Publications

Author Title [ Type(Desc)] Year
Filters: First Letter Of Last Name is B  [Clear All Filters]
Book Chapter
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.
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.
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.
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
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.
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.
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.
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.
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.
Hocky GM, Baker JL, Bradley MJ, Sinitskiy AV, De La Cruz EM, Voth GA. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits. J. Phys. Chem. B. 2016 ;120(20).
Hocky GM, 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).
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 .
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 .
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.
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 .
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.
Pak AJ, Yu A, Ke Z, Briggs JAG, Voth GA. Cooperative Multivalent Receptor Binding Promotes Exposure of the SARS-CoV-2 Fusion Machinery Core. Proc. Nat. Acad. Sci. USA . Submitted .
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).
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.
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, 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.
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.
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.
Harker AJ, Katkar HH, Bidone TC, Aydin F, Voth GA, Applewhite DA, Kovar DR. Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia crosslinker fascin. Molecular Biology of the Cell. 2019 ;30(7).
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.
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.
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.
Brewer ML, Schmitt UW, Voth GA. The Formation and Dynamics of Proton Wires in Channel Environments. Biophys J. 2001 ;80:1691-702.
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.
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.
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 .
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 .
Tan A, Pak AJ, Morado DR, Voth GA, Briggs JAG. Immature HIV-1 Assembles From Gag Dimers Leaving Partial Hexamers at Lattice Edges as Substrates for Proteolytic Maturation. Proc. Nat. Acad. Sci. USA . 2021 ;118(3):e2020054118.
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 .
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.
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 .
Ayton G, Bardenhagen S, McMurtry P, Sulsky D, Voth GA. Interfacing Continuum and Molecular Dynamics: An Application to Lipid Bilayers. J. Chem. Phys. 2001 ;114:6913-6924.
Ayton G, Smondyrev AM, Bardenhagen SG, McMurtry P, Voth GA. Interfacing Molecular Dynamics and Macro-scale Simulations for Lipid Bilayer Vesicles. Biophys J. 2002 ;83:1026-38.
Ayton G, 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.
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.
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.
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.
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.
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.
Jarin Z, Pak AJ, Bassereau P, Voth GA. Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins. Biophys. J. 2021 ;120:46-54.
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 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.
Ayton GS, Blood PD, Voth GA. Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation. Biophys J. 2007 ;92:3595-602.
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.
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.
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 .
Bidone TC, Skeeters AV, Oakes PW, Voth GA. Multiscale model of integrin adhesion assembly. POLS Computational Biology. 2019 ;15(6):e1007077.
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.
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.
Yang P, Voth GA, Xiao D, L. G. Hines J, Bartsch RA, Quitevis EL. Nanostructural Organization in Carbon Disulfide/Ionic Liquid Mixtures: Optical Kerr Effect Spectroscopy and Molecular Dynamics Simulations. J. Chem. Phys. 2011 ;135:034502.
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.
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.
Simunovic M, Bassereau P, Voth GA. Organizing Membrane-Curving Proteins: The Emerging Dynamical Picture. Curr. Opin. Struct. Biol. 2018 ;51:99-105 .
Blinov NV, Roy PN, Voth GA. Path Integral Formulation of Centroid Dynamics for Systems Obeying Bose-Einstein Statistics. J. Chem. Phys. 2001 ;115:4484.
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 .
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.
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.
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).
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, Voth GA. Role of Solvation Structure in the Shuttling of the Hydrated Excess Proton. J. Chem. Sci. 2017 ;129.
Yu A, Lee MY, Briggs JAG, Ganser-Pornillos BK, Pornillos O, Voth GA. Strain and Crack Propagation of HIV-1 Capsids During Uncoating. Proc. Nat. Acad. Sci. USA . Submitted .
Blake NP, Petersen MK, Voth GA, Metiu H. Structure of Hydrated Na−Nafion Polymer Membranes. J Phys Chem B. 2005 ;109:24244-53.
Zhou S, He P, Dhindwal S, Grum-Tokars VL, K. Li PY, Modica JA, Bleher R, R. Reis dos, Zuchniarz J, Dravid VP, et al. Synthesis, Characterization and Simulation of Four-Armed Megamolecules. Biomacromolecules. 2021 ;22(6):2363–2372.
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.
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.
Simunovic M, Voth GA, Callan-Jones A, Bassereau P. When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol. 2015 .