Publications
] . Reconstructing Protein Remodeled Membranes in Molecular Detail From Mesoscopic Models. Phys. Chem. Chem. Phys. 2011 :10430–10436.
. Water Under the BAR. Biophys. J. 2010 ;99:1783–1790.
. Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins. Biophys. J. 2008 ;95:4183–4192.
. A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor. Structure. 2009 ;17:1660–1668.
. Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining. J. Chem. Theor. Comp. 2010 ;6:954-965.
. Proton Transfer in the Enzyme Carbonic Anhydrase: An ab Initio Study. Journal of the American Chemical Society. 1998 ;120:4006-4014.
. Fitting coarse-grained distribution functions through an iterative force-matching method. J. Chem. Phys. 2013 ;139:1-10.
. Molecular Dynamics Simulations of Human Carbonic Anhydrase II: Insight into Experimental Results and the Role of Solvation. Proteins. 1998 ;33:119-34.
. The Multiscale Coarse-Graining Method. VII. Free Energy Decomposition of Coarse-Grained Effective Potentials. J. Chem. Phys. 2011 ;134:224107.
. Systematic Coarse-graining of a Multi-component Lipid Bilayer. J. Phys. Chem. B. 2009 ;113:1501-1510.
. 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.
. Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Structural Models. J. Phys. Chem. Submitted .
. A Path Integral Study of Electronic Polarization and Nonlinear Coupling Effects in Condensed Phase Proton Transfer Reactions. The Journal of Chemical Physics. 1994 ;100:3039-3047.
. Calculation of Quantum Activation Free Energies for Proton Transfer Reactions in Polar Solvents. Chem. Phys. Lett. 1992 ;198:311-315.
. 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.
. A Partial Averaging Strategy for Low Temperature Fourier Path Integral Monte Carlo Calculations. The Journal of Chemical Physics. 1992 ;97:4205-4214.
. A Quantum Model for Water: Equilibrium and Dynamical Properties. The Journal of Chemical Physics. 1997 ;106:2400-2410.
. The Quantum Dynamics of an Excess Proton in Water. The Journal of Chemical Physics. 1996 ;104:2056-2069.
. Reconstructing Atomistic Detail from Coarse-grained Models with Resolution Exchange. J. Chem. Phys. 2008 ;129:114103.
. Mesoscale Study of Proton Transport in Proton Exchange Membranes: Role of Morphology. J. Phys. Chem. C. 2015 ;119:1753-1762.
. Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins. J. Phys. Chem. B. 2022 ;126(49):10452–10459.
. Multiscale Coarse-Graining of Monosaccharides. J. Phys. Chem. B. 2007 ;111:11566-11575.
. A Bayesian Statistics Approach to Multiscale Coarse-graining. J. Chem. Phys. 2008 ;129:214114.
. Key Computational Findings Reveal Proton Transfer as Driving the Functional Cycle in the Phosphate Transporter PiPT. Proc. Natl. Acad. Sci. USA. 2021 ;118(25):e2101932118.
. Smart Resolution Replica Exchange: an Efficient Algorithm for Exploring Complex Energy Landscapes. J Chem Phys. 2007 ;126:045106.
. Numerical Approaches for Computing Nonadiabatic Electron Transfer Rate Constants. J. Chem. Phys. 2002 ;116:9174-9187.
. A Centroid Molecular Dynamics Approach for Nonadiabatic Dynamical Processes in Condensed Phases: The Spin-Boson Case. J. Phys. Chem. B. 2002 ;106:8449-8455.
. Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2014 ;111:9396-9401.
. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA . 2017 ;114.
. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J. Chem. Theor. Comp. 2014 ;10(1):451–462.
. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
. Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA. 2016 ;(113):7420-7425.
. Feynman Path Integral Approach for Studying Intramolecular Effects in Proton-transfer Reactions. The Journal of Physical Chemistry. 1991 ;95:10425-10431.
. A Solid-Solid Phase Transition in Carbon Dioxide at High Pressures and Intermediate Temperatures. Nat. Commun. 2013 ;4.
. Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys. J. 2022 ;121(12):2266–2278.
. Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1. J. Mol. Biol. 2011 ;407:607–620.
. What Coordinate Best Describes the Affinity of the Hydrated Excess Proton for the Air-Water Interface?. J. Phys. Chem. B. 2020 ;124(24):5039–5046.
. 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.
. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. J. Phys. Chem. B. 2021 ;125(37):10471–10480 .
. Interactions of Protein Kinase C-α C1A and C1B Domains with Membranes: A Combined Computational and Experimental Study. J. Am. Chem. Soc. 2014 ;136(33):11757–11766.
. Calculation of ESR Linewidths for Hydrogen Atom Impurities in Solid para-Hydrogen. J. Chem. Phys. 1994 ;100:1785-1796.
. Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles. Phys. Chem. Chem. Phys. 2020 ;22(19):10753–10763.
. A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces. Proc. Natl. Acad. Sci. USA. 2021 ;118(49 ):e2113141118.
. A Variational Model for the Thermodynamical and Structural Properties of Impurities in Low Temperature Solids. J. Chem. Phys. 1993 ;98:5734-5746.
. Static and Dynamic Correlations in Water: Classical Ab Initio Molecular Dynamics Run at an Elevated Temperature May Not Capture Well Explicit Nuclear Quantum Effects at Ambient Temperature. J. Chem. Theory Comput. 2022 ;18(4):2124–2131.
. A Path integral Einstein Model for Characterizing the Equilibrium States of Low Temperature Solids. The Journal of Chemical Physics. 1992 ;96:5340-5353.
. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(2):599–604.
. Ligand-Dependent Activation and Deactivation of a G Protein-Coupled Receptor. J. Am. Chem. Soc. 2013 ;135:8749-8759.
. Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale. Biophys. J. 2020 ;119(5):1033–1040.
. Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface. J. Chem. Theory Comput. 2021 ;17(9):5759–5765.
. 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.
. Further Developments in the Local-Orbital Density-Functional-Theory Tight-Binding Method. Phys. Rev. B. 2001 ;64:195103.
. 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.
. A Multi-State Empirical Valence Bond Approach to a Polarizable and Flexible Water Model. J. Phys. Chem. B. 2001 ;105:6628-6637.
. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. J. Am. Chem. Soc. . 2016 .
. The Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. J. Am. Chem. Soc. 2010 ;132:16225–16239.
. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comp. . 2016 ;12:879-891.
. Multiscale Simulations Reveal the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophys. J. 2016 ;110(6):1334–1345.
. Quantum and Classical Energy Transfer Between Ligands of a Heavy Metal Atom. Chem. Phys. Lett. 1986 ;124:93-98.
. Vibrational Energy Redistribution Across a Heavy Atom. Chem. Phys. 1989 ;139:171-184.
. The Multiscale Coarse-Graining Method. VI. Implementation of Three-Body Coarse-Grained Potentials. J. Chem. Phys. 2010 ;132:164107.
. A Bond-order Analysis of the Mechanism for Hydrated Proton Mobility in Liquid Water. J Chem Phys. 2005 ;122:14506.
. A Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations. J. Chem. Theor. Comp. 2013 ;9:4018–4025.
. Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKCα C2 Domain: A Combined Molecular Dynamics and Experimental Study. J. Mol. Biol. 2010 ;402:301–310.
. Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain. J. Mol. Biol. 2012 ;423:800-817.
. Molecular Mechanism of Membrane Binding of the GRP1 PH Domain. J. Mol. Biol. 2013 ;425(17):3073-3090.