Publications
] . Infrared Laser-induced Chaos and Conformational Disorder in a Model Polymer Crystal: Melting vs Ablation. The Journal of Chemical Physics. 1990 ;93:6081-6091.
. 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 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.
. Studies on the Influence of Nonlinearity in Classical Activated Rate Processes. The Journal of Chemical Physics. 1992 ;96:5460-5470.
. A Computer Simulation Study of Free Energy Curves in Heterogeneous Electron Transfer. The Journal of Physical Chemistry. 1993 ;97:7388-7391.
. Manifestations of Spatially Dependent Friction in Classical Activated Rate Processes. The Journal of Chemical Physics. 1993 ;98:4082-4097.
. Nature of Lithium Trapping Sites in the Quantum Solids Para-hydrogen and Ortho-deuterium. The Journal of Chemical Physics. 1993 ;99:9013-9020.
. Path Integral Calculation of Hydrogen Diffusion Rates on Metal Surfaces. The Journal of Chemical Physics. 1993 ;98:7451-7458.
. A Semiclassical Reactive Flux Method for the Calculation of Condensed Phase Activated Rate Constants. Chem. Phys. 1994 ;180:167-180.
. Vibrational Energy Relaxation Dynamics of C–H Stretching Modes on the Hydrogen-terminated H/C(111)1 x 1 Surface. The Journal of Chemical Physics. 1994 ;100:3247-3251.
. 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.
. Vibrational Energy Relaxation Dynamics of Si–H Stretching Modes on Stepped H/Si(111)1x1 Surfaces. Chem. Phys. 1995 ;20:357-368.
. Structure and Dynamics of Hydronium in the Ion Channel Gramicidin A. Biophys J. 1996 ;70:2043-51.
. Classical Molecular Dynamics Simulation of the Photoinduced Electron Transfer Dynamics of Plastocyanin. Biophys J. 1997 ;72:5-17.
. Multistate Empirical Valence Bond Model for Proton Transport in Water. The Journal of Physical Chemistry B. 1998 ;102:5547-5551.
. The Semiclassical Calculation of Nonadiabatic Tunneling Rates. The Journal of Chemical Physics. 1998 ;108:1055-1062.
. The Computer Simulation of Proton Transport in Water. The Journal of Chemical Physics. 1999 ;111:9361-9381.
. Extension of Path Integral Quantum Transition State Theory to the Case of Nonadiabatic Activated Dynamics. The Journal of Chemical Physics. 1999 ;111:2869-2877.
. A Modification of Path Integral Quantum Transition State Theory for Asymmetric and Metastable Potentials. The Journal of Physical Chemistry A. 1999 ;103:9527-9538.
. Molecular Dynamics of Synthetic Leucine-serine Ion Channels in a Phospholipid Membrane. Biophys J. 1999 ;77:2400-10.
. Quantum Properties of the Excess Proton in Liquid Water. Israeli J. Chem. 1999 ;39:483-492.
. 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.
. 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.
. The Isotope Substitution Effect on the Hydrated Proton. Chem. Phys. Lett. 2000 ;329:36-41.
. The Mechanism of Hydrated Proton Transport in Water. Journal of the American Chemical Society. 2000 ;122:12027-12028.
. A Multi-State Empirical Valence Bond Model for Acid-Base Chemistry in Aqueous Solution. Chem. Phys. Lett. 2000 ;258:187.
. The Quantum Vibrational Dynamics of Cl[sup -](H[sub 2]O)[sub n] Clusters. The Journal of Chemical Physics. 2000 ;113:5171-5178.
. Simulating Accidental Fires and Explosions. Computing in Science and Engineering. 2000 ;2:64-76.
. 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. 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. J. Chem. Phys. 2001 ;114:9758-9763.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. J. Chem. Phys. 2001 ;114:9758-9763.
. The Formation and Dynamics of Proton Wires in Channel Environments. Biophys J. 2001 ;80:1691-702.
. Interfacing Continuum and Molecular Dynamics: An Application to Lipid Bilayers. J. Chem. Phys. 2001 ;114:6913-6924.
. Interfacing Molecular Dynamics with Continuum Dynamics in Computer Simulation: Toward an Application to Biological Membranes. IBM J. Res. Dev. 2001 ;45:417-426.
. A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution. J. Phys. Chem. A. 2001 ;105:2814-2823.
. Quantum Mechanical Reaction Rate Constants from Centroid Molecular Dynamics Simulations. J. Chem. Phys. 2001 ;115:9209-9222.
. 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: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics. J. Chem. Phys. 2002 ;117:8694-8704.
. Calculating the Bulk Modulus for a Lipid Bilayer with Nonequilibrium Molecular Dynamics Simulation. Biophys J. 2002 ;82:1226-38.
. Interfacing Molecular Dynamics and Macro-scale Simulations for Lipid Bilayer Vesicles. Biophys J. 2002 ;83:1026-38.
. Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane. Biophys J. 2002 ;82:1460-8.
. Molecular Dynamics Simulation of Proton Transport through the Influenza A Virus M2 Channel. Biophys J. 2002 ;83:1987-96.
. A Second Generation Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems. J. Chem. Phys. 2002 ;117:5839-5849.
. A Second Generation Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems. J. Chem. Phys. 2002 ;117:5839-5849.
. The Vibrational Spectrum of the Hydrated Proton: Comparison of Experiment, Simulation, and Normal Mode Analysis. J. Chem. Phys. 2002 ;116:737-746.
. The Vibrational Spectrum of the Hydrated Proton: Comparison of Experiment, Simulation, and Normal Mode Analysis. J. Chem. Phys. 2002 ;116:737-746.
. 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. IV. Formal Analysis of the Deviations from Born-Oppenheimer Dynamics. Israel. J. Chem. 2003 ;42:191-202.
. Atom-centered Density Matrix Propagation (ADMP): Generalizations using Bohmian Mechanics. J. Phys. Chem. 2003 ;107:7269-7277.
. Massively Parallel Linear-scaling Algorithm in an ab initio Local-orbital Total-energy Method. J. Comp. Phys. 2003 ;188:1-15.
. Massively Parallel Linear-scaling Algorithm in an ab initio Local-orbital Total-energy Method. J. Comp. Phys. 2003 ;188:1-15.
. The Theory of Electron Transfer Reactions: What May Be Missing?. J Am Chem Soc. 2003 ;125:7470-8.
. Hybrid Ab Initio Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach. J. Phys. Chem. B. 2004 ;108:4210 - 4220.
. Kinetic Monte Carlo-Molecular Dynamics Approach To Model Soot Inception. Combust. Sci. and Tech. 2004 ;176:991-1005.
. The Mechanism of Proton Exclusion in Aquaporin Channels. Proteins. 2004 ;55:223-8.
. Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers. Biophys J. 2005 ;89:2385-94.
. Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel. J Phys Chem B. 2006 ;110:15045-8.
. A Multistate Empirical Valence Bond Description of Protonatable Amino Acids. J Phys Chem A. 2006 ;110:631-9.
. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
. Charge Delocalization in Proton Channels, I: the Aquaporin Channels and Proton Blockage. Biophys J. 2007 ;92:46-60.
. Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations. J Phys Chem B. 2007 ;111:4300-14.
. 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.
. Storage of an Excess Proton in the Hydrogen-bonded Network of the D-pathway of Cytochrome c Oxidase: Identification of a Protonated Water Cluster. J Am Chem Soc [Internet]. 2007 ;129:2910-3.
. 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.
. Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations. Biophys. J. 2008 ;95:1866-1876.
. Origins of Enhanced Proton Transport in the Y7F Mutant of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2008 ;130:11399–11408.
. Origins of Enhanced Proton Transport in the Y7F Mutant of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2008 ;130:11399–11408.
. Reconstructing Atomistic Detail from Coarse-grained Models with Resolution Exchange. J. Chem. Phys. 2008 ;129:114103.
. A Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations. J. Chem. Theory. Comp. 2009 ;5:949-961.
. A Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations. J. Chem. Theory. Comp. 2009 ;5:949-961.
. Effect of Active-site Mutations at Asn67 on the Proton Transfer Mechanism of Human Carbonic Anhydrase II. Biochem. 2009 ;48:7996-8005.
. Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2009 ;131:7598-7608.
. New Insights into BAR Domain Induced Membrane Remodeling. Biophys. J. 2009 ;97:1616–1625.
. A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor. Structure. 2009 ;17:1660–1668.
. The Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. J. Am. Chem. Soc. 2010 ;132:16225–16239.
. The Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. J. Am. Chem. Soc. 2010 ;132:16225–16239.
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 Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology. J. Chem. Theor. Comp. 2010 ;6:2566–2580.
. Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2011 ;133:6223–6234.
. Key Inter-molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis. J. Am. Chem. Soc. 2011 ;133:16828-16838.
. Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis. J. Mol. Biol. 2011 ;413:279-291.
. Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies. J. Phys. Chem. B. 2012 ;116:8045-8057.
. Coarse-graining of Multi-Protein Assemblies. Curr. Opin. Struct. Biol. 2012 ;22:144-150.
. Coarse-Graining Provides Insight on the Essential Nature of Heterogeneity in Actin Filaments. Biophys. J. 2012 ;103:1334-1342.
. Comparison Between Actin Filament Models: Coarse-Graining Reveals Essential Differences. Structure. 2012 ;20:641-653.
. Effect of Polymer Morphology on Proton Solvation and Transport in Proton Exchange Membranes. J. Phys. Chem C. 2012 ;116:19104-19116.
. Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90. Biophys. J. 2012 ;103:284-292.
. Nanostructural Organization in Acetonitrile/Ionic Liquid Mixtures: Molecular Dynamics Simulations and Optical Kerr Effect Spectroscopy. ChemPhysChem. 2012 ;13:1687-1700.
. 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.
. Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes. J. Phys. Chem. B. 2012 ;116:8363-8374.
. Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes. J. Phys. Chem. B. 2012 ;116:8363-8374.
. Proton Conduction in Exchange Membranes Across Multiple Length Scales. Acc. Chem. Res. 2012 ;45:2002-2010.
. Proton Transport Pathways in [NiFe]-Hydrogenase. J. Phys. Chem. B. 2012 ;116:2917–2926.
. Coarse-graining Methods for Computational Biology. Annu. Rev. Biophysics. 2013 ;42:73-93.
. Coarse-Graining of Proteins Based on Elastic Network Models. Chem. Phys. 2013 ;422:165-174.
. Diffusion Mechanisms in Smectic Ionic Liquid Crystals: Insights from Coarse-grained MD Simulations. Soft Matter. 2013 ;9:5716-5725.
. A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models. J. Chem. Theor. Comp. 2013 ;9:750-765.
. Ligand-Dependent Activation and Deactivation of a G Protein-Coupled Receptor. J. Am. Chem. Soc. 2013 ;135:8749-8759.
. Linear Aggregation of Proteins on the Membrane as a Prelude to Membrane Remodeling. Proc. Natl. Acad. Sci. 2013 ;110(51).
. Linear Aggregation of Proteins on the Membrane as a Prelude to Membrane Remodeling. Proc. Natl. Acad. Sci. 2013 ;110(51).
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
. Minimizing Memory as an Objective for Coarse-Graining. J. Chem. Phys. 2013 ;138.
. Molecular Mechanism of Membrane Binding of the GRP1 PH Domain. J. Mol. Biol. 2013 ;425(17):3073-3090.
. Molecular Origins of Cofilin-linked Changes in Actin Filament Mechanics. J. Mol. Biol. 2013 ;425(7).
. Protein-Mediated Transformation of Lipid Vesicles into Tubular Networks. Biophys. J. 2013 ;105(3):711-719.
. The Role of Amino Acid Sequence in the Self-Association of Therapeutic Monoclonal Antibodies: Insights from Coarse Grained Modeling. J. Chem. Phys. B. 2013 .
. A Solid-Solid Phase Transition in Carbon Dioxide at High Pressures and Intermediate Temperatures. Nat. Commun. 2013 ;4.
. Theory of Ultra Coarse-Graining. I. General Principles. J. Chem. Theor. Comp. 2013 ;9:2466−2480.
. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J. Chem. Theor. Comp. 2014 ;10(1):451–462.
. Can the Ring Polymer Molecular Dynamics Method be Interpreted as Real Time Quantum Dynamics?. J. Chem. Phys. 2014 ;140:1-11.
. Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems. J. Phys. Chem. C. 2014 ;118:845-853.
. An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane. Angewandte Chemie. 2014 ;53:1953-1958.
. An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane. Angewandte Chemie. 2014 ;53:1953-1958.
. An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane. Angewandte Chemie. 2014 ;53:1953-1958.
. Electron Transfer Activation of a Second Water Channel for Proton Transport in [FeFe]-Hydrogenase. J. Chem. Phys. 2014 ;141(22D527):1-9.
. Insights into the Transport of Aqueous Quaternary Ammonium Cations: A Combined Experimental and Computational Study. J. Phys. Chem. B. 2014 ;118:1363-1372.
. 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.
. Nucleotide Regulation of the Structure and Dynamics of G-actin. Biophys. J. 2014 ;106:1710-1720.
. Persistent Sub-diffusive Proton Transport in Perfluorosulfonic Acid Membranes. J. Phys. Chem. Lett. . 2014 ;(5(17):3037–3042.
. The Proton Transport Mechanism of Perfluorosulfonic Acid Membranes. J. Phys. Chem. C. 2014 ;118(31):17436–17445.
. Solvent-Free Highly Coarse-Grained Models for Charged Lipid Systems. J. Chem. Theor. Comp. . 2014 ;(10):4730-4744.
. The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation. J. Chem. Theory Comp. . 2014 ;10:5265-5275.
. Unraveling the Mystery of ATP Hydrolysis in Actin Filaments. J. Am. Chem. Soc. . 2014 ;136(37):13053–13058.
. 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 .
. Hydrated Excess Protons Can Create Their Own Water Wires. J. Phys. Chem. B. 2015 ;(119).
. Membrane Tension Controls the Assembly of Curvature-Generating Proteins. Nature Communications. 2015 ;6(7219):1-8.
. Mesoscale Study of Proton Transport in Proton Exchange Membranes: Role of Morphology. J. Phys. Chem. C. 2015 ;119:1753-1762.
. A Reductionist Perspective on Quantum Statistical Mechanics: Coarse-Graining of Path Integrals. J. Chem. Phys. 2015 ;143(094104):1-10.
. When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol. 2015 .
. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits. J. Phys. Chem. B. 2016 ;120(20).
. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comp. . 2016 ;12:879-891.
. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J. Phys. Chem. B. 2016 :8389−8404 .
. 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.
. Fascin and α-Actinin-bundled Networks Contain Intrinsic Structural Features That Drive Protein Sorting. Current Biology. 2016 ;26(20):2697–2706.
. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Nat. Acad. Sci. USA. 2016 .
. Multiscale Simulations of Protein Facilitated Membrane Remodeling. J. Struct. Biol. 2016 .
. Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA. 2016 ;(113):7420-7425.
. Multiscale Simulations Reveal the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophys. J. 2016 ;110(6):1334–1345.
. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. J. Am. Chem. Soc. . 2016 .
. Proton Solvation and Transport in Realistic Proton Exchange Membrane Morphologies. J. Phys. Chem. C. 2016 ;120(6):3176–3186.
. Simulation of Proton Transport in Proton Exchange Membranes with Reactive Molecular Dynamics. Fuel Cells. 2016 ;0000:1-9.
. Transition-Tempered Metadynamics is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes. J. Chem. Theory Comp. . 2016 .
. Actin Filament Strain Promotes Severing and Cofilin Dissociation. Biophys J. 2017 ;112.
. Highly Coarse-grained Representations of Transmembrane Proteins. J. Chem. Theory Comput. 2017 ;13.
. Immature HIV-1 Lattice Assembly Dynamics are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane. Proc. Nat. Acad. Sci. USA . 2017 ;114:E10056-E10065 .
. Immature HIV-1 Lattice Assembly Dynamics are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane. Proc. Nat. Acad. Sci. USA . 2017 ;114:E10056-E10065 .
. Lipid Membrane Mediates Long-Range Interactions Between Linear Filaments of Membrane-Curving Proteins. ACS Cen. Sci. 2017 ;3:1246-1253 .
. Lipid Membrane Mediates Long-Range Interactions Between Linear Filaments of Membrane-Curving Proteins. ACS Cen. Sci. 2017 ;3:1246-1253 .
. The Mesoscopic Membrane with Proteins Model (MesM-P). J. Chem. Phys. 2017 ;147.
Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
Proton Movement and Coupling in the POT Family of Peptide Transporters. Proc. Nat. Acad. Sci. USA . 2017 ;114(13182).
Proton Movement and Coupling in the POT Family of Peptide Transporters. Proc. Nat. Acad. Sci. USA . 2017 ;114(13182).
. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics. J. Chem. Theory Comput. 2017 ;13.
. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics. J. Chem. Theory Comput. 2017 ;13.
. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA . 2017 ;114.
. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophys. J. 2018 ;115(18):1589–1602.
. The Lamellipodia is a Myosin Independent Mechanosensor. Proc. Nat. Acad. Sci. USA. 2018 ;115(11):2646–2651.
. Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux. J Am. Chem. Soc. 2018 ;140(48):16535–16543.
. Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants. J. Chem. Phys. 2018 ;149(7):072310.
. Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants. J. Chem. Phys. 2018 ;149(7):072310.
. Multiscale Kinetic Modeling Reveals Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter. J. Am. Chem. Soc. 2018 ;140(5):1793–1804.
. Organizing Membrane-Curving Proteins: The Emerging Dynamical Picture. Curr. Opin. Struct. Biol. 2018 ;51:99–105 .
. Quantum Mechanics/Coarse-Grained Molecular Mechanics (QM/CG-MM). J. Chem. Phys. 2018 ;148(1):014102.
. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys. J. 2019 ;116(6):1000–1010 .
. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J. Am. Chem. Soc. 2019 ;141(34):13421–13433.
. Mechanical and Kinetic Factors Drive Sorting of F-actin Crosslinkers on Bundles. Proc. Natl. Acad. Sci. USA. 2019 ;116(13):16192–16197.
. Multiconfigurational Coarse-Grained Molecular Dynamics. J. Chem. Theory Comput. 2019 ;15(5):3306–3315.
. Multiscale model of integrin adhesion assembly. PLoS Comput. Biol. 2019 ;15(6):e1007077.
. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophys. J. 2019 ;117(3):453–463.
. Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. J. Am. Chem. Soc. 2019 ;141(29):11667–11676.
. Local conformational dynamics regulating transport properties of a Cl–/H+ antiporter. J. Comput. Chem. 2020 ;41(6):513–519 .
. TRIM5α Self-Assembly and Compartmentalization of the HIV-1 Viral Capsid. Nat. Commun. 2020 ;11:1307.
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.
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.
. Integrin-Based Mechanosensing through Conformational Activation. Biophys. J. 2021 ;120(20):4349–4359 .
. 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.
. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296:100337.
. 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.
. Computational Studies of Lipid Droplets. J. Phys. Chem. B. 2022 ;126(11):2145–2154.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
. Coarse-Graining with Equivariant Neural Networks: A Path Towards Accurate and Data-Efficient Structural Models. J. Phys. Chem. 2023 ;127:10564–10572.
. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 2023 ;127:8537–8550.
The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification. Nat. Commun. 2023 ;14:3533.
. Understanding Dynamics in Coarse-Grained Models: I. Universal Excess Entropy Scaling Relationship. J. Chem. Phys. 2023 ;158(3):034103.
. Understanding Dynamics in Coarse-Grained Models: II. Coarse-Grained Diffusion Modeled Using Hard Sphere Theory. J. Chem. Phys. 2023 ;158(3):034104.
. Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles. J. Chem. Theory Comput. 2023 ;19(14):4402–4413.
. The SARS-Cov-2 Nucleoprotein Associates With Anionic Lipid Membranes. J. Bio. Chem. Submitted .
. The SARS-Cov-2 Nucleoprotein Associates With Anionic Lipid Membranes. J. Bio. Chem. Submitted .