Publications

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2010
Ayton GS, Lyman E, G. A. Voth, “” 144 (2010. Hierarchical Coarse-graining Strategy for Protein-Membrane Systems to Access Mesoscopic Scales. Faraday Disc. Chem. Soc. 2010 ;144:347–357.
Ayton GS, Voth GA. Multiscale Computer Simulation of the Immature HIV-1 Virion. Biophys. J. 2010 ;99:2757–2765.
Ayton GS, Voth GA. Multiscale Simulation of Protein Mediated Membrane Remodeling. Seminars in Cell and Developmental Biology. 2010 ;21:357-362.
Krishna V, Ayton GS, Voth GA. Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-grained Analysis. Biophys. J. 2010 ;98:18-26.
2009
Ayton GS, Voth GA. A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales. J. Phys. Chem. B. 2009 ;113:4413-4424.
Cui H, Ayton GS, Voth GA. Membrane Binding by the Endophilin N-BAR Domain. Biophys. J. 2009 ;97:2746-2753.
Ayton GS, Lyman E, Krishna V, Swenson RD, Mim C, Unger V, Voth GA. New Insights into BAR Domain Induced Membrane Remodeling. Biophys. J. 2009 ;97:1616–1625.
Ayton GS, Voth GA. Systematic Multiscale Simulation of Membrane Protein Systems. Curr. Opin. Struct. Biol. 2009 ;19:138-144.
2008
Ceotto M, Ayton GS, Voth GA. Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems. J. Chem. Theor. Comp. 2008 ;4:560-568.
Noid WG, Chu J-W, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC. The Multiscale Coarse-graining Method I: A Rigorous Bridge between Atomistic and Coarse-grained Models. J. Chem. Phys. 2008 ;128:244114.
Noid WG, Liu P, Wang Y, Chu J-W, Ayton GS, Izvekov S, Andersen HC, Voth GA. The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models. J. Chem. Phys. 2008 ;128:244115.
Ayton GS, Izvekov S, Noid WG, Voth GA. Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior. Current Topics in Membranes. 2008 ;60:181-225.
2007
Mirijanian DT, Chu JW, Ayton GS, Voth GA. Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility. J Mol Biol. 2007 ;365:523-34.
Chu JW, Izvekov S, Ayton GS, Voth GA. Emerging Methods for Multiscale Simulation of Biomolecular Systems. Mol. Phys. 2007 ;105:167-175.
Paramore S, Ayton GS, Voth GA. Extending the Fluctuation Theorem to Describe Reaction Coordinates. J Chem Phys. 2007 ;126:051102.
Ayton GS, Blood PD, Voth GA. Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation. Biophys J. 2007 ;92:3595-602.
Noid WG, Chu JW, Ayton GS, Voth GA. Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory. J Phys Chem B. 2007 ;111:4116-27.
Ayton GS, Noid WG, Voth GA. Multiscale Modeling of Biomolecular Systems: in Serial and in Parallel. Curr Opin Struct Biol. 2007 ;17:192-8.
Ayton GS, Voth GA. Multiscale Simulation of Transmembrane Proteins. J Struct Biol. 2007 ;157:570-8.
Ayton GS, Noid WG, Voth GA. Systematic Coarse-graining of Biomolecular and Soft Matter Systems. MRS Bulletin. 2007 ;32:929-934.
Paramore S, Ayton GS, Voth GA. Transient Violations of the Second Law of Thermodynamics in Protein Unfolding Examined using Synthetic Atomic Force Microscopy and the Fluctuation Theorem. J. Chem. Phys. 2007 ;127:105105.
2006
Paramore S, Ayton GS, Mirijanian DT, Voth GA. Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response. Biophys J. 2006 ;90:92-100.
Paramore S, Ayton GS, Voth GA. Extending a Spectrin Repeat Unit. II: Rupture Behavior. Biophys J. 2006 ;90:101-11.
Gebremichael Y, Ayton GS, Voth GA. Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics. Biophys J. 2006 ;91:3640-52.
Ayton GS, McWhirter JL, Voth GA. A Second Generation Mesoscopic Lipid Bilayer Model: Connections to Field-Theory Descriptions of Membranes and Nonlocal Hydrodynamics. J Chem Phys. 2006 ;124:64906.
2005
Ayton GS, McWhirter JL, McMurtry P, Voth GA. Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles. Biophys J. 2005 ;88:3855-69.
Chang R, Ayton GS, Voth GA. Multiscale Coupling of Mesoscopic- and Atomistic-level Lipid Bilayer Simulations. J Chem Phys. 2005 ;122:244716.
Blood PD, Ayton GS, Voth GA. Probing the Molecular-Scale Lipid Bilayer Response to Shear Flow Using Nonequilibrium Molecular Dynamics. J Phys Chem B. 2005 ;109:18673-9.
2004
Ayton GS, Voth GA. Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys J. 2004 ;87:3299-311.
Ayton GS, Tepper HL, Mirijanian DT, Voth GA. A New Perspective on the Coarse-grained Dynamics of Fluids. J Chem Phys. 2004 ;120:4074-88.
Ayton GS, Voth GA. The Simulation of Biomolecular Systems at Multiple Length and Time Scales. Int. J. for Multiscale Comp. Eng. 2004 ;2:291-311.