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.
. 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.