Publications

Author Title [ Type(Desc)] Year
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Book Chapter
Wu Y, Voth GA. Computer Simulations of Proton Transport Through the M2 Channel of the Influenza A Virus. In: Fischer W Viral Membrane Proteins: Structure, Function and Drug Design. Viral Membrane Proteins: Structure, Function and Drug Design. New York: Kluwer Academic/Plenum Publishers; 2004.
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.
Journal Article
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.
Wu Y, Ilan B, Voth GA. Charge Delocalization in Proton Channels, II: The Synthetic LS2 Channel and Proton Selectivity. Biophys J. 2007 ;92:61-9.
Tse Y-LS, Lindberg GE, Sarode HN, Witten TA, Yang Y, Herring AM, Voth GA. Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems. J. Phys. Chem. C. 2014 ;118:845-853.
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.
Dannenhoffer-Lafage T, Wagner JW, Durumeric AEP, Voth GA. Compatible Observable Decompositions for Coarse-grained Representations of Real Molecular Systems. J. Chem. Phys. Submitted .
Wu Y, Voth GA. Computational Studies of Proton Transport through the M2 Channel. FEBS Lett. 2003 ;552:23-7.
Wu Y, Voth GA. A Computational Study of the Closed and Open States of the Influenza A M2 Proton Channel. Biophys J. 2005 ;89:2402-11.
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.
Wu Y, Voth GA. A Computer Simulation Study of the Hydrated Proton in a Synthetic Proton Channel. Biophys J. 2003 ;85:864-75.
White AD, Dama JF, Voth GA. Designing Free Energy Surfaces that Match Experimental Data with Metadynamics. J. Chem. Theor. Comp. 2015 ;11.
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.
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.
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.
Wang Y, Noid WG, Liu P, Voth GA. Effective Force Coarse-Graining. Phys. Chem. Chem. Phys. 2009 ;11:2002-2015.
White A, Voth G. Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data. J. Chem. Theor. Comp. 2014 ;10(8):3023–3030.
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.
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.
Wagner JW, Dannenhoffer-Lafage T, Jin J, Voth GA. Extending the Range and Physical Accuracy of Coarse-grained Models: Order Parameter Dependent Interactions. J. Chem. Phys. 2017 .
Winkelman JD, Suarez C, Hocky GM, Harker AJ, Christensen JR, Morganthaler AN, Voth GA, Bartles JR, Kovar DR. Fascin and α-Actinin-bundled Networks Contain Intrinsic Structural Features That Drive Protein Sorting. Current Biology. 2016 ;26(20):2697–2706.
Wu Y, Tepper HL, Voth GA. Flexible Simple Point-charge Water Model with Improved Liquid-State Properties. J Chem Phys. 2006 ;124:024503.
White AD, Knight C, Hocky GM, Voth GA. Improved Ab Initio Molecular Dynamics by Minimally Biasing with Experimental Data. J. Chem. Phys. 2017 ;146.
Wu Y, Chen H, Wang F, Paesani F, Voth GA. An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport. J. Phys. Chem. B. 2008 ;112:467-482.
Wu Y, Chen H, Wang F, Paesani F, Voth GA. An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport. J. Phys. Chem. B. 2008 ;112:467-482.
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.
Tse Y-LS, Voth GA, Witten TA. Ion Mixing, Hydration, and Transport in Aqueous Ionic Systems. J. Chem. Phys. 2015 ;142(184905):1-7.
Oakes PW, Bidone TC, Beckham Y, Skeeters AV, San Juan GRRamirez, Winter SP, Voth GA, Gardel ML. The Lamellipodia is a Myosin Independent Mechanosensor. Proc. Nat. Acad. Sci. USA . 2018 ;115(11):2646-2651.
Wang F, Voth GA. A Linear-scaling Self-consistent Generalization of the Multistate Empirical Valence Bond Method for Multiple Excess Protons in Aqueous Systems. J Chem Phys. 2005 ;122:144105.
Wang Z, Swanson JMJ, Voth GA. Local Conformational Dynamics Regulating Transport Properties of a Cl–/H+ Antiporter. J. Comp. Chem. Submitted .
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.
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. In Press .
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.
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.
Wang Z, Swanson JMJ, Voth GA. Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux. J Am. Chem. 2018 ;140(48):16535–16543.
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, 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.
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.
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.
Noid WG, Liu P, Wang Y, Chu J-W, Ayton GS, Izvekov S, Andersen HC, Voth GA. The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models. J. Chem. Phys. 2008 ;128:244115.
Wang Y, Izvekov S, Yan T, Voth GA. Multiscale Coarse-Graining of Ionic Liquids. J Phys Chem B. 2006 ;110:3564-75.
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.
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.
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.
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.
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.
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.
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.
Watkins LC, Liang R, Swanson JMJ, DeGrado WF, Voth GA. Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. J. Am. Chem. Soc. Submitted .
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).
Swanson JM, Maupin CM, Chen H, Petersen MK, Xu J, Wu Y, Voth GA. Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations. J Phys Chem B. 2007 ;111:4300-14.
Wong KF, Sonnenberg JL, Paesani F, Yamamoto T, Vaníček J, Zhang W, Schlegel HB, Case DA, T. E. Cheatham III, Miller WH, et al. Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology. J. Chem. Theor. Comp. 2010 ;6:2566–2580.
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.
Wang D, Voth GA. Proton Transport Pathway in the ClC Cl–/H+ Antiporter. Biophys. J. 2009 ;97:121-131.
Han Y, Jin J, Wagner J, Voth GA. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148:102335.
Wagner JW, Dama JF, Durumeric AEP, Voth GA. On the Representability Problem and the Physical Meaning of Coarse-Grained Models. J. Chem. Phys. 2016 ;145(044108):1-12.
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.
Wang Y, Voth GA. Tail Aggregation and Domain Diffusion in Ionic Liquids. J Phys Chem B. 2006 ;110:18601-8.
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.
Wang Y, Feng S, Voth GA. Transferable Coarse-Grained Models for Ionic Liquids. J. Chem. Theor. Comp. 2009 ;5:1091-1098.
Wang Y, Jiang W, Yan T, Voth GA. Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations. Acc Chem Res. 2007 ;40:1193-9.
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.
Wang Y, Voth GA. Unique Spatial Heterogeneity in Ionic Liquids. J Am Chem Soc. 2005 ;127:12192-3.
Wang F, Izvekov S, Voth GA. Unusual ‘Amphiphilic’ Association of Hydrated Protons in Strong Acid Solution. J. Am. Chem. Soc. 2008 ;130:3120-3126.