Bulletin of the American Physical Society
2008 APS March Meeting
Volume 53, Number 2
Monday–Friday, March 10–14, 2008; New Orleans, Louisiana
Session W25: Focus Session: Biopolymers: Molecules, Solutions and Networks II |
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Sponsoring Units: DPOLY DBP Chair: Ting Xu, University of California, Berkeley Room: Morial Convention Center 217 |
Thursday, March 13, 2008 2:30PM - 3:06PM |
W25.00001: Design of Responsive Peptide-based Hydrogels as Therapeutics Invited Speaker: Hydrogels composed of self-assembled peptides have been designed to allow minimally invasive delivery of cells in-vivo. These peptides undergo sol-gel phase transitions in response to biological media enabling the three-dimensional encapsulation of cells. Peptides are designed such that when dissolved in aqueous solution, exist in an ensemble of random coil conformations rendering them fully soluble. The addition of an exogenous stimulus results in peptide folding into beta-hairpin conformation. This folded structure undergoes rapid self-assembly into a highly crosslinked hydrogel network whose nanostructure is defined and controllable. This mechanism, which links intramolecular peptide folding to self-assembly, allows temporally resolved material formation. In general, peptides can be designed to fold and assemble affording hydrogel in response to changes in pH or ionic strength, the addition of heat or even light. In addition to these stimuli, DMEM cell culture media is able to initiate folding and consequent self-assembly. DMEM-induced gels are cytocompatible towards NIH 3T3 murine fibroblasts, mesenchymal stem cells, hepatocytes, osteoblasts and chondrocytes. As an added bonus, many of these hydrogels possess broad spectrum antibacterial activity suggesting that adventitious bacterial infections that may occur during surgical manipulations and after implantation can be greatly reduced. Lastly, when hydrogelation is triggered in the presence of cells, gels become impregnated and can serve as a delivery vehicle. A unique characteristic of these gels is that when an appropriate shear stress is applied, the gel will shear-thin, becoming an injectable low viscosity gel. However, after the application of shear has stopped, the material quickly self-heals producing a gel with mechanical rigidity nearly identical to the original hydrogel. This attribute allows cell-impregnated gels to be delivered to target tissues via syringe where they quickly recover complementing the shape of the tissue defect. This shear-thin delivery method is a convenient way to introduce cells to wound sites. [Preview Abstract] |
Thursday, March 13, 2008 3:06PM - 3:18PM |
W25.00002: Synchrotron x-ray diffraction study on the size distribution and mechanical stability of microtubules by microtubule-associated-protein (MAP) tau M.C. Choi, U. Raviv, H. Miller, M. Gaylord, E. Kiris, D. Ventimiglia, L. Wilson, M.W. Kim, S. Feinstein, C.R. Safinya In neurons, microtubules (MTs), 25nm protein nanotubes, are used extensively as tracks for transporting nutrients and cellular components between the cell body and axons. MAP tau regulates microtubule assembly and, in a poorly understood manner, inter-MT interactions. Altered tau-MT interactions leads to MT depolymerization and tau tangles, which is implicated in a large number of neurodegenerative diseases. We will show that the size distribution and the enhanced mechanical stability of MTs by tau bindings are dependent on tau isoforms. Supported by DOE DE-FG02-06ER46314, NSF DMR-0503347, and NIH GM-59288, NIHI RO1-NS35010. [Preview Abstract] |
Thursday, March 13, 2008 3:18PM - 3:30PM |
W25.00003: Effect of Mg Ions on Microrheological Properties of F-actin Solution across Isotropic-Nematic Phase Transition Jun He, Michael Mak, Yifeng Liu, Jay Tang We studied microrheological properties of F-actin across the isotropic-nematic phase transition region by video particle tracking and laser deflection particle tracking methods. The two methods give consistent results. As the nematic order parameter increases with the actin concentration, G$'_{x}$ (along the alignment) and G$'_{y}$ grow apart, with G$'_{y}$ larger than G$'_{x}$. The moduli scale with actin concentration as $G'_{x}\propto c^{0.54 \pm0.13}$ and $G'_{y}\propto c^{1.38\pm0.15}$. Furthermore, G$'$ and G$''$ dependence on [Mg$^{2+}$] were measured and compared for 1 mg/ml isotropic and 4 mg/ml nematic F-actin solutions. For isotropic phase, G$'$ increase with [Mg$^{2+}$] up to 6 mM and then plateaus; for nematic phase, G$'_{y}$ is larger and both G$'_{x}$ and G$'_{y}$ increase with [Mg$^{2+}$] monotonically all the way up to 16 mM, above which F-actin bundle formation occurs. In both isotropic and nematic phases, G$''$ only weakly depends on [Mg$^{2+}$]. In conclusion, particle tracking microrheology reveals rich rheological features of F-actin affected by I-N phase transition and by tuning weak electrostatic interactions among the filaments. [Preview Abstract] |
Thursday, March 13, 2008 3:30PM - 3:42PM |
W25.00004: The stability of cellulose Tongye Shen, S. Gnanakaran Stabilities and dynamics of known forms of crystalline cellulose (an ordered assembly of beta-glucose polysaccharide chains) are dominated by hydrogen bonding (HB) interactions. A detailed understanding on how HB interactions contribute to overall thermostability of crystalline cellulose is essential for efficient enzymatic degradation of cellulosic structures and the eventual conversion to ethanol. We construct a statistical mechanical model of cellulose at the resolution of explicit HB networks. This model takes into account the essential physical interaction in terms of both intramolecular bonding between neighboring glucose units within a chain and intermolecular bonding between different cellulose chains. These calculations reveal stabilities of HB networks under various conditions, and the microscopic details (at the resolution of individual bonds) of breaking of HB network that leads to instability. By combining these observations with all-atom replica exchange dynamics simulations of short cellulose chains, we are able to capture the local disorder and amorphous nature of crystalline cellulose where the directionality of HB interactions play a critical role. [Preview Abstract] |
Thursday, March 13, 2008 3:42PM - 3:54PM |
W25.00005: ABSTRACT WITHDRAWN |
Thursday, March 13, 2008 3:54PM - 4:06PM |
W25.00006: Transient Binding and Viscous Dissipation in Semi-flexible Polymer Networks Oliver Lieleg, Mireille Claessens, Andreas Bausch Nature specifically chooses from a myriad of actin binding proteins (ABPs) to tailor the cytoskeletal microstructure. Herein, cells rely on the dynamics of the cytoskeleton as its structural and mechanical adaptability is crucial to allow for dynamic processes. A molecular understanding of such biological complexity calls for an in vitro system with well-defined structural rearrangements and cross-linker dynamics to elucidate the physical origin of the unique viscoelastic properties of cells. As we present here, the frequency-dependent viscoelastic response of cross-linked in vitro actin networks is determined by the binding kinetics of cross-linking molecules. Independent from the particular network structure, the viscous dissipation (loss modulus) exhibits a pronounced minimum in an intermediate frequency which is dominated by elasticity. We show that in this frequency regime the molecular origin of the viscoelastic response is given by the non-static nature of actin/ABP bonds as they are subjugated to chemical on/off kinetics. The time scale of the resulting stress release is set by the lifetime distribution of the cross-linking molecule and therefore can be tuned independently from other relaxation mechanisms. We speculate that unbinding of distinct cross-links might be the molecular mechanism employed by cells for mechanosensing. [Preview Abstract] |
Thursday, March 13, 2008 4:06PM - 4:18PM |
W25.00007: : Microtubule Self- Assembly YongSeok Jho, M.C. Choi, O. Farago, MahnWon Kim, P.A. Pincus Microtubules are important structural elements for neurons. Microtubles are cylindrical pipes that are self-assembled from tubulin dimers, These structures are intimately related to the neuron transport system. Abnormal microtubule disintegration contributes to neuro-disease. For several decades, experimentalists investigated the structure of the microtubules using TEM and Cryo-EM. However, the detailed structure at a molecular level remain incompletely understood. . In this presentation, we report numerically studies of the self-assembly process using a toy model for tubulin dimers. We investigate the nature of the interactions which are essential to stabilize such the cylindrical assembly of protofilaments. We use Monte Carlo simulations to suggest the pathways for assembly and disassembly of the microtubules. [Preview Abstract] |
Thursday, March 13, 2008 4:18PM - 4:30PM |
W25.00008: Direct Observation of Early-Time Hydrogelation in $\beta $-Hairpin Peptide Self-Assembly Tuna Yucel, Joel Schneider, Darrin Pochan Triggered hydrogelation of MAX 1 peptide (NH$_{2}$-(VK)$_{4}$-V$^{D}$PPT-(KV)$_{4}$-CONH$_{2})$ proceeds through peptide intramolecular folding into $\beta $-hairpins and immediate self-assembly into branched clusters of well defined (uniform, 3 nm cross section), semi-flexible, $\beta $-sheet-rich nanofibrils. Cryogenic transmission electron microscopy indicates that dangling fibrils extend from one growing cluster to another and lead to early, intercluster communication in solution. At the apparent percolation threshold, the dynamic shear modulus measured by oscillatory rheology ($G'(\omega ),G"(\omega )\propto \omega ^n)$ and the field-intensity autocorrelation function measured by dynamic light scattering ($g_1 (\tau )\propto \tau ^{-\beta '})$ show power-law behavior with comparable critical dynamic exponents ($n \quad \approx $ 0.47 and \textit{$\beta \prime $} $\approx $ 0.45). Finite interpenetration of percolating cluster with smaller clusters, along with permanent intercluster entanglements, increase the network rigidity. The self-assembly of MAX 1 peptide was compared and contrasted with the assembly of other biopolymeric networks in literature. [Preview Abstract] |
Thursday, March 13, 2008 4:30PM - 4:42PM |
W25.00009: Loop Closure Dynamics of Flexible and Semi-flexible Polymer Jen-Fang Chang, Yeng-Long Chen It is widely believed that DNA looping due to multi-site DNA-binding proteins is important for DNA transcription, replication, and recombination. The chain closure problem has been studied in several Monte Carlo simulations to determine the chain closure probabilities and the chain conformation to infer dynamic properties. In this work, we investigate how the loop closure dynamics of flexible and semi-flexible polymers depend on the polymer length and the reactive site position using Brownian dynamics simulation, accounting for hydrodynamic interactions. Our study examines the probability of closing for two reactive sites along the chain and the shape of the loop formed by closing. In addition, intrachain hydrodynamic interactions are found to affect the diffusivity of circular chains compared to linear chains, in accord with experimental observations. We also consider the dynamics of chain closing under strong slit-like confinement as a function of slit height. [Preview Abstract] |
Thursday, March 13, 2008 4:42PM - 4:54PM |
W25.00010: Equilibrium Size Distribution of Twisted Biopolymer Bundles Gregory Grason, Robijn Bruinsma Using a continuum elastic model of hexagonal filament packing, we demonstrate that molecular-scale chirality strongly affects the equilibrium properties of aggregates, or bundles, of biopolymers, such as DNA and F-actin. We show that biopolymers tend to form bundles with long-range, chiral stress patterns, twisting or braiding helically around the central bundle axis. Due to the build-up of elastic stress on the outer surface, the cohesive energy of chiral filament bundles has a non-monotonic dependence on filament number. As a consequence, we demonstrate for two cases--bundles with 1) columnar-hexagonal order and 2) columnar-solid order--that a stable phase of dispersed bundles is thermodynamically stable below the point of bulk condensation and below a critical surface energy for the bundle exterior. This work suggests that the large characteristic radius biopolymer bundles observed in {\it in vitro} studies of is not a product of some mysterious long-range force or kinetic limitations of bundle growth, but rather in-plane elastic stresses which result from the local preference for the chiral packing of filaments. [Preview Abstract] |
Thursday, March 13, 2008 4:54PM - 5:06PM |
W25.00011: The Dependence of Actin Filament Assembly on Linking Agent Concentration Lam Nguyen, Qi Wang, Wei Yang, Linda Hirst This experimental and computational study focused on the properties of actin filament bundles and networks induced by the actin filament cross-linker, $\alpha $-actinin. Structural properties of actin filament networks linked by the $\alpha $-actinin protein were studied experimentally by using confocal microscopy. We varied the concentrations of actin and linking agents to study their effects on the properties of the bundles and networks. The study showed that the molar ratio of $\alpha $-actinin to actin played an important role in the properties of the network structure, determining the branching frequency of the bundles. An experimentally guided simulation based on the $\alpha $-actinin/actin filament system was carried out using CHARMM to attempt to replicate the features of the real system and therefore to study the physics behind the actin filament assembly process in different regimes. [Preview Abstract] |
Thursday, March 13, 2008 5:06PM - 5:18PM |
W25.00012: Dimensional percolation of sheared nano-rod dispersions and consequences for highly anisotropic property tensors M. Gregory Forest, Xiaoyu Zheng, Ruhai Zhou, Richard Vaia The Doi-Hess theory for flowing nano-rod dispersion yields orientational probability distribution functions for the nano-particle phase in flow-processed thin films. These numerical databases for variable shear rate, particle aspect ratio and volume fraction are then combined with a Monte Carlo algorithm to populate sheared dispersions. Nano-rod cluster statistics are then computed to determine percolation thresholds, which yield transitions from zero to one, two and three dimensional percolating paths. Finally, effective property enhancements are computed which include standard volume-averaged homogenization and percolation cluster statistics. [Preview Abstract] |
Thursday, March 13, 2008 5:18PM - 5:30PM |
W25.00013: Polymer Crystallization-Driven Gelation of an Ionic Liquid David Hoagland, John Harner Polyethylene glycol dissolves in the room temperature ionic liquid 1-ethyl-3-methylimidiazolium ethyl sulfate [EMIM][EtSO4] when heated above about 60C, the neat polymer's melting temperature. At typical polymer molecular weight and concentration, the homogeneous, slightly viscous solution solidifies during subsequent cooling, forming a semitransparent gel. For example, a 5 wt. percent solution of 6000 MW polymer produces a gel with modulus exceeding 1 KPa at 45C; cooled further to room temperature, the gel's modulus rises to a temperature-insensitive plateau of over 100 KPa. By DSC, rheology, and optical microscopy, gelation of the liquid is traced to kinetically frustrated polymer crystallization, a phenomenon previously reported for many pairings of crystallizable polymer and traditional solvent. Polarized optical microscopy reveals nucleation and growth of fibrillar polymer crystals during cooling, and these crystals, here with largest dimenions of tens to hundreds of microns, act as junction points. Melting is at a temperature higher than for gelation. Surprisingly, gelation can occur even when the starting polymer concentration is an order of magnitude below coil overlap. [EMIM][EtSO4] is hygroscopic, and with water uptake, the modulus drops. [Preview Abstract] |
Thursday, March 13, 2008 5:30PM - 5:42PM |
W25.00014: Avalanches, hardening and softening in dense cross-linked actin networks Jan Astrom, Sunil Kumar, Ilpo Vattulainen, Mikko Karttunen Actin filament networks enable the cytoskeleton to adjust to internal and external forcing. These active networks can adapt to changes by dynamically adjusting their crosslinks. Here, we study actin filaments as elastic fibers having finite dimensions. We employ a full three-dimensional model to study the elastic properties of actin networks by computer simulations. We model a dense actin network with the crosslinks being approximately 1$\mu$m apart. The results show that dense actin networks, without any pre-straining, are characterized by (a) strain hardening without entropic elasticity, (b) 'viscotic' hysteresis in the case of strong crosslinks, (c) avalanches of crosslink slippage leading to strain softening in the case of breakable crosslinks, and (d) spontaneous formation of stress fibers in the case of active crosslink formation and destruction. We will discuss the relation to recent experimental observations. [Preview Abstract] |
Thursday, March 13, 2008 5:42PM - 5:54PM |
W25.00015: Crystal aggregation in kidney stones; a polymer aggregation problem? J. Wesson, A. Beshensky, P. Viswanathan, W. Zachowicz, J. Kleinman Kidney stones most frequently form as aggregates of calcium oxalate monohydrate (COM) crystals with organic layers between them, and the organic layers contain principally proteins. The pathway leading to the formation of these crystal aggregates in affected people has not been identified, but stone forming patients are thought to have a defect in the structure or distribution of urinary proteins, which normally protect against stone formation. We have developed two polyelectrolyte models that will induce COM crystal aggregation \textit{in vitro}, and both are consistent with possible urinary protein compositions. The first model was based on mixing polyanionic and polycationic proteins, in portions such that the combined protein charge is near zero. The second model was based on reducing the charge density on partially charged polyanionic proteins, specifically Tamm-Horsfall protein, the second most abundant protein in urine. Both models demonstrated polymer phase separation at solution conditions where COM crystal aggregation was observed. Correlation with data from other bulk crystallization measurements suggest that the anionic side chains form critical binding interactions with COM surfaces that are necessary along with the phase separation process to induce COM crystal aggregation. [Preview Abstract] |
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