@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 {648, title = {Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane}, journal = {Biophys J}, volume = {82}, number = {3}, year = {2002}, note = {Smondyrev, Alexander M Voth, Gregory A GM53148/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):1460-8.}, pages = {1460-8}, abstract = {

The structural and dynamical properties of a hydrated proton near the surface of DMPC membrane were studied using a molecular dynamics simulation. The proton transport between water molecules was modeled using the second generation multistate empirical valence bond model. The proton diffusion was found to be inhibited at the membrane surface. The potential of mean force for the proton adsorption to the membrane surface and its release back into the bulk water was also determined, yielding a small barrier in each direction. An efficient algorithm for Ewald summation calculations for the multistate empirical valence bond model is also introduced.

}, keywords = {Adsorption Algorithms Biological Transport Cell Membrane/*metabolism Diffusion Dimyristoylphosphatidylcholine/chemistry Lipids/chemistry Models, Molecular Models, Statistical Phospholipids/*chemistry *Protons Water/chemistry}, doi = {10.1016/S0006-3495(02)75500-8}, author = {Smondyrev, A. M. and G. A. Voth} } @article {647, title = {Molecular Dynamics Simulation of Proton Transport through the Influenza A Virus M2 Channel}, journal = {Biophys J}, volume = {83}, number = {4}, year = {2002}, note = {Smondyrev, Alexander M Voth, Gregory A GM-53148/GM/NIGMS NIH HHS/United States Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2002 Oct;83(4):1987-96.}, pages = {1987-96}, abstract = {

The structural and dynamical properties of a solvated proton in the influenza A virus M2 channel are studied using a molecular dynamics (MD) simulation technique. The second-generation multi-state empirical valence bond (MS-EVB2) model was used to describe the interaction between the excess proton and the channel environment. Solvation structures of the excess proton and its mobility characteristics along the channel were determined. It was found that the excess proton is capable of crossing the channel gate formed by the ring of four histidine residues even though the gate was only partially open. Although the hydronium ion itself did not cross the channel gate by traditional diffusion, the excess proton was able to transport through the ring of histidine residues by hopping between two water molecules located at the opposite sides of the gate. Our data also indicate that the proton diffusion through the channel may be correlated with the changes in channel conformations. To validate this observation, a separate simulation of the proton in a "frozen" channel has been conducted, which showed that the proton mobility becomes inhibited.

}, keywords = {Biological Transport Biophysical Phenomena Biophysics Carbon/chemistry Computer Simulation Diffusion Dimyristoylphosphatidylcholine/chemistry Influenza A virus/*metabolism Ion Channel Gating Ion Channels/chemistry/physiology Lipid Bilayers/*chemistry Mode, Molecular Models, Statistical Protons Time Factors Viral Matrix Proteins/*chemistry/*physiology}, doi = {10.1016/S0006-3495(02)73960-X}, author = {Smondyrev, A. M. and G. A. Voth} }