Publications
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Systematic Multiscale Simulation of Membrane Protein Systems. Curr. Opin. Struct. Biol. 2009 ;19:138-144.
. Systematic Coarse-graining of Biomolecular and Soft Matter Systems. MRS Bulletin. 2007 ;32:929-934.
. Structure and Function of Lipid Droplet Assembly Complexes. Curr. Opin. Struct. Biol. 2023 ;80:102606.
. Special Pair Dance and Partner Selection: Elementary Steps in Proton Transport in Liquid Water. J. Phys. Chem. B. 2008 ;112:9456-9466.
. 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.
. 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.
. . . Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-grained Analysis. Biophys. J. 2010 ;98:18-26.
. Reactive Molecular Dynamics Models from Ab Initio Molecular Dynamics Data Using Relative Entropy Minimization. Chem. Phys. Lett. 2017 ;683.
. Quantum Molecular Dynamics and Spectral Simulation of a Boron Impurity in Solid Para-hydrogen. The Journal of Chemical Physics. 2000 ;113:9079-9089.
. Probing the Molecular-Scale Lipid Bilayer Response to Shear Flow Using Nonequilibrium Molecular Dynamics. J Phys Chem B. 2005 ;109:18673-9.
. 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.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
Prediction of the essential intermolecular contacts for side-binding of VASP on F-Actin. Cytoskeleton. Submitted .
. Path Integral Molecular Dynamics Simulation of Solid Para-Hydrogen with an Aluminum Impurity. Chem. Phys. Lett. 2002 ;365:487-493.
. On the Origin of Proton Mobility Suppression in Aqueous Solutions of Amphiphiles. J. Phys. Chem. B . 2013 ;117(49):15426-15435.
. A New Perspective on the Coarse-grained Dynamics of Fluids. J Chem Phys. 2004 ;120:4074-88.
. New Insights into BAR Domain Induced Membrane Remodeling. Biophys. J. 2009 ;97:1616–1625.
. 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 Simulation of Actin Filaments and Actin-Associated Proteins. Biophys. Rev. 2018 ;10(6):1521–1535.
. Multiscale Modeling of Biomolecular Systems: in Serial and in Parallel. Curr Opin Struct Biol. 2007 ;17:192-8.
. 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.
. 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. II. Numerical Implementation for Coarse-grained Molecular Models. J. Chem. Phys. 2008 ;128:244115.
. 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.
. The Multiscale Coarse-graining Method I: A Rigorous Bridge between Atomistic and Coarse-grained Models. J. Chem. Phys. 2008 ;128:244114.
. Multiscale Coarse-graining and Structural Correlations: Connections to Liquid State Theory. J Phys Chem B. 2007 ;111:4116-27.
. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 ;120(6):1097–1104.
. Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics. Biophys J. 2006 ;91:3640-52.
. Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys J. 2004 ;87:3299-311.
. Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation. Biophys J. 2007 ;92:3595-602.
. Membrane Binding by the Endophilin N-BAR Domain. Biophys. J. 2009 ;97:2746-2753.
. Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
Loss of the F-BAR Protein CIP4 Reduces Platelet Production by Impairing Membrane-Cytoskeleton Remodeling. Blood. 2013 ;122:1695-1706.
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.
. Integrin-Based Mechanosensing through Conformational Activation. Biophys. J. 2021 ;120(20):4349–4359 .
. A Hybrid Coarse-graining Approach for Lipid Bilayers at Large Length and Time Scales. J. Phys. Chem. B. 2009 ;113:4413-4424.
. The Hopping Mechanism of the Hydrated Excess Proton and Its Contribution to Proton Diffusion in Water. J. Chem. Phys. 2021 ;154(19):194506.
. Hierarchical Coarse-graining Strategy for Protein-Membrane Systems to Access Mesoscopic Scales. Faraday Disc. Chem. Soc. 2010 ;144:347–357.
. Gating mechanisms during actin filament elongation by formins. eLife. 2018 ;7:e37342.
. Formin Cdc12’s Specific Actin Assembly Properties are Tailored for Cytokinesis in Fission Yeast. Mol. Biol. Cell. 2021 ;120(15):2984–2997.
. 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.
. Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia crosslinker fascin. Mol. Biol. Cell. 2019 ;30(7):851–862.
. Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia crosslinker fascin. Mol. Biol. Cell. 2019 ;30(7):851–862.
. Emerging Methods for Multiscale Simulation of Biomolecular Systems. Mol. Phys. 2007 ;105:167-175.
. Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining. J. Chem. Theor. Comp. 2010 ;6:954-965.
. Dynamic Force Matching: Construction of Dynamic Coarse-Grained Models with Realistic Short Time Dynamics and Accurate Long Time Dynamics. J Chem Phys. 2016 ;145:224107.
. Dynamic Force Matching: A Method for Constructing Dynamical Coarse-Grained Models with Realistic Time Dependence. J. Chem. Phys. 2015 ;142(154104):1-21.
. . Coupling Field Theory with Mesoscopic Dynamical Simulations of Multicomponent Lipid Bilayers. Biophys J. 2004 ;87:3242-63.
. Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles. Biophys J. 2005 ;88:3855-69.
. Calculating the Bulk Modulus for a Lipid Bilayer with Nonequilibrium Molecular Dynamics Simulation. Biophys J. 2002 ;82:1226-38.
. Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers. Biophys J. 2002 ;83:3357-70.
. A Bond-order Analysis of the Mechanism for Hydrated Proton Mobility in Liquid Water. J Chem Phys. 2005 ;122:14506.
. Atomistic Modeling of the Electrode-Electrolyte Interface in Li-ion Energy Storage Systems: Electrolyte Structuring. J. Phys. Chem. C. 2013 ;17.
. Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility. J Mol Biol. 2007 ;365:523-34.
. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
. Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems. J. Chem. Theor. Comp. 2008 ;4:560-568.
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