Publications

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Journal Article
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.
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.
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 .
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.
Day TJF, Schmitt UW, Voth GA. The Mechanism of Hydrated Proton Transport in Water. Journal of the American Chemical Society. 2000 ;122:12027-12028.
Cui H, Lyman E, Voth GA. Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins. Biophys. J. 2011 ;100:1271-1279.
Ilan B, Tajkhorshid E, Schulten K, Voth GA. The Mechanism of Proton Exclusion in Aquaporin Channels. Proteins. 2004 ;55:223-8.
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.
Tepper HL, Voth GA. Mechanisms of Passive Ion Permeation through Lipid Bilayers: Insights from Simulations. J Phys Chem B. 2006 ;110:21327-37.
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).
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.
Cui H, Ayton GS, Voth GA. Membrane Binding by the Endophilin N-BAR Domain. Biophys. J. 2009 ;97:2746-2753.
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.
Ayton GS, Blood PD, Voth GA. Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation. Biophys J. 2007 ;92:3595-602.
Simunovic M, Voth GA. Membrane Tension Controls the Assembly of Curvature-Generating Proteins. Nature Communications. 2015 ;6(7219):1-8.
Jorn R, Voth GA. Mesoscale Simulation of Proton Transport in Proton Exchange Membranes. J. Phys. Chem. C. 2012 ;116:935-944.
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.
Han Y, Dama JF, Voth GA. Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. J. Chem. Phys. 2018 ;149.
Ayton GS, Voth GA. Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys J. 2004 ;87:3299-311.
Davtyan A, Simunovic M, Voth GA. The Mesoscopic Membrane with Proteins Model (MesM-P). J. Chem. Phys. 2017 ;147.
Gebremichael Y, Ayton GS, Voth GA. Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics. Biophys J. 2006 ;91:3640-52.
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.
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.
Izvekov S, Voth GA. Mixed Resolution Modeling of Interactions in Condensed Phase Systems. J. Chem. Theor. Comp. 2009 ;5:3232–3244.
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.
Cao J, Voth GA. Modeling Physical Systems by Effective Harmonic Oscillators: The Optimized Quadratic Approximation. The Journal of Chemical Physics. 1995 ;102:3337-3348.
Izvekov S, Voth GA. Modeling Real Dynamics in the Coarse-grained Representation of Condensed Phase Systems. J Chem Phys. 2006 ;125:151101.
Matyushov D, Voth GA. Modeling the Free Energy Surfaces of Electron Transfer in Condensed Phases. J. Chem. Phys. 2000 ;113:5413-5424.
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.
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.
Simunovic M, Voth GA. Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90. Biophys. J. 2012 ;103:284-292.
Koper MTM, G. A. Voth, " (HA)" (2000). Molecular Dynamics of Bond-Breaking Electron-Transfer Reactions at Metal-Liquid Interfaces. CATTECH 4. 2000 :51-55.
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.
Pfaendtner J, Voth GA. Molecular Dynamics Simulation and Coarse-grained Analysis of the Arp2/3 Complex. Biophys. J. 2008 ;95:5324-5333.
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.
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.
Smondyrev AM, Voth GA. Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane. Biophys J. 2002 ;82:1460-8.
Smondyrev AM, Voth GA. Molecular Dynamics Simulation of Proton Transport through the Influenza A Virus M2 Channel. Biophys J. 2002 ;83:1987-96.
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.
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.
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.
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.
Tse Y-LS, Herring AM, Voth GA. Molecular Dynamics Simulations of Proton Transport in 3M and Nafion Perfluorosulfonic Acid Membranes. J. Phys. Chem. C. 2013 .
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.
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 .
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).
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.
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.
Chu JW, Izvekov S, Voth GA. The Multiscale Challenge for Biomolecular Systems: Coarse-grained Modeling. Mol. Sim. 2006 ;32:211-218.
Izvekov S, Voth GA. Multiscale Coarse Graining of Liquid-state Systems. J Chem Phys. 2005 ;123:134105.
Noid WG, Chu JW, Ayton GS, Voth GA. Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory. J Phys Chem B. 2007 ;111:4116-27.
Izvekov S, Voth GA. A Multiscale Coarse-Graining Method for Biomolecular Systems. J Phys Chem B. 2005 ;109:2469-73.
Noid WG, Chu J-W, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC. The Multiscale Coarse-graining Method I: A Rigorous Bridge between Atomistic and Coarse-grained Models. J. Chem. Phys. 2008 ;128:244114.
Noid WG, Liu P, Wang Y, Chu J-W, Ayton GS, Izvekov S, Andersen HC, Voth GA. The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models. J. Chem. Phys. 2008 ;128:244115.
Krishna V, Noid WG, Voth GA. The Multiscale Coarse-graining Method. IV. Transferring Coarse-grained Potentials Between Temperatures. J. Chem. Phys. 2009 ;131:024103.
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.
Lu L, Voth GA. The Multiscale Coarse-Graining Method. VII. Free Energy Decomposition of Coarse-Grained Effective Potentials. J. Chem. Phys. 2011 ;134:224107.
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.
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.
Wang Y, Izvekov S, Yan T, Voth GA. Multiscale Coarse-Graining of Ionic Liquids. J Phys Chem B. 2006 ;110:3564-75.
Izvekov S, Voth GA. Multiscale Coarse-graining of Mixed Phospholipid/Cholesterol Bilayer. J. Chem. Theory Comp. 2006 ;2:637-648.
Liu P, Izvekov S, Voth GA. Multiscale Coarse-Graining of Monosaccharides. J. Phys. Chem. B. 2007 ;111:11566-11575.
Jr. HRD, Lu L, Voth GA. Multiscale Coarse-Graining of the Protein Energy Landscape. PLoS Comp. Bio. 2010 ;6:e1000827.
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.
Ayton GS, Voth GA. Multiscale Computer Simulation of the Immature HIV-1 Virion. Biophys. J. 2010 ;99:2757–2765.
Chang R, Ayton GS, Voth GA. Multiscale Coupling of Mesoscopic- and Atomistic-level Lipid Bilayer Simulations. J Chem Phys. 2005 ;122:244716.
Voth GA. A Multiscale Description of Biological Active Matter: The Chemistry Underlying Many Life Processes. Acc. Chem. Res. 2017 ;50.
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.
Bidone TC, Skeeters AV, Oakes PW, Voth GA. Multiscale model of integrin adhesion assembly. POLS Computational Biology. 2019 ;15(6):e1007077.
Ayton GS, Noid WG, Voth GA. Multiscale Modeling of Biomolecular Systems: in Serial and in Parallel. Curr Opin Struct Biol. 2007 ;17:192-8.
Shi Q, Voth GA. Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers. Biophys J. 2005 ;89:2385-94.
Knight C, Lindberg G, Voth GA. Multiscale Reactive Molecular Dynamics. J. Chem. Phys. 2012 ;137:22A525.
Aydin F, Katkar HH, Voth GA. Multiscale Simulation of Actin Filaments and Actin-Associated Proteins. Biophys Rev. 2018 ;10:1521-1535.
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. Multiscale Simulation of Protein Mediated Membrane Remodeling. Seminars in Cell and Developmental Biology. 2010 ;21:357-362.
Ayton GS, Voth GA. Multiscale Simulation of Transmembrane Proteins. J Struct Biol. 2007 ;157:570-8.
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.
Davtyan A, Simunovic M, Voth GA. Multiscale Simulations of Protein Facilitated Membrane Remodeling. J. Struct. Biol. 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.
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.
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.
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.
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.
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.
Schmitt UW, Voth GA. Multistate Empirical Valence Bond Model for Proton Transport in Water. The Journal of Physical Chemistry B. 1998 ;102:5547-5551.
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.