@article {368, title = {Hierarchical Coarse-graining Strategy for Protein-Membrane Systems to Access Mesoscopic Scales}, journal = {Faraday Disc. Chem. Soc.}, volume = {144}, year = {2010}, pages = {347{\textendash}357}, doi = {10.1039/B901996K}, author = {Ayton, G. S. and Lyman, E. and G. A. Voth, {\textquotedblleft}{\textquotedblright}, 144, (2010).} } @article {380, title = {Multiscale Computer Simulation of the Immature HIV-1 Virion}, journal = {Biophys. J.}, volume = {99}, year = {2010}, pages = {2757{\textendash}2765}, doi = {10.1016/j.bpj.2010.08.018}, author = {Ayton, G. S. and G. A. Voth} } @article {381, title = {Multiscale Simulation of Protein Mediated Membrane Remodeling}, journal = {Seminars in Cell and Developmental Biology}, volume = {21}, year = {2010}, pages = {357-362}, doi = {10.1016/j.semcdb.2009.11.011}, author = {Ayton, G. S. and G. A. Voth} } @article {520, title = {Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-grained Analysis}, journal = {Biophys. J.}, volume = {98}, year = {2010}, pages = {18-26}, doi = {10.1016/j.bpj.2009.09.049}, author = {Krishna, V. and Ayton, G. S. and G. A. Voth} } @article {379, title = {A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales}, journal = {J. Phys. Chem. B}, volume = {113}, year = {2009}, pages = {4413-4424}, doi = {10.1021/jp8087868}, author = {Ayton, G. S. and G. A. Voth} } @article {434, title = {Membrane Binding by the Endophilin N-BAR Domain}, journal = {Biophys. J.}, volume = {97}, year = {2009}, pages = {2746-2753}, doi = {10.1016/j.bpj.2009.08.043}, author = {Cui, H. and Ayton, G. S. and G. A. Voth} } @article {369, title = {New Insights into BAR Domain Induced Membrane Remodeling}, journal = {Biophys. J.}, volume = {97}, year = {2009}, pages = {1616{\textendash}1625}, doi = {10.1016/j.bpj.2009.06.036}, author = {Ayton, G. S. and Lyman, E. and Krishna, V. and Swenson, R. D. and Mim, C. and Unger, V. and G. A. Voth} } @article {378, title = {Systematic Multiscale Simulation of Membrane Protein Systems}, journal = {Curr. Opin. Struct. Biol.}, volume = {19}, year = {2009}, pages = {138-144}, doi = {10.1016/j.sbi.2009.03.001}, author = {Ayton, G. S. and G. A. Voth} } @article {418, title = {Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems}, journal = {J. Chem. Theor. Comp.}, volume = {4}, year = {2008}, pages = {560-568}, doi = {10.1021/ct7003275}, author = {Ceotto, M. and Ayton, G. S. and G. A. Voth} } @article {583, title = {The Multiscale Coarse-graining Method I: A Rigorous Bridge between Atomistic and Coarse-grained Models}, journal = {J. Chem. Phys.}, volume = {128}, year = {2008}, pages = {244114}, doi = {10.1063/1.2938860}, author = {Noid, W. G. and Chu, J.-W. and Ayton, G. S. and Krishna, V. and Izvekov, S. and G. A. Voth and Das, A. and Andersen, H. C.} } @article {585, title = {The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models}, journal = {J. Chem. Phys.}, volume = {128}, year = {2008}, pages = {244115}, doi = {10.1063/1.2938857}, author = {Noid, W. G. and Liu, P. and Wang, Y. and Chu, J.-W. and Ayton, G. S. and Izvekov, S. and Andersen, H. C. and G. A. Voth} } @article {367, title = {Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior}, journal = {Current Topics in Membranes}, volume = {60}, year = {2008}, pages = {181-225}, doi = {10.1016/S1063-5823(08)00007-0}, author = {Ayton, G. S. and Izvekov, S. and Noid, W. G. and G. A. Voth} } @article {579, title = {Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility}, journal = {J Mol Biol}, volume = {365}, number = {2}, year = {2007}, note = {Mirijanian, Dina T Chu, Jhih-Wei Ayton, Gary S Voth, Gregory A 1S10 RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. England Journal of molecular biology J Mol Biol. 2007 Jan 12;365(2):523-34. Epub 2006 Oct 6.}, pages = {523-34}, abstract = {

Spectrin is an ubiquitous protein in metazoan cells, and its flexibility is one of the keys to maintaining cellular structure and organization. Both alpha-spectrin and beta-spectrin polypeptides consist primarily of triple coiled-coil modular repeat units, and two important factors that determine spectrin flexibility are the bending flexibility between two consecutive repeat units and the conformational flexibility of individual repeat units. Atomistic molecular dynamics (MD) simulations are used here to study double spectrin repeat units (DSRUs) from the human erythrocyte beta-spectrin (HEbeta89) and the chicken brain alpha-spectrin (CBalpha1617). From the results of MD simulations, a highly conserved Trp residue in the A-helix of most repeat units that has been suggested to be important in conferring stability to the coiled-coil structures is found not to have a significant effect on the conformational flexibility of individual repeat units. Characterization of the bending flexibility for two consecutive repeats of spectrin via atomistic simulations and coarse-grained (CG) modeling indicate that the bending flexibility is governed by the interactions between the AB-loop of the first repeat unit, the BC-loop of the second repeat unit and the linker region. Specifically, interactions between residues in these regions can lead to a strong directionality in the bending behavior of two repeat units. The biological implications of these finding are discussed.

}, keywords = {Amino Acid Sequence Humans Models, Amino Acid Spectrin/*chemistry, Molecular Protein Conformation *Repetitive Sequences}, doi = {10.1016/j.jmb.2006.10.003}, author = {D. T. Mirijanian and Chu, J. W. and Ayton, G. S. and G. A. Voth} } @article {429, title = {Emerging Methods for Multiscale Simulation of Biomolecular Systems}, journal = {Mol. Phys.}, volume = {105}, year = {2007}, pages = {167-175}, doi = {10.1080/00268970701256696}, author = {Chu, J. W. and Izvekov, S. and Ayton, G. S. and G. A. Voth} } @article {598, title = {Extending the Fluctuation Theorem to Describe Reaction Coordinates}, journal = {J Chem Phys}, volume = {126}, number = {5}, year = {2007}, note = {Paramore, Sterling Ayton, Gary S Voth, Gregory A Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The Journal of chemical physics J Chem Phys. 2007 Feb 7;126(5):051102.}, pages = {051102}, abstract = {

The fluctuation theorem describes the distribution of work done on small systems which have been pushed out of equilibrium in response to an external field. The theorem has recently been a subject of much interest for describing single-molecule experiments and simulations. In this communication, it is shown how the fluctuation theorem can be extended to describe fluctuations not only in the work done on a system, but also in a reaction coordinate. The extension explored in this work allows for a generalized derivation of Hummer and Szabo{\textquoteright}s expression (G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. 98, 3658 (2001)) for reconstructing the potential of mean force from nonequilibrium trajectories. The derivation demonstrates how implementation of this expression can be more easily facilitated. Atomistic simulations of a biomolecular system are presented which support these results.

}, keywords = {*Algorithms *Computational Biology *Computer Simulation Diffusion *Energy Transfer Models, Molecular Statistical Distributions Thermodynamics}, doi = {10.1063/1.2463306}, author = {S. Paramore and Ayton, G. S. and G. A. Voth} } @article {366, title = {Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation}, journal = {Biophys J}, volume = {92}, number = {10}, year = {2007}, note = {Ayton, Gary S Blood, Philip D Voth, Gregory A 5 R01 GM063796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States Biophysical journal Biophys J. 2007 May 15;92(10):3595-602. Epub 2007 Feb 26.}, pages = {3595-602}, abstract = {

Liposome remodeling processes (e.g., vesiculation and tubulation) due to N-BAR domain interactions with the lipid bilayer are explored with a multi-scale simulation approach. Results from atomistic-level molecular dynamics simulations of membrane binding to the concave face of N-BAR domains are used along with discretized mesoscopic field-theoretic simulations to examine how the spontaneous curvature fields generated by N-BAR domains result in membrane remodeling. It is found that tubulation can be generated by anisotropic N-BAR spontaneous curvature fields, whereas vesiculation is only observed with isotropic N-BAR spontaneous curvature fields at high density. The results of the multi-scale simulations provide insight into recent experimental observations.

}, keywords = {Binding Sites Computer Simulation Lipid Bilayers/*chemistry Liposomes/*chemistry *Membrane Fluidity *Models, Chemical *Models, Molecular Molecular Conformation Nerve Tissue Proteins/*chemistry/*ultrastructure Protein Binding Protein Structure, Tertiary}, doi = {10.1529/biophysj.106.101709}, author = {Ayton, G. S. and Blood, P. D. and G. A. Voth} } @article {584, title = {Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory}, journal = {J Phys Chem B}, volume = {111}, number = {16}, year = {2007}, note = {Noid, W G Chu, Jhih-Wei Ayton, Gary S Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States 5F32GM076839-02/GM/NIGMS NIH HHS/United States F32 GM076839-02/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States The journal of physical chemistry. B J Phys Chem B. 2007 Apr 26;111(16):4116-27. Epub 2007 Mar 30.}, pages = {4116-27}, abstract = {

A statistical mechanical framework elucidates the significance of structural correlations between coarse-grained (CG) sites in the multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105). If no approximations are made, then the MS-CG method yields a many-body multidimensional potential of mean force describing the interactions between CG sites. However, numerical applications of the MS-CG method typically employ a set of pair potentials to describe nonbonded interactions. The analogy between coarse-graining and the inverse problem of liquid-state theory clarifies the general significance of three-particle correlations for the development of such CG pair potentials. It is demonstrated that the MS-CG methodology incorporates critical three-body correlation effects and that, for isotropic homogeneous systems evolving under a central pair potential, the MS-CG equations are a discretized representation of the well-known Yvon-Born-Green equation. Numerical calculations validate the theory and illustrate the role of these structural correlations in the MS-CG method.

}, keywords = {*Models, Theoretical}, doi = {10.1021/jp068549t}, author = {Noid, W. G. and Chu, J. W. and Ayton, G. S. and G. A. Voth} } @article {373, title = {Multiscale Modeling of Biomolecular Systems: in Serial and in Parallel}, journal = {Curr Opin Struct Biol}, volume = {17}, number = {2}, year = {2007}, note = {Ayton, Gary S Noid, Will G Voth, Gregory A 5 F32 GM076839-02/GM/NIGMS NIH HHS/United States GM063796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. Review England Current opinion in structural biology Curr Opin Struct Biol. 2007 Apr;17(2):192-8. Epub 2007 Mar 23.}, pages = {192-8}, abstract = {

Considerable progress has been recently achieved in the multiscale modeling of complex biological processes. Multiscale models have now investigated the structure and dynamics of lipid membranes, proteins, peptides and DNA over length and time scales ranging from the atomic to the macroscopic. Serial multiscale methods that parameterize low-resolution coarse-grained models with data from high-resolution models have studied long time or length scale phenomena that cannot be investigated with atomically detailed models. Parallel multiscale methods that directly couple high- and low-resolution models have efficiently explored slow structural transitions and the importance of long-wavelength fluctuations for biological molecules. The success of such models relies upon new theories and methods for constructing accurate multiscale bridges that transfer information between models with different resolutions.

}, keywords = {Computer Simulation DNA/chemistry Membrane Lipids/chemistry *Models, Molecular Peptides/chemistry Proteins/chemistry *Systems Biology}, doi = {10.1016/j.sbi.2007.03.004}, author = {Ayton, G. S. and Noid, W. G. and G. A. Voth} } @article {377, title = {Multiscale Simulation of Transmembrane Proteins}, journal = {J Struct Biol}, volume = {157}, number = {3}, year = {2007}, note = {Ayton, Gary S Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t United States Journal of structural biology J Struct Biol. 2007 Mar;157(3):570-8. Epub 2006 Oct 27.}, pages = {570-8}, abstract = {

Multiscale simulation is employed to examine changes in atomistic-level protein structure due to long wavelength membrane undulations and plane stress fields. An ensemble of atomistic-level simulations of a model of a transmembrane influenza A virus M2 proton channel in a dimyristoylphosphatidylcholine (DMPC) bilayer is coupled to a corresponding mesoscopic model of a DMPC bilayer in an explicit mesoscopic solvent. Structural variations in the key proton gating His37 residues of the M2 channel are examined. Small, but distinct variations in the structure of the His37 residues are observed in both the open and closed states of the channel as a result of the coupling to mesoscopic-level membrane motions.

}, keywords = {Dimyristoylphosphatidylcholine/chemistry Histidine/chemistry Lipid Bilayers/chemistry Membrane Proteins/*chemistry Protein Conformation Solvents/chemistry Viral Matrix Proteins/*chemistry}, doi = {10.1016/j.jsb.2006.10.020}, author = {Ayton, G. S. and G. A. Voth} } @article {372, title = {Systematic Coarse-graining of Biomolecular and Soft Matter Systems}, journal = {MRS Bulletin}, volume = {32}, year = {2007}, pages = {929-934}, doi = {10.1557/mrs2007.190}, author = {Ayton, G. S. and Noid, W. G. and G. A. Voth} } @article {597, title = {Transient Violations of the Second Law of Thermodynamics in Protein Unfolding Examined using Synthetic Atomic Force Microscopy and the Fluctuation Theorem}, journal = {J. Chem. Phys.}, volume = {127}, year = {2007}, pages = {105105}, doi = {10.1063/1.2764487}, author = {S. Paramore and Ayton, G. S. and G. A. Voth} } @article {595, title = {Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response}, journal = {Biophys J}, volume = {90}, number = {1}, year = {2006}, note = {Paramore, Sterling Ayton, Gary S Mirijanian, Dina T Voth, Gregory A Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2006 Jan 1;90(1):92-100. Epub 2005 Oct 14.}, pages = {92-100}, abstract = {

Nonequilibrium molecular dynamics simulations were used to calculate the elastic properties of a spectrin repeat unit. A contiguous alpha-helical linker was constructed by employing periodic boundary conditions, allowing a novel scheme for evaluating the thermodynamic force as a function of extension. By measuring the force-extension response under small extensions, spectrin was observed to behave primarily as an elastic material with a spring constant of 1700 +/- 100 pN/nm. The implications of this spring constant, in terms of the properties of the spectrin tetramer, are also discussed.

}, keywords = {Algorithms Animals Biophysics/*methods Brain/metabolism Carbon/chemistry Chickens Computer Simulation Cytoskeleton/chemistry Magnetic Resonance Spectroscopy Microscopy, Atomic Force/methods Models, Biological Models, Secondary Software Spectrin/*chemistry/metabolism Thermodynamics Water/chemistry, Statistical Molecular Conformation Protein Conformation Protein Denaturation Protein Folding Protein Structure}, doi = {10.1529/biophysj.105.066969}, author = {S. Paramore and Ayton, G. S. and D. T. Mirijanian and G. A. Voth} } @article {596, title = {Extending a Spectrin Repeat Unit. II: Rupture Behavior}, journal = {Biophys J}, volume = {90}, number = {1}, year = {2006}, note = {Paramore, Sterling Ayton, Gary S Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. United States Biophysical journal Biophys J. 2006 Jan 1;90(1):101-11. Epub 2005 Oct 14.}, pages = {101-11}, abstract = {

A spectrin repeat unit was subject to extension using cyclic expansion nonequilibrium molecular dynamics. Periodic boundary conditions were used to examine the effects of the contiguous alpha-helical linker on the force response. The measured force-extension curve shows a linear increase in the force response when the spectrin repeat unit is extended by approximately 0.4 nm. After that point, the force response peaks and subsequently declines. The peak in the force response marks the point where the spectrin repeat unit undergoes a change in its material properties from a strongly elastic material to a mostly viscous one, on the timescales of the simulations. The force peak is also correlated with rupture of the alpha-helical linker, and is likely the event responsible for the peaks in the sawtooth-pattern force-extension curves measured by atomic force microscopy experiments. Rupture of the linker involves simultaneously breaking approximately four hydrogen bonds that maintain the alpha-helical linker. After this initial rupture, the linker undergoes simple helix-to-coil transitions as the spectrin repeat unit continues to be extended. The implications of linker rupture in the interpretation of unfolding and atomic force microscopy experiments are also discussed.

}, keywords = {Animals Brain/metabolism Chickens Computer Simulation Hydrogen Bonding Microscopy, Atomic Force Models, Molecular Molecular Conformation Protein Conformation Protein Denaturation Protein Folding Protein Structure, Secondary Protein Structure, Tertiary Software Spectrin/*chemistry Time Factors}, doi = {10.1529/biophysj.105.066977}, author = {S. Paramore and Ayton, G. S. and G. A. Voth} } @article {450, title = {Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics}, journal = {Biophys J}, volume = {91}, number = {10}, year = {2006}, note = {Gebremichael, Yeshitila Ayton, Gary S Voth, Gregory A GM053148/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States Biophysical journal Biophys J. 2006 Nov 15;91(10):3640-52. Epub 2006 Aug 25.}, pages = {3640-52}, abstract = {

A particle-based hybrid method of elastic network model and smooth-particle hydrodynamics has been employed to describe the propulsion of bacterial flagella in a viscous hydrodynamic environment. The method explicitly models the two aspects of bacterial propulsion that involve flagellar flexibility and long-range hydrodynamic interaction of low-Reynolds-number flow. The model further incorporates the molecular organization of the flagellar filament at a coarse-grained level in terms of the 11 protofilaments. Each of these protofilaments is represented by a collection of material points that represent the flagellin proteins. A computational model of a single flexible helical segment representing the filament of a bacterial flagellum is presented. The propulsive dynamics and the flow fields generated by the motion of the model filament are examined. The nature of flagellar deformation and the influence of hydrodynamics in determining the shape of deformations are examined based on the helical filament.

}, keywords = {*Bacterial Physiological Phenomena Computer Simulation Flagella/*physiology Microfluidics/*methods *Models, Biological Motion}, doi = {10.1529/biophysj.106.091314}, author = {Gebremichael, Y. and Ayton, G. S. and G. A. Voth} } @article {371, title = {A Second Generation Mesoscopic Lipid Bilayer Model: Connections to Field-Theory Descriptions of Membranes and Nonlocal Hydrodynamics}, journal = {J Chem Phys}, volume = {124}, number = {6}, year = {2006}, note = {Ayton, Gary S McWhirter, J Liam Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States The Journal of chemical physics J Chem Phys. 2006 Feb 14;124(6):64906.}, pages = {64906}, abstract = {

A new mesoscopic membrane model is developed in order to examine long-wavelength structural and dynamical membrane phenomena. Two different explicit mesoscopic solvent models are employed. The first mesoscopic solvent is denoted the big liquid oscillating blob system, which is parametrized to model water at a coarse-grained level and is motivated by a Langevin-like approach; the resulting membrane dynamics predict a solvent viscosity dependence consistent with the known viscosity of water. The second mesoscopic solvent is a Weeks-Chandler-Anderson model. Here, it is found that the correct mesoscopic hydrodynamic scaling of the membrane undulation dynamics is still preserved, although accelerated. When the behavior of the two membranes in close proximity to one another is examined, very little correlated motion is observed. However, the theoretically predicted scaling of the entropic undulation energy is confirmed, demonstrating that the entropic interaction between two membranes becomes increasingly repulsive with decreasing separation.

}, keywords = {*Algorithms Computer Simulation Diffusion Entropy Lipid Bilayers/*chemistry *Membrane Fluidity Models, Biological Solvents/chemistry Surface Properties}, doi = {10.1063/1.2165194}, author = {Ayton, G. S. and McWhirter, J. L. and G. A. Voth} } @article {370, title = {Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles}, journal = {Biophys J}, volume = {88}, number = {6}, year = {2005}, note = {Ayton, Gary S McWhirter, J Liam McMurtry, Patrick Voth, Gregory A GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States Biophysical journal Biophys J. 2005 Jun;88(6):3855-69. Epub 2005 Mar 25.}, pages = {3855-69}, abstract = {

Domain formation is modeled on the surface of giant unilamellar vesicles using a Landau field theory model for phase coexistence coupled to elastic deformation mechanics (e.g., membrane curvature). Smooth particle applied mechanics, a form of smoothed particle continuum mechanics, is used to solve either the time-dependent Landau-Ginzburg or Cahn-Hilliard free-energy models for the composition dynamics. At the same time, the underlying elastic membrane is modeled using smooth particle applied mechanics, resulting in a unified computational scheme capable of treating the response of the composition fields to arbitrary deformations of the vesicle and vice versa. The results indicate that curvature coupling, along with the field theory model for composition free energy, gives domain formations that are correlated with surface defects on the vesicle. In the case that external deformations are included, the domain structures are seen to respond to such deformations. The present simulation capability provides a significant step forward toward the simulation of realistic cellular membrane processes.

}, keywords = {Biomechanics Biophysical Phenomena Biophysics Elasticity Liposomes/*chemistry Models, Chemical Thermodynamics}, doi = {10.1529/biophysj.105.059436}, author = {Ayton, G. S. and McWhirter, J. L. and P. McMurtry and G. A. Voth} } @article {419, title = {Multiscale Coupling of Mesoscopic- and Atomistic-level Lipid Bilayer Simulations}, journal = {J Chem Phys}, volume = {122}, number = {24}, year = {2005}, note = {Chang, Rakwoo Ayton, Gary S Voth, Gregory A 1 S10 RR17214-01/RR/NCRR NIH HHS/United States R01-GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States The Journal of chemical physics J Chem Phys. 2005 Jun 22;122(24):244716.}, pages = {244716}, abstract = {

A multiscale method is presented to bridge between the atomistic and mesoscopic membrane systems. The atomistic model in this case is the united atom dimyristoylphosphatidylcholine membrane system, although the method is completely general. Atomistic molecular dynamics provides the expansion modulus which is used to parametrize a mesoscopic elastic membrane model. The resulting elastic membrane model, including explicit mesoscopic solvent, shows appropriate static and dynamic undulation behaviors. Large membranes of approximately 100 nm in length can then be easily simulated using the mesoscopic membrane system. The critical feedback from the mesoscopic system back down to the atomistic-scale system is accomplished by bridging the stress (or surface tension) of a small region in the mesoscopic membrane to the corresponding atomistic membrane system. Because of long length-scale modes of membranes such as undulation and buckling, the local tension responds differently from the frame tension, when subjected to external perturbations. The effect of these membrane modes is shown for the stress response of a local membrane region and therefore the atomistic membrane system. In addition, certain equilibrium static and dynamic properties of stand-alone and multiscale coupled systems are presented for several different membrane sizes. Although static properties such as two-dimensional pair-correlation function and order parameters show no noticeable discrepancy for the different systems, lipid self-diffusion and the rotational relaxation of lipid dipoles have a strong dependence on the membrane size (or long-wavelength membrane motions), which is properly modeled by the present multiscale method.

}, keywords = {*Algorithms Carbon/chemistry *Computer Simulation Diffusion Dimyristoylphosphatidylcholine/chemistry Lipid Bilayers/*chemistry *Membrane Fluidity Stress, Mechanical Surface Properties Surface Tension Time Factors}, doi = {10.1063/1.1931651}, author = {R. Chang and Ayton, G. S. and G. A. Voth} } @article {387, title = {Probing the Molecular-Scale Lipid Bilayer Response to Shear Flow Using Nonequilibrium Molecular Dynamics}, journal = {J Phys Chem B}, volume = {109}, number = {39}, year = {2005}, note = {Blood, Philip D Ayton, Gary S Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural United States The journal of physical chemistry. B J Phys Chem B. 2005 Oct 6;109(39):18673-9.}, pages = {18673-9}, abstract = {

A nonequilibrium molecular dynamics simulation of the response of dimyristoylphosphatidylcholine (DMPC) bilayers to a solvent shear flow is presented. Application of shear flow to planar, stationary DMPC bilayers results in a redistribution of the membrane density profile along the bilayer normal due to the alignment of the lipids in the direction of flow and an increase in average lipid chain length. An increase in the intermolecular and intramolecular order of the lipids in response to the shear flow is also observed. This study provides groundwork for understanding the mechanism of the full response of lipid bilayers to externally imposed solvent shear flows, beginning with the response in the absence of collective lipid motions such as undulations and bilayer flow.

}, keywords = {*Lipid Bilayers *Molecular Probes}, doi = {10.1021/jp0530449}, author = {Blood, P. D. and Ayton, G. S. and G. A. Voth} } @article {375, title = {Mesoscopic Lateral Diffusion in Lipid Bilayers}, journal = {Biophys J}, volume = {87}, number = {5}, year = {2004}, note = {Ayton, Gary S 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. 2004 Nov;87(5):3299-311. Epub 2004 Aug 31.}, pages = {3299-311}, abstract = {

The lateral diffusion in bilayers is modeled with a multiscale mesoscopic simulation. The methodology consists of two simulations, where the first employs atomistic models to obtain exact results for the mesoscopic model. The second simulation takes the results obtained from the first to parameterize an effective force field that is employed in a new coarse-grained model. The multiscale aspect of this scheme occurs at the point where the microscopic time-averaged results of the first simulation are employed to parameterize the second simulation that operates in a higher spatial and temporal domain. The results of both simulation schemes give quantitative information on the details associated with lipid lateral diffusion.

}, keywords = {Artificial *Models, Chemical *Models, Cholesterol/chemistry Computer Simulation *Diffusion Dimyristoylphosphatidylcholine/chemistry Lipid Bilayers/*chemistry *Membrane Fluidity Membranes, Molecular Molecular Probes/*chemistry Motion Nanotubes/*chemistry}, doi = {10.1529/biophysj.104.047811}, author = {Ayton, G. S. and G. A. Voth} } @article {374, title = {A New Perspective on the Coarse-grained Dynamics of Fluids}, journal = {J Chem Phys}, volume = {120}, number = {9}, year = {2004}, note = {Ayton, Gary S Tepper, Harald L Mirijanian, Dina T Voth, Gregory A R01 GM63796/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, P.H.S. United States The Journal of chemical physics J Chem Phys. 2004 Mar 1;120(9):4074-88.}, pages = {4074-88}, abstract = {

A computational methodology is presented that is designed to model, at a coarse-grained level, the mesoscale dynamics of fluids and potentially other forms of soft matter. Within a molecular dynamics simulation, "ghost" particles of a specific size, corresponding to the fundamental length-scale of coarse-graining, are used as micro-probes designed to respond to local mesoscale fluid flows and stress gradients. A subsequent coarse-grained model is then developed that incorporates both the coarse-grained mesoscale dynamics and isothermal compressibility of the original microscopic system. The method is applied to water and methanol. A contrast with dissipative particle dynamics (DPD) is also presented.

}, keywords = {Chemical *Models, Colloids/*chemistry Computer Simulation Microfluidics/*methods *Models, Mechanical, Molecular Models, Statistical Molecular Conformation Motion Nanostructures/*chemistry Phase Transition Stress}, doi = {10.1063/1.1644092}, author = {Ayton, G. S. and H. L. Tepper and D. T. Mirijanian and G. A. Voth} } @article {376, title = {The Simulation of Biomolecular Systems at Multiple Length and Time Scales}, journal = {Int. J. for Multiscale Comp. Eng.}, volume = {2}, year = {2004}, pages = {291-311}, doi = {10.1615/IntJMultCompEng.v2.i2.80 }, author = {Ayton, G. S. and G. A. Voth} }