Publications

Author Title [ Type(Asc)] Year
Filters: First Letter Of Last Name is Y  [Clear All Filters]
Journal Article
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.
Yu A, Skorupka K, Pak AJ, Ganser-Pornillos BK, Pornillos O, Voth GA. TRIM5α Self-Assembly and Compartmentalization of the HIV-1 Viral Capsid. Nature Comm. 2020 ;11:1-10.
Jin J, Yu A, Voth GA. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J. Chem. Theory Comp. 2020 ;16(11):6823–6842.
Yan T, Li S, Jiang W, Gao X, Xiang B, Voth GA. Structure of the Liquid−Vacuum Interface of Room-Temperature Ionic Liquids:  A Molecular Dynamics Study. J Phys Chem B. 2006 ;110:1800-6.
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 . 2022 ;119:e2117781119.
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 .
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.
Li C, Yue Z, Newstead S, Voth GA. Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys. J. In Press .
Yamashita T, Voth GA. Properties of Hydrated Excess Protons Near Phospholipid Bilayers. J. Phys. Chem. B. 2010 ;114:592–603.
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 .
Xu J, Yamashita T, Agmon N, Voth GA. On the Origin of Proton Mobility Suppression in Aqueous Solutions of Amphiphiles. J. Phys. Chem. B . 2013 ;117(49):15426-15435.
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.
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.
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.
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.
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.
Wang Y, Izvekov S, Yan T, Voth GA. Multiscale Coarse-Graining of Ionic Liquids. J Phys Chem B. 2006 ;110:3564-75.
Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 .
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.
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.
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.
Yue Z, Wang Z, Voth GA. Ion Permeation, Selectivity, and Electronic Polarization in Fluoride Channels. Biophys. J. 2022 ;121:1336–1347.
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.
Yamashita T, Voth GA. Insights into the Mechanism of Proton Transport in Cytochrome c Oxidase. J. Am. Chem. Soc. 2012 ;134:1147-1152.
Yamashita T, Voth GA. Insights into the Mechanism of Proton Transport in Cytochrome c Oxidase. J. Am. Chem. Soc. 2011 ;134(2):1147–1152.
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 .
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 .
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 .
Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J. Am. Chem. Soc. 2019 ;141:13421-13433.
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.
Chen H, Yan T, Voth GA. A Computer Simulation Model for Proton Transport in Liquid Imidazole. J. Phys. Chem. A. 2009 ;113:4507-4517.
Yamashita T, Peng Y, Knight C, Voth GA. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics. J. Chem. Theory Comput. 2012 ;8:4863-4875.
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.
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.
Yu A, Lee EMY, Jin J, Voth GA. Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6). Science Advances. 2020 ;6(36).
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.
Book Chapter
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.
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.