Publications

Author Title [ Type(Desc)] Year
Filters: Author is Voth, GA  [Clear All Filters]
Book
Voth GA. Coarse-Graining of Condensed Phase and Biomolecular Systems. Boca Raton, FL: CRC Press/Taylor and Francis Group; 2009.
Journal Article
Li C, Voth GA. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. J. Phys. Chem B . 2021 ;125(37):10471-10480 .
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.
Pak AJ, Voth GA. Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Current Opinion in Structural Biology. 2018 ;52:119-126.
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).
Galvan-Monjee V, Voth GA. Binding Mechanism of the Matrix Domain of HIV-1 Gag to Lipid Membranes. eLife . 2020 ;9.
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 .
Jarin Z, Newhouse J, Voth GA. Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover. J. Chem. Theory Comp. 2021 ;17(2):1170-1180.
Mani S, Katkar HH, Voth GA. Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments. J. Phys. Chem. B . 2021 ;17(3):1900-1913.
Han Y, Jin J, Voth GA. Constructing Many-body Mesoscopic Models of Fluids from Bottom-up Coarse-graining. J. Chem. Phys. 2021 ;154:084122.
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 .
Mironenko AV, Voth GA. Density Functional Theory-based Quantum Mechanics/Coarse-grained Molecular Mechanics: Theory and Implementation. J. Chem. Theory Comp. 2020 ;16(10):6329–6342.
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).
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.
Ryu WH, Voth GA. Generalized Langevin Equation Analysis of Ring Polymer Molecular Dynamics. J. Chem. Phys. Submitted .
Arntsen C, Chen C, Calio PB, Li C, Voth GA. The Hopping Mechanism of the Hydrated Excess Proton and Its Contribution to Proton Diffusion in Water. J. Chem. Phys. 2021 ;154:194506.
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.
Watkins LC, DeGrado WF, Voth GA. Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics. J. Am. Chem. Soc. 2020 ;142(41):17425–17433.
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. Biophysical Journal. 2018 ;115(18):1589-1602.
Driscoll T, Bidone TC, Ahn S, Goisman A, Voth GA, Schwartz MA. Integrin-Based Mechanosensing through Conformational Activation. eLife. In Press .
Li J, Ziemba BP, Falke JJ, Voth GA. Interactions of Protein Kinase C-α C1A and C1B Domains with Membranes: A Combined Computational and Experimental Study. J. Am. Chem. Soc. 2014 ;136(33):11757–11766.
Li Z, Voth GA. Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles. Phys. Chem. Chem. Phys. 2020 ;22(19):10753-10763.
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.
Calio PB, Hocky GM, Voth GA. A Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water. J. Chem. Theory. Comp. 2020 ;16(9):5675–5684 .
Monje-Galvan V, Voth GA. Molecular Interactions of the M And E Integral Membrane Proteins of SARS-CoV-2. Faraday Discussions. In Press .
Calio PB, Li C, Voth GA. Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions. J. Phys. Chem. B. 2020 ;124(40):8868–8876.
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.
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 .
Bidone TC, Skeeters AV, Oakes PW, Voth GA. Multiscale model of integrin adhesion assembly. POLS Computational Biology. 2019 ;15(6):e1007077.
Aydin F, Katkar HH, Voth GA. Multiscale Simulation of Actin Filaments and Actin-Associated Proteins. Biophys Rev. 2018 ;10:1521-1535.
Watkins LC, DeGrado WF, Voth GA. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior. J. Am. Chem. Soc. Submitted .
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.
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 ;154:044104.
Jin J, Pak AJ, Voth GA. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-Body Projected Water (BUMPer). II. Temperature Transferability and Structural Properties at Low Temperature. J. Chem. Phys. 2021 ;154:044105.
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.
Simunovic M, Bassereau P, Voth GA. Organizing Membrane-Curving Proteins: The Emerging Dynamical Picture. Curr. Opin. Struct. Biol. 2018 ;51:99-105 .
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.
Kim S, Voth GA. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis. J. Phys. Chem. B . 2021 ;125:6872-6888.
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. Submitted .
Li C, Yue Z, Newstead S, Voth GA. Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. eLife . Submitted .
Li C, Voth GA. A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces. Proc. Nat. Acad. Sci. USA . Submitted .
Han Y, Jin J, Wagner J, Voth GA. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148:102335.
Dannenhoffer-Lafage T, Voth GA. Reactive Coarse-grained Molecular Dynamics. J. Chem. Theory. Comp. 2020 ;16(4):2541−2549.
Calio PB, Li C, Voth GA. Resolving the Structural Debate for the Hydrated Excess Proton in Water. J. Am. Chem. Soc. In Press .
Srivastava A, Voth GA. Solvent-Free Highly Coarse-Grained Models for Charged Lipid Systems. J. Chem. Theor. Comp. . 2014 ;(10):4730-4744.
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.
Zsolnay V, Katkar HH, Chou SZ, Pollard TD, Voth GA. Structural Basis for Polarized Elongation of Actin Filaments. Proc. Nat. Acad. Sci. USA. 2020 .
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.
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.
Jin J, Yu A, Voth GA. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J. Chem. Theory Comp. 2020 ;16(11):6823–6842.
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 .
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, Han Y, Voth GA. Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding. J. Chem. Theory Comput. 2018 ;14(12):6159-6174.
Jin J, Voth GA. Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. J. Chem. Theory Comp. 2018 ;14(4):2180-2197.
McCullagh M, Saunders MG, Voth GA. Unraveling the Mystery of ATP Hydrolysis in Actin Filaments. J. Am. Chem. Soc. . 2014 ;136(37):13053–13058.
Li C, Voth GA. Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface. J. Chem. Theory Comp. . 2021 ;125(37):10471-10480 .
Ma X, Li C, Martinson ABF, Voth GA. Water Assisted Proton Transport in Confined Nanochannels. J. Phys. Chem. C. 2020 ;124:16186−16201.