Publications
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.
. Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems. J. Chem. Theor. Comp. 2008 ;4:560-568.
. An Accurate and Simple Quantum Model for Liquid Water. J Chem Phys. 2006 ;125:184507.
. An Accurate and Simple Quantum Model for Liquid Water. J Chem Phys. 2006 ;125:184507.
. Acidic Conditions Impact Hydrophobe Transfer Across the Oil-Water Interface in Unusual Ways. J. Phys. Chem. B. 2023 ;127(17):3911–3918.
. Actin Filament Remodeling by Actin Depolymerization Factor/Cofilin. Proc. Natl. Acad. Sci. USA. 2010 ;107:7299–7304.
. Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
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.
Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-grained Analysis. Proc Natl Acad Sci U S A. 2005 ;102:13111-6.
. 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.
. Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility. J Mol Biol. 2007 ;365:523-34.
. Calculation of Solvent Free Energies for Heterogeneous Electron Transfer at the Water–metal Interface: Classical Versus Quantum Behavior. The Journal of Chemical Physics. 1995 ;102:529-539.
. Charge Delocalization in Proton Channels, I: the Aquaporin Channels and Proton Blockage. Biophys J. 2007 ;92:46-60.
. Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2011 ;133:6223–6234.
. 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 .
. Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model. Biophys. J. 2007 ;93:3860-3871.
. Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations. Biophys J. 2006 ;90:1572-82.
. Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies. J. Phys. Chem. B. 2012 ;116:8045-8057.
. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys. J. 2019 ;116(6):1000–1010 .
. Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks. eLife. 2017 ;6.
. The Computation of Electron Transfer Rates: The Nonadiabatic Instanton Solution. The Journal of Chemical Physics. 1995 ;103:1391-1399.
. A Computer Simulation Model for Proton Transport in Liquid Imidazole. J. Phys. Chem. A. 2009 ;113:4507-4517.
. The Computer Simulation of Correlated Electron Transfer Across the Electrode/Electrolyte Interface Involving Multiple Redox Species. The Journal of Chemical Physics. 1998 ;109:4569-4575.
. The Computer Simulation of Electron Transfer Processes Across the Electrode/Electrolyte Interface: A Treatment of Solvent and Electrode Polarizability. J. Electroanal. Chem. 1998 ;450:253-264.
. Delocalization and Stretch-Bend Mixing of the HOH Bend in Liquid Water. J. Chem. Phys. 2017 ;147(084503).
. Development of Reactive Force Fields Using Ab Initio Molecular Dynamics Simulation Minimally Biased to Experimental Data. J. Chem. Phys. 2017 .
. An Efficient Multi-State Reactive Molecular Dynamics Approach Based on Short-Ranged Effective Potentials. J. Chem. Theor. Comp. 2010 ;6:3039–3047.
. Electrochemical Bond-Breaking Reactions: A Comparison of Large Scale Simulation Results with Analytical Theory. The Journal of Physical Chemistry B. 1999 ;103:3442-3448.
. Electron Transfer Across the Electrode/Electrolyte Interface: Influence of Redox Ion Mobility and Counterions. The Journal of Physical Chemistry. 1996 ;100:10746-10753.
. Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure. 2015 ;23.
. Emerging Methods for Multiscale Simulation of Biomolecular Systems. Mol. Phys. 2007 ;105:167-175.
. Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1. J. Mol. Biol. 2011 ;407:607–620.
. Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1. J. Mol. Biol. 2011 ;407:607–620.
. Exact Exchange in ab initio Molecular Dynamics: An Efficient Plane-wave based Algorithm. The Journal of Chemical Physics. 1998 ;108:4697-4700.
. 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.
. Fascin and α-Actinin-bundled Networks Contain Intrinsic Structural Features That Drive Protein Sorting. Current Biology. 2016 ;26(20):2697–2706.
. On the Feynman Path Centroid Density as a Phase Space Distribution in Quantum Statistical Mechanics. The Journal of Chemical Physics. 1995 ;103:5018-5026.
. A First-Principles Simulation of the Semiconductor/Water Interface. The Journal of Chemical Physics. 1997 ;106:2811-2818.
. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. IV. Algorithms for Centroid Molecular Dynamics. The Journal of Chemical Physics. 1994 ;101:6168-6183.
. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. III. Phase Space Formalism and Analysis of Centroid Molecular Dynamics. The Journal of Chemical Physics. 1994 ;101:6157-6167.
. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. II. Dynamical Properties. The Journal of Chemical Physics. 1994 ;100:5106-5117.
. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. V. Quantum Instantaneous Normal Mode Theory of Liquids. The Journal of Chemical Physics. 1994 ;101:6184-6192.
. The Formulation of Quantum Statistical Mechanics based on the Feynman Path Centroid Density. I. Equilibrium Properties. The Journal of Chemical Physics. 1994 ;100:5093-5105.
. Gating mechanisms during actin filament elongation by formins. eLife. 2018 ;7:e37342.
. The Hopping Mechanism of the Hydrated Excess Proton and Its Contribution to Proton Diffusion in Water. J. Chem. Phys. 2021 ;154(19):194506.
. The Hopping Mechanism of the Hydrated Excess Proton and Its Contribution to Proton Diffusion in Water. J. Chem. Phys. 2021 ;154(19):194506.
. How Does Electronic Polarizability or Scaled-Charge Affect the Interfacial Properties of Room Temperature Ionic Liquids?. J. Phys. Chem. B. 2023 ;127(5):1264–1275.
. The Hydrated Excess Proton at Water-Hydrophobic Interfaces. J. Phys. Chem. B. 2009 ;113:4017-4030.
. Hydrated Proton Structure and Diffusion at Platinum Surfaces. J. Phys. Chem. C. 2015 ;119:7516-7521.
. Hydroxide Solvation and Transport in Anion Exchange Membranes. J. Am. Chem. Soc. 2016 ;138(3):991-1000.
. Hyper-Parallel Algorithms for Centroid Molecular Dynamics: Application to Liquid para–Hydrogen. Chem. Phys. Lett. 1996 ;262:415-420.
. 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 .
. An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport. J. Phys. Chem. B. 2008 ;112:467-482.
. Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis. Biophys. J. 2008 ;95:2487-2499.
. Ion Transport through Ultra-Thin Electrolyte under Applied Voltages. J. Phys. Chem. B. 2015 ;119:7516-7521.
. IR Spectral Assignments for the Hydrated Excess Proton in Liquid Water. J. Chem. Phys. 2017 ;146.
. Isotope Effects in Electron Transfer across the Electrode-Electrolyte Interface: A Measure of Solvent Mode Quantization. The Journal of Physical Chemistry B. 1998 ;102:8563-8568.
. On the Key Influence of Amino Acid Ionic Liquid Anions on CO2 Capture. J. Am. Chem. Soc. 2024 ;146:1612 - 1618.
. The Kinetics of Proton Migration in Liquid Water. J. Phys. Chem. B. 2010 ;114:333–339.
. Largescale Computer Simulation of an Electrochemical Bond Breaking Reaction. Chem. Phys. Lett. 1999 ;305:94-100.
. Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
Mechanism of Fast Proton Transport along One-Dimensional Water Chains Confined in Carbon Nanotubes. J. Am. Chem. Soc. 2010 ;132:11395–11397.
. Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins. Biophys. J. 2011 ;100:1271-1279.
. Mechanism of Targeting of Amphipathic Helix-Containing Proteins to Lipid Droplets. Dev. Cell. 2018 ;44(1):73–86.
. Membrane Binding by the Endophilin N-BAR Domain. Biophys. J. 2009 ;97:2746-2753.
. 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 .
. Modeling Physical Systems by Effective Harmonic Oscillators: The Optimized Quadratic Approximation. The Journal of Chemical Physics. 1995 ;102:3337-3348.
. Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water. J. Chem. Phys. . 2016 .
. Molecular Origins of Cofilin-linked Changes in Actin Filament Mechanics. J. Mol. Biol. 2013 ;425(7).
. Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions. J. Phys. Chem. B. 2020 ;124(40):8868–8876.
. The Multiscale Challenge for Biomolecular Systems: Coarse-grained Modeling. Mol. Sim. 2006 ;32:211-218.
. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 ;120(6):1097–1104.
. Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory. J Phys Chem B. 2007 ;111:4116-27.
. The Multiscale Coarse-graining Method I: A Rigorous Bridge between Atomistic and Coarse-grained Models. J. Chem. Phys. 2008 ;128:244114.
. The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models. J. Chem. Phys. 2008 ;128:244115.
. The Multiscale Coarse-Graining Method. XI. Accurate Interactions Based on the Centers of Charge of Coarse-Grained Sites. J. Chem. Phys. 2015 ;143(243116):1-11.
. Multiscale Coupling of Mesoscopic- and Atomistic-level Lipid Bilayer Simulations. J Chem Phys. 2005 ;122:244716.
. A Multi-State Empirical Valence Bond Model for Acid-Base Chemistry in Aqueous Solution. Chem. Phys. Lett. 2000 ;258:187.
. A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution. J. Phys. Chem. A. 2001 ;105:2814-2823.
. A New Perspective on Quantum Time Correlation Functions. The Journal of Chemical Physics. 1993 ;99:10070-10073.
. A Novel Method for Simulating Quantum Dissipative Systems. The Journal of Chemical Physics. 1996 ;104:4189-4197.
. Origins of Proton Transport Behavior from Selectivity Domain Mutations of the Aquaporin-1 Channel. Biophys J. 2006 ;90:L73-5.
. Path Integral Coarse-graining Replica Exchange Method for Enhanced Sampling. J. Chem. Theor. Comp. 2014 ;10 (9 ):3634–3640.
. Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface. J. Am. Chem. Soc. 2015 ;137(39):12610-12616.
. Proton Dissociation and Delocalization Under Stepwise Hydration of Zeolite HZSM-5. J. Phys. Chem. C. 2023 ;127:16175-16186.
. Proton Movement and Coupling in the POT Family of Peptide Transporters. Proc. Nat. Acad. Sci. USA . 2017 ;114(13182).
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 Behavior Through the Influenza A M2 Channel: Insights from Molecular Simulation. Biophys. J. 2007 ;93:3470-3479.
. Proton Transport Under External Applied Voltage. J. Phys. Chem. B. 2014 .
. Quantum Effects and the Excess Proton in Water. The Journal of Chemical Physics. 1997 ;107:7428-7432.
. Reactive Molecular Dynamics Models from Ab Initio Molecular Dynamics Data Using Relative Entropy Minimization. Chem. Phys. Lett. 2017 ;683.
. Reconstructing Protein Remodeled Membranes in Molecular Detail From Mesoscopic Models. Phys. Chem. Chem. Phys. 2011 :10430–10436.
. Resolving the Structural Debate for the Hydrated Excess Proton in Water. J. Am. Chem. Soc. 2021 ;143(44):18672−18683.
. Rigorous Formulation of Quantum Transition State Theory and its Dynamical Corrections. The Journal of Chemical Physics. 1989 ;91:7749-7760.
. The Role of Amino Acid Sequence in the Self-Association of Therapeutic Monoclonal Antibodies: Insights from Coarse Grained Modeling. J. Chem. Phys. B. 2013 .
. A Second Generation Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems. J. Chem. Phys. 2002 ;117:5839-5849.
. Seipin Transmembrane Segments Critically Function in Triglyceride Nucleation and Droplet Budding from the Membrane. eLife. 2022 ;11:e75808.
. Semiclassical Approximations to Quantum Dynamical Time Correlation Functions. The Journal of Chemical Physics. 1996 ;104:273-285.
. A Semiclassical Reactive Flux Method for the Calculation of Condensed Phase Activated Rate Constants. Chem. Phys. 1994 ;180:167-180.
. Solvated Excess Proton as the Active Site in Methanol Dehydration: Beyond the Hydrated Hydronium Ion. Submitted .
. Solvent Free Ionic Solution Models from Multiscale Coarse-Graining. J Chem Theory Comput. 2013 ;9:172-178.
. Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water. J. Phys. Chem. B. 2008 ;112:9456-9466.
. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296:100337.
. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296:100337.
. Structural Basis for Polarized Elongation of Actin Filaments. Proc. Natl. Acad. Sci. USA. 2020 ;117(48):30458–30464.
. 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.
. Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites. J. Am. Chem. Soc. 2021 ;143(27):10203–10213.
. A Theory for Electron Transfer across the Electrode/Electrolyte Interface Involving more than One Redox Ion. The Journal of Chemical Physics. 1997 ;107:8940-8954.
. A Theory for the Quantum Activated Rate Constant in Dissipative Systems. Chem. Phys. Lett. 1996 ;261:111-116.
. A Theory for Time Correlation Functions in Liquids. The Journal of Chemical Physics. 1995 ;103:4211-4220.
. Time Correlation Function and Path Integral Analysis of Quantum Rate Constants. The Journal of Physical Chemistry. 1989 ;93:7009-7015.
. Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling. Biophys. J. 2013 ;104:404-411.
. A Unified Framework for Quantum Activated Rate Processes. I. General Theory. The Journal of Chemical Physics. 1996 ;105:6856-6870.
. A Unified Framework for Quantum Activated Rate Processes. II. The Nonadiabatic Limit. The Journal of Chemical Physics. 1997 ;106:1769-1779.
. Unusual Hydrophobic Interactions in Acidic Aqueous Solutions. J. Phys. Chem. B. 2009 ;113:7291-7297.
. Water Under the BAR. Biophys. J. 2010 ;99:1783–1790.
. When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol. 2015 .
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