Publications
] . Cracked Actin Filaments as Mechanosensitive Receptors. Proc. Natl. Acad. Sci. U.S.A. Submitted .
. Can a Coarse-grained Water Model Capture the Key Physical Features of the Hydrophobic Effect?. J. Chem. Phys. 2023 ;159:224105.
. Critical Mechanistic Features of HIV-1 Viral Capsid Assembly. Sci. Adv. 2023 ;9(1):eadd7434.
. Gaussian Representation of Coarse-Grained Interactions of Liquids: Theory, Parametrization, and Transferability. J. Chem. Phys. 2023 ;159:184105.
. Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly Towards Kinetically-Trapped Morphologies. J. Am. Chem. Soc. 2022 ;144(23):10417–10428.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
. Strain and Rapture of HIV-1 Capsids During Uncoating. Proc. Nat. Acad. Sci. USA. 2022 ;119(10):e2117781119.
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.
. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 ;120(6):1097–1104.
Synthesis, Characterization and Simulation of Four-Armed Megamolecules. Biomacromolecules. 2021 ;22(6):2363–2372.
. Binding Mechanism of the Matrix Domain of HIV-1 Gag to Lipid Membranes. eLife. 2020 ;9.
. TRIM5α Self-Assembly and Compartmentalization of the HIV-1 Viral Capsid. Nat. Commun. 2020 ;11:1307.
. 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.
. Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc. Natl. Acad. Sci. USA. 2018 ;115(37):E8595–E8603.
. The Lamellipodia is a Myosin Independent Mechanosensor. Proc. Nat. Acad. Sci. USA. 2018 ;115(11):2646–2651.
. 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 .
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 .
. Coarse-grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly. Nat. Comm. 2016 ;7(1156):1-11.
. Coarse-grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly. Nat. Comm. 2016 ;7(1156):1-11.
. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Nat. Acad. Sci. USA. 2016 .
. Highly Scalable and Memory Efficient Ultra-coarse-grained Molecular Dynamics Simulations. J. Chem. Theor. Comp. 2014 ;10:423-431.
. Minimizing Memory as an Objective for Coarse-Graining. J. Chem. Phys. 2013 ;138.
. Nucleotide-dependent Lateral and Longitudinal Interactions in Microtubules. J. Mol. Biol. 2013 .
. Early Stages of the HIV-1 Capsid Protein Lattice Formation. Biophys. J. 2012 ;103:1774-1783.
. Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain. J. Mol. Biol. 2012 ;423:800-817.
. Structural Basis of Membrane Bending by the N-BAR Protein Endophilin. Cell. 2012 ;149.
. An Exploration of Transferability in Multiscale Coarse-grained Peptide Models. J. Phys. Chem. B. 2011 ;115:11911-11926.
. Intrinsic Bending of Microtubule Protofilaments. Structure. 2011 ;19:409–417.
. Hierarchical Coarse-graining Strategy for Protein-Membrane Systems to Access Mesoscopic Scales. Faraday Disc. Chem. Soc. 2010 ;144:347–357.
. The Intricate Role of Water in Proton Transport through Cytochrome c Oxidase. J. Am. Chem. Soc. 2010 ;132:16225–16239.
. Proton Transport in Carbonic Anhydrase: Insights from Molecular Simulation. Biochim. et Biophys. Acta - Proteins and Proteomics. 2010 ;1804:332-341.
. Defining Coarse-grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models. Biophys. J. 2009 ;97:2327-2337.
. Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis. Biophys. J. 2008 ;95:2487-2499.
. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
. Mesoscopic Modeling of Bacterial Flagellar Microhydrodynamics. Biophys J. 2006 ;91:3640-52.
. Structure of the Liquid−Vacuum Interface of Room-Temperature Ionic Liquids: A Molecular Dynamics Study. J Phys Chem B. 2006 ;110:1800-6.
. 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.
. Massively Parallel Linear-scaling Algorithm in an ab initio Local-orbital Total-energy Method. J. Comp. Phys. 2003 ;188:1-15.
. The Vibrational Spectrum of the Hydrated Proton: Comparison of Experiment, Simulation, and Normal Mode Analysis. J. Chem. Phys. 2002 ;116:737-746.
. Further Developments in the Local-Orbital Density-Functional-Theory Tight-Binding Method. Phys. Rev. B. 2001 ;64:195103.
. Quantum Mechanical Reaction Rate Constants from Centroid Molecular Dynamics Simulations. J. Chem. Phys. 2001 ;115:9209-9222.
. Ab Initio Calculations of Reactive Pathways for α-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (α-HMX). The Journal of Physical Chemistry A. 2000 ;104:11384-11389.
. Molecular Dynamics of Bond-Breaking Electron-Transfer Reactions at Metal-Liquid Interfaces. CATTECH 4. 2000 :51-55.
. The Quantum Vibrational Dynamics of Cl[sup -](H[sub 2]O)[sub n] Clusters. The Journal of Chemical Physics. 2000 ;113:5171-5178.
. Ab initio Centroid Molecular Dynamics: A Fully Quantum Method for Condensed Phase Dynamics Simulations. Chem. Phys. Lett. 1999 ;300:93-98.
. Vibrational Energy Relaxation Dynamics of Si–H Stretching Modes on Stepped H/Si(111)1x1 Surfaces. Chem. Phys. 1995 ;20:357-368.
. First-principles Molecular Dynamics Study of Surface Vibrations and Vibrational Mode Coupling on the H/Si(111)1 x 1 Surface. The Journal of Chemical Physics. 1994 ;101:1734-1737.
. 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 Relaxation Dynamics of Si–H Stretching Modes on the H/Si(111)11 Surface. J. Chem. Phys. 1993 ;99:740-743.
. A Computer Simulation Method for Studying the Ablation of Polymer Surfaces by Ultraviolet Laser Radiation. Journal of Applied Physics. 1992 ;71:1415-1420.
. 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.
. 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.