Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session Y21: Focus Session: Multiscale Analysis in Biology: Computation |
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Sponsoring Units: DBP Chair: Robert Eisenberg, Rush Medical Center Room: LACC 409A |
Friday, March 25, 2005 11:15AM - 11:51AM |
Y21.00001: Hierarchy of computational electronics approaches for multiscale charge transport simulation Invited Speaker: Semiconductor device simulation has been developed over several decades resulting in a hierarchy of computational electronics tools and approaches that are uniquely powerful for treating self-consistently the transport of charged particles. These methodologies, originally conceived for electronic transport in solid state systems, can be extended to other fields, particularly ionic transport in aqueous solutions, as found in biological systems. This talk will outline the hierarchy and the most important features of these transport model and discuss the new challenges encountered in treating general molecular systems as devices. Emphasis will be placed on discussing the approaches which are more suitable for future practical applications for engineering and design of molecular systems and devices, including multi-scale problems. [Preview Abstract] |
Friday, March 25, 2005 11:51AM - 12:03PM |
Y21.00002: Multiscale Modeling of Heterogeneous Lipid Bilayers Roland Faller, Sandra Bennun-Serrano, Allison Dickey The first line of defense for a cell against intrusive molecules is the membrane which must be resilient to prevent unwanted molecules from passing through as a change in the intracellular ion balance could be detrimental. Experimentally, it has been shown that as chain length and concentration of alcohols near a membrane increase, the area per lipid expands, increasing the likelihood of permeation. Additionally, there is evidence for pattern formation in cell membranes due to the presence of various lipids. These patterns or rafts are believed to play important roles in cell signaling. Here, we use MD to study the interactions between alcohols and pure lipid bilayers as well as pattern formation in mixed membranes using atomistic and coarse-grained models. We characterize the effect of alcohol chain-length and concentration on the lipid bilayer through area per head group, order parameter, and density profile. We also examine the effects of lipid-alcohol interactions on membrane curvature with the CG model and find satisfactory system representation. We use a mixture of DLPC and DSPC as model system for phase separation. Different concentrations and temperatures are used to reproduce phase transitions. We obtain agreement with experiments for area per lipid head group and deuterium order parameter. At high DSPC concentrations phase separation into a gel and liquid state is found. Simulations confirm that increasing DLPC concentrations lower the transition temperature. [Preview Abstract] |
Friday, March 25, 2005 12:03PM - 12:39PM |
Y21.00003: MultiScale, Renomalization, and Biology Invited Speaker: Is biology renormalizable and amenable to multiscale simulation methods? Multiscale simulations provide a comprehensive computational model, spanning many length and time scales, starting with the characteristic molecular assemblies, and connecting them to meso scale and finally macro scale material properties. A hierarchy of overlapping calculations in space and time are performed. Parameters are input to each calculation based on the calculations from a smaller length and time scale and checked with calculations at a larger length scale. In this lecture examples will include the properties of proteins in an ultracentrifuge and the elastic properties of DNA from the atomic to the material length scales. These problems have an explicit coupling of length-scales from the microscopic correlations between molecules in the assembly to the shape of the resulting assembly to the continuum elastic properties. The results are tested against experiments and checked for consistency with known thermodynamic and structural data. The question of the renormalizablility of biology is shown to be linked to intrinsic complexity in space and time. [Preview Abstract] |
Friday, March 25, 2005 12:39PM - 12:51PM |
Y21.00004: Flexible lipid bilayers in implicit solvent Grace Brannigan, Peter Phillips, Frank Brown A minimalist simulation model for lipid bilayers is presented. Each lipid is represented by a flexible chain of beads in implicit solvent. The hydrophobic effect is mimicked through an intermolecular pair potential localized at the ``water''/hydrocarbon tail interface. This potential guarantees realistic interfacial tensions for lipids in a bilayer geometry. Lipids self assemble into bilayer structures that display fluidity and elastic properties consistent with experimental model membrane systems. Varying molecular flexibility allows for tuning of elastic moduli and area/molecule over a range of values seen in experimental systems. [Preview Abstract] |
Friday, March 25, 2005 12:51PM - 1:03PM |
Y21.00005: Simulation of lipid bilayers using coarse grained methods Mark Stevens There are many important biological processes involving lipid bilayers on times scales beyond that accessible by atomistic simulations. We have developed coarse-grained, bead-spring models of lipid molecules to treat membrane fusion, domain formation and the general physical characteristics of lipid bilayers. A key aspect of these coarse-grained models is that the liquid nature of a bilayer is explicitly present in the simulations; the lipids diffuse far beyond their neighbors in contrast to atomistic simulations. With these models self-assembly into a bilayer starting from a random configuration of lipids and solvent is readily simulated. We have performed extensive simulations to characterize these lipid models in single component lipid bilayers. For a variety of tail lengths, the area per lipid as a function of temperature has been calculated; the liquid-gel transition has been characterized. Models have been developed for a variety of lipids including double bonds in the lipid tails. Simulation results will be presented for fusion and domain formation. [Preview Abstract] |
Friday, March 25, 2005 1:03PM - 1:15PM |
Y21.00006: Efficient tunable generic model for self-assembling fluid bilayer membranes Markus Deserno, Ira R. Cooke, Kurt Kremer We present a new model for the simulation of generic lipid bilayers in the mesoscopic regime (between a few nanometers and many tens of nanometers), which is very robust, versatile, and extremely efficient, since it avoids the need for an embedding solvent. Based entirely on simple pair potentials, it features a wide region of unassisted self assembly into fluid bilayers without the need for careful parameter tuning. The resulting membranes display the correct continuum elastic behavior with bending constants in the experimentally relevant range. It can be readily used to study events like bilayer fusion, bilayer melting, lipid mixtures, rafts, and protein-bilayer interactions. [Preview Abstract] |
Friday, March 25, 2005 1:15PM - 1:27PM |
Y21.00007: Membrane Geometry and Forces Eric Peterson, Rob Phillips, Paul Wiggins, Feng Feng, William Klug Recent advances in cryo-electron microscopy have enabled biologists to reconstruct detailed three-dimensional structures of cellular-scale biological systems via tomography. In particular, tomography can be exploited to capture lipid bilayer membrane conformations of membrane bound organelles and membrane-mediated cellular functions such as transport, mobility and viral budding. We propose to exploit the observed membrane geometry to measure the forces applied on submicron length scales by the protein machines responsible for cellular function. We discuss the computational technique and present preliminary in vitro experimental results for liposomes. [Preview Abstract] |
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Y21.00008: On the translocation of stiff chains Roya Zandi, William Gelbart, Joseph Rudnick, David Reguera We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the length of the chain inside, for different concentrations of binding particles. As a consequence of the interactions with these particles, the chain experiences a net force along its length whose calculated value from the simulations accounts for the velocity at which it enters the cell. This force can in turn be obtained from the solution of a generalized diffusion equation incorporating an effective Langmuir adsorption free energy for the chain plus binding particles. These results suggest a role of binding particles in the translocation process which is in general quite different from that of a Brownian ratchet. Furthermore, non-equilibrium effects contribute significantly to the dynamics, \emph{e.g.}, the chain often enters the cell faster than particle binding can be saturated, resulting in a force several times smaller than the equilibrium value. [Preview Abstract] |
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