Publications
Well-tempered Metadynamics Converges Asymptotically. Phys. Rev. Lett. 2014 ;112:1-6.
. Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys. J. 2019 ;117(3):553–562.
. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J. Phys. Chem. Lett. 2019 ;10(16):4549–4557.
. TRIM5α Self-Assembly and Compartmentalization of the HIV-1 Viral Capsid. Nat. Commun. 2020 ;11:1307.
. 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 .
. 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.
. A Theory for the Thermally Activated Rate Constant in Systems with Spatially Dependent Friction. Chem. Phys. Lett. 1993 ;207:309-316.
. 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-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites. J. Chem. Theory Comput. 2019 ;15(3):2087–2100.
. 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.
. 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.
. Structural Basis for Polarized Elongation of Actin Filaments. Proc. Natl. Acad. Sci. USA. 2020 ;117(48):30458–30464.
. Strain and Rapture of HIV-1 Capsids During Uncoating. Proc. Nat. Acad. Sci. USA. 2022 ;119(10):e2117781119.
. 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.
. Solvated Excess Proton as the Active Site in Methanol Dehydration: Beyond the Hydrated Hydronium Ion. Submitted .
. Simulating Accidental Fires and Explosions. Computing in Science and Engineering. 2000 ;2:64-76.
. . The Role of Amino Acid Sequence in the Self-Association of Therapeutic Monoclonal Antibodies: Insights from Coarse Grained Modeling. J. Chem. Phys. B. 2013 .
. Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water. J. Phys. Chem. 1999 ;103:925-931.
. 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.
. 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.
. 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.
. Proton Transport Under External Applied Voltage. J. Phys. Chem. B. 2014 .
. 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 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).
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.
. Preservation of HIV-1 Gag Helical Bundle Symmetry by Bevirimat is Central to Maturation Inhibition. J. Am. Chem. Soc. 2021 ;143(45):19137−19148 .
. Preservation of HIV-1 Gag Helical Bundle Symmetry by Bevirimat is Central to Maturation Inhibition. J. Am. Chem. Soc. 2021 ;143(45):19137−19148 .
. Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
Path Integral Coarse-graining Replica Exchange Method for Enhanced Sampling. J. Chem. Theor. Comp. 2014 ;10 (9 ):3634–3640.
. Orientational Dynamics of Water in the Nafion Polymer Electrolyte Membrane and Its Relationship to Proton Transport. J. Phys. Chem. B. 2008 ;112:7754–7761.
. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 2023 ;127:8537–8550.
. 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.
. Nucleotide-Dependent Conformational States of Actin. Proc. Natl. Acad. Sci. USA. 2009 ;106:12723–12728.
. Nucleotide-Dependent Conformational States of Actin. Proc. Natl. Acad. Sci. USA. 2009 ;106:12723–12728.
. Nucleotide-Dependent Conformational States of Actin. Proc. Natl. Acad. Sci. USA. 2009 ;106:12723–12728.
. Nonlinear Quantum Time Correlation Functions from Centroid Molecular Dynamics and the Maximum Entropy Method. J. Chem. Phys. 2008 ;129:194113.
. . Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA. 2016 ;(113):7420-7425.
. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 ;120(6):1097–1104.
. Molecular Mechanism of Membrane Binding of the GRP1 PH Domain. J. Mol. Biol. 2013 ;425(17):3073-3090.
. 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.
. Modeling Condensed Phase Chemistry Through Molecular Dynamics Simulation. Computers in Science and Engineering. 2003 ;5:31-35.
. 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).
. Mechanism of Targeting of Amphipathic Helix-Containing Proteins to Lipid Droplets. Dev. Cell. 2018 ;44(1):73–86.
. Mechanism of Phosphate Release from Actin Filaments. Proc. Natl. Acad. Sci. U.S.A. Submitted .
. Mechanism of Fast Proton Transport along One-Dimensional Water Chains Confined in Carbon Nanotubes. J. Am. Chem. Soc. 2010 ;132:11395–11397.
. Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins. Biophys. J. 2021 ;120(1):46–54.
. Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation. J. Mol. Biol. 2012 ;416:148–161.
. Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation. J. Mol. Biol. 2012 ;416:148–161.
. Ion Transport through Ultra-Thin Electrolyte under Applied Voltages. J. Phys. Chem. B. 2015 ;119:7516-7521.
. Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly Towards Kinetically-Trapped Morphologies. J. Am. Chem. Soc. 2022 ;144(23):10417–10428.
. Infrared Spectroscopy and Hydrogen-Bond Dynamics in Liquid Water from Quantum Simulations. J. Phys. Chem. B. 2009 ;113:13118–13130.
. An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport. J. Phys. Chem. B. 2008 ;112:467-482.
. 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 Assembles from Gag Dimers Leaving Partial Hexamers at Lattice Edges as Substrates for Proteolytic Maturation. Proc. Natl. Acad. Sci. USA. 2021 ;118(3):e2020054118.
. Hyper-Parallel Algorithms for Centroid Molecular Dynamics: Application to Liquid para–Hydrogen. Chem. Phys. Lett. 1996 ;262:415-420.
. Hydrated Proton Structure and Diffusion at Platinum Surfaces. J. Phys. Chem. C. 2015 ;119:7516-7521.
. The Hydrated Proton at the Water Liquid/Vapor Interface. J. Phys. Chem. B. 2004 ;108:14804-14806.
. Hydrated Excess Protons Can Create Their Own Water Wires. J. Phys. Chem. B. 2015 ;(119).
. The Hydrated Excess Proton at Water-Hydrophobic Interfaces. J. Phys. Chem. B. 2009 ;113:4017-4030.
. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Nat. Acad. Sci. USA. 2016 .
. A Helical Assembly of Human ESCRT-I Scaffolds Reverse-Topology Membrane Scission. Nat. Struct. Mol. Biol. 2020 ;27(6):570–580.
Gating mechanisms during actin filament elongation by formins. eLife. 2018 ;7:e37342.
. Extending the Fluctuation Theorem to Describe Reaction Coordinates. J Chem Phys. 2007 ;126:051102.
. Extending a Spectrin Repeat Unit. II: Rupture Behavior. Biophys J. 2006 ;90:101-11.
. Extending a Spectrin Repeat Unit. I: Linear Force-Extension Response. Biophys J. 2006 ;90:92-100.
. Expanding the View of Proton Pumping in Cytochrome c Oxidase through Computer Simulation. Biochim. et Biophys. Acta-Bioenergetics. 2012 ;1817:518-525.
. Excess Proton Solvation and Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion. J Phys Chem B. 2005 ;109:3727-30.
. Examining the Influence of Linkers and Tertiary Structure in the Forced Unfolding of Multiple-Repeat Spectrin Molecules. Biophys J. 2006 ;91:3436-45.
. Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure. 2015 ;23.
. Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure. 2015 ;23.
. Effective Force Fields for Condensed Phase Systems from ab initio Molecular Dynamics Simulation: a New Method for Force-matching. J Chem Phys. 2004 ;120:10896-913.
. Discovering Crystals Using Shape Matching and Machine Learning. Soft Matter. 2013 ;9:8552.
. Defining Coarse-grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models. Biophys. J. 2009 ;97:2327-2337.
. DA Theory for the Activated Barrier Crossing Rate Constant in Systems Influenced by Space and Time Dependent Friction. The Journal of Chemical Physics. 1994 ;101:7811-7822.
. Critical Mechanistic Features of HIV-1 Viral Capsid Assembly. Sci. Adv. 2023 ;9(1):eadd7434.
. Cooperative Multivalent Receptor Binding Promotes Exposure of the SARS-CoV-2 Fusion Machinery Core. Nat. Commun. 2022 ;13:1002.
. A Computationally Efficient Treatment of Polarizable Electrochemical Cells Held at a Constant Potential. J. Phys. Chem. C. 2012 ;116:4903-4912.
. Computationally Efficient Multiconfigurational Reactive Molecular Dynamics. J. Chem. Theory Comput. 2012 ;8:4863-4875.
. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys. J. 2019 ;116(6):1000–1010 .
. Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies. J. Phys. Chem. B. 2012 ;116:8045-8057.
. Characterization of the Solvation and Transport of the Hydrated Proton in the Perfluorosulfonic Acid Membrane Nafion. J Phys Chem B. 2006 ;110:18594-600.
. Centroid Molecular Dynamics: A Quantum Dynamics Method Suitable for the Parallel Computer. Parallel Computing. 2000 ;26:1025-1041.
. Bottom-up Coarse-Graining: Principles and Perspectives. J. Chem. Theory Comput. 2022 ;18(10):5759–5791.
. A Bond-order Analysis of the Mechanism for Hydrated Proton Mobility in Liquid Water. J Chem Phys. 2005 ;122:14506.
. Amphiphilic Character of the Hydrated Proton in Methanol−Water Solutions. J Phys Chem B. 2006 ;110:7085-9.
. Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Curr. Opin. Struct. Biol. 2018 ;52:119–126.
. Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
Actin Filament Remodeling by Actin Depolymerization Factor/Cofilin. Proc. Natl. Acad. Sci. USA. 2010 ;107:7299–7304.
. An Accurate and Simple Quantum Model for Liquid Water. J Chem Phys. 2006 ;125:184507.
. Ab initio Centroid Molecular Dynamics: A Fully Quantum Method for Condensed Phase Dynamics Simulations. Chem. Phys. Lett. 1999 ;300:93-98.
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