Publications
Coarse-Graining of Condensed Phase and Biomolecular Systems. Boca Raton, FL: CRC Press/Taylor and Francis Group; 2009.
. Computer Simulations of Proton Transport Through the M2 Channel of the Influenza A Virus. In: Viral Membrane Proteins: Structure, Function and Drug Design. Viral Membrane Proteins: Structure, Function and Drug Design. New York: Kluwer Academic/Plenum Publishers; 2004.
. Feynman Path Centroid Dynamics. In: Progress in Theoretical Chemistry and Physics. Vol. 5. Progress in Theoretical Chemistry and Physics. Dordrecht: Kluwer; 2000. pp. 47-68.
. A Feynman Path Integral Formulation of Quantum Mechanical Transition State Theory. In: New Trends in Kramers' Reaction Rate Theory. New Trends in Kramers' Reaction Rate Theory. The Netherlands: Kluwer Academic Publishers; 1993.
. 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.
. OKE Spectroscopy and Molecular Dynamics Simulations of Polar and Nonpolar Molecules in Ionic Liquids. In: Ionic Liquids: Science and Applications. ACS Symposium Series 1117th ed. Ionic Liquids: Science and Applications. Washington, DC: American Chemical Society; 2012. pp. 271-287.
. 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.
. Quantum Rate Theory: A Path Integral Centroid Perspective. In: Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. ; 2005.
. Spatial Heterogeneity in Ionic Liquids. In: Ionic Liquids IV. Not Just Solvents Anymore. Ionic Liquids IV. Not Just Solvents Anymore. Washington DC: American Chemical Society; 2007. pp. 272-307.
. Ab Initio Calculations of Reactive Pathways for α-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (α-HMX). The Journal of Physical Chemistry A. 2000 ;104:11384-11389.
. Ab initio Centroid Molecular Dynamics: A Fully Quantum Method for Condensed Phase Dynamics Simulations. Chem. Phys. Lett. 1999 ;300:93-98.
. 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. J. Chem. Phys. 2001 ;114:9758-9763.
. 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: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics. J. Chem. Phys. 2002 ;117:8694-8704.
. Ab initio Molecular Dynamics Simulation of the Ag(111)–Water Interface. J. Chem. Phys. 2001 ;115:7196-7206.
. Ab initio Molecular Dynamics Simulation of the Cu(110)–Water Interface. J. Chem. Phys. 2001 ;114:3248.
. Ab initio Molecular Dynamics Simulation of the H/InP(100)–Water Interface. J. Chem. Phys. 2002 ;117:872-884.
. Ab Initio Molecular-dynamics Simulation of Aqueous Proton Solvation and Transport Revisited. J Chem Phys. 2005 ;123:044505.
. 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.
. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. J. Phys. Chem. B. 2021 ;125(37):10471–10480 .
. 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.
. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
. 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.
. 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.
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.
Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Curr. Opin. Struct. Biol. 2018 ;52:119–126.
. Adversarial-Residual-Coarse-Graining: Applying Machine Learning Theory to Systematic Molecular Coarse-Graining. J. Chem. Phys. 2019 ;151(12):124110.
. Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-grained Analysis. Proc Natl Acad Sci U S A. 2005 ;102:13111-6.
. On the Amphiphilic Behavior of the Hydrated Proton: An Ab Initio Molecular Dynamics Study. Int. J. Mass. Spec. 2005 ;241:197-204.
. Amphiphilic Character of the Hydrated Proton in Methanol−Water Solutions. J Phys Chem B. 2006 ;110:7085-9.
. An Analysis of Hydrated Proton Diffusion in Ab Initio Molecular Dynamics. J. Chem. Phys. 2015 ;142(014104):1-13.
. Analytic Expression for the Transmission Coefficient in Quantum Mechanical Transition State Theory. Chem. Phys. Lett. 1990 ;170:289-296.
. 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.
. Applications Of Higher Order Composite Factorization Schemes In Imaginary Time Path Integral Simulations. J. Chem. Phys. 2001 ;115:7832-7842.
. Approximate Coupled Equations for Multiphoton Processes Induced by One or More Lasers. Chem. Phys. Lett. 1986 ;129:315-320.
. Aqueous Solutions and their Interfaces. J. Phys. Chem. B. 2009 ;113:3997.
. Are Many-body Electronic Polarization Effects Important in Liquid Water?. J Chem Phys. 2007 ;126:124505.
. Atom-centered Density Matrix Propagation (ADMP): Generalizations using Bohmian Mechanics. J. Phys. Chem. 2003 ;107:7269-7277.
. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
. Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6). Sci. Adv. 2020 ;6(36).
. Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility. J Mol Biol. 2007 ;365:523-34.
. Atomistic Modeling of the Electrode-Electrolyte Interface in Li-ion Energy Storage Systems: Electrolyte Structuring. J. Phys. Chem. C. 2013 ;17.
. Autoinhibition of Endophilin in Solution via Inter-domain Interactions. Biophys. J. 2013 ;104:396-403.
. A Bayesian Statistics Approach to Multiscale Coarse-graining. J. Chem. Phys. 2008 ;129:214114.
. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J. Chem. Theor. Comp. 2014 ;10(1):451–462.
. . A Bond-order Analysis of the Mechanism for Hydrated Proton Mobility in Liquid Water. J Chem Phys. 2005 ;122:14506.
. Bottom-up Coarse-Graining: Principles and Perspectives. J. Chem. Theory Comput. 2022 ;18(10):5759–5791.
. Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers. Biophys J. 2002 ;83:3357-70.
. Calculating the Bulk Modulus for a Lipid Bilayer with Nonequilibrium Molecular Dynamics Simulation. Biophys J. 2002 ;82:1226-38.
. Calculation of Equilibrium Averages with Feynman-Hibbs Effective Classical Potentials and Similar Variational Approximations. Phys Rev A. 1991 ;44:5302-5305.
. Calculation of ESR Linewidths for Hydrogen Atom Impurities in Solid para-Hydrogen. J. Chem. Phys. 1994 ;100:1785-1796.
. Calculation of Quantum Activation Free Energies for Proton Transfer Reactions in Polar Solvents. Chem. Phys. Lett. 1992 ;198:311-315.
. 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.
. Can a Coarse-grained Water Model Capture the Key Physical Features of the Hydrophobic Effect?. J. Chem. Phys. 2023 ;159:224105.
. Can Quantum Transition State Theory be Defined as a t = 0+ Limit?. J. Chem. Phys. 2016 ;144(084110):1-12.
. Can the Ring Polymer Molecular Dynamics Method be Interpreted as Real Time Quantum Dynamics?. J. Chem. Phys. 2014 ;140:1-11.
. Car-Parrinello Molecular Dynamics Simulation of Liquid Water: New Results. J. Chem. Phys. 2002 ;116:10372-10376.
. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits. J. Phys. Chem. B. 2016 ;120(20).
. Centroid Molecular Dynamics: A Quantum Dynamics Method Suitable for the Parallel Computer. Parallel Computing. 2000 ;26:1025-1041.
. A Centroid Molecular Dynamics Approach for Nonadiabatic Dynamical Processes in Condensed Phases: The Spin-Boson Case. J. Phys. Chem. B. 2002 ;106:8449-8455.
. 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.
. A Centroid Molecular Dynamics Study of Liquid Para-hydrogen and Ortho-deuterium. J Chem Phys. 2004 ;121:6412-22.
. Characterization of the Solvation and Transport of the Hydrated Proton in the Perfluorosulfonic Acid Membrane Nafion. J Phys Chem B. 2006 ;110:18594-600.
. Charge Delocalization in Proton Channels, I: the Aquaporin Channels and Proton Blockage. Biophys J. 2007 ;92:46-60.
. Charge Delocalization in Proton Channels, II: The Synthetic LS2 Channel and Proton Selectivity. Biophys J. 2007 ;92:61-9.
. Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2011 ;133:6223–6234.
. Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems. J. Phys. Chem. C. 2014 ;118:845-853.
. 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 Simulation of Electron Transfer Through a Polypeptide. The Journal of Physical Chemistry B. 1999 ;103:7367-7382.
. Classical and Quantum Transition State Theory for the Diffusion of Helium in Silica Sodalite. The Journal of Physical Chemistry B. 1997 ;101:491-503.
. Classical Molecular Dynamics Simulation of the Photoinduced Electron Transfer Dynamics of Plastocyanin. Biophys J. 1997 ;72:5-17.
. Coarse-Grained Directed Simulation. J. Chem. Theory Comput. 2017 .
. Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover. J. Chem. Theory Comput. 2021 ;17(2):1170–1180.
. Coarse-Grained Free Energy Functions for Studying Protein Conformational Changes: A Double-Well Network Model. Biophys. J. 2007 ;93:3860-3871.
. A Coarse-grained Model for Double-helix Molecules in Solution: Spontaneous Helix Formation and Equilibrium Properties. J Chem Phys. 2005 ;122:124906.
. 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 Peptide Modeling Using a Systematic Multiscale Approach. Biophys J. 2007 ;92:4289-303.
. Coarse-Grained Representations of Large Biomolecular Complexes from Low Resolution Structural Data. J. Chem. Theor. Comp. 2010 ;6:2990–3002.
. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys. J. 2019 ;116(6):1000–1010 .
. Coarse-grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly. Nat. Comm. 2016 ;7(1156):1-11.
. Coarse-graining Away Electronic Structure: A Rigorous Route to Accurate Condensed Phase Interaction Potentials. Mol. Phys. 2012 ;110:935-944.
. Coarse-graining in Interaction Space: A Systematic Approach for Replacing Long-ranged Electrostatics by Short-ranged Effective Potentials. J. Phys. Chem. B. 2008 ;112:4711-4724.
. Coarse-Graining in Interaction Space: An Analytical Approximation for the Effective Short-Ranged Electrostatics. J. Phys. Chem. B. 2008 ;112:16230–16237.
. Coarse-Graining Involving Virtual Sites: Centers of Symmetry Coarse-Graining. J. Chem. Phys. 2019 ;150(15):154103.
. Coarse-graining Methods for Computational Biology. Annu. Rev. Biophysics. 2013 ;42:73-93.
. Coarse-Graining of Imaginary Time Feynman Path Integrals: Inclusion of Intramolecular Interactions and Bottom-up Force-Matching. J. Phys. Chem. A. 2022 ;126(35):6004–6019.
. Coarse-graining of many-body path integrals: Theory and numerical approximations. J. Chem. Phys. 2019 ;150(24):244103.
. Coarse-graining of Multi-Protein Assemblies. Curr. Opin. Struct. Biol. 2012 ;22:144-150.
. Coarse-Graining of Proteins Based on Elastic Network Models. Chem. Phys. 2013 ;422:165-174.
. Coarse-Graining Provides Insight on the Essential Nature of Heterogeneity in Actin Filaments. Biophys. J. 2012 ;103:1334-1342.
. Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Structural Models. J. Phys. Chem. 2023 ;127:10564–10572.
. A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles. J. Chem. Theor. Comp. 2011 ;7:2277-2283.
. Combining the Semiclassical Initial Value Representation with Centroid Dynamics. J. Phys. Chem. B. 2004 ;108:6883-6892.
. A Comparative Study of Imaginary Time Path Integral Based Methods for Quantum Dynamics. J Chem Phys. 2006 ;124:154103.
. Comparison Between Actin Filament Models: Coarse-Graining Reveals Essential Differences. Structure. 2012 ;20:641-653.
. Compatible Observable Decompositions for Coarse-grained Representations of Real Molecular Systems. J. Chem. Phys. 2019 ;151(13):134115.
. 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.
. Computational Studies of Lipid Droplets. J. Phys. Chem. B. 2022 ;126(11):2145–2154.
. Computational Studies of Proton Transport through the M2 Channel. FEBS Lett. 2003 ;552:23-7.
. A Computational Study of the Closed and Open States of the Influenza A M2 Proton Channel. Biophys J. 2005 ;89:2402-11.
. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics. J. Chem. Theory Comput. 2012 ;8:4863-4875.
. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comp. . 2016 ;12:879-891.
. A Computationally Efficient Treatment of Polarizable Electrochemical Cells Held at a Constant Potential. J. Phys. Chem. C. 2012 ;116:4903-4912.
. A Computer Simulation Method for Studying the Ablation of Polymer Surfaces by Ultraviolet Laser Radiation. Journal of Applied Physics. 1992 ;71:1415-1420.
. 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.
. Computer Simulation of Explicit Proton Translocation in Cytochrome c Oxidase: the D-pathway. Proc Natl Acad Sci U S A. 2005 ;102:6795-800.
. Computer Simulation of Proton Solvation and Transport in Aqueous and Biomolecular Systems. Acc Chem Res. 2006 ;39:143-50.
. The Computer Simulation of Proton Transport in Biomolecular Systems. Front Biosci. 2003 ;8:s1384-79.
. The Computer Simulation of Proton Transport in Water. The Journal of Chemical Physics. 1999 ;111:9361-9381.
. A Computer Simulation Study of Free Energy Curves in Heterogeneous Electron Transfer. The Journal of Physical Chemistry. 1993 ;97:7388-7391.
. A Computer Simulation Study of the Hydrated Proton in a Synthetic Proton Channel. Biophys J. 2003 ;85:864-75.
. Conformational Switching Between Protein Substates Studied with 2D IR Vibrational Echo Spectroscopy and Molecular Dynamics Simulations. J. Phys. Chem. B. 2010 ;114:17187–17193.
. Conformational Transitions of the HIV-1 Gag Polyprotein Upon Multimerization and gRNA Binding. Biophys. J. 2024 ;123:42 - 56.
. Constructing Many-body Mesoscopic Models of Fluids from Bottom-up Coarse-graining. J. Chem. Phys. 2021 ;154(8):084122.
. Cooperative Membrane Binding of HIV-1 Matrix Proteins. J. Phys. Chem. B. Submitted .
. Cooperative Multivalent Receptor Binding Promotes Exposure of the SARS-CoV-2 Fusion Machinery Core. Nat. Commun. 2022 ;13:1002.
. The Coupled Proton Transport in the ClC-ec1 Cl-/H+ Antiporter. Biophys. J. 2011 ;101:L47-L49.
. 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 .
. Cracked Actin Filaments as Mechanosensitive Receptors. Proc. Natl. Acad. Sci. U.S.A. Submitted .
. 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.
. Critical Mechanistic Features of HIV-1 Viral Capsid Assembly. Sci. Adv. 2023 ;9(1):eadd7434.
. The C-terminus of the Multi-Drug Efflux Pump EmrE Prevents Proton Leak by Gating Transport. Proc. Nat. Acad. Sci. USA. Submitted .
. The Curious Case of the Hydrated Proton. Acc. Chem. Res. 2012 ;45:101-109.
. 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.
. Deciphering the Dynamic Codes: Advances in Biomolecular Modeling and Simulation. Curr. Opin. Struct. Biol. 2023 ;81:102642.
. Defining Coarse-grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models. Biophys. J. 2009 ;97:2327-2337.
. 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.
. Delocalization and Stretch-Bend Mixing of the HOH Bend in Liquid Water. J. Chem. Phys. 2017 ;147(084503).
. Density Functional Theory-based Quantum Mechanics/Coarse-grained Molecular Mechanics: Theory and Implementation. J. Chem. Theory Comput. 2020 ;16(10):6329–6342.
. 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.
. A Derivation of Centroid Molecular Dynamics and Other Approximate Time Evolution Methods for Path Integral Centroid Variables. The Journal of Chemical Physics. 1999 ;111:2371-2384.
. Designing Free Energy Surfaces that Match Experimental Data with Metadynamics. J. Chem. Theor. Comp. 2015 ;11.
. Development of Reactive Force Fields Using Ab Initio Molecular Dynamics Simulation Minimally Biased to Experimental Data. J. Chem. Phys. 2017 .
. Diffusion Mechanisms in Smectic Ionic Liquid Crystals: Insights from Coarse-grained MD Simulations. Soft Matter. 2013 ;9:5716-5725.
. A Direct Method for Incorporating Experimental Data into Multiscale Coarse-grained Models. J Chem Theory Comp. 2016 ;12(5):2144-2153.
. Direct Observation of Bin/amphiphysin/Rvs (BAR) Domain-induced Membrane Curvature by Means of Molecular Dynamics Simulations. Proc Natl Acad Sci U S A. 2006 ;103:15068-72.
. Discovering Crystals Using Shape Matching and Machine Learning. Soft Matter. 2013 ;9:8552.
. A Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations. J. Chem. Theory. Comp. 2009 ;5:949-961.
. Divergent spike mutations impact the activation of the fusion core in Delta and Omicron variants of SARS-CoV-2. Sci. Adv. Submitted .
. Dynamic Force Matching: A Method for Constructing Dynamical Coarse-Grained Models with Realistic Time Dependence. J. Chem. Phys. 2015 ;142(154104):1-21.
. Dynamic Force Matching: Construction of Dynamic Coarse-Grained Models with Realistic Short Time Dynamics and Accurate Long Time Dynamics. J Chem Phys. 2016 ;145:224107.
. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J. Am. Chem. Soc. 2019 ;141(34):13421–13433.
. The Dynamic Stress Responses to Area Change in Planar Lipid Bilayer Membranes. Biophys J. 2005 ;88:1104-19.
. Dynamics of Upstream ESCRT Organization at the HIV-1 Budding Site. Biophys. J. 2023 ;122(13):2655–2674.
. Early Stages of the HIV-1 Capsid Protein Lattice Formation. Biophys. J. 2012 ;103:1774-1783.
. Effect of Active-site Mutations at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II. Biochem. 2009 ;48:7996-8005.
. Effect of Membrane Environment on Proton Permeation through Gramicidin A Channels. J. Phys. Chem. B. 2007 ;111:9931-9939.
. Effect of Nonlinear Dissipation on Quantum-activated Rate Processes in Condensed Phases. Phys Rev A. 1992 ;46:2143-2146.
. Effect of Polymer Morphology on Proton Solvation and Transport in Proton Exchange Membranes. J. Phys. Chem C. 2012 ;116:19104-19116.
. Effect of Solvent on Semiconductor Surface Electronic States: A First-principles Study. The Journal of Chemical Physics. 1995 ;103:7569-7575.
. An Effective Barrier Model for Describing Quantum Mechanical Activated Rate Processes in Condensed Phases. The Journal of Chemical Physics. 1991 ;94:7342-7352.
. Effective Force Coarse-Graining. Phys. Chem. Chem. Phys. 2009 ;11:2002-2015.
. Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio Molecular Dynamics Simulation Using the Force-Matching Method. J Phys Chem B. 2005 ;109:6573-86.
. Effective Force Fields for Condensed Phase Systems from ab initio Molecular Dynamics Simulation: a New Method for Force-matching. J Chem Phys. 2004 ;120:10896-913.
. An Effective Golden Rule Decay Rate Expression for Quasidissipative IVR Processes. The Journal of Chemical Physics. 1988 ;88:5547-5552.
. Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain. Biophys. J. 2013 ;105(7):1624-1634.
. An Efficient and Accurate Implementation of Centroid Molecular Dynamics Using a Gaussian Approximation. J Phys Chem A. 2005 ;109:11609-17.
. Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data. J. Chem. Theor. Comp. 2014 ;10(8):3023–3030.
. An Efficient Multi-State Reactive Molecular Dynamics Approach Based on Short-Ranged Effective Potentials. J. Chem. Theor. Comp. 2010 ;6:3039–3047.
. Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining. J. Chem. Theor. Comp. 2010 ;6:954-965.
. Electrochemical Bond-Breaking Reactions: A Comparison of Large Scale Simulation Results with Analytical Theory. The Journal of Physical Chemistry B. 1999 ;103:3442-3448.
. An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane. Angewandte Chemie. 2014 ;53:1953-1958.
. Electron Transfer Across the Electrode/Electrolyte Interface: Influence of Redox Ion Mobility and Counterions. The Journal of Physical Chemistry. 1996 ;100:10746-10753.
. Electron Transfer Activation of a Second Water Channel for Proton Transport in [FeFe]-Hydrogenase. J. Chem. Phys. 2014 ;141(22D527):1-9.
. Electronic Structure Calculation of the Structures and Energies of the Three Pure Polymorphic Forms of Crystalline HMX. The Journal of Physical Chemistry B. 2000 ;104:1009-1013.
. Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure. 2015 ;23.
. Elucidating the Molecular Mechanism of CO2 Capture by Amino Acid Ionic Liquids. J. Am. Chem. Soc. 2023 ;145(29):15663–15667.
. Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2009 ;131:7598-7608.
. Emerging Methods for Multiscale Simulation of Biomolecular Systems. Mol. Phys. 2007 ;105:167-175.
. 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.
. Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1. J. Mol. Biol. 2011 ;407:607–620.
. Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc. Natl. Acad. Sci. USA. 2018 ;115(37):E8595–E8603.
. Evaluation of Nonlinear Quantum Time Correlation Functions within the Centroid Dynamics Formulation. J Phys Chem B. 2006 ;110:18953-7.
. Exact Exchange in ab initio Molecular Dynamics: An Efficient Plane-wave based Algorithm. The Journal of Chemical Physics. 1998 ;108:4697-4700.
. Examining the Influence of Linkers and Tertiary Structure in the Forced Unfolding of Multiple-Repeat Spectrin Molecules. Biophys J. 2006 ;91:3436-45.
. Excess Proton Solvation and Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion. J Phys Chem B. 2005 ;109:3727-30.
. Expanding the View of Proton Pumping in Cytochrome c Oxidase through Computer Simulation. Biochim. et Biophys. Acta-Bioenergetics. 2012 ;1817:518-525.
. An Exploration of Transferability in Multiscale Coarse-grained Peptide Models. J. Phys. Chem. B. 2011 ;115:11911-11926.
. Exploring the Behavior of the Hydrated Excess Proton at Hydrophobic Interfaces. Faraday Discussions. 2013 .
. 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 .
. Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response. Biophys J. 2006 ;90:92-100.
. Extending a Spectrin Repeat Unit. II: Rupture Behavior. Biophys J. 2006 ;90:101-11.
. Extending the Fluctuation Theorem to Describe Reaction Coordinates. J Chem Phys. 2007 ;126:051102.
. Extending the Range and Physical Accuracy of Coarse-grained Models: Order Parameter Dependent Interactions. J. Chem. Phys. 2017 .
. Extension of Path Integral Quantum Transition State Theory to the Case of Nonadiabatic Activated Dynamics. The Journal of Chemical Physics. 1999 ;111:2869-2877.
. 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.
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