Publications

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2023
Chen S, Li Z, Voth GA. Acidic Conditions Impact Hydrophobe Transfer Across the Oil-Water Interface in Unusual Ways. J. Phys. Chem. B. 2023 ;127(17):3911–3918.
Ghosh K, Loose TD, Voth GA. Can a Coarse-grained Water Model Capture the Key Physical Features of the Hydrophobic Effect?. J. Chem. Phys. 2023 ;159:224105.
Loose TD, Sahrmann PG, Qu TS, Voth GA. Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Structural Models. J. Phys. Chem. 2023 ;127:10564–10572.
Peng Y, Pak AJ, Durumeric AEP, Mani S, Jin J, Sahrmann PG, Loose TD, Beiter J, Voth GA. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 2023 ;127:8537–8550.
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.
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.
Yue Z, Li C, Voth GA. The Role of Conformational Change and Key Glutamic Acid Residues in the ClC-ec1 Antiporter. Biophys. J. 2023 ;122(6):1068–1085.
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.
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.
Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Liu L, Voth GA, DeGrado WF. Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins. Nat. Chem. 2023 ;15(7):1012–1021.
Jin J, Lee EK, Voth GA. Understanding Dynamics in Coarse-Grained Models: III. Roles of Rotational Motion and Translation-Rotation Coupling in Coarse-Grained Dynamics. J. Chem. Phys. 2023 ;159:164102.
Sahrmann PG, Loose TD, Durumeric AEP, Voth GA. Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles. J. Chem. Theory Comput. 2023 ;19(14):4402–4413.
2022
Zuchniarz J, Liu Y, Li C, Voth GA. Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values. J. Phys. Chem. B. 2022 ;126(38):7321–7330.
Zuchniarz J, Liu Y, Li C, Voth GA. Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values. J. Phys. Chem. B. 2022 ;126(38):7321–7330.
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.
Jin J, Pak AJ, Durumeric AEP, Loose TD, Voth GA. Bottom-up Coarse-Graining: Principles and Perspectives. J. Chem. Theory Comput. 2022 ;18(10):5759–5791.
Loose TD, Sahrmann PG, Voth GA. Centroid Molecular Dynamics Can Be Greatly Accelerated through Neural Network Learned Centroid Forces Derived from Path Integral Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(10):5856–5863.
Liu Y, Li C, Voth GA. Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins. J. Phys. Chem. B. 2022 ;126(49):10452–10459.
Liu Y, Li C, Voth GA. Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins. J. Phys. Chem. B. 2022 ;126(49):10452–10459.
Kim S, Li C, Jr RVFarese, Walther TC, Voth GA. Key Factors Governing Initial Stages of Lipid Droplet Formation. J. Phys. Chem. B. 2022 ;126(2):453–462.
Li C, Yue Z, Newstead S, Voth GA. Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys. J. 2022 ;121(12):2266–2278.
Li C, Paesani F, Voth GA. Static and Dynamic Correlations in Water: Classical Ab Initio Molecular Dynamics Run at an Elevated Temperature May Not Capture Well Explicit Nuclear Quantum Effects at Ambient Temperature. J. Chem. Theory Comput. 2022 ;18(4):2124–2131.
Yu A, Lee MY, Briggs JAG, Ganser-Pornillos BK, Pornillos O, Voth GA. Strain and Rapture of HIV-1 Capsids During Uncoating. Proc. Nat. Acad. Sci. USA. 2022 ;119(10):e2117781119.
Li C, Voth GA. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(2):599–604.
2021
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.
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.
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(19):194506.
Liu Y, Li C, Gupta M, Finer-Moore J, Verma N, Johri AK, Stroud RM, Voth GA. Key Computational Findings Reveal Proton Transfer as Driving the Functional Cycle in the Phosphate Transporter PiPT. Proc. Natl. Acad. Sci. USA. 2021 ;118(25):e2101932118.
Liu Y, Li C, Gupta M, Finer-Moore J, Verma N, Johri AK, Stroud RM, Voth GA. Key Computational Findings Reveal Proton Transfer as Driving the Functional Cycle in the Phosphate Transporter PiPT. Proc. Natl. Acad. Sci. USA. 2021 ;118(25):e2101932118.
Li C, Voth GA. A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces. Proc. Natl. Acad. Sci. USA. 2021 ;118(49 ):e2113141118.
Calio PB, Li C, Voth GA. Resolving the Structural Debate for the Hydrated Excess Proton in Water. J. Am. Chem. Soc. 2021 ;143(44):18672−18683.
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.
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.
Li C, Voth GA. Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface. J. Chem. Theory Comput. 2021 ;17(9):5759–5765.
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 .
Lee S, Liang R, Voth GA, Swason JMJ. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comp. . 2016 ;12:879-891.
Lee S, Liang R, Voth GA, Swason JMJ. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comp. . 2016 ;12:879-891.
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.
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 .
Chen C, Tse Y-LS, Lindberg GE, Knight C, Voth GA. Hydroxide Solvation and Transport in Anion Exchange Membranes. J. Am. Chem. Soc. 2016 ;138(3):991-1000.
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.
Lee S, Swanson JMJ, Voth GA. Multiscale Simulations Reveal the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophys. J. 2016 ;110(6):1334–1345.
Lee S, Mayes HB, Swanson JMJ, Voth GA. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. J. Am. Chem. Soc. . 2016 .
2014
Liang R, Swanson JMJ, Voth GA. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J. Chem. Theor. Comp. 2014 ;10(1):451–462.
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.
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.
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.
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.
Liang R, Li H, Swanson JMJ, Voth GA. Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2014 ;111:9396-9401.
Liang R, Li H, Swanson JMJ, Voth GA. Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2014 ;111:9396-9401.
Ziemba BP, Li J, Landgraf KE, Knight JD, Voth GA, Falke JJ. Single Molecule Studies Reveal A Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C alpha. Biochemistry. 2014 ;53:1697-1713.
Ziemba BP, Li J, Landgraf KE, Knight JD, Voth GA, Falke JJ. Single Molecule Studies Reveal A Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C alpha. Biochemistry. 2014 ;53:1697-1713.
2013
Choi TH, Liang R, Maupin CM, Voth GA. Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions. J. Phys. Chem. B . 2013 ;117:5165-5179.
Lu L, Dama JF, Voth GA. Fitting coarse-grained distribution functions through an iterative force-matching method. J. Chem. Phys. 2013 ;139:1-10.
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.
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.
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.
Lange AW, Voth GA. A Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations. J. Chem. Theor. Comp. 2013 ;9:4018–4025.
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.
Cao Z, Dama JF, Lu L, Voth GA. Solvent Free Ionic Solution Models from Multiscale Coarse-Graining. J Chem Theory Comput. 2013 ;9:172-178.
Cui H, Mim C, Lyman E, Unger VM, Voth GA. Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling. Biophys. J. 2013 ;104:404-411.
2010
Chen H, Liu P, Voth GA. An Efficient Multi-State Reactive Molecular Dynamics Approach Based on Short-Ranged Effective Potentials. J. Chem. Theor. Comp. 2010 ;6:3039–3047.
Lu L, Izvekov S, Das A, Andersen HC, Voth GA. Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining. J. Chem. Theor. Comp. 2010 ;6:954-965.
Ayton GS, Lyman E, G. A. Voth, “” 144 (2010. Hierarchical Coarse-graining Strategy for Protein-Membrane Systems to Access Mesoscopic Scales. Faraday Disc. Chem. Soc. 2010 ;144:347–357.
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.
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.
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.
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.
Lai C-L, Landgraf KE, Voth GA, Falke JJ. Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKCα C2 Domain: A Combined Molecular Dynamics and Experimental Study. J. Mol. Biol. 2010 ;402:301–310.
Lai C-L, Landgraf KE, Voth GA, Falke JJ. Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKCα C2 Domain: A Combined Molecular Dynamics and Experimental Study. J. Mol. Biol. 2010 ;402:301–310.
Larini L, Lu L, Voth GA. The Multiscale Coarse-Graining Method. VI. Implementation of Three-Body Coarse-Grained Potentials. J. Chem. Phys. 2010 ;132:164107.
Larini L, Lu L, Voth GA. The Multiscale Coarse-Graining Method. VI. Implementation of Three-Body Coarse-Grained Potentials. J. Chem. Phys. 2010 ;132:164107.
Jr. HRD, Lu L, Voth GA. Multiscale Coarse-Graining of the Protein Energy Landscape. PLoS Comp. Bio. 2010 ;6:e1000827.
Pfaendtner J, Lyman E, Pollard TD, Voth GA. Structure and Dynamics of the Actin Filament. J. Mol. Biol. 2010 ;396:252–263.
Lyman E, Cui H, Voth GA. Water Under the BAR. Biophys. J. 2010 ;99:1783–1790.
1997
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.
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.
Lobaugh J, Voth GA. A Quantum Model for Water: Equilibrium and Dynamical Properties. The Journal of Chemical Physics. 1997 ;106:2400-2410.
1996
Lobaugh J, Voth GA. The Quantum Dynamics of an Excess Proton in Water. The Journal of Chemical Physics. 1996 ;104:2056-2069.
1994
Li DH, Voth GA. Calculation of ESR Linewidths for Hydrogen Atom Impurities in Solid para-Hydrogen. J. Chem. Phys. 1994 ;100:1785-1796.
Lobaugh J, Voth GA. A Path Integral Study of Electronic Polarization and Nonlinear Coupling Effects in Condensed Phase Proton Transfer Reactions. The Journal of Chemical Physics. 1994 ;100:3039-3047.
Lobaugh J, Voth GA. Quantum Mechanical Calculations of Tunneling Rates in Condensed Phases Systems. In: Reaction Dynamics in Clusters and Condensed Phases. Reaction Dynamics in Clusters and Condensed Phases. The Netherlands: Kluwer Academic Publishers; 1994. pp. 411-422.