Publications
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.
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