotion with 3D Printed Electroactive Hydrogel

Electro-responsive hydrogel (ERH) which exhibits large deformation in response to an electric field has received great attention as a smart material for soft actuators because of their reliable control, fast actuation, and materials property similar to that of natural muscles. Despite their unique advantages, their application has been limited due to fabrication techniques that are inherently two-dimensional (2D) such as molding and lithography.
Here we demonstrate soft robotic manipulation and locomotion with 3D printed ERH. We use a digital light processing (DLP) based micro 3D printing technique, projection micro-stereolithography (PµSL). Photo-curable ERH resin was prepared and printed into 3D ERH micro actuators using PµSL. Gripping and transporting an object were achieved by 3D printed soft robotic ERH actuators. Also, a locomotion of a 3D printed ERH structure was demonstrated by using alternating electric fields and corresponding shift of the center of mass due to large deformation. 3D printed ERH will have potential impact on a variety of applications, such as soft robots, electro-active sensors, and artificial muscles.   

Thermal and Mechanical Properties of 3D Printed Polymers (Polylactic Acid, Acrylonitrile Butadiene Styrene and Polyurethane)

The effect of processing on the properties of three polymers commonly used in 3D printing was studied. Mechanical testing was uniaxial compression/tension tests performed at room temperature for Young’s modulus, Poisson’s ratio, and yield stress. Thermal testing was Differential Scanning Calorimetry (DSC) for glass transition temperature, melting point and degree of crystallinity. Processing was found to have a pronounced effect in most cases and is most obviously seen in the DSC thermograms where evidence of partial crystallinity and physical aging is seen, both of which are strongly cooling rate dependent.   

3D Printed Mechanical Sensors using Block Copolymer Nanocomposites

3D printing has been widely applied to design and manufacturing processes in diverse industries. However, few available materials and a lack of understanding of their behaviors limit the possibilities to produce smart devices with 3D printers. Here, 3D printable functional materials using block copolymers and nanoparticles are introduced. Changes in mechanical and electrical properties as a function of different block copolymer morphologies and nanoparticle concentrations were investigated. This new functional material can be used to fabricate high quality piezo-resistive sensors applicable to wearable electronics, soft robotics, and nano-bio research.   

Real Time FTIR study on Hydrogen Bonded Complex of Epoxides and Oxetanes in Photo-initiated Cationic Polymerization

The importance of study on photo-initiated polymerization continue to increase, because its understanding and control is a key factor to accurate result of 3D printing. We studied the thermal stability of the hydrogen bonded complex of epoxy and oxetane monomers with Brønsted acid, as being generated during photo-initiated cationic polymerization. In particular, we investigated how its thermal stability affects the induction period in the polymerization. The chemical structure of monomers with glycidyl or methylene ether groups next to epoxy or oxetane groups form an intermediate metastable state of secondary oxonium ions with generated superacid. It stabilizes the photo-acid and is responsible for the induction time in the cationic photo-polymerization. Using temperature-controlled FTIR with in-situ UV irradiation, we performed a series of real-time FTIR (RT-FTIR) experiments to support that the induction time is originated from the thermal stability of the hydrogen bonded complex that is strongly influenced by the heat conduction environment for the study of photo-polymerization.   

Elucidating Reaction Pathways in the Synthesis of Block Copolymer-Derived Crystalline Inorganic Materials via In Situ SAXS/WAXS and XAS

Block copolymer-inorganic hybrid co-assembly is a tunable, versatile basis for synthesis of ordered mesoporous transition metal oxides and nitrides used in electrochemical energy conversion and storage, catalysis, and discovery of novel electronic properties. Despite decades of experimental work in the synthesis such materials, the interplay of crystallinity and mesostructure retention during high temperature treatments remains a significant challenge for further fundamental and applied studies on such materials. For example, the only route to superconducting block copolymer-derived mesoporous niobium nitride involves a poorly-understood two step heat treatment in flowing ammonia gas at temperatures above 850 C to produce materials with a significantly depressed superconducting transition. We have employed in situ small- and wide- angle X-ray scattering and XANES during such anneals to elucidate reaction pathways and synthesize materials with improved transition temperature and mesostructure retention. These studies have also allowed the expansion of this process from custom-synthesised ABC triblock terpolymers to commercially available Pluronic ABA triblock copolymers, enabling the broader application of block copolymer-derived mesoporous nitrides.   

Hierarchical morphology of ABC mikto-arm terpolymer

The morphology of a ABC mikto-arm terpolymer consisting of polystyrene, polyisoprene and poly(2-vinylpyridine) (PS-PI-P2VP) was studied by combining small angle neutron and X-ray scattering (SANS and SAXS) with transmission electron microscopy (TEM). Because of the complex electron density differences between each block, SAXS is limited to the observation of interferences arising from all three phases, leading to ambiguity in the determination of the morphology. To overcome this ambiguity, SANS and resonance soft x-ray scattering was used to elucidate the morphology by isotopic labeling of the PS with deuterium and by varying the x-ray energy to change the electron density of each component. The experimentally determined morphology was compared to simulations where the key input parameters are the segmental interactions between the components. The morphology determined is a new complex lamellae structure.   

Selective Evaluation of Molecular Aggregation Structure in Soft Materials using Wide-Range of X-ray Energy

To understand an elemental distribution and molecular aggregation structure of polymeric materials are essential for fabricating functional materials. A use of tender X-ray (2-5 keV) is important to achieve the characterization of elemental distribution in polymeric materials because the absorption of light elements exists in these energies. The use of tender X-ray enables to detect lower scattering angle within the limitation of camera length. Small-angle X-ray scattering (SAXS) with higher than 0.5 nm wavelength can evaluate the sample with larger than 300 nm domain spacing. Furthermore, the population of each micro crystalline structure in thin film depending on depth can also trace using grazing-incidence wide-angle X-ray diffraction (GI-WAXD) with tender X-ray because penetration depth to the sample gradually changes. In this study, we introduce the results of SAXS, GI-WAXD, and X-ray reflectivity using wide-range of X-ray energy. Combination of these measurement techniques is of use to achieve the real visualization of the structure in thin films.   

Analysis of SANS Patterns from 1D Symmetrically Confined Polymers

Understanding how polymer chain conformations are altered under nanoconfinement is critical for understanding polymer behavior in applications ranging from nanoscale lithography to polymer nanocomposites. Previous work that measured polymer conformations under 1D confinement has been limited to using “open face” thin films, where at least one confining surface is free. In these samples, changes in the polymer conformations perpendicular to the confining surfaces have proven difficult to measure. Our study uses a new and unique sample geometry, consisting of long, narrow, and deep polymer filled channels that rigidly confine the polymer on both sides. This geometry should allow SANS to simultaneously probe chain conformation parallel and perpendicular to the confining surfaces. The resulting anisotropic SANS patterns from empty templates are fit using a dynamical theory based on the Bloch wave expansion of the neutron wave function to account for the complex nature of the template. Here we present our initial results developing the fitting theory and extracting polymer R_g in the confined and unconfined dimensions.   

Characterization of Charge Transport and Microstructure of Non-Fullerene Molecular Networks in Bulk Heterojunction Thin Films

A large effort exists to explore non-fullerene small-molecules for organic photovoltaic devices, however, there is a fundamental lack of understanding of how the chemical structure of polymer and small-molecule influence the hierarchical microstructure of bulk-heterojunction (BHJ) thin films. Two photophysical processes that dictate device performance – charge separation and transport – depend intimately on the hierarchical length scales of phase separation and interpenetrating polymer/small molecule networks. To elucidate the relationship between BHJ microstructure and chemical structure, we interrogate a series of bay-annulated isoindigo dye molecules with varied connectivity of pi-stacking faces in polymer blends and couple transmission electron microscopy with real-space pair distance distribution functions generated from the generalized indirect Fourier transform of resonant elastic X-ray scattering data. To connect the nanoscale morphology with charge transport, we use dark current injection measurements in diode configuration devices to interrogate the formation of percolated charge transfer channels. We find that the geometry of the small-molecule frontier electronic wavefunctions has a very large influence on the molecular network that forms inside the polymer matrix.   

Probing the local dynamics in three-dimensional colloid-polymer assemblies using single particle tracking

We use single particle tracking (SPT) to understand the local environment around colloidal probe particles in colloid-polymer hybrid structures. These hybrids were prepared using ice templating. We have shown that variation in the crosslinking protocol for hybrid formation can dramatically alter their mechanical response¹. Elastic, compressible sponges or plastic monoliths can be prepared by varying crosslinking conditions. We use SPT to probe the microstructural differences that underlie the different mechanical response of elastic and plastic assemblies. We apply wavelet transforms to trajectories obtained from epifluorescence microscopy to eliminate error due to stage drift. This yields a spatial resolution of 2 nm in particle tracking. The mean squared displacements (MSD) showed subdiffusive behavior in both elastic and plastic scaffolds. However, the MSD and van Hove distribution for plastic scaffolds indicate larger spatial heterogeneity, in contrast to elastic sponges. This corresponds to heterogeneity in the local crosslinked polymer environment. We interpret this in terms of nonuniform distribution of crosslinks in plastic assemblies.
¹Langmuir 2016, 32, 11623−11630

  

An Automated, High-Throughput System for GISAXS and GIWAXS Measurements of Thin Films

Grazing incidence small-angle X-ray scattering (GISAXS) and grazing incidence wide-angle X-ray scattering (GIWAXS) are important techniques for characterizing thin films. In order to meet rapidly increasing demand, the SAXSWAXS beamline at the Advanced Light Source (beamline 7.3.3) has implemented a fully automated, high-throughput system to conduct GISAXS and GIWAXS measurements. An automated robot arm transfers samples from a holding tray to a measurement stage. Intelligent software aligns each sample in turn, and measures each according to user-defined specifications. Users mail in trays of samples on individually barcoded pucks, and can download and view their data remotely. Data will be pipelined to the NERSC supercomputing facility, and will be available to users via a web portal that facilitates highly parallelized analysis.
  

Imaging polymer:fullerene bulk heterojunctions with X-ry ptychography

Improving the efficiency of organic photovoltaics (OPV) requires a comprehensive understanding of the relationship between microstructure and device function. Most OPVs are blends of polymers (or small molecule) donors and fullerene derivative acceptors (or increasingly polymers or small molecules) in bulk heterojunctions (BHJs). Microstructure characterization is challenging due to the similarity of the donor and acceptors and to easily damaged nature of organics. We have demonstrated that X-ray ptychography can be used to achieve this goal and to directly image the BHJ morphology. Ptychography is a technique that scans across a sample, collecting X-ray scattering images at localized but overlapping positions, and reconstructs real space images. We have used this technique to characterize the morphology in BHJs of PTB7 and PC71BM, allowing identification of the PTB7 and PC71BM domains and how these vary with the additive 1,8-diiodooctane (DIO).   

Evaluation of the Interaction Parameter for Poly(solketal methacrylate)-block-polystyrene Copolymers

A series of symmetric poly(solketal methacrylate-b-styrene) (PSM-b-PS) copolymers that can transform a hydrophobic PSM block to a hydrophilic poly(glycerol mono-methacrylate) (PGM) block through an acid hydrolysis was investigated. This simple method significantly enhances the segmental interaction parameter (χ), enabling a phase-mixed block copolymer (BCP) to microphase separate without any additives. Temperature-dependent small-angle X-ray scattering (SAXS) measurements as a function of the degree of polymerization (16 ≤ N ≤ 316) and PSM hydrolysis conversion were conducted to characterize the order-to-disorder transition (ODT) behavior, as well as the lamellar microdomain features. Using a mean-field correlation-hole analysis of the scattering, the χ value for PSM and PS was determined as a function of the conversion of PSM to PGM. For 100% conversion of PSM to PGM, the χ with PS was found to be given by χ = 0.3144 + 36.91/T, with χ = 0.438 at 25 °C, which is ~13 times larger in magnitude than χ parameter for PSM-b-PS copolymer (~0.035 at 25 °C). With this large increase in χ, full pitch lamellar microdomains of sub-3 nm were achieved by the lowest molar mass sample.   

Directed self-assembly of Janus Bottlebrush Polymers from A-Branch-B Diblock Macromonomers

Recent advances in polymerization strategies have facilitated the synthesis of precisely controlled polymer architectures. Bottlebrush block copolymers BBCPs is a distinct structure that is characterized by side-chains densely grafted on a linear backbone. BBCPs exhibit novel properties such as reduced entanglement density, improved micro-phase separation, and dense functionality. Here, we study a particular form of BBCPs constituting of a series of tethered AB linear diblock chains. Hence, the A and B blocks phase separate with the backbone serving as an interface. The added constraint imposed by the polymer backbone on the equilibrium spacing of the neighboring AB diblocks directly manifests itself in the resulting morphologies. Simulations using self-consistent field theory SCFT reveal the structural effects on the characteristics of micro-phase separation. In particular, the effect of grafting density on domain spacing and effective segregation. In addition, the self-assembly of BBCPs under confinement shows distinct orientation preferences compared to its linear AB counterpart. Free energy calculation reveals regions of stability of different orientations based on segregation strength and molecular architecture. ”
  

Vertically Oriented Nanostructures of Poly(3-dodecylthiophene)-Containing Rod-Coil Block Copolymers

We introduced a star-shape molecular structure, 18 arm PS-b-P3DDT (STAR-SDDT) copolymers, to overcome large difference in surface tension. The STAR-SDDT with 47 % weight fraction of P3DDT block (w_P3DDT = 0.47) was synthesized by a combination of atom-transfer radical polymerization (ATRP) and click reaction. Both transmission electron microscopy (TEM) and small angle X-ray scattering (SAXS) revealed lamellar morphology of STAR-SDDT in bulk. When STAR-SDDT is spin-coated on a silicon substrate, vertically oriented lamellar microdomains were observed by tapping mode atomic-force microscopy (AFM) and grazing incidence small angle X-ray scattering (GISAXS). On the other hand, linear PS-b-P3DDT (LINEAR-SDDT) having lamellar structures only showed parallel structures with fibrils at surface in film. Also, we confirmed that the P3DDT crystalline locating inside microdomain is well formed, verified by the existence of (100) and (200) peaks of grazing incidence wide angle X-ray scattering (GIWAXS) spectrum.   

Block Copolymer Templated Anisotropic Plasmonic Nanostructure

The anisotropic nanostructures of noble metals are of great interest for plasmonic applications due to their narrow-band localized surface plasmon resonance and larger local field enhancement. This work reports a simple and promising fabrication method of anisotropic gold (Au) nanostructures film using poly (styrene-b-2-vinylpyridine (PS-b-P2VP) block copolymers (BCP) as template. In this process, PS-b-P2VP spherical micelles were first synthesized as template followed by selective deposition of Au compound HAuCl₄ inside P2VP core of the micelles. Subsequently, heat treatment of the Au deposited BCP films followed by complete removal of the BCP template produced edged gold nanostructures of various shapes with a dependence on the annealing temperature and time. Moreover, optical extinction spectra showed presence of signature near infra-red peaks of anisotropic Au nanostructure, suggesting its potential for applications in plasmonic devices.
  

Block copolymer nanoparticles

Block copolymers tend to microphase separate at certain conditions. The formed nano-structures can be of different symmetries, which can be influenced by confinement. We perform computer simulations of block copolymers forming compact particles. We investigate different block copolymer compositions, and found a large zoo of fascinating morphologies. Confinement induces many non-bulk morphologies. The results of computer simulations are compared with both other theoretical investigations and with the experiments [1].
[1] Takeshi Higuchi, Marco Pinna, Andrei V. Zvelindovsky, Hiroshi Jinnai, Hiroshi Yabu, J. Polym. Sci., Part B: Polym. Phys.(2016).
  

Hybrid Particle-Field Simulations for Studying Polymers Containing Strong Interaction Sites

Development of next-generation polymeric materials involves judicious combinations of functional capability and mesoscale structural properties. A small amount of strongly interacting “moieties” are often introduced to polymers for performing specific functionalities and/or controlling assembled microstructures. Drastic changes in material’s properties often result from their inclusion. A fundamental understanding of these effects from computational studies is of critical interest to material designs in experiments. Particle-based simulations are often computationally demanding when applied to systems with mesoscale features, while field-based methods lack microscopic description of the strong interactions of interest. To address this challenge, a hybrid particle-field simulation scheme is developed that explicitly account for interactions among the “moieties”, while being computationally efficient to access experimentally relevant length scales. The scheme can be applied to study interactions of various natures (e.g. hydrogen and coordination bonds, etc.). To illustrate the method’s versatility and performance, applications to several polymeric systems, including polymers containing ionic groups, hydrogen-bonding sites, and polymers in explicit solvent models are presented.   

Mesoscopic Simulations for Transport of Water and Salt Through Desalination Membranes

We extend our studied the influence of multicomponent salt solutions on water and salt transport in charged membranes at the mesoscale using dissipative particle dynamics (DPD) simulations. This technique allow us to reach the larger and time scales that can bridge the gap between atomistic and mesoscopic simulations. This insight will show a basic understanding for the future design of desalination membranes for water purification technologies. The polymer, salts, and water are modeled by course-grained beads interacting via standard short-range soft repulsion and smeared charge electrostatic potentials. Our simulations reproduce the results in good agreement with experimental and our atomistic simulations works, showing that diffusion of salt and water are influenced by cation sizes (mono and divalent), salt concentrations, and ionic strength of polymers.   

typyPRISM: A Computational Tool for Liquid-State Theory Calculations of Macromolecular Materials

The Polymer Reference Interaction Site Model (PRISM) theory describes the equilibrium spatial-correlations of liquid-like polymer systems including melts, blends, solutions, block copolymers, ionomers, liquid crystal forming polymers and nanocomposites. Using PRISM theory, one can calculate thermodynamic (second virial coefficient, χ interaction parameters, potential of mean force) and structural (pair correlation functions, structure factor) information for these macromolecular materials. Here, we present a Python-based, open-source framework, typyPRISM, for conducting PRISM theory calculations. This framework aims to simplify PRISM-based studies by providing a user-friendly scripting interface for setting up and numerically solving the PRISM equations. typyPRISM also provides data structures, functions, and classes that streamline PRISM calculations, allowing typyPRISM to be extended for use in other tasks such as the coarse-graining of atomistic simulation force-fields or the modeling of experimental scattering data. The goal of providing this framework is to reduce the barrier to correctly and appropriately using PRISM theory and to provide a platform for rapid calculations of the structure and thermodynamics of polymeric fluids and nanocomposites.   

Temperature Dependent Scaling Behavior of Poly(ethylene oxide) in an Ionic Liquid [BMIM][BF4] Predicted Using First Principles-Based Force Fields

Mixtures of polymers with ionic liquids (ILs) exhibit many interesting thermodynamic properties including lower critical solution temperature (LCST) phase behavior, for which a better molecular level understanding is desired. While microscopic insight may be provided by molecular dynamics (MD) simulations, the applicability to polymer/IL mixtures is challenging due to uncertain accuracy of the interaction potentials as well as the significant computational cost. In this work, we develop a cost effective, first-principles united atom (UA) force field for poly(ethylene oxide) (PEO)/[BMIM][BF4] mixtures that importantly allows access to the multi-microsecond simulation time-scales necessary to obtain converged statistics for dillute polymer chains in IL solvents. The UA force field is benchmarked against ab initio calculations without any implicit fitting. We use MD simulations to predict the temperature-dependent scaling of polymer size for single-chain PEO in IL solvent. We find that [BMIM][BF4] changes from a good solvent to a theta solvent for PEO as the temperature increses, which agrees perfectly with recent experiment. We highlight specific coordination structures of the PEO chains enclosing its neighboring BMIM cations to illustrate the entropic mechanism for the LCST.   

Segmental Dynamics Revealed from All-atom Simulations of Concatenated Polyethylene Rings

Predicting entanglement molecular weight from all-atom simulations remains challenging. We present all-atom MD simulation results for concatenated rings of polyethylenes with up to 1600 carbon atoms. The chain-end effects are suppressed, and the entanglement topology is equilibrated by temporarily turning off and on the intermolecular pairing potential that prevents chain segments to cross. The bead mean squared displacement and stress relaxation data covering the reptation plateau are reported, and are analyzed using the tube model adapted to ring polymers. It is found that the monomer relaxation is slowed down substantially by angle and dihedral restrictions. A characteristic subdiffusion 3/4 scaling around the entanglement time is identified for all molecular weights investigated, which supersedes the 1/2 Rouse scaling expected for flexible chains.   

Effect of Metal Ions on Polyelectrolyte Nanofiber Mechanics

Polyelectrolyte based hydrogel fibers can mimic extracellular matrix and have applications such as drug delivery and tissue scaffolding. Metal ions play a critical role in hydrogel fiber stability via electrostatic interactions, but knowledge of how they modulate mechanical properties of individual polyelectrolyte polymers is lacking. In this study, electrospun polyacrylic acid with chitosan is used as a model system to evaluate ferric ion effect on nanofiber mechanics. Using dark field microscopy imaging and persistence length analysis, we demonstrate that ferric ions modulate the bending stiffness of nanofibers. Young’s modulus of individual nanofibers is estimated at values of a few kilopascals, suggesting that electrospun nanofibers possibly exist in a hydrated state. Furthermore, Fourier Transform Infrared (FTIR) spectra indicate the effect of ferric ions on polyacrylic acid molecular bonds. Our results suggest that metal ions can regulate single nanofiber stiffness, thereby providing designs to fabricate hydrogels in a tunable fashion.   

Polyaniline and CN-functionalized polyaniline as organic cathodes for lithium and sodium ion batteries: a combined molecular dynamics and Density Functional Tight Binding Study in solid state

We present the first atomic-scale simulation of the discharge process of polyaniline (PANI) based polymeric cathode materials for electrochemical batteries in solid state. The oxidation of PANI and of cyano groups (CN) functionalized PANI induced by coordination to the electrolyte anions is computed and voltage curves are estimated. The cyano functionalized PANI is expected to not suffer from irreversible formation of pernigraniline base at high degrees of oxidation, which could nearly double the reversible capacity. To deal with the large required numbers of atoms and structures, a combination of molecular dynamics and Density Functional Tight Binding (DFTB) is used. The DFTB is benchmarked to Density Functional Theory (DFT) calculations using different functionals to confirm its accuracy. The voltages computed with the solid state model are in good agreement with available experimental data and ab initio models based on oligomers. The solid state model also predicts substantially increased voltage with PANI functionalized with cyano groups.   

Chain Dynamics in Li-neutralized Precise Acid-Containing Polyethylenes

Single ion conductors have the potential for higher transference numbers, improved mechanical stability, and reduced degradation compared to traditional polymer electrolytes. This study investigates the dynamics of Li-neutralized poly (ethylene-co-acrylic acid) ionomers (pnAA), a linear polyethylene backbone where n is the carbon spacing length between pendant acrylic acid groups (p9AA, p15AA, p21AA). Quasi-elastic neutron scattering experiments and atomistic molecular dynamics simulations are used to understand how changing Li neutralization affects ion aggregation and polymer dynamics in these systems. We directly compare the intermediate scattering structure factor derived from experiments and simulations, and determine dynamic properties such as polymer relaxation times and heterogeneity of motion. Neutralizing the precise ionomers with lithium introduces an additional relaxation time as compared with the parent acid copolymer, and slows the primary relaxation of the systems by 1-3 orders of magnitude.
  

The Influence of Thiophene Moieties on the Molecular Orientation and Interface Properties of Low Band Gap Polymers

The properties of low band gap (LBG) polymers in donor-acceptor based bulk heterojunction (BHJ) solar cells are strongly influenced by their morphology and ability for self-organization in thin-films. For two related polymer pairs the influence of the introduction of additional (hexyl-) thiophene moieties on both the electronic structure and the ability for self-organization in thin films is studied using Ultraviolet Photoelectron spectroscopy (UPS) and Near-Edge X-Ray Absorption Fine Structure spectroscopy (NEXAFS). NEXAFS in fluorescence detection mode at the sulfur K edge was used to investigate molecular orientation. Exemplary NEXAFS spectra are compared to DFT calculations. We find that the introduction of additional (hexyl-) thiophene moieties in the polymer structure does not affect significantly basic electronic parameters and the energy level alignment at interfaces, but has a strong impact on their self-organization properties.[1] This will affect the behavior of such polymers in devices. We thank the group of Prof. Scherf (University of Wuppertal, Germany) for the synthesis of LBG polymers.

[1] M. Ivanovic et al., Solar Energy Materials and Solar Cells, 157 (2016) 286-294   

Force Spinning of PEO-Based Nanofibers

Nanofibers have been obtained by force spinning solutions of polyethylene oxide (PEO) in distilled water at various spinning rates, ranging between 1,000 to 10,000 rpm. The polymer, PEO, was purchased from Sigma Aldrich. A detailed analysis of the nanofibers’ production as a function of the concentrations of PEO solutions and of the spinning rate is presented. The as-obtained PEO nanofibers have been collected as mats and analyzed by several spectroscopic techniques such as Raman (532 and 785 nm), X-Ray, and XPS. Optical and electron microscopy was used to evaluate the distribution of the diameters of PEO nanofibers and to quantify the effect of PEO concentration and spinning rate. To determine the effect of the fast spinning on the morphology of PEO nanofibers, pristine PEO films have been obtained by the evaporation of PEO solutions used to obtain the nanofibers. This analysis was focused on the effect of spinning rate on the crystallinity of PEO mats. Complementary data have been obtained by DSC measurements. Tentatively, the effect of solvents (toluene, acetone, and chloroform) on the morphology of PEO nanofibers will be analyzed.   

Non-equilibrium Conformation of a DNA Segment Outside a Capsid and its Effect on the DNA Packaging Rate

DNA is packaged into a nanometer-sized capsid by a motor protein, where the internal pressure is so high that DNA segment inside the capsid (trans segment) is almost jammed. Recent experiments showed that the trans segment was in non-equilibrium states, which substantially retarded the packaging process. However, the conformation of a cis segment (i.e. DNA outside the capsid) and its effect on packaging rate have attracted little attention, partly because of limits of experiments. In this study, we illustrate that the conformation of cis segment is a major determinant for packaging rate, contrary to previous expectations. The conformation of cis segment is also significantly away from its equilibrium due to tension propagation along the chain. We perform LD simulations of polymer packaging and mimic the recent experiment: the motor protein is stalled and restarted repeatedly, which allows the polymer to have equilibrium conformations during packaging. By analyzing the effect of cis and trans segment separately, we find that the conformational relaxation of the cis segment (strongly tensed) substantially accelerates packaging process and effects of trans segment are marginal under strong motor forces.   

Sorting ring polymers by knot type using modulated nanochannels

In this theoretical study we discuss a novel method for sorting ring polymers according to their topological, knotted state. The proposed approach harnesses the rich dynamical behaviour of polymers confined inside spatially-modulated nanochannels. The longitudinal mobility of the rings is shown to have two key properties that are ideally suited for knot sorting. First, at fixed topology, the mobility has an intriguing oscillatory dependence on chain length. Second, the mobility ranking of different knot types is inverted upon increasing the chain length. We show that this complex interplay of channel geometry, chain length and topology can be rationalised within a simple theoretical framework based on Fick–Jacobs’s diffusive theory. The results and the interpretative scheme ought to be useful for designing microfluidic devices with optimal topological sorting capabilities [Marenda et al., Soft Matt. 2017].   

The effects of DNA Entanglement in Viral Capsids on the Conformational Relaxation and the DNA Ejection Rate

DNA ejects from a small viral capsid due to a large repulsion force, thus infecting the host cells. Because the DNA confined within a small viral capsid which is jammed and entangled significantly, the DNA conformation does not usually relax to equilibrium conformation during the ejection. In this work, we delineate the importance of the DNA entanglement by allowing the conformational relaxation via strand-crossings during ejection. We carry out Langevin Dynamics simulations of a single chain with 1024 monomers. The viral capsid is modeled as a cubic box with a long tail, through which the DNA is ejected. By tuning the force constant of FENE (Finitely Extensible Non-linear Elastic) model for the chain, we either allow or disallow the chain to undergo strand-crossing. We employ two types of initial configuration of the DNA; (1) ordered and (2) disordered. We find that strand-crossings help the DNA relax, not only segments of DNA near the pore but entire parts of the DNA, thus making the ejection fast despite its disordered initial conformation. When the strand-crossing is forbidden, the ejection rate becomes slow by a factor of two or more in disordered initial conformations.   

Polymer Folding in Cylindrical Confinement

A polymer chain with sufficiently short-range interactions can undergo a direct first-order-like folding transition from an expanded coil to an ordered crystallite. This all-or-none transition is analogous to the folding transition exhibited by many small proteins [1] and is of interest for smart materials applications. Here we investigate the effects of cylindrical confinement on this transition. We study a flexible square-well-sphere chain end-tethered at the base of a hard-wall cylinder of diameter D. We carry out Wang-Landau simulations to construct the density of states, and thus the thermodynamics, for this system. For a wide cylinder an entropic stabilization of the folded state is observed [2]. However, as the cylinder diameter approaches the size of the folded state we find a destabilization effect. For cylinder diameters smaller than the native ground-state, the chain folds into a different, higher energy, ground state ensemble and the T vs D phase diagram displays non-monotonic behavior as the system is forced into different ground states for different ranges of D. The folding transition remains first-order-like until the cylinder is so narrow that only 1D folding is possible. [1] J. Chem. Phys. 145, 174903 (2016); [2] Macromolecules 50, 6967 (2017).   

Folding of a Square-Well Chain in a Hard-Sphere Brush

Macromolecular crowding and geometric confinement can alter the phase behavior of biomacromolecules. Here we study the folding transition of a flexible polymer chain end tethered to a hard surface within an athermal brush composed of flexible hard-sphere chains (thus we combine confinement and crowding effects). Our model polymer is a square-well-sphere chain with short-range interaction that undergoes a first-order like coil-crystal folding transition, analogous to the all-nor-none folding of many small proteins. This chain is surrounded by a set of tangent-hard-sphere chains end-tethered on a square grid and we vary the crowding effect by changing the grid spacing. We carry out Wang-Landau simulations to construct the density of states, and thus the complete thermodynamics, for this system. In the dense brush, the folding transition temperature is suppressed, although it maintains a first-order character, indicating a destabilization of the folded state. Thus, crowding near the tethering point shifts the folding equilibrium in favor of the expanded state. This effect is opposite that seen for a similar chain in either geometric confinement [1] or crowded solution conditions [2]. [1] Macromolecules 50, 6967 (2017); [2] J. Chem. Phys. 147, 166101 (2017).   

Driven Translocation of a Star Polymer from a Confined Cylindrical Cavity with a Finite Volume

We performed a coarse-grained Langevin Dynamics simulation to investigate the translocation process of homogeneous star polymers through a nanopore in the case where the polymer is initially confined inside a cylindrical cavity. The translocation time is investigated in terms of the total number of beads for three- and four-armed star polymers. Moreover, the geometry of the cavity, that is, its volume and its aspect ratio has an obvious impact on the polymer conformation as it crosses the nanopore, and hence a significant influence on the translocation times distribution. That is why polymer translocation times were also computed by varying the volume and the aspect ratio of the cylindrical cavity.   

Noncovalent Interactions with a Synthetic Random Heteropolymer Allow for Protein Stabilization in Nonnatural Environments

Proteins possess a vast array of functions stemming from their rich chemical diversity and hierarchical structures. For instance, enzymes exhibit catalytic properties that are more efficient than their synthetic counterparts; certain proteins can be programmed to respond to external stimuli with high selectivity and sensitivity; other proteins are critical for disease treatment. Thus, materials constructed using functional natural proteins may lead to new opportunities to address a range of scientific and technological challenges.
However, since many materials processing techniques require the use of organic solvents, proteins must be stabilized in nonnatural environments in order to develop homogenous active materials. We have developed a synthetic random heteropolymer (RHP) comprising different chemical moieties to induce multivalent interactions with the surface of proteins that are collectively strong enough to solubilize and stabilize the proteins in organic solvents. Computational simulations coupled with spectroscopic, kinetic, and light scattering experiments provide valuable insights into the nature of these interactions. Our studies show that the interactions depend highly on the physiochemical properties of the organic solvent used to dissolve the protein.   

Polymer-Mediated Synthesis and Incorporation of Membrane Protein in Phospholipid Vesicles

Membrane proteins play significant roles in cellular activities, and remain attractive pharmacological targets. Studying membrane protein folding out of biological environments remains an intriguing endeavor for both biophysical and biological communities. Small molecular detergents are generally used to solubilize membrane proteins during in vitro characterization, which usually perturb protein structures and functions. Here, we show a synthetic polymer system that mimics protein folding chaperones by tailoring polymer amphiphilicity and charges. Specifically, a series of polymers have been developed that enable direct cell-free synthesis of a channel protein, PepTso (peptide transporter) and a water channel protein Aquaporin Z, which fold properly in aqueous environment. Protein synthesis in the presence of both liposomes and the polymers result in the incorporation of proteins into phospholipid bilayers, and allow proteins to transport oligopeptides and waters across liposome membrane respectively. Notably, the results validate our hypothesis that the polymer can serve as a synthetic chaperone that sequesters the membrane proteins from water and still retains their structures and functionalities.   

Non-topochemical Solid State Polymerization of Benzene Monomer into Diamond Nanothread Single Crystals

Diamond nanothreads are a new type of 1D sp³ carbon nanomaterial, synthesized by solid state reaction of benzene (Nat. Mater., 2015). In view of their stiffness and unlike most polymers, they readily form hexagonally-packed single crystals of threads, as demonstrated by XRD (JACS, 2017). We investigated the polymerization reaction under pressure. The stacks of benzene molecules in the reactant crystal must contract dramatically along the thread axis (by 40–50%) while the symmetry increases from monoclinic to hexagonal as nanothreads form. Thus it doesn't proceed with commensuration of periodicities from reactant crystal to polymer crystal as is found in topochemical reactions. In some sense, the applied mechanochemical stress “templates” the reaction to form single crystal nanothreads from polycrystalline benzene monomer. It is surprising that well-ordered 1D crystals can be obtained from an uncatalyzed, room T reaction directly forming C-C bonds with large changes in symmetry and distances. Breaking the constraint of topochemical reaction to form single crystals of polymers and carbon nanomaterials may allow for the synthesis of a large, new family of materials.   

Real-Time High-Resolution AFM of Crystallization Process of Isotactic Poly(methyl methacrylate) Monolayer under High Humidity

We have successfully observed the formation of a folded-chain crystal (FCC) from an amorphous state at the molecular level using atomic force microscopy (AFM). We previously showed that FCC of an isotactic poly(methyl methacrylate) (it-PMMA) formed in its Langmuir monolayer upon compression and after being deposited on mica could be visualized at the molecular level by AFM (Kumaki et al. JACS 2005, 127, 5788; J. Phys. Chem. B 2013, 117, 5594). Recently, we found that an amorphous it-PMMA monolayer deposited at a low surface pressure crystallized under high humidity at room temperature, and successfully visualized the FCC formation process at the molecular level by AFM in real time. We will discuss the various crystallization processes observed at the molecular level and their dependence on the humidity and the surface pressure during the deposition.   

Reorganization and Recrystallization in αc-Mobile and Crystal-Fixed Semicrystalline Polymers Studied by Fast Scanning Calorimetry (Flash-DSC) and SAXS

Semi-crystalline polymers can undergo processes of reorganization/recrystallization during a heating scan in a DSC measurement. As a result, several melting peaks are observed or the melting peak shifts depending on the applied heating rate. We investigated these processes by a Flash-DSC for α_c-mobile and crystal-fixed polymers in comparison. With NMR it is possible to distinguish these classes of sc polymers, depending on the presence of α_c-relaxation - an intra-crystalline chain mobility. As model samples we chose PEO (α_c-mobile) and PCL (crystal-fixed). Typical experiments consist of heating scans after isothermal crystallization with a broad range of different heating rates which in the limit of large heating rates allow a suppression of the reorganization. At such high heating rates additional experimental effects like thermal lag and superheating become important and need to be taken into account. Our results show that crystallization of PCL leads to the formation of marginally stable crystallites that constantly reorganize during heating, while in PEO due to the presence of the α_c-relaxation, much more stable lamellar crystals form, which melt only at much higher T. Crystallization at low T on the other hand seems to suppress the α_c-induced stabilization in PEO.
  

Flow-induced Crystallization of Nylon 6/6

When a semi-crystalline polymer melt is subjected to intense flow before crystallization, the crystallization kinetics are accelerated and the crystal morphology is changed from isotropic spherulites to smaller anisotropic structures, which is termed flow-induced crystallization (FIC). In this study, FIC of Nylon 6/6 was characterized using rheology and polarized optical microscopy. Using a rotational rheometer, a wide range of specific works (10 ~ 10^7 Pa) was imposed prior to crystallization (Ts=270 ^oC) above the melting temperature (Tm=265 ^oC). Small amplitude oscillatory shear was then used to monitor the acceleration of crystallization kinetics at a lower crystallization temperature (Tc=245 ^oC). When the imposed specific work increased from 10 to 10^7 Pa before crystallization, the onset time of crystallization was accelerated from 628 to 26 s. The shear-induced structures were directly observed through a polarized optical microscope equipped with a hot stage under nitrogen. With a Nylon 6/6 disc, which was sheared at 10 s^-1 between two parallel plates, large spherulites were observed at the center (~0 s^-1), while a mixture of smaller spherulites and anisotropic cylindrites were observed at the edge (~10 s^-1).
  

Self-Poisoning in Crystallization of Helices

Crystallization of complex molecules such as polymers sometimes shows peculiarities absent in atomic or small-molecule systems. They are due to tortuous kinetic pathways that involves complex conformational ordering additional to the simple adoption of correct position and orientation. One such anomaly is the growth rate minimum as a function of crystallization temperature or solution concentration, or multiple minima, exhibited by monodisperse long-chain alkanes.¹ These occur at the transition from extended to folded-chain growth, or once-folded to twice-folded etc. The slow-down and even complete cessation of growth are due to the numerous but not quite stable folded-chain depositions blocking the productive extended-chain ones at the growth surface.
Such stark anomalies tell us much about the self-poisoning that takes place at the growth surface of all polymers. However, growth rate minima and self-poisoning should not be restricted to chain folding. Here we consider the possibility of self-poisoning in polymers due to incorrect helical order blocking the growth of crystals with ordered helical chains. We show, using two different kinetic models, that growth rate minima due to “helical self-poisoning” are possible.

1. G. Ungar et al., PRL 2000, 85, 4397.   

Mesoscopic Heterogeneity in Curing Process of An Epoxy Reaction System

To confer desirable mechanical properties onto an epoxy resin, it is necessary to understand and control a spatial heterogeneity induced in it upon the curing process. In this study, the spatial heterogeneity in a mixture of hydrogenated bisphenol-A diglycidyl ether and 1,4-cyclohexanebis(methylamine) with a molar ratio of 2:1 was examined at a given temperature as a function of time by a particle tracking technique, in which local physical properties can be examined on the basis of the thermal motion of a probe particle. Polystyrene particles with diameters of 200, 120 and 50 nm were used as a probe, leading to observations with different length scales. We could successfully track the time evolution of spatial heterogeneity in the system during the curing reaction and combine the bulk mechanical properties of the resultant resin.   

Determining Forces in Macroscopic Fiber Networks Using Conductive Fabric

Fiber networks are present in various systems from textiles and paper to the cytoskeleton and tissues. Simulations of fiber networks have unveiled interesting emergent phenomena. However, it has proven difficult to experimentally probe how forces are distributed across individual fibers in such networks. Here we are able to determine the force distribution through multiple geometries of macroscopic networks in both two and three dimensions in a simple manner. We construct networks out of macroscopic strips of conductive fabric. We measure the change in resistivity of each element of conductive fabric as a network is perturbed to determine the force on each element simultaneously. We investigate the magnitudes of the forces within the network and how those forces are spatially distributed through the network. Our model system makes determining the stress throughout a large system quite simple, and can be applied to large and three-dimensional systems.
  

Structure and Mechanics of Random Networks of Fiber Bundles Stabilized by Adhesion

Nanofibers self-organize under the action of strong adhesive forces. Examples of such systems are collagen networks in connective tissue, carbon nanotubes and nanoribbons, and polymeric electrospun nanofibers. Self-organization leads to the formation of fiber bundles which then assemble in networks of bundles with a cellular structure. In this work we study the self-organization process and classify the resulting structures, indicating the range of system parameters corresponding to each type of network. The mechanics of adhesion-stabilized networks of bundles is then studied and compared with the mechanical behavior of networks of equivalent density and fiber properties without adhesion. The presentation provides a comprehensive overview of the conditions of existence and properties of such systems.   

Liquid Letters

Using the interfacial jamming of cellulose nanocrystal (CNC) surfactants, we introduce a new concept, termed all-liquid molding, to produce all-liquid objects that retain the shape and details of the mold with high fidelity, yet remain completely liquid. This simple process, where the viscosity of the CNC dispersion can range from that of water to a cross-linked gel, opens tremendous opportunities for next generation soft materials. The process described is generally applicable to any functionalized nanoparticles dispersed in one liquid and polymer ligands having complementary functionality dissolved in a second immiscible liquid. Such sculpted liquids retain all the characteristics of the liquids but retain shape indefinitely, very much like a solid. These molded objects are fully liquid, have long-term stability, and can adapt or respond to external stimuli, providing a new platform for encapsulation, delivery systems, the development of sensors, and liquid electronic devices.   

How to Measure Work of Adhesion and Surface Tension of Soft Material

Knowledge of the work of adhesion and surface tension plays an important role in design of new materials for applications as coatings, adhesives and lubricants. We develop an approach for obtaining work of adhesion and substrate surface tension from analysis of the equilibrium indentation data of rigid particles in contact with elastic surfaces. By comparing predictions of different models of a rigid particle in contact with a soft elastic surface we show that a crossover expression taking into account contributions of the elastic energy of the contact and surface free energy change outside and in the contact area is the best in describing the results of the coarse-grained molecular dynamics simulations. This crossover expression is applied to obtain work of adhesion and surface tension of glass particles on PDMS substrates. In particular, we study the indentations produced by silica particles with sizes varying between 0.2 and 1.5 μm on super-soft, solvent-free PDMS elastomers with brush-like network strands. By varying the side chain grafting density and the crosslinking density of the networks, we control their elastic modulus from ~3 to 600 kPa.   

Quantification of Crumpling in Graphene Oxide via Ultra-Small-Angle X-Ray Scattering

Graphene oxide and related two-dimensional nanostructures have been of significant interest in the last decade for their potential applications in catalysis, energy materials, nanoscale electronics, and other areas. Previous work has found that crumpling of sheet-like nanostructures can be used to enhance dispersion, tune electronic properties, and develop nanomechanical devices. An understanding of the topological details of such structures has revealed various qualitative features driven by thermodynamics and interfacial chemistry. Here, we present a scaling model for these structures which, coupled with small-angle scattering data, can quantify their crumpling. We introduce two key parameters that quantify this crumpling: the tortuosity of a path across the sheet, Φ_m, and the size of the average two-dimensional persistence of the structure, the Kuhn area l_k². This work enables prediction of properties of sheet-like nanostructures and development of structure-property relationships through statistical quantification of the crumpling in the structure.   

Investigating pressure denaturation using the high pressure small angle x-ray scattering

The continuous progress in the field of basic molecular biosciences has a persistent goal of establishing and utilizing the rational correlations amongst the molecular structure and function of biomolecules. As a fundamental thermodynamic parameter, pressure affects a process that leads to decrease in overall volume in a closed system, following the Le Chateliers’s principle. Exposure to a high-pressure (hp) environment causes proteins to unfold in a way that allows structural information to be accessed, not accessible otherwise. Pressure also affects the tertiary structure by collapsing the internal cavities unlike chemically or thermally induced denaturation. Small angle x-ray scattering (SAXS) provides direct information of the structure and hence the deviations in the volume of macromolecules. The presentation will elaborate upon the recent advances in the multidimensional hp sciences, specifically oriented towards the application of the hp-SAXS capabilities at the Cornell High Energy Synchrotron Source, which is complimentary in nature to the information obtained using NMR and fluorescence spectroscopies.   

Photothermal Actuation of Liquid Crystal Elastomer Nanocomposites

Photoactive liquid crystal elastomers are a powerful platform for generating work from light. Material systems incorporating azo-based dyes and carbon nanomaterials into liquid crystal elastomers have been shown to drive actuation upon light illumination through isomerization and photothermal heating, respectively. However, little work has been done on the incorporation of metallic nanoparticles into liquid crystal networks for photothermal actuation. Here we demonstrate the preparation of nanorod-containing liquid crystal elastomers by post-synthesis doping of aligned networks. Upon illumination with visible light, these materials generate up to 30% strain due to photothermal heating. An investigation of optical properties, mechanical properties, deformation kinetics, and a simple heat transfer model are also presented. Finally, we discuss opportunities for the use of these materials in deformable optics and future avenues for development.   

Useful Defects on the Surfaces of Chiral Liquid Crystalline Polymers

Materials found in nature are often classified as being in the liquid, solid or gas state. Some materials such as nematic liquid crystals flow like liquids but orient themselves along a common axis. Chiral nematic crystals additionally form periodical helical structures which leads to selective reflection of light and formation of a number of defects including focal conic domains. Chiral liquid crystalline polymers and oligomers which can vitrify are of special interest because defects formed on their surface can be manipulating in a variety of ways. Changing the temperature or the chemical nature of the surface interface as well as decorating the defects with metal nanoparticles/metallizing the surface allowed for unique patterns. The defects were studied in chiral liquid crystal siloxanes, oligomers and networks, and their formations were studied under an atmosphere of volatile organic compounds and liquid concentrations. Next, the surfaces were decorated and/or metallized by silver and studied under Atomic Force Microscopy. The surface patterns created were found to be very sensitive to changes in the atmosphere of volatile organic compounds. Applications of the metallized liquid crystal polymers are far reaching and can find use to create diffraction gratings and much more.
  

Sub 10-nm Self-Assembly of Mesogen-containing Diblock Macromonomers and their Graft-through Polymers

We explore the morphology and phase behavior of branched diblock macromonomers and their grafted-through polymers. A library of materials was synthesized based on a recently developed architecture, with each macromonomer in the library consisting of a polydimethylsiloxane (PDMS) homopolymer branch and a branch containing 1, 2, or 3 cyanobiphenyl (CB) mesogens. Each macromonomer was then polymerized to 3 different degrees of polymerization (N=10, 25, or 50). Due to the immiscibility of the two branches, the molecules self-assemble to form classically observed microphase-separated structures, including spheres, hexagonally packed cylinders, bicontinuous gyroid, or lamellae. We report the observation of well-ordered lamellae and cylinders with d-spacings as low as 6.1 and 8.0 nm, respectively. We find that the coil-branch-rod(s) structure leads to an asymmetric phase diagram. Other unique features of the samples in this library include highly birefringent textures observed by polarized optical microscopy and a distortion of microstructure for some samples due to crystallization. The small d-spacings and large grain sizes observed here highlight the versatility and potential utility of this molecular architecture for designing and engineering new functional materials.



  

Going to Nanoscale by Surface Patterning

Polymers forming glassy states are notable for the creation of nanostructures on their surfaces. Liquid crystalline glassy polymers are of interest due to the inherently higher molecular order they possess. This allows for creation and observation of a number of unique patterns on their surfaces. These patterns may be induced by intelligent heating or light irradiation. In this work we used conventional polymer glasses and nanoparticles to decorate and replicate such patterns on the surface of glassy chiral liquid crystalline polymers. The polymers were studied by Atomic Force Microscopy. It was observed that both chiral polymers and replicas can be decorated with nanoparticles and form a variety of surface patterns. The possibility of using these patterns for the creation of metamaterials is discussed.   

Glassy Oligomer Sensitivity to Volatile Organic Compounds

The sensitivity of chiral liquid crystals (CLCs) to their surrounding environments enables them to be useful gas sensors. The various CLCs used in this experiment were studied to determine their sensitivity to certain volatile organic compounds (VOCs), namely toluene, cyclohexane, and ethanol. Liquid crystal siloxane oligomers have a high melting point and form a glassy state at room temperature; they were “physically” modified by being blended with low molar mass compounds with a lower melting point. The liquid crystalline blends were placed in a vacuum-sealed container filled with a gaseous VOC for fifteen minutes. The samples were examined by optical and atomic force microscopies (AFM). Responses to VOC treatment were found in all experiments. AFM studies are especially interesting as they point to subtle changes in the very thin surface layer and, therefore, occur during much shorter times of treatment and/or lower concentrations of VOCs. Each solvent was found to have its own impact on surface pattern studied by AFM. The changes observed in AFM are also discussed from theoretical viewpoint.   

The calorimetric signature of aging in an epoxy glass following mechanical rejuvenation

Diglycidyl ether of bisphenol A (DGEBA) epoxy is cured with diethanolamine and then aged at 20°C below Tg for varying amounts of time. The samples are uniaxially compressed (“mechanically rejuvenated”) through yield and then further aged at room temperature. DSC temperature ramps are run on both (1) samples aged but not compressed and (2) samples aged after rejuvenation. Thermograms of samples aged at Tg-20°C exhibit the typical aging peak near or above Tg. It is found that compression erases the physical aging peak as expected from previous studies. The post-compression samples aged at room temperature show complex thermograms with a small “pre-Tg” peak and a broad “post-Tg” peak. Both of these peaks become more pronounced with increased post-rejuvenation aging time.   

Free Surface Flows and Extensional Rheology of Polymer Solutions

Free-surface flows -- jetting, spraying, atomization during fuel injection, roller-coating, gravure printing, several microfluidic drop/particle formation techniques, and screen-printing -- all involve the formation of axisymmetric fluid elements that spontaneously break into droplets by a surface-tension-driven instability. The growth of the capillary-driven instability and pinch-off dynamics are dictated by a complex interplay of inertial, viscous and capillary stresses for simple fluids. Additional contributions by elasticity, extensibility and extensional viscosity play a role for complex fluids. We show that visualization and analysis of capillary-driven thinning and pinch-off dynamics of the columnar neck in an asymmetric liquid bridge created by dripping-onto-substrate (DoS) can be used for characterizing the extensional rheology of complex fluids. Using a wide variety of complex fluids, we show the measurement of the extensional relaxation time, extensional viscosity, power-law index and shear viscosity. Lastly, we elucidate how polymer composition, flexibility, and molecular weight determine the thinning and pinch-off dynamics of polymeric complex fluids.   

Mesoscopic Model with Vectorial Structure Parameter for Star Polymers

In a previous study on non-equilibrium interactions between star polymers (Briels et al., JCP, 134, 124901, (2011)), we presented a mesoscopic model to describe transient forces where one star polymer is fixed at the origin and the other star polymer is dragged past at a constant velocity. When the moving star is directly above the fixed star, the force along x-direction is zero, in disagreement with small-scale simulations (Singh et al., PRL, 107, 158301, (2011)).

Motivated by this disparity, we present an updated mesoscopic model for transient forces between two star polymers (Fitzgerald and Briels (2017)). Calculation of the transient forces is based on the response of a vectorial structure parameter rather than a scalar parameter, thus allowing for the description of both mixing and deformation processes. This simple model that takes these processes into account turns out to fit into an obvious generalisation of the coarse-grained RaPiD model introduced by us some time ago. The model reproduces forces from the simulation quite well, and at the same time removes an unphysical feature of the RaPiD model used so far.   

Effects of Dipolar Interactions on Microphase Separation in Diblock Copolymer Melts

We have studied the effects of dipolar interactions on the thermodynamics of microphase separation in diblock copolymer melts using a field theory approach along side coarse-grained molecular dynamics simulations. The effects of mismatch in the dipole moments of the monomers on the disorder-order transition as well as on the domain spacing of the lamellar morphology will be presented. Not only do the coarse-grained simulations confirm predictions of the field theory approach (valid for freely-rotating point dipoles) but also they provide insights into the effects of orientation dependent dipolar interactions. The effects of dipolar interactions on the segregation strength in lamellar morphology will also be discussed.   

A Model for Dry-Wet Spinning of Cellulose Fibers

Polymeric fibers are manufactured by spinning from polymer melts or solutions. For the latter, coagulation occurs through precipitating in liquid bath (wet spinning) or evaporating the solvent in air (dry spinning). Recent development of dry-wet spinning combines the two coagulation mechanisms, resulting in better control of spinning cellulose fibers from ionic liquid solutions. We discuss the mechanism of dry-wet spinning in general terms using a model that incorporates both constitutive equations of fluid dyanmics and continuouse structural transformation during two stages of spinning processes.   

Dissolution and Precipitation of Oligomeric Cellulose in Lithium Hydroxide Solutions

The dissolution and precipitation processes for oligomeric cellulose with degree of polymerization 15 in lithium hydroxide/water solution were studied. A phase diagram of dissolution was mapped based on mole ratios between cellulose anhydrous glucose units, lithium hydroxide ions and water. The solution showed lower critical solution temperature (LCST) behavior or precipitation upon heating up to 90°C. The precipitates redissolve after cooling to near 0°C. The LCST behavior and large temperature hysteresis is attributed to hydrogen bond formation between cellulose and hydrated ions. The precipitates from lithium hydroxide were found to be cellulose in the type II crystal form but the intensity ratio between (200) and (110) peaks was reversed, which differs from the precipitates from sodium hydroxide solutions.   

Modeling directed motion of polymer gels

We utilize the 3D computational gel lattice spring approach to model the directed motion of polymer gels. We consider a lower critical solution temperature (LCST) gel, which is placed between two parallel plates. Upon a decrease in temperature, the plates constrain the swelling of the gel to the direction parallel to the surface. We assume that in the course of swelling, the gel slides along the confining surfaces with a local friction coefficient that is proportional to the normal stress (Newtonian friction). Using the gel lattice spring model, we demonstrate that the gel can attain directed motion with the application of an externally controlled temperature stimulus. In a system containing several gel pieces, the gels self-organize to exhibit concerted movement. The reported results can be used to design advanced gel-based actuators.   

Solidification of poly(2-methoxyethyl acrylate) via block copolymerization with poly(methyl methacrylate)

Antithrombogenicity is one of the most important properties required for a material used in the biomedical applications, especially for the devices used in direct contact with blood. It is known that poly(2-methoxyethyl acrylate) (PMEA) has an excellent antithrombogenicity. However, due to its low Tg (~ -20°C), a PMEA homopolymer is liquid-like, which cannot be directly used as a solid material. In this study, we attempted to solidify the PMEA by the block copolymerization with poly(methyl methacrylate) (PMMA) as a hard segment, possessing a high Tg (~ 110°C). The synthesized MMA-MEA-MMA triblock copolymer exhibited two Tgs due to the PMEA block (~ -20°C) and the PMMA blocks (~ 110°C). The triblock copolymer could be mold-pressed at 180°C, and the resulting molded film exhibited elastomeric characteristics. Moreover, when the volume fraction of MMA was below 0.4, the triblock copolymer exhibited an excellent antithrombogenicity similar to that of a PMEA homopolymer. The triblock copolymer could be used as a rubber-like material with thermoplastic and antithrombogenic properties.   

Mean-Field Critical Behavior of End-Linked Polymer Networks with Loops

The Flory-Stockmayer (F-S) theory of gelation has been a paradigm for understanding chemical gelation. In the F-S mean-field model, monomers are placed at the sites of a Bethe lattice, and the process of end-linked network formation becomes equivalent to the bond percolation process on such a lattice. Extension of F-S theory to non-ideal networks shows that bond percolation for either purely branching networks or networks containing uncorrelated loops exhibits the same classical F-S critical exponents, regardless of the exact topology of the underlying network. However, the regime where loop formation is prevalent and loops are heavily correlated has not been investigated. Here, using a mean-field kinetic Monte Carlo simulation, we demonstrate that the critical exponents deviate significantly from the classical F-S values when loops becomes strongly correlated. We show that for networks with small loop fractions, finite size scaling gives the classical critical exponents; when loop fraction is increased, the calculated critical exponents deviate from the classical values, suggesting that the introduction of loops significantly alters the topology of the network formed.   

Fracture of polymeric gels

A polymeric gel is a cross-linked polymer network swollen with a solvent. If the concentration of the solvent or the deformation is increased to substantial levels, especially in the presence of flaws, then the gel may rupture. Although various theoretical aspects of coupling of fluid permeation with large deformation of polymeric gels are reasonably well-understood and modeled in the literature, the understanding of the effects of fluid diffusion on the damage and fracture of polymeric gels is still in its infancy. A simple model which has the predictive capacity is still lacking.

In this talk, we will show a recent proposed model for fracture of polymeric gels, by embedding the following central idea in the model: the chain of polymers start to break as the stored internal energy attain a certain value. Many interesting phenomena of soft materials can be explored then: i). Swelling induced fracture. ii). Delayed fracture, and iii). Rate-dependent toughness due to diffusion. Also in the talk, we will systematically explore the fast deswelling induced fracture in a typical soft material, by theoretical, experimental and numerical analysis.   

Self-doped Block Polymer Electrolytes for Lithium-ion Batteries

As a result of their ability to self-assemble on nanometer length scales, block polymer (BP) electrolytes offer an attractive strategy to tackle the competing constraints of high conductivity and mechanical/thermal stability that hamper optimization of traditional electrolyte materials. Herein, we report on the behavior of a new self-doped diblock terpolymer electrolyte, in which one block was a high modulus material and the other was comprised of high ion-conductivity and self-doped monomer segments. Unlike traditional salt-doped BP electrolytes, which require the addition of a lithium salt to bestow conductivity, these self-doped BPs minimize counterion motion that reduce efficiency and cause concentration polarization in the electrolyte. These single-ion BPs were synthesized with a series of self-doped lithium concentrations, and the nanoscale morphologies were determined using small angle X-ray scattering and transmission electron microscopy. Electrolyte transport properties were measured via AC impedance spectroscopy and DC polarization. With this enhanced physical understanding, the chemistries, monomer segment distribution, and ion content of the self-doped BP can be used to inform BP electrolyte designs.   

Tuning structure and properties of lamellar sulfonated pentablock terpolymer films

Thin films of sulfonated block copolymers are widely studied for applications in water purification and electrochemical devices. When films are cast from solution, the ultimate structures are strongly influenced by the solvent’s polarity. These structures are often not well-defined, presenting a challenge for fundamental studies of structure and properties. In this work, we demonstrate lamellar self-assembly in 16-µm films of a sulfonated pentablock terpolymer cast from solvent mixtures. As the polarity of the solvent mixture is increased, the lamellar structure becomes more disordered. Both surface and bulk properties are impacted by these changes: the surface becomes more hydrophilic, and water uptake increases by a factor of 1.5. This increase in water uptake comes at the expense of mechanics, as the films become tacky and disintegrate over time in water. These results demonstrate that continuity of the sulfonated domains can be tuned through processing. The knowledge acquired from this work can facilitate structure-property-processing relations of these highly complex materials.   

Molecular weight dependence of chain conformation of polyelectrolytes

Molecular conformation of permanently charged polyelectrolytes is investigated at single molecular level by fluorescence correlation spectroscopy (FCS). By taking sodium polystyrene sulfonate (NaPSS) and quarternized poly 4-vinylpyridine (QP4VP) as model systems, the hydrodynamic radius (R_h) was measured for a series of samples covering molecular weight about an order of magnitude. The results show that the scaling power index depends on the ionic strength in the aqueous solution, and especially under moderate ionic strength, the scaling power index differs depending on the molecular weight of the polyelectrolyte, indicating the dependence of molecular conformation on the molecular weight, a process of conformation change from rod-like to random coil. The physical origin is found to be the enhancement of counterion adsorption (binding) to the charged chain.   

Synthesis and Self-Assembly of PS-b-PDMS Bottle Brush Block Copolymers

Recently, brush block copolymers (BBCPs) have attracted significant interest due to their ability to rapidly self-assemble into phase separated nanoscale morphologies. The precise control over side chain chemistry/length and backbone M_w has opened many new opportunities for designing a diverse library of nanostructures. Here, we report the successful synthesis of Poly(styrene)-block-Poly(dimethyl siloxane) (PS-b-PDMS) BBCPs by ring opening metathesis polymerization (ROMP) of norbornene functionalized macromonomers of variable side chain length (PS M_n = 2.9 and 4.7 kg/mol, PDMS M_n = 4.8 kg/mol). BBCPs synthesized over a wide range of M_w (M_w = 195 to 982 kg/mol) at symmetric volume fraction microphase separate into ordered lamellar morphologies via rapid self-assembly after thermal annealing. The lamellar spacing (d) was determined by small angle X-ray scattering and scales with the overall degree of polymerization (d ~ DP^a). The scaling exponents of a = 0.70 and 0.82 for the two series of side chains indicate an extended backbone conformation when compared to linear BCPs in the strong phase segregation limit. The PDMS side chains appear to impart additional flexibility when compared to previously reported BBCP systems, and this is directly influenced by the side chain length.
  

Phase Transition of Binary Block Copolymer Blends and Pressure Dependence

Three types of phase transitions were identified in the miscible block copolymer blends of polystyrene-b-poly(n-butyl methacrylate) (PS-b-PnBMA) and polystyrene-b-poly(n-hexyl methacrylate) (dPS-b-PnHMA), which were known as order-to-disorder transition (ODT), lower disorder-to-order transition (LDOT), and upper order-to-disorder transition (UODT). Interestingly, the closed-loop transition was found in a specific volume range (0.511~0.514) of one block. Small-angle X-ray scattering (SAXS) and depolarized light scattering (DPLS) were used to measure the composition-dependent phase transitions, and transmission electron microscopy (TEM) was used to confirm each results. These phase transition boundaries were demonstrated in a 3D phase transition diagram of the BCP blends with other variable of (d)PS volume fraction. Such diverse phase transitions and the closed-loop transition showed high pressure-sensitive baroplastic nature, arising from entropic compressibility.   

Composition Fluctuation at Order-to-Disorder Transition: χN effects of Symmetric Diblock Copolymers

We report that the thermodynamic segregation power of cN where χ is the Flory-Huggins interaction parameter and N is the overall degree of polymerization will also be an important parameter for block copolymers (BCPs) to influence the composition fluctuation inhomogeneity at order-to-disorder transition (ODT). For this purpose, a series of symmetric BCPs of polystyrene-b-poly(2-vinlyprydine) (PS-b-P2VP), PS-b-poly(methyl methacrylate) (PS-b-PMMA), and PS-b-poly(n-hexyl methacrylate) (PS-b-PnHMA) with modest molecular weights were prepared to represent the (χN)_ODT sequence of . The latent heat (ΔH_ODT) at ODTs were estimated by differential scanning calorimetry (DSC) and Porod invariant (Q) at ODTs from the small angle x-ray scattering (SAXS), and the properties of local composition profiles at ODTs are described in terms of (χN)_ODT of BCPs.   

Comparison of phase behavior of 18-arm star-shaped polystyrene-block-poly(methyl methacrylate) copolymers depending on degrees of second block initiations

We investigated, vis electron microscopy and small-angle X-ray scattering, the difference of phase diagram of 18-arm star-shaped polystyrene-block-poly(methyl methacrylate) copolymers ((PS-b-PMMA)₁₈) depending on the degree of initiation of the second PMMA. Star-shaped block copolymers, using different catalysts CuBr and CuCl, were synthesized by using α-cyclodextrin (α-CD) as a core of the star-shape. When CuBr was used for catalyst, PMMA was linked to only 75% of PS arm and, in the case of CuCl for calatlyst, PMMA was linked to 100% of PS arms perfectly. The reason is that, using CuCl for catalyst, reaction rate of propagation of PMMA to PS whose end is bromine is similar to that of PMMA to PMMA whose end is chloride. Because of this difference, phase diagram depending on shell part volume fraction was different. Those block copolymers were characterized by gel permeation chromatography and nuclear magnetic resonance. Morphology of Star-shaped block copolymer was characterized by TEM and small angle X-ray scattering.   

Universal Behaviors for Chirality Effect on Self-Assembly of Block Copolymers

Here, we aim to investigate the universal behaviors of the chirality effect on the self-assembly of chiral block copolymers (BCPs*). A new type of BCP*, poly(cyclohexylglycolide) (PCG)-containing block copolymer (BCP) (i.e., poly(benzyl methacrylate)-b-poly(D-cyclohexylglycolide) (PBnMA-PDCG)), are designed and synthesized for self-assembly. Exclusive handedness of PCG polymer chain in the enantiomeric BCPs* can be found due to intramolecular chiral interaction of chiral entities as evidenced by coupling of carbonyl group (C=O) in vibrational circular dichroism (VCD) spectra. By taking advantage of intermolecular chiral interaction, the self-assembly of the PCG-containing BCP* gives the formation of helical phase (H*), suggesting the chirality effect on BCP self-assembly. Most interestingly, with the high twisting power, the metastability of forming H* can be significantly affected, resulting in the tendency to give H* with higher thermodynamic stability. The observed phase behaviors of the PCG-containing BCP*s are in line with theoretical prediction based on chiral orientational self-consistent field theory at which the chiral PCG behaves like mesogenic liquid crystal as evidenced by the mirror-imaged VCD signals of C-O-C vibration.   

Measurement and Predictability of baroplasticity in polystyrene-b-poly(ethyl hexyl acrylate) copolymers

Baroplasticity in deuterated polystyrene-b-poly(ethyl hexyl acrylate) (dPS-b-PEHA) melts is measured through small-angle neutron scattering (SANS) experiments at selected pressures. The order-to-disorder transition (ODT) temperatures for the copolymer is shown to decrease upon the pressure increase. In order to acquire predictability of its phase behaviors, we theoretically analyze our SANS measurements. A compressible random-phase approximation (cRPA) theory based on an off-lattice molecular equation-of-state model is chosen for our purpose. The necessary homopolymer properties for PEHA are first determined by using its PVT data. The ODTs and their pressure dependence for the copolymer are used to elicit a proper cross-interaction parameters between the constituents. We discuss our prediction for the phase behaviors of dPS-b-PEHA/dPS or dPS-b-PEHA/PEHA blends.   

Double Diamond of Self-Assembled Chiral Diblock Copolymers

Here, a double diamond (DD) phase was found in the self-assembly of chiral block copolymer, polystyrene-b-poly(L-lactide) (PS-PLLA). The tetrapod with four fold symmetry in the DD phase can be directly visualized by transmittance electron microscope tomography (i.e., 3D TEM) and further identified by small angle x-ray scattering with fitting of effective sphere model for two-node dihedral texture. In contrast to the double gyroid (DG) phase from achiral block copolymer, polystyrene-b- poly(D,L-lactide) (PS-PLA), the excessive frustration in the center of the node of the DD phase can be alleviated by the formation of helical polymer chain with higher persistent length (helical persistent length); the helical conformation with preferred handedness can be evidenced by the vibrational circular dichroism (VCD) at which the split-type Cotton effect can be clearly recognized. Moreover, interesting phase transitions among DD and DG as well as helical phase from the chiral PS-PLLA were systematically examined in comparison with the DG from achiral PS-PLA. The corresponding transition mechanisms were examined by the real-space imaging and the reciprocal scattering as well as the spectroscopic results of VCD for the metastability study of self-assembled phases from chiral block copolymers.   

Role of Polymer Chain Helicity in Block Copolymer Self-Assembly

While coil–coil and rod–coil block copolymer self-assembly are well understood, the details of how chain conformational asymmetry affects the thermodynamics of self-assembly are still unclear. Here, we use polypeptoid-containing block copolymers to achieve direct control of chain conformation. By incorporating homochiral, bulky side chains, a helical conformation is induced in the polypeptoid block, while a racemic mixture of the same side chains generates an unstructured polypeptoid chain. Block copolymers with a helical polypeptoid chain have increased domain spacings relative to the unstructured counterpart, due to chain stretching penalty and packing frustration. Thermodynamically, the chain conformation is expected to affect the Flory–Huggins parameter χ through an effective coordination number. The interaction parameter between the two chemically distinct blocks, poly(methacrylate) and polypeptoid (helical or unstructured), can be extracted from interfacial segregation of the block copolymers to a homopolymer interface using secondary ion mass spectrometry (SIMS). This polypeptoid-containing system will offer new insights into the effects of chain helicity on the thermodynamic interactions and self-assembled structures of block copolymers.   

Characterizing the Microscale Mobility and Viscoelasticity of Entangled Blends of DNA of Varying Lengths and Topologies

Due to the complexity of entangled polymer systems, the majority of previous studies have focused on monodisperse systems of linear polymers. However, systems that exhibit the most intriguing and useful properties – those that make up biological cells and fluids and are used to develop new materials – are blends of polymers of different lengths or topologies.
To elucidate the viscoelastic properties of entangled polymer blends, we use DNA as a model polymer system that naturally occurs in ring and linear form with wide-ranging lengths. We use particle-tracking microrheology to characterize the viscoelastic properties of entangled blends of: (1) 45 kbp linear and ring DNA and (2) 11 kbp and 111 kbp linear DNA. Specifically, we track the brownian motion of embedded microspheres to quantify the diffusive characteristics and viscoelastic moduli of blends. We systematically determine the dependence of these properties on the ratio of the two different blend species ((1) ring vs linear and (2) short vs long). Results of our systematic study shed new light on a currently intractable problem in polymer physics, and provide design principles for engineering new biopolymeric materials.   

Spinodal nanostructures in polymer blends and the Cahn-Hilliard lengthscale prediction

Spinodal decomposition of partially miscible polymer blends has the potential to generate well-defined polymeric nanostructured materials, with precise control of lengthscale and connectivity, and vast applications ranging from membranes to photovoltaics. We examine experimentally the validity of the classical Cahn-Hilliard theory prediction for the initial spinodal lengthscale q*=sqrt(-G''/4k), where G’’ is the second derivative of the free energy of mixing with respect to composition, and k is the prefactor of the square gradient term, accounting for additional free energy arising from concentration gradients. We contrast an unprecedented series of Λ≡2π/q* estimates, self-consistent with the theory, and independent -G’’(T) and k measurements, and overall find the prediction to be remarkably accurate for all blends and conditions examined. No breakdown of this prediction is observed at the smallest Λ recorded experimentally, which are however still several times larger than Rg. Finally, we outline design considerations and limitations for generating polymeric materials via spinodal decomposition, bound by thermodynamics of available polymer systems, coarsening kinetics governed by rheology, as well as by engineering constraints.   

Raman Investigations on PS-PERB-PS – Graphene Nanocomposites

Polystyrene-Block-Poly(ethylene-ran-butylene)-Block-Polystyrene (PS-PERB-PS) and chloroform were purchased from Sigma Aldrich. Graphene was purchased from Cheaptubes. The block copolymer was dissolved in chloroform. Then the graphene powder was added to the solution. The obtained mixture was stirred at 2500 rpm for about 8 hours. Then, a high-power sonication homogenization step (500 W, 30 minutes) was necessary to obtain a good dispersion of graphene. During the sonication, the temperature of the mixture increased up to about 80 ^oC. The viscous solutions were poured on microscope slides and were introduced in an oven at 90 ^oC for 12 hours. Thermogravimetric analysis (using TA Instruments Q 50 equipment) was used to confirm the full removal of the solvent and to assess the effect of the nanofiller on the thermal stability of the polymeric matrix. Various nanocomposites containing different fractions of graphene in the block copolymer have been synthesized and investigated. Raman measurements at 532 nm and 785 nm have been performed using a Renishaw InVia spectrometer, at room temperature. The effect of the interactions between the polymeric matrix and the graphene nanofiller, as revealed by the shift of the main Raman lines assigned to graphene and PS-PERB-PS will be discussed.   

Swelling of Composite Graphene/Polymer Foams

Composite graphene/polymer foams, made through templated polymerization of the continuous monomer phase in graphene stabilized monomer/water emulsions, have unique solvent selectivity and displays electrical conductivity that is sensitive to deformation. We use a combination of the experimental techniques and coarse-grained molecular dynamics simulations to elucidate factors influencing foam selectivity and dynamics of the swelling process. In particular, we have studied swelling ability of the composite graphene poly(butyl acrylate) foams in 17 different solvents. Analysis of the swelling data shows direct correlation between solubility parameter and degree of the foam swelling. The equilibrium swelling ratio of the foam changes with the degree of crosslinking as expected for swelling of the polymer networks in selective solvents. MD simulations of the composite graphene/polymer foams indicate that the capillary forces first drive the liquid to fill up the foam cells which is followed by swelling of the surrounding polymer network. This swelling process changes overlap between graphene sheets coating the foam cell. This rearrangement of sheets manifests itself in change of the foam conductivity upon swelling.   

MOF-Random Copolymer Mixed Matrix Membrane Monolayer

Inorganic-organic mixed matrix membrane is an interesting family of materials. MOF-polymer mixed matrix membranes combine the porous property of MOF nanoparticles and processibility of polymers, which can be used in large-scale gas separation. However, the bottleneck is how to enhance the compatibility of MOF and polymer and form homogeneous mixture. Herein, we propose to use random copolymer to modify the surface of MOF nanocrystals. In detail, we investigated UiO-67 nanocrystals with polystyrene-random-poly(4-vinylpyridine). Moreover, we generate MOF-random copolymer mixed matrix membrane monolayer by interfacial assembly. We investigated the nanostructure of mixed matrix membrane monolayer as a function of MOF nanoparticle concentration, polymer chain length and polymer composition. These monolayers are defect free in macroscopic scale and exhibit promising properties in gas separation.   

From Graphene Stabilized Emulsions to Foams

The unique electrical, thermal, and mechanical properties of graphene make it a perfect candidate for applications in graphene/graphite based polymer composites. Recently shown surface activity of the graphene sheets to oil-water interphase has opened a new path for design of graphene based polymeric materials. We use molecular dynamics simulations and theoretical techniques to elucidate factors responsible for surface activity and emulsion stabilization of 2D graphene sheets. In particular, we use large scale coarse-grained molecular dynamics simulations to study affinity of the 2D elastic sheets to interface between two immiscible solvent as a function of the sheet sizes and degree of substitution of atoms on the 2D sheets. The established envelop of parameters for sheets’ surface activity is used to model emulsion assembly and emulsion polymerization producing polymeric foams which cells are coated with 2D elastic sheets. The mechanical properties of foams are studied as a function of the crosslinking density, 2D-sheet/monomer affinity, and sheets bending rigidity. The results of the computer simulations are compared with corresponding experimental studies of the graphene stabilized emulsions and composite graphene/polymer foams.   

Electrospun Carbon Nanofibers; structural and electrical properties

CNF were prepared by electrospinning polyacrylonitrile nanofibers followed by stabilization and carbonization.Electrical transport and Hall Effect on carbon nanofibers annealed at 700 °C–1400 °C was studied. It has been observed that the ratio of the D to G peaks in Raman spectroscopy and the FWHM of 100% peak (26 °) in the XRD spectra decreases as the annealing temperature increases, hence the crystallinity of CNF increases as the temperature increases. Also, the diameter of the carbon nanofibers decreases from 51.17 nm to 15.89 nm as the annealing temperature increases. CNF have been found to exhibit a semiconducting behavior in the temperature range of 350-10 K with their room temperature resistivity’s varying from 10 to 50 mOhm.cm. The Hall Effect show that Hall coefficient value was -5.6x10^-10 cm³/C at 300 K for the CNF that were annealed at 1200 °C.The electron carrier concentration and their mobility were calculated to be 1.1x10²⁰/cm³ and 25.8 cm²/Vs.The electronic charge carrier concentration is almost an order of magnitude higher than the values reported for CNF synthesized under similar conditions. Due to semiconducting nature of CNF, superior carrier concentration, and carrier mobility CNF have the potential to be used in non-silicon based integrated circuits.
  

Neutron reflectivity, water dynamics and performance of polyamide nanofilms for water desalination

We investigate the structure and hydration of polyamide (PA) membranes, with a combination of neutron and X-ray reflectivity, and benchmark their performance in reverse osmosis water desalination. Neutron spectroscopy provides further insight into the dynamics of water and the PA membrane under various hydration states. PA membranes were synthesised by the interfacial polymerization of m-phenylenediamine (MPD) and trimesoyl chloride (TMC), varying systematically reaction time, concentration and stoichiometry, to yield large-area, planar films of ≈10 nm thickness. Reflectivity precisely determined membrane thickness and roughness, as well as the (TMC/MPD) concentration profile, and response to hydration in the vapour phase. The resulting film thickness is found to be predominantly set by the MPD concentration, while TMC regulates water uptake. A favourable correlation is found between higher swelling and water uptake with permeance. The confined water dynamics were resolved and found to be coupled with the polymer relaxation dynamics. Our data provide quantitative insight into the film formation mechanisms and correlate reaction conditions, cross-sectional nanostructure and performance of the PA active layer in RO membranes for desalination.   

Mobility of Star Polymers under Confinement

Thin polymer films made of star polymers have applications in biomedical coatings and microelectronics. As the thickness of the films decreases, the surface and interfacial behavior of the polymer chains play a major role in determining the physical properties of the materials. Interdiffusion measurements can reveal the mobility of polymer chains at the interfaces. Here we have determined the thickness dependence of diffusion coefficients of the star polystyrene (PS) chains in thin films as a function of the number of polymer arms and the molecular weight per arm using neutron reflectivity (NR) and compare our results with linear chains of identical total molecular weight. Bilayer samples of 4-arm and 8-arm protonated PS (hPS) and deuterated PS (dPS) were used to elucidate the effect of polymer chain architecture on interdiffusion. NR measurements indicate that the mobility of polymer chains in thin films get faster as the number of polymer arms increases and the arm molecular weight decreases. The apparent diffusion coefficient of star PS chains has a weak dependence on the thickness of the bottom layer most likely due to the adsorption of chains on the substrate.
  

Degrafting polyelectrolyte brushes by elastic force

Polymer brushes grafted on a surface at high densities have been of great interest in the past two decades due to their high stability at the interface. Previous reports have revealed that covalent bonds between the polymer brush and the surface can break in buffer solutions, leading to degrafting of polymer chains from the surface. We report a systematic study of degrafting covalently attached polyelectrolyte brushes. Poly(2-dimethylaminoethyl methacrylate) (PDMAEMA) brushes were grown on silicon substrates by surface-initiated atom transfer radical polymerization (SI-ATRP) and incubated in aqueous solutions at varying pH with constant ionic strength. Increasing the degree of quaternization increases the swelling ratio and the elastic force. By degrafting at different pH, with constant elastic force, the main mechanism of degrafting is shown to be base-catalyzed hydrolysis at the Si-O groups and/or the ester group of the SI-ATRP initiator. Stronger elastic force on the initiator induces more degrafting. Brush degrafting increases slightly with increasing the molecular weight of the brush.   

Effect of Flory-Huggins Interaction Parameter of Block Copolymers on the Shape of Block Copolymer Particles

Systematic modulation of shape-anisotropy of block copolymer (BCP) particles is of great importance in tuning their shape-dependent properties. Herein, we investigate the effect of Flory-Huggins interaction parameter (χ) on the shape of BCP particles. Four different poly(styrene-b-butadiene) (PS-b-PB), poly(styrene-b-dimethylsiloxane) (PS-b-PDMS), poly(styrene-b-(4-vinylpyridine)) (PS-b-P4VP), and poly(dimethylsiloxane-b-(2-vinylpyridine)) (PDMS-b-P2VP) with different χ values but similar degree of polymerization (N) were used to produce two different anisotropic BCP particles (i.e., striped ellipsoidal particles and convex-lens particles). Lamellae-forming BCPs with higher χ assembled into ellipsoidal particles with more elongation. In particular, the aspect ratio (AR) of PDMS-b-P2VP ellipsoidal particles increased more than 3-fold over PS-b-PB. Similarly, cylinder-forming BCPs with higher χ assembled into flatter convex lens-like particles, resulting in an increase in AR greater than 10. Fine-tuning of shape anisotropy depending on χ was supported with theoretic calculation of particle free energy.   

Hybrid Monte Carlo / Self-Consistent Field Theory for Modeling Zwitterionic Polymers

The antifouling and biocompatibility properties of zwitterionic polymers have led to their use in surface modifications in biotechnological applications. Surfaces modified with zwitterionic polymer brushes have been shown to exhibit ultralow fouling properties. Zwitterionic polymer conjugation has been used to stabilize therapeutic proteins. The antifouling and stabilizing properties of zwitterionic polymers are hypothesized to be due to the strong hydration exhibited by the zwitterions. Theoretical models for describing zwitterionic polymers behavior are currently lacking. In this work we present a hybrid Monte-Carlo simulation and Self-Consistent Field Theory to model zwitterionic polymers in solution and on the surface. This hybrid approach has been successfully employed in modeling complex coacervation. We apply coarse-grained modeling in an NVT MC simulation with Widom Insertion to generate free energy landscapes for a polymer, salt, and solvent system. These landscapes are used to inform a SCFT describing the system. This approach allows us to capture phase behavior in solution, as well as interfacial properties on the surface. This formalism can be extended to describe interactions with other charged species such as aptamers and polypeptides.   

Design and Fabrication of Wettability Gradients with Tunable Profiles Through Degrafting Organosilane Layers from Silica Surfaces by Tetrabutylammonium Fluoride

Surface-bound gradients allow for a high-throughput approach to evaluate surface interactions for many biological and chemical processes. We fabricate surface-bound gradients using a simple, two-step procedure that permits precise tuning of the gradient profile. We deposit a homogeneous self-assembled monolayer (SAM) of silane and generate a surface coverage gradient by vertically immersing the sample into the solution of tetrabutylammonium fluoride which cleaves the Si-O bonds at the surface. We model the kinetic of degrafting using a series of first order rate equations, based on the number of broken attachment points. Degrafting of mono-functional silanes exhibits an exponential decay in surface coverage as a function of degrafting time. The degrafting of tri-functional silanes is delayed due to the presence of multiple attachment points. We examine the effects of degrafting temperature and time and demonstrate the ability to control reliably the silane gradient profile. We observe a relatively homogenous coverage of silane throughout the process, when compared to additive approaches of gradient formation. We design and form linear gradients in silane coverage to demonstrate the reproducibility and tuneability of this approach.   

Interpretation of the roughness at interfaces of photoresists from a perspective molecular aspect

Developing new materials or process conditions for photoresists, to reduce the roughness in the pattern while maintaining the high resolution and sensitivity upon light exposure, has been considered as a key for the success of high resolution (sub-10 nm) patterning technology. While inherent uncertainties due to the photon shot noise and photochemistry are considered as one of main sources of the roughness, additional factors due to the configurations of polymer chains and its distribution at the interface should be taken into account as the required roughness scales down to the molecule size. Hence beyond the former stochastic modeling, we attempted to introduce molecular simulation/modeling approach to find the inherent limits on the sharpness at the interface focusing on width and fluctuations of the interface between the exposed and unexposed area, and chain configurations during/after development. Coarse-grained polymer chain models allow us to understand the relation between the system conditions and relevant chain configurations near the interfaces.   

VO2 Nanodots Array Using Block Copolymer-Based Nanoporous Templates

We present the highly ordered array of vanadium oxide (VO₂) nanodots using nanoporous templates fabricated by block copolymers-based lithography. Thin layers of poly(vinyl alcohol) (PVA) and polystyrene-block-poly(2-vinyl pyridine) (S2VP) were subsequently prepared on a silicon (Si) substrate by spin-coating method. Then, the S2VP thin film on the PVA layer was solvent-annealed in tetrahydrofuran vapor for its self-assembly, so that hexagonally packed P2VP cylinders oriented vertically to the surface were achieved. After surface reconstruction of the S2VP thin film in ethanol, the resulting film showed hexagonally packed nanoporous structures for template-assisted self-assembly of VO₂ nanodots. Then, colloidal VO₂ nanocrystals (NCs) were deposited on the nanoporous templates. The samples were thermally treated to induce VO₂ nanodots array while organic components were completely degraded during the thermal process. Furthermore, morphologies and electrical properties of the samples were investigated by using conductive atomic force microscopy.   

Temperature-Dependent Shape and Morphology Transformation of Colloidal Particles by Controlled Assembly of Thermoresponsive Polymers

Recently, colloidal particles that exhibit real-time tailored properties in response to external stimulus have recently been in the spotlight due to their diverse range of applications. Herein, we developed a simple and practical method for producing colloidal particle with temperature-driven transformation of shape and morphology via temperature-dependent assembly of polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) block copolymer (BCP) and poly(N-isopropylacryamide) (PNIPAM) in a chloroform-in-water emulsion. Depending on the surrounding temperature, convex lens-shaped particle and pupa-like particle can be prepared by precise positioning of PNIPAM. At the lower temperature than LCST of PNIPAM, PNIPAM was dissolved from chloroform to water, producing convex lens-shaped particles with vertical cylinders. In contrast, the PNIPAM was localized preferentially in the P4VP domains in chloroform when the temperature is higher than LCST of PNIPAM, producing pupa-like particles with axially stacked lamellar. Importantly, we successfully demonstrated reversible transformation between anisotropic shapes of BCP particles using solvent-adsorption annealing method, suggesting a great promise for use in sensor, detector, and drug delivery applications.
  

Mechanism of High Extensibility in Entangled Associative Protein Hydrogels

When topological entanglements are incorporated into physically associating polymer gels, they can exhibit remarkably large ultimate extensions, exceeding 3,000% engineering strain. Here, we show that these large strains are related to molecular alignment within the gel under deformation that is not observed in unentangled gels. Uniaxial strain-induced structural changes are investigated in an associative protein hydrogel up to ~600% engineering strain using in situ laser light scattering and small-angle X-ray scattering. These methods reveal that the hydrogel develops an anisotropic optical response to uniaxial strain at the nano-, micro-, and macro-scales. Macroscale anisotropy suggests bulk chain alignment occurs along the straining axis, which is confirmed with depolarized light scattering. This behavior does not emerge in hydrogels with molecular weight below the entanglement cutoff. The findings suggest that both entanglements and freedom of individual chains to align at the nanoscale due to junction relaxation are critical to achieving high extension in physical gels.   

Multiscale Simulation Study of Synthetic Melanin Nanoparticle Self-Assembly

Self-assembled melanin-containing structures are leveraged by multiple organisms to create so-called structural colors; these biomaterials exhibit tunable color and iridescence based on the ordering and spacing of the melanin-containing assemblies. Recent work has demonstrated similar structural colors in micron-sized supraballs created using reverse emulsion assembly of ~100 nm polydopamine nanoparticles [Xiao et al. Sci. Adv. 2017, 3 (9), e1701151]. However, the supraball structure at multiple lengthscales (nm to micron), and how these structures can be controllably tuned to obtain a specific color response, remains unclear. In this poster, we describe our multiscale molecular dynamics simulation approach to explore a wide parameter space of nanoparticle chemistries, sizes, and emulsion assembly conditions and study their effects on the supraball structure. We use atomistic simulations to understand molecule-level structure and interactions between synthetic melanin monomers and common reverse emulsion solvents (water, octanol). These results inform nm-scale coarse-grained simulations to explore interactions between nanoparticles and the boundary of the emulsion droplet, which then parameterize ultra-coarse-grained simulations that mimic the micron-scale supraball assembly.   

Clustering and dynamic relaxation of microphase former in one-dimensional system

Microphases ubiquitously form in systems of particles interacting through short-range attraction and long-range repulsion. Depending on the conditions, these microphases can be both ordered or disordered. Although the latter are typical materials targets, their assembly requires a dynamical understanding of the former. By considering a one-dimensional model that can be analyzed using both simulations and theory, we pinpoint the microscopic origin of the rich and dynamically complex behavior of disordered microphases.   

Transport and Regulation of Water Molecules and Ions in Restricted Nanostructures

Worldwide commercial interest in single-walled carbon nanotubes (SWCNTs) reflected in the use of nanofluidic devices. Recently, with the rapid development of molecular dynamics simulation, single-walled carbon nanotubes are usually used in a variety of pipeline simulation, such as simulation of cell membrane ion channel mechanism. Although the working mechanism of ion switch in bio-ion channels has been studied extensively in the field of biology, most of them are based on macroscopic studies .In this paper, we focus on the control behavior of the ion in the pipeline for a very short time in the nanometer scale, trying to find microscopic patterns of ion switch. We also try to find special places to fix the ion so that we can control the transport of water molecules. The regulation process of ions in ion channels were studied and discussed.
  

When don’t colloids order into cubic-close packings?

The hard sphere system has been utilized as a model system to understand the mechanism of self-assembly. Advances in synthesis techniques and the drive towards materials discovery has led to research on polyhedral shapes that are easily synthesized in the lab, and how their self-assembly compares to that of spheres. Hard spheres assemble into the face-centered cubic (FCC) lattice type, with cubic-close packing (CCP) structure at packing fractions of 0.5–0.7. Here we ask: which polyhedral shapes will likewise assemble CCP? Literature has offered some guidelines to the assembly of plastic crystals with CCP structure from symmetric polyhedral particles [1], but a general understanding is lacking. We examine one parameter that influences the assembly structure, the sphericity of a particle shape, and the role it plays in the likelihood of assembling CCP from polyhedral particles of various shapes and vertex numbers.

[1] P. Damasceno, M. Engel, and S.C. Glotzer, Science 337 (2012).   

Mechanical response of 2D polymer networks: role of topology, rate dependence and damage accumulation

The skeleton of many natural and artificial soft materials can be abstracted as networks of fibers/ polymers interacting in a non-linear fashion. Here we present a numerical model for networks of nonlinear elastic polymer chains with rate dependent crosslinkers similar to what is found in gels. The model combines the work-like chain models at the chain level with the transition state theory for bond dynamics.We study the damage evolution and the force displacement response of these networks under uniaxial stretching for di erent loading rates, network topology, and crosslinking density. Our results suggest a complex nonmonotonic response as the loading rate or the crosslinking density increases. We discuss this in terms of the microscopic deformation mechanisms and suggest a novel framework for increasing toughness and ductility of polymer networks using a bio-inspired Sacrificial bonds and Hidden Length (SBHL) mechanism. This works highlights the role of local network characteristics on macroscopic mechanical observables and opens new pathways for designing tough
polymer networks.   

Nonlinear elasticity, and stability of semiflexible filament networks

Networks of semiflexible or stiff filament exhibit unique mechanic properties. We construct an analytic form of the free energy of a model semiflexible network, with its constitutive relation, by assuming 3-chain configuration of the network structure. There are only two parameters: stiffness of individual filaments, and pre-tension of these filaments in equilibrium network. The model fits nonlinear strain-stress experiments for numerous filament networks, such as actin, collagen, vimentin, fibrin, etc. This model successfully explains why networks of stiff filaments show negative Poynting effect (negative normal stress), which remained a mystery in this area since its observation. We also discuss the marginal rigidity of the network, and the phenomenon of tensegrity, where the pre-tension of the strands determines the linear shear modulus of the network. As a result, we present a ‘phase diagram’ in variables of filament stiffness and pre-tension, and identify the transitions between regions of stable/unstable network, and positive/negative normal stress. Curiously, all cytoskeletal or extra-cellular network we have examined lie very close to the marginal rigidity boundary. The model is portable and adaptable to meet specific demands in experiment and industrial applications.   

Controllable Dynamic Reconfiguration in Fiber-decorated Thermo-responsive Gels

Using computational modeling, we simulate gels where elastic fibers are localized on the surface of the polymer network. Our computational approach, the gel lattice spring model, allows us to numerically solve the elastodynamic equations that characterize the behavior of thermo-responsive polymer gels. Via this model, we determine how to arrange the fibers on the outer layer(s) of the gel to achieve new shape changes that could not be achieved with the fibers localized in the bulk of the material. We focus on gels with a lower critical solubility temperature (LCST) and show that the fibers inhibit the swelling of the gel as the temperature is lowered and inhibit the shrinking of the gel as the temperature is increased. This behavior can lead to novel 3D shape changes, such as gels that encompass negative Gaussian curvature around a saddle point. We show that if an arrangement of fibers is placed on the top of an initially planar gel and the same arrangement is placed in an adjacent region at the bottom of the gel, the system be dynamically and reversibly switched between a planar and corrugated geometry with variations in temperature. In this manner, we are attempting to design gels with 3D architectures that undergo structural reconfiguration and enable new functionality.   

Investigating ordered phases of organic molecules with density-of-states simulations

Thin films of molecular semiconductors may show a range of ordered phases depending on properties of the molecules, of confining surfaces, and of the thermodynamic state. Computer simulations of such systems are challenging since the molecules are complex, the state space is multidimensional, and systems may be trapped in metastable states. To address these challenges we perform density-of-states simulations of a coarse-grained model in strategically chosen statistical ensembles. In recent work, we developed a model for alpha-oligothiophenes, where each molecule is represented as a linear chain of Gay-Berne disks. In this work, we perform Wang-Landau type simulations of the model to investigate crystalline and liquid crystalline phases in the bulk as well as ordering near surfaces. Simulations over a two-dimensional (volume-energy) state space allow us to reach very low energy conformations and analyze the bulk crystalline state. To investigate the structure of adsorbed layers under experimental conditions, we work with a revised state space and introduce confining fields. By combining simulations in different ensembles, we will follow the system from sub-monolayer coverage to bulk conditions.   

Fabrication of Non-spherical Particles and Self-wrinkling of the Surfaces by Non-uniform Crosslinking of the Polymer at a Water/Oil Interface

Fabrication of non-spherical shapes or wrinkles on the curved surfaces may help us to understand an aspect of morphological development found in nature such as pollens, fruits, and vegetables. Popular methods to fabricate microparticles of various geometries rely on molding or 2D lithography, which have challenges in creating 3D shapes. Moreover, in order to create wrinkles on them, additional processes are required to form an outer layer of different material properties and impose stress. We present a simple system of UV-curable hydrogel droplets dispersed in oil, of which initial spherical shapes by a water-oil interfacial tension are subjected to non-uniform UV crosslinking resulting in shape deformations. We also find that the presence of crosslinking gradient in the cured droplets induces surface wrinkles by self-swelling, and we can control the pattern of wrinkles with the shapes of particles or by spatially varying UV exposure. Further research will develop applications such as fabrication of nanochannels and patterns on 3D objects to impart multifunctionality.   

Scaling relation for convective velocity in an intermittently vibrated granular packing

When a granular packing is mechanically vibrated in a container, convective motion of constituent particles (granular convection) is often induced. A scaling relation has been experimentally obtained for granular convective velocity under the steady vibration condition [Yamada & Katsuragi, Planet. Space Sci. 100, 79 (2014)]. However, the scaling relation for convective velocity in an intermittently vibrated granular packing has not been quantitatively obtained so far. In this study, we experimentally measured the granular convective motion in a two-dimensional granular packing under the successive intermittent tappings (each tapping event consists of a single period of sinusoidal oscillation). We calculated particle velocities using by the particle tracking velocimetry method. In addition, we investigated a vibration-condition dependence of convective velocity by systematically varying the amplitude and period of tappings. As a result, we found the scaling relation for convective velocity in an intermittently vibrated granular packing is almost identical to the scaling obtained with a steady vibration. Therefore, we conclude the intermittency of vibration doesn’t affect the velocity of granular convection.   

Dynamics of Stratification in Micellar Foam Films

Ultrathin films exhibit stratification due to confinement-induced structuring and layering of small molecules in simple fluids, and of supramolecular structures like micelles, lipid layers and nanoparticles in complex fluids. Stratification proceeds by the formation and growth of thinner domains at the expense of surrounding thicker film, and flows and instabilities drive the formation of nanoscopic terraces, ridges and mesas within a film. The detailed mechanisms underlying stratification are still under debate, and are resolved in this contribution by addressing long-standing experimental and theoretical challenges. Thickness variations in stratifying films are visualized and analyzed using interferometry, digital imaging and optical microscopy (IDIOM) protocols, with unprecedented high spatial (thickness < 100 nm, lateral ~500 nm) and temporal resolution (< 1 ms). Using IDIOM protocols we developed recently, we characterize the shape and the growth dynamics of nanoridges and mesas that flank the expanding domains in micellar thin films. We show that topographical changes including ridge growth and instability, and the overall stratification dynamics, can be described quantitatively by nonlinear thin film equation, amended with supramolecular oscillatory surface forces.   

Rotational Drag and Hydrodynamics of Single Dipolar Colloids and Linear Colloidal Strings under an Oscillating Drive

Fluid dynamics plays an essential role in the mechanics of colloidal dispersions. While much attention is paid to high-density systems, low-density systems have received much less attention. This could be attributed to the fact that the impact of hydrodynamics on colloidal mechanics and assemblies in low densities is only very localized and, thus, less pronounced effects might be expected; but it is equally true that quantities such as mechanical drag and flow fields at the microscale remain difficult to examine for many micron-sized objects and in non-homogeneous environments. Here, we investigate the rotational drag and the role of hydrodynamics of dispersed magnetic Janus beads close to a wall. For single Janus particles as well as particles in small, linear assemblies, we demonstrate how the Stokes coefficient of rotational drag can be obtained experimentally from driven torsional oscillations. Furthermore, we simulate the fluid around the oscillating single particles and particle strings close to a wall using fluctuating Lattice Boltzmann simulations. Comparing experimental and numerical results, we are able to estimate the impact of hydrodynamic effects in such low-density systems.   

Relaxation dynamics of a vibro-fluidized granular pile

Relaxation is one of the phenomena lying at the center of soft matter physics. As for granular media, heap structure (e.g. sand pile) shows relaxation toward a horizontally-flat surface in gravitational field when subjected to perturbations such as vibration. The complete understanding of this dynamics has not yet been achieved, although this kind of relaxation has been observed in broad research fields from general soft matter physics to civil engineering and geophysics. Motivated by this fact, in this study nonlinear relaxation dynamics of a vertically-vibrated granular pile is experimentally studied. In the experiment, the flux and slope on a vibro-fluidized pile are measured by using a high-speed laser profiler. To explain the relation of these quantities, we propose the nonlinear transport law based on the assumption that an entire pile is uniformly fluidized by vibration. By the continuity equation with this proposed model, the actual relaxation is successfully reproduced. The fitting parameter of the model is only the relaxation efficiency, which characterizes the energy conversion rate from vertical vibration into horizontal transport. We finally demonstrate that this value is a universal constant independent of experimental conditions.   

Impact of Salt Ions on the Structure and Dynamics of Water

Water is a fundamental substance in characterizing many biological and chemical processes. Despite its simple appearance, water possesses a wide variety of dynamic and structural anomalies that still elude complete understanding. Since water is often found in ion solutions, studying the effects of ions on the anomalies and structure and dynamics of water is of great interest. With computer simulations of NaCl aqueous solution, we found that ions have different effects on water’s structure and dynamics at different temperatures. At room temperature, Na+ and Cl- ions retard water's motion by electrostatic drag. At lower temperatures, ions facilitate water’s movement within a medium range by breaking the immobile locally favored structures. The former effect supports the traditional classification of NaCl as a structure maker, whereas the latter leads to its “unusual” structure-breaker nature at low temperatures. Our results reveal the dual effects of ions on water’s structure and dynamics, which challenges the old concept of structure maker and breaker traditionally defined at room temperature, and advances our understanding of aqueous solutions in a wide range of temperature and salt concentration.   

Phase Transition and Chain Formation in Dipolar Fluids

Gibbs ensemble simulations are reported for the Lennard-Jones potential with embedded dipoles and quadrupoles of varying strengths. The reduced dipole moments ranged from 0.1 to 0.5 and the reduced quadrupole moments had values ranging from 0.1 to 5.0. The simulation data are analyzed to estimate the critical properties of the polar fluid, vapor-liquid coexistence and their dependence on the strength, λ, of the dispersive force. Chain formation is observed for the dipole in both phases to a degree that depends on the number density and strength of the dipolar interactions. Our simulation results clearly indicate that one can get vapor-liquid coexistence in the presence of quadrupole moments even at the smallest value of λ.   

The study of self-assembly of colloidal particles under confinement using Langevin dynamics

One of the topics popular in the field of soft matter is the self-assembling phenomena in which the ordering appears in the system without microscopic manipulation of system components. The self-assembly of colloidal particles is also actively researched in this trend. The recent advance in self-assembly of colloidal particles is the self-assembly under spherical confinement in the work of De Nijs et al. in 2014. We investigated diverse aspects of self-assembling phenomena from confinement and discovered new geometry appears in the system with Langevin dynamics using the well-known molecular dynamics package, LAMMPS. The new geometry is also observed in experiment too and its appearance and stability are discussed in the analysis of thermodynamics.   

Energy dissipation and fluctuations in a driven liquid

Minimal models of active and driven particles have recently been used to elucidate many properties of non-equilibrium systems. However, the relation between energy consumption and changes in the structure and transport properties of these non-equilibrium materials remains to be explored. We explore this relation in a minimal model of a driven liquid that settles into a time periodic steady state. Using concepts from stochastic thermodynamics and liquid state theories, we show how the work performed on the system by various non-conservative, time dependent forces this quantifies a violation of time reversal symmetry modifies the structural, transport, and phase transition properties of the driven liquid.   

From effective interactions to the interfacial phase behavior and pressure of active particles

We employ classical density functional theory to study the self-organization in active systems.
Using a first-principles approach, we map the self-propulsion onto an effective
pair interaction potential, which has been shown to account for the motility-induced
phase separation (MIPS) observed for active Brownian particles. We further introduce an
effective external potential and define a free energy to investigate inhomogeneous
situations. Solely as a result of their activity, we predict that active (Brownian) particles
undergo a variety of interfacial phase transitions, e.g., wetting and capillary condensation
in purely repulsive systems or drying and capillary evaporation of attractive colloids.

We also explain why the effective thermodynamic pressure and interfacial tension do not satisfy
the mechanical force-balance condition derived for the present effective equilibrium
model and show how to define more appropriate (rescaled) expressions for
the mechanical pressure and interfacial tension. Finally, we demonstrate that
our theory can also be applied to situations with a non-vanishing particle current
and to mixtures of particles with different activities.   

Boundary Effects on Low Reynolds Number Bacterial Robots

The dynamics of prokaryotic motility at low Reynolds number is important in a wide range of fields. Our experiment models the locomotion of a bacterium near a boundary using a robotic swimmer. Our robot uses a computer controlled DC motor that drives a helical flagellum made of wire. We maintain a low Reynolds number by placing the robot in highly viscous silicone oil with viscosity 10⁵ that of water and measure the forces and torques on the flagellum. Previous research measured helical propulsion far from a boundary (Rodenborn et al., PNAS 2013), but proximity to a boundary strongly affects the results. We have designed a system to precisely control the distance from the flagellum to the tank wall, and have made some of the first macroscopic measurements of boundary effects on helical propulsion. We find an approximately exponential dependence of the propulsive force and torque near the boundary, but we also find and unexpected asymmetry between CW and CCW rotation caused by the flow induced by the flagellum.   

The Robophysics of the Three Link Swimmer

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 under the assumption that 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.   

Selective patterning of metallic layers on the 3D printed polymers based on hygroscopic swelling behavior of two different materials

A novel process to fabricate three-dimensional (3D) metallic patterns from 3D printed polymeric structures was developed by utilizing hygroscopic swelling behavior of two different polymeric materials. The “Swollen-off”, an evolution of the lift-off process commonly used in the micro-fabrication process. The Swollen-off process demonstrated in this research provides a simple way of producing electrical devices on complex 3D surfaces. 3D patterns are printed with two different polymers as cube shape. The substrate, as well as the sacrificial material, were produced using a material jetting printer capable of creating multi-material parts. The surface of the 3D printed polymeric structures is plated with nickel by an electroless plating method. The nickel patterns on the surface of the 3D printed cube shape structure are formed by removing sacrificial layers using the difference in the rate of hygroscopic swelling between two printing polymer materials. The hygroscopic behavior on the interfaced structure was modeled with COMSOL Multiphysics. The surface and electrical properties of the fabricated three-dimensional patterns were analyzed and characterized.   

Effects of Charge Distribution on Lithium Dendrite Growth

Microscopic fibers of lithium, or so-called "dendrites", often lead to a short circuit in lithium-ion batteries that may cause them to catch fire. However, the mechanism for dendrite growth in electrolytes remains unclear. To overcome this problem, we have developed a new Monte Carlo simulation method that simultaneously accounts for dendrite growth and the electrostatic potential in liquids with a minimal set of parameters. Our theory provides a fractal dimension that can be measured experimentally. We consider various charge distributions. Specifically, we examined a case of highly concentrated charges toward a study of dendrite growth in ionic liquids. Our results produced two key features: (1) Charge distribution can substantially affect the fractal structure of dendrites, and (2) dendrites may grow more uniformly at high ionic strengths.   

Colloidal Assembly by Directional ice Templating

Here, we investigate the directional ice templating of aqueous colloidal particle dispersions. We coat micron size silica colloids with crosslinkable polymer; we add crosslinker and subject this dispersion to unidirectional freezing. We work at very low colloid concentrations. When the aqueous dispersion freezes, ice crystals force polymer-coated particles and cross-linker into close proximity so that crosslinked clusters are formed at ice crystal boundaries. We varied the particle concentration from 10⁶ /ml to 10⁹ /ml and observed that there is a transition from isolated single particles to increasingly large size clusters. Most of the clusters formed under these conditions are either linear, two particle wide chains or sheet like aggregates. The size distribution (P_N) for the clusters (N<30) is strongly dependent on the particle concentration. The exponent (ν) of the power law (P_N~N^ν) increases with the particle concentration and gets saturated at higher concentration. To understand the system better we performed kinetic simulations that ignore hydrodynamic interactions and instabilities at the growing ice front. We demonstrate that aggregate structure of colloidal assemblies is predominantly governed by the exclusion by growing ice crystals.   

Nanoparticle-Polymer Surfactant Covered Monodispersed Droplets using Microfluidics

We present droplet interfaces covered with elastic, responsive monolayers of nanoparticle (NP)-surfactants. Due to the interactions between functional groups on NPs dispersed in one liquid and polymers having complementary end-functionality dissolved in a second immiscible fluid, the anchoring of a self-regulated number of polymer chains onto the NPs leads to the formation of NP-surfactants that assemble at the interface and reduce the interfacial energy. Due to the presence of an elastic layer at the interface, the droplets offer a greater resistance to coalescence and can prevent the exchange of materials across interfaces. Our results show the successful encapsulation of nanoparticles, dyes, and proteins with diameters in the 2.4–30 nm range. Further, we show that stable water-in-oil droplets can be generated for various combinations of polymer ligands and nanoparticles bearing complementary functionalities. These NP-surfactant stabilized microfluidic emulsions enable new applications requiring liquid-liquid interfaces that can adapt and respond to external stimuli, and whose mechanical properties can be easily tailored.   

Osmotic Compressibility of Colloidal Crystals and Suspensions Measured by Dielectrophoresis and Fluorescence Microscopy

Osmotic compressibility is the relative volume change upon the change in pressure. For colloids, it is measured traditionally by scattering methods, which limit to only dilute solutions below 1.0 wt%. Between 1.0 and 2.0 wt%, highly repulsive colloids can form Wigner crystals. There is no experimental study to date of the compressibility near such phase transition. We present a new method for measuring compressibility of colloids using fluorescence microscopy and non-invasive dielectrophoretic force field generated from radiofrequency electric field. With known force field and spatial distribution of particle concentration determined from fluorescence microscopy, we can use Einstein’s osmotic equilibrium theory to calculate the osmotic pressure and hence construct the equation of state and determine the compressibility. With this method, we can determine the compressibility for colloids from the disordered phase to crystalline phase by either changing salt or particle concentration. To validate our method, we compare our results with charge renormalization theory by Alexander et. al. (J. Chem. Phys. 1984, 80, 5776) and computer simulations.   

Visualizing Nanoscopic Topography and Patterns in Freely Standing Thin Films

Thin liquid films containing micelles, nanoparticles, polyelectrolyte-surfactant complexes and smectic liquid crystals undergo thinning in a discontinuous, step-wise fashion. The discontinuous jumps in thickness are often characterized by quantifying changes in the intensity of reflected monochromatic light, modulated by thin film interference from a region of interest. Stratifying thin films exhibit a mosaic pattern in reflected white light microscopy, attributed to the coexistence of domains with various thicknesses, separated by steps. Using Interferometry Digital Imaging Optical Microscopy (IDIOM) protocols developed in the course of this study, we spatially resolve for the first time, the landscape of stratifying freestanding thin films. In particular, for thin films containing micelles of sodium dodecyl sulfate (SDS), discontinuous, thickness transitions with concentration-dependent steps of 5-25 nm are visualized and analyzed using IDIOM~protocols. We distinguish~nanoscopic rims, mesas and craters and show that the~non-flat features are sculpted by oscillatory, periodic, supramolecular structural forces that arise in confined fluids   

Salt effects on transition temperatures and orientational order of lyotropic chromonic liquid crystals.

Lyotropic chromonic liquid crystals (LCLCs) differ from conventional liquid crystals since the constituent units are self-assembled aggregates rather than individual molecules. The aggregates are stabilized by π-π interaction of poly-aromatic cores and ionic interactions between side groups. Hence, the aggregation behavior is sensitive to ionic impurities which interfere with the electrostatic interactions. In this study, we used monovalent salts to investigate salt effects on LCLC self-assembly by measuring transition temperatures and order parameters. We found that the size of cation plays a crucial role on the stability of nematic phase but the size of anion makes no difference. A mechanism is proposed based on the screening of electrostatic repulsion between adjacent molecules and aggregates. The order parameters of LCLCs at transition temperature are reduced by the addition of salts, which cannot be explained by Onsager model. The roles of temperature, LCLC concentration, and salts are separated when plotting the order parameters as a function of reduced temperature. The order parameters dependence on reduced temperature is independent of LCLC concentration, salt concentration, or cation size.   

Cellulose nanocrystals confined to cylinders

Liquid crystals that are confined within curved boundaries are of interest to many scientists due to their important role in optoelectronic technologies. As such, intensive research has been conducted with various types of liquid crystals constrained to droplets or cylindrical environments. Since curvature of liquid crystals costs energy, we can observe rich physical phenomena such as change in director field. Most of the fundamental studies of liquid crystalline phase of the CNCs were conducted as a film type or in the cells with flat boundaries, limited to certain concentration and time. Herein, we report the fundamental study of liquid crystalline phase of CNCs confined in cylindrical capillaries. Time, concentration, and size of the capillaries were systemically varied. We observed the formation of a chiral nematic phase of 4 wt % CNCs in 200 µm cylinders at different time periods. Specifically, small rod-like structures were observed at t = 0 h, then developed into small tactoids with periodic bands in less than an hour. After 24 h, we observed long-range fingerprint structure. We believe the study of the evolution of CNC liquid crystals in a curved geometry will provide us deeper understanding into the structure formation of the chiral nematic phase in confinement.   

Unravelling what governs the fluctuation spectra of active membranes

We detect thermal and activity-driven fluctuations of lipid vesicles over the exceptionally broad frequency range of 0.1 to 1,000 Hz with an amplitude resolution of 0.1 nm. Thermal fluctuations, understood phenomenologically from the classical Helfrich theory, are modified by active protein pumps to enhance high-frequency fluctuations. This enhancement yields surprises regarding underlying processes occurring in the membrane.   

Light Scattering Study of the Size and Shape of Mixed Elastin-Like Polypeptide Micelles

Elastin-Like Polypeptides (ELP) formed thermoreversible nanoparticles by having three-armed star polypeptides (each with 20 repeats of (GVGVP) amino acid sequence) extending from the negatively charged foldon domain. In addition, linear constructs composed of 40 repeats of the (GVGVP) sequence were introduced into the system. The mixed ELP polymer system is soluble at room temperature and becomes insoluble at ~ 50 forming micelles with the foldons on the exterior and linear constructs at the core. Above the transition, the size and shape of the mixed micelles are dependent on the pH of the solution, concentration of the PBS, and the ratio of the linear to foldon concentration. The Depolarized Dynamic Light Scattering was employed to study the structure and dynamics of the mixed micelles at 62 ^oC and pH of 7.3 - 7.5. The ELP foldon micelles have a radius of 10nm; the introduction of the linear ELP chains leads to a growth of mixed micelles at a linear rate, at fixed PBS and foldon concentrations. A developed molar volumes model explains the linear size growth of the mixed system. Static Light Scattering results largely support the model. However, the apparent VH signal found can indicate elongation in geometry of the particles or anisotropic properties of the micelle core.   

Experiment and Modeling of Enzymatic Degradation Kinetics Using Autofluorescent BSA Microspheres

Autofluorescent bovine serum albumin (BSA) hydrogel microspheres are synthesized through spray-drying of glutaraldehyde cross-linked BSA nanoparticles. The as-synthesized microspheres are employed for the study of enzyme degradation in an aqueous solution. Experimental results from confocal imaging and phenomenological modeling are presented to quantify the degradation process as well as the release of synthesized fluorophores. The coupling of swelling dynamics of the gel and the transient distribution of fluorophores are optically tracked. It is found the concentration of the enzyme proteinase K within the Tris buffer plays the primary role that controls BSA gel degradation. The model considers linear elastic deformation of the hydrogel coupled with fluorophore transport and enzyme degradation kinetics. The study provides fundamental investigation of the degradation and release kinetics of protein-based materials, which can potentially be extended to in vivo applications in drug delivery or tissue engineering.   

Effect of Surface Energy and Confinement on Cavitation in Soft Gels

The sudden expansion of a cavity in soft solids subjected to an internal pressure is a commonly observed phenomenon. Such phenomenon has been harnessed in developing cavitation rheology (CR) technique for probing the local mechanical properties of various soft materials. In this experiment, a small defect within a soft material is pressurized and the critical pressure corresponding to the sudden expansion of the defect is recorded. The critical pressure is dictated by the elasticity of the material, surface energy, and geometric factors. We have developed a finite element based framework to capture the critical pressure for a spherical cavity growth in an infinite media and for the CR geometry. Presence of a needle in the CR geometry increases the critical pressure, in comparison to the growth of spherical cavity in an infinite media. The effect of confinement on the critical pressure is captured by varying the distance between the needle tip and the sample boundaries. The simulation results are compared with that obtained experimentally for triblock gels consisting of poly(styrene)-poly(isoprene)-poly(styrene) in mineral oil.   

Effects of Microstructure Formation on the Stability of Vapor Deposited Glasses

Glasses formed by physical vapor deposition (PVD) are an interesting new class of materials, exhibiting properties thought to be equivalent to those aged for thousands of years. Exerting control over the properties of PVD glasses formed with different types of glass forming molecules is now an emerging challenge. In this work, we study coarse grained models of organic glass formers containing fluorocarbon tails of increasing length, corresponding to an increased tendency to form microstructures. We use simulated PVD to examine how the presence of the microphase separated domains influences the ability to form stable glasses. This model suggests that increasing molecule tail length results in decreased kinetic stability and a shift towards out of plane orientation of the molecules in PVD films. We find that the relaxation time near the surface of ordinary glass films formed by these molecules remains essentially bulk-like, and the surface diffusion is markedly reduced due to a trapping mechanism where the tails are unable to move between local phase separated domains on our simulation time scales. Together, these results are consistent with theories which suggest surface mobility is the driving force behind enhanced PVD glass properties.   

Distributions of pore sizes and atomic densities in binary LJ glasses revealed by molecular dynamics simulations

We report on the results of a molecular dynamics simulation study of binodal glassy systems, formed in the process of isochoric rapid quenching from a high-temperature fluid phase. The transition to vitreous state occurs due to concurrent spinodal decomposition and solidification of the matter. The study is focused on topographies of the porous solid structures and their dependence on temperature and average density. To quantify the pore-size distributions, we put forth a scaling relation that provides a robust data collapse in systems with high porosity. We also find that the local density of glassy phases is broadly distributed, and, with increasing average glass density, a distinct peak in the local density distribution is displaced toward higher values.   

Force network and mechanical stability in an ageing 2D glass

The concept of force network as a heterogeneous load bearing structure comes from the physics of jamming and granular matter. Recently, extension of this idea to thermal systems is gaining considerable attention to understand the nature of mechanical equilibrium in glass [1]. We study a weakly poly-dispersed almost hard sphere glass in two dimensions. In the deeply aged regime, we find the structural relaxation in our system is intermittent - long quiescent stage followed by rapid avalanches, and a long-lived force network is developed. By analyzing the topology of this emergent force network, the structural defects and the dynamics, we find evidence that suggests a close connection between the changes in the force network in the quiescent stage, and the large particle displacements during avalanche.
Ref:
1. T. Yanagashima, J. Russo, H. Tanaka, Nat. Comm., 8, 15954 (2017).   

Nonlinear dielectric features of highly polar glass formers: Derivatives of propylene carbonate

We have measured the nonlinear dielectric behavior of several highly polar propylene carbonate (PC) derivatives near T_g. Focus is on the effects of a large DC field on the frequency dependent permittivity and on the cubic susceptibility measured using a high AC field. Vinyl-PC shows both dielectric saturation and a field induced increase of dielectric relaxation times. The extent of the shift of the loss profile caused by the field correlates strongly with the peak magnitude of the cubic susceptibility, |χ₃|, showing a potential link between the |χ₃| 'hump' and electro-rheological behavior. Further support of this picture emerges from the observation that the most polar of these liquids, (S)-(-)-methoxy-PC ε_s ≈ 250, lacks both the electro-rheological effect in ε'(ω) as well as the 'hump' typically observed in |χ₃(ω)|. The absence of sensitivity of the dynamics to an electric field is contrary to the expectation that the electro-rheological effect correlates with the field induced entropy change. The results suggest that the dependence of the relaxation time on the electric field is not directly linked to the entropy change.   

Frictional Properties of Zinc Oxide Thin Films: Interplay of oxygen vacancies, ambient humidity and surface roughness

Being able to manipulate the frictional properties of materials at the nanoscale is important for future development of nano-electro-mechanical systems (NEMS), where moving components are inevitably present. By means of atomic force microscopy (AFM), we investigated the frictional properties of ZnO thin films with nanoscale surface roughness. Photo-catalytic effect (PCE) is used to induce oxygen vacancies in the surface layer of ZnO, which can act as binding sites for ambient water molecules, further converting the ZnO surface from being hydrophobic to superhydrophilic. Due to the capillary effect, nanoscale water bridges can form between the surface asperities in the contact zone of AFM tip and superhydrophilic ZnO surface. Therefore, the measured friction exhibits a negative dependence on the logarithm of tip sliding velocity. Such dependence is found to be a strong function of both ambient humidity and the concentration of oxygen vacancies, and can be reversibly manipulated by the PCE. These results might find applications in future ZnO based NEMS.¹

1. Langmuir 33, 8362 (2017)   

Theory and computation of fracture formation in polymer electrolyte membranes

We present a physical-statistical model of fracture formation in polymer electrolyte membranes. The membrane is considered as a cross-linked network of ionomer bundles. Water that fills the pore spaces between bundles causes stress on them, incurring bundle breakage. The problem of fracture formation and propagation is mapped onto a bond percolation problem. It was solved previously for the random percolation case of the weak-stress regime (Melchy and Eikerling, J. Phys. Condens. Matter 27, 325103, 2015). This work focuses on the high-stress regime where breakage events become correlated because of the stress redistribution upon bundle breakage. We have implemented a rejection-free kinetic Monte Carlo method to simulate correlated bundle breakage events on regular lattices. Fracture rates of bundles are expressed through an exponential breakdown rule. So far, we have evaluated a global power-law stress redistribution scheme. Using this approach, we study the effect of the initial stress, correlation length and lattice anisotropy on fracture propagation. Different regimes or fracture propagation corresponding to random and correlated percolation are identified and the impact of relevant parameters transitions between these regimes as well as on the time to fracture is analyzed.   

The study on self-assembly structure of diblock copolymer melts using molecular dynamics with soft potential and potential recovery

Various self-assembled microstructures with block copolymers are obtained by using molecular dynamics (MD) simulation method. Typically, it requires substantial computational cost to prepare initial configurations of various self-assembled structures with MD because of topological constraints. Furthermore, manual preparation often becomes a complicated and time-consuming procedure even for a lamellar phase, not to mention complex phases, such as a bi-continuous gyroid phase. The problem may be overcome by introducing a soft potential to allow the system to reach a self-assembled state fast. Once a self-assembled microstructure is established, the normal potential, like Weeks-Chandler-Andersen (WCA) potential, is reinstated and equilibration runs are performed to get equilibrated melts and calculate both static and dynamic properties of the microstructures. Various equilibrated phase structures—including S (spherical), H (hexagonal), G (gyroid), and L (lamellar) phases—are obtained and, to verify our method, static and dynamic properties of the lamellar phase are analyzed with previous results.   

Interfacial Assembly and Jamming Behavior of Polymeric Janus Particles at Liquid Interfaces

The self-assembly and interfacial jamming of spherical Janus nanoparticles (JNPs) at the water/oil interface is presented. Polymeric JNPs, made by cross-linking polystyrene-block-polybutadiene-block-poly(methyl methacrylate)(PS-PB-PMMA), with a high interfacial activity assemble at the water/oil interface. Even though none of the building blocks are water soluble, JNPs can self-assemble at interface, prevent direct contact between water and oil, and reduce interfacial energy. Unlike hard particles, the JNPs are composed of polymer chains that can reconfigure at the liquid−liquid interface to maximize coverage at relatively low areal densities of the JNPs. Interpenetration of the polymer chains causes the JNPs to form a solid-like interfacial assembly, resulting in the formation of wrinkles when the interfacial area is decreased. The wrinkling behavior, the retention of the wrinkles, or the slow relaxation of the liquid drop back to its original equilibrium shape was found to depend upon the pH. The soft characteristic of this polymeric JNPs arouse interesting interfacial behavior that has not been found with hard nanoparticles at liquid interfaces.   

Directed Self-assembly of Dendrimer Columns with High Aspect Ratio Patterns

Directed self-assembly has considerable attention to form highly ordered and dense nanopatterns compared to conventional top-down lithography. Especially, directed self-assembly of dendrimers shows small feature size (~ 4.7 nm), ultra-dense structures, and fast self-assembly. Herein, we report directed self-assembly of dendrimers for long-range ordering on the macroscopic area. Graphoepitaxy by high resolution (~ 20 nm) and high aspect ratio (> 10) line patterns controls dendrimer columns over large-area (4 cm x 4 cm) with minimal dead spaces (~ 1%). Significant point is that ordering behavior of dendrimer columns is controllable by the dimension of guiding template and dendrimer film thickness. Dendrimer columns perpendicular to the line pattern direction are generated in the narrow guiding template. On the other hand, dendrimer columns which are parallel to the line pattern direction are represented in very specific condition, narrow guiding template and control of the ratio of dendrimer film thickness to the pattern height are necessary. These approaches exhibit opportunities for lithographic applications, which are based on directed self-assembly of dendrimers.
  

Bending dynamics of single-walled carbon nanotubes in viscoelastic media

The mechanics and dynamics of cells and tissues are dominated by semi-flexible polymer networks, whose bending stiffness leads to nontrivial dynamics. Micron-sized beads are commonly used in microrheology approaches to measure the viscoelasticity of such systems. Insertion of such probes can lead to artefacts and is often not possibly in confined geometries in living cells. Here we introduce single-walled carbon nanotubes (SWNTs), themselves semi-flexible polymers with non-photobleaching near-infrared fluorescence, as multiscale “stealth probes” for microrheology. We investigate the bending dynamics of SWNTs embedded in viscoelastic media and analyze their thermally driven shape fluctuations. We discuss how the bending dynamics of SWNTs embedded in soft media can be used to probe the viscoelastic properties of such media.   

Synchronization conditions of N Coupled Maps using Periodicities

Using the synchrony factor and its periodicity, we are able to identify not only complete synchronization but also in-phase synchronization. The analysis of the periodicities of the synchrony factor allows to obtain a phase diagram that contains all the information of synchronous behaviour in a wide range of parameters. This method constitutes a new and useful tool to characterize synchronization. We are working in extend our results to many maps.   

Increasing Information Storage Capacity in Computing Devices Formed from Self-Oscillating Gels

We recently designed an example of “materials that compute”, where the material and computer are one and the same entity, and demonstrated the ability of these systems to perform pattern recognition. Each basic unit in the system encompasses a self-oscillating polymer gel undergoing the Belousov-Zhabotinsky (BZ) reaction and an overlaying piezoelectric (PZ) cantilever. Driven by the BZ reaction, each gel periodically swells and shrinks in volume and thereby deflects the overlaying PZ cantilever. The periodic deflection of the PZ plate generates an oscillating electrical voltage, which is transmitted to other units through electrical wires. As a result, the chemo-mechanical oscillation of one BZ gel affects the oscillations of all the other gels. Eventually, the oscillations of the BZ-PZ units achieve in-phase or anti-phase synchronization, enabling the BZ-PZ oscillator network to store and recognize binary patterns. Here, we show that introducing capacitors into the system allows us to modify the system dynamics and create additional stable synchronization modes, thus increasing the information storage capacity in a given BZ-PZ network. We then demonstrate how this extended information storage enhances the functionality of the BZ-PZ networks in performing computational tasks.   

Coarse-grained dynamics simulation of a two-dimensional auxetic lattice.

We present the dynamical behavior of the geometric degrees of freedom of a 2D lattice obtained by the tessellation of the C4-symmetric protein L-rhamnulose-1-phosphate aldolase (RhuA). We analyze the relevance of the parameters defining said kind of lattice on the configurations and dynamical behaviors exhibited by it. Constrained dynamics calculations, including holonomic and nonholonomic constraints, provide essential information towards the understanding of the coherent behavior observed experimentally, as well as intriguing insight on the auxetic character of this arrangement.   

Interlocked Fragmented Continua: A State Between Continuum and Granular Matter

We study the mechanical behavior of three-dimensional, randomly microcracked continua for crack densities up to and above the transport percolation threshold. We show the existence of a fully fragmented material state in which stiffness is preserved due to topological interlocking of fragments. This material state is different from both the continuum and granular states. In this regime, the mechanical behavior is controlled by the contacts between fragments and becomes non-linear. The range of system parameters in which the material is found in this state is identified, including the upper limit which represents the stiffness percolation threshold. The variation of the effective material stiffness for crack densities ranging from zero to the stiffness percolation threshold is reported.   

A Reconfigurable Shape-memory Surface

The mechanical response of a graphene monolayer with equal numbers of pentagon and heptagon disclinations arranged in a kagome-like superlattice is modeled with semiclassical molecular dynamics. The pentagon disclinations form cones with an Ising degree of freedom in their up/down orientation, yielding a reconfigurable surface with a large number of distinct metastable shapes, unlike traditional membranes which typically have a single metastable shape. A complete 'zoo' of such shapes for a small patch of this material is enumerated and analyzed to uncover the “density of shapes” and the effective interactions between these Ising degrees of mechanical freedom.   

Bayesian Inference of Global Statistics on Complex Networks using Random Walks

The study of complex networks is ubiquitous across physics, biology, and computer science, as well as many other disciplines. Examples include protein-protein interaction networks, the Worldwide Web, etc. Complete querying of these enormous systems is often impractical or impossible. We have developed a theoretical methodology for rapid Bayesian inference of the statistical properties of these complex networks based on the sampling method of random walks for networks with weighted or unweighted edges. The statistics of interest include, but are not limited to, the node degree distribution, the average degree of nearest-neighbor nodes, and the node clustering coefficient. Surprisingly, our formalism yields high-accuracy estimates of these statistics, and of the network size, after only a small fraction of network nodes have been explored. The Bayesian nature of our approach provides rigorous estimates of all parameter uncertainties. We have demonstrated our framework on several standard examples, including random, scale-free, and small-world networks, and have applied it to the network formed by the links between Wikipedia pages.   

Phonon Network Topology in Spatially Modulated Nonlinear Lattices

Even in the simplest structures, the presence of nonlinear phonon-phonon scattering can produce phonon dynamics of surprising complexity. The nonlinear resonances can be understood as forming an anharmonic network of coupled phonon modes. We examine the topology of these networks for a broad class of nonlinear lattices and show how the inclusion of a spatially modulated anharmonicity can produce large changes in this underlying topology. We further show how this graph topology impacts the dynamics of the coupled phonons.   

Data-driven Computational Screening of Solid Electrolytes for Mechanical Suppression of Dendrites

Solid electrolytes present a new avenue to tackling the problem of safety and energy density in current Li-ion batteries. Recent work has shown that the mechanical properties of the solid electrolyte determine the stability of electrodeposition with Li metal anode [1, 2]. An exhaustive search for candidate materials with required properties through experimental or ab initio methods can be expensive and time-consuming. We approach this problem through a data-driven computational screening method. We train a neural network model to the training data consisting of structural descriptors and elastic tensors of ~300 materials from materials project database, computed through density functional theory calculations [3]. Using the neural network model, we predict the elastic tensor and electrodeposition stability of ~12,000 compounds. These materials could be used for enabling Li metal anode in Li-ion and beyond Li-ion batteries.

References
[1] Z. Ahmad and V. Viswanathan, Phys. Rev. Lett. 119, 056003 (2017).
[2] Z. Ahmad and V. Viswanathan, Phys. Rev. Materials 1, 055403 (2017).
[3] M. De Jong, W. Chen, T. Angsten, A. Jain, R. Notestine, A. Gamst, M. Sluiter, C. K. Ande, S. Van Der Zwaag, J. J. Plata, et al., Sci. Data 2, 150009 (2015).
  

Active Lévy matter: Hydrodynamic description and linear stability analysis

Collective ordered motion can emerge spontaneously in many biological systems, such as bird flocks, insect swarms and tissue under dynamic re-organization. This phenomenon is typically modelled under the active fluid formalism. However, anomalous diffusion, characterizing particles whose position mean-square displacement scales non-linearly in time, is also widespread in biology. For instance, Lévy walks exhibiting super-diffusion can represent an optimal foraging strategy under specific environmental conditions. Surprisingly, the emergence of collective motion in systems displaying such anomalous diffusive behaviour has not yet been discussed. Here, we will investigate a system of active particles performing Levy flights and endowed with alignment interactions. We will derive the model equation in the hydrodynamic limit and investigate the stability of its ordered and disordered phases. This analysis aims at developing a framework integrating both anomalous diffusive motility and inter-particle interactions, thus paving the way for the definition of more realistic active matter models.   

Influence of the network properties on the phase transition of the SIR epidemic model

Out of equilibrium simulations have been used as a technique for characterization of many systems in statistical mechanics. Epidemic models as SI, SIR, SIS and SIRS and have been studied using differential equations and also Monte Carlo simulations. In the latter, usually, a square lattice is used as a network and each vertex is one individual. The positions of the individuals and the interaction between them do not change with time. The phase transitions and the critical exponent theta have been obtained with this kind of network. In this work, we explore the influence of the network allowing it to evolve during the time evolution. This is accomplished by considering each individual as a random walker moving by a fixed quantity in an arbitrary direction. Instantaneous and different networks are thus formed in each iteration. Now the interaction will be defined by the distances between the individuals, making these interactions changes in each iteration. Within this model, we identified the new phase transition, the critical exponent theta and the features of the aggregated weighted network (the weight distribution and correlation of the interactions).   

Bipartite Fidelity and Loschmidt Echo of Bosonic Conformal Interface

We study the quantum quench problem for a class of bosonic conformal interfaces by computing the Loschmidt echo and the bipartite fidelity. The quench can be viewed as a sudden change of boundary conditions parameterized by $\theta$ when connecting two one-dimensional critical systems. They are classified by $S(\theta)$ matrices associated with the current scattering processes on the interface. The resulting Loschmidt echo of the quench has long time algebraic decay $t^{-\alpha}$, whose exponent also appears in the finite size bipartite fidelity as $L^{-\frac{\alpha}{2}}$. We perform analytic and numerical calculations of the exponent $\alpha$, and find that it has a quadratic dependence on the change of $\theta$ if the prior and post quench boundary conditions are in the same type of $S$, while remains $\frac{1}{4}$ otherwise. Possible physical realizations of these interfaces include for instance connecting different quantum wires (Luttinger liquids), quench of the topological phase edge states \etc and the exponent can be detected in a X-ray edge singularity type experiment.   

Four States Epidemiologic model (FSEM) in the random transverse-field Ising universality class

We analyze the critical properties of a four states epidemic model by a mean field pair approximation and by Monte Carlo simulations on a cubic lattice. The mean field pair approximation solution suggests that this model spreads the infection in two different steps. The first step decides which sites can be infected, and the second step spreads the infection among those sites. Comparing these mean field equations with those of the Susceptible-Exposed-Infected (SEI) model and the Contact Process (CP), we conclude that the first step generates clusters according to the SEI rules and the second simulates the CP in those clusters. Since the SEI model is in the Dynamical Percolation universality class, this mean field solution suggests that this four states epidemic model should be in the same universality class of the CP with quenched disorder, which is expected to be in the random transverse field Ising (RTFI) universality class. By performing Monte Carlo simulations near the critical point, we are able to verify this hypothesis and estimate the critical exponents which are compatible with those in the random transverse field Ising model.   

Polariton condensation in 2D Lieb lattice with distributed dissipation

While one flat band appears in the 2D Lieb lattice in the tight binding model, it is hard to yield any flatness in realistic continuous models for polaritons propagating in the presence of lateral potential mimicking the Lieb lattice structure. Nevertheless, in this work, we show the exciton-polariton condensation can happen in the states possessing the symmetry of compact localized states that characterize the flat band. We consider the two-dimensional system of exciton-polaritons in semiconductor microcavity patterned with the Lieb potential. Due to the dissipative nature of this system, the single polariton motion is described by the complex periodic 2D potential, where the dissipation rate from the quantum wells differs from dissipation rate from the potential barriers. This reflects the typical experimental situation of different leakage from the wells and the barriers. Solving the Gross-Pitaevskii equation coupled to an external reservoir, we show that, under certain conditions, it becomes easier for the second (nearly flat) band to reach the condensation threshold. Thus, the condensate is formed in a non-trivial many-body state. The properties of this state are characterized by calculation of the first-order spatial correlation function g⁽¹⁾ for different lattice sites.   

Strain Bursts and Dislocation Avalanches in Obstacle-Hardened Materials

We develop a hybrid continuum-discrete model for the collective dynamics of dislocations in dense obstacle fields. The density of obstacles is described by continuum conservation equations, and solved numerically. With this hybrid model, we unravel the mystery of how and why irradiation-induced defects enhance or inhibit strain bursts in submicron single crystals. It is shown that smaller strain burst amplitudes in irradiated nano- and micro-pillars are obtained under stress control conditions. However, under strain control conditions, bursts are found not to be sensitive to irradiation, despite the arresting effect of radiation defects. This feature is a result of rapid stress relaxation truncating the strain burst, compared with the influence of irradiation-induced defects. The influence of dislocation-defect interaction mechanisms, cross slip, irradiation dose, as well as loading mode on strain bursts is systematically investigated, and the results compared with experimental observations. We also present results showing the relationship to spatial localization of plastic flow.   

Collective oscillations of DNA methylation during exit from pluripotency

Pluripotency is associated with the erasure of parental epigenetic memory with naïve pluripotent cells exhibiting global DNA hypomethylation both in vitro and in vivo. Symmetry breaking in the early embryo and priming for differentiation into somatic lineages is accompanied by genome-wide de novo DNA methylation. During this phase, we find that the paradoxical co-expression of enzymes that promote methylation and demethylation, DNMT3s and TETs, promotes cell-to-cell variability in DNA methylation. We use a combination of novel single-cell sequencing techniques and methods from statistical physics, such as renormalization, to show that these factors drive coherent, genome-scale oscillations of DNA methylation. Analysis of parallel single-cell transcriptional and epigenetic profiling provides evidence for the same oscillatory dynamics in the living mouse embryo. These observations provide fresh insights into the emergence of collective epigenetic dynamics during early embryo development, suggesting that dynamic changes in DNA methylation may assist in regulating early fate decisions.   

A System Of Pressure Sensors To Characterize Duration And Area Of Avalanches On A Conical Bead Pile

A system of pressure sensors is used to measure the area of avalanches on a conical bead pile. The bead pile is a slowly driven critical system of 3 mm steel beads. The pile comprises roughly 20,000 steel spheres atop a circular base; it is driven by adding one bead at a time to the apex of the pile. Avalanches are recorded by the change in mass as beads fall off the pile. To create cohesion between beads, a pair of Helmholtz coils is used to apply a uniform magnetic field and induce magnetization of the beads. As cohesion is added, the size and number of the largest avalanches in the system increase. To more fully compare the experiment to models, we want to characterize the fraction of the pile involved in a given avalanche to determine which avalanches are system-spanning. Thus we added a set of eight pressure sensors at the edge of the base of the pile to detect dynamic changes in the pile during an avalanche. The signals from the force-sensitive resistors are amplified through a custom circuit board and each signal is read via Arduino. The sensors provide a sensitive response to changes in the force chains within the pile, and allow us to characterize the fraction of the pile involved in an avalanche at any time during the avalanche.   

Use Of Particle Image Velocimetry To Characterize The Dynamics Of Avalanches On A Conical Bead Pile

We experimentally investigate avalanche behavior using a critical bead pile system. The pile is slowly driven by dropping individual 3 mm steel beads onto the apex of the pile. Our previous work [Lehman, Gran Matt 14, 553 (2012)] explored how the probability distribution function for avalanches of different size scaled with drop height; these results match well with a mean-field model of slip avalanches [Dahmen, Nat Phys 7, 554 (2011)]. This analysis is based on statistical data for a series of avalanches. To gain information about the dynamic motion for individual avalanches and enable a deeper comparison with the model predictions, we now image the pile using a high-speed camera and analyze the motion using particle image velocimetry (PIV). With this approach, the mean velocity at different locations on the surface of the pile is tracked and analyzed for every frame during the avalanche. Our preliminary results of avalanche duration for data runs at different levels of cohesion (due to an applied magnetic field) show that the effect of cohesion on the avalanche dynamics varies according to the avalanche size. While smaller avalanches become longer in duration for higher cohesion, large avalanches are shorter in duration at high cohesion.
  

Free Cooling of a Granular Gas in Microgravity

Granular gases as dilute ensembles of particles in random motion are not only at the basis of elementary structure-forming processes in the universe and involved in many industrial and natural phenomena, but also excellent models to study fundamental statistical dynamics. A vast number of theoretical and numerical investigations have dealt with this seemingly simple non-equilibrium system. The essential difference to molecular gases is the energy dissipation in particle collisions, a subtle distinction with immense impact on their global dynamics. Its most striking manifestation is the so-called granular cooling, the gradual loss of mechanical energy in absence of external excitation. We report the first experimental study of homogeneous cooling of three-dimensional (3D) granular gases in microgravity. The asymptotic scaling E(t)∼ t^-2 obtained by Haff's minimal model [J. Fluid Mech. 134 401 (1983)] proves to be robust, despite the violation of several of its central assumptions.   

Formation of Force Conduits Give Rise to Mechanical Self-Organization Across Microscopic Length Scales

Mechanical self-organization is uniquely found in cells, which organize forces from nanometer to micron length scales with remarkable precision to perform functions like locomotion and cell division. Presently, we are unable to design systems with similar capabilities due to a lack of governing principles for mechanical self-organization. Here, we identify a fundamental mechanism of mechanical self-organization in a minimal biochemical system we re-engineered. We find that forces can be controlled across length scales through the self-organization of structures that act as force conduits. The system contains filaments and light controlled molecular motors that, when activated, form pairs and pull on adjacent filaments. We show that, within localized regions of light, filaments organize into radially aligned asters. Furthermore, asters generate piconewton pulling forces when linked together with light, where the vectors of the pulling forces are determined by both the spatial arrangement of the asters and the geometry of the light that links them. Using the properties of aster interactions, we design and implement schemes for force-actuated logic gates and micron scale control over the transport of beads, which may be further developed to build adaptive micron-scale machines.   

Self-assembling dragons from charismatic birds

Agents able to move in 3 spatial dimensions or "birds" have been shown to give rise to various kinds of ordered phases whereby either some spatial order or some kinematic order or a combination of both would emerge by tuning parameters controlling the rules with which these agents move and interact. In this study we ascribe to each bird a certain degree of charisma related to its rank in a given hierarchical social structure. We investigate the case where such birds follow a rule where they would tend to go where other birds they look up to seem to be gathering. As a consequence, birds at the bottom of the hirearchy would tend to follow any neighbouring group of birds whereas birds at the top of the hierarchy would not follow any other bird. By combining this new hierarchical rule with more traditional rules of avoidance and stochasticity we report a range of parameter values where such birds self-assemble into a directional 3D structure which bears a resemblance to the dragons of Asian mythology. We finally probe the stability of these structures against various models of predators.   

Application of The Density Matrix Renormalization Group Algorithm to Classical Driven Diffusive Systems in One and Two Dimensions

The Density Matrix Renormalization Group (DMRG) algorithm is recognized as one of the most accurate quantum chemistry methods for calculations involving strongly-correlated particles. Its utility has recently been expanded from quantum systems to classical non-equilibrium systems such as the Symmetric Exclusion Process (SEP), which fall into the category of driven diffussive systems. Here, I first introduce the DMRG algorithm from the Matrix Product States paradigm and describe how it can be used to calculate the steady-state properties of the SEP in one and two dimensions. Last, the phase behavior of the SEP is discussed in both dimensions with comparison to analytic solutions and Monte Carlo calculations.   

Discussion on Temperatures on the basis of the Tsallis Entropy Determined by the Excited-State Populations of Hydrogen Atoms in Hydrogen Plasma

We reconsider what the temperature should be determined in plasmas in a state of non-equilibrium on the basis of Tsallis statistics. We calculate number densities N_i of hydrogen atoms with its principal quantum number i (≥ 2) of the hydrogen plasma by collisional radiative model, where we can treat N_i as functions of electron temperature T_e, density N_e, and density of the ground-state hydrogen atoms N₁. When we apply the Tsallis entropy S_q = -kΣ^N_i=1 p_i^q ln_q p_i, q-average energy U_q = (Σ^N_i=1 p_i^qε_i)/(Σ^N_j=1 p_j^q) and probabilities p_i = 1/Z_qexp_q(-β_q(ε_i-U_q)), we can determine the physical temperature as T_phys = (1+(1-q)S_q/k)/(∂U_q/∂S_q) on the basis of Tsallis statistics. Then, we can apply this equation to the excited-state N_i of hydrogen plasmas to determine T_phys. We discuss the dependence of T_phys on T_e in the range of 1 ≤ T_e [eV] ≤ 10.   

Capillary length measurements and noise-driven sidebranches in the dendritic crystal growth of ammonium chloride.

Dendritic crystal growth is an important example of nonequilibrium pattern formation that involves both nonlinear and noise-driven effects. The large-scale structures are sensitively dependent on relatively small effects, such as surface tension, and on small anisotropies in those quantities. Testing theoretical models requires careful measurements of the relevant materials parameters. For the growth of ammonium chloride crystals from aqueous solution, previous published estimates of the capillary length have varied by over a factor of 20. We report the results of a new technique for non-faceted materials. This method uses a nearly spherical crystal held near unstable equilibrium in an oscillating temperature field. We find that the product of the chemical diffusion constant D and the capillary length d₀ is approximately 0.5 μm³/s. We also consider noise-driven models of sidebranch growth. No simple power law describes either the growth of the average sidebranch amplitude or the average sidebranch envelope. Instead, the effective power law exponent appears to increase as a function of distance from the dendritic tip. Based on our new capillary length measurement, the sidebranch amplitude is larger than predicted by models of noise-driven sidebranching.   

Dynamical phase transitions in generalized Kuramoto model with distributed Sakaguchi phase

In this computational work, we have studied the disorder driven phase transitions in the paradigmatic Kuramoto–Sakaguchi model of synchronizing phase oscillators. We plot the steady state phase diagrams for quenched and annealed kinds of disorder in the Sakaguchi parameters, using the various order parameters quantifying strength of incoherence and discontinuity measures. The order of various transitions is confirmed by a study of the distribution of the order parameter and its fourth order Binder’s cumulant across the transition for an ensemble of initial distribution of phases. The system is shown to possess both continuous and discontinuous phase transitions depending on the disorder strength and coupling range. We also elucidate the role of chimeralike states in the synchronizing transition of the system, and study how disorder affects the formation and evolution of these states. Finally, we apply the Ott–Antonsen ansatz and show that theoretical results agree well with numerical findings.   

Purely General Relativistic Effects Can Suppress Astrophysical Chaos

The emergence of chaos in a spacetime deviating from Kerr in the mass quadrupole is governed only by the presence of that parameter. Space time around sources with more complex multipole structure can show the emergence of high order rotationally-induced multipoles that leaves its own imprint in the gravitational field of the source. The role of the rotation in the generation of chaos in the geodesic motion is comprehensively analyzed. The novel characteristic discussed in this work is that starting from a chaotic static configuration, the purely relativistic effects are capable of rebuilding broken tori by the quadrupole deformation by increasing slightly the rotation parameter of the source. This makes difficult the distinction between an integrable background by means of the observation of the gravitational waves.   

Sliding on a Massive Spinning Asteroid

While Newton’s sphere theorem allows us to model spherically symmetric objects as points, a spherical approximation is insufficient for some objects, such as irregular asteroids. Even Earth is not a true sphere but is closer to an oblate spheroid. We study the trajectory of a point mass sliding on a massive rotating ellipsoidal asteroid by numerically integrating the equations of motion in Mathematica. We calculate the maximum Lyapunov exponent and plot Poincare sections for the motion. We find that the system exhibits a variety of chaotic and regular behaviors and that its chaotic nature is closely related to the centrifugal and Coriolis pseudoforces and to the asteroid's gravity.   

Designed waveforms with enhanced probability to target lossy elements embedded in chaotic enclosures

The prospect of utilizing electromagnetic radiation in order to efficiently target objects (e.g. sensitive electronic circuit elements, antennas, etc) has been intensely pursued during the last few years. We propose an algorithm that provides coherent waveforms which aim to target, with high probability, lossy elements inside a chaotic enclosure. Our scheme relies on Random Matrix Theory considerations and utilizes the universal rules that characterize the statistical properties of chaotic wavefunctions.   

Physics Must Empasize Stronger the Role of Magnetic Fields in the Universe and Man

Physics still does not emphasize enough the role magnetic fields play in the activity of stars, galaxies, and black holes, as well as the increased activity of the Sun and the increased volcanic activity of the planets orbiting it at planetary alignment when the magnetic dipole moments of the aligned planets sum up. We know that the solar activity is ruled by magnetic fields, but we wouldn’t consider the impact of the summed-up magnetic dipole moments of the aligned planets on the sun. The fact that in the whole Material Universe only L-molecules (left-handed molecules) are present tell us that magnetic field played a major role in the Universe creation. Nonlinear physics could even explain the type of magnetic field involved. Our body contains only L-molecules and when we hydrogenize vegetable oils to make margarine both D-molecules and L-molecules are present. It was found that the D-molecules cause cancer. Isn’t it time for the physics to step in and offer the use of magnetic field at the synthesis, which would produce only L-molecules? Also, by measuring the body energy (magnetic) balance, we could diagnose and cure diseases because once we restore the magnetic balance we restore the health.   

Continuum Percolation of Anisotropically-Distributed Disks

Many problems of practical significance can be mapped onto a model of continuum percolation with circular disks, including overlapping images of fluorescent molecules in superresolution localization microscopy. In many such problems the positions of the disks are correlated or anisotopically distributed, e.g. in fluorescent labeling of the cytoskeleton. We have adapted the commonly-used Newman-Ziff algorithm to determine the percoclation thresholds of such systems, studying the percolation threshold as a function of the degree of anisotropy in the system, and comparing with percolation thresholds in systems of ellipses with uncorrelated positions but varying degrees of eccentricity.   

Exact Calculation of Typical Hyper-Parameter Posterior Distribution of Gaussian Markov Random Field model.

We investigated a hyper-parameter estimation method using posterior distributions for a Gaussian Markov random field (GMRF) model. GMRF is a modelling tool of gray scale images. Our GMRF model has hyper-parameters which are related to physical quantities such as a diffusion coefficient [1]. We analyzed the negative logarithm of posterior distributions called free-energy based on an analogy with statistical mechanics and exactly calculated the configurational average of free energy with respect to data. We found that the contour lines of free energy typically shrink as the amount of data increases and posterior distributions work well in evaluating the confidence of estimated values of hyper-parameters [2].
[1] Y. Nakanishi-Ohno, K. Nagata, H. Shouno, and M. Okada, J. Phys. A: Mathematical and Theoretical, 47, 045001, (2014).
[2] H. Sakamoto, Y. Nakanishi-Ohno and M. Okada, J. Phys. Soc. Jpn., 85, [6], 063801, (2016).   

Bridges in Complex Networks

A bridge in a graph is an edge whose removal disconnects the graph and increases the number of connected components. We calculate the fraction of bridges in a wide range of real-world networks and their randomized counterparts. We nd that real networks typically have more bridges than their completely randomized counterparts, but very similar fraction of bridges as their degreepreserving randomizations. We de ne a new edge centrality measure, called bridgeness, to quantify the importance of a bridge in damaging a network. We nd that certain real networks have very large average and variance of bridgeness compared to their degree-preserving randomizations and other real networks. Finally, we o er an analytical framework to calculate the bridge fraction, the average and variance of bridgeness for uncorrelated random networks with arbitrary degree distributions.   

Using Degree Correlation to Amplify Contagion in Networks

Networks facilitate the spread of contagious phenomena, wherein the behavior of an individual node is affected by the interactions with its neighbors. We investigate how the structure of a network affects the outcome of a contagious process. By accounting for the joint degree-degree distribution of the network within a message passing model, we can characterize how degree assortativity affects both the onset of global outbreaks in a network and the size of outbreaks triggered by individual nodes. We find that the critical point defining the onset of global outbreaks has a non-monotonic relationship with degree-degree correlation. In addition, the choice of nodes to seed largest outbreak is also largely affected by the degree-degree correlation. Specifically, when this correlation is negative, the largest degree nodes, hubs, trigger biggest outbreaks. However, when assortativity is positive, then contrary to traditional wisdom, low degree nodes are more likely to generate largest outbreaks. Our work suggests that it may be possible to tailor the spread of contagions by manipulating higher order structure of networks.   

From Quenched Disorder to Continuous Time Random Walk

The presented work focuses on quantitative representation of transport in systems with quenched disorder. Explicit mapping of the quenched trap model to continuous time random walk is presented. We will show that linear temporal transformation: t→ t/Λ^1/α for transient process in the sub-diffusive regime, is sufficient for asymptotic mapping. Exact form of the constant Λ^1/α is established. Disorder averaged position probability density function for quenched trap model is obtained and analytic expressions for the diffusion coefficient and drift are provided.   

Exact enumeration of self-avoiding walks on critical percolation clusters in two to seven dimensions

We study self-avoiding walks on critical percolation clusters by means of a recently developed exact enumeration method, which can handle walks of several thousand steps. We had previously presented results for the two- and three-dimensional cases; here we take a wider perspective and vary the system's dimensions up to D=7, beyond the supposed upper critical dimension of D_uc=6. These results may serve as a check of analytical predictions and help understand how the medium's fractal structure impacts on the walks' scaling behavior. For the physically relevant, smaller dimensions, the scaling exponent \nu for the end-to-end distance turns out to be smaller than previously thought and appears to be the same on the backbones as on full clusters. For the number of conformations, the "partition function", we find strong evidence against the widely assumed scaling law and propose an alternative, which perfectly fits our data.   

Uniformity Transition for Ray Intensities in Random Media

We analyse a model for the intensity of distribution for rays
propagating without absorption in a random medium. The random medium
is modelled as a dynamical map. After N iterations, the intensity is modelled as
a sum of M contributions from different trajectories, each of which is
a product of N independent identically distributed random variables, representing
successive focussing or de-focussing events. The number of ray
trajectories reaching a given point is assumed to proliferate
exponentially: M=A^N, for some constant A.
We investigate the probability distribution of the sum.
We find a phase transition as
parameters of the model are varied. There is a phase where the
fluctuations are suppressed as N increases, and a phase where
theintensity has large fluctuations, for which we provide a large deviation
analysis.   

Structure of Medellin Gangs Netwrok

For more than two decades, 1980 to 2000, Medellin has been considered one of the most dangerous cities around the world. In a joint effort with the National Center for Historical Memory, the structure of the network of gangs of Medellin is constructed out of the testimony of former paramilitary groups. The multilayer network comprises confrontation, collaboration, relation with legal actors and sponsorship networks for six analysis periods. It is shown that the parameters of the confrontation network correlates with the evolution of crime indexes of the city for the same periods.   

Computational Modeling of Neuromoscular Junction and Evaluation of A Novel Treatment For Neuromuscular Disease

The structure and organization of transmitter release sites is known to be of importance to synapse function. We combine MCell diffusion-reaction computer simulations of a realistic nerve terminal with physiology to advance our understanding of terminal release site organization. We developed healthy and diseased frog and mouse neuromuscular synapse models. We evaluated the effects of varying the spatial distribution of calcium channels and synaptic vesicles in transmission release, studied sub-active zone distribution and function of calcium-activated potassium (BK) channels, predicted changes in action potential shape and its effects on transmitter release. These models are compared and constrained by physiological recordings.

We used our control MCell model (validated by its ability to predict physiology) as a starting point for modeling the current treatments for the neuromuscular disease Lambert-Eaton Myasthenic Syndrome (LEMS). We modeled: A) the current treatment for LEMS, DAP (a potassium channel blocker), B) a newly developed drug (GV-58) that is a calcium channel gating modifier, and C) a combination of the two drugs. We evaluated the model-predicted effects on transmitter release of using different concentration combinations of each drug for future pre-clinical testing.   

Quantifying Nucleic Acid Base Pairing Free Energy and Entropic Contribution

The free energy of base pairing and base stacking is key to the stability of double-stranded DNA. This free energy can be attributed to various sources. Pairing interactions are of special interest because of their importance in controlling DNA complementarity. The entropy cost of forming hydrogen bonds between base pairs is offset by the concomitant release of water molecules originally hydrogen-bonded to the individual bases and this has been suggested as an important determinant of base pairing stability, but so far these entropic factors not been carefully quantified. Here we study a pair of nucleobases (A:T or G:C) in an aqueous solvent with up to 5,000 TIP3P water molecules using Monte Carlo simulations and umbrella sampling with full electrostatics and Ewald summation. The free energy of an A:T or a G:C pair is calculated to be stable by 7 to 8 kcal/mol. Calculating the entropic contributions separately, we find that the majority of this stability is due to the release of water as hydrogen bonds between the bases are made. Using these results, we are able to quantify for the first time how solvent entropy dominates DNA base-pairing complementarity.   

Light, Imaging, Vision: An interdisciplinary undergraduate course

Students in physical and life science, and in engineering, need to know about the physics and biology of light. In the 21st century, it has become increasingly clear that the quantum nature of light is essential both for the latest imaging modalities and even to advance our knowledge of fundamental processes, such as photosynthesis and human vision. But many optics courses remain rooted in classical physics, with photons as an afterthought. I'll describe a new undergraduate course, for students in several science and engineering majors, that starts from the rudiments of probability theory to modern methods like fluorescence imaging and Förster resonance energy transfer. After a digression into color vision, students then see how the Feynman principle explains the apparently wavelike phenomena associated to light, including applications like diffraction limit, subdiffraction imaging, total internal reflection and TIRF microscopy. Then we see how scientists documented the single-quantum sensitivity of the eye seven decades earlier than `ought' to have been possible, and finally close with the remarkable signaling cascade that delivers such outstanding performance. A new textbook embodying this course has been published by Princeton University Press.   

Open system perspective on incoherent excitation of light-harvesting systems

The nature of excited states of open quantum systems produced by incoherent natural thermal light is analyzed based on a description of the quantum dynamical map. Natural thermal light is shown to generate long-lasting coherent dynamics because of (i) the super-Ohmic character of the radiation, and (ii) the absence of pure dephasing dynamics. In the presence of an environment, the long-lasting coherences induced by suddenly turned-on incoherent light dissipate and stationary coherences are established. Dynamics in a subunit of the PC645 light-harvesting complex is considered where it is further shown that aspects of the energy pathways landscape depend on the nature of the exciting light and number of chromophores excited. Specifically, pulsed laser and natural broadband incoherent excitation induce significantly different energy transfer pathways. We note an important difference in the phase of system coherences when coupled to blackbody radiation or when coupled to a phonon background.   

Energetic funnel facilitates facilitated diffusion

It has been established that transcription factors find their target on DNA by facilitated diffusion, i.e. by alternating 3D diffusion and 1D random walk along the DNA. This implies that the genetic context, i.e. the DNA energy landscape around a specific target finding can play an important role for the transcription factor kinetics. By analyzing DNA sequences from E.Coli, I will show how genetic context can be used to speed-up target search. Predictions are tested by an extensive computational study of a stochastic model of protein sliding events. I will conclude by discussing possible evolutionary implications of this finding.   

Mapping The Cold Denaturation Landscape of Proteins

We are exploring the fundamental basis of an importnat but little understood key component of globular protein stability and function: protein cold denaturation. Cold denaturation is not a commonly known phenomena, yet probably all globular proteins have a free energy minimum in the vicinity of 20-40 C and have increasing free energies at both higher and lower temperatures, for different physical chemistry reasons that are equally important. We belive understanding this fundamental puzzle of globular protein metastability will get at the heart of understanding globular protein stability in the cell. We are using low-temperature microfluidics and single molecule spectroscopy to monitor protein stability at both low and high temperatures.   

Following protein conformational fluctuations during ligand binding, catalysis, and inhibition

A single-molecule nanocircuit technique is applied to trace protein conformational fluctuations that control dynamic interactions between a single enzyme lysozyme and various ligands including peptidoglycan substrates and synthetic peptide inhibitors. The electronic recordings directly revealed the ligand-dependent, wide conformational fluctuations such as precluded catalytically important conformation states and their timing or additional conformational states. We have identified several kinetic parameters and compared them for each ligand to elucidate the role of such fluctuations for enzyme activities such as binding, catalysis, and inhibition. These results help understand the molecular mechanism governing lysozyme’s interaction with inhibitors as well as design more effective drugs, such as mechanism-based inhibitors.   

CRISPR−Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling and Molecular Dynamics

The RNA-guided CRISPR−associated Cas9 has revolutionized genome engineering, yet its mechanism for DNA target selection is not fully understood. A crucial step in Cas9 target recognition involves unwinding of the DNA duplex. Our work demonstrates direct detection of Cas9-mediated DNA unwinding by a combination of site-directed spin labeling experiments and molecular dynamics simulations. The results support a model in which the unwound nontarget strand is stabilized by a positively charged patch between the two nuclease domains of Cas9 and reveal uneven increase in flexibility along the unwound nontarget strand upon scissions of the DNA backbone. Analysis of Cas9 with mutations along the positive patch reveal the role of this protein domain in specificity. This work establishes the synergistic combination of spin-labeling and molecular dynamics to directly monitor Cas9-mediated DNA conformational changes and yields information on the target DNA in different stages of Cas9 function, thus advancing mechanistic understanding of CRISPR−Cas9 and aiding future technological development.   

The inverse and direct Hofmeister series of Hen egg lysozyme at pH below isoelectric point (pI) as seen by SAXS

Protein interaction and aggregation processes are important in understanding many physiological processes in living organisms. Diseases such as Alzheimer’s, Creutzfeldt-Jakob and Parkinson’s are associated with protein or peptide aggregation phenomena. We are focused on determining the shape, size, and nature of interactions between the protein molecules (lysozyme) in solution at low and high salt concentration of various sodium salts at certain pH by using Small-angle X-ray scattering (SAXS).
Results show that for protein at 10mg/ml and 200mg/ml the shape and size of the protein is spherical with radius 15.5 Å and 16.7 Å respectively. At 60mg/ml with 0.1M sodium salt, the shape and size of the protein is ellipsoidal with the average polar radius of 38.5 Å and equatorial radius 15.5Å. There is no interaction among proteins at 10mg/ml and 60mg/ml whereas at 200mg/ml we see a coulomb repulsive interaction with effective radius 20.3 Å. The variation of the polar radius of protein at 60mg/ml at pH 9.0 with 0.1M of various Hofmeister sodium salts shows an elongation of the protein as we go from left to right in the Hofmeister series. We are currently focusing on determining the mechanism of elongation and impact on aggregation in the protein induced by Hofmeister salts.   

A Comparative Study of Thermodynamic Properties of Hydration Layer of the Amyloid Precursors of Alzheimer’s Disease and Type II diabetes using Dielectric Relaxation Spectroscopy

Recent reports suggest a biological link between Alzheimer’s disease (AD) and Type 2 diabetes (T2D). AD and T2D involves the aggregation of amyloidogenic peptides of amyloid beta 42 (Aβ42) and human islet amyloid polypeptide (hIAPP). During aggregation process, the biological water at their surface tends to redistribute itself. The thermodynamic changes accompanying this redistribution provides better insight into the understanding of the correlation between amyloidogenesis of Aβ42 and hIAPP peptides. Here, we present the variations in thermodynamic parameters of activation entropy, enthalpy, Gibbs free energy, and heat capacity for Aβ42 and hIAPP precursors as a function of incubation time (0-24 h) and temperature (133K- 283K) using dielectric relaxation spectroscopy over the frequency domain of 10^-3-10⁷ Hz. The dielectric processes corresponding to different amyloid aggregates of Aβ42 and hIAPP showed closely related values of enthalpies and entropies, indicating a lesser degree of hydrogen bonding for the bound water than bulk water. Our results showed a thermodynamic correspondence in the behaviors of Aβ42 and h-IAPP peptides which further support the relationship between AD and T2D.   

Protein Transport in Curved Lipid Bilayer Membranes: An Extended Saffman-Delbruck Approach Incorporating Hydrodynamics in Curvatured Fluid Intefaces

We develop fluctuating hydrodynamics approaches to extend Saffman-Delbruck theory to capture the collective drift-diffusion dynamics of proteins within curved lipid bilayer membranes. Our approach is at the level of fluid interfaces having any curved radial manifold shape. We take into account the two dimensional hydrodynamics of the two curved leaflets of the bilayer coupled with the three dimensional hydrodynamics of the surrounding bulk fluid. Using analytic and computational approaches, we show how Gaussian curvature can significantly impact dissipation within the curved two dimensional membrane fluid to augment the collective drift-diffusion dynamics of protein inclusions. We further show for the self-assembly of protein clusters that these effects contribute significant kinetic contributions giving differences with widely used non-hydrodynamic theories. We also present general results on the collective drift-diffusion dynamics when heterogeneous curved structures are present in the membrane geometry showing how these local Gaussian curvature effects influence hydrodynamic coupling in some interesting ways.   

Circulating Traveling Wave Enhance the Maturation of Cardiomyocytes in Self-organized Tissue Ring.

Directed differentiation methods allowed high purity cardiomyocytes (CMs) differentiated from human pluripotent stem cells (hPSCs). However, their immaturity nature indicated early cardiac development, and might limit the applications in drug development and regenerative therapy. Here we showed a platform that promote the three-dimensional self-organized tissue rings (SOTRs) within which high-frequency action potential, named travelling waves (TWs), spontaneously originated and travelled robustly and continuously for months without any external stimulation. A mathematical model was used to simulate and interpret the origination of TWs within SOTRs. After two weeks training, SOTRs with TWs showed matured structural organization, increased cardiac gene expression and enhanced Ca²⁺ handling properties in a frequency-related manner, compared with control group without TWs. Thus, the self-pacing SOTRs may be used for promoting the cardiomyocytes maturation and the platform can serve as an economical and practical system for future scaling-up production of matured hPSCs-CMs.
  

Effects of Physical Parameters on Structural Maturation of Marine Mussel Adhesive Plaques

Marine mussels have evolved to produce extremely effective wet adhesives. In order to create synthetic versions of these adhesives, we would like to understand the division between the biological and physical parameters involved in their formation and structural maturation. Mussel adhesives exist as acellular, thin films, known as plaques, consisting of mussel foot proteins (mfps). In the case of Mytilus californianus, cross-linked mfps form a foam architecture that incorporates iron and calcium. The origin and role of iron and calcium, among other metals, in the structural maturation process is unknown. Using electron microscopy, inductively coupled plasma mass spectrometry, and amino acid analysis, we examine the composition, the effect of iron and calcium, and the role of pH on the time evolution of the plaque’s maturation. Our results suggest that physical, rather than biological, processes are critical to the formation of the final structure.   

Investigating Bacterial Detachment on Polymeric Biomaterial Nanopillared Surfaces Under Shear Stress

Pseudomonas aeruginosa is an opportunistic biofilm forming bacterium that exhibits the ability to twitch upstream in fluid flow environments. The upstream movement is facilitated by the retraction and extension of their type iv pili mechanosensor ATPase motors pilT and pilU when adhered to a surface. Here, motility prohibition and detachment of P. aeruginosa are studied on polymer biomaterial surfaces structures with arrays of nanopillared geometries under fluid flow. The arrays of nanopillars range in periodicity from 200, 300, to 600 nanometers. Upstream movement direction, detachment, and velocity of wild-type P. aeruginosa expressing GFP were monitored in flow channels of flat and nanopillared surfaces and quantified using fluorescence microscopy. The cell motility prohibition and detachment under shear stress was observed to have a nanopillar surfaced periodicity dependence. This bacteria-biomaterial interaction allows us to design our surface interfaces with specific nanopillared geometries for structurally controlling cell motility and detachment under fluid flow. The disruption of surface attached bacterium upstream movement that lead to colonization and biofilm formation is crucial in preventing harmful infection from contaminated medical devices such as catheters.   

The cooperative effect of amelogenin and enamelin in the nucleation of calcium phosphate

Amelogenin is the major matrix proteins templating the nucleation of numerous calcium phosphate phases during enamel formation. Besides matrix protein, the other proteins like enamelin are also believed to have important role in the formation of enamel apatite. The delicate enamel architecture is believed to form under the control of amelogenin together with other non-amelogenous proteins including enamelin. Thus, understanding the interplay between amelogenin and enamelin may enable us to manufacture complex protein-mineral structure for tissue engineering. Here the nucleation of calcium phosphate on these surfaces is studied by in-situ AFM. The result showed that the nucleation rate of calcium phosphate showes an optimal enamelin/amelogenin ratio, when the enamelin/amelogenin ratio is below the critical value, nucleation rate increase as the enamelin increase, while above the critical value, the nucleation is inhibited. The reason for existence of such critical value is proposed and proved by gold nanoparticle labeling.   

Can sixth extinction be avoided

Sixth mass extinction is coming!
We suppose a balance system between the sun and a dark sun which is made up of the dark matter-dark energy. It decides the structure among the matter, dark matter, and DNA; and it has periodic dark impaction to make mass extinction on the earth.
Supposing spacetime center of negative Einstein field equation, balance structure between spacetime (wave) and massenergy (particle), balance between dark matter-energy and general matter, probability effect of spacetime structure, new atom model, new uncertainty relation, and bid bang of spacetime, that can explain of the inertial system, the dark energy, dark matter, Hubble’s red shift, Galaxy rotation curves, a flat structure of universe, inflationary theory, two slit Interference, and photoelectric effect.
Since 2002, I had finished the experiments that consciousness used a probability effect of the spacetime structure of brain’s wave to change the photo-voltages of the solar cells and a balance structure between Electron Clouds and electron holes of P-N Junction.
Studying two kinds of Big bangs and advance consciousness, Human should use the dark matter-energy to balance the structure of the dark impaction, evolutive DNA, and avoid sixth mass extinction.
http://meetings.aps.org/Meeting/APR16/Session/M13.8   

Computational Study of Antibody-Antigen Coevolution Using a Shape-Space Model

B lymphocytes in the adaptive immune system can produce antibody molecules that bind and remove foreign substances (antigen). The binding affinity of antibodies for an antigen can be improved through affinity maturation (AM) – a Darwinian process occurring in the microenvironment called germinal centers (GC). Studying AM process is crucial for understanding how the immune repertoire evolves and for developing efficient vaccine strategies.

In this work, we focus on B cell maturation against HIV infection, where the antigen is also rapidly evolving, creating an evolutionary “arms race”. We develop a shape-space model to describe antibody-antigen coevolution and use stochastic simulations to study how GC compartmentalization and initial antigen diversity affect the course of affinity maturation. We have identified important determinants of maturation outcome and found a critical role played by the degree of conservation of the antigen.   

Activity and Effects of Retroelements in Bacteria

Retroelements (RTEs) are abundant in eukaryotic genomes but less numerous in bacteria as group II introns. It has been hypothesized that eukaryotic spliceosomal introns and retrotransposons may have evolved as a result of invasion by bacterial group II introns. However, it remains unclear what limits RTE proliferation in bacteria and archaea and what enables it in eukaryotes. We quantify the effects of the human RTE LINE-1 and the bacterial group II intron Ll.LtrB in Escherichia coli and Bacillus subtilis. We find that RTE expression is detrimental to both species, that LINE-1 successfully integrates into the chromosomes, and that the ability to repair DNA breaks with bacterial non-homologous end joining systems increases retrotransposition efficiency. Our results show that RTEs place a significant burden on organisms poorly equipped to handle their effects, and that the capacity of the last eukaryotic common ancestor for NHEJ may have enabled the proliferation of RTEs and the evolution of eukaryotes.   

A new analytical model for studying the energy of DNA with and without proteins

We introduce a new analytical rod model to describe the configuration of DNA with and without proteins. The model incorporates any pathway of protein-bound DNA, including those found in high-resolution structures, and allows for the treatment of circular and looped molecules. We determined the mathematical equation for linkers that can smoothly connect two protein-bound DNA segments with arbitrary positions and orientations. The smooth linker is a quartic function with five coefficients which can be expressed in terms of its boundary values. We first considered ideal protein-bound DNA segments containing left-handed and right-handed helical supercoils with complete and partial turns.
We are using these supercoils and the smooth linkers as building blocks to study more complicated structures like the SV40 minichromosome. We are studying the effects of electrostatic and elastic energy on the stable configurations of these systems.   

The Standard Genetic Code Facilitates Exploration of the Space of Functional Nucleotide Sequences

Mutations occur in the genomic DNA while most cellular functions are carried out by proteins, which largely determine the organism’s phenotype. Governing the translation of genomic transcripts into proteins, the genetic code plays a crucial role in steering molecular evolution. We investigated the number of functional variants of the E. coli PhoQ protein explored at different numbers of mutational steps under translation using different genetic codes and found that the standard code was optimized for exploring a greater number of functional PhoQ variants at intermediate time scales as compared to random such codes. Greater genetic diversity in the population is beneficial in response to environmental changes which are more likely to occur at these intermediate time scales. Our results indicated that, independent of the property of the standard code to minimize the phenotypic effects of mutations, the property to explore more functional sequence variants arises from a balance between robustness and flexibility in the face of mutations. We propose that selection for this property while minimizing phenotypic effects of mutations contributed towards the emergence of the standard code as the universal genetic code.   

Synchronized Cellular Mechanosensing due to External Periodic Driving

The response of cells to periodic driving is important for many biological processes, particularly for proper blood flow and heart functioning. Our research analyzes the collective shear stress response of fibroblast cells due to a periodic driving frequency. When cells experience shear stress, they release calcium into the cytosol. To quantify the shear stress response of the cells, we use calcium imaging and single-cell level analysis. We have observed the collective response of a monolayer of fibroblast cells due to a periodic shear stress. The average calcium dynamics of the cells do not have the same frequency as the applied shear stress profile. This suggests that a collective response of cells may exhibit rich dynamics beyond intuitive expectation. We did simple theoretical modeling to explain the discontinuity of the nonlinear signaling dynamics observed.   

Modeling and Inference of Hepatic Transport Kinetics

The liver performs critical physiological functions, including metabolizing and removing substances such as toxins and medications from the bloodstream. Intravital microscopy (IVM) has developed into a versatile tool to monitor hepatic transport kinetics and its data is poised to provide greater insight into hepatotoxicity. Hepatotoxicity itself is intimately linked to abnormal hepatic transport and liver injuries remain the primary reason drugs in development fail and approved drugs are withdrawn from the market. Here we propose new tools to learn, from IVM data, transport kinetics of fluorescein across liver compartments which, due to their chemical composition, differentially impact fluorescein’s emission properties. We propose a way by which IVM data may be turned into a quantitative differential equation transport model by introducing fluorophore “visibility parameters" across different regions that we infer jointly alongside transport rates (kinetic parameters). To perform the parameter inference, we adapt the method of parameter cascades which ensures fast and precise parameter estimates from noisy time traces under conditions of curve smoothness. We test our approach on both synthetic data and apply our method to experimental data.   

Temporal precision of regulated gene expression

Important cellular processes such as cell migration, differentiation, and division often rely on precise timing. Yet, the molecular machinery that regulates timing is inherently noisy. How do cells achieve precise timing with noisy components? We investigate this question using a first-passage-time approach, for an event triggered by a molecule that crosses an abundance threshold and that is regulated by either an accumulating activator or a degrading repressor. We find that the optimal strategy corresponds to a nonlinear increase of the target molecule over time. The optimality arises from a tradeoff between minimizing the extrinsic timing noise of the regulator, and minimizing the intrinsic timing noise of the target molecule itself. Although either activation or repression outperforms an unregulated strategy, we find that repression outperforms activation in the presence of cell division that occurs late in the process. Our results explain the nonlinear increase and low noise of mig-1 gene expression in migrating neuroblast cells during C. elegans development, and suggest that mig-1 regulation is dominated by repression for maximal temporal precision. These findings suggest that dynamic regulation may be a simple and powerful strategy for precise cellular timekeeping.   

Exploring Cellular Constriction Chain Dynamics in Drosophila Embryo

Several potential mechanisms of mechanical coordination of the constriction of the cell apices in groups of cells have been proposed. Our previous computational studies have shown a connection between tensile mechanical feedback and Cellular Constriction Chains (CCCs) that propagate during the first phase of Ventral Furrow Formation (VFF) in the Drosophila melanogaster embryo. Detailed imaging of the underside of the embryo allows us to analyze how morphological aspects of cell clusters change over time. We have used confocal microscopy to take high-resolution time-lapsed images of living Spider-GFP embryos, mutants that have Green Fluorescence Protein (GFP) embedded in their cell membranes. Monitoring the progression of individual cell shape through image analysis, we have explored the nature of mechanical coordination responsible and established a method for evaluating the underlying cause of cellular group formations.
  

Influence of periodical mechanical stimulus on cardiac cell aggregates

In Physiology, numerous studies have provided evidence for electrical-mechanical interactions between cardiac cells in order to regulate the heartbeat. To investigate such interactions experimentally, a periodical mechanical stimulus has been applied to cardiac cell aggregates in a culture dish. The motion of the tip for the stimulus, tapping, replicated the intrinsic beat motion of the contraction and relaxation of the cell aggregates. Cardiac cell aggregates synchronize the beat with a periodical electrical stimulus in culture medium as the electrical stimulus is used for peacemaker. On the other hand, our mechanical tapping by a tungsten probe limited the area of the deformation on the aggregate surface. We will present the response of spontaneous aggregate beats to mechanical tapping, single or periodical at room temperature and in a standard culture condition. The results showed cardiac cell aggregates are not sensitive to mechanical stimulus relative to electrical stimulus, particularly in the culture condition. However, the partial synchronization and the spontaneous beat rate change under the stimulus in 24-48h indicates the biological modification may occur.   

Biological Cell Manipulation by Magnetic Nanoparticles

We report a manipulation of biological cells (erythrocytes) by magnetite (Fe₃O₄) nanoparticles in the presence of magnetic field. The experiment was accomplished on the top of the micro-electromagnet consisting of two magnetic field generating contours. An electric current flowing through the contour(s) produces a non-uniform magnetic field, which is about 1.4mT/1µm at 100mA current in the vicinity of the current-carrying wire. It makes magnetic nanoparticles to move towards the magnetic energy minima. In turn, magnetic nanoparticles drag biological cells in the same direction. We present experimental data showing cell manipulation by controlling the electric currents. This technique allows us to capture and to move cells located in the vicinity (10-20 microns) of the current-carrying wires. One of the most interesting results shows a periodic motion of erythrocytes between the two conducting contours, which frequency is controlled by the electric circuit. The obtained results demonstrate the feasibility of non-destructive cell manipulation by magnetic nanoparticles with micrometer-scale precision.   

Effect of Weak Magnetic Field on Neural SIgnals

Biosensors are devices that employ specific biochemical reactions mediated by enzymes, tissues, organelles or whole signals by electrical, thermal or optical signals. Biochemical production is affected by external magnetic field and the electrical and chemical signals may also interact with external fields. We study the effect of weak magnetic field on electrochemical signal transport and its impact on biosensors and neural signals.   

Dynamics of Approach-Avoidance Conflict during Exploration of Novel Objects in Mice

Novelty poses a complex challenge to animals: in a potentially risky encounter with the unknown, they must balance exploration with safety. Indeed, many animals respond to novelty with a mix of curiosity and caution. Typically, when presented with conflicting incentives to approach and avoid a stimulus, animals oscillate between the two behaviors. Here, we reconstruct the phase space of oscillatory behaviors elicited by novel objects in mice from experimental data. We show that the mice's behavior in a 1D circular maze can be characterized as a 2D dynamical system of the form d²θ/dt²=F(θ,dθ/dt). Interestingly, the mice behave as though they experience a different "force" F near the object depending on whether they are moving toward or away from it. The dependence of F on velocity is inconsistent with a popular model of approach-avoidance conflict, according to which the appetitive and aversive aspects of a stimulus create overlapping motivational "potential fields", and F is the gradient of the summed potentials. Transitions between this and other types of exploratory behaviors require time-dependence of F.   

Cooperation mitigates diversity loss during spatial range expansions

Spatially expanding populations are known to experience rapid diversity loss because of the serial founder effect - the small number of individuals at the tip of the expansion wave, that seed the population in a new territory, makes them susceptible to demographic fluctuations, leading to loss of diversity. However, this is only true in competitively growing populations, in which the per capita growth rate of the population decreases monontonically with increasing density. For cooperative populations, which grow the fastest at intermediate optimal densities, the founder effect is mitigated because of migration from the fast-growing high density bulk of the expansion wave. In previous work, we have demonstrated that yeast populations undergo a transition from pulled to pushed expansion waves as cooperation is increased. Here, we extend the experimental system to demonstrate that pushed waves, caused by increased cooperation, indeed mitigate the rate of diversity loss. We also experimentally quantify the effective population size during expansions and its scaling relationship with the bulk population size.   

Interspecies Bacterial Competitive Outcomes in C. elegans Intestine Reveal the Principles of Community Assembly in a Simple Animal Gut

Animals throughout the tree of life contain complex multi-species gut communities that play an important role in health and disease. However, the complexity of these gut microbiomes often constrains our ability to gain a mechanistic understanding of how these communities assemble and function. We colonize the gut of the worm C. elegans, a tractable experimental system, with 11 bacterial species in singles, all possible pairs, and selected trios. We find a mixture of coexistence and competitive exclusion with a hierarchical structure lacking any rock-paper-scissors interactions. With the intention of associating the characteristics of these one, two, and three species microbiomes, we find a correlation between the monoculture colonization capacity of a bacteria and its average fraction at pairwise competition, and we encounter that the fractions of pairwise competitions possess good predictive power of trio outcomes. We further show that the C. elegans gut environment changes the outcome a pair of species would have outside of the host, with the low intestinal pH being one of the causes. These results highlight that a bottom-up approach to microbiome community assembly may provide valuable insight into the structure and function of complex microbial communities.
  

The "Goldilocks" Point for the Emergence of Antibiotic Resistance in Spatial Bacterial Populations

Low antibiotic concentration in a microenvironment allows for a large bacterial population, facilitating the emergence of a resistant mutant. It also implies a low fitness advantage for the mutant over the wild type which impedes mutant fixation. Using computer simulations to investigate the emergence of antibiotic resistance amidst a linear antibiotic gradient in one- and two-dimensional geometries, we found that the mutant fixed at higher antibiotic concentrations on increasing the rate of bacterial movement between microenvironments up to a threshold, beyond which the mutants had a higher chance of fixing at low antibiotic concentrations. The mechanism of mutant fixation was different on the two sides of the threshold and we describe a theory for the two scenarios. Dynamics in the one- and two-dimensional cases were qualitatively similar, with a higher rate of mutant fixation in the two-dimensional case. The results indicated that a trade-off between wild type population size and fitness advantage of the mutant governs the emergence of antibiotic resistance in spatial bacterial populations, and this “goldilocks” point for mutant fixation exhibits non-trivial dependence on the movement rate of the bacteria.   

Percolation and cooperation with mobile agents: Geometric and strategy clusters

We study the conditions for persistent cooperation in an off-lattice model of mobile agents playing the Prisoner's Dilemma (PD) game with pure strategies: C-cooperators, D-defectors. Each agent has an exclusion radius r_P and an interaction radius r_int that defines the instantaneous contact network. The agents undergo random diffusion and strategy evolution follows the finite-population analog of replicator dynamics. We show that, differently from the r_P = 0 case, the model with finite sized agents presents a coexistence phase. Moreover, there are also two absorbing phases in which either C's or D's dominate. We provide a geometric interpretation of the transitions between phases and present a phase diagram of the PD dynamics as a function of both r_P and r_int. In analogy with lattice models, geometric percolation of the contact network enhances cooperation. More importantly, we show that the percolation of D's is an essential condition for their survival. Differently from compact clusters of C's, isolated groups of D's will eventually become extinct if not percolating, independently of their size. Our results are robust for a great range of mobilities and of the temptation parameter in the PD game.   

Active systems learning at the microscale

Living organisms are able to sense and process information about the environment they live in. They are also able to update this information in order to contruct solutions for real life problems such as finding food or avoiding danger. This active adaption process that in the long run drives the evolution of species is the result of a short time scale evolution of the knowledge of an organism that we know as learning. At the microscale the learning is hampered by stochasticity given that the intrinsic Brownian noise makes critical to build a feedback between stimulus and action. Here, we present a system based on a self-themophoretic microswimmer that allows the application of artifical intelligence algorithms at the microscale. Using reinforcement learning we show that even under noise conditions a system is able to learn how to optimize a simple navigation task. We study the influence of noise and the situation where multiple agents can share information to carry out specific tasks. This way we show how adaptation and intelligent collective behavior can be studied in artificial microswimmers systems.   

Coarse-Grained and Statistical Mechanical Modeling of Dynamic, Mechanically Compliant DNA Hinges

Structural DNA nanotechnology takes advantage of base-pairing interactions to assemble DNA strands into rigid 2D and 3D nanostructures of exquisite geometries and complexity. Recently, this approach has been used to design dynamic, mechanically-compliant DNA nanostructures by exploiting differences in the mechanical properties of single- and double-stranded DNA. Here, we use coarse-grained molecular dynamics simulations to provide some of the first insights into the conformational dynamics of a mechanically-compliant nanostructure, a DNA origami hinge recently designed and studied experimentally. We show that the simulations can accurately reproduce the experimentally measured equilibrium angles between hinge arms for a range of hinge designs. The simulations also reveal important insights into the structural and mechanical properties of the hinges that are challenging to obtain experimentally. We also introduce a novel approach for rapidly predicting equilibrium hinge conformations based on the force-deformation characteristics of its components. Lastly, we present a statistical-mechanical model for describing salt-triggered actuation that is currently being used to guide ongoing experimental efforts towards designing DNA hinge-based actuators.   

Emergent Polar Organization and Bundling of Nematic Filaments Driven by Crosslinking Motors

Mixtures of cytoskeletal filaments and molecular motors can create active nematic liquid crystals with remarkable properties, including spontaneously generated extensile stress, active turbulent flow, and complex defect dynamics. We have developed a minimal computational model of a network of rigid filaments that undergoes bundling and sliding by crosslinking motor proteins. Here, we map the phase diagram as motor activity and concentration are varied. Increasing the concentration of passive crosslinkers drives a transition from isolated, laterally extended bundles to horizontally extended nematic domains. Low driving of the bundled state maintains the extended bundle organization but polarity sorts these rod aggregates. Sufficiently high driving leads to large, fluctuating polar domains and apparent polar phase separation. We characterize the polarity-dependent filament transport that leads to emergent polar organization of the non-equilibrium steady state.   

Mechanism of force-induced restarting of protein synthesis in SecM-stalled ribosomes

Stalling peptides are a class of proteins that induce long-timescale pauses in ribosomal translation as they are synthesized. Since this stalling can be relieved with a physical force applied to the end of the nascent protein, they have been utilized as force sensors for biological processes. Despite their utility, the mechanism through which an applied force leads to the restart of synthesis is still unclear. We run molecular dynamics simulations of a stalling peptide in the ribosome exit tunnel. By directly applying a force to the end of the peptide, we are able to characterize several intermediate states in the stall breaking pathway. Identification of these states allows for the rational design of stalling peptides sensitive to different force ranges. Through repeated measurements of the forces required to induce transitions between these states, we characterize the free energy landscape of the stall, and use it to make predictions about stall-breaking as it occurs in experimentally realistic force-regimes and timescales.   

Dynamical Instability in Rigor Fibers?

When muscle fibers are in rigor, most of the crossbridges are thought to exist in a "rigid" type of mobility state. This is due to strong attachment to binding sites of actin ("thin") filaments. Using EPR spectroscopy, we have studied changes in crossbridge mobility state as a function of time. We observed both small and large oscillatory changes over timescales ranging from minutes to hours. The large changes would correspond to long-range correlations in space. They could be taken to arise from slow dynamics of rigor cluster rearrangements in space. The mixed mobility state of the entire fiber could then be viewed as a type of structural phase coexistence. Finally, the slow dynamic rearrangements could be viewed as heterophase fluctuations that undergo avalanche-like excursions - in both directions. These spontaneous directional switching events may then correspond to some type of extreme dynamical instability existing within the rigor-state fiber.   

Probabilistically Patterned: Synthesis and Characterization of Random Copolymers in Ensemble and at the Single Chain Level.

Living polymerization techniques have enabled polymer scientists to create random copolymers combining a breadth of interesting monomers, with precise control over composition, molecular weight, and architecture. These materials, with their multi-functional ligands and well-defined features, begin to approach the complexity achieved in natural biopolymers. Recent studies have been performed on their ability to produce proton specific membranes and to stabilize enzymes in organic solvents, enabling active hybrid biomaterials production. However, most of the materials characterization is done on ensembles of polymer chains. What if, in the application, we are seeing the achievements of a few outlier sequences? Herein we use computational and experimental approaches to characterize random copolymers at both ensemble and single chain levels to further our understanding of the relationship between aggregate properties, sequence specificity, and activity.   

Unveiling Molecular Mechanisms of Kinesin-5 Function Using Multiscale Computational Techniques

Molecular motor protein Kinesin-5 (Eg5) is a member of kinesin superfamily that is critical for bipolar spindle assembly and spindle maintenance during mitosis. As a result it is a promising chemotherapeutic target for cancer treatment. While a number of small-molecule drugs that interact with Eg5 have been identified, little is known about the molecular mechanisms by which they inhibit Eg5 function. Furthermore, multi-motor systems can exhibit qualitatively diverse behavior for different drugs, in some cases showing non-linear dependence of motor velocity on drug concentration. We study molecular mechanisms behind function of individual Eg5 and multi-motor systems involving it using computational modeling techniques. Besides apparent fundamental value this work has direct implications for clinical applications, where in depth understanding of Eg5-drug interaction is important.   

Governing Factors for Active Transport in the Actin Cytoskeleton

Active transport driven by molecular motors in the cytoskeleton is of great importance for various cellular processes, such as secretion of molecules and endocytosis. Thus, the active transport phenomena have been studied in several previous models. However, those models have critical limitations in many aspects. In this study, we employed an agent-based computational model that overcomes the limitations of the previous models, in order to investigate how diverse properties of the actin cytoskeleton affect characteristics and efficiency of the active transport. We found that force dependence of walking velocity of motors that has been neglected in many models plays a very significant role in the active transport. Mobility of motors is lower if an actin network is more elastic because motors are stalled easily at cross-linking points between actin filaments in such an elastic network. We also found that bias in orientation of actin filaments critically regulates motions of motors. In addition, we uncovered how the amount and properties of motors affect movements of motors. Our findings provide new insights into mechanisms by which cells regulate motions of motors in the actin cytoskeleton for the active transport.   

The effect of microtubule deformation on the efficiency of motor protein walkers

Microtubules are an important component of the cytoskeleton of cells. They provide not only structural support, but also connectivity between different regions of the cell. Motor proteins transport tethered cargo by walking along microtubules, which may be deformed in the complex environment of the cell. Since the length of the microtubule is measured in micrometers, while motor proteins operate on the nanometer scale, computer simulations of walking motor proteins have to bridge multiple length scales. In recent work, Zhang and Wang [1] developed a micromechanical microtubule model that can be efficiently simulated with finite element methods and mapped back to an interaction site model on the nanometer scale. In this work, we simulate motor proteins walking on deformed microtubules by combining finite element calculations of microtubules under stress with Brownian dynamics simulations of a coarse-grained model for motor proteins. We report on our method for bridging the length scales and present results for the effect of microtubule deformation on the efficiency of motor protein walkers.
[1] J. Zhang and C. Wang. Biomech. Model Mechanobiol. 13, 1175 (2014).   

Photobleaching of Microplastics from Recyclable Plastics

When improperly disposed recyclable plastics break down, microscopic pieces of the material become environmental pollutants. The physical properties of microplastics can be determined using fluorescence microscopy. However, persistent illumination of microplastics at the fluorescence excitation wavelength results in photobleaching, which reduces the fluorescence intensity of the sample, often irreversibly. The effects of photobleaching are analyzed by exposing microplastic samples to 405 nm laser light at two different intensities for an experimentally relevant time of 30 minutes while taking a video recording of the resulting fluorescence decay. This is followed by taking periodic single images to examine possible fluorescence recovery. Our results set experimental constraints on the imaging intensity and imaging time for fluorescence microscopy studies of microplastics. Implications for further analysis of microplastics using secondary fluorescence techniques are also evident. Investigators can use our results to create more effective experimental designs, which will allow for more accurate investigations into the environmental consequences of microplastics.   

Negative differential resistance behavior on charge transport through strained and tilted DNA molecules

A double-stranded DNA molecule subject to either an electrical bias voltage or a small mechanical strain exhibits a negative differential resistance (NDR). Using an advanced two-dimensional tight-binding model including hopping integrals for the next nearest-neighbors, we implement a strain-dependent DNA helix conformation in conjunction with the theories of Slater-Koster and linear elasticity. Contour plots, which show nonlinear current-voltage (I-V) characteristics, as functions of tilted angles (or percentage strains) and source-drain voltage for fixed percentage strains (or tilted angles) are presented. The observed NDR in the I-V curve is characterized by a peak-to-valley ratio (PVR). We show that a high value of PVR is achieved as either percentage strains or tilted angles increase. This higher value of PVR for an I-V curve implies a greater ability for the realization of potential applications such as logic switches and reflection amplifiers.
  

Actin Density Distribution in C17.2 Cells

Single-walled carbon nanotubes (SWCNTs) have great potential in the biomedical field as a means to deliver materials such as drugs and genes due to their size and chemistry. However, the long-term consequences to the body are still unknown. For example, carbon nanotubes have been previously shown to alter the differentiation process of C17.2 stem cells. To understand the underlying mechanism, we investigated the change in actin distribution in the cells. We developed a catalogue of actin density distribution in C17.2 cells which we would like to compare to cells assimilated with carbon nanotubes. Initial results will be discussed.
  

Conformational landscape of a virus from single-particle scattering using a X-ray Free Electron Laser

Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and continuous conformational landscape of the PR772 virus. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome[1]. We have shown that XFEL-based single-particle imaging, when combined with novel data analytical approaches, has the potential to reveal important conformational changes in biological entities, identify the conformational coordinates controlling key processes, and map the conformational landscapes associated with individual or multiple conformational coordinates. The emerging capability of XFELs to generate very large data sets promises unprecedented access to rarely occupied rate-limiting conformations, which control the course of important biological processes. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.

[1] Hosseinizadeh, A. et al. Conformational landscape of a virus by single-particle X-ray scattering. Nat. Methods (2017). doi:10.1038/nmeth.4395   

Facilitated Dissociation Kinetics of Transcription Factor Proteins from Single DNA Binding Sites

The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits TF off-rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key E. coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate ~1 × 104 M−1s−1, establishing that FD of Fis occurs at the single-binding-site level, and we find that the off-rate saturates at large Fis concentrations in solution. While spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that facilitated dissociation depends only weakly on salt.   

Development of Single Particle Manipulation and Detection using Quadrupole-Electrode Integtrated Nanopore Devices by Dielectrophoresis

Nanopore sensing methods have been attracted for biological research fields because various bio-sample particles, i.e., liposome, exosome, mitochondria, can be detected at single-particle level. In principle, when a particle passes through a sensing nanopore, an ionic current drops is observed and its current-time profile represents its characteristic physical properties, i.e., volume and shape. In order to realize high-throughput analysis with nanopore device, it is important not only to detect and but also to manipulate particles around sensing nanopore because particle-clogging events are frequently occurred and its pore-sensing is interrupted under random sample-particle behaviors. In this study, we newly fabricated pore-devices integrated with quadruple-electrode, which is used for dielectrophoretic manipulation/separation of sample particles. By applying AC electric voltage between the quadruple-electrodes around a sensing-pore, it is found that sample-particles moved toward the pore and particle-sensing frequency is increased. This repulsion behavior around the pore is due to negative-dielectrophoresis by its AC electrical field. This dielectrophoretic manipulation by this type of pore devices can be a promising method for high-throughput nanopore sensing.
  

Development of Single-Molecule Electrophoretic Control Method For Single-Molecule Tunnel-Current based Nucleotide Identification by Nano-fluid integrated Nano-gap Devices

Single-molecule tunnel-current detection is promising for identification of biopolymers. Until now, by using nano-gap-electrode devices, we measured tunneling-current time-traces during its translocation of nucleotide molecules through a nano-gap-electrode and, based on the conductance-intensity, the base-sequence are assigned. From the assigned sequence, most of the signals are found to be the partial sequences, which would be due to partial translocation of sample, which may be influenced by random-flow such as Brownian motion. In order to obtain longer right-read signals, the control of translocation behavior is necessary for biopolymer sequencing. In this study, we developed the nano-fluid integrated nano-gap device, in which also a pair of silver/silver chloride electrode is located. When dc voltage is applied through the fluid, negatively charged nucleotide translocate through the gap electrodes by electrophoresis. It is found that the fluid around nano-gap can strongly confine the nucleotide translocation route and molecular orientation so that integrated nano-fluidics straightly guide nucleotide molecules into the nano-gap electrode, resulting in frequent detections of longer-right read signals. This methodology would be useful for biopolymer electrical sensing.   

Development of a Behavioral Assay using a Fluidic Device to Study Learning and Memory in Cuttlefish Larvae

Cuttlefish are marine organisms that exhibit complex social behaviors: they camouflage in response to visual stimuli, display intellectual behaviors such as flashing and stunning of prey, or avoid predators, suggesting that a cuttlefish brain has evolved learning and memory mechanisms. Early exposure of cuttlefish larvae to cues from predator and prey shows embryonic learning, as they know to differentiate between them for life. In this work we developed a behavioral assay to investigate complex behaviors by designing a fluidic device to manipulate flow of chemicals, delivery times, and allow event recording. We used mathematical models to predict diffusion coefficients of molecules based on molecular shape, bond lengths and angles. Since behavioral assays for aquatic species require a flow-through design, our chip consists of joined channels, and diffusion coefficients allow calculation of lateral diffusion lengths, rate of flows, and channel size limitations. Controls are used to verify our model's accuracy. Analysis of cuttlefish behavior to selected stimuli and response are presented. Such results allow one to quantify the learning and behavior in the embryos. This work can stimulate further studies in learning and memory mechanisms displayed by the cuttlefish.   

The effect of Cytoskeletal crowding on the Mobility and Conformational Dynamics of circular and linear DNA

In order to carry out processes such as gene transcription and cell replication, DNA must diffuse through a highly crowded cellular environment. Previous studies aimed at understanding intracellular DNA transport have mainly focused on the effect of small mobile crowders. However, the cytoskeleton, composed of filamentous proteins such as semiflexible actin and rigid microtubules, has been identified as a key factor suppressing viral transfection and gene therapy. Here, we investigate the effect that cytoskeletal proteins have on the transport properties of linear and circular DNA. Specifically, we use fluorescence microscopy and custom single-molecule tracking algorithms to measure center-of-mass transport and time-varying conformational changes of single DNA molecules diffusing in in vitro composite networks of actin and microtubules. We determine the role that DNA topology as well as cytoskeletal filament rigidity (actin vs microtubules) has on DNA transport and conformational states. We specifically quantify DNA diffusion coefficients, degrees of anomalous diffusion, and conformational changes within protein networks of varying concentrations and polymerization states.   

Developing Resilient DNA Polymers for Operation in an E. coli Transcription-Translation System

DNA nanotechnology is a growing field with potential intracellular applications. Interfacing DNA nanostructures with biology, however, faces many challenges, a major one being the resilience of such devices in vivo. In this work, we use an Escherichia coli cell-free transcription–translation (TXTL) system to assay the robustness of DNA nanotubes in a cytoplasmic environment. TXTL recapitulates physiological conditions as well as strong linear DNA degradation through the RecBCD complex, the major exonuclease in E. coli. We demonstrate that chemical modifications of the tiles making up DNA nanotubes extend their viability in TXTL for more than 24 hours, with phosphorothioation of the sticky end backbone being the most effective. Furthermore, we show that a Chi-site dsDNA, an inhibitor of the RecBCD complex, extends DNA nanotube lifetime significantly. These complementary approaches are a first step towards a systematic prototyping of DNA nanostructures in active cell-free cytoplasmic environments and expand the scope of TXTL utilization for bioengineering.   

Dynamics of Myoglobin in Light and Heavy Water Probed by Dielectric Relaxation Spectroscopy

It is largely accepted that the hydration water plays an important role in the function and dynamics of proteins. However, yet, the detailed nature of protein – hydration water interactions, is still unclear. Here, we investigated the protein-solvent interactions by measuring the dielectric response of myoglobin (Mb) in light and heavy water as a function of frequency (10^-3 Hz to 10⁷Hz), temperature (133K to 283K), and hydration ratio (100 to 2). In light water, we observed an additional peak in the dielectric spectra as compared to heavy water. We used two Havriliak- Negami functions plus conductivity to fit the relaxation processes. We determined the relaxation time for all observed processes and calculated the corresponding activation energies. We further determined the electric dipole moment of myoglobin in light and heavy water and its behavior as a function of temperature and hydration. As predicted, our data shows that the additional relaxation observed in the myoglobin-light water solutions corresponds to the hydration layer.
  

Propagation of a thermo-mechanical signal on a lipid bilayer

A simplified model of a neuron consists of an artificial lipid membrane that possesses interesting thermodynamic properties as it changes from a gel to a liquid state. The propagation of sound waves on lipid monolayers supported on water has been previously studied during the melting transition. However, a lipid bilayer is a more approximate model of a cell membrane. A solitary wave has been thought to occur when a tiny section of a membrane in its fluid phase is brought to the gel phase. In this work, we designed and built an experimental setup to assemble long artificial lipid bilayers under water, comparable in length to a large real neuron (0.1 m). To trigger a melting transition at one end of the membrane, we applied localized heat stimulation. At the other end, we found the arrival of a thermo-mechanical perturbation. Our findings may support the existence of solitary waves, which may confirm that not only electrical signals explain the propagation of information along the nerves as it has been traditionally thought, but thermodynamics may also play an important role in the propagation of isentropic signals together with the action potential.   

Three Vital Roles of Membranes in Electrical Communication in Lives

Electrical signals play the primary role in rapid signal transmission in lives, especially in nerve system. This kind of signals are actually electromagnetic (EM) signals, whose generation and propagation rely on the bio-membrane.
Membranes, play three vital roles in electrical communication in lives. Firstly, membranes serve as the capacitive power supply in lives. They are also the framework supporting protein channels where EM signals are generated by the transient transmembrane ionic currents. In addition, membranes, together with bilateral ionic solutions, compose the softmaterial waveguide, which enable the effective transmission of the EM pulses generated by the transient ionic currents.
Furthermore, softmaterial waveguide network model is built to explain the uniform electrical communication mechanism in organism lives, plants and higher vertebrates by analyzing and summarizing the existing phenomena and data on the movement of paramecium, the prey behavior of flytraps and the synchronistic discharge activity in electric eels. To be specific, the network behaves as the biological membrane in unicellular organisms, plasmodesmata and sieve tubes in plants, and nervous system mostly in higher vertebrates.   

Macromolecular crowding modulates actin filament bending dynamics and mechanics

Cellular environment is crowded with high concentrations of macromolecules such as polysaccharides and proteins limiting the amount of unoccupied space within eukaryotic cells. Actin filaments are semiflexible protein biopolymers that play a dynamic role in cellular structural support, movement, and intracellular transport. Although the effects of molecular crowding on actin filament assembly have been shown, how crowded environments affect filament mechanics remains to be elucidated. In this study, we investigate how macromolecular crowding affects the mechanical properties and bending dynamics of actin filaments in vitro. We simulate crowded cellular environments by using inert/polymer molecular crowders, sucrose and polyethylene glycol. Visualization of filaments in crowded environments by fluorescence microscopy allows for the quantification of filament bending modes and stiffness. Our finding suggests that molecular crowding enhances filament mechanics and modulates thermal bending dynamics, thereby potentially regulating interactions with actin binding proteins in vivo.   

Simulations of Branching Actin Filament Networks at the Leading Edge of Moving Cells

Branched filamentous actin networks provide the driving force for lamellipodial protrusions in motile cells. Structural network changes occur due to filaments polymerizing, depolymerizing, capping, severing, and nucleating either as branches or de novo. The actin network in lamellipodia has been studied in prior mathematical and computational models; however, little is known about how network remodeling away from leading edge regulates its size and structural properties. We developed a 3D simulation of this network at the level of individual filaments, defining various processes as occurring with defined rate constants. Through changing of rates, effects on the network’s structure and size due to different parameters were observed. In particular, it was seen that increased severing leads to a faster drop off in actin concentration, resulting in a shorter lamellipodium. In addition, branching not limited to occurring near the leading edge extends the depth of the lamellipodium, by allowing away from leading edge nucleation of filaments. Orientation of branches dependent on the actin helix repeat, there is a distinct pattern in spacing between branches on the same mother filament when branching is restricted to a near 2D plane.   

Electrostatic Specifications of Single Cancer vs. Brain Microtubules In Vitro Obtained from Their Electro-orientation Behavior

Microtubules, one of the intracellular components, are involved in many cellular functions including, but not limited to, cell division and intracellular transportations. Tubulins, which are the building block of microtubules, may be expressed in different isotypes. The recently reported results indicate that the biomechanical functions of microtubules can be affected due to the distribution of different tubulin isotypes in their compositional structures. The difference in the electric charge of the carboxy-terminal tails of tubulin isotypes is the major reason that these isotypes are distinct from each other. Two groups of microtubules, cancer microtubules and brain microtubules, are structured from significantly different distributions of beta tubulin isotypes. In this study, we compare the electro-orientation behavior of individual human breast cancer microtubules vs. porcine brain microtubules inside a uniform electric field in vitro. We will discuss our recently reported results related to the electrostatic specifications of these two groups of microtubules.   

Electrostatic Specifications of single Cancer vs. brain microtubules in vitro obtained from their electro-orientation behavior

Microtubules, one of the intracellular components, are involved in many cellular functions including, but not limited to, cell division and intracellular transportations. Tubulins, which are building block of microtubules, may be expressed in different isotypes. The recently reported results indicate that the biomechanical functions of microtubules can be affected due to the distribution of different tubulin isotypes in their compositional structures. The difference in the electric charge of the carboxy-terminal tails of tubulin isotypes is the major reason that these isotypes are distinct from each other. Two groups of microtubules, cancer microtubules and brain microtubules, are structured from significantly different distributions of beta tubulin isotypes. In this study, we compare the electro-orientation behavior of individual human breast cancer microtubules vs. porcine brain microtubules inside a uniform electric field in vitro. We will discuss our recently reported results related to the electrostatic specifications of these two groups of microtubules.
  

Electronic and Optical Properties of Self-Assembled Peptide Nucleic Acids.

In this work, we analyze theoretically electronic and optical properties of self-assembled GC and GG di-peptide nucleic acids (PNAs) that were characterized experimentally (Berger, et al., Nat. Nanotechnol. 2015, 10, 353). To assess their potential as electronic and optical materials by using density functional theory (DFT), we first predict that the lattice constants, Watson-Crick hydrogen bond and stacking distances of GC PNA are close to the experimental structure, while for GG, where the structure has not been determined experimentally, we propose a well-converged crystal structure. The band gap for GC is found to be consistent with the measured emission, while a larger bandgap is predicted for GG. Calculated optical absorption spectra for GC and GG PNAs using time-dependent DFT will be discussed. In addition, based on electron transport calculations for the GC PNA along the stacking direction by using a non-equilibrium Green’s function method with DFT, derivation of a phenomenological scattering potential and transport channels near the Fermi level will be described.
  

Investigating Three-Helix Micelles Transport and Accumulation in Tumors

Long-circulating three-helix micelles (3HM) developed in our lab has been found to selectively accumulate & penetrate through several solid tumor models in vivo. However, the underlying 3HM transport mechanism has yet to be fully understood. In solid tumors, while leaky blood vessels permit nanoparticle extravasation, high interstitial pressure prevents convective transport to the necrotic core. Additionally, dense tumor extracellular matrix presents a size-exclusion barrier to large nanoparticles (e.g. 100 nm liposomes) penetrating through the tumor. We hypothesize that 3HM tumor transport is mainly governed by Fick's laws of diffusion, advantageous to its small size (sub-20 nm) and long plasma half-life (~30 hours in mice). Solving diffusive flux for particle extravasation yields an equation that links the observed 3HM tumor accumulation to its plasma elimination time constant, with respect to tumor vessel permeability. Additionally, we have found that 3HM in vivo tumor penetration agrees with mathematical modeling of non-steady state diffusion profile. As such, 3HM represents a prime example of a small and stable nanoparticle with high diffusivity that is well-suited for passive tumor targeting.   

Using Massively Parallel Reporter Assays to Dissect the Molecular Mechanisms of Transcriptional Regulation of Bacterial Promoters.

Organisms across all domains of life must make regulatory decisions in response to changing environments. The decision about when and where to turn on transcription in bacteria is mainly controlled through the binding of transcription factors to promoter regions of the DNA. However, even for the organism Escherichia coli, whose regulation is arguably best understood, we still have no indication if or how more than half of the genes are regulated. Here we use a RNA-seq based massively-parallel reporter assays and information-theoretic modeling to dissect the mechanism of regulation for a group of both well studied and unannotated bacterial promoters. We quantitatively compare the RNA-seq based massively-parallel reporter assay to a previously used fluorescent reporter based methodology. We recover nucleotide-resolution models of transcription factor to DNA binding energy and demonstrate that we can scale up the method to cover all promoters in E. coli.
  

Mapping Operator Sequence to Transcription Factor Binding Energy In Vivo

Despite the central importance of transcriptional regulation in systems biology, it has proven difficult to determine the precise regulatory mechanisms of individual genes, let alone entire gene networks. The advent of readily-available DNA sequencing has opened up numerous ways to interrogate promoters and transcription factors. Yet, it is still challenging to integrate the various aspects of transcriptional regulation into a cohesive understanding of a given promoter or transcription factor. One promising avenue for elucidating multiple aspects of transcriptional regulation with a single assay is through Sort-Seq, a high-throughput in vivo assay which associates expression measurements with the sequences of millions of promoter mutants. Here, we show how Sort-Seq can be used to accurately map binding site sequence to binding energy and predict the binding energies of operator mutants to within 1 k_BT of their measured values. We further explore how such a sequence-energy mapping can be used to address key scientific challenges, such as designing specific induction responses, analyzing the probability that a mutation will affect the fitness of a promoter, or determining how regulatory context affects sequence specificity.   

Quantifying the energetics of microbial growth

Energetics is central to microbial life. The strategies by which microbes harbor and spend energy comprise an essential link between the geochemical and biological makeup in an ecosystem. A quantitative understanding of these strategies and their underlying mechanisms can provide useful insight into the microbial component in the global cycling of carbon, nitrogen, sulfur, and other elements. We study the growth of various environmentally relevant microbes using calorimetry, which measures the heat dissipation. We combine this approach with other biological and geochemical methods to dissect energy flow in various types of microbial metabolism.   

A Predictive Theory of Allosteric Regulation in Transcription

Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. To that end, we present a theory of allosteric transcriptional regulation using the Monod-Wyman-Changeux model which applies to a variety of regulatory architectures. We rigorously test this model using the ubiquitous simple repression motif in bacteria by first predicting the behavior of strains that span a large range of repressor copy numbers and DNA binding strengths and then constructing and measuring their response. Our model accurately captures the induction profiles of these strains and enables us to derive analytic expressions for key properties such as the dynamic range, [EC₅₀], and steepness of response. Finally, we derive an expression for the free energy of repressors which enables us to collapse our experimental data onto a single master curve that captures the diverse phenomenology of the induction profiles.   

Find Topologies Exhibit Adaptation and Oscillation

Understanding the relationship between the topology and its function remain an important question in nonlinear physics. Previous works taught us that negative feedback is essential for the topology to show oscillation while positive feedback is essential for the appearance of bistable states. Many signaling systems show different behaviors when they are stimulated by different level of input signal. For example, when the system is stimulated by low input signal, it shows adaptation. When it is stimulated by high input signal, it shows oscillation. We found all simple transcriptional regulatory network topologies that could perform adaptation and oscillation, then we investigate how the system switches between two functions. We found that some topologies can transform two function by changing one parameter while others cannot. Finally, we find some biological network correspond to our findings.   

Population Dynamics and Pattern Formation in Antigen Antibody Co-evolution

The adaptive immune system provides specific protection against foreign threats by removing recognized antigens. Nevertheless, rapidly mutating viruses such as HIV can cause chronic infections by evading antibody recognition, leading to an evolutionary arms race. Here we introduce a minimal predator-prey model to study co-evolution of antibody and antigen. We show that intermediate replication rate and mutation rate of the antigen can lead to chronic infection. The effect of cross-reactivity, represented by a nonlocal interaction, is investigated. Interestingly, asymmetric cross-reactivity may lead to pattern formation in the shape space, indicating localization of antigens. On the one hand, instability resulting from the asymmetry could enable late clearance of antigens. On the other hand, an escape phase could emerge under homeostatic constraints.   

Is Human Atrial Fibrillation Stochastic or Deterministic?

A reason why the mechanism that maintains human atrial fibrillation (AF) remain unclear may derive from the stochasticity of cardiac dynamics. Using forbidden ordinal patterns (FOP) with Bandt-Pompe symbolization, we characterize the intracardiac bipolar electrograms of AF from 15 patients. We calculate normalized Shannon entropy and Jansen-Shannon statistical complexity. We compare the results with stochastic time series as well as simulated bipolar spiral waves with different levels of white Gaussian noise. For all series, we construct surrogate data with the same frequency spectrum and autocorrelation, and estimate the ratio of FOP decay in the first 6,000 timepoints. Human AF exhibit a median of 460 FOP (range 357-525) which is significantly higher from surrogate data (range 0-103, p<0.05) and all stochastic series (range 0-5, p<0.05). The ratio of FOP decay in time series over surrogate data is significantly lower in AF compared to any stochastic series. On the causal entropy-complexity plane, human AF is of lower entropy, higher complexity than stochastic series, and of higher entropy, higher complexity than simulated spiral waves. We conclude that, although human AF is quantitatively different from simulated spiral waves, it has little evidence to suggest stochasticity.   

Modeling Statistical Multiplicity of Infection to Update Methods of Virus Quantification and Infectivity Assays

Many biological assays are employed in virological studies in order to quantify physical parameters of interest such as the number of viruses present in a solution or the ability of a viral strain to successfully infect a host cell. At the dilute concentrations that virus quantification assays operate, the results can be subject to the stochastic variability in the virus-cell interactions. At the other extreme, large numbers of virus particles are used in infectivity assays, resulting in a statistical multiplicity of infection (SMOI) where each cell is infected by multiple particles. In many cases, the SMOI may lead to significant variability in estimations of desired physical parameters. In our study, we develop probabilistic models for SMOI at low and high viral particle concentrations and apply them to several assays used in virological studies including plaque assays, endpoint dilution, and luciferase reporter assays. After performing a detailed analysis of statistical effects, we propose improved estimates for inferring experimental and biophysical parameters from the results of these assays.   

Needle- and Laser-Induced Cavitation Techniques to Study Extreme Deformation and Strain-Sensitivity of Intact Brain Tissue

Despite growing support that cavitation damage contributes to traumatic brain injury (TBI), current diagnostic testing is incapable of detecting cavitation-related tissue damage. One limitation is that the mechanism of damage, be it formation/expansion of a cavitation bubble, collapse of that bubble, or strain propagation through heterogeneous material, is unknown. Cavitation rheology is a powerful technique to characterize and understand the mechanical properties of soft materials, such as biological tissues. This method introduces a defect within a material at the tip of a needle, initiating an unstable void expansion followed by collapse. This technique can be used to quantify the deformation of brain tissue in low strain regimes. A complementary method, laser-induced cavitation (LIC), applies high strain deformations with a focused laser light to vaporize a particle resulting in rapid expansion of a void at extremely short timescales. I will present data on brain deformation at low and high strain rates using these methods as well as how boundary conditions impact deformation at an interface. This data is pertinent to understanding the interface dynamics and strain sensitivity of brain tissue during cavitation and how that damage manifests in TBI patients.   

Subdiffusive motion of phages through mucus

In the mucus, a viscoelastic fluid that coats many organs, phages can dramatically increase their ability to infect bacteria. It is expected that understanding the mechanisms underlying the beneficiary role of mucus will provide insight into how phages interact with their bacterial hosts, infectious diseases and their cures in general. Possible mechanisms by which mucus could help phages find their hosts are: (1) by sticking to mucus, phages could increase the encounter rate with bacteria; (2) the motion of bacteria could influence the viscolestic properties of the mucus network and induce a mechanical response to attract phages. A key element is the observed sub-diffusive motion of the phages. This could be caused by fractional Brownian motion or a Continuous Time Random Walk. Numerically generated data sets are currently employed to investigate the number and length of data tracks needed to discern between origins of subdiffusion and set them apart from normal Fickian diffusion. Experiments performed using nanoparticles to mimic phages will be analyzed and compared with those previously published for phage diffusion through mucus*. Recommendations will be made for future measurements.
* Barr et al. Proc. Natl. Acad. Sci. 112,13675 (2015)   

E. coli Filaments Doing the Twist

Some bacteria in response to stress conditions, form extraordinarily long filaments with multiple chromosomes. It is the consequence of filamentation in which DNA duplication and cellular growth continues while cell division stops. Filamentation has been considered as a general survival strategy in repose to hostile environment. Here we further studied the motility of E. coli filaments treated by ciprofloxacin. We observed that despite different radii, different rotational frequency and different length varying from 4 microns to 50 microns, E. coli filaments retain constant swimming velocity of 20 microns per seconds as the normal 2 micron long E. coli mono-cell and do not tumble but only reversing their direction. Using high-speed confocal imaging, we show that these filaments are right-handed helices and move by rotating around the helix axis driven by a synchronous rotation of flagella along the entire filament and thus twisting through the media. The reversal motion of the filaments are accomplished by the synchronous reversal of the flagella. This swimming mechanism results a high diffusion coefficient due to very long velocity reversal persistence length enables bacterial filaments to leave the region of high stress quickly.   

Effects of Electromagnetic Radiation on the Measurements on Optical Density of Staphylococcus aureus

We investigate the effects of electromagnetic energy on the absorbance rate of Staphylococcus aureus. One bacterial sample used as control was incubated at room temperature whereas the other two were grown over the static and time-varying magnetic fields. The effect of external electromagnetic radiation was then observed on bacteria exposed to magnetic field and the effect was compared with the control. After 48 hours of growth, the optical density was compared at different wavelengths ranging from 350-950nm.   

Visible Light Reverts the Effect in Motility Produced by Temperature in Mouse Sperm.

The effects of visible light on biological systems have been studied for several years, from mammal spermatozoa motility to protein structural changes. The data have shown that these systems interact in certain ways with light but the origin and mechanisms are still far from being understood. Thus more work on the subject is needed. In the present work we study the effects of green light (490-540 nm) on the motility of mouse spermatozoa with an optical technique of time-resolved correlation adapted to study several samples simultaneously. Image correlation analysis is used to follow the temporal behavior of the sperm samples at 10 degrees Celsius and 37 degrees Celsius . At these contrasting temperatures, the motility is radically different: at the lower one the prevalence is the lengthiest, according to a previous finding reported by us. Our present results show that while green light extends the prevalence of sperm motility at 37 degrees Celsius, it reduces it at 10 degrees Celsius. This evidence suggests that green light is playing an important role in the spermatozoa motility. We speculate about the possibility that these opposed effects are related to elastic changes that spermatozoa suffer during irradiation.   

Impact of Electromagnetic Radiation on Measurements of Optical Density of E.coli

Recent studies show that optical density in E.coli is affected by electromagnetic energy. Cells were cultured under controlled conditions, so any changes in optical density could be detected when comparing the exposed sample to the control sample. One sample was exposed to a static magnetic field while the other sample was grown in slowly varying magnetic field. After a period of 48 hours of growth, the optical density of both samples was measured by scanning from 350-950 nm. Small changes in the OD were detected. It is likely that magnetic field effects could impact the cell or environmental conditions that could explain the changes in OD.   

Spacetime Structure and Evolution among Consciousness, Nervous, and DNA

The author had brought forward spacetime structure and massenergy structure.

The dark matter-energy which has a ring structure (spacetime center structure) impact to the stellar matter which has a open structure (massenergy center structure) to make or break the structures of lives.

So the structures both of nervous and DNA which are made up of spacetime center structure and massenergy center structure together.

Consciousness has an effect and relationship with the dark matter-energy (spacetime center structure) and the general-matter (massenergy center structure).

According a relationship between the cerebrum and cerebellum, we will consider a evolutive and degenerative relationship among consciousness, nervous, and DNA.
http://meetings.aps.org/Meeting/MAR16/Session/M1.59
http://meetings.aps.org/Meeting/APR16/Session/M13.8   

Effects of noise on dynamics of Hodgkin Huxley style neuronal model

We studied the effect of noise on the dynamics of a single neuron that is described by the generic Hodgkin Huxley model. We model a channel noise by adding the Gaussian noise to inactivation of Na+ current, activation variable of potassium current and the h-current. The characteristics of the neural dynamics such as the burst duration, interburst interval and period were affected by noise. These effects are more pronounced for the noise added to the inactivation of Na+ current(hNa). For hNa variable, there is a critical noise amplitude at which the average interburst interval reaches its minimum. This minimum is well pronounced, e.g., if for a neuron without noise the interburst interval is 100 s, then the minimum interburst interval, at the critical noise value, is around 20 s. Such highly nonmonotic behavior is realized only for a range of parameters of the neuron model, for which the noise-free interburst interval is greater than 20 s. But if the interburst interval of the noise-free model is less than 20 s then the system does not show any minimum and the interburst interval monotonically increases with the noise.   

Humeral bone strength and hunting strategies in dromaeosaur and troodont dinosaurs

Dromaeosaur and troodont dinosaurs were small predatory theropods. Dromaeosaurids had stronger feet than troodontids and are believed to have used a stealthy ambush predatory strategy, adapted for relatively large prey. By contrast, troodontids had a longer metatarsus, presumably, allowing for speed. This allowed for a more precise, but weaker grip. This suggests that they were swift runners who probably took relatively smaller prey. Dromaeosaurids are believed to have attacked larger prey animals than the troodontids. In this work, we find that the dromaeosaurids had stronger humeri (i.e., with a larger section modulus) than the troodontids. This is consistent with the hypothesis that the dromaeosaurids attacked larger prey than troodontids. Humeral stresses are expected to be larger when engaging a larger prey animal.   

Femoral bone strength in extant quadrupedal animals from Microtus ochrogaster to Loxodonta africana

The femoral bone strength in extant quadrupedal animals from Microtus ochrogaster (meadow mouse) to Loxodonta africana (African elephant) has been studied as a function of mass of the animal. The masses of these animals vary by more than five orders of magnitude. Given the finite resources available, each organ of an animal is as big as it needs to be, but no bigger. In this work, we study what limits the strength of the femur. The femoral cortical area at the narrowest part gives the measure of the strength of the femur to support the longitudinal stress due to the weight of the animal. The femoral section modulus at the narrowest part is a measure of the ability to resist transverse stresses. Both the cortical area and the section modulus are found to be power laws of the mass. The exponent of the power law is about 0.70 for the cortical area and about 1.0 for the section modulus. This suggests that transverse stresses are the limiting factor for the bones of the legs of these quadrupedal animals.   

Curvature-Driven Phase-Separation of Spherical Vesicle Membranes: Insights from Single-Bead Lipid Models

Motivated by the role of the collective dynamics of lipids in many biological processes, we explore the morphology and kinetics of phase separation in spherical lipid bilayer vesicles. We use single-bead implicit-solvent coarse-grained models based on anisotropic pair potentials to simulate coarsening dynamics and preferred curvatures. We find for molecular mixtures with different preferred curvatures that several interesting phenomena can arise, such as curvature-induced stalling of coarsening and for more extreme curvature variations even the occurrence of budding events of small vesicles. We report on our findings and related theory describing the kinetics of domain formation, coarsening arrest, and related phenomena as curvature is varied.   

NUCLEATION RATES OF WATER USING STATISTICAL ASSOCIATION FLUID THEORY

The SAFT EOS recently showed relatively successful calculations of the phase-equilibrium properties and the classical-nonclassical nucleation rates of methanol. In this work, the effective temperature-dependent hard sphere diameter was adjusted for the SAFT-0 EOS in a away that it produces the water binodal lines and also the vapor pressures in a good agreement with the experimental data, in particular within the temperature range of anomalous density behavior below 277.15 K. The Gibbsian form of classical nucleation theory (CNT) (known as the P-form) and nonclassical gradient theory (GT) calculations were carried out using the SAFT-0 EOS with and without including this adjusted diameter. Calculated rates were compared to the experimental values of W\"olk and Strey [J. Phys. Chem., B 2001, 105, 11683-11701]. In addition to the phase-equilibrium properties, this adjustment improved the nucleation rates from both GT and CNT by factors of 500 and 100, respectively. To explore this further, the GT and experimental rates were analyzed using Hale's scaled model [J. Chem. Phys., 2005, 122, 204509]. This analysis shows that the predictions of GT scale well and relatively conform with that of the experimental data.   

Reactivity of Model Inverse Catalysts Prepared by Mass-Selected Cluster Deposition

Electronic interactions at the interface between supported metals and reducible oxides play an important role in a wide range of catalytic processes, including water-gas-shift for clean hydrogen production and CO/CO₂ hydrogenation for liquid fuels. The enhanced catalytic activity of these systems has been linked to oxygen vacancy formations on the reducible oxide, which act as active sites for reactant binding. In this study, we investigated the electronic and reactivity properties of model “inverse” catalytic systems prepared by the deposition of size-selected metal oxide nanoclusters onto supporting metal surface. Size-selected deposition provides selection of the cluster stoichiometry with atomic precision, which allows for the introduction of oxygen “vacancies”,and variation of metal cation coordination and average oxidation state. Results will be presented for the study of MO_x/Cu(111) surfaces using ambient pressure x-ray photoelectron spectroscopy (AP-XPS) which probe the chemical state of the oxide and metal support, and the formation of surface intermediates under AP conditions.   

Concentration and Solvent Dependence of the Hierarchical Organization of Asphaltenes in Solution.

Asphaltenes are a group of planar molecules found in crude oil and are prone to aggregation which often causes blockage of pipes along the oil production stream. Asphaltene concentration and solvent composition on the hierarchical structure of asphaltenes in solution was studied using small-angle x-ray scattering (SAXS). SAXS, a technique to study nanostructure was used to study modified asphaltenes with polar groups removed at concentrations of 1, 5, 10, and 50 mg/ml in toluene. After collecting scattering data on a 2-D detector, SASView was used to analyze the results by fitting them with a mass fractal model over a Q-range: 0.008 - 0.4 Å^-1. Results will be compared and integrated with statistical mechanics theories such as the DLVO (Derjaguin–Landau–Verwey–Overbeek) theory that models absorption and the aggregation of nanoparticles in aqueous systems and describes the stability of colloidal dispersions. Future work will include the use of other solvents, as well as the impact of pressure and temperature on the nanostructure of these systems.   

Plasmon-exciton polariton condensation set by quasi-long range order and nonlinearities

Bose-Einstein Condensation of exciton-polaritons, quasi-particles formed by strong coupling of cavity photons and excitons, have been a subject of intensive study. The appearance of the long-range order and extended spatial coherence is one of the underlying properties of Bose-Einstein condensates. We use a lattice of metal nanoparticles supporting propagating modes, which can couple with the electronic transitions of organic molecules. Above the condensation threshold, we observe the formation of extended spatial coherence over distances longer than the excitation spot. This extension can be explained by the presence of the repulsive interactions among the exciton-polaritons within the condensate. We support this hypothesis with time-resolved photoluminescence measurements of the condensate, observing an initial blue-shift consequence of exciton-polariton interactions, followed by a red-shift at later times as a consequence of the reduction of the density of exciton-polaritons.   

Absorption and Photoluminescence in Organic Cavity Quantum Electrodynamics

Organic microcavities can be engineered to reach exotic quantum regimes of strong and ultrastrong light-matter coupling. However, the microscopic interpretation of their spectroscopic signals can be challenging due to the competition between coherent and dissipative processes involving electrons, vibrations, and cavity photons. We develop here a theoretical framework based on the Holstein-Tavis-Cummings model and a Markovian treatment of dissipation to account for previously unexplained spectroscopic features of organic microcavities consistently. We identify conditions for the formation of dark vibronic polaritons, a class of light-matter excitations that are not visible in absorption but lead to strong photoluminescence lines. We show that photon leakage from dark vibronic polaritons can be responsible for enhancing photoluminescence at the lower polariton frequency, and also can explain the apparent breakdown of reciprocity between absorption and emission in the vicinity of the bare molecular transition frequency. Successful comparison with experimental data demonstrates the applicability of our theory.

[1] F. Herrera and F. C. Spano, Phys. Rev. A 95, 053867 (2017)
[2] F. Herrera and F. C. Spano, Phys. Rev. Lett. 118, 223601 (2017)   

Tailoring Energy Transfer from Hot Electrons to Adsorbate Vibrations for Plasmon-Enhanced Catalysis

Chemical reactions can be enhanced on surfaces of bimetallic nanoparticles composed of a core plasmonic metal and a catalytically active shell when illuminated with light. One critical process is the non-adiabatic energy transfer from hot electrons that transiently populate the unoccupied electronic orbitals of the adsorbate to the vibrational modes of the adsorbed reactants. This occurs via electron-vibration coupling and could potentially be tailored by changing the composition of the shell. Here, we apply an ab initio method based on density functional theory to investigate this coupling at various sp- and d-band metal-adsorbate interfaces. Our calculations demonstrate the importance of d-bands in enhancing and tuning this energy transfer at the interface. We extract a simple descriptor (dependent on the coupling matrix element and equilibrium bond length) that can account for the coupling strength at a metal-adsorbate interface, thus representing a valuable tool for rational shell design for different reactions. The introduction of this descriptor should also impact other processes such as light-triggerred drug release that exploit hot electrons, and surface-enhanced Raman spectroscopy, where electron-vibration coupling plays a key role.   

Entangled Photon-Pair Two-Dimensional Fluorescence Spectroscopy

The entangled photon-pair two-dimensional fluorescence spectroscopy (EPP-2DFS) is extended to include contributions from the singly-exited manifold. Experimental advantages and quantum-enhanced characteristics are discussed.   

Extending the Runge-Gross Theorem for the Inclusion of Non-analytic Potentials and Densities

The Runge-Gross theorem reveals the existence of an invertible map between time-dependent (TD) electronic densities and external scalar potentials, provided the initial state of the system is fixed. This result provides solid footing to the TDDFT research field. The original version of the theorem, however, excluded potentials and densities that are not Taylor-expandable around the initial time of the propagation. This talk presents new developments that extend the theorem to include TD non-analytic potentials and densities. Relation with previous work, current limitations, and future directions are discussed.
Reference: J. Chem. Phys., 147, 134110.   

Calculations of optical properties of organic molecules and crystals avoidng some drawbacks of TD-DFT and dipole approximations

Commonly used methods to compute optical properties based on DFT (density functional theory) - time dependent DFT, often used for molecules and clusters, and the dipole approximation, often used for solids - suffer from significant errors having to do with reliance on orbital energies and shapes, as they critically depend on integrals over overlapping orbitals. One consequence of that is strong underestimation of excitation energies with GGA functionals, another is artificial redshift of computed spectra of large molecules or molecular aggregates. We use an alternative approach in which we compute frequency dependent polarizability which does not as strongly depend on orbitals, and from there, the real, then the imaginary part of the dielectric constant, and ultimately the spectrum. We present calculations of absorption spectra of dyes and molecular aggregates that show that this approach is less sensitive to the specific DFT setup than (linear response) TD-DFT and the dipole approximation.   

Excitons in Defective Monolayer WSe2.

To understand the role of localized excitons in defective 2D WSe₂, for example as single-photon emission sources, we aim in this work to confirm theoretically the type of defects that will result in defect-induced states that were experimentally characterized, and to predict excitations for larger engineered defects. First, by applying many-body G₀W₀ and G₀W₀-BSE methods, including spin-orbit coupling, calculations of dark and bright excitons of pristine 2D WSe₂ will be described. Next, we note that single and double Se vacancies incorporated in the monolayer resulted in red-shifted localized excitons consistent with measurements, while interestingly, results for experimentally observed three-fold rotational defects demonstrated significantly larger red-shifts from the X_A exciton. Finally, calculations of Raman band intensities of defective monolayer WSe₂ will be discussed, indicating that such Raman signatures could be used for characterization of defects in these 2D structures.   

Investigating Size-Dependent Accuracy of Real-Time Time-Dependent Density Functional Theory

Real-time time-dependent density functional theory (RT-TDDFT) has been used to simulate electronic response properties (e.g., ionization, charge transfer) within one of the most widespread approximations within RT-TDDFT: temporal adiabaticity, i.e. the adiabatic approximation. However, for small systems, RT-TDDFT within the adiabatic approximation can lead to incorrect charge transfer. The size-dependency of this popular approximation is not well-understood. By comparing RT-TDDFT densities to those obtained via time-dependent configuration interaction methods, this work attempts to elucidate the relation between system size and the applicability of RT-TDDFT in modeling charge transfer.   

SAXS Studies of Nanostructure of Ionic Liquid - Organic Solvent Mixtures: Concentration, Temperature, and Polarity Effects

Room-temperature ionic liquid (RTIL) mixtures, as electrolytes in supercapacitors, have desirable properties in comparison to conventional electrolytes. We studied the nanostructural properties of mixtures of RTILs (e.g., BMIM+[TFSI]−) with organic solvents: acetonitrile, dichloromethane, benzene, toluene, and tetrahydrofuran. The mass % at which macroscopic phase separation is visible, in the BMIM+[TFSI]−/ solvent mixtures, was determined by slowing increasing the solvent concentration. SAXS measurements at RTIL mass % lower than the phase separation concentration were carried out to determine whether nano-heterogeneity is present leading up to macroscopic phase separation, and to characterize its structural properties; this same measurements were then replicated at different temperatures ranging from -10°C to 60°C. We used the range of .01Å^-1 to 2.6Å^-1 for our scattering measurements. We find an excess scattering at low-Q compared to the expected scattering from a simple mixture of two liquids, suggesting nanometer-scale composition fluctuations. We describe the system’s heterogeneity, in a 11Å length scale, dependence on temperature. Results and analysis of the length scales of the heterogeneity, and changes in intermolecular coordination in these systems will be discussed.   

Liquid Water Under Strong Electric Fields: Understanding the Phenomenon of Electrofreezing

Motivated by the crucial role that strong electric fields play in many aqueous systems, we have carried out molecular dynamics simulations, to probe, how the structure and properties of water change when it is subjected to strong external fields. In agreement with previous studies, we have found, that when a conventional classical force field is used, at field strengths above ~0.1 V/nm, the water dipoles are increasingly forced to align with the field, giving rise to a somewhat more viscous phase akin to a nematic liquid crystal. It has also been shown, that under even stronger fields, water will eventually freeze, however in contrast to previous studies, we have found, that in simulations at constant pressure, with sufficiently long trajectories, TIP4P-2005 water already electrofreezes at RT and 1 atm at a field strength of 2.2 V/nm. Crucially, this is lower, than the field strength at which significant auto-ionization is predicted to occur in liquid H₂O. The structural changes that facilitate crystallization will be discussed, the possibility of probing the competition between electrofreezing and ion conduction experimentally, or using reactive (classical or ab-initio) simulations will be examined, and preliminary results from reactive simulations will be presented.   

Crystal Structure, molecular, electronic and spectral analysis of (E)-2-iodo-N-((5-nitrothiophen-2-yl)methylene)aniline using experimental and theoretical approaches

Schiff bases compounds are of the great interest in many fields of chemistry and biochemistry. In this study, a new Schiff base compound C₁₁H₇IN₂O₂S has been synthesized and characterized using FT-IR and single-crystal X-ray diffraction method. The compound crystallizes in the monoclinic space group P21/n. The molecular geometry obtained from the X-ray structure determination was optimized using Density Functional Theory (DFT/B3LYP) method with the 6-311G++(d, p) basis set in ground state [1]. The vibrational frequencies, gauge including atomic orbital (GIAO) 1H and 13C -NMR chemical shift values and electronic properties in the ground state were investigated same level of theory. For the purpose of the structural conformity of the title molecule, the theoretical results were compared with the experimental values and similar literature [2, 3]. This comparison indicated that the theoretically calculated results are in agreement with the experimental data on the whole.   

Probing Charge Transfer to Cold Molecules Within Superfluid Helium Nanodroplets

Helium nanodroplet isolation is a powerful and broadly applicable tool for the investigation and manipulation of cold molecules. One source of uncertainty in the mass spectrometry of droplet-embedded molecules is their ionization probability, i.e., the process of charge transfer from the helium matrix to the dopant molecule. We investigate this process by means of our recently developed deflection technique, whereby a beam of superfluid He nanodroplets doped with polar molecules is deflected by an external inhomogeneous electric field. The almost complete orientation of the cold embedded molecules results in a remarkably large beam deviation. Among the various applications of this technique is its ability to spread the deflected neutral beam according to the droplet size. Using this tool, we parameterize the intra-droplet charge transfer probability as a function of droplet size. The results are compared with theoretical models of charge hopping within the liquid helium medium.   

Dielectric properties of a-RDX and its vibrational modes: Quantum chemistry calculations

The effect of an external electric field on the dielectric constant of crystalline a-RDX and vibrational modes thereof are studied using quantum chemistry methods. An artificial neural network method was employed to obtain an improved set of parameters for the XDM dispersion corrections. It is shown that the empirical XDM corrections in the improved form make it possible to reproduce the crystal properties and vibrational modes in excellent agreement with available experimental data. The dielectric constant is computed as a function of an external electric field. The obtained results are fit to the Booth model and a satisfactory agreement is achieved.   

Low-Field Ion Extraction and Coincident Electron Detection in a Tabletop Setup Help Resolve Ambiguities in Identifying Combustion Intermediates

Most combustion reactions are exceedingly complex and difficult to model due to hundreds of chemical intermediates, many of which have not even been identified. Photoionization mass spectrometry (PIMS) has become a common tool for identifying these intermediates for two reasons: this technique is very sensitive to low-concentration species, and very little prior knowledge of the reaction is required. Here, we improve on the traditional fixed-wavelength PIMS measurement in two ways. First, we use a low electric field to extract ions in order to distinguish thermally-induced fragmentation in the reactor from dissociative ionization caused by the laser. Second, we use electron-ion coincidence detection to measure a photoelectron spectrum for each observed mass simultaneously. We provide proof of principle that the electron spectrum can distinguish isomers that have sufficiently different ionization potentials. These improvements were completed in a tabletop setup, rather than at a national facility, enabling year-round data collection. Here, we use a pyrolysis microreactor jet to cause thermal fragmentation of fuels, but the detection techniques can be generalized to other reactors.   

Effects of Fluid Flow on Chemical Excitation Waves with Normal and Anomalous Dispersion Relations

Reaction-Diffusion (RD) waves are autocatalytic reaction zones that propagate via molecular diffusion without mass transport. They arise from the interplay of nonlinear reaction kinetics of an activator and an inhibitor species and diffusion-mediated spatial coupling (e.g., action potentials in nerves, forest fires, or stadium waves). Introducing fluid flow in a liquid chemical RD system has a huge effect on the propagation behavior of the wave. By using glass capillary tubes to create a quasi-1D system, it is possible to develop stationary waves by advecting the liquid solution opposite to the direction of wave propagation. This occurs when fluid flow velocity is equal and opposite to diffusion. In our experiments, we used the Belousov-Zhabotinsky reaction with monotonic increasing (typical) and non-monotonic (anomalous) speed-wavelength relationships. After initiating waves at one end of a capillary, the reaction solution was advected in the opposite direction. The effect of flow rate on i) the propagation speed and ii) the front shape was investigated. We also present stationary chemical waves observed in both systems and report on the effect of advection on different types of anomalous wave dispersion.   

Generating Converged Quantum-Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semi-Empirical Model

Molecular dynamics using density functional theory (DFT) is a highly accurate approach to predict chemistry, but the extreme computational cost often harshly limits the exploration of long time scale phenomena and many thermodynamic states. We present a general force-matching approach to parameterize quantum-based semi-empirical models that can retain DFT-level accuracy while affording up to a thousandfold reduction in cost. Accelerated sampling is used to simultaneously generate DFT training data and validate the force-matched model for particular reaction paths. We show that a force-matched semi-empirical model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experiments. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate, which is accessible with high-throughput models such as those presented here. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.   

Theoretical Study on the Mechanism of Palladium-Catalyzed Synthesis of 5,10-Dihydrophenazasilines via 1,5-Palladium Migration

Previously, we reported a palladium-catalyzed asymmetric synthesis of silicon-stereogenic dibenzosiloles through intramolecular C−H arylation of prochiral 2-(diarylsilyl)aryl triflates. During the course of this study, we found that 3-amino-2-(diarylsilyl)aryl triflates six-membered heterocycle did not provide corresponding dibenzosilole at all under the same condition and instead, six-membered nitrogen-containing heterocycle, 5,10-dihydrophenazasiline, was obtained. This unexpected transformation is supposed to proceed via 1,5-palladium migration and C−N bond-forming reductive elimination. A series of mechanistic investigations were carried out to probe the catalytic cycle of this process, and the 1,5-palladium migration step was suggested to be the enantiodetermining step. However, the origin of the chemo- and stereoselectivity of this process were not theoretically proved. In this work, we theoretically investigate the reaction mechanism by using DFT calculation and elucidate the origin of the selectivity of this reaction.   

Mathematical modeling of a pilot-scale methanol synthesis reactor: Experimental validation

Methanol is used extensively as a raw material for the production of chemicals such as formaldehyde, methyl tert-butyl ether, and acetic acid, and for electricity by direct oxidization with air to water and carbon dioxide in a direct methanol fuel cell. In this study, a process for the methanol synthesis using syngas was considered. After the effectiveness factor was determined for a pellet-type catalyst using experimental data in a bench-scale reactor, a mathematical model for a pilot-scale (10 ton per day) was developed by considering reactor dynamics. The validity of the model was corroborated by comparing with experimental data. Further analysis showed that the overall heat transfer coefficient, which is one of the important parameters for reactor design, is correlated with linear velocity in the catalytic bed, and the model could be used to determine the operating window for thermally safe and highly productive operation in the open-loop case.   

Tip Induced Isomerization of Azobenzene Derivatives

The adsorption and trans-cis isomerization of azobenzyl thiols (ABT) on the Ag tip and Ag(111) surface are studied using density functional theory (DFT) calculations. The trans states is the most stable adsorption configuration on both Ag tip and Ag(111) surface. However, their switching behaviours are distinct. The trans-cis ismoerization of ABT is suppressed on Ag(111) surface, while the swithcing energy barrier is dramatically decreased by the Ag tip. The driving mechanisms are investigated by charge transfers to reveal the physical inisights and to provide guidance for the realization of molecular-based swithcing devices. Further more, we have calculated the Raman spectral to directily compare with the experiment.   

From Arrhenius to non-Arrhenius: Variable Energy of activation and the kinetic compensation effect

The kinetic compensation effect, observed in many different areas of science, is the observed systematic change in the magnitudes of the Arrhenius parameters the energy of activation, E_a, and the preexponential factor, ν, as a response to external perturbations. Its existence continues to be debated as it has not been explicitly demonstrated and its physical origins remain poorly understood. As part of a systematic study of the different factors that alter the energy of activation during thermal desorption, we perform numerical studies on the effects of adsorbate-adsorbate interactions, changes in surface morphology and variations in the concentration of different chemical species.Our aim is to provide a deeper understanding into how, and to what extent, these factors produce variations in the Arrhenius parameters, and wether they yield a compensation effect. These results may help provide a deeper understanding of the microscopic events that originate compensation effects, not only in our system, but also in other fields where these effects have been reported.   

Universal nature of different methods of obtaining the exact Kohn-Sham exchange-correlation potential for a given density

Finding the external potential or the Kohn-Sham potential for a given ground state density is a fundamental inverse problem in density functional theory. Furthermore, it is important in generating the exact exchange-correlation potential for a density which can then serve as a benchmark for testingthe accuracy of an exchange-correlation energy functional. Over the years different methods have been proposed to do the density-to-potential inversion and all of these appear to be disjoint. In this paper we show that these methods are connected to one general algorithm that utilizes two forms of the equation for the density; these are the Kohn-Sham equation in terms of orbitals and the Euler equations in terms of the density. We derive the condition for the convergence of the general method and show that all the other methods considered by us satisfy this condition. We demonstrate the method and its flexibility by obtaining the Kohn-Sham potential for some spherical systems in a variety of ways.   

Analytical Nuclear Gradients for Projection-based Wavefunction-in-Density Functional Theory Embedding

Projection-based wavefunction-in-density functional theory (WF-in-DFT) embedding provides a simple framework for embedding WF theories within DFT. It has been successfully used to retain the high accuracy of WF methods while still benefitting from the low cost of DFT. Even though this method has performed well for single-point energy calculations, it has lacked analytical nuclear gradients, preventing the efficient exploration of the potential energy surface. Here, we present recent work on the development of analytical nuclear gradients for the projection-based WF-in-DFT embedding method so we can perform tasks such as geometry optimizations and study reaction pathways. We illustrate the application of projection-based WF-in-DFT gradients on a number of simple systems with the aim to model conical intersections.   

Lone-Pair Electrons Lead to Strong Phonon Anharmonicity and Anomalous Strain Enhancement of Thermal Conductivity

Manipulating heat conduction is an appealing thermophysical problem with enormous practical implications, which requires insight into the lattice dynamics. Lone-pair electrons have long been proposed to induce strong phonon anharmonicity. However, no direct evidence is available from a fundamental point of view and the electronic origin still remains untouched. In this Letter, by performing comparative study of thermal transport in two-dimensional group III-nitrides (h-BN, h-AlN, h-GaN) and graphene, we establish a microscopic picture to provide direct evidence for the interaction between lone-pair non-bonding electrons and covalently bonding electrons based on the analysis of orbital-projected electronic structures, which demonstrates how nonlinear restoring forces arise from atomic motions. The microscopic picture of lone-pair electrons driving strong phonon anharmonicity not only provides coherent understanding of the diverse thermal transport properties of the monolayer group III-nitrides compared to graphene, but also successfully explains their anomalous positive response of thermal conductivity to the external tensile strain.   

Study of Physical and Chemical Properties of the Sodium Montmorillonite Compound through First Principles Calculations

The montmorillonite (MMT) M_xAl₃Si₈O₂₄H₄Na (M_x: Mg²⁺, Fe²⁺) clay is a lamellar silicate mineral that is found in nature or synthesized in order to create structures, such as polymer matrix nanocomposites. These materials have several remarkable physicochemical properties, opening up a wide variety of industrial applications. Each lamella of anhydrous or hydrated MMT consists of two tetrahedral layers involving an octahedral one. The aluminum Al³⁺ in the octahedral layer may optionally be substituted by other cations generating negative charges, and to keep electroneutrality a cation is added between the lamellae. As sodium cations are present between the lamellae the clay is called sodium montmorillonite (MMT-Na⁺). This work shows results of investigation through ab initio calculations of the physicochemical properties of MMT-Na⁺ isomorphically replaced by Mg²⁺ and Fe²⁺. The electronic properties were obtained by calculating the band structures and density of states, and a comparison is made with experimental results from visible and ultraviolet spectroscopy of the natural MMT-Na⁺ (Cloisite®). Our results pave the way for understanding the behavior of MMT nanocomposites upon chemical and structural changes due to inclusions.   

Counteraction of Urea-Denaturation of Proteins by TMAO in Mixed Urea-TMAO Solutions

In marine animals such as rays, sharks and cartilaginous fishes, the detrimental protein-denaturing effects of urea are counteracted by the presence of naturally occurring osmolyte trimethylamine N-oxide (TMAO). Using replica-exchange molecular dynamics (REMD) and the theory of solvation thermodynamics we shed new lights on the molecular mechanism behind the aforementioned counteraction process. Using two model peptides, polyalanine and the R2 fragment of the Tau protein, we find that TMAO counteracts the effects of urea by inhibiting the preferential interaction of urea with the peptide. In addition, TMAO promotes compact conformations of the R2 peptide by stabilizing lysine-aspartic acid salt-bridge which is responsible for an end-to-end contact in the R2 peptide. We also identify the deficiencies in the existing urea and TMAO force-fields with respect to correctly capturing the solvation thermodynamics of ternary urea-TMAO-water solutions and propose a unified force-field for urea-TMAO mixtures.   

Quantitative Prediction of Multivalent Ligand-Receptor Binding Affinities for Influenza, Cholera and Anthrax Inhibition

Multivalency achieves strong, yet reversible binding by the simultaneous formation of multiple weak bonds. It is a key interaction principle in biology and promising for the synthesis of high-affinity inhibitors of pathogens. We present a model for the binding affinity of synthetic multivalent ligands onto multivalent receptors consisting of n receptor units arranged on a regular polygon. Ligands consist of a rigid polygonal core to which monovalent ligand units are attached via flexible linker polymers. The calculated binding affinities quantitatively agree with experimental studies for cholera toxin (n=5) and anthrax receptor (n=7). We find that maximal binding affinity is achieved for a core that matches the receptor size and for linkers that have an equilibrium end-to-end distance that is slightly larger than the difference between core-size and receptor-size. We compare mono- and multivalent binding affinities, from which we conclude that multivalent ligands against influenza viral hemagglutinin (n=3), cholera toxin (n=5) and anthrax receptor (n=7) can outperform monovalent ligands only for a monovalent ligand affinity that exceeds a core-size dependent threshold value.   

Method for the Growth and Stabilization of Rare Earth Nano-Particles

We are developing a process to produce rare-earth nano-particles, (NPs), to study how quantum confinement affects the magnetic and electrical properties of rare-earth metals. The primary obstacle to producing and stabilizing rare-earth NPs is the reactive nature of rare-earth elements, which have an oxidation potential around -2 V or higher. Rare-earth elements require a strong reducing agent to form from an oxidized state, and are oxidized by common materials such as moisture and oxygen in the air.
For forming the NPs we are testing the use of electride/alkalide solutions, since they are some of the strongest reducing agents and can overcome the high oxidation potential. As for the stabilization and protection of the NPs, we are interested in using ligands since they bond to the surface of the NP, possibly providing a more effective barrier compared to micelles.
Since last year we have improved our process by installing an oxygen sensor and drying our solvents with molecular sieves, allowing us to ensure an inert environment in our glovebox. From observing the products and byproducts in a recent growth, we can see there is an improvement over last year’s results.
  

Characteristic Adsorption of Amino Acids on Surface of Al2O3 (0001) Single Crystal in Water Solution

We have been interested in a study to control cellular configuration on various functional oxides as an immobilization substrate for cell adhesion protein. For this purpose, adsorption interaction of various amino acids to terrace, step and kink (surface nanostructures) on the atomically flat surface of functional oxides should be studied with atomic scale as a preliminary experiment.
In this study, we investigate the adsorption behaviors of glycine, phenylalanine and alanine by using atomic force microscope (AFM) on the surface of Al₂O₃ (0001) that surface annealed at 1100 °C (single-step) and 1400 °C (multi-step) in air for 3 hours. The AFM images were taken for Al₂O₃ (0001) surfaces in the ultra pure water, water solution of glycine, alanine and phenylalanine (10^-3 mol/l). From the AFM images, the specific adsorption of glycine can be found only for the multi-step surface. However, phenylalanine and alanine adsorbed even on the single-step surface while glycine did not.   

Long- and Short- Range Order in Silicate Glasses Following Silver Ion Exchange

Infrared reflectance spectra have been shown to be sensitive to the intermediate-range order (IRO, 2-5 nm) and short-range order (SRO, 1-2 nm) of silica and silicates due to changes in fictive temperature and the diffusion of ions like Ag into the silica matrix. As the diffusion of metal ions in silica is affected by the IRO and SRO, knowledge of the structure changes induced provides us with how the metal ions can be expected to nucleate and grow into metal nanoparticles (MNPs) with thermal or laser annealing. Understanding this process may provide pathways to control the formation and growth of the MNPs, their location in the substrate, and their optical properties. Because of the very small scale of the SRO and IRO, these changes in the SRO-IRO order are difficult to measure except by the changes it brings to the more global matrix responses such as to the infrared and Raman spectra of the silica matrix. Using FTIR and optical measurements, we show that silicates can behave like an effective sponge, keeping their structure while loading the matrix with metal nanoparticles of Ag using the ion exchange process   

Effect of Diameter on Performance of Vortex Unit

Vortex unit is a proposed new suction device. It consists of a nozzle, a circular chamber and a skirt. Compressed air is injected into the circular chamber to form a rotating flow. The rotating flow produces a negative pressure inside the circular chamber, just like the center of typhoon. Because of the internal and external pressure difference, vortex unit can produce a suction force. Vortex unit has two characteristics: (1) Vacuum chuck has a limitation on working surfaces, it only works on smooth surfaces. But vortex unit overcomes this defect, vortex unit can work on rough surfaces. (2) Vortex unit has no direct contact with the sucked objects and can be applied to some special occasions such as gripping the semiconductor wafer.Vortex unit's optimized design is important. It has several important structural parameters, the radius of the circular chamber (denoted as R) is one of them. We measured the suction force of vortex unit, and calculated its input energy and found that R increases and the input energy decreases when the suction forces of vortex unit with different R are the same. In other words, In this paper, we will explore the relationship between R and vortex unit by experiment and theory, and achieve the goal of optimizing the vortex unit.   

Ordered Nanobody Arrays for Enhanced Biosensor Sensitivity and Selectivity

Nanobodies are an emerging class of proteins composed of a single antibody domain that have demonstrated significant potential for use as therapeutics, antigen tracers, and biosensors. For biosensing applications these proteins are incorporated onto a surface, where performance is dependent upon achieving sufficient protein density with easily accessible binding sites and adequate analyte transport. Here, we demonstrate the self-assembly of nanobody-polymer conjugates into domains of densely-packed, well-oriented nanobodies and domains of polymer meshes that can exclude molecules from the block copolymer assembly based on particle size. Small-angle X-ray scattering (SAXS) measurements indicate that the conjugates assemble into lamellae with alternating domains of nanobody and polymer. Enzyme immunoassays (EIAs) are performed using thin films of the conjugates, displaying orders of magnitude decrease in limit of detection compared to surface-immobilized nanobodies. It is further demonstrated that tuning the polymer molecular weight serves as a method to control the diffusion of molecules into the films.   

Structural Pattern Formation of Composite Particles with CeO2 and Polymer Brushes

The particle dispersibility in organic solution is important to fabricate a self-assembly film with ordered structure. In this study, surface modification of CeO₂ nano particles with high-density poly-methyl methacrylate (PMMA) brushes was conducted to improve its dispersibility and tried to make the self-assembly film of these polymer-inorganic composite particles.
The CeO₂ composite particles with PMMA brushes (PMMA-CeO₂) showed a good dispersibility in organic solvents. The particle structure of PMMA-CeO₂ was investigated by ultra small-angle X-ray scattering measurement and it was confirmed that its shape was almost a hard-sphere. The self-assembly film with PMMA-CeO₂ was fabricated by drop cast method and observed by the scanning electron microscope. The monolayer film of PMMA-CeO₂ with close-packed structure was fabricated via the chain structure depending on the volume fraction of PMMA-CeO₂ in solution. Furthermore, at quite low volume fraction, it was suggested that PMMA-CeO₂ were isolated at equal intervals with hexagonal coordination.   

Understanding the Flow Structure of Low Reynolds Number Flows

We consider a variety of low Reynolds number experimental flows including a Stokes multi-gyre flow and a four roll mill. An investigation of the underlying Lagrangian Coherent Structures (LCS) is performed using images of passive tracer (dye) and with finite-time Lyapunov exponent (FTLE) fields computed via particle imaging velocimetry (PIV). In addition we consider the dynamics of inertial particles in these flows along with the associated inertial LCS for these particle. Results are confirmed with theoretical/numerical models and provide improved understanding of transport in these fluid flows.   

Hydrodynamic Equilibrium and Structures of Compact Objects

Tidal disruption events (TDEs) occur when stars can no longer maintain hydrodynamic equilibrium as it begins to accrete onto compact supermassive objects. During this process, matter ejection takes place out of the object, and the constituent particles transferred to the compact objects fall in to circular orbit around their individual centers with various energies. Using the standard equations of fluid motion, we can determine the energies of each species of particle during accretion with the goal of determining when the equations of motion produce a solution, and which solutions lead to the specific conditions under which the star destabilizes. We compute these solutions to identify and further investigate the corresponding compact objects.   

Trantision of a compressible square cylinder wake structures subjected to free-stream disturbance

The flow around a square cylinder and its three-dimensionalization which leads to a turbulent wake are analyzed by a series of high-resolution simulations of the subsonic wake at Mach 0.3.
By examining the effects of upstream velocity disturbances on the wake flow structure, the following results are obtained.
In the preprimary study, the two-dimensional numerical simulation indicates that the Karman vortex street behind the cylinder is generated, when the base flow loses its symmetry around the critical point in the near wake region of the squire cylinder due to the round-off error.
The wake is well stimulated by the disturbance with an angular frequency close to the most unstable frequency of the wake.
The disturbances with an antisymmetric feature are well amplified, even if the angular frequency of the disturbance is far from the most unstable one. Bypassing secondary instability of the wake column structure, Roller-like structures which are often observed in the far wake flow.
A phase diagram of u and v fluctuations in the region indicates a turbulent state.   

Hybrid Simulation of Kelvin-Helmholtz Instabilities in the Presence of Radially Varying Flow

This paper summarizes the hybrid simulation results of plasma flow
curvature effects on the growth of the Kelvin-Helmholtz instability
(KHI). It is found that KHI growth rate is higher when the shear flow
has a negative initial curvature than linearly sheared initial flow. The
growth rate is lower when the initial shear flow has a positive curvature.
The growth rate under positive curvature decreases with increasing
positive curvature.   

Modeling anisotropic turbulence with Rapid Distortion Theory

Rapid Distortion Theory (RDT) describes how a turbulent flow changes under a sudden large scale geometric deformation. Under the assumption of rapid distortion, the flow field follows a simplified dynamics. In this project we develop numerical schemes to model isotropic turbulence undergoing a sudden shear under the RDT framework. We pay attention to the stability of the numerical method and justify our results with known RDT properties. This project is at the inital stage of researching shear flows, and we will present primary results. We expect to expand our investigations to particle dynamics in such flows in the next stage.   

Computer Simulation of Fluid Flow in Microfluidic Devices

Computer simulations of fluids can be an efficient way to model the behavior of fluid flow without the need to build and test a physical device. To help expedite the design of microfluidic devices and reduce the cost of the production of such devices, a computer simulation is being developed using the scientific computing library SciPy. The fluid flow in microfluidic devices can then be simulated to accurately predict the behavior of fluids in microfluidic channels via the numerical computation of the Naiver-Stokes equations with the appropriate boundary conditions. This can drastically improve the ability to fabricate devices compared to purely experimental techniques. The effectiveness of the model will be tested to determine the advantage of using a simulation to aid in the process of the development of microfluidic devices. By using technique, future undergraduate researchers will be able to further refine the simulation, adding more features and bringing the simulation results into agreement with experimental data.   

Dynamics of chemically active membranes

We numerically study the dynamics of a chemically active membrane in a reactive solvent. Catalytic sites on the membrane decompose the reagents present in the fluid and thus create a local chemical gradient. In this self-generated gradient, the membrane spontaneously undergoes a wiggling motion that, in turn, results in the directed movement of the membrane. We quantify the dynamics of the moving membrane, studying the effects of hydrodynamic interactions and an externally imposed gradients. Our results show novel membrane oscillations, which could be used to design chemically-powered autonomous films with specific applications.   

Silo outflow of soft frictionless spheres

Outflow of granular materials from silos is a remarkably complex physical phenomenon that has been extensively studied with simple objects like monodisperse hard disks in two dimensions (2D) and hard spheres in 2D and 3D. For those materials, empirical equations were found that describe the discharge characteristics. Softness adds qualitatively new features to the dynamics and to the character of the flow. We report a study of the outflow of soft, practically frictionless hydrogel spheres from a quasi-2D bin. Prominent features are intermittent clogs, peculiar flow fields in the container and a pronounced dependence of the flow rate and clogging statistics on the container fill height. The latter is a consequence of the ineffectiveness of Janssen's law: the pressure at the bottom of a bin containing hydrogel spheres grows linearly with the fill height.   

3D Phase Field Modeling on Fusion and Void Formation of Triplet Metallic Powders

Laser-based additive manufacturing (AM) process is important in aerospace and biomedical industry due to the request for superior quality and liability on shape-complicated parts. However, the multiphase dynamics involved in the high temperature AM manufacturing process is complicated by for examples the interplays of spot laser heating, dynamic powder-powder interactions, melting and solidification of pure and alloy-based metallic powders, evaporation, and the strong thermal capillary flow of the molten metal. A full process simulation including a broad range of thermophysical properties can be an overwhelming task even for pure metals. We focus on quantifying the dynamic void or defect formation due to incomplete melting or fusion of three metallic powders. This is important in predicting surface defect which may lead to crack or early failure of AM produced parts. The small scale analysis based on phase field formulation has successfully characterized the dynamic coupling of three phase evolution, solid-liquid phase transition, and the thermal capillary flow driven by a fixed or scanning laser beam. The simplified analysis on the triplet powder interaction provides a primitive model for describing complicated many or hybrid powder interactions.   

Experimental and Theoretical Investigation of Constant Flux Bidensity Particle Laden Flows on an Incline

Previous research [Lee et. al. 2014, Wong et. al. 2016] shows that gravitational and shear forces play an important role on the dynamics of particle laden flows down an incline. These effects can be characterized by two regimes, settled and ridged. In the past, experimental results were focused on the finite volume case for one and two species of particles, whereas we change the initial conditions to consider the constant flux case with the aid of a pump. Our experiments on bidensity slurries contain two negatively buoyant species with the same diameter and different densities. We develop numerical simulations of the mathematical model which are validated through the experimental comparisons, showing the front position evolving as x(t) ~ t. We also produce a phase diagram indicating the transition between the settled and ridged regimes, obtained through a careful study varying the angle of inclination and volume ratio between particles. Additional comparisons include measurements of the film height, the time required for a regime to emerge, among others.   

Plasma simulation of a two-stage electric propulsion system for spacecraft

Space-based technology is allowing for smaller and more cost-effective satellites to be produced. By working in large swarms, many small satellites can provide additional capabilities while reducing risk. The high exhaust velocity and propellant efficiency of plasma-based electric propulsion makes it ideally suited for low thrust missions. The two dominant types of electric propulsion, namely ion thrusters and Hall thrusters, excel in different mission types. In this work, an electric hybrid propulsion design is modelled to enhance understanding of key plasma phenomena and evaluate performance. Specifically, the modelled hybrid thruster seeks to overcome issues with existing Ion and Hall thruster designs. A two-stage Hall thruster is investigated and the potential feasibility of coupling the two stages to produce the ion-beam is evaluated. The ionization and acceleration events are investigated via multiphysics simulations. The key trends ranging from the discharge inception, amplification and drift to formation of the ion beam are discussed and characterized.   

Direct Comparison of 3D Printed and Conventionally Produced Microfluidic Devices

Microfluidic devices are currently produced mainly by the expensive and time-consuming process of photolithography. Previous research done by this laboratory has shown that it is possible to produce microfluidic devices using a MakerBot 3D printer. This research evaluated the effectiveness of the 3D printed design method in comparison to the conventional lithography methods. First a variety of devices were designed, followed by their fabrication by the two methods described above. Following fabrication, the flow of the devices was compared qualitatively through use of optical microscopy. During the fabrication process a comparison of length of time necessary to produce the devices as well as the cost of device production was recorded and compared. It is believed that the method of 3D printing devices will be able to significantly reduce device cost and time of fabrication, while maintaining similar flow quality.   

Effect of Magnetic Field on Blood Viscosity and the development of Atherosclerotic Plaque in Mice

Risk of cardiac diseases increase greatly with high viscosity of blood. Also, atherosclerotic plaque develops in vasculature due to turbulence in blood flow. Medicines, like Aspirin, may reduce blood viscosity, however, only to worsen the turbulence because the Reynolds number goes up as the viscosity lowers. Here, we will report our Magneto-Rheology research that addresses both turbulence suppression and viscosity reduction simultaneously. When a strong magnetic field is applied along the blood flow direction, red blood cells are polarized, and aggregated into short chains, which lowers the viscosity along the flow direction. Concurrently, viscosity is increased in the directions perpendicular to the flow. We studied the effect of magnet on mice to test our hypothesis. A small magnet was surgically implanted adjacent to the jugular vein in mice. Afterwards we measure the viscosity of blood collected from sacrificed mice. Also, plaque formation in the aortic arch was analyzed. Preliminary results suggest that viscosity is reduced with lesser plaque, i.e., suppressed turbulence. We expect to design and develop a device for human, which will control plaque, and thus will prevent Heart Attack and Strokes.   

Application of different wavelet families and thresholding methods for low-dose computed tomography denoising

X-ray Computed Tomography (CT) is one the predominant imaging devices. X-ray photons are generated in a vacuum tube, and directed towards the patient body. A reconstruction algorithm such as filtered back projection (FBP) is normally used to reconstruct the 3D-volume image of the patient from the projection data. Since CT imaging is based on transmission and absorption of X-ray photons, it will deposit radiation dose inside the patient, which has the risk of producing unhealthy biological events. However, reducing the radiation flux will generate quantum mottle noise in the CT images. In this study, wavelet denoising was successfully applied in order to reduce the noise in a low-dose CT image. The low-dose CT image had 75% less dose compared to its normal dose version. Different types of wavelets and thresholding methods were applied. The denoising performance of each one was evaluated using structural similarity index (SSIM). The results showed that the selection of thresholding method and threshold value are the most important factors in CT image denoising using wavelet transform.   

A novel L-shell x-ray fluorescence bone lead quantification method based on direct x-ray soft tissue attenuation measurement using a microbeam and a bone and soft tissue phantom assembly

Lead (Pb) is a well-known toxic element residing in the human bone for many years. Therefore, in vivo measurement of bone Pb concentration is a metric of long-term human exposure. The L-shell x-ray fluorescence (LXRF) large population bone Pb surveys can be designed with portable x-ray tubes and detectors. In the past studies the x-ray attenuation of the soft tissue (XAST) overlying the bone was accounted for using ultrasound and average elemental compositions to calculate its linear attenuation coefficient (μ). The procedure proved inaccurate. A cylindrical plaster-of-Paris (bone) and a 3-mm thick cylindrical-shell polyoxymethylene (POM) (soft tissue) were used in a scanning microbeam XAST measurement. The μ_POM measurements were in excellent agreement (<5%) with the μ_POM calculations using the POM chemical formula (CH₂O)_n and the NIST XCOM database. A relationship between the XAST and the Pb calibration line slopes for 0, 1, and 3 mm POM thickness values was recently demonstrated by our group which can lead to a more accurate in vivo Pb LXRF measurement method.   

Effects of Transcranial Magnetic Stimulation on Parkinsonian Motor Neurons

Parkinson’s disease (PD) is a neurological condition which affects millions of people and can lead to fatal complications. Patients often receive deep brain stimulation (DBS), an invasive but effective treatment in which a probe is inserted into nuclei deep in the brain. This probe provides continuous current and the treatment has been shown to alleviate various symptoms of PD. Recent studies have also shown that it is possible to use transcranial magnetic stimulation (TMS) to alleviate parkinsonian symptoms by stimulating motor areas of the brain. While DBS and TMS are significant medical advancements, their exact cellular mechanisms are poorly understood. We explore the firing rates and patterns of motor pathway neurons using a novel computational model. We have developed healthy and PD motor pathway models with similar firing rates as those observed from in vivo studies. We then induce DBS-like current in the PD neurons and observe the consequent neuron firing patterns, and manipulate various parameters of TMS to observe the deep brain effects of cortical non-invasive TMS. Results indicate that it may be possible to emulate DBS firing using non-invasive cortical TMS if a pulse rate of 50 Hz can be achieved and any side effects such as overstimulation of tissue can be avoided.   

Localizing Rotors in Human Atrial Fibrillation Using Differential Entropy.

Rotors sustain atrial fibrillation (AF) and are targeted during AF ablation with variable results. Although Shannon entropy was shown to identify rotors of spiral waves in experimental settings, it fails to detect rotors in human atrial fibrillation (AF). We previously showed that the accuracy of identification sensitively depends on the number of rotors and spatial resolution of signal recording. Another possible limitation of the approach is discretization of probability distribution from continuous unipolar electrograms. Therefore, we assessed the value of differential entropy (DE), which does not require discretization of probability distribution, to locate rotors of human AF using intracardiac 64-electrode basket catheter recordings from 33 patients. The area of maximum DE and rotors precisely overlapped in 9% of the recordings, and was one electrode away in 36%. When the maximum DE was defined as the highest 5^th percentile, the area of maximum DE and rotors precisely overlapped in 22% of the recordings, and was one electrode away in 59%. We conclude that DE is a promising metric to locate rotors in human AF, but the accuracy is modest.   

Qualitative Comparison of the Cytotoxic and Immunologic Consequences of Spatially Homogeneous and Heterogeneous Radiation Dosing

In radiotherapy the standard of care (SOC) is homogeneous tumor dosing. Spatially fractionated dosing (GRID) has recently been studied in the clinic. Radiation induces cytotoxicity on both tumor and immune cells, but it is hypothesized that it also elicits an immune response. To explore radiation-induced immunity, three tumors of similar mass were grown in silico and radiated with SOC homogeneous and GRID dose distributions. A stochastic agent based model described the dynamic interactions between the cancer and immune cells. This was supplemented with an ODE approach. All simulations without radiation-induced immunity did not control tumors. Simulations under conventional dosing with radiation-induced immunity resulted in tumor control. GRID radiation with large single doses correlated with lower cancer to immune cell ratios. Simulations revealed that in addition to inducing a powerful immune response, the tumor did not decrease in mass without radiation-induced immunity. GRID dosing may be effective in treatment of tumors assuming robust immune response. High dose, single GRID fractions showed promise in reducing tumor burden due to the large number of immune cells generated and spared.   

Distance Running: Computational Reconstruction of Physiological Profiles

Low level of aerobic fitness is an inevitable consequence of physical inactivity and sedentary lifestyle that is believed to be one of the most important public health problem of the 21st century. Physical inactivity and poor physical fitness (measured in terms of a person’s maximal oxygen uptake) are associated with several health problems, such as cardiovascular diseases, metabolic disorders, musculoskeletal disorders, pulmonary diseases, cancer, psychological problems and more. Positively, improvements in aerobic fitness have been shown to reduce all-cause mortality. Hence, it is important to be able to asses physiological profiles which are associated wtih exercise. We observed the running world records from 1000m up to the Marathon show exponential scaling regimes when the race time is plotted over the race velocity. Based on that, we have develop a model that reconstructs the running economy (oxygen uptake as function of running velocity) and endurance (time over which a fraction of maximal oxygen uptake can be sustained) for an individual runner from her/his performances in competitions and the heart rate data measured during training. Studies with runners have been performed to validate the model.   

A Self-Consistent Gaussian Study On Phase Transition and Critical Exponents of Kagome Lattice

The low temperature dynamics of the classical Heisenberg antiferromagnet with nearest neighbor interaction on the frustrated kagome lattice is studied by using a self-consistent Gaussian method (SCGA). The structure factor of this lattice for different temperatures has been calculated and plotted. It has been seen that by decreasing the temperature, several maxima with same height has been appeared which reveals that the system doesn’t have a certain ground state. By projecting the structure factor on the plane, pinch point behavior is also considered, and it has been shown that by decreasing the temperature, pinch points are becoming sharper, which suggests a highly frustrated lattice. Then the single-ion anisotropy term is added to Hamiltonian and phase transition temperature and critical exponents of kagome lattice has been calculated by using the SCGA method. It has been seen that by decreasing the single ion anisotropy coefficient from D=1 to D=0.2, phase transition temperature decreases from Tc=0.4 to 0.15K which are well consistent with Monte Carlo simulation results.
  

Bismuth Sulfide Nanostructures as Contrast Agents for Computed Tomography

CT contrast agents based on iodinated compounds have been studied for imaging since 1920s. Despite effective attenuation, versatile synthesis methods and body tissue tolerance, these agents suffer from limitation in circulation times (<10 min) that results in poor contrast. Bismuth sulfide nanoparticles have circulation times up to 140 min¹. Also their high X-ray attenuation and low cost make them good candidates for X-ray-based imaging.
In this work, a chemical methodology for the synthesis of uniform Bi₂S₃ nanostructures is reported. The reaction is in a mixture of primary (oleylamine) and tertiary (trioctylamine) solution at moderate temperature (<200^oC) using Bi(Ac)₃ as Bi3+ source. XRD analysis shows the single phase Bi₂S₃ nanoparticles, while TEM measurements used for the morphological characterization. Both amines are important for the structural and morphological control of the synthesized materials. Additionally, by changing the molecular ratio of the amines we are able to control shape and size of the particles. Our goal is to coat the Bi₂S₃ nanorods with Fe₃O₄ nanoparticles to produce a multifunctional contrast agent for CT and MRI scans.
¹Rabin O,Perez JM,Grimm J,Wojtkiewicz G,Weissleder R (2006)   

Parallel Multicanonical Simulations and their Application

Generalized-ensemble simulations are advanced Monte Carlo tools to solve problems involving large free-energy barriers and strongly suppressed states, such as first-order phase transitions or rare-event distributions. A particular approach is the multicanonical method, replacing the canonical Boltzmann weight by an auxiliary weight function. The weight function is iteratively adapted to produce a flat histogram. The beauty of this approach is that each iteration samples from an equilibrium distribution due to fixed weights. Consequently, this process can be parallelized very easily and very efficiently. We will present in detail this parallel scheme for CPU and GPU architectures and show its close-to-perfect scaling up to $\mathcal{O}(10^5)$ threads. In addition, we present some recent applications using parallel multicanonical simulations to study cluster formation in particle and polymer systems, reaching previously inaccessible scaling regimes.   

Magnetic Critical Fluctuations Of Ising-like Antiferromagnet DyScO3

Orthorhombic perovskites provide a perfect playground for investigations of novel magnetic phenomena. We here report on detailed low temperature magnetic properties of the DyScO3 by means of single crystal and powder neutron scattering, and magnetization measurements. We show that Dy3+ has an Ising-like anisotropy with easy axis of magnetization lying in ab plane, consistent with the calculated wave functions of the ground doublets, which is mostly contributed from |±15/2>. Below TN =3.2 K, Dy3+ ising moments orders antiferromagnetically, with the ground state configuration AxGy, selected by the dipole-dipole interaction. Magnetic diffuse scattering in the elastic channel were observed over a wide temperature range, indicating the existence of strong critical fluctuations associated with the Ising ground states. The ground state wave function indicates that conventional transverse fluctuations like magnons are strongly suppressed. On the other side, the longitudinal fluctuations are ‘hidden’ to neutrons, restricted by the selection rules ΔS=1.   

Isomerism for substituted nanothreads with chemical formula ((CH)5X)n and regularities in their energetics

Pressure-driven polymerization of solid pyridine to one-dimensional crystalline “nanothreads” has been recently achieved experimentally through non-topochemical reaction. This route might also be feasible for the polymerization of other hetero-substituted or functionalized aromatic molecules to form one-dimensional saturated structures. The atomic structures of these threads have not yet been fully determined due to experimentally challenges in synthesis and characterization. We systematically enumerated the isomeric possibilities for substituted nanothreads with chemical formula ((CH)₅X)_n (X=heteroatom or –CR substituent) under a symmetry-conditioned permutation constraint and limit on unit cell size. Isomerization for these systems encompasses both changes in heteroatom position within a given framework and also changes in the connectivity of the sp³ framework itself. Regularities in their isomerization energetics have been investigated.   

Non-density driven liquid-liquid transition in pure gallium melt

A liquid may have two or more isotropic phases of the same composition, the transition between them is called liquid-liquid transition (LLT). LLT has been reported in several systems where LLT is associated with dramatic change of density. However, it is suggested that the structural change in liquid cannot be sufficiently described by density. Several attempts are made to reveal the non-density driven LLT. But the existence of non-density driven LLT is still controversial due to the lack of adequate experimental evidences. In this work, we capture a non-density driven LLT in pure Gallium at far above its melting temperature. The structural change of liquid without significant density change is revealed by a kink in the Knight shift (K_s) curve during heating. The first order character of LLT is revealed by the hysteresis of heating and cooling curve of Knight shift (K_s). The latent heat of LLT can be reflected by an endothermic peak measured in the Differential Scanning Calorimetry experiment. Our observations of the LLT in the single element system support density is not the only order parameter in the description of liquid structure, and additional order parameters are needed.   

Investigation of Electromagnetic Hotspots in Metal Infiltrated Metalattices Using Electron Energy Loss Spectroscopy (EELS)

Metalattices are 3D periodic, ordered and interconnected nanostructures with periodicity size range between 1 nm – 100 nm. Tuning the functional properties of metalattice can happen by infiltrating them with semiconductor materials (like Si, Ge etc) and/or metals (Ag, Pt, Pd, Ni etc). In this research, monochromated Scanning Transmission Electron Microscopy (STEM) and Electron Energy Loss Spectroscopy (EELS) are shown as promising techniques in characterizing both the spatial and spectral properties enabling direct mapping of electromagnetic hotspots associated with the localized surface plasmon resonances at the nanoscale which can give us a depth understanding of plasmonic behavior in infiltrated nano-opals. Of particular interest are metal filled nano-opals that exhibit dark plasmon modes resulting from vanishing dipole moments that can lead to storing electromagnetic energy more efficiently and making them as future candidates for various applications such as enhanced biological and chemical sensors.