Publications

[ Author(Desc)] Title Type Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
A
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.
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(19):194506.
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.
Aydin F, Katkar HH, Morganthaler AN, Harker AJ, Kovar DR, Voth GA. Prediction of the essential intermolecular contacts for side-binding of VASP on F-Actin. Cytoskeleton. Submitted .
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(6):1521–1535.
Ayton G, Voth GA. Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers. Biophys J. 2002 ;83:3357-70.
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, 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.
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 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, 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 Simulation of Transmembrane Proteins. J Struct Biol. 2007 ;157:570-8.
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 GS, Noid WG, Voth GA. Systematic Coarse-graining of Biomolecular and Soft Matter Systems. MRS Bulletin. 2007 ;32:929-934.
Ayton GS, Voth GA. Multiscale Simulation of Protein Mediated Membrane Remodeling. Seminars in Cell and Developmental Biology. 2010 ;21:357-362.
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, Voth GA. The Simulation of Biomolecular Systems at Multiple Length and Time Scales. Int. J. for Multiscale Comp. Eng. 2004 ;2:291-311.
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 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, Voth GA. Multiscale Computer Simulation of the Immature HIV-1 Virion. Biophys. J. 2010 ;99:2757–2765.
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, Voth GA. Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys J. 2004 ;87:3299-311.
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 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, Voth GA. A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales. J. Phys. Chem. B. 2009 ;113:4413-4424.
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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.
Banerjee P, Voth GA. Conformational Transitions of the HIV-1 Gag Polyprotein Upon Multimerization and gRNA Binding. Biophys. J. 2024 ;123:42 - 56.
Banerjee P, Monje-Galvan V, Voth GA. Cooperative Membrane Binding of HIV-1 Matrix Proteins. J. Phys. Chem. B. Submitted .
Banerjee P, Qu K, Briggs JAG, Voth GA. Molecular Dynamics Simulations of HIV-1 Matrix-Membrane Interactions at Different Stages of Viral Maturation. Biophys. J. In Press .
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.
Beckett D, Voth GA. Unveiling the catalytic mechanism of GTP hydrolysis in microtubules. Proc. Natl. Acad. Sci. U.S.A. 2023 ;120(27):e2305899120.
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. PLoS Comput. Biol. 2019 ;15(6):e1007077.
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 .
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, Fournier JA, Voth GA, Tokmakoff A. IR Spectral Assignments for the Hydrated Excess Proton in Liquid Water. J. Chem. Phys. 2017 ;146.
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, 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, 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, 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 YG, Voth GA. A Theory for Adiabatic Electron Transfer Processes across the Semiconductor/Electrolyte Interface. The Journal of Chemical Physics. 1996 ;104:6168-6183.
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 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.
Brewer ML, Schmitt UW, Voth GA. The Formation and Dynamics of Proton Wires in Channel Environments. Biophys J. 2001 ;80:1691-702.
Brousseau M, Thomas NE, Teng D, Voth GA, Henzler-Wildman KA. The C-terminus of the Multi-Drug Efflux Pump EmrE Prevents Proton Leak by Gating Transport. Proc. Nat. Acad. Sci. USA. Submitted .
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. Largescale Computer Simulation of an Electrochemical Bond Breaking Reaction. Chem. Phys. Lett. 1999 ;305:94-100.
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, 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, 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. 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, 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. 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, 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.
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. Comput. 2020 ;16(9):5675–5684 .
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. A Theory for the Quantum Activated Rate Constant in Dissipative Systems. Chem. Phys. Lett. 1996 ;261:111-116.
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 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.
Cao J, Voth GA. A New Perspective on Quantum Time Correlation Functions. The Journal of Chemical Physics. 1993 ;99:10070-10073.
Cao Z, Kumar R, Peng Y, Voth GA. Proton Transport Under External Applied Voltage. J. Phys. Chem. B. 2014 .
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 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 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, 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. Semiclassical Approximations to Quantum Dynamical Time Correlation Functions. The Journal of Chemical Physics. 1996 ;104:273-285.
Cao Z, Peng Y, Voth GA. Ion Transport through Ultra-Thin Electrolyte under Applied Voltages. J. Phys. Chem. B. 2015 ;119:7516-7521.
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 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 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 Z, Kumar R, Peng Y, Voth GA. Hydrated Proton Structure and Diffusion at Platinum Surfaces. J. Phys. Chem. C. 2015 ;119:7516-7521.
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. 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. A Unified Framework for Quantum Activated Rate Processes. II. The Nonadiabatic Limit. The Journal of Chemical Physics. 1997 ;106:1769-1779.
Cao J, Voth GA. Modeling Physical Systems by Effective Harmonic Oscillators: The Optimized Quadratic Approximation. The Journal of Chemical Physics. 1995 ;102:3337-3348.
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 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 H, Voth GA. The Kinetics of Proton Migration in Liquid Water. J. Phys. Chem. B. 2010 ;114:333–339.
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 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, Xu J, Voth GA. Unusual Hydrophobic Interactions in Acidic Aqueous Solutions. J. Phys. Chem. B. 2009 ;113:7291-7297.
Chen S, Voth GA. How Does Electronic Polarizability or Scaled-Charge Affect the Interfacial Properties of Room Temperature Ionic Liquids?. J. Phys. Chem. B. 2023 ;127(5):1264–1275.
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 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 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 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 .
Chen S, Li Z, Voth GA. Acidic Conditions Impact Hydrophobe Transfer Across the Oil-Water Interface in Unusual Ways. J. Phys. Chem. B. 2023 ;127(17):3911–3918.
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.
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, Voth GA. Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model. Biophys. J. 2007 ;93:3860-3871.
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. Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-grained Analysis. Proc Natl Acad Sci U S A. 2005 ;102:13111-6.
Chu JW, Izvekov S, Voth GA. The Multiscale Challenge for Biomolecular Systems: Coarse-grained Modeling. Mol. Sim. 2006 ;32:211-218.
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.
Cui H, Lyman E, Voth GA. Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins. Biophys. J. 2011 ;100:1271-1279.
Cui H, Ayton GS, Voth GA. Membrane Binding by the Endophilin N-BAR Domain. Biophys. J. 2009 ;97:2746-2753.
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.
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.
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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.
Dama JF, Parrinello M, Voth GA. Well-tempered Metadynamics Converges Asymptotically. Phys. Rev. Lett. 2014 ;112:1-6.
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.
Dannenhoffer-Lafage T, Voth GA. Reactive Coarse-grained Molecular Dynamics. J. Chem. Theory. Comput. 2020 ;16(4):2541−2549.
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(13):134115.
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, Simunovic M, Voth GA. Multiscale Simulations of Protein Facilitated Membrane Remodeling. J. Struct. Biol. 2016 .
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, 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.
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.
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.
Day TJF, Schmitt UW, Voth GA. The Mechanism of Hydrated Proton Transport in Water. Journal of the American Chemical Society. 2000 ;122:12027-12028.
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(12):124110.
Durumeric AEP, Voth GA. Using classifiers to understand coarse-grained models and their fidelity with the underlying all-atom systems. J. Chem. Phys. 2023 ;158(23):234101.
Dutta M, Su Y, Voth GA, Stahelin RV. The SARS-Cov-2 Nucleoprotein Associates With Anionic Lipid Membranes. J. Bio. Chem. Submitted .
Dutta M, Voth GA. Divergent spike mutations impact the activation of the fusion core in Delta and Omicron variants of SARS-CoV-2. Sci. Adv. Submitted .
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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, 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.
Feng S, Voth GA. Proton Solvation and Transport in Hydrated Nafion. J. Phys. Chem. B. 2011 ;115:5903-5912.
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 ;27(6):570–580.
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. Proc. Natl. Acad. Sci. USA. 2019 ;116(13):16192–16197.
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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.
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. A Computer Simulation Method for Studying the Ablation of Polymer Surfaces by Ultraviolet Laser Radiation. Journal of Applied Physics. 1992 ;71:1415-1420.
Galvan-Monjee V, Voth GA. Binding Mechanism of the Matrix Domain of HIV-1 Gag to Lipid Membranes. eLife. 2020 ;9.
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.
Gebremichael Y, Ayton GS, Voth GA. Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics. Biophys J. 2006 ;91:3640-52.
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.
Geva E, Shi Q, Voth GA. Quantum Mechanical Reaction Rate Constants from Centroid Molecular Dynamics Simulations. J. Chem. Phys. 2001 ;115:9209-9222.
Ghosh K, Loose TD, Voth GA. Can a Coarse-grained Water Model Capture the Key Physical Features of the Hydrophobic Effect?. J. Chem. Phys. 2023 ;159:224105.
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 Features of HIV-1 Viral Capsid Assembly. Sci. Adv. 2023 ;9(1):eadd7434.
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.
Hack JH, Ma X, Chen JP, Dombrowski JP, Lewis NHC, Li C, Kung HH, Voth GA, Tokmakoff A. Proton Dissociation and Delocalization Under Stepwise Hydration of Zeolite HZSM-5. J. Phys. Chem. C. 2023 ;127:16175-16186.
Han Y, Jin J, Wagner J, Voth GA. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148(10):102335.
Han Y, Dama JF, Voth GA. Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. J. Chem. Phys. 2018 ;149(4):044104.
Han Y, Jin J, Voth GA. Constructing Many-body Mesoscopic Models of Fluids from Bottom-up Coarse-graining. J. Chem. Phys. 2021 ;154(8):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. Mol. Biol. Cell. 2019 ;30(7):851–862.
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, 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.
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. 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. 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.
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, Voth GA. Quantum Time Correlation Functions and Classical Coherence. Chem. Phys. 1998 ;233:243-255.
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.
Hocky GM, Sindelar VC, Cao W, Voth GA, Cruz DLEM. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296:100337.
Hocky GM, Dannenhoffer-Lafage T, Voth GA. Coarse-Grained Directed Simulation. J. Chem. Theory Comput. 2017 .
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).
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, 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, 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, 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. Dynamics of Upstream ESCRT Organization at the HIV-1 Budding Site. Biophys. J. 2023 ;122(13):2655–2674.
Hudait A, Voth GA. HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex. Proc. Nat. Acad. Sci. USA. 2024 ;121:e2313737121.
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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, Izvekov S, Voth GA. Are Many-body Electronic Polarization Effects Important in Liquid Water?. J Chem Phys. 2007 ;126:124505.
Iuchi S, Chen H, Paesani F, Voth GA. The Hydrated Excess Proton at Water-Hydrophobic Interfaces. J. Phys. Chem. B. 2009 ;113:4017-4030.
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, 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, 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, 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, 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.
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.
Izvekov S, Voth GA. A Solvent Free Lipid Bilayer Model Using Multiscale Coarse-graining. J. Phys. Chem. B. 2009 ;113:4443-4455.
Izvekov S, Voth GA. A Multiscale Coarse-Graining Method for Biomolecular Systems. J Phys Chem B. 2005 ;109:2469-73.
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. Mixed Resolution Modeling of Interactions in Condensed Phase Systems. J. Chem. Theor. Comp. 2009 ;5:3232–3244.
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, 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, Voth GA. Multiscale Coarse-graining of Mixed Phospholipid/Cholesterol Bilayer. J. Chem. Theory Comp. 2006 ;2:637-648.
Izvekov S, Voth GA. Multiscale Coarse Graining of Liquid-state Systems. J Chem Phys. 2005 ;123:134105.
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, Voth GA. Modeling Real Dynamics in the Coarse-grained Representation of Condensed Phase Systems. J Chem Phys. 2006 ;125:151101.
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. Ab Initio Molecular-dynamics Simulation of Aqueous Proton Solvation and Transport Revisited. J Chem Phys. 2005 ;123:044505.
Izvekov S, Voth GA. Ab initio Molecular Dynamics Simulation of the Ag(111)–Water Interface. J. Chem. Phys. 2001 ;115:7196-7206.
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, Voth GA. Can Quantum Transition State Theory be Defined as a t = 0+ Limit?. J. Chem. Phys. 2016 ;144(084110):1-12.
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, Voth GA. Non-Uniqueness of Quantum Transition State Theory and General Dividing Surfaces in the Path Integral Space. J. Chem. Phys. 2017 ;146.
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 Relationship between Centroid Dynamics and Path Integral Quantum Transition State Theory. The Journal of Chemical Physics. 2000 ;112:8747-8757.
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, 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. 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, 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, 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, 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, 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.
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 Comput. 2021 ;17(2):1170–1180.
Jarin Z, Pak AJ, Bassereau P, Voth GA. Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins. Biophys. J. 2021 ;120(1):46–54.
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.
Jeon J, Lefohn AE, Voth GA. An Improved Polarflex Water Model. J. Chem. Phys. 2003 ;118:7504-7518.
Jeon J, Voth GA. Gating of the Mechanosensitive Channel Protein MscL: The Interplay of Membrane and Protein. Biophys. J. 2008 ;94:3497-3511.
Jeon J, Voth GA. The Dynamic Stress Responses to Area Change in Planar Lipid Bilayer Membranes. Biophys J. 2005 ;88:1104-19.
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.
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, Wang Y, Voth GA. Molecular Dynamics Simulation of Nanostructural Organization in Ionic Liquid/Water Mixtures. J Phys Chem B. 2007 ;111:4812-8.
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, Lee EK, Voth GA. Understanding Dynamics in Coarse-Grained Models: III. Roles of Rotational Motion and Translation-Rotation Coupling in Coarse-Grained Dynamics. J. Chem. Phys. 2023 ;159:164102.
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(4):044105.
Jin J, Voth GA. Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. J. Chem. Theory Comput. 2018 ;14(4):2180–2197.
Jin J, Schweizer KS, Voth GA. Understanding Dynamics in Coarse-Grained Models: II. Coarse-Grained Diffusion Modeled Using Hard Sphere Theory. J. Chem. Phys. 2023 ;158(3):034104.
Jin J, Yu A, Voth GA. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J. Chem. Theory Comput. 2020 ;16(11):6823–6842.
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. 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(4):044104.
Jin J, Pak AJ, Voth GA. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J. Phys. Chem. Lett. 2019 ;10(16):4549–4557.
Jin J, Schweizer KS, Voth GA. Understanding Dynamics in Coarse-Grained Models: I. Universal Excess Entropy Scaling Relationship. J. Chem. Phys. 2023 ;158(3):034103.
Jin J, Han Y, Voth GA. Coarse-Graining Involving Virtual Sites: Centers of Symmetry Coarse-Graining. J. Chem. Phys. 2019 ;150(15):154103.
Jin J, Hwang J, GA V. Gaussian Representation of Coarse-Grained Interactions of Liquids: Theory, Parametrization, and Transferability. J. Chem. Phys. 2023 ;159:184105.
Jin J, Voth GA. Statistical Mechanical Design Principles for Coarse-grained Interactions Across Different Conformational Free Energy Surfaces. J. Phys. Chem. Lett. 2023 ;14(6):1354–1362.
Jorn R, Voth GA. Mesoscale Simulation of Proton Transport in Proton Exchange Membranes. J. Phys. Chem. C. 2012 ;116:935-944.
Jorn R, Savage J, Voth GA. Proton Conduction in Exchange Membranes Across Multiple Length Scales. Acc. Chem. Res. 2012 ;45:2002-2010.
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.
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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. Biophys. J. 2018 ;115(18):1589–1602.
Kim S, Swanson JMJ, Voth GA. Computational Studies of Lipid Droplets. J. Phys. Chem. B. 2022 ;126(11):2145–2154.
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, Voth GA. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis. J. Phys. Chem. B. 2021 ;125(25):6872–6888.
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.
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.
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, Voth GA. Coarse-graining Away Electronic Structure: A Rigorous Route to Accurate Condensed Phase Interaction Potentials. Mol. Phys. 2012 ;110:935-944.
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, 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, Voth GA. A Theory for Adiabatic Bond Breaking Electron Transfer Reactions at Metal Electrodes. Chem. Phys. Lett. 1998 ;282:100-106.
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, G. A. Voth, " (HA)" (2000). Molecular Dynamics of Bond-Breaking Electron-Transfer Reactions at Metal-Liquid Interfaces. CATTECH 4. 2000 :51-55.
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. 2023 ;15(7):1012–1021.
Krishna V, Voth GA. Evaluation of Nonlinear Quantum Time Correlation Functions within the Centroid Dynamics Formulation. J Phys Chem B. 2006 ;110:18953-7.
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, 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.
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, Voth GA, Marcus RA. Quantum and Classical Energy Transfer Between Ligands of a Heavy Metal Atom. Chem. Phys. Lett. 1986 ;124:93-98.
Lederman SM, Lopez V, Fairen V, Voth GA, Marcus RA. Vibrational Energy Redistribution Across a Heavy Atom. Chem. Phys. 1989 ;139:171-184.
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, 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.
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, 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.
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, 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 ;124(24):5039–5046.
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 C, Voth GA. A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces. Proc. Natl. Acad. Sci. USA. 2021 ;118(49 ):e2113141118.
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 C, Voth GA. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(2):599–604.
Li C, Voth GA. Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface. J. Chem. Theory Comput. 2021 ;17(9):5759–5765.
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 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 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 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 DH, Voth GA. Calculation of ESR Linewidths for Hydrogen Atom Impurities in Solid para-Hydrogen. J. Chem. Phys. 1994 ;100:1785-1796.
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 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 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 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 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 Comput. 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, 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, 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, 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 .
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.
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, Shi Q, Lyman E, Voth GA. Reconstructing Atomistic Detail from Coarse-grained Models with Resolution Exchange. J. Chem. Phys. 2008 ;129:114103.
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 P, Izvekov S, Voth GA. Multiscale Coarse-Graining of Monosaccharides. J. Phys. Chem. B. 2007 ;111:11566-11575.
Liu Y, Li C, Voth GA. Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins. J. Phys. Chem. B. 2022 ;126(49):10452–10459.
Liu P, III DH, Voth GA. A Bayesian Statistics Approach to Multiscale Coarse-graining. J. Chem. Phys. 2008 ;129:214114.
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. Natl. Acad. Sci. USA. 2021 ;118(25):e2101932118.
Liu P, Voth GA. Smart Resolution Replica Exchange: an Efficient Algorithm for Exploring Complex Energy Landscapes. J Chem Phys. 2007 ;126:045106.
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 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. 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 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. 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.
Lobaugh J, Voth GA. A Quantum Model for Water: Equilibrium and Dynamical Properties. The Journal of Chemical Physics. 1997 ;106:2400-2410.
Loose TD, Sahrmann PG, Qu TS, Voth GA. Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Structural Models. J. Phys. Chem. 2023 ;127:10564–10572.
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 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, Dama JF, Voth GA. Fitting coarse-grained distribution functions through an iterative force-matching method. J. Chem. Phys. 2013 ;139:1-10.
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 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 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, Voth GA. Systematic Coarse-graining of a Multi-component Lipid Bilayer. J. Phys. Chem. B. 2009 ;113:1501-1510.
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, Cui H, Voth GA. Reconstructing Protein Remodeled Membranes in Molecular Detail From Mesoscopic Models. Phys. Chem. Chem. Phys. 2011 :10430–10436.
Lyman E, Cui H, Voth GA. Water Under the BAR. Biophys. J. 2010 ;99:1783–1790.
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(29):16186−16201.
Madsen JJ, Sinitskiy AV, Li J, Voth GA. Highly Coarse-grained Representations of Transmembrane Proteins. J. Chem. Theory Comput. 2017 ;13.
Madsen JJ, Grime JMA, Rossman JS, Voth GA. Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc. Natl. Acad. Sci. USA. 2018 ;115(37):E8595–E8603.
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.
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.
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 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 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. 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.
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. A Perturbation Theory for Solvation Thermodynamics: Dipolar–quadrupolar Liquids. The Journal of Chemical Physics. 1999 ;111:3630-3638.
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, 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, Voth GA. Preferred Orientations of His-64 in Human Carbonic Anhydrase II. Biochemistry. 2007 ;46:2938-47.
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, 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, 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, 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.
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.
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, 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.
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, Alexander MH, Voth GA. Path Integral Molecular Dynamics Simulation of Solid Para-Hydrogen with an Aluminum Impurity. Chem. Phys. Lett. 2002 ;365:487-493.
Mironenko AV, Voth GA. Density Functional Theory-based Quantum Mechanics/Coarse-grained Molecular Mechanics: Theory and Implementation. J. Chem. Theory Comput. 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 Discuss. 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, Voth GA. The Properties of Water: Insights from Quantum Simulations. J. Phys. Chem. B. 2009 ;113:5702–5719.
Paesani F, Voth GA. Quantum Effects Strongly Influence the Surface Premelting of Ice. J. Phys. Chem. C. 2008 ;112:324-327.
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.
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, 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, 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. 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.
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, Voth GA. Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Curr. Opin. Struct. Biol. 2018 ;52:119–126.
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, 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, 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, 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.
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.
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.
Paramore S, Ayton GS, Voth GA. Extending the Fluctuation Theorem to Describe Reaction Coordinates. J Chem Phys. 2007 ;126:051102.
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 a Spectrin Repeat Unit. II: Rupture Behavior. Biophys J. 2006 ;90:101-11.
Paramore S, Ayton GS, Mirijanian DT, Voth GA. Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response. Biophys J. 2006 ;90:92-100.
Parker LJ, 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, Voth GA. Quantum and Classical Simulations of an Excess Proton in Water. Ber. Bunsenges. Phys. Chem. 1998 ;102:527-532.
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, Jang S, Voth GA. Centroid Molecular Dynamics: A Quantum Dynamics Method Suitable for the Parallel Computer. Parallel Computing. 2000 ;26:1025-1041.
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, 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.
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).
Peng Y, Pak AJ, Durumeric AEP, Mani S, Jin J, Sahrmann PG, Loose TD, Beiter J, Voth GA. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 2023 ;127:8537–8550.
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, Voth GA. Expanding the View of Proton Pumping in Cytochrome c Oxidase through Computer Simulation. Biochim. et Biophys. Acta-Bioenergetics. 2012 ;1817:518-525.
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, 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, 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.
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, Voth GA. Amphiphilic Character of the Hydrated Proton in Methanol−Water Solutions. J Phys Chem B. 2006 ;110:7085-9.
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.
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, 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, Voth GA. Molecular Dynamics Simulation and Coarse-grained Analysis of the Arp2/3 Complex. Biophys. J. 2008 ;95:5324-5333.
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, Lyman E, Pollard TD, Voth GA. Structure and Dynamics of the Actin Filament. J. Mol. Biol. 2010 ;396:252–263.
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, Jr. RVFarese, 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, Voth GA. Self-consistent Harmonic Theory of Solvation in Glassy Systems: Quantum Solvation. The Journal of Chemical Physics. 2000 ;112:3280-3284.
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: Classical Solvation. The Journal of Chemical Physics. 2000 ;112:3267-3279.
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.
Roy P-N, Jang S, Voth GA. Feynman Path Centroid Dynamics for Fermi–Dirac Statistics. The Journal of Chemical Physics. 1999 ;111:5303-5305.
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.
Ryu WH, Han Y, Voth GA. Coarse-graining of many-body path integrals: Theory and numerical approximations. J. Chem. Phys. 2019 ;150(24):244103.
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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.
Sahrmann PG, Loose TD, Durumeric AEP, Voth GA. Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles. J. Chem. Theory Comput. 2023 ;19(14):4402–4413.
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. Coarse-graining of Multi-Protein Assemblies. Curr. Opin. Struct. Biol. 2012 ;22:144-150.
Saunders MG, Voth GA. Comparison Between Actin Filament Models: Coarse-Graining Reveals Essential Differences. Structure. 2012 ;20:641-653.
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, 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.
Saunders MG, Voth GA. Coarse-graining Methods for Computational Biology. Annu. Rev. Biophysics. 2013 ;42:73-93.
Savage J, Voth G. Persistent Sub-diffusive Proton Transport in Perfluorosulfonic Acid Membranes. J. Phys. Chem. Lett. . 2014 ;(5(17):3037–3042.
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 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, 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.
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.
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. 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 Isotope Substitution Effect on the Hydrated Proton. Chem. Phys. Lett. 2000 ;329:36-41.
Schmitt UW, Voth GA. Quantum Properties of the Excess Proton in Liquid Water. Israeli J. Chem. 1999 ;39:483-492.
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.
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.
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Schwieters CD, Voth GA. The Semiclassical Calculation of Nonadiabatic Tunneling Rates. The Journal of Chemical Physics. 1998 ;108:1055-1062.
Sharp ME, Vázquez FX, Wagner JW, Dannenhoffer-Lafage T, Voth GA. Multiconfigurational Coarse-Grained Molecular Dynamics. J. Chem. Theory Comput. 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, Voth GA. Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers. Biophys J. 2005 ;89:2385-94.
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, 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.
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, Voth GA. Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90. Biophys. J. 2012 ;103:284-292.
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Simunovic M, Bassereau P, Voth GA. Organizing Membrane-Curving Proteins: The Emerging Dynamical Picture. Curr. Opin. Struct. Biol. 2018 ;51:99–105 .
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).
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.
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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. Natl. Acad. Sci. USA. 2021 ;118(3):e2020054118.
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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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Yamashita T, Voth GA. Insights into the Mechanism of Proton Transport in Cytochrome c Oxidase. J. Am. Chem. Soc. 2012 ;134:1147-1152.
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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.
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