Publications
] . New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases. In: Reviews in Computational Chemistry. Vol. 18. Reviews in Computational Chemistry. New York: John Wiley and Sons; 2002. pp. 147-210.
. A New Perspective on Quantum Mechanical Transition State Theory. In: Quantum Simulations of Condensed Matter Phenomena. Quantum Simulations of Condensed Matter Phenomena. Singapore: World Scientific; 1990. pp. 391-400.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. J. Chem. Phys. 2001 ;114:9758-9763.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. IV. Formal Analysis of the Deviations from Born-Oppenheimer Dynamics. Israel. J. Chem. 2003 ;42:191-202.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics. J. Chem. Phys. 2002 ;117:8694-8704.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. II. Generalization based on Mass-weighting, Idempotency, Energy Conservation, and Choice of Initial Conditions. J. Chem. Phys. 2001 :10291-10302.
. Ab initio Molecular Dynamics Simulation of the Cu(110)–Water Interface. J. Chem. Phys. 2001 ;114:3248.
. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
. Actin Filament Strain Promotes Severing and Cofilin Dissociation. Biophys J. 2017 ;112.
Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
. Adiabatically Reduced Coupled Equations for Intramolecular Dynamics Calculations. The Journal of Chemical Physics. 1986 ;84:2254-2261.
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.
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.
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.
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.
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.
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.
. Anisotropic Motions of Fibrils Dictated by Their Orientations in the Lamella: A Coarse-Grained Model of a Plant Cell Wall. J. Phys. Chem. B. 2020 ;124(17):3527–3539.
. Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions. J. Phys. Chem. B . 2013 ;117:5165-5179.
. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
. Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility. J Mol Biol. 2007 ;365:523-34.
. Calculating the Bulk Modulus for a Lipid Bilayer with Nonequilibrium Molecular Dynamics Simulation. Biophys J. 2002 ;82:1226-38.
. Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2011 ;133:6223–6234.
. Cholesterol Alters the Membrane Orientation and Activity of the Influenza Virus M2 Amphipathic Helix. J. Phys. Chem. B. 2020 ;124(31):6738–6747 .
. Cholesterol Alters the Membrane Orientation and Activity of the Influenza Virus M2 Amphipathic Helix. J. Phys. Chem. B. 2020 ;124(31):6738–6747 .
. Classical and Quantum Transition State Theory for the Diffusion of Helium in Silica Sodalite. The Journal of Physical Chemistry B. 1997 ;101:491-503.
. Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks. eLife. 2017 ;6.
. Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments. J. Phys. Chem. B. 2021 ;17(3):1900–1913.
. The Computation of Electron Transfer Rates: The Nonadiabatic Instanton Solution. The Journal of Chemical Physics. 1995 ;103:1391-1399.
. Cooperative Membrane Binding of HIV-1 Matrix Proteins. J. Phys. Chem. B. Submitted .
. Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles. Biophys J. 2005 ;88:3855-69.
. Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles. Biophys J. 2005 ;88:3855-69.
. Coupling Field Theory with Mesoscopic Dynamical Simulations of Multicomponent Lipid Bilayers. Biophys J. 2004 ;87:3242-63.
. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J. Phys. Chem. B. 2016 :8389−8404 .
. 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.
. Defining Condensed Phase Reactive Force Fields From Ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton. J. Chem. Theor. Comp. 2010 ;6:3223–3232.
. Density Functional Theory-based Quantum Mechanics/Coarse-grained Molecular Mechanics: Theory and Implementation. J. Chem. Theory Comput. 2020 ;16(10):6329–6342.
. Effect of Active-site Mutations at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II. Biochem. 2009 ;48:7996-8005.
. Effect of Active-site Mutations at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II. Biochem. 2009 ;48:7996-8005.
. Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure. 2015 ;23.
. Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2009 ;131:7598-7608.
. Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2009 ;131:7598-7608.
. Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc. Natl. Acad. Sci. USA. 2018 ;115(37):E8595–E8603.
. Excess Proton Solvation and Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion. J Phys Chem B. 2005 ;109:3727-30.
. Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response. Biophys J. 2006 ;90:92-100.
. Fascin and α-Actinin-bundled Networks Contain Intrinsic Structural Features That Drive Protein Sorting. Current Biology. 2016 ;26(20):2697–2706.
. Highly Coarse-grained Representations of Transmembrane Proteins. J. Chem. Theory Comput. 2017 ;13.
. The Highly Excited C-H Stretching States of CHD3, CHT3, and CH3D. J. Chem. Phys. 1984 ;81:5494-5507.
. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Nat. Acad. Sci. USA. 2016 .
. Immature HIV-1 Assembles from Gag Dimers Leaving Partial Hexamers at Lattice Edges as Substrates for Proteolytic Maturation. Proc. Natl. Acad. Sci. USA. 2021 ;118(3):e2020054118.
. Interfacing Continuum and Molecular Dynamics: An Application to Lipid Bilayers. J. Chem. Phys. 2001 ;114:6913-6924.
. Interfacing Molecular Dynamics and Macro-scale Simulations for Lipid Bilayer Vesicles. Biophys J. 2002 ;83:1026-38.
. Interfacing Molecular Dynamics with Continuum Dynamics in Computer Simulation: Toward an Application to Biological Membranes. IBM J. Res. Dev. 2001 ;45:417-426.
. Iteratively Determined Effective Hamiltonians for the Adiabatically Reduced Coupled Equations Approach to Intramolecular Dynamics Calculations. J. Chem. Phys. 1986 ;85:5019-5026.
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
. Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain. J. Mol. Biol. 2012 ;423:800-817.
. Modeling the Free Energy Surfaces of Electron Transfer in Condensed Phases. J. Chem. Phys. 2000 ;113:5413-5424.
. Molecular Interactions of the M and E Integral Membrane Proteins of SARS-CoV-2. Faraday Discuss. 2021 ;232:49–67 .
. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 ;120(6):1097–1104.
. Multiscale Kinetic Modeling Reveals Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter. J. Am. Chem. Soc. 2018 ;140(5):1793–1804.
. A Multistate Empirical Valence Bond Description of Protonatable Amino Acids. J Phys Chem A. 2006 ;110:631-9.
. Nature of Lithium Trapping Sites in the Quantum Solids Para-hydrogen and Ortho-deuterium. The Journal of Chemical Physics. 1993 ;99:9013-9020.
. New Insights into BAR Domain Induced Membrane Remodeling. Biophys. J. 2009 ;97:1616–1625.
. A New Perspective on the Coarse-grained Dynamics of Fluids. J Chem Phys. 2004 ;120:4074-88.
. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 2023 ;127:8537–8550.
. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. J. Am. Chem. Soc. . 2016 .
. Origins of Enhanced Proton Transport in the Y7F Mutant of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2008 ;130:11399–11408.
. Origins of Enhanced Proton Transport in the Y7F Mutant of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2008 ;130:11399–11408.
. Path Integral Molecular Dynamics Simulation of Solid Para-Hydrogen with an Aluminum Impurity. Chem. Phys. Lett. 2002 ;365:487-493.
. A Perturbation Theory for Solvation Thermodynamics: Dipolar–quadrupolar Liquids. The Journal of Chemical Physics. 1999 ;111:3630-3638.
. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophys. J. 2019 ;117(3):453–463.
. Potential Energy Surfaces for Chemical Reactions: An Analytical Representation from Coarse Grained Data with an Application to Proton Transfer in Water. The Journal of Physical Chemistry B. 1997 ;101:4544-4552.
. Prediction of the essential intermolecular contacts for side-binding of VASP on F-Actin. Cytoskeleton. Submitted .
. Preferred Orientations of His-64 in Human Carbonic Anhydrase II. Biochemistry. 2007 ;46:2938-47.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
. Protein-Mediated Transformation of Lipid Vesicles into Tubular Networks. Biophys. J. 2013 ;105(3):711-719.
. Protein-Mediated Transformation of Lipid Vesicles into Tubular Networks. Biophys. J. 2013 ;105(3):711-719.
. Proton Dissociation and Delocalization Under Stepwise Hydration of Zeolite HZSM-5. J. Phys. Chem. C. 2023 ;127:16175-16186.
. Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations. J Phys Chem B. 2007 ;111:4300-14.
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.
. Proton Transport in Carbonic Anhydrase: Insights from Molecular Simulation. Biochim. et Biophys. Acta - Proteins and Proteomics. 2010 ;1804:332-341.
. Quantum and Classical Energy Transfer Between Ligands of a Heavy Metal Atom. Chem. Phys. Lett. 1986 ;124:93-98.
. Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 1. Charge Transfer Reactions. The Journal of Physical Chemistry A. 2000 ;104:6470-6484.
. Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 2. Optical Spectra. The Journal of Physical Chemistry A. 2000 ;104:6485-6494.
. Rigorous Formulation of Quantum Transition State Theory and its Dynamical Corrections. The Journal of Chemical Physics. 1989 ;91:7749-7760.
. A Second Generation Mesoscopic Lipid Bilayer Model: Connections to Field-Theory Descriptions of Membranes and Nonlocal Hydrodynamics. J Chem Phys. 2006 ;124:64906.
. The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations. J. Phys. Chem. B. 2010 ;114:6922-6931.
. Semiclassical Dressed State Theory for the Vibrational Excitation of a Morse Oscillator by Radiation. The Journal of Physical Chemistry. 1985 ;89:2208-2213.
. Semiclassical Theory of Fermi Resonance between Stretching and Bending Modes in Polyatomic Molecules. The Journal of Chemical Physics. 1985 ;82:4064-4072.
. Simulating Accidental Fires and Explosions. Computing in Science and Engineering. 2000 ;2:64-76.
. Solvated Excess Proton as the Active Site in Methanol Dehydration: Beyond the Hydrated Hydronium Ion. Submitted .
. Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water. J. Phys. Chem. B. 2008 ;112:9456-9466.
. Structural Basis of Membrane Bending by the N-BAR Protein Endophilin. Cell. 2012 ;149.
. Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites. J. Am. Chem. Soc. 2021 ;143(27):10203–10213.
. Structure of Hydrated Na−Nafion Polymer Membranes. J Phys Chem B. 2005 ;109:24244-53.
Synthesis, Characterization and Simulation of Four-Armed Megamolecules. Biomacromolecules. 2021 ;22(6):2363–2372.
Synthesis, Characterization and Simulation of Four-Armed Megamolecules. Biomacromolecules. 2021 ;22(6):2363–2372.
. Temperature Dependence of the Solvent Reorganization Energy of Electron Transfer in Highly Polar Solvents. J. Phys. Chem. B. 1999 ;103:9130-9140.
. A Theory of Electron Transfer and Steady-State Optical Spectra of Chromophores with Varying Electronic Polarizability. The Journal of Physical Chemistry A. 1999 ;103:10981-10992.
. The Theory of Electron Transfer Reactions: What May Be Missing?. J Am Chem Soc. 2003 ;125:7470-8.
. Theory of Ultra Coarse-Graining. I. General Principles. J. Chem. Theor. Comp. 2013 ;9:2466−2480.
. Time Correlation Function and Path Integral Analysis of Quantum Rate Constants. The Journal of Physical Chemistry. 1989 ;93:7009-7015.
. Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins. Nat. Chem. 2023 ;15(7):1012–1021.
. Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling. Biophys. J. 2013 ;104:404-411.
. Unique Elastic Properties of the Spectrin Tetramer as Revealed by Multiscale Coarse-Grained Modeling. Proc. Natl. Acad. Sci. USA. 2008 ;105:1204-1208.
. Unraveling the Mystery of ATP Hydrolysis in Actin Filaments. J. Am. Chem. Soc. . 2014 ;136(37):13053–13058.
. Unraveling the Role of the Protein Environment for [FeFe]-Hydrogenase Charge Transfer: A New Application of Coarse-Graining. J. Phys. Chem. B. 2013 ;17:4062−4071.
. Vibrational Energy Redistribution Across a Heavy Atom. Chem. Phys. 1989 ;139:171-184.
. Water Assisted Proton Transport in Confined Nanochannels. J. Phys. Chem. C. 2020 ;124(29):16186−16201.
. Water Assisted Proton Transport in Confined Nanochannels. J. Phys. Chem. C. 2020 ;124(29):16186−16201.