Publications
When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol. 2015 .
. 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.
. Well-tempered Metadynamics Converges Asymptotically. Phys. Rev. Lett. 2014 ;112:1-6.
. Water Under the BAR. Biophys. J. 2010 ;99:1783–1790.
. 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.
. Water Assisted Proton Transport in Confined Nanochannels. J. Phys. Chem. C. 2020 ;124(29):16186−16201.
. The Vibrational Spectrum of the Hydrated Proton: Comparison of Experiment, Simulation, and Normal Mode Analysis. J. Chem. Phys. 2002 ;116:737-746.
. Vibrational Energy Relaxation Dynamics of Si–H Stretching Modes on Stepped H/Si(111)1x1 Surfaces. Chem. Phys. 1995 ;20:357-368.
. Vibrational Energy Relaxation Dynamics of Si–H Stretching Modes on the H/Si(111)11 Surface. J. Chem. Phys. 1993 ;99:740-743.
. 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.
. Vibrational Energy Redistribution Across a Heavy Atom. Chem. Phys. 1989 ;139:171-184.
. A Variational Model for the Thermodynamical and Structural Properties of Impurities in Low Temperature Solids. J. Chem. Phys. 1993 ;98:5734-5746.
. 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.
. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(2):599–604.
. 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.
. Using classifiers to understand coarse-grained models and their fidelity with the underlying all-atom systems. J. Chem. Phys. 2023 ;158(23):234101.
. On the Use of Feynman–Hibbs Effective Potentials to Calculate Quantum Mechanical Free Energies of Activation. The Journal of Chemical Physics. 1991 ;94:4095-4096.
. Unveiling the catalytic mechanism of GTP hydrolysis in microtubules. Proc. Natl. Acad. Sci. U.S.A. 2023 ;120(27):e2305899120.
. Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys. J. 2019 ;117(3):553–562.
. Unusual Hydrophobic Interactions in Acidic Aqueous Solutions. J. Phys. Chem. B. 2009 ;113:7291-7297.
. Unusual ‘Amphiphilic’ Association of Hydrated Protons in Strong Acid Solution. J. Am. Chem. Soc. 2008 ;130:3120-3126.
. Unraveling the Role of the Protein Environment for [FeFe]-Hydrogenase Charge Transfer: A New Application of Coarse-Graining. J. Phys. Chem. B. 2013 ;17:4062−4071.
. Unraveling the Mystery of ATP Hydrolysis in Actin Filaments. J. Am. Chem. Soc. . 2014 ;136(37):13053–13058.
. Unique Spatial Heterogeneity in Ionic Liquids. J Am Chem Soc. 2005 ;127:12192-3.
. Unique Elastic Properties of the Spectrin Tetramer as Revealed by Multiscale Coarse-Grained Modeling. Proc. Natl. Acad. Sci. USA. 2008 ;105:1204-1208.
. A Unified Framework for Quantum Activated Rate Processes. II. The Nonadiabatic Limit. The Journal of Chemical Physics. 1997 ;106:1769-1779.
. A Unified Framework for Quantum Activated Rate Processes. I. General Theory. The Journal of Chemical Physics. 1996 ;105:6856-6870.
. Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling. Biophys. J. 2013 ;104:404-411.
. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA . 2017 ;114.
. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J. Phys. Chem. Lett. 2019 ;10(16):4549–4557.
. Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations. Acc Chem Res. 2007 ;40:1193-9.
. Understanding Dynamics in Coarse-Grained Models: III. Roles of Rotational Motion and Translation-Rotation Coupling in Coarse-Grained Dynamics. J. Chem. Phys. 2023 ;159:164102.
. Understanding Dynamics in Coarse-Grained Models: II. Coarse-Grained Diffusion Modeled Using Hard Sphere Theory. J. Chem. Phys. 2023 ;158(3):034104.
. Understanding Dynamics in Coarse-Grained Models: I. Universal Excess Entropy Scaling Relationship. J. Chem. Phys. 2023 ;158(3):034103.
. Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. J. Chem. Theory Comput. 2018 ;14(4):2180–2197.
. Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding. J. Chem. Theory Comput. 2018 ;14(12):6159–6174.
. TRIM5α Self-Assembly and Compartmentalization of the HIV-1 Viral Capsid. Nat. Commun. 2020 ;11:1307.
. Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-The-Fly Transition Barrier Estimation. J. Chem. Theor. Comp. 2014 .
. Transition-Tempered Metadynamics is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes. J. Chem. Theory Comp. . 2016 .
. Transition State Dynamics and Relaxation Processes in Solutions: A Frontier of Physical Chemistry. The Journal of Physical Chemistry. 1996 ;100:13034-13049.
. Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins. Nat. Chem. 2023 ;15(7):1012–1021.
. Transient Violations of the Second Law of Thermodynamics in Protein Unfolding Examined using Synthetic Atomic Force Microscopy and the Fluctuation Theorem. J. Chem. Phys. 2007 ;127:105105.
. Transferable Coarse-Grained Models for Ionic Liquids. J. Chem. Theor. Comp. 2009 ;5:1091-1098.
. Time Correlation Function and Path Integral Analysis of Quantum Rate Constants. The Journal of Physical Chemistry. 1989 ;93:7009-7015.
. A Three-dimensional Potential Energy Surface for Dissociative Adsorption and Associative Desorption at Metal Electrodes. The Journal of Chemical Physics. 1998 ;109:1991-2001.
. The Theory of Ultra-Coarse-Graining. 3. Coarse-grained Sites with Rapid Local Equilibrium of Internal States. J. Chem. Theory Comput. 2017 ;13.
. The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation. J. Chem. Theory Comp. . 2014 ;10:5265-5275.
. Theory of Ultra Coarse-Graining. I. General Principles. J. Chem. Theor. Comp. 2013 ;9:2466−2480.
. The Theory of Electron Transfer Reactions: What May Be Missing?. J Am Chem Soc. 2003 ;125:7470-8.
. A Theory of Electron Transfer and Steady-State Optical Spectra of Chromophores with Varying Electronic Polarizability. The Journal of Physical Chemistry A. 1999 ;103:10981-10992.
. A Theory for Treating Spatially-dependent Friction in Classical Activated Rate Processes. The Journal of Chemical Physics. 1992 ;97:5908-5910.
. A Theory for Time Correlation Functions in Liquids. The Journal of Chemical Physics. 1995 ;103:4211-4220.
. A Theory for the Thermally Activated Rate Constant in Systems with Spatially Dependent Friction. Chem. Phys. Lett. 1993 ;207:309-316.
. A Theory for the Quantum Activated Rate Constant in Dissipative Systems. Chem. Phys. Lett. 1996 ;261:111-116.
. A Theory for Electron Transfer between an Electrode and a Multilevel Acceptor/Donor Species in an Electrolyte Solution. J. Electroanal. Chem. 1998 ;450:95-107.
. A Theory for Electron Transfer across the Electrode/Electrolyte Interface Involving more than One Redox Ion. The Journal of Chemical Physics. 1997 ;107:8940-8954.
. A Theory for Adiabatic Electron Transfer Processes across the Semiconductor/Electrolyte Interface. The Journal of Chemical Physics. 1996 ;104:6168-6183.
. A Theory for Adiabatic Bond Breaking Electron Transfer Reactions at Metal Electrodes. Chem. Phys. Lett. 1998 ;282:100-106.
. Temperature Dependence of the Solvent Reorganization Energy of Electron Transfer in Highly Polar Solvents. J. Phys. Chem. B. 1999 ;103:9130-9140.
. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J. Chem. Theory Comput. 2020 ;16(11):6823–6842.
. Tail Aggregation and Domain Diffusion in Ionic Liquids. J Phys Chem B. 2006 ;110:18601-8.
. Systematic Multiscale Simulation of Membrane Protein Systems. Curr. Opin. Struct. Biol. 2009 ;19:138-144.
. Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins. Biophys. J. 2008 ;95:4183–4192.
. A Systematic Methodology for Defining Coarse-grained Sites in Large Biomolecules. Biophys. J. 2008 ;95:5073-5083.
. Systematic Coarse-Graining of Nanoparticle Interactions in Molecular Dynamics Simulation. J Phys Chem B. 2005 ;109:17019-24.
. Systematic Coarse-graining of Biomolecular and Soft Matter Systems. MRS Bulletin. 2007 ;32:929-934.
. Systematic Coarse-graining of a Multi-component Lipid Bilayer. J. Phys. Chem. B. 2009 ;113:1501-1510.
. Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites. J. Chem. Theory Comput. 2019 ;15(3):2087–2100.
. Synthesis, Characterization and Simulation of Four-Armed Megamolecules. Biomacromolecules. 2021 ;22(6):2363–2372.
Superposition State Molecular Dynamics. J. Chem. Theory Comp. 2005 ;1:36-40.
. Studies on the Influence of Nonlinearity in Classical Activated Rate Processes. The Journal of Chemical Physics. 1992 ;96:5460-5470.
. Structure of the Liquid−Vacuum Interface of Room-Temperature Ionic Liquids: A Molecular Dynamics Study. J Phys Chem B. 2006 ;110:1800-6.
. Structure of SARS-CoV-2 M protein in lipid nanodiscs. eLife. 2022 ;11:e81702.
. The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification. Nat. Commun. 2023 ;14:3533.
Structure of Hydrated Na−Nafion Polymer Membranes. J Phys Chem B. 2005 ;109:24244-53.
. Structure and Function of Lipid Droplet Assembly Complexes. Curr. Opin. Struct. Biol. 2023 ;80:102606.
. Structure and Dynamics of the Actin Filament. J. Mol. Biol. 2010 ;396:252–263.
. On the Structure and Dynamics of Ionic Liquids. J. Phys. Chem. B. 2004 ;108:1744-1752.
. Structure and Dynamics of Hydronium in the Ion Channel Gramicidin A. Biophys J. 1996 ;70:2043-51.
. Structure and Dynamics of Concentrated Hydrochloric Acid Solutions. J. Phys. Chem. B. 2010 ;114:9555–9562.
. Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites. J. Am. Chem. Soc. 2021 ;143(27):10203–10213.
. Structural Basis of Membrane Bending by the N-BAR Protein Endophilin. Cell. 2012 ;149.
. Structural Basis for Polarized Elongation of Actin Filaments. Proc. Natl. Acad. Sci. USA. 2020 ;117(48):30458–30464.
. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296:100337.
. Strain and Rapture of HIV-1 Capsids During Uncoating. Proc. Nat. Acad. Sci. USA. 2022 ;119(10):e2117781119.
. 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.
. Statistical Mechanical Design Principles for Coarse-grained Interactions Across Different Conformational Free Energy Surfaces. J. Phys. Chem. Lett. 2023 ;14(6):1354–1362.
. 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.
. Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water. J. Phys. Chem. B. 2008 ;112:9456-9466.
. Solvent-Free Highly Coarse-Grained Models for Charged Lipid Systems. J. Chem. Theor. Comp. . 2014 ;(10):4730-4744.
. A Solvent Free Lipid Bilayer Model Using Multiscale Coarse-graining. J. Phys. Chem. B. 2009 ;113:4443-4455.
. Solvent Free Ionic Solution Models from Multiscale Coarse-Graining. J Chem Theory Comput. 2013 ;9:172-178.
. Solvated Excess Proton as the Active Site in Methanol Dehydration: Beyond the Hydrated Hydronium Ion. Submitted .
. A Solid-Solid Phase Transition in Carbon Dioxide at High Pressures and Intermediate Temperatures. Nat. Commun. 2013 ;4.
. Smart Resolution Replica Exchange: an Efficient Algorithm for Exploring Complex Energy Landscapes. J Chem Phys. 2007 ;126:045106.
. Single Molecule Studies Reveal A Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C alpha. Biochemistry. 2014 ;53:1697-1713.
. Simulation of Proton Transport in Proton Exchange Membranes with Reactive Molecular Dynamics. Fuel Cells. 2016 ;0000:1-9.
. The Simulation of Biomolecular Systems at Multiple Length and Time Scales. Int. J. for Multiscale Comp. Eng. 2004 ;2:291-311.
. 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 Accidental Fires and Explosions. Computing in Science and Engineering. 2000 ;2:64-76.
. Simple Reversible Molecular Dynamics Algorithms for Nos[e-acute]–Hoover Chain Dynamics. The Journal of Chemical Physics. 1997 ;107:9514-9526.
. Semiclassical Theory of Fermi Resonance between Stretching and Bending Modes in Polyatomic Molecules. The Journal of Chemical Physics. 1985 ;82:4064-4072.
. A Semiclassical Reactive Flux Method for the Calculation of Condensed Phase Activated Rate Constants. Chem. Phys. 1994 ;180:167-180.
. Semiclassical Molecular Dynamics Computation of Spontaneous Light Emission in the Condensed Phase: Resonance Raman Spectra. J. Chem. Phys. 2001 ;114:7130-7143.
. Semiclassical Dressed State Theory for the Vibrational Excitation of a Morse Oscillator by Radiation. The Journal of Physical Chemistry. 1985 ;89:2208-2213.
. The Semiclassical Calculation of Nonadiabatic Tunneling Rates. The Journal of Chemical Physics. 1998 ;108:1055-1062.
. Semiclassical Approximations to Quantum Dynamical Time Correlation Functions. The Journal of Chemical Physics. 1996 ;104:273-285.
. Self-consistent Harmonic Theory of Solvation in Glassy Systems: Quantum Solvation. The Journal of Chemical Physics. 2000 ;112:3280-3284.
. Self-consistent Harmonic Theory of Solvation in Glassy Systems: Classical Solvation. The Journal of Chemical Physics. 2000 ;112:3267-3279.
. The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations. J. Phys. Chem. B. 2010 ;114:6922-6931.
. Seipin Transmembrane Segments Critically Function in Triglyceride Nucleation and Droplet Budding from the Membrane. eLife. 2022 ;11:e75808.
. 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 Mesoscopic Lipid Bilayer Model: Connections to Field-Theory Descriptions of Membranes and Nonlocal Hydrodynamics. J Chem Phys. 2006 ;124:64906.
. The SARS-Cov-2 Nucleoprotein Associates With Anionic Lipid Membranes. J. Bio. Chem. Submitted .
. Role of Solvation Structure in the Shuttling of the Hydrated Excess Proton. J. Chem. Sci. 2017 ;129.
. Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-grained Analysis. Biophys. J. 2010 ;98:18-26.
. Role of Pre-Solvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport. J. Phys. Chem. B . 2016 ;120(8):1793–1804.
. The Role of Conformational Change and Key Glutamic Acid Residues in the ClC-ec1 Antiporter. Biophys. J. 2023 ;122(6):1068–1085.
. 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 Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor. Structure. 2009 ;17:1660–1668.
. Rigorous Formulation of Quantum Transition State Theory and its Dynamical Corrections. The Journal of Chemical Physics. 1989 ;91:7749-7760.
. Resolving the Structural Debate for the Hydrated Excess Proton in Water. J. Am. Chem. Soc. 2021 ;143(44):18672−18683.
. On the Representability Problem and the Physical Meaning of Coarse-Grained Models. J. Chem. Phys. 2016 ;145(044108):1-12.
. Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 2. Optical Spectra. The Journal of Physical Chemistry A. 2000 ;104:6485-6494.
. Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 1. Charge Transfer Reactions. The Journal of Physical Chemistry A. 2000 ;104:6470-6484.
. A Relationship between Centroid Dynamics and Path Integral Quantum Transition State Theory. The Journal of Chemical Physics. 2000 ;112:8747-8757.
. A Reductionist Perspective on Quantum Statistical Mechanics: Coarse-Graining of Path Integrals. J. Chem. Phys. 2015 ;143(094104):1-10.
. Redox-Coupled Proton Pumping in Cytochrome c Oxidase: Further Insights from Computer Simulation. Biochim. et Biophys. Acta-Bioenergetics. 2008 ;1777:196-201.
. Reconstructing Protein Remodeled Membranes in Molecular Detail From Mesoscopic Models. Phys. Chem. Chem. Phys. 2011 :10430–10436.
. Reconstructing Atomistic Detail from Coarse-grained Models with Resolution Exchange. J. Chem. Phys. 2008 ;129:114103.
. Reactive Molecular Dynamics Models from Ab Initio Molecular Dynamics Data Using Relative Entropy Minimization. Chem. Phys. Lett. 2017 ;683.
. Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water. J. Phys. Chem. 1999 ;103:925-931.
. Reactive Coarse-grained Molecular Dynamics. J. Chem. Theory. Comput. 2020 ;16(4):2541−2549.
. Reaction-Coordinate-Dependent Friction in Classical Activated Barrier Crossing Dynamics: When it Matters and When it Doesn't. The Journal of Chemical Physics. 1995 ;103:10176-10182.
. Quasidissipative Intramolecular Dynamics: An Adiabatically Reduced Coupled Equations Approach. The Journal of Chemical Physics. 1987 ;87:5272-5279.
. The Quantum Vibrational Dynamics of Cl[sup -](H[sub 2]O)[sub n] Clusters. The Journal of Chemical Physics. 2000 ;113:5171-5178.
. Quantum Time Correlation Functions and Classical Coherence. Chem. Phys. 1998 ;233:243-255.
. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148(10):102335.
. Quantum Properties of the Excess Proton in Liquid Water. Israeli J. Chem. 1999 ;39:483-492.
. Quantum Molecular Dynamics Simulations of Low-Temperature High Energy Density Matter: Solid p-H2/Li and p-H2/B. The Journal of Physical Chemistry A. 1999 ;103:9512-9520.
. Quantum Molecular Dynamics and Spectral Simulation of a Boron Impurity in Solid Para-hydrogen. The Journal of Chemical Physics. 2000 ;113:9079-9089.
. A Quantum Model for Water: Equilibrium and Dynamical Properties. The Journal of Chemical Physics. 1997 ;106:2400-2410.
. Quantum Mechanics/Coarse-Grained Molecular Mechanics (QM/CG-MM). J. Chem. Phys. 2018 ;148(1):014102.
. Quantum Mechanical Reaction Rate Constants from Centroid Molecular Dynamics Simulations. J. Chem. Phys. 2001 ;115:9209-9222.
. Quantum Effects Strongly Influence the Surface Premelting of Ice. J. Phys. Chem. C. 2008 ;112:324-327.
. Quantum Effects in Liquid Water from an Ab Initio-Based Polarizable Force Field. J. Chem. Phys. 2007 ;127:074506.
. Quantum Effects and the Excess Proton in Water. The Journal of Chemical Physics. 1997 ;107:7428-7432.
. The Quantum Dynamics of an Excess Proton in Water. The Journal of Chemical Physics. 1996 ;104:2056-2069.
. Quantum Dynamical Simulation of the Energy Relaxation Rate of the CN- Ion in Water. The Journal of Physical Chemistry A. 1999 ;103:10289-10293.
. Quantum and Classical Simulations of an Excess Proton in Water. Ber. Bunsenges. Phys. Chem. 1998 ;102:527-532.
. Quantum and Classical Energy Transfer Between Ligands of a Heavy Metal Atom. Chem. Phys. Lett. 1986 ;124:93-98.
. A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces. Proc. Natl. Acad. Sci. USA. 2021 ;118(49 ):e2113141118.
. A Quantitative Assessment of the Accuracy of Centroid Molecular Dynamics for the Calculation of the Infrared Spectrum of Liquid Water. J. Chem. Phys. 2010 ;132:014105.
. Pseudopotentials for Centroid Molecular Dynamics: Application to Self-Diffusion in Liquid para-Hydrogen. Chem. Phys. Lett. 1996 ;249:231-236.
. Protons May Leak through Pure Lipid Bilayers via a Concerted Mechanism. Biophys J. 2005 ;88:3095-108.
. Proton Transport Under External Applied Voltage. J. Phys. Chem. B. 2014 .
. Proton Transport Pathways in [NiFe]-Hydrogenase. J. Phys. Chem. B. 2012 ;116:2917–2926.
. Proton Transport Pathway in the ClC Cl–/H+ Antiporter. Biophys. J. 2009 ;97:121-131.
. The Proton Transport Mechanism of Perfluorosulfonic Acid Membranes. J. Phys. Chem. C. 2014 ;118(31):17436–17445.
. Proton Transport in Carbonic Anhydrase: Insights from Molecular Simulation. Biochim. et Biophys. Acta - Proteins and Proteomics. 2010 ;1804:332-341.
. Proton Transport Behavior Through the Influenza A M2 Channel: Insights from Molecular Simulation. Biophys. J. 2007 ;93:3470-3479.
. 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 in the Enzyme Carbonic Anhydrase: An ab Initio Study. Journal of the American Chemical Society. 1998 ;120:4006-4014.
. Proton Solvation and Transport in Realistic Proton Exchange Membrane Morphologies. J. Phys. Chem. C. 2016 ;120(6):3176–3186.
. Proton Solvation and Transport in Hydrated Nafion. J. Phys. Chem. B. 2011 ;115:5903-5912.
. Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations. J Phys Chem B. 2007 ;111:4300-14.
. Proton Movement and Coupling in the POT Family of Peptide Transporters. Proc. Nat. Acad. Sci. USA . 2017 ;114(13182).
Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. J. Am. Chem. Soc. 2019 ;141(29):11667–11676.
. Proton Dissociation and Delocalization Under Stepwise Hydration of Zeolite HZSM-5. J. Phys. Chem. C. 2023 ;127:16175-16186.
. Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys. J. 2022 ;121(12):2266–2278.
. Proton Conduction in Exchange Membranes Across Multiple Length Scales. Acc. Chem. Res. 2012 ;45:2002-2010.
. Protein-Mediated Transformation of Lipid Vesicles into Tubular Networks. Biophys. J. 2013 ;105(3):711-719.
. The Properties of Water: Insights from Quantum Simulations. J. Phys. Chem. B. 2009 ;113:5702–5719.
. The Properties of Ion-water Clusters. II. Solvation Structures of Na+, Cl-, and H+ Clusters as a Function of Temperature. J Chem Phys. 2006 ;124:024327.
. The Properties of Ion-water Clusters. I. The Protonated 21-water Cluster. J Chem Phys. 2005 ;123:084309.
. Properties of Hydrated Excess Protons Near Phospholipid Bilayers. J. Phys. Chem. B. 2010 ;114:592–603.
. Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface. J. Am. Chem. Soc. 2015 ;137(39):12610-12616.
. Probing the Molecular-Scale Lipid Bilayer Response to Shear Flow Using Nonequilibrium Molecular Dynamics. J Phys Chem B. 2005 ;109:18673-9.
. Probing Selected Morphological Models of Hydrated Nafion Using Large Scale Molecular Dynamics Simulations. J. Phys. Chem. B. 2010 ;114:3205–3218.
. Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
Preservation of HIV-1 Gag Helical Bundle Symmetry by Bevirimat is Central to Maturation Inhibition. J. Am. Chem. Soc. 2021 ;143(45):19137−19148 .
. Preferred Orientations of His-64 in Human Carbonic Anhydrase II. Biochemistry. 2007 ;46:2938-47.
. Prediction of the essential intermolecular contacts for side-binding of VASP on F-Actin. Cytoskeleton. Submitted .
. Predicting the Sensitivity of Multiscale Coarse-grained Models to their Underlying Fine-grained Model Parameters. J. Chem. Theory Comp. . 2015 ;11:3547-3560.
. Potential Energy Surfaces for Chemical Reactions: An Analytical Representation from Coarse Grained Data with an Application to Proton Transfer in Water. The Journal of Physical Chemistry B. 1997 ;101:4544-4552.
. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophys. J. 2019 ;117(3):453–463.
. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis. J. Phys. Chem. B. 2021 ;125(25):6872–6888.
. Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
A Perturbation Theory for Solvation Thermodynamics: Dipolar–quadrupolar Liquids. The Journal of Chemical Physics. 1999 ;111:3630-3638.
. Persistent Sub-diffusive Proton Transport in Perfluorosulfonic Acid Membranes. J. Phys. Chem. Lett. . 2014 ;(5(17):3037–3042.
. Peptide Folding Using Multiscale Coarse-grained Models. J. Phys. Chem. B. 2008 ;112:13079–13090.
. 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.
. Path Integral Molecular Dynamics Simulation of Solid Para-Hydrogen with an Aluminum Impurity. Chem. Phys. Lett. 2002 ;365:487-493.
. Path Integral Formulation of Centroid Dynamics for Systems Obeying Bose-Einstein Statistics. J. Chem. Phys. 2001 ;115:4484.
. A Path integral Einstein Model for Characterizing the Equilibrium States of Low Temperature Solids. The Journal of Chemical Physics. 1992 ;96:5340-5353.
. Path Integral Coarse-graining Replica Exchange Method for Enhanced Sampling. J. Chem. Theor. Comp. 2014 ;10 (9 ):3634–3640.
. Path Integral Centroid Variables and the Formulation of their Exact Real Time Dynamics. The Journal of Chemical Physics. 1999 ;111:2357-2370.
. Path Integral Centroid Methods in Quantum Statistical Mechanics and Dynamics. Adv. Chem. Phys. 1996 ;93:135-218.
. Path Integral Calculation of Hydrogen Diffusion Rates on Metal Surfaces. The Journal of Chemical Physics. 1993 ;98:7451-7458.
. A Partial Averaging Strategy for Low Temperature Fourier Path Integral Monte Carlo Calculations. The Journal of Chemical Physics. 1992 ;97:4205-4214.
. Origins of Proton Transport Behavior from Selectivity Domain Mutations of the Aquaporin-1 Channel. Biophys J. 2006 ;90:L73-5.
. Origins of Enhanced Proton Transport in the Y7F Mutant of Human Carbonic Anhydrase II. J. Am. Chem. Soc. 2008 ;130:11399–11408.
. On the Origin of Proton Mobility Suppression in Aqueous Solutions of Amphiphiles. J. Phys. Chem. B . 2013 ;117(49):15426-15435.
. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. J. Am. Chem. Soc. . 2016 .
. Orientational Dynamics of Water in the Nafion Polymer Electrolyte Membrane and Its Relationship to Proton Transport. J. Phys. Chem. B. 2008 ;112:7754–7761.
. Organizing Membrane-Curving Proteins: The Emerging Dynamical Picture. Curr. Opin. Struct. Biol. 2018 ;51:99–105 .
. Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes. J. Phys. Chem. B. 2012 ;116:8363-8374.
. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 2023 ;127:8537–8550.
. Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation. J. Am. Chem. Soc. 2019 ;141(26):10214–10224.
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