Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session Y66: Biological Systems, Components and MoleculesRecordings Available
|
Hide Abstracts |
Chair: Ping Yu, University of Missouri Room: Hyatt Regency Hotel -Grant Park D |
Friday, March 18, 2022 8:00AM - 8:12AM |
Y66.00001: Impact of protein crystal contact forces on intramolecular picosecond dynamics Jeffrey A McKinney, Deepu K George, Xiaotong Zhang, Jason Benedict, Alexander J McNulty-Romaguera, Tod Romo, Andrea G Markelz While many protein dynamics studies depend on crystal phase measurements, it is not known how the intermolecular interactions effect these dynamics. We examine the dynamical impact of intermolecular interactions by measuring the collective structural vibrations using anisotropic terahertz microspectroscopy and tuning interactions through controlled dehydration of the crystal water content. For tetragonal and triclinic crystals no frequency shifts are observed. Instead, the bands initially narrow then broaden with dehydration, consistent with increased and then decreased ordering as found in X-ray crystallography. For monoclinic crystals on the other hand, we find strong anisotropic bands at 14.8 and 21.6 cm-1, which blue shift by 5.0 and 3.1 cm-1 respectively. This blue shift in the vibrations suggests a stiffening of the potential due to either a reduction in the solvent, an increase in the interaction with the neighboring molecules or both. Monoclinic lysozyme crystals are known to reversibly transform to another monoclinic form due to dehydration, thus it is possible that the spectral shifts are associated with this new ordering and not changes in the interactions. We explore these different possible mechanisms by comparison with Normal Mode Ensemble Analysis calculations. |
Friday, March 18, 2022 8:12AM - 8:24AM |
Y66.00002: Quasi-two-dimensional clustering of Brownian particles with competitive interactions: Phase diagram, structures, and dynamics Zihan Tan, Jan Dhont, Gerhard Nägele Three-dimensional (3D) bulk dispersions of Brownian particles with competitive short-range attractive (SA) and long-range repulsive (LR) interactions show rich phase behavior, and peculiar diffusion and rheological properties. In comparison, little is known about quasi-two-dimensional (Q2D) SALR dispersions of particles confined to a liquid interface or membrane, despite their biological relevance. For instance, the antagonistic interplay of SA forces (due, e.g., to lipid-mediated depletion, wetting) and LR forces (induced, e.g., by mechanical deformations or membrane fluctuations) in membrane proteins is crucial for forming protein clusters. These clusters, in turn, are pivotal in signal transduction and protein processing. We present mesoscale simulation results on the phase behavior, cluster structures, and dynamics of planar monolayers of SALR Brownian particles embedded in a bulk fluid. Salient differences and similarities between Q2D and 3D SALR particles are highlighted[1]. Insights on the dynamics of clusters are gained from analyzing mean-squared displacements, cluster correlation and hexagonal order correlation functions, and intermediate scattering functions. Furthermore, we discuss the effects of hydrodynamic interactions on dynamic clustering[2]. |
Friday, March 18, 2022 8:24AM - 8:36AM |
Y66.00003: Biomechanics of microvasculature on blood vessel-on-a-chip Paul Salipante, Steven D Hudson, Stella Alimperti We use a three-dimensional 3D model blood vessel platform to measure the elasticity and membrane permeability of the endothelial cell layer. The microfluidic platform is connected to a pneumatic pressure controller to apply hydrostatic pressure. The deformation is measured by tracking the mean vessel diameter under varying pressures up to 300 Pa. We obtain a value for the Young's modulus of the cell layer in low strain where a linear elastic response is observed and use a hyperelastic model that describes the strain hardening observed at larger strains. Fluorescent dye is used to track the flow through the cell layer while pressurized to determine the membrane flow resistance as a function of applied pressure. Finally, we track the 3D positions of cell nuclei while the vessel is pressurized to observe local deformation and correlate inter-cell deformation with the local structure of the cell layer. This approach can probe the mechanical properties of blood vessels in vitro and provides a methodology for investigating microvascular related diseases. |
Friday, March 18, 2022 8:36AM - 8:48AM |
Y66.00004: Charge regulation in colloidal system Leticia Lopez-Flores, Monica Olvera De La Cruz The acid-base equilibrium in a system directly influences the functionality and behavior of particles in a system. In most cases, the particles win or lose charge due to the ionization of the acidic or basic groups. The degree of ionization and their intermolecular electrostatic interactions are controlled by varying pH and the salt concentration of the solution in the system. Although the pH can be tuned in experiments, it is hard to model the effect by simulations or with theoretical approaches. This is because of the difficulty in treating charge regulation effects in each particle to be considered in the system. In this work, we analyze pH effects as a function of the density of colloidal particles via simulations and find the phase diagram of the system. |
Friday, March 18, 2022 8:48AM - 9:00AM |
Y66.00005: A Molecular-scale Perspective of Competitive Interactions Induced by Phase-modifiers in Organic Solvents Biswajit Sadhu, Aurora E Clark The self-assembly of amphiphiles leads to complex, multi-component soft-matter structures that underpin a wide-range of colloidal and engineering applications. Separations methods, for eg. liquid-liquid extraction, are heavily influenced by soft-matter self-aggregation. In addition to the amphiphile extractant, so-called "phase-modifier" amphiphiles are often added into the organic phase to influence the self-assembly process with the aim of preventing undesirable phase phenomena. It is believed that the behavior of a phase-modifier can be explained in the context of "cosurfactant" and/or "cosolvent" characteristics. However, there remain experimental challenges for identifying the true composition of aggregates, which results in dearth of molecular level knowledge on the phase-modifier's working principles. This work employs molecular dynamics with graph theoretical analyses to unravel the working mechanism of phase-modifiers. We focus upon N,N-dihexyloctanamide (DHOA) and tributyl phosphate (TBP) that are commonly used as phase-modifier with actinide selective amphiphile extractant N, N, N', N'-tetraalkyl diglycolamide (TODGA). We demonstrate that the hydrogen bonding ability of the modifiers introduces competition to the interactions among extractant and polar solvent molecules (e.g., water and nitric acid). As an important consequence, the modifiers limit the association of polar solvent molecules similar to a chaotropic agent, and therefore hinder the prerequisite steps of developing a microemulsion by restricting the formation of large polar cores. The hydrogen bonding ability of a phase-modifier allows it to sequester solvent molecules from the TODGA extractant, therefore decreasing the solvent-assisted self-aggregation of primary extractant and supporting the well-documented observation of increase in critical aggregate concentration from the prior experimental studies. |
Friday, March 18, 2022 9:00AM - 9:12AM |
Y66.00006: Dynamics of Semiflexible Viruses in Polyelectrolyte Solutions Farshad Safi Samghabadi, Ali H Slim, Jacinta C Conrad The structure and dynamics of polyelectrolytes differ from those of neutral polymers. How these differences affect the transport of anisotropic particles remains incompletely understood. Here, we study the dynamics of semiflexible, rodlike M13 bacteriophage (phage) in aqueous semidilute solutions of sodium poly(styrene sulfonate) with various ionic strengths using fluorescence microscopy. Phage exhibit approximately diffusive dynamics and non-Gaussian distribution of displacements across all polymer concentrations. The phage dynamics are faster than nanospheres of the same hydrodynamic size and monotonically deviate from predictions for the diffusivity of rods based on the bulk viscosity across all polymer length scales. Available scaling theories for neutral polymers can only partially collapse dynamics as a function of normalized length scales onto a master curve. Furthermore, the non-Gaussian parameter exhibits concentration-dependent temporal evolution. These results suggest the presence of multiple diffusive modes due to the anisotropic structure of the filamentous viruses and the confining time and length scales set by polymer structure and dynamics. |
Friday, March 18, 2022 9:12AM - 9:24AM |
Y66.00007: Modeling Knotted Topological Configurations in Confined Polymers using a Field Theoretic Approach Rajeev Kumar In this talk, I will present our work related to a new field theoretic approach for modeling knotted configurations in confined polymers. Divergences appearing due to crossings in knotted configurations are treated using invariance of the single chain partition to an arbitrary gradient term in a vector field encoding orientational interactions. Results obtained for homopolymers with free chain ends forming torus knots inside spherical cavities will be presented. Specifically, monomer density distribution along with the free energy cost for the formation of torus knots inside spherical cavities will be presented. |
Friday, March 18, 2022 9:24AM - 9:36AM |
Y66.00008: Ring-o-rings: joining the ends of poly[n]-catenanes to capture supramolecular torsion Luca Tubiana, Franco Ferrari, Enzo Orlandini Recent advancements in chemical synthesis and self-assembly as well as modelling and simulations have offered a framework to design systems of interlocked rings with controllable properties. These systems can be produced at scales varying from a few nanometers to several micrometers, and have been proposed for applications ranging from smart materials, to catalyzers and nano-machines. Of particular interest are poly[n]-catenanes, sequences of n mechanically interlocked circular molecules, which can be synthesised through self assembly. Here we show that, by joining the two ends of a linear poly[n]-catenane to form a supramolecular ring, it is possible to capture different amount of twist, which alter significantly the average extension of the structure and the relative orientation of the elementary rings along the backbone. |
Friday, March 18, 2022 9:36AM - 9:48AM |
Y66.00009: Composite Entanglement Topology and Extensional Deformation In Ring-Linear Polymer Blends Thomas C O'Connor, Ting Ge, Gary S Grest Large-scale molecular simulations are applied to characterize the entanglement structure, topology, and dynamics of architectural blends of ring and linear polymer chains. The mixture of the two chain shapes produces a composite network formed by a combination of conventional linear-chain entanglements and threading of linear chains through ring polymers. We systematically study these networks for symmetric blends of well entangled polymers with the ring fraction $\phi_R$ varying from 0.05 to 0.95. Primitive path analyses are used to visualize and quantify the network structure and measure the quantity of ring-linear threading and linear-linear entanglement as a function of $\phi_R$. We find that the density of topological constraints of the network has a maximum with respect to $\phi_R$ at a ring fraction $\phi_R\approx0.4$, which we can rationalize with simple constraint-counting arguments. Complimentary simulations of blend elongation are also reported and demonstrate how the changing entanglement structure of blends with $\phi_R$ gives rise to qualitative changes in macroscopic extensional stresses during deformation. |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700