Publications

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Journal Article
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.
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.
Pfaendtner J, Cruz DLEM, Voth GA. Actin Filament Remodeling by Actin Depolymerization Factor/Cofilin. Proc. Natl. Acad. Sci. USA. 2010 ;107:7299–7304.
Pak AJ, Voth GA. Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Current Opinion in Structural Biology. 2018 ;52:119-126.
Petersen MK, Voth GA. Amphiphilic Character of the Hydrated Proton in Methanol−Water Solutions. J Phys Chem B. 2006 ;110:7085-9.
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.
Pavese M, Jang S, Voth GA. Centroid Molecular Dynamics: A Quantum Dynamics Method Suitable for the Parallel Computer. Parallel Computing. 2000 ;26:1025-1041.
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.
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.
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 .
Yamashita T, Peng Y, Knight C, Voth GA. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics. J. Chem. Theory Comput. 2012 ;8:4863-4875.
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.
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.
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.
Phillips CL, Voth GA. Discovering Crystals Using Shape Matching and Machine Learning. Soft Matter. 2013 ;9:8552.
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.
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.
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.
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.
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.
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.
Paramore S, Ayton GS, Mirijanian DT, Voth GA. Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response. Biophys J. 2006 ;90:92-100.
Paramore S, Ayton GS, Voth GA. Extending a Spectrin Repeat Unit. II: Rupture Behavior. Biophys J. 2006 ;90:101-11.
Paramore S, Ayton GS, Voth GA. Extending the Fluctuation Theorem to Describe Reaction Coordinates. J Chem Phys. 2007 ;126:051102.
Simunovic M, Manneville J-B, Renard H-F, Evergren E, Raghunathan K, Kenworthy AK, Voth GA, Prost J, McMahon HT, Johannes L, et al. Friction Mediates Scission of Tubular Membranes Scaffolded by BAR Proteins. Cell. 2017 ;170.
Aydin F, Courtemanche N, Pollard TD, Voth GA. Gating mechanisms during actin filament elongation by formins. eLife. 2018 ;7:e37342.
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 .
Iuchi S, Chen H, Paesani F, Voth GA. The Hydrated Excess Proton at Water-Hydrophobic Interfaces. J. Phys. Chem. B. 2009 ;113:4017-4030.
Peng Y, Swanson JMJ, Kang S, Zhou R, Voth GA. Hydrated Excess Protons Can Create Their Own Water Wires. J. Phys. Chem. B. 2015 ;(119).
Petersen MK, Iyengar SS, Day TJF, Voth GA. The Hydrated Proton at the Water Liquid/Vapor Interface. J. Phys. Chem. B. 2004 ;108:14804-14806.
Cao Z, Kumar R, Peng Y, Voth GA. Hydrated Proton Structure and Diffusion at Platinum Surfaces. J. Phys. Chem. C. 2015 ;119:7516-7521.
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.
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 .
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.
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.
Cao Z, Peng Y, Voth GA. Ion Transport through Ultra-Thin Electrolyte under Applied Voltages. J. Phys. Chem. B. 2015 ;119:7516-7521.
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, 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.
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.
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.
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.
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.
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.
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.
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.
Paesani F, Voth GA. Nonlinear Quantum Time Correlation Functions from Centroid Molecular Dynamics and the Maximum Entropy Method. J. Chem. Phys. 2008 ;129:194113.
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, 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, Branduardi D, Pollard TD, Parrinello M, Voth GA. Nucleotide-Dependent Conformational States of Actin. Proc. Natl. Acad. Sci. USA. 2009 ;106:12723–12728.
Jarin Z, Tsai F-C, Davtyan A, Pak AJ, Bassereau P, Voth GA. Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys. J. 2019 ;117(3):553-562.
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.
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.
Elam WA, Cao W, Kang H, Huehn A, Hocky GM, Prochniewicz E, Schramm AC, Negrón K, Garcia J, Bonello TT, et al. Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
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.
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.
Paesani F, Voth GA. The Properties of Water: Insights from Quantum Simulations. J. Phys. Chem. B. 2009 ;113:5702–5719.
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.
Cao Z, Kumar R, Peng Y, Voth GA. Proton Transport Under External Applied Voltage. J. Phys. Chem. B. 2014 .
Pavese M, Voth GA. Pseudopotentials for Centroid Molecular Dynamics: Application to Self-Diffusion in Liquid para-Hydrogen. Chem. Phys. Lett. 1996 ;249:231-236.
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.
Pavese M, Voth GA. Quantum and Classical Simulations of an Excess Proton in Water. Ber. Bunsenges. Phys. Chem. 1998 ;102:527-532.
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.
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.
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. Quantum Effects Strongly Influence the Surface Premelting of Ice. J. Phys. Chem. C. 2008 ;112:324-327.
Pak Y, Voth GA. Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water. J. Phys. Chem. 1999 ;103:925-931.
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 .
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.
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.
Popolo DMG, Voth GA. On the Structure and Dynamics of Ionic Liquids. J. Phys. Chem. B. 2004 ;108:1744-1752.
Pfaendtner J, Lyman E, Pollard TD, Voth GA. Structure and Dynamics of the Actin Filament. J. Mol. Biol. 2010 ;396:252–263.
Pfaendtner J, Lyman E, Pollard TD, Voth GA. Structure and Dynamics of the Actin Filament. J. Mol. Biol. 2010 ;396:252–263.
Blake NP, Petersen MK, Voth GA, Metiu H. Structure of Hydrated Na−Nafion Polymer Membranes. J Phys Chem B. 2005 ;109:24244-53.
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.
Zhang Z, Lu L, Noid WG, Krishna V, Pfaendtner J, Voth GA. A Systematic Methodology for Defining Coarse-grained Sites in Large Biomolecules. Biophys. J. 2008 ;95:5073-5083.
Lyman E, Pfaendtner J, Voth GA. Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins. Biophys. J. 2008 ;95:4183–4192.
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.
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.
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 .
Jin J, Pak AJ, Voth GA. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J. Chem. Phys. Lett. Submitted .
Dama JF, Parrinello M, Voth GA. Well-tempered Metadynamics Converges Asymptotically. Phys. Rev. Lett. 2014 ;112:1-6.