Publications

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Submitted
Brousseau M, Thomas NE, Teng D, Voth GA, Henzler-Wildman KA. The C-terminus of the Multi-Drug Efflux Pump EmrE Prevents Proton Leak by Gating Transport. Proc. Nat. Acad. Sci. USA. Submitted .
Aydin F, Katkar HH, Morganthaler AN, Harker AJ, Kovar DR, Voth GA. Prediction of the essential intermolecular contacts for side-binding of VASP on F-Actin. Cytoskeleton. Submitted .
Chen Y, Ma X, Hack JH, Zhang S, Peng A, Dombrowski JP, Voth GA, Tokmakoff A, Kung MC, Kung HH. Solvated Excess Proton as the Active Site in Methanol Dehydration: Beyond the Hydrated Hydronium Ion. Submitted .
2024
Hudait A, Voth GA. HIV-1 capsid shape, orientation, and entropic elasticity regulate translocation into the nuclear pore complex. Proc. Nat. Acad. Sci. USA. 2024 ;121:e2313737121.
2023
Voth GA, Haliloglu T. Deciphering the Dynamic Codes: Advances in Biomolecular Modeling and Simulation. Curr. Opin. Struct. Biol. 2023 ;81:102642.
Hudait A, Hurley JH, Voth GA. Dynamics of Upstream ESCRT Organization at the HIV-1 Budding Site. Biophys. J. 2023 ;122(13):2655–2674.
Hudait A, Hurley JH, Voth GA. Dynamics of Upstream ESCRT Organization at the HIV-1 Budding Site. Biophys. J. 2023 ;122(13):2655–2674.
Jin J, Hwang J, GA V. Gaussian Representation of Coarse-Grained Interactions of Liquids: Theory, Parametrization, and Transferability. J. Chem. Phys. 2023 ;159:184105.
Hack JH, Ma X, Chen JP, Dombrowski JP, Lewis NHC, Li C, Kung HH, Voth GA, Tokmakoff A. Proton Dissociation and Delocalization Under Stepwise Hydration of Zeolite HZSM-5. J. Phys. Chem. C. 2023 ;127:16175-16186.
Wang K, Lee CW, Sui X, Kim S, Wang S, Higgs AB, Baublis AJ, Voth GA, Liao M, Walther T, et al. The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification. Nat. Commun. 2023 ;14:3533.
2022
Tsai F-C, Henderson JM, Jarin Z, Kremneva E, Pernier J, Mikhajlov O, Manzi J, Clainche LC, Voth GA, Lappalainen P, et al. Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
Wei G, Iqbal N, Courouble VV, AC F, Singh PK, Hudait A, Annamalai AS, Bester S, Huang S-W, Shkriabai N, et al. Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
Wei G, Iqbal N, Courouble VV, AC F, Singh PK, Hudait A, Annamalai AS, Bester S, Huang S-W, Shkriabai N, et al. Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
Wei G, Iqbal N, Courouble VV, AC F, Singh PK, Hudait A, Annamalai AS, Bester S, Huang S-W, Shkriabai N, et al. Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
2021
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.
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.
Han Y, Jin J, Voth GA. Constructing Many-body Mesoscopic Models of Fluids from Bottom-up Coarse-graining. J. Chem. Phys. 2021 ;154(8):084122.
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.
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 ;120(6):1097–1104.
Jin J, Han Y, Voth GA. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-body Projected Water (BUMPer). I. General Theory and Model. J. Chem. Phys. 2021 ;154(4):044104.
Hocky GM, Sindelar VC, Cao W, Voth GA, Cruz DLEM. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296:100337.
Hack JH, Dombrowski JP, Ma X, Chen Y, Lewis NHC, Carpenter WB, Li C, Voth GA, Kung HH, Tokmakoff A. Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites. J. Am. Chem. Soc. 2021 ;143(27):10203–10213.
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.
2020
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 ;27(6):570–580.
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 ;27(6):570–580.
Calio PB, Hocky GM, Voth GA. Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water. J. Chem. Theory. Comput. 2020 ;16(9):5675–5684 .
2019
Jin J, Han Y, Voth GA. Coarse-Graining Involving Virtual Sites: Centers of Symmetry Coarse-Graining. J. Chem. Phys. 2019 ;150(15):154103.
Ryu WH, Han Y, Voth GA. Coarse-graining of many-body path integrals: Theory and numerical approximations. J. Chem. Phys. 2019 ;150(24):244103.
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. Mol. Biol. Cell. 2019 ;30(7):851–862.
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. Proc. Natl. Acad. Sci. USA. 2019 ;116(13):16192–16197.
Schramm AC, Hocky GM, Voth GA, Martiel J-L, De La Cruz EM. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophys. J. 2019 ;117(3):453–463.
2018
Katkar HH, Davtyan A, Durumeric AEP, Hocky GM, Schramm CS, De La Cruz EM, Voth GA. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophys. J. 2018 ;115(18):1589–1602.
Han Y, Dama JF, Voth GA. Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. J. Chem. Phys. 2018 ;149(4):044104.
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(7):072310.
Han Y, Jin J, Wagner J, Voth GA. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148(10):102335.
Jin J, Han Y, Voth GA. Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding. J. Chem. Theory Comput. 2018 ;14(12):6159–6174.
2017
Schramm AC, Hocky GM, Voth GA, .Blanchoin L, Martiel J-L, De La Cruz EM. Actin Filament Strain Promotes Severing and Cofilin Dissociation. Biophys J. 2017 ;112.
Hocky GM, Dannenhoffer-Lafage T, Voth GA. Coarse-Grained Directed Simulation. J. Chem. Theory Comput. 2017 .
Christensen JR, Hocky GM, Morganthaler AN, Homa KE, Hitchcock-DeGregori SE, Voth GA, Kovar DR. Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks. eLife. 2017 ;6.
Christensen JR, Hocky GM, Morganthaler AN, Homa KE, Hitchcock-DeGregori SE, Voth GA, Kovar DR. Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks. eLife. 2017 ;6.
Christensen JR, Hocky GM, Morganthaler AN, Homa KE, Hitchcock-DeGregori SE, Voth GA, Kovar DR. Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks. eLife. 2017 ;6.
White AD, Knight C, Hocky GM, Voth GA. Improved Ab Initio Molecular Dynamics by Minimally Biasing with Experimental Data. J. Chem. Phys. 2017 ;146.
Simunovic M, Šarić A, Henderson JM, Lee K-YC, Voth GA. Lipid Membrane Mediates Long-Range Interactions Between Linear Filaments of Membrane-Curving Proteins. ACS Cen. Sci. 2017 ;3:1246-1253 .
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).
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).
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 .
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 .
2016
Liang R, Swanson JMJ, Madsen JJ, Hong M, DeGrado WF, Voth GA. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
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).
Li Y, Christensen JR, Homa KE, Hocky GM, Fok A, Sees JA, Voth GA, Kovar DR. The F-Actin Bundler α-Actinin Ain1 is Tailored for Ring Assembly and Constriction during Cytokinesis in Fission Yeast. Mol Biol Cell. 2016 ;27(11):1821-1833.
Li Y, Christensen JR, Homa KE, Hocky GM, Fok A, Sees JA, Voth GA, Kovar DR. The F-Actin Bundler α-Actinin Ain1 is Tailored for Ring Assembly and Constriction during Cytokinesis in Fission Yeast. Mol Biol Cell. 2016 ;27(11):1821-1833.
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.
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.
2015
Dama JF, Hocky GM, Sun R, Voth GA. Exploring Valleys Without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction. J. Chem. Theory Comp. 2015 .
2014
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.
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.
2013
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 .
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).
Li J, Sode O, Voth GA, Hirata S. A Solid-Solid Phase Transition in Carbon Dioxide at High Pressures and Intermediate Temperatures. Nat. Commun. 2013 ;4.
2012
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.
2009
Lyman E, Higgs C, Kim B, Lupyan D, Shelley JC, Farid R, Voth GA. A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor. Structure. 2009 ;17:1660–1668.
2008
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.
2006
Hone TD, Rossky PJ, Voth GA. A Comparative Study of Imaginary Time Path Integral Based Methods for Quantum Dynamics. J Chem Phys. 2006 ;124:154103.
2005
Hone TD, Izvekov S, Voth GA. Fast Centroid Molecular Dynamics: a Force-matching Approach for the Predetermination of the Effective Centroid Forces. J Chem Phys. 2005 ;122:54105.
2004
Hone TD, Voth GA. A Centroid Molecular Dynamics Study of Liquid Para-hydrogen and Ortho-deuterium. J Chem Phys. 2004 ;121:6412-22.
2000
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.
1998
Hernandez R, Voth GA. Quantum Time Correlation Functions and Classical Coherence. Chem. Phys. 1998 ;233:243-255.
1996
Voth GA, Hochstrasser RM. Transition State Dynamics and Relaxation Processes in Solutions: A Frontier of Physical Chemistry. The Journal of Physical Chemistry. 1996 ;100:13034-13049.
1995
Hernandez R, Cao J, Voth GA. On the Feynman Path Centroid Density as a Phase Space Distribution in Quantum Statistical Mechanics. The Journal of Chemical Physics. 1995 ;103:5018-5026.
Haynes GR, Voth GA. Reaction-Coordinate-Dependent Friction in Classical Activated Barrier Crossing Dynamics: When it Matters and When it Doesn't. The Journal of Chemical Physics. 1995 ;103:10176-10182.
1994
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.
1993
Haynes GR, Voth GA. The Dependence of the Potential of Mean Force on the Solvent Friction: Consequences for Condensed Phase activated Rate Theories. The Journal of Chemical Physics. 1993 ;99:8005-8008.
Voth GA. A Feynman Path Integral Formulation of Quantum Mechanical Transition State Theory. In: Talkner P, Hänggi P New Trends in Kramers' Reaction Rate Theory. New Trends in Kramers' Reaction Rate Theory. The Netherlands: Kluwer Academic Publishers; 1993.
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.
1992
McRae RP, Schenter GK, Garrett BC, Haynes GR, Voth GA, Schatz GC. Critical Comparison of Approximate and Accurate Quantum-mechanical Calculations of Rate Constants for a Model Activated Reaction in Solution. The Journal of Chemical Physics. 1992 ;97:7392-7404.
Haynes GR, Voth GA. Effect of Nonlinear Dissipation on Quantum-activated Rate Processes in Condensed Phases. Phys Rev A. 1992 ;46:2143-2146.