Publications
] 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.
. 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.
. Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems. J. Phys. Chem. C. 2014 ;118:845-853.
. Coarse-grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly. Nat. Comm. 2016 ;7(1156):1-11.
. Compatible Observable Decompositions for Coarse-grained Representations of Real Molecular Systems. J. Chem. Phys. 2019 ;151(13):134115.
. 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.
. A Computationally Efficient Treatment of Polarizable Electrochemical Cells Held at a Constant Potential. J. Phys. Chem. C. 2012 ;116:4903-4912.
. A Computer Simulation Study of the Hydrated Proton in a Synthetic Proton Channel. Biophys J. 2003 ;85:864-75.
. 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.
. Designing Free Energy Surfaces that Match Experimental Data with Metadynamics. J. Chem. Theor. Comp. 2015 ;11.
. 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.
. A Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations. J. Chem. Theory. Comp. 2009 ;5:949-961.
. Effective Force Coarse-Graining. Phys. Chem. Chem. Phys. 2009 ;11:2002-2015.
. Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data. J. Chem. Theor. Comp. 2014 ;10(8):3023–3030.
. Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1. J. Mol. Biol. 2011 ;407:607–620.
. Excess Proton Solvation and Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion. J Phys Chem B. 2005 ;109:3727-30.
. Fascin and α-Actinin-bundled Networks Contain Intrinsic Structural Features That Drive Protein Sorting. Current Biology. 2016 ;26(20):2697–2706.
. Flexible Simple Point-charge Water Model with Improved Liquid-State Properties. J Chem Phys. 2006 ;124:024503.
A Helical Assembly of Human ESCRT-I Scaffolds Reverse-Topology Membrane Scission. Nat. Struct. Mol. Biol. 2020 ;27(6):570–580.
. Improved Ab Initio Molecular Dynamics by Minimally Biasing with Experimental Data. J. Chem. Phys. 2017 ;146.
. An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport. J. Phys. Chem. B. 2008 ;112:467-482.
. An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport. J. Phys. Chem. B. 2008 ;112:467-482.
. Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics. J. Am. Chem. Soc. 2020 ;142(41):17425–17433.
. Infrared Laser-induced Chaos and Conformational Disorder in a Model Polymer Crystal: Melting vs Ablation. The Journal of Chemical Physics. 1990 ;93:6081-6091.
. Ion Mixing, Hydration, and Transport in Aqueous Ionic Systems. J. Chem. Phys. 2015 ;142(184905):1-7.
. Ion Permeation, Selectivity, and Electronic Polarization in Fluoride Channels. Biophys. J. 2022 ;121(7):1336–1347.
. Key Factors Governing Initial Stages of Lipid Droplet Formation. J. Phys. Chem. B. 2022 ;126(2):453–462.
. K-Means Clustering Coarse-graining (KMC-CG): A Next Generation Methodology for Determining Optimal Coarse-grained Mappings of Large Biomolecules. J. Chem. Theory Comp. 2023 ;19:8987–8997.
. The Lamellipodia is a Myosin Independent Mechanosensor. Proc. Nat. Acad. Sci. USA. 2018 ;115(11):2646–2651.
. A Linear-scaling Self-consistent Generalization of the Multistate Empirical Valence Bond Method for Multiple Excess Protons in Aqueous Systems. J Chem Phys. 2005 ;122:144105.
. Local conformational dynamics regulating transport properties of a Cl–/H+ antiporter. J. Comput. Chem. 2020 ;41(6):513–519 .
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
. Mechanical and Kinetic Factors Drive Sorting of F-actin Crosslinkers on Bundles. Proc. Natl. Acad. Sci. USA. 2019 ;116(13):16192–16197.
. Mechanism of Phosphate Release from Actin Filaments. Proc. Natl. Acad. Sci. U.S.A. Submitted .
. Mechanism of Targeting of Amphipathic Helix-Containing Proteins to Lipid Droplets. Dev. Cell. 2018 ;44(1):73–86.
. Minimizing Memory as an Objective for Coarse-Graining. J. Chem. Phys. 2013 ;138.
. Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux. J Am. Chem. Soc. 2018 ;140(48):16535–16543.
. Molecular Dynamics Simulation of Nanostructural Organization in Ionic Liquid/Water Mixtures. J Phys Chem B. 2007 ;111:4812-8.
. Molecular Dynamics Simulation of the Energetic Room Temperature Ionic Liquid 1-Hydroxyethyl-4Amino-1, 2, 4-Triazolium Nitrate (HEATN). J. Phys. Chem. B. 2008 ;112:3121-3131.
. Molecular Dynamics Simulations of Polyglutamine Aggregation using Solvent-Free Multiscale Coarse-Grained Models. J. Phys. Chem. B. 2010 ;114:8735–8743.
. Multiconfigurational Coarse-Grained Molecular Dynamics. J. Chem. Theory Comput. 2019 ;15(5):3306–3315.
. The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models. J. Chem. Phys. 2008 ;128:244115.
. Multiscale Coarse-Graining of Ionic Liquids. J Phys Chem B. 2006 ;110:3564-75.
. A Multiscale Coarse-Graining Study of Liquid/Vacuum Interface of Room-Temperature Ionic Liquids with Alkyl Substituents of Different Lengths. J. Phys. Chem. C. 2008 ;112:1132-1139.
. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior. J. Am. Chem. Soc. 2022 ;144(2):769–776.
. Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA. 2016 ;(113):7420-7425.
. A Multistate Empirical Valence Bond Description of Protonatable Amino Acids. J Phys Chem A. 2006 ;110:631-9.
. Nonlinear Vibrational Dynamics of a Neon Atom in Fullerene (C60). The Journal of Physical Chemistry. 1992 ;96:7864-7869.
. Nucleotide Regulation of the Structure and Dynamics of G-actin. Biophys. J. 2014 ;106:1710-1720.
. Origins of Proton Transport Behavior from Selectivity Domain Mutations of the Aquaporin-1 Channel. Biophys J. 2006 ;90:L73-5.
. Predicting the Sensitivity of Multiscale Coarse-grained Models to their Underlying Fine-grained Model Parameters. J. Chem. Theory Comp. . 2015 ;11:3547-3560.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
. Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. J. Am. Chem. Soc. 2019 ;141(29):11667–11676.
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 Pathway in the ClC Cl–/H+ Antiporter. Biophys. J. 2009 ;97:121-131.
. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148(10):102335.
. On the Representability Problem and the Physical Meaning of Coarse-Grained Models. J. Chem. Phys. 2016 ;145(044108):1-12.
. Seipin Transmembrane Segments Critically Function in Triglyceride Nucleation and Droplet Budding from the Membrane. eLife. 2022 ;11:e75808.
. Simulating Accidental Fires and Explosions. Computing in Science and Engineering. 2000 ;2:64-76.
. 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.
. Structure and Function of Lipid Droplet Assembly Complexes. Curr. Opin. Struct. Biol. 2023 ;80:102606.
The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification. Nat. Commun. 2023 ;14:3533.
. Tail Aggregation and Domain Diffusion in Ionic Liquids. J Phys Chem B. 2006 ;110:18601-8.
. Theory of Ultra Coarse-Graining. I. General Principles. J. Chem. Theor. Comp. 2013 ;9:2466−2480.
. Transferable Coarse-Grained Models for Ionic Liquids. J. Chem. Theor. Comp. 2009 ;5:1091-1098.
. Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins. Nat. Chem. 2023 ;15(7):1012–1021.
. Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations. Acc Chem Res. 2007 ;40:1193-9.
. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA . 2017 ;114.
. Unique Spatial Heterogeneity in Ionic Liquids. J Am Chem Soc. 2005 ;127:12192-3.
. Unusual ‘Amphiphilic’ Association of Hydrated Protons in Strong Acid Solution. J. Am. Chem. Soc. 2008 ;130:3120-3126.
. 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.