Bulletin of the American Physical Society
11th Annual Meeting of the Northwest Section of APS
Volume 54, Number 6
Thursday–Saturday, May 14–16, 2009; Vancouver, BC, Canada
Session B3: Condensed Matter Physics II: Soft Matter/Biophysics |
Hide Abstracts |
Chair: Barbara Frisken, Simon Fraser University Room: Irving Barber Learning Center 155 |
Friday, May 15, 2009 1:00PM - 1:36PM |
B3.00001: Relaxation and deformation in glassy materials Invited Speaker: Amorphous solids such as glassy polymers, colloidal glasses, and physical gels are invariably characterized by slow dynamics. The inability to reach equilibrium on experimental timescales is due to the many geometric constraints that the molecules experience in dense, "jammed" configurations. The ensuing relaxation or aging processes modify material properties such as creep compliance and yield stress. Our understanding of how such amorphous materials yield and flow under the application of stress or strain is much less developed than in crystals, where well-defined defects such as dislocations are the carriers of plastic deformation. This talk will give an overview of recent work in my group, where we use molecular simulations and phenomenological models to gain insight into the microscopic origins of elastoplastic behavior of disordered solids. We will show how particle mobility controls plastic flow, and how aging appears to be reduced in solids under load. Interesting modifications to the structural relaxations can be achieved by adding nanoparticle fillers. By decomposing single particle trajectories into intermittent hopping events, we will obtain a statistical description of the molecular rearrangements in terms of a continuous time random walk, which provides insight into the origin of aging at the molecular level. [Preview Abstract] |
Friday, May 15, 2009 1:36PM - 1:48PM |
B3.00002: A Multiscale Modeling Procedure for Simulations of Polymer Melts James McCarty, Ivan Lyubimov, Marina Guenza One of the major ambitions in developing a coarse-grained model for macromolecular fluids is to provide a rigorous procedure to reintroduce the chemical details of the system. Such a scheme allows for the development of a multiscale modeling protocol. Here, a novel multiscaling scheme is presented that uses a hierarchical approach of combining mesoscopic and united atom molecular dynamic (UA MD) simulations. In this way, the multiple length and time scales of relevance to complex fluids are effectively bridged. The method is applied to various polymer melts of different architectures and chain lengths, and results are compared directly to UA MD simulations over the entire length-scale range of interest. It is shown that this approach reproduces pair correlation functions at a high computational efficiency, providing a method of extending simulations to very large length and time scales. Since the approach is analytical, it is applicable to a broad range of polymer systems. [Preview Abstract] |
Friday, May 15, 2009 1:48PM - 2:00PM |
B3.00003: Investigating the Microstructure of Carbopol by Light Scattering David Lee, Arthur Bailey, Barbara Frisken Carbopol, a family of cross-linked acrylic acid-based polymers and a well-known thickener used in personal care, household and industrial products, is often used as a model yield-stress fluid because it is transparent and its rheological properties can be precisely tuned by sample preparation conditions. Carbopol dispersions behave as an elastic solid but they will flow when the applied stress exceeds a sample-dependent yield value. Both the yield stress phenomena and the range of potential applications recommend study of the microscopic structure and properties of yield stress fluids as this will lead to a fundamental understanding of this behaviour. Light scattering experiments investigating Carbopol ETD2050 dispersed in water have revealed that the Carbopol microstructure consists of a highly cross-linked inner region surrounded by a lightly cross-linked outer region. Experiments also show that the length scales and mass fractal dimension depend on the sample concentration and pH. [Preview Abstract] |
Friday, May 15, 2009 2:00PM - 2:12PM |
B3.00004: Rescaling the Molecular Dynamics Simulation of Coarse-Grained Polymer Liquids Ivan Lyubimov, Marina Guenza Due to the limitations of theoretical approaches and computer simulations, coarse-graining of polymer systems facilitates the investigation of their dynamical and structural properties. A multiscaling description provides information at the whole range of time and length scales at which relevant phenomena take place. We use our analytical procedure to coarse-grain polymer liquids and produce mesoscale molecular dynamics simulations. Mesocalse simulations enable much longer times to be reached than in united atom simulations. However, the accelerated dynamics in mesoscale simulations need to be rescaled in order to correctly describe real time processes. We propose a rescaling procedure for mesoscale simulations of polymer liquids to allow for comparison it with united atom simulations. As a part of the rescaling procedure the friction coefficients for units of both mesoscale and united atom simulations were derived from the first principles. The rescaling procedure enhances the multiscaling modeling approach, substantially saving computational time. [Preview Abstract] |
Friday, May 15, 2009 2:12PM - 2:24PM |
B3.00005: Changes in the free energy of a protein in the presence of osmolytes Shirin Hadizadeh Changes in the free energy of a protein in the presence of osmolytes have their origin in the interaction between residues of the protein finding themselves in a sea of crowding agents, namely the depletion interaction. This interaction was first described by Asakura and Oosawa who showed that there is an osmotic imbalance pushing the particles together if they are within a distance from each other. Here we first derive the free energy of a protein as a function of its ``proper size'' and then analyze the changes to it as we add osmoltes. [Preview Abstract] |
Friday, May 15, 2009 2:24PM - 2:36PM |
B3.00006: Coarse-grained molecular dynamics simulations of DNA using ellipsoids Alex Morriss-Andrews We are developing a coarse-grained computational model of DNA using ellipsoids, and simulating the DNA using molecular dynamics simulations. We represent the bases using the RE2 potential, as these molecules are better represented by ellipsoids than spheres. Our model gives greater resolution than traditional coarse-grained models but requires less computational power than all-atom simulations. [Preview Abstract] |
Friday, May 15, 2009 2:36PM - 2:50PM |
B3.00007: BREAK
|
Friday, May 15, 2009 2:50PM - 3:02PM |
B3.00008: Identifying Unstable Regions of Proteins Involved in Misfolding Diseases Will Guest, Neil Cashman, Steven Plotkin Protein misfolding is a necessary step in the pathogenesis of many diseases, including Creutzfeldt-Jakob disease (CJD) and familial amyotrophic lateral sclerosis (fALS). Identifying unstable structural elements in their causative proteins elucidates the early events of misfolding and presents targets for inhibition of the disease process. An algorithm was developed to calculate the Gibbs free energy of unfolding for all sequence-contiguous regions of a protein using three methods to parameterize energy changes: a modified G\={o} model, changes in solvent-accessible surface area, and all-atoms molecular dynamics. The entropic effects of disulfide bonds and post-translational modifications are treated analytically. It incorporates a novel method for finding local dielectric constants inside a protein to accurately handle charge effects. We have predicted the unstable parts of prion protein and superoxide dismutase 1, the proteins involved in CJD and fALS respectively, and have used these regions as epitopes to prepare antibodies that are specific to the misfolded conformation and show promise as therapeutic agents. [Preview Abstract] |
Friday, May 15, 2009 3:02PM - 3:14PM |
B3.00009: Length Dependent Force Characteristics of Coiled-Coils Sara Sadeghi, Eldon Emberly Coiled-coil domains play an important role in mediating protein-protein interactions in biology. Each helix in a coiled-coil has a hydrophobic strip that winds around it, and it is the packing of these hydrophobic residues that leads to the superhelical structure. A recent continuum model [1] showed that the correspondence between the chirality of the pack to that of the underlying hydrophobic strip comes about because of the internal deformation energy associated with each helix in forming the superhelix. Here we use a coarse-grained atomistic model for coiled coils to examine the dependency of super-helical formation on the deformation energy. We then explore the force-extension properties of these model coiled-coils as a function helix length, and find surprising length dependence, with certain periodic lengths being stable to much higher pulling forces. \\[4pt] [1] S. Neukirch, A. Goriely and A.C. Hausrath, PRL, 100, 038105 (2008). [Preview Abstract] |
Friday, May 15, 2009 3:14PM - 3:26PM |
B3.00010: Using Optical Tweezers to Probe the Elasticity of Short Molecules Benjamin P.B. Downing, Astrid van der Horst, Ming Miao, Fred W. Keeley, Nancy R. Forde Stretching and relaxing single protein molecules provides quantitative information on their elasticity and other mechanical properties. Optical tweezers can be used to perform such experiments, but require the ends of the protein to be chemically tethered to polystyrene beads used to manipulate the molecule and measure its response. Our goal is to use this method to study the human structural protein elastin, whose mechanical properties are directly related to its physiological function. Elastin's contour length is approximately 170 nm, so the trapped beads must be manipulated at separations small compared to their micron dimensions. The close proximity of the beads introduces experimental complications, primarily the result of optical and hydrodynamic interactions. We discuss these complications along with our efforts to minimize and account for them in our measurements. We then show preliminary evidence addressing a critical question of whether elastin has higher order structure, where our results instead suggest that it exists in solution as a random polymer chain. [Preview Abstract] |
Friday, May 15, 2009 3:26PM - 3:38PM |
B3.00011: Melting Behaviour of Cell Death Lipids Sherry Leung, Jesus Sot, Felix Goni, Jenifer Thewalt Sphingomyelin is a major lipid constituent of mammalian cell plasma membranes. It is converted into ceramide during programmed cell death. It is hypothesized that this conversion induces a structural change in membranes that is responsible for downstream signaling. To characterize these structural changes, deuterium nuclear magnetic resonance spectroscopy is used to create a concentration-temperature phase diagram of palmitoyl sphingomyelin:ceramide multilamellar vesicles in excess water between 0-40 mol\% ceramide and 25-80$^{\circ}$C. The two lipids are fully miscible at high temperatures and at 40 mol\% ceramide. A variety of solid-liquid coexistence phase behavior is observed at lower concentrations. With increasing ceramide content, a gel phase is observed at progressively higher temperatures, implying that at physiological temperature, ceramide may increase the gel phase propensity of cell membranes. [Preview Abstract] |
Friday, May 15, 2009 3:38PM - 3:50PM |
B3.00012: The Effect of Cholesterol on the Partitioning of 1-Octanol into POPC Lipid Bilayers Roja Zakariaee, Barbara Frisken The exact mechanism of anesthesia is not yet completely understood. One common type of anesthetics is n-alkanol, a subgroup of hydrocarbon alcohols. In this work the partition coefficient of 1-octanol into liposomes containing both: 1-palmitoyl-2-oleoyl-sn-3-glycero-phosphatidylcholine (POPC), a semi-unsaturated lipid, and cholesterol was measured as a function of cholesterol molar concentration. This study was carried out by means of isothermal titration calorimetry, a calorimetric tool that measures heats of interactions. Our results indicate that the partition coefficient of 1-octanol in POPC bilayers at 45\r{ }C increases with increasing concentration of cholesterol. In contrast, previous studies have shown that the partition coefficient of alkanols into bilayers containing saturated lipids decreases with increasing cholesterol concentration. This may be due to the fact that bilayers composed of saturated lipids are more tightly packed than those composed of unsaturated lipids. Our results could therefore open a new window on different behaviors of these two types of lipid bilayers when interacting with n-alkanols. [Preview Abstract] |
Friday, May 15, 2009 3:50PM - 4:02PM |
B3.00013: The Physical Properties of Sphingomyelin/Cholesterol Membranes: a Deuterium NMR Study Amirmohamad Keyvanloo, Mehran Shaghaghi, Martin Zuckermann, Jenifer Thewalt We have used $^{2}$H NMR to study the effect of cholesterol on N-palmitoyl(D31)-D-erythro-sphingosylphosphorylcholine (PSM) membranes. NMR spectra were taken as a function of temperature and cholesterol concentration. The constructed phase diagram exhibits both solid-ordered (\textbf{so}) + liquid-ordered (\textbf{lo}) and liquid-disordered (\textbf{ld}) + \textbf{lo} phase coexistence regions with a clear three-phase line at 37$^{\circ}$C. The \textbf{ld} + \textbf{lo} region was characterized by examining the cholesterol dependence of the width of resolved peaks in the depaked spectra, as well as the average spectral width (M$_{1})$, at a given temperature. The \textbf{so} + \textbf{lo} region was defined using spectral subtraction. Analogous experiments were done using 1-palmitoyl,2-palmitoyl(D31)-\textit{sn}-glycero-3-phosphocholine (DPPC)/cholesterol membranes in order to carefully compare the data obtained using palmitoyl chains which have similar ``kinked'' conformations. The three-phase line in sn-2 perdeuterated DPPC/cholesterol is at 39$^{\circ}$C. The PSM/cholesterol membrane is significantly more ordered than the DPPC/cholesterol membrane in the liquid crystalline phase. This should be compared to the difference between the cholesterol-free membranes at, where the average order of PSM is more than that of DPPC. [Preview Abstract] |
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