Publications

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Arntsen C, Chen C, Voth GA. Reactive Molecular Dynamics Models from Ab Initio Molecular Dynamics Data Using Relative Entropy Minimization. Chem. Phys. Lett. 2017 ;683.
Arntsen C, Chen C, Calio PB, Li C, Voth GA. The Hopping Mechanism of the Hydrated Excess Proton and Its Contribution to Proton Diffusion in Water. J. Chem. Phys. 2021 ;154:194506.
Arntsen C, Savage J, Tse Y-LS, Voth GA. Simulation of Proton Transport in Proton Exchange Membranes with Reactive Molecular Dynamics. Fuel Cells. 2016 ;0000:1-9.
Aydin F, Courtemanche N, Pollard TD, Voth GA. Gating mechanisms during actin filament elongation by formins. eLife. 2018 ;7:e37342.
Aydin F, Katkar HH, Voth GA. Multiscale Simulation of Actin Filaments and Actin-Associated Proteins. Biophys Rev. 2018 ;10:1521-1535.
Ayton G, Bardenhagen S, McMurtry P, Sulsky D, Voth GA. Interfacing Continuum and Molecular Dynamics: An Application to Lipid Bilayers. J. Chem. Phys. 2001 ;114:6913-6924.
Ayton G, Bardenhagen S, McMurtry P, Sulsky D, Voth GA. Interfacing Molecular Dynamics with Continuum Dynamics in Computer Simulation: Toward an Application to Biological Membranes. IBM J. Res. Dev. 2001 ;45:417-426.
Ayton G, Smondyrev AM, Bardenhagen SG, McMurtry P, Voth GA. Interfacing Molecular Dynamics and Macro-scale Simulations for Lipid Bilayer Vesicles. Biophys J. 2002 ;83:1026-38.
Ayton G, Smondyrev AM, Bardenhagen SG, McMurtry P, Voth GA. Calculating the Bulk Modulus for a Lipid Bilayer with Nonequilibrium Molecular Dynamics Simulation. Biophys J. 2002 ;82:1226-38.
Ayton G, Voth GA. Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers. Biophys J. 2002 ;83:3357-70.
Ayton GS, Blood PD, Voth GA. Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation. Biophys J. 2007 ;92:3595-602.
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.
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, 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, 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.
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.
Ayton GS, Noid WG, Voth GA. Systematic Coarse-graining of Biomolecular and Soft Matter Systems. MRS Bulletin. 2007 ;32:929-934.
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, 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. Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys J. 2004 ;87:3299-311.
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.
Ayton GS, Voth GA. Multiscale Simulation of Transmembrane Proteins. J Struct Biol. 2007 ;157:570-8.
Ayton GS, Voth GA. Systematic Multiscale Simulation of Membrane Protein Systems. Curr. Opin. Struct. Biol. 2009 ;19:138-144.
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.
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.
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Bagchi S, Thorpe DG, Thorpe IF, Voth GA, Fayer MD. Conformational Switching Between Protein Substates Studied with 2D IR Vibrational Echo Spectroscopy and Molecular Dynamics Simulations. J. Phys. Chem. B. 2010 ;114:17187–17193.
Baker JL, Voth GA. Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain. Biophys. J. 2013 ;105(7):1624-1634.
Baker JL, Courtemanche DL, Parton DL, McCullagh M, Pollard TD, Voth GA. Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure. 2015 ;23.
Bardak F, Xiao D, Jr. HLG, Son P, Bartsch RA, Quitevis EL, Yang P, Voth GA. Nanostructural Organization in Acetonitrile/Ionic Liquid Mixtures: Molecular Dynamics Simulations and Optical Kerr Effect Spectroscopy. ChemPhysChem. 2012 ;13:1687-1700.
Barry E, Burns R, Chen W, de Hoe GX, de Oca JMM, de Pablo JJ, Dombrowski J, Elam JW, Felts AM, Gali G, et al. Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport. Chem Rev. 2021 ;121(21):9450−9501.
Bhattacharya-Kodali I, Voth GA. Integral Equation Calculation of Solvent Activation Free Energies for Electron- and Proton-transfer Reactions. The Journal of Physical Chemistry. 1993 ;97:11253-11257.
Bidone TC, Polley A, Jin J, Driscoll T, Iwamoto D, Calderwood D, Schwartz MA, Voth GA. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys J. 2019 ;116(6):1000-1010 .
Bidone TC, Skeeters AV, Oakes PW, Voth GA. Multiscale model of integrin adhesion assembly. POLS Computational Biology. 2019 ;15(6):e1007077.
Biswas R, Carpenter W, Fournier JA, Voth GA, Tokmakoff A. IR Spectral Assignments for the Hydrated Excess Proton in Liquid Water. J. Chem. Phys. 2017 ;146.
Biswas R, Voth GA. Role of Solvation Structure in the Shuttling of the Hydrated Excess Proton. J. Chem. Sci. 2017 ;129.
Biswas R, Tse Y-LS, Tokmakoff A, Voth GA. Role of Pre-Solvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport. J. Phys. Chem. B . 2016 ;120(8):1793–1804.
Biswas R, Carpenter W, Voth GA, Tokmakoff A. Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water. J. Chem. Phys. . 2016 .
Blake NP, Petersen MK, Voth GA, Metiu H. Structure of Hydrated Na−Nafion Polymer Membranes. J Phys Chem B. 2005 ;109:24244-53.
Blinov NV, Roy PN, Voth GA. Path Integral Formulation of Centroid Dynamics for Systems Obeying Bose-Einstein Statistics. J. Chem. Phys. 2001 ;115:4484.
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.
Blood PD, Swenson RD, Voth GA. Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations. Biophys. J. 2008 ;95:1866-1876.
Blood PD, Voth GA. Direct Observation of Bin/amphiphysin/Rvs (BAR) Domain-induced Membrane Curvature by Means of Molecular Dynamics Simulations. Proc Natl Acad Sci U S A. 2006 ;103:15068-72.
Boroda Y, Voth GA. A Theory for Electron Transfer between an Electrode and a Multilevel Acceptor/Donor Species in an Electrolyte Solution. J. Electroanal. Chem. 1998 ;450:95-107.
Boroda YG, Calhoun A, Voth GA. A Theory for Electron Transfer across the Electrode/Electrolyte Interface Involving more than One Redox Ion. The Journal of Chemical Physics. 1997 ;107:8940-8954.
Boroda YG, Voth GA. A Theory for Adiabatic Electron Transfer Processes across the Semiconductor/Electrolyte Interface. The Journal of Chemical Physics. 1996 ;104:6168-6183.
Brewer ML, Schmitt UW, Voth GA. The Formation and Dynamics of Proton Wires in Channel Environments. Biophys J. 2001 ;80:1691-702.
Bruns CJ, Li J, Frasconi ST, Schneebeli J, Iehl J, Jacquot de Rouville H-P, Stupp SI, Voth GA, Stoddart JF. An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane. Angewandte Chemie. 2014 ;53:1953-1958.
Bug ALR, Wilson A, Voth GA. Nonlinear Vibrational Dynamics of a Neon Atom in Fullerene (C60). The Journal of Physical Chemistry. 1992 ;96:7864-7869.
Burnham CJ, Petersen MK, Day TJ, Iyengar SS, Voth GA. The Properties of Ion-water Clusters. II. Solvation Structures of Na+, Cl-, and H+ Clusters as a Function of Temperature. J Chem Phys. 2006 ;124:024327.
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Calhoun A, Koper MTM, Voth GA. Electrochemical Bond-Breaking Reactions: A Comparison of Large Scale Simulation Results with Analytical Theory. The Journal of Physical Chemistry B. 1999 ;103:3442-3448.
Calhoun A, Koper MTM, Voth GA. Largescale Computer Simulation of an Electrochemical Bond Breaking Reaction. Chem. Phys. Lett. 1999 ;305:94-100.
Calhoun A, Pavese M, Voth GA. Hyper-Parallel Algorithms for Centroid Molecular Dynamics: Application to Liquid para–Hydrogen. Chem. Phys. Lett. 1996 ;262:415-420.
Calhoun A, Voth GA. Electron Transfer Across the Electrode/Electrolyte Interface: Influence of Redox Ion Mobility and Counterions. The Journal of Physical Chemistry. 1996 ;100:10746-10753.
Calhoun A, Voth GA. Isotope Effects in Electron Transfer across the Electrode-Electrolyte Interface: A Measure of Solvent Mode Quantization. The Journal of Physical Chemistry B. 1998 ;102:8563-8568.
Calhoun A, Voth GA. The Computer Simulation of Correlated Electron Transfer Across the Electrode/Electrolyte Interface Involving Multiple Redox Species. The Journal of Chemical Physics. 1998 ;109:4569-4575.
Calhoun A, Voth GA. The Computer Simulation of Electron Transfer Processes Across the Electrode/Electrolyte Interface: A Treatment of Solvent and Electrode Polarizability. J. Electroanal. Chem. 1998 ;450:253-264.
Calio PB, Hocky GM, Voth GA. Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water. J. Chem. Theory. Comp. 2020 ;16(9):5675–5684 .
Calio PB, Li C, Voth GA. Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions. J. Phys. Chem. B. 2020 ;124(40):8868–8876.
Calio PB, Li C, Voth GA. Resolving the Structural Debate for the Hydrated Excess Proton in Water. J. Am. Chem. Soc. 2021 ;143(44):18672−18683.
Cao J, Minichino C, Voth GA. The Computation of Electron Transfer Rates: The Nonadiabatic Instanton Solution. The Journal of Chemical Physics. 1995 ;103:1391-1399.
Cao J, Ungar LW, Voth GA. A Novel Method for Simulating Quantum Dissipative Systems. The Journal of Chemical Physics. 1996 ;104:4189-4197.
Cao J, Voth GA. A New Perspective on Quantum Time Correlation Functions. The Journal of Chemical Physics. 1993 ;99:10070-10073.
Cao J, Voth GA. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. I. Equilibrium Properties. The Journal of Chemical Physics. 1994 ;100:5093-5105.
Cao J, Voth GA. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. II. Dynamical Properties. The Journal of Chemical Physics. 1994 ;100:5106-5117.
Cao J, Voth GA. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. IV. Algorithms for Centroid Molecular Dynamics. The Journal of Chemical Physics. 1994 ;101:6168-6183.
Cao J, Voth GA. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. V. Quantum Instantaneous Normal Mode Theory of Liquids. The Journal of Chemical Physics. 1994 ;101:6184-6192.
Cao J, Voth GA. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. III. Phase Space Formalism and Analysis of Centroid Molecular Dynamics. The Journal of Chemical Physics. 1994 ;101:6157-6167.
Cao J, Voth GA. Modeling Physical Systems by Effective Harmonic Oscillators: The Optimized Quadratic Approximation. The Journal of Chemical Physics. 1995 ;102:3337-3348.
Cao J, Voth GA. A Theory for Time Correlation Functions in Liquids. The Journal of Chemical Physics. 1995 ;103:4211-4220.
Cao J, Voth GA. Semiclassical Approximations to Quantum Dynamical Time Correlation Functions. The Journal of Chemical Physics. 1996 ;104:273-285.
Cao J, Voth GA. A Unified Framework for Quantum Activated Rate Processes. I. General Theory. The Journal of Chemical Physics. 1996 ;105:6856-6870.
Cao J, Voth GA. A Theory for the Quantum Activated Rate Constant in Dissipative Systems. Chem. Phys. Lett. 1996 ;261:111-116.
Cao J, Voth GA. A Unified Framework for Quantum Activated Rate Processes. II. The Nonadiabatic Limit. The Journal of Chemical Physics. 1997 ;106:1769-1779.
Cao Z, Peng Y, Yan T, Li S, Li A, Voth GA. Mechanism of Fast Proton Transport along One-Dimensional Water Chains Confined in Carbon Nanotubes. J. Am. Chem. Soc. 2010 ;132:11395–11397.
Cao Z, Dama JF, Lu L, Voth GA. Solvent Free Ionic Solution Models from Multiscale Coarse-Graining. J Chem Theory Comput. 2013 ;9:172-178.
Cao Z, Kumar R, Peng Y, Voth GA. Proton Transport Under External Applied Voltage. J. Phys. Chem. B. 2014 .
Cao Z, Peng Y, Voth GA. Ion Transport through Ultra-Thin Electrolyte under Applied Voltages. J. Phys. Chem. B. 2015 ;119:7516-7521.
Cao Z, Kumar R, Peng Y, Voth GA. Hydrated Proton Structure and Diffusion at Platinum Surfaces. J. Phys. Chem. C. 2015 ;119:7516-7521.
Cao Z, Voth GA. The Multiscale Coarse-Graining Method. XI. Accurate Interactions Based on the Centers of Charge of Coarse-Grained Sites. J. Chem. Phys. 2015 ;143(243116):1-11.
Carpenter WB, Fournier JA, Biswas R, Voth GA. Delocalization and Stretch-Bend Mixing of the HOH Bend in Liquid Water. J. Chem. Phys. 2017 ;147(084503).
Ceotto M, Ayton GS, Voth GA. Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems. J. Chem. Theor. Comp. 2008 ;4:560-568.
Chang R, Ayton GS, Voth GA. Multiscale Coupling of Mesoscopic- and Atomistic-level Lipid Bilayer Simulations. J Chem Phys. 2005 ;122:244716.
Chaudhri A, Zarraga IE, Kamerzell TJ, Brandt JP, Patapoff TW, Shire SJ, Voth GA. Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies. J. Phys. Chem. B. 2012 ;116:8045-8057.
Chaudhri A, Zarraga IE, Yadav S, Patapoff TW, Shire SJ, Voth GA. The Role of Amino Acid Sequence in the Self-Association of Therapeutic Monoclonal Antibodies: Insights from Coarse Grained Modeling. J. Chem. Phys. B. 2013 .
Chawla S, Voth GA. Exact Exchange in ab initio Molecular Dynamics: An Efficient Plane-wave based Algorithm. The Journal of Chemical Physics. 1998 ;108:4697-4700.
Chen H, Ilan B, Wu Y, Zhu F, Schulten K, Voth GA. Charge Delocalization in Proton Channels, I: the Aquaporin Channels and Proton Blockage. Biophys J. 2007 ;92:46-60.
Chen H, Liu P, Voth GA. An Efficient Multi-State Reactive Molecular Dynamics Approach Based on Short-Ranged Effective Potentials. J. Chem. Theor. Comp. 2010 ;6:3039–3047.
Chen H, Voth GA. The Kinetics of Proton Migration in Liquid Water. J. Phys. Chem. B. 2010 ;114:333–339.
Chen H, Wu Y, Voth GA. Origins of Proton Transport Behavior from Selectivity Domain Mutations of the Aquaporin-1 Channel. Biophys J. 2006 ;90:L73-5.
Chen H, Wu Y, Voth GA. Proton Transport Behavior Through the Influenza A M2 Channel: Insights from Molecular Simulation. Biophys. J. 2007 ;93:3470-3479.
Chen H, Xu J, Voth GA. Unusual Hydrophobic Interactions in Acidic Aqueous Solutions. J. Phys. Chem. B. 2009 ;113:7291-7297.
Chen H, Yan T, Voth GA. A Computer Simulation Model for Proton Transport in Liquid Imidazole. J. Phys. Chem. A. 2009 ;113:4507-4517.
Chen Y, Aardema J, Kale S, Whichard ZL, Awomolo A, Blanchard E, Chang B, Myers DR, Ju L, Tran R, et al. Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
Chen C, Tse Y-LS, Lindberg GE, Knight C, Voth GA. Hydroxide Solvation and Transport in Anion Exchange Membranes. J. Am. Chem. Soc. 2016 ;138(3):991-1000.
Chen C, Arntsen C, Voth GA. Development of Reactive Force Fields Using Ab Initio Molecular Dynamics Simulation Minimally Biased to Experimental Data. J. Chem. Phys. 2017 .
Chen Y, Ma X, Hack JH, Zhang S, Peng A, Dombrowski JP, Voth GA, Tokmakoff A, Kung MC, Kung HH. Solvated Excess Proton as the Active Site in Methanol Dehydration: Beyond the Hydrated Hydronium Ion. Submitted .
Choi TH, Liang R, Maupin CM, Voth GA. Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions. J. Phys. Chem. B . 2013 ;117:5165-5179.
Christensen JR, Hocky GM, Morganthaler AN, Homa KE, Hitchcock-DeGregori SE, Voth GA, Kovar DR. Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks. eLife. 2017 ;6.
Chu JW, Izvekov S, Ayton GS, Voth GA. Emerging Methods for Multiscale Simulation of Biomolecular Systems. Mol. Phys. 2007 ;105:167-175.
Chu JW, Izvekov S, Voth GA. The Multiscale Challenge for Biomolecular Systems: Coarse-grained Modeling. Mol. Sim. 2006 ;32:211-218.
Chu JW, Voth GA. Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-grained Analysis. Proc Natl Acad Sci U S A. 2005 ;102:13111-6.
Chu JW, Voth GA. Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations. Biophys J. 2006 ;90:1572-82.
Chu JW, Voth GA. Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model. Biophys. J. 2007 ;93:3860-3871.
Cui H, Ayton GS, Voth GA. Membrane Binding by the Endophilin N-BAR Domain. Biophys. J. 2009 ;97:2746-2753.
Cui H, Lyman E, Voth GA. Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins. Biophys. J. 2011 ;100:1271-1279.
Cui H, Mim C, Lyman E, Unger VM, Voth GA. Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling. Biophys. J. 2013 ;104:404-411.
Cuma M, Schmitt UW, Voth GA. A Multi-State Empirical Valence Bond Model for Acid-Base Chemistry in Aqueous Solution. Chem. Phys. Lett. 2000 ;258:187.
Cuma M, Schmitt UW, Voth GA. A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution. J. Phys. Chem. A. 2001 ;105:2814-2823.
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Dama JF, Sinitskiy AV, McCullagh M, Weare J, Roux B, Dinner AR, Voth GA. Theory of Ultra Coarse-Graining. I. General Principles. J. Chem. Theor. Comp. 2013 ;9:2466−2480.
Dama JF, Parrinello M, Voth GA. Well-tempered Metadynamics Converges Asymptotically. Phys. Rev. Lett. 2014 ;112:1-6.
Dama JF, Rotskoff J, Parrinello M, Voth GA. Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-The-Fly Transition Barrier Estimation. J. Chem. Theor. Comp. 2014 .
Dama JF, Hocky GM, Sun R, Voth GA. Exploring Valleys Without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction. J. Chem. Theory Comp. 2015 .
Dama JF, Jin J, Voth GA. The Theory of Ultra-Coarse-Graining. 3. Coarse-grained Sites with Rapid Local Equilibrium of Internal States. J. Chem. Theory Comput. 2017 ;13.
Dannenhoffer-Lafage T, White AD, Voth GA. A Direct Method for Incorporating Experimental Data into Multiscale Coarse-grained Models. J Chem Theory Comp. 2016 ;12(5):2144-2153.
Dannenhoffer-Lafage T, Wagner JW, Durumeric AEP, Voth GA. Compatible Observable Decompositions for Coarse-grained Representations of Real Molecular Systems. J. Chem. Phys. 2019 ;151.
Dannenhoffer-Lafage T, Voth GA. Reactive Coarse-grained Molecular Dynamics. J. Chem. Theory. Comp. 2020 ;16(4):2541−2549.
Das A, Lu L, Andersen HC, Voth GA. The Multiscale Coarse-Graining Method. X. Improved Algorithms for Constructing Coarse-Grained Potentials for Molecular Systems. J. Chem. Phys. 2012 ;136:194115.
Davtyan A, Dama JF, Sinitskiy AV, Voth GA. The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation. J. Chem. Theory Comp. . 2014 ;10:5265-5275.
Davtyan A, Dama JF, Voth GA, Andersen HC. Dynamic Force Matching: A Method for Constructing Dynamical Coarse-Grained Models with Realistic Time Dependence. J. Chem. Phys. 2015 ;142(154104):1-21.
Davtyan A, Simunovic M, Voth GA. Multiscale Simulations of Protein Facilitated Membrane Remodeling. J. Struct. Biol. 2016 .
Davtyan A, Voth GA, Andersen HC. Dynamic Force Matching: Construction of Dynamic Coarse-Grained Models with Realistic Short Time Dynamics and Accurate Long Time Dynamics. J Chem Phys. 2016 ;145:224107.
Davtyan A, Simunovic M, Voth GA. The Mesoscopic Membrane with Proteins Model (MesM-P). J. Chem. Phys. 2017 ;147.
Day TJF, Schmitt UW, Voth GA. The Mechanism of Hydrated Proton Transport in Water. Journal of the American Chemical Society. 2000 ;122:12027-12028.
Day TJF, Soudackov AV, Cuma M, Schmitt UW, Voth GA. A Second Generation Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems. J. Chem. Phys. 2002 ;117:5839-5849.
Dolan KA, Dutta M, Kern DM, Kotecha A, Voth GA, Brown SG. Structure of SARS-CoV-2 M protein in lipid nanodiscs. eLife. 2022 ;11:e81702.
Driscoll T, Bidone TC, Ahn S, Goisman A, Voth GA, Schwartz MA. Integrin-Based Mechanosensing through Conformational Activation. Biophys. J. 2021 ;120(20):4349–4359 .
Durumeric AEP, Voth GA. Adversarial-Residual-Coarse-Graining: Applying Machine Learning Theory to Systematic Molecular Coarse-Graining. J. Chem. Phys. . 2019 ;151.
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Fan J, Saunders MG, Voth GA. Coarse-Graining Provides Insight on the Essential Nature of Heterogeneity in Actin Filaments. Biophys. J. 2012 ;103:1334-1342.
Fan J, Saunders MG, Haddadian EJ, Freed KF, Cruz DLEM, Voth GA. Molecular Origins of Cofilin-linked Changes in Actin Filament Mechanics. J. Mol. Biol. 2013 ;425(7).
Feng S, Voth GA. Molecular Dynamics Simulations of Imidazolium-based Ionic Liquid/Water Mixtures: Alkyl Side Chain Length and Anion Effects. Fluid Phase Equilibria (Special Issue). 2010 ;294:148–156.
Feng S, Voth GA. Proton Solvation and Transport in Hydrated Nafion. J. Phys. Chem. B. 2011 ;115:5903-5912.
Feng S, Savage J, Voth GA. Effect of Polymer Morphology on Proton Solvation and Transport in Proton Exchange Membranes. J. Phys. Chem C. 2012 ;116:19104-19116.
Fisher SZ, Maupin CM, Budayova-Spano M, Govindasamy L, Tu C, Agbandje-McKenna M, Silverman DN, Voth GA, McKenna R. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
Flower TG, Takahashi Y, Hudait A, Rose K, Tjahjono N, Pak AJ, Yokom AL, Liang X, Wang HG, Bouamr F, et al. A Helical Assembly of Human ESCRT-I Scaffolds Reverse-Topology Membrane Scission. Nat. Struct. Mol. Biol. 2020 .
Freedman SL, Suarez C, Winkelman JD, Kovar DR, Voth GA, Dinner AR, Hocky GM. Mechanical and Kinetic Factors Drive Sorting of F-actin Crosslinkers on Bundles. PNAS. 2019 ;116(13):16192-16197.
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Gai H, Voth GA. A Computer Simulation Method for Studying the Ablation of Polymer Surfaces by Ultraviolet Laser Radiation. Journal of Applied Physics. 1992 ;71:1415-1420.
Gai H, Voth GA. Vibrational Energy Relaxation Dynamics of Si–H Stretching Modes on the H/Si(111)11 Surface. J. Chem. Phys. 1993 ;99:740-743.
Gai H, Voth GA. First-principles Molecular Dynamics Study of Surface Vibrations and Vibrational Mode Coupling on the H/Si(111)1 x 1 Surface. The Journal of Chemical Physics. 1994 ;101:1734-1737.
Galvan-Monjee V, Voth GA. Binding Mechanism of the Matrix Domain of HIV-1 Gag to Lipid Membranes. eLife . 2020 ;9.
Gebremichael Y, Ayton GS, Voth GA. Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics. Biophys J. 2006 ;91:3640-52.
Gebremichael Y, Chu J-W, Voth GA. Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis. Biophys. J. 2008 ;95:2487-2499.
Geva E, Shi Q, Voth GA. Quantum Mechanical Reaction Rate Constants from Centroid Molecular Dynamics Simulations. J. Chem. Phys. 2001 ;115:9209-9222.
Geva E, Jang S, Voth GA. Quantum Rate Theory: A Path Integral Centroid Perspective. In: Yip S Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. ; 2005.
Grafmüller A, Voth GA. Intrinsic Bending of Microtubule Protofilaments. Structure. 2011 ;19:409–417.
Grafmuller A, Noya EG, Voth GA. Nucleotide-dependent Lateral and Longitudinal Interactions in Microtubules. J. Mol. Biol. 2013 .
Grime JMA, Voth GA. Early Stages of the HIV-1 Capsid Protein Lattice Formation. Biophys. J. 2012 ;103:1774-1783.
Grime JMA, Voth GA. Highly Scalable and Memory Efficient Ultra-coarse-grained Molecular Dynamics Simulations. J. Chem. Theor. Comp. 2014 ;10:423-431.
Grime JMA, Dama JF, Ganser-Pornillos BK, Woodward CL, Jensen GJ, Yeager MJ, Voth GA. Coarse-grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly. Nat. Comm. 2016 ;7(1156):1-11.
Gupta M, Pak AJ, Voth GA. Critical Mechanistic Role of Inositol Hexakisphosphate (IP6) in HIV-1 Viral Capsid Assembly. Sci. Adv. Submitted .
Guttenberg N, Dama JF, Saunders MG, Voth GA, Weare J, Dinner AR. Minimizing Memory as an Objective for Coarse-Graining. J. Chem. Phys. 2013 ;138.
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Hack JH, Dombrowski JP, Ma X, Chen Y, Lewis NHC, Carpenter WB, Li C, Voth GA, Kung HH, Tokmakoff A. Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites. J. Am. Chem. Soc. . 2021 ;143(27):10203–10213.
Han Y, Jin J, Wagner J, Voth GA. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148:102335.
Han Y, Dama JF, Voth GA. Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. J. Chem. Phys. 2018 ;149.
Han Y, Jin J, Voth GA. Constructing Many-body Mesoscopic Models of Fluids from Bottom-up Coarse-graining. J. Chem. Phys. 2021 ;154:084122.
Harker AJ, Katkar HH, Bidone TC, Aydin F, Voth GA, Applewhite DA, Kovar DR. Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia crosslinker fascin. Molecular Biology of the Cell. 2019 ;30(7).
Haynes GR, Voth GA. Effect of Nonlinear Dissipation on Quantum-activated Rate Processes in Condensed Phases. Phys Rev A. 1992 ;46:2143-2146.
Haynes GR, Voth GA. The Dependence of the Potential of Mean Force on the Solvent Friction: Consequences for Condensed Phase activated Rate Theories. The Journal of Chemical Physics. 1993 ;99:8005-8008.
Haynes GR, Voth GA. Reaction-Coordinate-Dependent Friction in Classical Activated Barrier Crossing Dynamics: When it Matters and When it Doesn't. The Journal of Chemical Physics. 1995 ;103:10176-10182.
Haynes GR, Voth GA, Pollak E. A Theory for the Thermally Activated Rate Constant in Systems with Spatially Dependent Friction. Chem. Phys. Lett. 1993 ;207:309-316.
Haynes GR, Voth GA, Pollak E. DA Theory for the Activated Barrier Crossing Rate Constant in Systems Influenced by Space and Time Dependent Friction. The Journal of Chemical Physics. 1994 ;101:7811-7822.
Henderson TC, McMurtry PA, Smith PJ, Voth GA, Wight CA, Pershing DW. Simulating Accidental Fires and Explosions. Computing in Science and Engineering. 2000 ;2:64-76.
Hernandez R, Cao J, Voth GA. On the Feynman Path Centroid Density as a Phase Space Distribution in Quantum Statistical Mechanics. The Journal of Chemical Physics. 1995 ;103:5018-5026.
Hernandez R, Voth GA. Quantum Time Correlation Functions and Classical Coherence. Chem. Phys. 1998 ;233:243-255.
Hocky GM, Baker JL, Bradley MJ, Sinitskiy AV, De La Cruz EM, Voth GA. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits. J. Phys. Chem. B. 2016 ;120(20).
Hocky GM, Dannenhoffer-Lafage T, Voth GA. Coarse-Grained Directed Simulation. J. Chem. Theory Comput. 2017 .
Hocky GM, Sindelar VC, Cao W, Voth GA, Cruz DLEM. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296.
Homa KE, Zsolnay V, Anderson CA, O’Connell ME, Neidt EM, Voth GA, Bidone TC, Kovar DR. Formin Cdc12’s Specific Actin Assembly Properties are Tailored for Cytokinesis in Fission Yeast. Mol. Biol. Cell . 2021 ;120(15):2984-2997.
Hone TD, Izvekov S, Voth GA. Fast Centroid Molecular Dynamics: a Force-matching Approach for the Predetermination of the Effective Centroid Forces. J Chem Phys. 2005 ;122:54105.
Hone TD, Rossky PJ, Voth GA. A Comparative Study of Imaginary Time Path Integral Based Methods for Quantum Dynamics. J Chem Phys. 2006 ;124:154103.
Hone TD, Voth GA. A Centroid Molecular Dynamics Study of Liquid Para-hydrogen and Ortho-deuterium. J Chem Phys. 2004 ;121:6412-22.
Hudait A, Hurley JH, Voth GA. Organization of Upstream ESCRT Machinery at the HIV-1 Budding Site. J. Biol. Chem. Submitted .
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Ilan B, Tajkhorshid E, Schulten K, Voth GA. The Mechanism of Proton Exclusion in Aquaporin Channels. Proteins. 2004 ;55:223-8.
Iuchi S, Chen H, Paesani F, Voth GA. The Hydrated Excess Proton at Water-Hydrophobic Interfaces. J. Phys. Chem. B. 2009 ;113:4017-4030.
Iuchi S, Izvekov S, Voth GA. Are Many-body Electronic Polarization Effects Important in Liquid Water?. J Chem Phys. 2007 ;126:124505.
Iyengar SS, Burnham CJ, Petersen MK, Voth GA. Modeling Condensed Phase Chemistry Through Molecular Dynamics Simulation. Computers in Science and Engineering. 2003 ;5:31-35.
Iyengar SS, Day TJF, Voth GA. On the Amphiphilic Behavior of the Hydrated Proton: An Ab Initio Molecular Dynamics Study. Int. J. Mass. Spec. 2005 ;241:197-204.
Iyengar SS, Petersen MK, Day TJ, Burnham CJ, Teige VE, Voth GA. The Properties of Ion-water Clusters. I. The Protonated 21-water Cluster. J Chem Phys. 2005 ;123:084309.
Iyengar SS, Schlegel HB, Millam JM, Voth GA, Scuseria GE, Frisch MJ. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. II. Generalization based on Mass-weighting, Idempotency, Energy Conservation, and Choice of Initial Conditions. J. Chem. Phys. 2001 :10291-10302.
Iyengar SS, Schlegel HB, Voth GA. Atom-centered Density Matrix Propagation (ADMP): Generalizations using Bohmian Mechanics. J. Phys. Chem. 2003 ;107:7269-7277.
Iyengar SS, Schlegel HB, Voth GA, Millam JM, Scuseria GE, Frisch MJ. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. IV. Formal Analysis of the Deviations from Born-Oppenheimer Dynamics. Israel. J. Chem. 2003 ;42:191-202.
Izvekov S, Mazzolo A, VanOpdorp K, Voth GA. Ab initio Molecular Dynamics Simulation of the Cu(110)–Water Interface. J. Chem. Phys. 2001 ;114:3248.
Izvekov S, Parrinello M, Burnham CJ, Voth GA. Effective Force Fields for Condensed Phase Systems from ab initio Molecular Dynamics Simulation: a New Method for Force-matching. J Chem Phys. 2004 ;120:10896-913.
Izvekov S, Violi A, Voth GA. Systematic Coarse-Graining of Nanoparticle Interactions in Molecular Dynamics Simulation. J Phys Chem B. 2005 ;109:17019-24.
Izvekov S, Voth GA. Ab initio Molecular Dynamics Simulation of the Ag(111)–Water Interface. J. Chem. Phys. 2001 ;115:7196-7206.
Izvekov S, Voth GA. Car-Parrinello Molecular Dynamics Simulation of Liquid Water: New Results. J. Chem. Phys. 2002 ;116:10372-10376.
Izvekov S, Voth GA. Multiscale Coarse Graining of Liquid-state Systems. J Chem Phys. 2005 ;123:134105.
Izvekov S, Voth GA. Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio Molecular Dynamics Simulation Using the Force-Matching Method. J Phys Chem B. 2005 ;109:6573-86.
Izvekov S, Voth GA. A Multiscale Coarse-Graining Method for Biomolecular Systems. J Phys Chem B. 2005 ;109:2469-73.
Izvekov S, Voth GA. Ab Initio Molecular-dynamics Simulation of Aqueous Proton Solvation and Transport Revisited. J Chem Phys. 2005 ;123:044505.
Izvekov S, Voth GA. Modeling Real Dynamics in the Coarse-grained Representation of Condensed Phase Systems. J Chem Phys. 2006 ;125:151101.
Izvekov S, Voth GA. Multiscale Coarse-graining of Mixed Phospholipid/Cholesterol Bilayer. J. Chem. Theory Comp. 2006 ;2:637-648.
Izvekov S, Voth GA. Mixed Resolution Modeling of Interactions in Condensed Phase Systems. J. Chem. Theor. Comp. 2009 ;5:3232–3244.
Izvekov S, Voth GA. A Solvent Free Lipid Bilayer Model Using Multiscale Coarse-graining. J. Phys. Chem. B. 2009 ;113:4443-4455.
Izvekov* S, Swanson* JMJ, Voth GA. Coarse-graining in Interaction Space: A Systematic Approach for Replacing Long-ranged Electrostatics by Short-ranged Effective Potentials. J. Phys. Chem. B. 2008 ;112:4711-4724.
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Jang S, Jang S, Voth GA. Quantum Molecular Dynamics Simulations of Low-Temperature High Energy Density Matter: Solid p-H2/Li and p-H2/B. The Journal of Physical Chemistry A. 1999 ;103:9512-9520.
Jang S, Jang S, Voth GA. Applications Of Higher Order Composite Factorization Schemes In Imaginary Time Path Integral Simulations. J. Chem. Phys. 2001 ;115:7832-7842.
Jang S, Pak Y, Voth GA. Quantum Dynamical Simulation of the Energy Relaxation Rate of the CN- Ion in Water. The Journal of Physical Chemistry A. 1999 ;103:10289-10293.
Jang S, Schwieters CD, Voth GA. A Modification of Path Integral Quantum Transition State Theory for Asymmetric and Metastable Potentials. The Journal of Physical Chemistry A. 1999 ;103:9527-9538.
Jang S, Voth GA. Simple Reversible Molecular Dynamics Algorithms for Nos[e-acute]–Hoover Chain Dynamics. The Journal of Chemical Physics. 1997 ;107:9514-9526.
Jang S, Voth GA. Lithium Impurity Recombination in Solid Para-hydrogen: A Path Integral Quantum Transition State Theory Study. The Journal of Chemical Physics. 1998 ;108:4098-4106.
Jang S, Voth GA. Path Integral Centroid Variables and the Formulation of their Exact Real Time Dynamics. The Journal of Chemical Physics. 1999 ;111:2357-2370.
Jang S, Voth GA. A Derivation of Centroid Molecular Dynamics and Other Approximate Time Evolution Methods for Path Integral Centroid Variables. The Journal of Chemical Physics. 1999 ;111:2371-2384.
Jang S, Voth GA. A Relationship between Centroid Dynamics and Path Integral Quantum Transition State Theory. The Journal of Chemical Physics. 2000 ;112:8747-8757.
Jang S, Sinitskiy AV, Voth GA. Can the Ring Polymer Molecular Dynamics Method be Interpreted as Real Time Quantum Dynamics?. J. Chem. Phys. 2014 ;140:1-11.
Jang S, Voth GA. Can Quantum Transition State Theory be Defined as a t = 0+ Limit?. J. Chem. Phys. 2016 ;144(084110):1-12.
Jang S, Voth GA. Non-Uniqueness of Quantum Transition State Theory and General Dividing Surfaces in the Path Integral Space. J. Chem. Phys. 2017 ;146.
Jarin Z, Tsai F-C, Davtyan A, Pak AJ, Bassereau P, Voth GA. Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys. J. 2019 ;117(3):553-562.
Jarin Z, Pak AJ, Bassereau P, Voth GA. Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins. Biophys. J. 2021 ;120:46-54.
Jarin Z, Newhouse J, Voth GA. Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover. J. Chem. Theory Comp. 2021 ;17(2):1170-1180.
Jeon J, Lefohn AE, Voth GA. An Improved Polarflex Water Model. J. Chem. Phys. 2003 ;118:7504-7518.
Jeon J, Voth GA. The Dynamic Stress Responses to Area Change in Planar Lipid Bilayer Membranes. Biophys J. 2005 ;88:1104-19.
Jeon J, Voth GA. Gating of the Mechanosensitive Channel Protein MscL: The Interplay of Membrane and Protein. Biophys. J. 2008 ;94:3497-3511.
Jiang W, Wang Y, Voth GA. Molecular Dynamics Simulation of Nanostructural Organization in Ionic Liquid/Water Mixtures. J Phys Chem B. 2007 ;111:4812-8.
Jiang W, Wang Y, Yan T, Voth GA. A Multiscale Coarse-Graining Study of Liquid/Vacuum Interface of Room-Temperature Ionic Liquids with Alkyl Substituents of Different Lengths. J. Phys. Chem. C. 2008 ;112:1132-1139.
Jiang W, Yan T, Wang Y, Voth GA. Molecular Dynamics Simulation of the Energetic Room Temperature Ionic Liquid 1-Hydroxyethyl-4Amino-1, 2, 4-Triazolium Nitrate (HEATN). J. Phys. Chem. B. 2008 ;112:3121-3131.
Jin J, Voth GA. Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. J. Chem. Theory Comp. 2018 ;14(4):2180-2197.
Jin J, Han Y, Voth GA. Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding. J. Chem. Theory Comput. 2018 ;14(12):6159-6174.
Jin J, Han Y, Voth GA. Coarse-Graining Involving Virtual Sites: Centers of Symmetry Coarse-Graining. J. Chem. Phys. 2019 ;150(15):1-15.
Jin J, Pak AJ, Voth GA. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J. Chem. Phys. Lett. 2019 ;10:4549-4557.
Jin J, Yu A, Voth GA. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J. Chem. Theory Comp. 2020 ;16(11):6823–6842.
Jin J, Han Y, Voth GA. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-body Projected Water (BUMPer). I. General Theory and Model. J. Chem. Phys. 2021 ;154:044104.
Jin J, Pak AJ, Voth GA. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-Body Projected Water (BUMPer). II. Temperature Transferability and Structural Properties at Low Temperature. J. Chem. Phys. 2021 ;154:044105.
Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J. Chem. Theory Comput. 2022 ;18(10):5759–5791.
Jin J, Schweizer KS, Voth GA. Understanding Dynamics in Coarse-Grained Models: I. Universal Excess Entropy Scaling Relationship. J. Chem. Phys. Submitted .
Jin J, Schweizer KS, Voth GA. Understanding Dynamics in Coarse-Grained Models: II. Coarse-Grained Diffusion Modeled Using Hard Sphere Theory. J. Chem. Phys. Submitted .
Jorn R, Savage J, Voth GA. Proton Conduction in Exchange Membranes Across Multiple Length Scales. Acc. Chem. Res. 2012 ;45:2002-2010.
Jorn R, Voth GA. Mesoscale Simulation of Proton Transport in Proton Exchange Membranes. J. Phys. Chem. C. 2012 ;116:935-944.
Jorn* R, Kumar* R, Abraham DP, Voth GA. Atomistic Modeling of the Electrode-Electrolyte Interface in Li-ion Energy Storage Systems: Electrolyte Structuring. J. Phys. Chem. C. 2013 ;17.
Jr. HRD, Lu L, Voth GA. Multiscale Coarse-Graining of the Protein Energy Landscape. PLoS Comp. Bio. 2010 ;6:e1000827.
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Ka BJ, Voth GA. Combining the Semiclassical Initial Value Representation with Centroid Dynamics. J. Phys. Chem. B. 2004 ;108:6883-6892.
Ka BJ, Voth GA. An Efficient and Accurate Implementation of Centroid Molecular Dynamics Using a Gaussian Approximation. J Phys Chem A. 2005 ;109:11609-17.
Katkar HH, Davtyan A, Durumeric AEP, Hocky GM, Schramm CS, De La Cruz EM, Voth GA. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophysical Journal. 2018 ;115(18):1589-1602.
Kim S, Voth GA. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis. J. Phys. Chem. B . 2021 ;125:6872-6888.
Kim S, Li C, Jr RVFarese, Walther TC, Voth GA. Key Factors Governing Initial Stages of Lipid Droplet Formation. J. Phys. Chem. B . 2022 ;126(2):453–462.
Kim S, Chung J, Arlt H, Pak AJ, Jr RVFarese, Walther TC, Voth GA. Seipin Transmembrane Segments Critically Function in Triglyceride Nucleation and Droplet Budding from the Membrane. eLife . 2022 ;11:e75808.
Kim S, Swanson JMJ, Voth GA. Computational Studies of Lipid Droplets. J. Phys. Chem. B . 2022 ;126(11):2145–2154.
Kim J, Schmitt UW, Gruetzmacher JA, Voth GA, Scherer NF. The Vibrational Spectrum of the Hydrated Proton: Comparison of Experiment, Simulation, and Normal Mode Analysis. J. Chem. Phys. 2002 ;116:737-746.
Klippenstein SJ, Voth GA, Marcus RA. Iteratively Determined Effective Hamiltonians for the Adiabatically Reduced Coupled Equations Approach to Intramolecular Dynamics Calculations. J. Chem. Phys. 1986 ;85:5019-5026.
Knight C, Maupin CM, Izvekov S, Voth GA. Defining Condensed Phase Reactive Force Fields From Ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton. J. Chem. Theor. Comp. 2010 ;6:3223–3232.
Knight C, Voth GA. Coarse-graining Away Electronic Structure: A Rigorous Route to Accurate Condensed Phase Interaction Potentials. Mol. Phys. 2012 ;110:935-944.
Knight C, Lindberg G, Voth GA. Multiscale Reactive Molecular Dynamics. J. Chem. Phys. 2012 ;137:22A525.
Knight C, Voth GA. The Curious Case of the Hydrated Proton. Acc. Chem. Res. 2012 ;45:101-109.
Knox CK, Voth GA. Probing Selected Morphological Models of Hydrated Nafion Using Large Scale Molecular Dynamics Simulations. J. Phys. Chem. B. 2010 ;114:3205–3218.
Koper MTM, G. A. Voth, " (HA)" (2000). Molecular Dynamics of Bond-Breaking Electron-Transfer Reactions at Metal-Liquid Interfaces. CATTECH 4. 2000 :51-55.
Koper MTM, Voth GA. A Three-dimensional Potential Energy Surface for Dissociative Adsorption and Associative Desorption at Metal Electrodes. The Journal of Chemical Physics. 1998 ;109:1991-2001.
Koper MTM, Voth GA. A Theory for Adiabatic Bond Breaking Electron Transfer Reactions at Metal Electrodes. Chem. Phys. Lett. 1998 ;282:100-106.
Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Liu L, Voth GA, DeGrado WF. Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins. Nat. Chem. Submitted .
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.
Krishna V, Noid WG, Voth GA. The Multiscale Coarse-graining Method. IV. Transferring Coarse-grained Potentials Between Temperatures. J. Chem. Phys. 2009 ;131:024103.
Krishna V, Voth GA. Evaluation of Nonlinear Quantum Time Correlation Functions within the Centroid Dynamics Formulation. J Phys Chem B. 2006 ;110:18953-7.
Krumrine JR, Jang S, Alexander MH, Voth GA. Quantum Molecular Dynamics and Spectral Simulation of a Boron Impurity in Solid Para-hydrogen. The Journal of Chemical Physics. 2000 ;113:9079-9089.
Kumar R, Knight C, Voth GA. Exploring the Behavior of the Hydrated Excess Proton at Hydrophobic Interfaces. Faraday Discussions. 2013 .
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Lai C-L, Jao CC, Lyman E, Gallop JL, Peter BJ, McMahon HT, Langen R, Voth GA. Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain. J. Mol. Biol. 2012 ;423:800-817.
Lai C-L, Landgraf KE, Voth GA, Falke JJ. Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKCα C2 Domain: A Combined Molecular Dynamics and Experimental Study. J. Mol. Biol. 2010 ;402:301–310.
Lai C-L, Srivastava A, Pilling C, Falke JJ, Voth GA. Molecular Mechanism of Membrane Binding of the GRP1 PH Domain. J. Mol. Biol. 2013 ;425(17):3073-3090.
Lange AW, Voth GA. A Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations. J. Chem. Theor. Comp. 2013 ;9:4018–4025.
Lapid H, Agmon N, Petersen MK, Voth GA. A Bond-order Analysis of the Mechanism for Hydrated Proton Mobility in Liquid Water. J Chem Phys. 2005 ;122:14506.
Larini L, Lu L, Voth GA. The Multiscale Coarse-Graining Method. VI. Implementation of Three-Body Coarse-Grained Potentials. J. Chem. Phys. 2010 ;132:164107.
Lederman SM, Lopez V, Fairen V, Voth GA, Marcus RA. Vibrational Energy Redistribution Across a Heavy Atom. Chem. Phys. 1989 ;139:171-184.
Lederman SM, Lopez V, Voth GA, Marcus RA. Quantum and Classical Energy Transfer Between Ligands of a Heavy Metal Atom. Chem. Phys. Lett. 1986 ;124:93-98.
Lee HJ, Svahn E, Swanson JMJ, Lepp H, Voth GA, Brzezinski P, Gennis RB. The Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. J. Am. Chem. Soc. 2010 ;132:16225–16239.
Lee S, Swanson JMJ, Voth GA. Multiscale Simulations Reveal the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophys. J. 2016 ;110(6):1334–1345.
Lee S, Liang R, Voth GA, Swason JMJ. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comp. . 2016 ;12:879-891.
Lee S, Mayes HB, Swanson JMJ, Voth GA. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. J. Am. Chem. Soc. . 2016 .
Lefohn AE, Ovchinnikov MV, Voth GA. A Multi-State Empirical Valence Bond Approach to a Polarizable and Flexible Water Model. J. Phys. Chem. B. 2001 ;105:6628-6637.
Lewis JP, Glaesemann KR, VanOpdorp K, Voth GA. Ab Initio Calculations of Reactive Pathways for α-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (α-HMX). The Journal of Physical Chemistry A. 2000 ;104:11384-11389.
Lewis JP, Glaesemann KR, Voth GA, Fritsch J, Demkov AA, Ortega J, O. F. Sankey, " " 64 1951. Further Developments in the Local-Orbital Density-Functional-Theory Tight-Binding Method. Phys. Rev. B. 2001 ;64:195103.
Lewis JP, Sewell TD, Evans RB, Voth GA. Electronic Structure Calculation of the Structures and Energies of the Three Pure Polymorphic Forms of Crystalline HMX. The Journal of Physical Chemistry B. 2000 ;104:1009-1013.
Li D, Voth GA. Feynman Path Integral Approach for Studying Intramolecular Effects in Proton-transfer Reactions. The Journal of Physical Chemistry. 1991 ;95:10425-10431.
Li D, Voth GA. A Path integral Einstein Model for Characterizing the Equilibrium States of Low Temperature Solids. The Journal of Chemical Physics. 1992 ;96:5340-5353.
Li DH, Voth GA. A Variational Model for the Thermodynamical and Structural Properties of Impurities in Low Temperature Solids. J. Chem. Phys. 1993 ;98:5734-5746.
Li DH, Voth GA. Calculation of ESR Linewidths for Hydrogen Atom Impurities in Solid para-Hydrogen. J. Chem. Phys. 1994 ;100:1785-1796.
Li H, Chen H, Zeuthen T, Conrad C, Wu B, Beitz E, Voth GA. Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1. J. Mol. Biol. 2011 ;407:607–620.
Li J, Jonsson AL, Shelley JC, Beuming T, Voth GA. Ligand-Dependent Activation and Deactivation of a G Protein-Coupled Receptor. J. Am. Chem. Soc. 2013 ;135:8749-8759.
Li J, Sode O, Voth GA, Hirata S. A Solid-Solid Phase Transition in Carbon Dioxide at High Pressures and Intermediate Temperatures. Nat. Commun. 2013 ;4.
Li J, Ziemba BP, Falke JJ, Voth GA. Interactions of Protein Kinase C-α C1A and C1B Domains with Membranes: A Combined Computational and Experimental Study. J. Am. Chem. Soc. 2014 ;136(33):11757–11766.
Li Y, Christensen JR, Homa KE, Hocky GM, Fok A, Sees JA, Voth GA, Kovar DR. The F-Actin Bundler α-Actinin Ain1 is Tailored for Ring Assembly and Constriction during Cytokinesis in Fission Yeast. Mol Biol Cell. 2016 ;27(11):1821-1833.
Li Z, Voth GA. Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles. Phys. Chem. Chem. Phys. 2020 ;22(19):10753-10763.
Li Z, Li C, Wang Z, Voth GA. What Coordinate Best Describes the Affinity of the Hydrated Excess Proton for the Air-Water Interface?. J. Phys. Chem. B . 2020 .
Li C, Yue Z, Espinoza-Fonseca LM, Voth GA. Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale. Biophys. J. 2020 ;119(5):1033-1040.
Li C, Voth GA. A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces. Proc. Nat. Acad. Sci. USA . 2021 ;118(no. 49 ):e2113141118.
Li C, Voth GA. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. J. Phys. Chem B . 2021 ;125(37):10471-10480 .
Li C, Yue Z, Newstead S, Voth GA. Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys. J. 2022 ;121(12):2266–2278.
Li C, Voth GA. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J. Chem. Theory Comp. . 2022 ;18(2):599–604.
Li C, Paesani F, Voth GA. Static and Dynamic Correlations in Water: Classical Ab Initio Molecular Dynamics Run at an Elevated Temperature May Not Capture Well Explicit Nuclear Quantum Effects at Ambient Temperature. J. Chem. Theory Comp. . 2022 ;18(4):2124–2131.
Liang R, Swanson JMJ, Wikstrom M, Voth GA. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA . 2017 ;114.
Liang R, Swanson JMJ, Voth GA. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J. Chem. Theor. Comp. 2014 ;10(1):451–462.
Liang R, Li H, Swanson JMJ, Voth GA. Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2014 ;111:9396-9401.
Liang R, Swanson JMJ, Peng Y, Nelson JG, Wikström M, Voth GA. Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA. 2016 ;(113):7420-7425.
Liang R, Swanson JMJ, Madsen JJ, Hong M, DeGrado WF, Voth GA. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
Liao JL, Voth GA. A Centroid Molecular Dynamics Approach for Nonadiabatic Dynamical Processes in Condensed Phases: The Spin-Boson Case. J. Phys. Chem. B. 2002 ;106:8449-8455.
Liao JL, Voth GA. Numerical Approaches for Computing Nonadiabatic Electron Transfer Rate Constants. J. Chem. Phys. 2002 ;116:9174-9187.
Liu P, III DH, Voth GA. A Bayesian Statistics Approach to Multiscale Coarse-graining. J. Chem. Phys. 2008 ;129:214114.
Liu P, Izvekov S, Voth GA. Multiscale Coarse-Graining of Monosaccharides. J. Phys. Chem. B. 2007 ;111:11566-11575.
Liu P, Shi Q, Lyman E, Voth GA. Reconstructing Atomistic Detail from Coarse-grained Models with Resolution Exchange. J. Chem. Phys. 2008 ;129:114103.
Liu P, Voth GA. Smart Resolution Replica Exchange: an Efficient Algorithm for Exploring Complex Energy Landscapes. J Chem Phys. 2007 ;126:045106.
Liu S, Savage J, Voth GA. Mesoscale Study of Proton Transport in Proton Exchange Membranes: Role of Morphology. J. Phys. Chem. C. 2015 ;119:1753-1762.
Liu Y, Li C, Gupta M, Finer-Moore J, Verma N, Johri AK, Stroud RM, Voth GA. Key Computational Findings Reveal Proton Transfer as Driving the Functional Cycle in the Phosphate Transporter PiPT. Proc. Nat. Acad. Sci. USA . 2021 ;118(25):e2101932118.
Liu Y, Li C, Voth GA. A Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins. J. Phys. Chem. B. Submitted .
Lobaugh J, Voth GA. A Partial Averaging Strategy for Low Temperature Fourier Path Integral Monte Carlo Calculations. The Journal of Chemical Physics. 1992 ;97:4205-4214.
Lobaugh J, Voth GA. Calculation of Quantum Activation Free Energies for Proton Transfer Reactions in Polar Solvents. Chem. Phys. Lett. 1992 ;198:311-315.
Lobaugh J, Voth GA. A Path Integral Study of Electronic Polarization and Nonlinear Coupling Effects in Condensed Phase Proton Transfer Reactions. The Journal of Chemical Physics. 1994 ;100:3039-3047.
Lobaugh J, Voth GA. The Quantum Dynamics of an Excess Proton in Water. The Journal of Chemical Physics. 1996 ;104:2056-2069.
Lobaugh J, Voth GA. A Quantum Model for Water: Equilibrium and Dynamical Properties. The Journal of Chemical Physics. 1997 ;106:2400-2410.
Lobaugh J, Voth GA. Quantum Mechanical Calculations of Tunneling Rates in Condensed Phases Systems. In: Reaction Dynamics in Clusters and Condensed Phases. Reaction Dynamics in Clusters and Condensed Phases. The Netherlands: Kluwer Academic Publishers; 1994. pp. 411-422.
Loose TD, Sahrmann PG, Voth GA. Centroid Molecular Dynamics Can Be Greatly Accelerated through Neural Network Learned Centroid Forces Derived from Path Integral Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(10):5856–5863.
Lu D, Voth GA. Molecular Dynamics Simulations of Human Carbonic Anhydrase II: Insight into Experimental Results and the Role of Solvation. Proteins. 1998 ;33:119-34.
Lu D, Voth GA. Proton Transfer in the Enzyme Carbonic Anhydrase: An ab Initio Study. Journal of the American Chemical Society. 1998 ;120:4006-4014.
Lu L, Izvekov S, Das A, Andersen HC, Voth GA. Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining. J. Chem. Theor. Comp. 2010 ;6:954-965.
Lu L, Voth GA. Systematic Coarse-graining of a Multi-component Lipid Bilayer. J. Phys. Chem. B. 2009 ;113:1501-1510.
Lu L, Voth GA. The Multiscale Coarse-Graining Method. VII. Free Energy Decomposition of Coarse-Grained Effective Potentials. J. Chem. Phys. 2011 ;134:224107.
Lu L, Dama JF, Voth GA. Fitting coarse-grained distribution functions through an iterative force-matching method. J. Chem. Phys. 2013 ;139:1-10.
Lyman E, Cui H, Voth GA. Water Under the BAR. Biophys. J. 2010 ;99:1783–1790.
Lyman E, Cui H, Voth GA. Reconstructing Protein Remodeled Membranes in Molecular Detail From Mesoscopic Models. Phys. Chem. Chem. Phys. 2011 :10430–10436.
Lyman E, Higgs C, Kim B, Lupyan D, Shelley JC, Farid R, Voth GA. A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor. Structure. 2009 ;17:1660–1668.
Lyman E, Pfaendtner J, Voth GA. Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins. Biophys. J. 2008 ;95:4183–4192.
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Ma X, Li C, Martinson ABF, Voth GA. Water Assisted Proton Transport in Confined Nanochannels. J. Phys. Chem. C. 2020 ;124:16186−16201.
Madsen JJ, Grime JMA, Rossman JS, Voth GA. Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. PNAS. 2018 ;115(37).
Madsen JJ, Sinitskiy AV, Li J, Voth GA. Highly Coarse-grained Representations of Transmembrane Proteins. J. Chem. Theory Comput. 2017 ;13.
Mani S, Cosgrove DJ, Voth GA. Anisotropic Motions of Fibrils Dictated by Their Orientations in the Lamella: A Coarse-Grained Model of a Plant Cell Wall. J. Phys. Chem. B . 2020 ;124(17):3527–3539.
Mani S, Katkar HH, Voth GA. Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments. J. Phys. Chem. B . 2021 ;17(3):1900-1913.
Markovitch O, Chen H, Izvekov S, Paesani F, Voth GA, Agmon N. Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water. J. Phys. Chem. B. 2008 ;112:9456-9466.
Martyna A, Bahsoun B, Madsen JJ, Clifton LA, Jackson FSJS, Badham MD, Voth GA, Rossman JS. Cholesterol Alters the Membrane Orientation and Activity of the Influenza Virus M2 Amphipathic Helix. J. Phys. Chem. B . 2020 ;124(31):6738-6747 .
Matyushov D, Voth GA. Modeling the Free Energy Surfaces of Electron Transfer in Condensed Phases. J. Chem. Phys. 2000 ;113:5413-5424.
Matyushov DV, Voth GA. A Theory of Electron Transfer and Steady-State Optical Spectra of Chromophores with Varying Electronic Polarizability. The Journal of Physical Chemistry A. 1999 ;103:10981-10992.
Matyushov DV, Voth GA. A Perturbation Theory for Solvation Thermodynamics: Dipolar–quadrupolar Liquids. The Journal of Chemical Physics. 1999 ;111:3630-3638.
Matyushov DV, Voth GA. Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 2. Optical Spectra. The Journal of Physical Chemistry A. 2000 ;104:6485-6494.
Matyushov DV, Voth GA. Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 1. Charge Transfer Reactions. The Journal of Physical Chemistry A. 2000 ;104:6470-6484.
Matyushov DV, Voth GA. New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases. In: Lipkowitz KB, Boyd DB Reviews in Computational Chemistry. Vol. 18. Reviews in Computational Chemistry. New York: John Wiley and Sons; 2002. pp. 147-210.
Maupin CM, Aradi B, Voth GA. The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations. J. Phys. Chem. B. 2010 ;114:6922-6931.
Maupin CM, Castillo N, Taraphder S, C. Tu MKR, Silverman DN, Voth GA. Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2011 ;133:6223–6234.
Maupin CM, G. A. Voth, “ 1804 (201. Proton Transport in Carbonic Anhydrase: Insights from Molecular Simulation. Biochim. et Biophys. Acta - Proteins and Proteomics. 2010 ;1804:332-341.
Maupin CM, McKenna R, Silverman DN, Voth GA. Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2009 ;131:7598-7608.
Maupin CM, Saunders MG, Thorpe IF, McKenna R, Silverman DN, Voth GA. Origins of Enhanced Proton Transport in the Y7F Mutant of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2008 ;130:11399–11408.
Maupin CM, Voth GA. Preferred Orientations of His-64 in Human Carbonic Anhydrase II. Biochemistry. 2007 ;46:2938-47.
Maupin CM, Wong KF, Soudackov AV, Kim S, Voth GA. A Multistate Empirical Valence Bond Description of Protonatable Amino Acids. J Phys Chem A. 2006 ;110:631-9.
Maupin CM, Zheng J, Tu C, McKenna R, Silverman DN, Voth GA. Effect of Active-site Mutations at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II. Biochem. 2009 ;48:7996-8005.
Mayes HB, Lee S, Voth GA, Swanson JMJ. Multiscale Kinetic Modeling Reveals Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter. J. Am. Chem. Soc. 2018 ;140(5):1793–1804.
McCullagh M, Voth GA. Unraveling the Role of the Protein Environment for [FeFe]-Hydrogenase Charge Transfer: A New Application of Coarse-Graining. J. Phys. Chem. B. 2013 ;17:4062−4071.
McCullagh M, Saunders MG, Voth GA. Unraveling the Mystery of ATP Hydrolysis in Actin Filaments. J. Am. Chem. Soc. . 2014 ;136(37):13053–13058.
McRae RP, Schenter GK, Garrett BC, Haynes GR, Voth GA, Schatz GC. Critical Comparison of Approximate and Accurate Quantum-mechanical Calculations of Rate Constants for a Model Activated Reaction in Solution. The Journal of Chemical Physics. 1992 ;97:7392-7404.
McWhirter JL, Ayton G, Voth GA. Coupling Field Theory with Mesoscopic Dynamical Simulations of Multicomponent Lipid Bilayers. Biophys J. 2004 ;87:3242-63.
Mim C, Cui H, Gawronski-Salerno JA, Frost A, Lyman E, Voth GA, Unger VM. Structural Basis of Membrane Bending by the N-BAR Protein Endophilin. Cell. 2012 ;149.
Minichino C, Voth GA. Potential Energy Surfaces for Chemical Reactions: An Analytical Representation from Coarse Grained Data with an Application to Proton Transfer in Water. The Journal of Physical Chemistry B. 1997 ;101:4544-4552.
Mirijanian DT, Alexander MH, Voth GA. Path Integral Molecular Dynamics Simulation of Solid Para-Hydrogen with an Aluminum Impurity. Chem. Phys. Lett. 2002 ;365:487-493.
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.
Mirijanian DT, Voth GA. Unique Elastic Properties of the Spectrin Tetramer as Revealed by Multiscale Coarse-Grained Modeling. Proc. Natl. Acad. Sci. USA. 2008 ;105:1204-1208.
Mironenko AV, Voth GA. Density Functional Theory-based Quantum Mechanics/Coarse-grained Molecular Mechanics: Theory and Implementation. J. Chem. Theory Comp. 2020 ;16(10):6329–6342.
Monje-Galvan V, Voth GA. Molecular Interactions of the M and E Integral Membrane Proteins of SARS-CoV-2. Faraday Discussions. 2021 ;232:49-67 .
Murphy MJ, Voth GA, Bug ALR. Classical and Quantum Transition State Theory for the Diffusion of Helium in Silica Sodalite. The Journal of Physical Chemistry B. 1997 ;101:491-503.
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Paesani F, Iuchi S, Voth GA. Quantum Effects in Liquid Water from an Ab Initio-Based Polarizable Force Field. J. Chem. Phys. 2007 ;127:074506.
Paesani F, Voth GA. Nonlinear Quantum Time Correlation Functions from Centroid Molecular Dynamics and the Maximum Entropy Method. J. Chem. Phys. 2008 ;129:194113.
Paesani F, Voth GA. Quantum Effects Strongly Influence the Surface Premelting of Ice. J. Phys. Chem. C. 2008 ;112:324-327.
Paesani F, Voth GA. The Properties of Water: Insights from Quantum Simulations. J. Phys. Chem. B. 2009 ;113:5702–5719.
Paesani F, Voth GA. A Quantitative Assessment of the Accuracy of Centroid Molecular Dynamics for the Calculation of the Infrared Spectrum of Liquid Water. J. Chem. Phys. 2010 ;132:014105.
Paesani F, Xantheas SS, Voth GA. Infrared Spectroscopy and Hydrogen-Bond Dynamics in Liquid Water from Quantum Simulations. J. Phys. Chem. B. 2009 ;113:13118–13130.
Paesani F, Zhang W, Case DA, Cheatham, T. E. 3rd, Voth GA. An Accurate and Simple Quantum Model for Liquid Water. J Chem Phys. 2006 ;125:184507.
Pak Y, Voth GA. Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water. J. Phys. Chem. 1999 ;103:925-931.
Pak AJ, Grime JMA, Sengupta P, Chen AK, Durumeric AEP, Srivastava A, Yeager M, Briggs JAG, Lippincott-Schwartz J, Voth GA. Immature HIV-1 Lattice Assembly Dynamics are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane. Proc. Nat. Acad. Sci. USA . 2017 ;114:E10056-E10065 .
Pak AJ, Voth GA. Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Current Opinion in Structural Biology. 2018 ;52:119-126.
Pak AJ, Dannenhoffer-Lafage T, Voth GA. Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites. J Chem Theory Comput. 2019 ;15(3):2087–2100.
Pak AJ, Grime JMA, Yu A, Voth GA. Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation. J. Am. Chem. Soc. 2019 ;141(26):10214-10224.
Pak AJ, Purdy MD, Yeager M, Voth GA. Preservation of HIV-1 Gag Helical Bundle Symmetry by Bevirimat is Central to Maturation Inhibition. J. Am. Chem. Soc. 2021 ;143(45):19137−19148 .
Pak AJ, Yu A, Ke Z, Briggs JAG, Voth GA. Cooperative Multivalent Receptor Binding Promotes Exposure of the SARS-CoV-2 Fusion Machinery Core. Nat. Commun. 2022 ;13:1002.
Pak AJ, Gupta M, Yeager M, Voth GA. Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly Towards Kinetically-Trapped Morphologies. J. Am. Chem. Soc. 2022 ;144(23):10417–10428.
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.
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.
Paramore S, Ayton GS, Voth GA. Extending the Fluctuation Theorem to Describe Reaction Coordinates. J Chem Phys. 2007 ;126:051102.
Paramore S, Voth GA. Examining the Influence of Linkers and Tertiary Structure in the Forced Unfolding of Multiple-Repeat Spectrin Molecules. Biophys J. 2006 ;91:3436-45.
Parker JL, Li C, Brinth A, Wang Z, Vogeley L, Solcan N, Ledderboge-Vucinic G, Swanson JMJ, Caffrey M, Voth GA, et al. Proton Movement and Coupling in the POT Family of Peptide Transporters. Proc. Nat. Acad. Sci. USA . 2017 ;114(13182).
Pavese M, Berard DR, G. A. Voth, " " 300 (19. Ab initio Centroid Molecular Dynamics: A Fully Quantum Method for Condensed Phase Dynamics Simulations. Chem. Phys. Lett. 1999 ;300:93-98.
Pavese M, Chawla S, Lu D, Lobaugh J, Voth GA. Quantum Effects and the Excess Proton in Water. The Journal of Chemical Physics. 1997 ;107:7428-7432.
Pavese M, Jang S, Voth GA. Centroid Molecular Dynamics: A Quantum Dynamics Method Suitable for the Parallel Computer. Parallel Computing. 2000 ;26:1025-1041.
Pavese M, Voth GA. Pseudopotentials for Centroid Molecular Dynamics: Application to Self-Diffusion in Liquid para-Hydrogen. Chem. Phys. Lett. 1996 ;249:231-236.
Pavese M, Voth GA. Quantum and Classical Simulations of an Excess Proton in Water. Ber. Bunsenges. Phys. Chem. 1998 ;102:527-532.
Peng Y, Voth GA. Expanding the View of Proton Pumping in Cytochrome c Oxidase through Computer Simulation. Biochim. et Biophys. Acta-Bioenergetics. 2012 ;1817:518-525.
Peng Y, Cao Z, Zhou R, Voth GA. Path Integral Coarse-graining Replica Exchange Method for Enhanced Sampling. J. Chem. Theor. Comp. 2014 ;10 (9 ):3634–3640.
Peng Y, Swanson JMJ, Kang S, Zhou R, Voth GA. Hydrated Excess Protons Can Create Their Own Water Wires. J. Phys. Chem. B. 2015 ;(119).
Petersen MK, Hatt AJ, Voth GA. Orientational Dynamics of Water in the Nafion Polymer Electrolyte Membrane and Its Relationship to Proton Transport. J. Phys. Chem. B. 2008 ;112:7754–7761.
Petersen MK, Iyengar SS, Day TJF, Voth GA. The Hydrated Proton at the Water Liquid/Vapor Interface. J. Phys. Chem. B. 2004 ;108:14804-14806.
Petersen MK, Kumar R, White HS, Voth GA. A Computationally Efficient Treatment of Polarizable Electrochemical Cells Held at a Constant Potential. J. Phys. Chem. C. 2012 ;116:4903-4912.
Petersen MK, Voth GA. Characterization of the Solvation and Transport of the Hydrated Proton in the Perfluorosulfonic Acid Membrane Nafion. J Phys Chem B. 2006 ;110:18594-600.
Petersen MK, Voth GA. Amphiphilic Character of the Hydrated Proton in Methanol−Water Solutions. J Phys Chem B. 2006 ;110:7085-9.
Petersen MK, Wang F, Blake NP, Metiu H, Voth GA. Excess Proton Solvation and Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion. J Phys Chem B. 2005 ;109:3727-30.
Pfaendtner J, Branduardi D, Pollard TD, Parrinello M, Voth GA. Nucleotide-Dependent Conformational States of Actin. Proc. Natl. Acad. Sci. USA. 2009 ;106:12723–12728.
Pfaendtner J, Cruz DLEM, Voth GA. Actin Filament Remodeling by Actin Depolymerization Factor/Cofilin. Proc. Natl. Acad. Sci. USA. 2010 ;107:7299–7304.
Pfaendtner J, Lyman E, Pollard TD, Voth GA. Structure and Dynamics of the Actin Filament. J. Mol. Biol. 2010 ;396:252–263.
Pfaendtner J, Volkmann N, Hanein D, Dalhaimer P, Pollard TD, Voth GA. Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation. J. Mol. Biol. 2012 ;416:148–161.
Pfaendtner J, Voth GA. Molecular Dynamics Simulation and Coarse-grained Analysis of the Arp2/3 Complex. Biophys. J. 2008 ;95:5324-5333.
Phillips CL, Voth GA. Discovering Crystals Using Shape Matching and Machine Learning. Soft Matter. 2013 ;9:8552.
Popolo DMG, Voth GA. On the Structure and Dynamics of Ionic Liquids. J. Phys. Chem. B. 2004 ;108:1744-1752.
Prévost C, Cohen ME, Kory N, Lin Q, Voth GA, Farese, Jr. RV, Walther TC. Mechanism of Targeting of Amphipathic Helix-Containing Proteins to Lipid Droplets. Dev. Cell. 2018 ;44(1):73-86.
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Qin Z, Tepper HL, Voth GA. Effect of Membrane Environment on Proton Permeation through Gramicidin A Channels. J. Phys. Chem. B. 2007 ;111:9931-9939.
Quitevis EL, Bardak F, Xiao D, L. G. Hines J, Son P, Bartsch RA, Yang P, Voth GA. OKE Spectroscopy and Molecular Dynamics Simulations of Polar and Nonpolar Molecules in Ionic Liquids. In: Ionic Liquids: Science and Applications. ACS Symposium Series 1117th ed. Ionic Liquids: Science and Applications. Washington, DC: American Chemical Society; 2012. pp. 271-287.
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Randa HS, Forrest LR, Voth GA, Sansom MS. Molecular Dynamics of Synthetic Leucine-serine Ion Channels in a Phospholipid Membrane. Biophys J. 1999 ;77:2400-10.
Rega N, Iyengar SS, Voth GA, Schlegel HB, Vreven T, Frisch MJ. Hybrid Ab Initio Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach. J. Phys. Chem. B. 2004 ;108:4210 - 4220.
Reichman DR, Roy P-N, Jang S, Voth GA. A Feynman Path Centroid Dynamics Approach for the Computation of Time Correlation Functions Involving Nonlinear Operators. The Journal of Chemical Physics. 2000 ;113:919-929.
Reichman DR, Voth GA. Self-consistent Harmonic Theory of Solvation in Glassy Systems: Quantum Solvation. The Journal of Chemical Physics. 2000 ;112:3280-3284.
Reichman DR, Voth GA. Self-consistent Harmonic Theory of Solvation in Glassy Systems: Classical Solvation. The Journal of Chemical Physics. 2000 ;112:3267-3279.
Roy P-N, Jang S, Voth GA. Feynman Path Centroid Dynamics for Fermi–Dirac Statistics. The Journal of Chemical Physics. 1999 ;111:5303-5305.
Roy P-N, Voth GA. On the Feynman Path Centroid Density for Bose-Einstein and Fermi-Dirac Statistics. The Journal of Chemical Physics. 1999 ;110:3647-3652.
Ryu WH, Han Y, Voth G. Coarse-graining of many-body path integrals: Theory and numerical approximations. J. Chem. Phys. 2019 ;150(24).
Ryu WH, Voth GA. Coarse-Graining of Imaginary Time Feynman Path Integrals: Inclusion of Intramolecular Interactions and Bottom-up Force-Matching. J. Phys. Chem. A. 2022 ;126(35):6004–6019.
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Sagnella DE, Cao J, Voth GA. A Semiclassical Reactive Flux Method for the Calculation of Condensed Phase Activated Rate Constants. Chem. Phys. 1994 ;180:167-180.
Sagnella DE, Voth GA. Structure and Dynamics of Hydronium in the Ion Channel Gramicidin A. Biophys J. 1996 ;70:2043-51.
Saielli G, Voth GA, Wang Y. Diffusion Mechanisms in Smectic Ionic Liquid Crystals: Insights from Coarse-grained MD Simulations. Soft Matter. 2013 ;9:5716-5725.
Sarode* HN, Lindberg* GE, Yang Y, Felberg LE, Voth GA, Herring AM. Insights into the Transport of Aqueous Quaternary Ammonium Cations: A Combined Experimental and Computational Study. J. Phys. Chem. B. 2014 ;118:1363-1372.
Saunders MG, Voth GA. Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis. J. Mol. Biol. 2011 ;413:279-291.
Saunders MG, Voth GA. Comparison Between Actin Filament Models: Coarse-Graining Reveals Essential Differences. Structure. 2012 ;20:641-653.
Saunders MG, Voth GA. Coarse-graining of Multi-Protein Assemblies. Curr. Opin. Struct. Biol. 2012 ;22:144-150.
Saunders MG, Voth GA. Coarse-graining Methods for Computational Biology. Annu. Rev. Biophysics. 2013 ;42:73-93.
Saunders MG, Tempkin J, Weare J, Dinner AR, Roux B, Voth GA. Nucleotide Regulation of the Structure and Dynamics of G-actin. Biophys. J. 2014 ;106:1710-1720.
Savage J, Tse Y-LS, Voth GA. The Proton Transport Mechanism of Perfluorosulfonic Acid Membranes. J. Phys. Chem. C. 2014 ;118(31):17436–17445.
Savage J, Voth G. Persistent Sub-diffusive Proton Transport in Perfluorosulfonic Acid Membranes. J. Phys. Chem. Lett. . 2014 ;(5(17):3037–3042.
Savage J, Voth GA. Proton Solvation and Transport in Realistic Proton Exchange Membrane Morphologies. J. Phys. Chem. C. 2016 ;120(6):3176–3186.
Scharf D, Martyna GJ, Li D, Voth GA, Klein ML. Nature of Lithium Trapping Sites in the Quantum Solids Para-hydrogen and Ortho-deuterium. The Journal of Chemical Physics. 1993 ;99:9013-9020.
Schenter GK, Garrett BC, Voth GA. The Quantum Vibrational Dynamics of Cl[sup -](H[sub 2]O)[sub n] Clusters. The Journal of Chemical Physics. 2000 ;113:5171-5178.
Schlegel HB, Iyengar SS, Li X, Millam JM, Voth GA, Scuseria GE, Frisch MJ. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics. J. Chem. Phys. 2002 ;117:8694-8704.
Schlegel HB, Millam JM, Iyengar SS, Voth GA, Daniels AD, Scuseria GE, Frisch MJ. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. J. Chem. Phys. 2001 ;114:9758-9763.
Schmitt UW, Voth GA. Multistate Empirical Valence Bond Model for Proton Transport in Water. The Journal of Physical Chemistry B. 1998 ;102:5547-5551.
Schmitt UW, Voth GA. The Computer Simulation of Proton Transport in Water. The Journal of Chemical Physics. 1999 ;111:9361-9381.
Schmitt UW, Voth GA. Quantum Properties of the Excess Proton in Liquid Water. Israeli J. Chem. 1999 ;39:483-492.
Schmitt UW, Voth GA. The Isotope Substitution Effect on the Hydrated Proton. Chem. Phys. Lett. 2000 ;329:36-41.
Schramm AC, Hocky GM, Voth GA, .Blanchoin L, Martiel J-L, De La Cruz EM. Actin Filament Strain Promotes Severing and Cofilin Dissociation. Biophys J. 2017 ;112.
Schramm AC, Hocky GM, Voth GA, Martiel J-L, De La Cruz EM. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophys. J. 2019 ;117(3):453-463.
Schwieters CD, Voth GA. The Semiclassical Calculation of Nonadiabatic Tunneling Rates. The Journal of Chemical Physics. 1998 ;108:1055-1062.
Schwieters CD, Voth GA. Extension of Path Integral Quantum Transition State Theory to the Case of Nonadiabatic Activated Dynamics. The Journal of Chemical Physics. 1999 ;111:2869-2877.
Sharp ME, Vázquez FX, Wagner JW, Dannenhoffer-Lafage T, Voth GA. Multiconfigurational Coarse-Grained Molecular Dynamics. J. Chem. Theory Comp. 2019 ;15(5):3306–3315.
Shellman SD, Lewis JP, Glaesemann KR, Sikorski K, Voth GA. Massively Parallel Linear-scaling Algorithm in an ab initio Local-orbital Total-energy Method. J. Comp. Phys. 2003 ;188:1-15.
Shi Q, Izvekov S, Voth GA. Mixed Atomistic and Coarse-Grained Molecular Dynamics:  Simulation of a Membrane-Bound Ion Channel. J Phys Chem B. 2006 ;110:15045-8.
Shi Q, Liu P, Voth GA. Coarse-Graining in Interaction Space: An Analytical Approximation for the Effective Short-Ranged Electrostatics. J. Phys. Chem. B. 2008 ;112:16230–16237.
Shi Q, Voth GA. Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers. Biophys J. 2005 ;89:2385-94.
Simunovic M, Voth GA. Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90. Biophys. J. 2012 ;103:284-292.
Simunovic M, Srivastava A, Voth GA. Linear Aggregation of Proteins on the Membrane as a Prelude to Membrane Remodeling. Proc. Natl. Acad. Sci. 2013 ;110(51).
Simunovic M, Mim C, Marlovits T, Resch G, Unger G, Voth GA. Protein-Mediated Transformation of Lipid Vesicles into Tubular Networks. Biophys. J. 2013 ;105(3):711-719.
Simunovic M, Voth GA. Membrane Tension Controls the Assembly of Curvature-Generating Proteins. Nature Communications. 2015 ;6(7219):1-8.
Simunovic M, Voth GA, Callan-Jones A, Bassereau P. When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol. 2015 .
Simunovic M, Šarić A, Henderson JM, Lee K-YC, Voth GA. Lipid Membrane Mediates Long-Range Interactions Between Linear Filaments of Membrane-Curving Proteins. ACS Cen. Sci. 2017 ;3:1246-1253 .
Simunovic M, Evergren E, Golushko I, Prévost C, Renard H-F, Johannes L, McMahon H, Lorman V, Voth GA, Bassereau P. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Nat. Acad. Sci. USA. 2016 .
Simunovic M, Manneville J-B, Renard H-F, Evergren E, Raghunathan K, Kenworthy AK, Voth GA, Prost J, McMahon HT, Johannes L, et al. Friction Mediates Scission of Tubular Membranes Scaffolded by BAR Proteins. Cell. 2017 ;170.
Simunovic M, Bassereau P, Voth GA. Organizing Membrane-Curving Proteins: The Emerging Dynamical Picture. Curr. Opin. Struct. Biol. 2018 ;51:99-105 .
Sinitskiy A, Voth GA. Quantum Mechanics / Coarse-Grained Molecular Mechanics (QM/CG-MM). J Chem Phys. 2018 ;148(102335):1-15.
Sinitskiy AV, Saunders MG, Voth GA. Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes. J. Phys. Chem. B. 2012 ;116:8363-8374.
Sinitskiy AV, Voth GA. Coarse-Graining of Proteins Based on Elastic Network Models. Chem. Phys. 2013 ;422:165-174.
Sinitskiy AV, Voth GA. A Reductionist Perspective on Quantum Statistical Mechanics: Coarse-Graining of Path Integrals. J. Chem. Phys. 2015 ;143(094104):1-10.
Small DW, Matyushov DV, Voth GA. The Theory of Electron Transfer Reactions:  What May Be Missing?. J Am Chem Soc. 2003 ;125:7470-8.
Smondyrev AM, Voth GA. Molecular Dynamics Simulation of Proton Transport through the Influenza A Virus M2 Channel. Biophys J. 2002 ;83:1987-96.
Smondyrev AM, Voth GA. Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane. Biophys J. 2002 ;82:1460-8.
Sode O, Voth GA. Electron Transfer Activation of a Second Water Channel for Proton Transport in [FeFe]-Hydrogenase. J. Chem. Phys. 2014 ;141(22D527):1-9.
Sonnenberg JL, Wong KF, Voth GA, Schlegel HB. A Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations. J. Chem. Theory. Comp. 2009 ;5:949-961.
Srivastava A, Voth GA. A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models. J. Chem. Theor. Comp. 2013 ;9:750-765.
Srivastava A, Voth GA. Solvent-Free Highly Coarse-Grained Models for Charged Lipid Systems. J. Chem. Theor. Comp. . 2014 ;(10):4730-4744.
Straus JB, Calhoun A, Voth GA. Calculation of Solvent Free Energies for Heterogeneous Electron Transfer at the Water–metal Interface: Classical Versus Quantum Behavior. The Journal of Chemical Physics. 1995 ;102:529-539.
Straus JB, Llorente JGM, Voth GA. Manifestations of Spatially Dependent Friction in Classical Activated Rate Processes. The Journal of Chemical Physics. 1993 ;98:4082-4097.
Straus JB, Voth GA. Studies on the Influence of Nonlinearity in Classical Activated Rate Processes. The Journal of Chemical Physics. 1992 ;96:5460-5470.
Straus JB, Voth GA. A Computer Simulation Study of Free Energy Curves in Heterogeneous Electron Transfer. The Journal of Physical Chemistry. 1993 ;97:7388-7391.
Sumner I, Voth GA. Proton Transport Pathways in [NiFe]-Hydrogenase. J. Phys. Chem. B. 2012 ;116:2917–2926.
Sumpter BG, Voth GA, Noid DW, Wunderlich B. Infrared Laser-induced Chaos and Conformational Disorder in a Model Polymer Crystal: Melting vs Ablation. The Journal of Chemical Physics. 1990 ;93:6081-6091.
Sun Y-C, Gai H, Voth GA. Vibrational Energy Relaxation Dynamics of C–H Stretching Modes on the Hydrogen-terminated H/C(111)1 x 1 Surface. The Journal of Chemical Physics. 1994 ;100:3247-3251.
Sun Y-C, Gai H, Voth GA. Vibrational Energy Relaxation Dynamics of Si–H Stretching Modes on Stepped H/Si(111)1x1 Surfaces. Chem. Phys. 1995 ;20:357-368.
Sun Y-C, Voth GA. Path Integral Calculation of Hydrogen Diffusion Rates on Metal Surfaces. The Journal of Chemical Physics. 1993 ;98:7451-7458.
Sun R, Dama JF, Tan JS, Rose JP, Voth GA. Transition-Tempered Metadynamics is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes. J. Chem. Theory Comp. . 2016 .
Sun R, Sode O, Dama JF, Voth GA. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics. J. Chem. Theory Comput. 2017 ;13.
Sun R, Han Y, Swanson JMJ, Tan JS, Rose JP, Voth GA. Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants. J. Chem. Phys. 2018 ;149.
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Tan A, Pak AJ, Morado DR, Voth GA, Briggs JAG. Immature HIV-1 Assembles from Gag Dimers Leaving Partial Hexamers at Lattice Edges as Substrates for Proteolytic Maturation. Proc. Nat. Acad. Sci. USA . 2021 ;118(3):e2020054118.
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Tepper HL, Voth GA. A Coarse-grained Model for Double-helix Molecules in Solution: Spontaneous Helix Formation and Equilibrium Properties. J Chem Phys. 2005 ;122:124906.
Tepper HL, Voth GA. Protons May Leak through Pure Lipid Bilayers via a Concerted Mechanism. Biophys J. 2005 ;88:3095-108.
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Thorpe IF, Goldenberg DP, Voth GA. An Exploration of Transferability in Multiscale Coarse-grained Peptide Models. J. Phys. Chem. B. 2011 ;115:11911-11926.
Thorpe IF, Zhou J, Voth GA. Peptide Folding Using Multiscale Coarse-grained Models. J. Phys. Chem. B. 2008 ;112:13079–13090.
Tong D, Voth GA. Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability. Biophys. J. . 2020 ;118(12):2938-2951.
Tsai F-C, Henderson JM, Jarin Z, Kremneva E, Pernier J, Mikhajlov O, Manzi J, Clainche LC, Voth GA, Lappalainen P, et al. Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
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Vath P, Zimmt MB, Matyushov DV, Voth GA. Temperature Dependence of the Solvent Reorganization Energy of Electron Transfer in Highly Polar Solvents. J. Phys. Chem. B. 1999 ;103:9130-9140.
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Voth GA. Approximate Coupled Equations for Multiphoton Processes Induced by One or More Lasers. Chem. Phys. Lett. 1986 ;129:315-320.
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Wagner JW, Dama JF, Voth GA. Predicting the Sensitivity of Multiscale Coarse-grained Models to their Underlying Fine-grained Model Parameters. J. Chem. Theory Comp. . 2015 ;11:3547-3560.
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Wang Y, Voth GA. Molecular Dynamics Simulations of Polyglutamine Aggregation using Solvent-Free Multiscale Coarse-Grained Models. J. Phys. Chem. B. 2010 ;114:8735–8743.
Wang Y, Jiang W, Voth GA. Spatial Heterogeneity in Ionic Liquids. In: Brennecke JF, Rogers RD, Seddon KR Ionic Liquids IV. Not Just Solvents Anymore. Ionic Liquids IV. Not Just Solvents Anymore. Washington DC: American Chemical Society; 2007. pp. 272-307.
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Watkins LC, DeGrado WF, Voth GA. Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics. J. Am. Chem. Soc. 2020 ;142(41):17425–17433.
Watkins LC, DeGrado WF, Voth GA. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior. J. Am. Chem. Soc. 2022 ;144(2):776–776.
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White AD, Knight C, Hocky GM, Voth GA. Improved Ab Initio Molecular Dynamics by Minimally Biasing with Experimental Data. J. Chem. Phys. 2017 ;146.
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Yamashita T, Voth GA. Properties of Hydrated Excess Protons Near Phospholipid Bilayers. J. Phys. Chem. B. 2010 ;114:592–603.
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Yan T, Burnham CJ, Popolo DMG, Voth GA. Molecular Dynamics Simulation of Ionic Liquids: The Effect of Electronic Polarizability. J. Phys. Chem. B. 2004 ;108:11877-11881.
Yan T, Li S, Jiang W, Gao X, Xiang B, Voth GA. Structure of the Liquid−Vacuum Interface of Room-Temperature Ionic Liquids:  A Molecular Dynamics Study. J Phys Chem B. 2006 ;110:1800-6.
Yang P, Voth GA, Xiao D, L. G. Hines J, Bartsch RA, Quitevis EL. Nanostructural Organization in Carbon Disulfide/Ionic Liquid Mixtures: Optical Kerr Effect Spectroscopy and Molecular Dynamics Simulations. J. Chem. Phys. 2011 ;135:034502.
Yu A, Skorupka K, Pak AJ, Ganser-Pornillos BK, Pornillos O, Voth GA. TRIM5α Self-Assembly and Compartmentalization of the HIV-1 Viral Capsid. Nature Comm. 2020 ;11:1-10.
Yu A, Lee EMY, Jin J, Voth GA. Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6). Science Advances. 2020 ;6(36).
Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 .
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Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J. Am. Chem. Soc. 2019 ;141:13421-13433.
Yue Z, Wang Z, Voth GA. Ion Permeation, Selectivity, and Electronic Polarization in Fluoride Channels. Biophys. J. 2022 ;121:1336–1347.
Yue Z, Li C, Voth GA. The Role of Conformational Change and Key Glutamic Acid Residues in the ClC-ec1 Antiporter. Biophys. J. Submitted .
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Zhang Y, Voth GA. A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles. J. Chem. Theor. Comp. 2011 ;7:2277-2283.
Zhang Z, Lu L, Noid WG, Krishna V, Pfaendtner J, Voth GA. A Systematic Methodology for Defining Coarse-grained Sites in Large Biomolecules. Biophys. J. 2008 ;95:5073-5083.
Zhang Z, Pfaendtner J, Grafmüller A, Voth GA. Defining Coarse-grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models. Biophys. J. 2009 ;97:2327-2337.
Zhang Z, Sanbonmatsu KY, Voth GA. Key Inter-molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis. J. Am. Chem. Soc. 2011 ;133:16828-16838.
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Zhang Y, Voth GA. The Coupled Proton Transport in the ClC-ec1 Cl-/H+ Antiporter. Biophys. J. 2011 ;101:L47-L49.
Zhou J, Thorpe IF, Izvekov S, Voth GA. Coarse-Grained Peptide Modeling Using a Systematic Multiscale Approach. Biophys J. 2007 ;92:4289-303.
Zhou S, He P, Dhindwal S, Grum-Tokars VL, K. Li PY, Modica JA, Bleher R, R. Reis dos, Zuchniarz J, Dravid VP, et al. Synthesis, Characterization and Simulation of Four-Armed Megamolecules. Biomacromolecules. 2021 ;22(6):2363–2372.
Ziemba BP, Li J, Landgraf KE, Knight JD, Voth GA, Falke JJ. Single Molecule Studies Reveal A Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C alpha. Biochemistry. 2014 ;53:1697-1713.
Zimmerman D, Homa KE, Hocky GM, Pollard LW, De La Cruz EM, Voth GA, Trybus KM, Kovar DR. Mechanosensitive Inhibition of Formin Facilitates Contractile Actomyosin Ring Assembly. Nat. Comm. 2017 ;8 (703).
Zsolnay V, Katkar HH, Chou SZ, Pollard TD, Voth GA. Structural Basis for Polarized Elongation of Actin Filaments. Proc. Nat. Acad. Sci. USA. 2020 .
Zuchniarz J, Liu Y, Li C, Voth GA. Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values. J. Phys. Chem. B. 2022 ;126(38):7321–7330.