@article {575, title = {Coupling Field Theory with Mesoscopic Dynamical Simulations of Multicomponent Lipid Bilayers}, journal = {Biophys J}, volume = {87}, number = {5}, year = {2004}, note = {McWhirter, J Liam Ayton, Gary Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2004 Nov;87(5):3242-63. Epub 2004 Sep 3.}, pages = {3242-63}, abstract = {

A method for simulating a two-component lipid bilayer membrane in the mesoscopic regime is presented. The membrane is modeled as an elastic network of bonded points; the spring constants of these bonds are parameterized by the microscopic bulk modulus estimated from earlier atomistic nonequilibrium molecular dynamics simulations for several bilayer mixtures of DMPC and cholesterol. The modulus depends on the composition of a point in the elastic membrane model. The dynamics of the composition field is governed by the Cahn-Hilliard equation where a free energy functional models the coupling between the composition and curvature fields. The strength of the bonds in the elastic network are then modulated noting local changes in the composition and using a fit to the nonequilibrium molecular dynamics simulation data. Estimates for the magnitude and sign of the coupling parameter in the free energy model are made treating the bending modulus as a function of composition. A procedure for assigning the remaining parameters in the free energy model is also outlined. It is found that the square of the mean curvature averaged over the entire simulation box is enhanced if the strength of the bonds in the elastic network are modulated in response to local changes in the composition field. We suggest that this simulation method could also be used to determine if phase coexistence affects the stress response of the membrane to uniform dilations in area. This response, measured in the mesoscopic regime, is already known to be conditioned or renormalized by thermal undulations.

}, keywords = {Chemical *Models, Computer Simulation Lipid Bilayers/*chemistry Macromolecular Substances/chemistry *Membrane Fluidity *Models, Molecular Molecular Conformation Motion Phase Transition Surface Properties}, doi = {10.1529/biophysj.104.045716}, author = {McWhirter, J. L. and G. Ayton and G. A. Voth} } @article {365, title = {Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers}, journal = {Biophys J}, volume = {83}, number = {6}, year = {2002}, note = {Ayton, Gary Voth, Gregory A GM 63796/GM/NIGMS NIH HHS/United States Evaluation Studies Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2002 Dec;83(6):3357-70.}, pages = {3357-70}, abstract = {

A lipid bilayer is modeled using a mesoscopic model designed to bridge atomistic bilayer simulations with macro-scale continuum-level simulation. Key material properties obtained from detailed atomistic-level simulations are used to parameterize the meso-scale model. The fundamental length and time scale of the meso-scale simulation are at least an order of magnitude beyond that used at the atomistic level. Dissipative particle dynamics cast in a new membrane formulation provides the simulation methodology. A meso-scale representation of a dimyristoylphosphatidylcholine membrane is examined in the high and low surface tension regimes. At high surface tensions, the calculated modulus is found to be slightly less than the atomistically determined value. This result agrees with the theoretical prediction that high-strain thermal undulations still persist, which have the effect of reducing the value of the atomistically determined modulus. Zero surface tension simulations indicate the presence of strong thermal undulatory modes, whereas the undulation spectrum and the calculated bending modulus are in excellent agreement with theoretical predictions and experiment.

}, keywords = {*Algorithms Cell Membrane/chemistry Computer Simulation Dimyristoylphosphatidylcholine/chemistry Elasticity Lipid Bilayers/*chemistry *Membrane Fluidity Membranes, Artificial *Models, Chemical *Models, Mechanical Surface Tension, Molecular Molecular Conformation Molecular Structure Motion Stress}, doi = {10.1016/S0006-3495(02)75336-8}, author = {G. Ayton and G. A. Voth} } @article {364, title = {Calculating the Bulk Modulus for a Lipid Bilayer with Nonequilibrium Molecular Dynamics Simulation}, journal = {Biophys J}, volume = {82}, number = {3}, year = {2002}, note = {Ayton, Gary Smondyrev, Alexander M Bardenhagen, Scott G McMurtry, Patrick Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2002 Mar;82(3):1226-38.}, pages = {1226-38}, abstract = {

Nonequilibrium molecular dynamics (NEMD) computer simulations are used to calculated the bulk modulus for a dimyristoylphosphatidylcholine bilayer. A methodology is developed whereby NEMD can be effectively used to calculate material properties for complex systems that undergo long time-scale conformational changes. It is found that the bulk modulus upon expansion from a zero stress state agrees well with experimental estimates. However, it is also found that the modulus upon contraction from a zero stress state is larger. From a molecular perspective, it is possible to explain this phenomena by examining the molecular origins of the pressure response. The finding that the two moduli are not equal upon compression and expansion is in apparent contradiction to osmotic stress experiments where the area modulus was found to be the same upon expansion and contraction. This issue is addressed.

}, keywords = {Algorithms Computer Simulation Lipid Bilayers/*chemistry Osmosis Protein Conformation Temperature Time Factors Water/chemistry}, doi = {10.1016/S0006-3495(02)75479-9}, author = {G. Ayton and Smondyrev, A. M. and Bardenhagen, S. G. and P. McMurtry and G. A. Voth} } @article {363, title = {Interfacing Molecular Dynamics and Macro-scale Simulations for Lipid Bilayer Vesicles}, journal = {Biophys J}, volume = {83}, number = {2}, year = {2002}, note = {Ayton, Gary Smondyrev, Alexander M Bardenhagen, Scott G McMurtry, Patrick Voth, Gregory A United States Biophysical journal Biophys J. 2002 Aug;83(2):1026-38.}, pages = {1026-38}, abstract = {

A continuum-level model for a giant unilamellar vesicle (GUV) is bridged to a corresponding atomistic model of a dimyristoylphosphatidylcholine (DMPC) bilayer at various cholesterol concentrations via computation of the bulk modulus. The bulk modulus and other microscopically determined parameters are passed to a continuum-level model operating in time- and length-scales orders of magnitude beyond that which is accessible by atomistic-level simulation. The continuum-level simulation method used is the material point method (MPM), and the particular variation used here takes advantage of the spherical nature of many GUVs. An osmotic pressure gradient due to a solvent concentration change is incorporated into the continuum-level simulation, resulting in osmotic swelling of the vesicle. The model is then extended to treat mixtures of DMPC and cholesterol, where small domains of different composition are considered.

}, keywords = {Algorithms Biophysical Phenomena Biophysics Carbon/chemistry Cholesterol/chemistry Computer Simulation Dimyristoylphosphatidylcholine/chemistry Lipid Bilayers/*chemistry Membranes/chemistry Models, Statistical Osmosis Protein Structure, Tertiary Time Factors}, doi = {10.1016/S0006-3495(02)75228-4}, author = {G. Ayton and Smondyrev, A. M. and Bardenhagen, S. G. and P. McMurtry and G. A. Voth} } @article {361, title = {Interfacing Continuum and Molecular Dynamics: An Application to Lipid Bilayers}, journal = {J. Chem. Phys.}, volume = {114}, year = {2001}, pages = {6913-6924}, doi = {10.1063/1.1356001}, author = {G. Ayton and S Bardenhagen and P. McMurtry and D. Sulsky and G. A. Voth} } @article {362, title = {Interfacing Molecular Dynamics with Continuum Dynamics in Computer Simulation: Toward an Application to Biological Membranes}, journal = {IBM J. Res. Dev.}, volume = {45}, year = {2001}, pages = {417-426}, doi = {10.1147/rd.453.0417}, author = {G. Ayton and S Bardenhagen and P. McMurtry and D. Sulsky and G. A. Voth} }