Publications
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.
. 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 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.
. 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.
. 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.
. Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling. Biophys. J. 2013 ;104:404-411.
. 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.
. Transition-Tempered Metadynamics is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes. J. Chem. Theory Comp. . 2016 .
. 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.
. 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 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 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.
. 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.
. 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.
. 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 Hydrated Na−Nafion Polymer Membranes. J Phys Chem B. 2005 ;109:24244-53.
. 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 Basis of Membrane Bending by the N-BAR Protein Endophilin. Cell. 2012 ;149.
. 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.
. Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water. J. Phys. Chem. B. 2008 ;112:9456-9466.
. 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.
. 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.
. 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.
. 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.
. 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.
. A Second Generation Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems. J. Chem. Phys. 2002 ;117:5839-5849.
. . 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.
. 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.
. On the Representability Problem and the Physical Meaning of Coarse-Grained Models. J. Chem. Phys. 2016 ;145(044108):1-12.
. 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.
. Quantum Time Correlation Functions and Classical Coherence. Chem. Phys. 1998 ;233:243-255.
. Quantum Rate Theory: A Path Integral Centroid Perspective. In: Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. Encyclopedia of Materials Modeling: Vol. I, Fundamental Models and Methods. ; 2005.
. Quantum Properties of the Excess Proton in Liquid Water. Israeli J. Chem. 1999 ;39:483-492.
. Quantum Mechanical Reaction Rate Constants from Centroid Molecular Dynamics Simulations. J. Chem. Phys. 2001 ;115:9209-9222.
. 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.
. 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 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 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 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 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 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.
. Preferred Orientations of His-64 in Human Carbonic Anhydrase II. Biochemistry. 2007 ;46:2938-47.
. Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
Peptide Folding Using Multiscale Coarse-grained Models. J. Phys. Chem. B. 2008 ;112:13079–13090.
. 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.
. Path Integral Centroid Methods in Quantum Statistical Mechanics and Dynamics. Adv. Chem. Phys. 1996 ;93:135-218.
. 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.
. Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes. J. Phys. Chem. B. 2012 ;116:8363-8374.
. 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.
. Numerical Approaches for Computing Nonadiabatic Electron Transfer Rate Constants. J. Chem. Phys. 2002 ;116:9174-9187.
. Nucleotide-dependent Lateral and Longitudinal Interactions in Microtubules. J. Mol. Biol. 2013 .
. Nucleotide-Dependent Conformational States of Actin. Proc. Natl. Acad. Sci. USA. 2009 ;106:12723–12728.
. Nucleotide Regulation of the Structure and Dynamics of G-actin. Biophys. J. 2014 ;106:1710-1720.
. Nonlinear Quantum Time Correlation Functions from Centroid Molecular Dynamics and the Maximum Entropy Method. J. Chem. Phys. 2008 ;129:194113.
. A New Perspective on the Coarse-grained Dynamics of Fluids. J Chem Phys. 2004 ;120:4074-88.
. A New Perspective on Quantum Mechanical Transition State Theory. In: Quantum Simulations of Condensed Matter Phenomena. Quantum Simulations of Condensed Matter Phenomena. Singapore: World Scientific; 1990. pp. 391-400.
. New Insights into BAR Domain Induced Membrane Remodeling. Biophys. J. 2009 ;97:1616–1625.
. New Developments in the Theoretical Description of Charge-Transfer Reactions in Condensed Phases. In: Reviews in Computational Chemistry. Vol. 18. Reviews in Computational Chemistry. New York: John Wiley and Sons; 2002. pp. 147-210.
. New and Notable: Key New Insights into Membrane Targeting by Proteins. Biophys. J. 2013 ;104:517-519.
. Nanostructural Organization in Carbon Disulfide/Ionic Liquid Mixtures: Optical Kerr Effect Spectroscopy and Molecular Dynamics Simulations. J. Chem. Phys. 2011 ;135:034502.
. Nanostructural Organization in Acetonitrile/Ionic Liquid Mixtures: Molecular Dynamics Simulations and Optical Kerr Effect Spectroscopy. ChemPhysChem. 2012 ;13:1687-1700.
. A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution. J. Phys. Chem. A. 2001 ;105:2814-2823.
. A Multi-State Empirical Valence Bond Model for Acid-Base Chemistry in Aqueous Solution. Chem. Phys. Lett. 2000 ;258:187.
. A Multistate Empirical Valence Bond Description of Protonatable Amino Acids. J Phys Chem A. 2006 ;110:631-9.
. A Multi-State Empirical Valence Bond Approach to a Polarizable and Flexible Water Model. J. Phys. Chem. B. 2001 ;105:6628-6637.
. A Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations. J. Chem. Theor. Comp. 2013 ;9:4018–4025.
. Multiscale Simulations of Protein Facilitated Membrane Remodeling. J. Struct. Biol. 2016 .
. 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.
. Multiscale Simulation of Transmembrane Proteins. J Struct Biol. 2007 ;157:570-8.
. Multiscale Simulation of Protein Mediated Membrane Remodeling. Seminars in Cell and Developmental Biology. 2010 ;21:357-362.
. Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior. Current Topics in Membranes. 2008 ;60:181-225.
. Multiscale Reactive Molecular Dynamics. J. Chem. Phys. 2012 ;137:22A525.
. Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers. Biophys J. 2005 ;89:2385-94.
. Multiscale Modeling of Biomolecular Systems: in Serial and in Parallel. Curr Opin Struct Biol. 2007 ;17:192-8.
. A Multiscale Description of Biological Active Matter: The Chemistry Underlying Many Life Processes. Acc. Chem. Res. 2017 ;50.
. Multiscale Coupling of Mesoscopic- and Atomistic-level Lipid Bilayer Simulations. J Chem Phys. 2005 ;122:244716.
. Multiscale Computer Simulation of the Immature HIV-1 Virion. Biophys. J. 2010 ;99:2757–2765.
. 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 Coarse-Graining of the Protein Energy Landscape. PLoS Comp. Bio. 2010 ;6:e1000827.
. Multiscale Coarse-Graining of Monosaccharides. J. Phys. Chem. B. 2007 ;111:11566-11575.
. Multiscale Coarse-graining of Mixed Phospholipid/Cholesterol Bilayer. J. Chem. Theory Comp. 2006 ;2:637-648.
. Multiscale Coarse-Graining of Ionic Liquids. J Phys Chem B. 2006 ;110:3564-75.
. The Multiscale Coarse-Graining Method. X. Improved Algorithms for Constructing Coarse-Grained Potentials for Molecular Systems. J. Chem. Phys. 2012 ;136:194115.
. The Multiscale Coarse-Graining Method. VII. Free Energy Decomposition of Coarse-Grained Effective Potentials. J. Chem. Phys. 2011 ;134:224107.
. The Multiscale Coarse-Graining Method. VI. Implementation of Three-Body Coarse-Grained Potentials. J. Chem. Phys. 2010 ;132:164107.
. The Multiscale Coarse-graining Method. IV. Transferring Coarse-grained Potentials Between Temperatures. J. Chem. Phys. 2009 ;131:024103.
. The Multiscale Coarse-graining Method. II. Numerical Implementation for Coarse-grained Molecular Models. J. Chem. Phys. 2008 ;128:244115.
. The Multiscale Coarse-graining Method I: A Rigorous Bridge between Atomistic and Coarse-grained Models. J. Chem. Phys. 2008 ;128:244114.
. A Multiscale Coarse-Graining Method for Biomolecular Systems. J Phys Chem B. 2005 ;109:2469-73.
. Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory. J Phys Chem B. 2007 ;111:4116-27.
. Multiscale Coarse Graining of Liquid-state Systems. J Chem Phys. 2005 ;123:134105.
. The Multiscale Challenge for Biomolecular Systems: Coarse-grained Modeling. Mol. Sim. 2006 ;32:211-218.
. Molecular Origins of Cofilin-linked Changes in Actin Filament Mechanics. J. Mol. Biol. 2013 ;425(7).
. Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water. J. Chem. Phys. . 2016 .
. Molecular Mechanism of Membrane Binding of the GRP1 PH Domain. J. Mol. Biol. 2013 ;425(17):3073-3090.
. Molecular Dynamics Simulations of Proton Transport in 3M and Nafion Perfluorosulfonic Acid Membranes. J. Phys. Chem. C. 2013 .
. Molecular Dynamics Simulations of Polyglutamine Aggregation using Solvent-Free Multiscale Coarse-Grained Models. J. Phys. Chem. B. 2010 ;114:8735–8743.
. Molecular Dynamics Simulations of Imidazolium-based Ionic Liquid/Water Mixtures: Alkyl Side Chain Length and Anion Effects. Fluid Phase Equilibria (Special Issue). 2010 ;294:148–156.
. Molecular Dynamics Simulations of Human Carbonic Anhydrase II: Insight into Experimental Results and the Role of Solvation. Proteins. 1998 ;33:119-34.
. 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 Simulation of Proton Transport through the Influenza A Virus M2 Channel. Biophys J. 2002 ;83:1987-96.
. Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane. Biophys J. 2002 ;82:1460-8.
. Molecular Dynamics Simulation of Nanostructural Organization in Ionic Liquid/Water Mixtures. J Phys Chem B. 2007 ;111:4812-8.
. Molecular Dynamics Simulation of Ionic Liquids: The Effect of Electronic Polarizability. J. Phys. Chem. B. 2004 ;108:11877-11881.
. Molecular Dynamics Simulation and Coarse-grained Analysis of the Arp2/3 Complex. Biophys. J. 2008 ;95:5324-5333.
. Molecular Dynamics of Synthetic Leucine-serine Ion Channels in a Phospholipid Membrane. Biophys J. 1999 ;77:2400-10.
. Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90. Biophys. J. 2012 ;103:284-292.
. Modeling the Free Energy Surfaces of Electron Transfer in Condensed Phases. J. Chem. Phys. 2000 ;113:5413-5424.
. Modeling Real Dynamics in the Coarse-grained Representation of Condensed Phase Systems. J Chem Phys. 2006 ;125:151101.
. Modeling Condensed Phase Chemistry Through Molecular Dynamics Simulation. Computers in Science and Engineering. 2003 ;5:31-35.
. Mixed Resolution Modeling of Interactions in Condensed Phase Systems. J. Chem. Theor. Comp. 2009 ;5:3232–3244.
. Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel. J Phys Chem B. 2006 ;110:15045-8.
. Minimizing Memory as an Objective for Coarse-Graining. J. Chem. Phys. 2013 ;138.
. Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics. Biophys J. 2006 ;91:3640-52.
. Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys J. 2004 ;87:3299-311.
. Mesoscale Simulation of Proton Transport in Proton Exchange Membranes. J. Phys. Chem. C. 2012 ;116:935-944.
. Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation. Biophys J. 2007 ;92:3595-602.
. 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 by the Endophilin N-BAR Domain. Biophys. J. 2009 ;97:2746-2753.
. Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain. J. Mol. Biol. 2012 ;423:800-817.
. Mechanosensitive Inhibition of Formin Facilitates Contractile Actomyosin Ring Assembly. Nat. Comm. 2017 ;8 (703).
. Mechanisms of Passive Ion Permeation through Lipid Bilayers: Insights from Simulations. J Phys Chem B. 2006 ;110:21327-37.
. The Mechanism of Proton Exclusion in Aquaporin Channels. Proteins. 2004 ;55:223-8.
. Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins. Biophys. J. 2011 ;100:1271-1279.
. Mechanism of Fast Proton Transport along One-Dimensional Water Chains Confined in Carbon Nanotubes. J. Am. Chem. Soc. 2010 ;132:11395–11397.
. Massively Parallel Linear-scaling Algorithm in an ab initio Local-orbital Total-energy Method. J. Comp. Phys. 2003 ;188:1-15.
. Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
Lipid Membrane Mediates Long-Range Interactions Between Linear Filaments of Membrane-Curving Proteins. ACS Cen. Sci. 2017 ;3:1246-1253 .
. 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.
. Linear Aggregation of Proteins on the Membrane as a Prelude to Membrane Remodeling. Proc. Natl. Acad. Sci. 2013 ;110(51).
. Ligand-Dependent Activation and Deactivation of a G Protein-Coupled Receptor. J. Am. Chem. Soc. 2013 ;135:8749-8759.
. Largescale Computer Simulation of an Electrochemical Bond Breaking Reaction. Chem. Phys. Lett. 1999 ;305:94-100.
. The Kinetics of Proton Migration in Liquid Water. J. Phys. Chem. B. 2010 ;114:333–339.
. Kinetic Monte Carlo-Molecular Dynamics Approach To Model Soot Inception. Combust. Sci. and Tech. 2004 ;176:991-1005.
. Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation. J. Mol. Biol. 2012 ;416:148–161.
. Key Inter-molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis. J. Am. Chem. Soc. 2011 ;133:16828-16838.
. Iteratively Determined Effective Hamiltonians for the Adiabatically Reduced Coupled Equations Approach to Intramolecular Dynamics Calculations. J. Chem. Phys. 1986 ;85:5019-5026.
. The Isotope Substitution Effect on the Hydrated Proton. Chem. Phys. Lett. 2000 ;329:36-41.
. IR Spectral Assignments for the Hydrated Excess Proton in Liquid Water. J. Chem. Phys. 2017 ;146.
. Ion Transport through Ultra-Thin Electrolyte under Applied Voltages. J. Phys. Chem. B. 2015 ;119:7516-7521.
. Intrinsic Bending of Microtubule Protofilaments. Structure. 2011 ;19:409–417.
. Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis. Biophys. J. 2008 ;95:2487-2499.
. The Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. J. Am. Chem. Soc. 2010 ;132:16225–16239.
. Interfacing Molecular Dynamics with Continuum Dynamics in Computer Simulation: Toward an Application to Biological Membranes. IBM J. Res. Dev. 2001 ;45:417-426.
. Interfacing Molecular Dynamics and Macro-scale Simulations for Lipid Bilayer Vesicles. Biophys J. 2002 ;83:1026-38.
. Interfacing Continuum and Molecular Dynamics: An Application to Lipid Bilayers. J. Chem. Phys. 2001 ;114:6913-6924.
. Insights into the Transport of Aqueous Quaternary Ammonium Cations: A Combined Experimental and Computational Study. J. Phys. Chem. B. 2014 ;118:1363-1372.
. Insights into the Mechanism of Proton Transport in Cytochrome c Oxidase. J. Am. Chem. Soc. 2012 ;134:1147-1152.
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