Publications
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.
. Ab initio Centroid Molecular Dynamics: A Fully Quantum Method for Condensed Phase Dynamics Simulations. Chem. Phys. Lett. 1999 ;300:93-98.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. J. Chem. Phys. 2001 ;114:9758-9763.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. IV. Formal Analysis of the Deviations from Born-Oppenheimer Dynamics. Israel. J. Chem. 2003 ;42:191-202.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. II. Generalization based on Mass-weighting, Idempotency, Energy Conservation, and Choice of Initial Conditions. J. Chem. Phys. 2001 :10291-10302.
. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III. Comparison with Born-Oppenheimer Dynamics. J. Chem. Phys. 2002 ;117:8694-8704.
. Ab initio Molecular Dynamics Simulation of the Ag(111)–Water Interface. J. Chem. Phys. 2001 ;115:7196-7206.
. Ab initio Molecular Dynamics Simulation of the Cu(110)–Water Interface. J. Chem. Phys. 2001 ;114:3248.
. Ab initio Molecular Dynamics Simulation of the H/InP(100)–Water Interface. J. Chem. Phys. 2002 ;117:872-884.
. Ab Initio Molecular-dynamics Simulation of Aqueous Proton Solvation and Transport Revisited. J Chem Phys. 2005 ;123:044505.
. Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems. J. Chem. Theor. Comp. 2008 ;4:560-568.
. An Accurate and Simple Quantum Model for Liquid Water. J Chem Phys. 2006 ;125:184507.
. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. J. Phys. Chem. B. 2021 ;125(37):10471–10480 .
. Accurate pKa Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values. J. Phys. Chem. B. 2022 ;126(38):7321–7330.
. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
. Acidic Conditions Impact Hydrophobe Transfer Across the Oil-Water Interface in Unusual Ways. J. Phys. Chem. B. 2023 ;127(17):3911–3918.
. Actin Filament Remodeling by Actin Depolymerization Factor/Cofilin. Proc. Natl. Acad. Sci. USA. 2010 ;107:7299–7304.
. Actin Filament Strain Promotes Severing and Cofilin Dissociation. Biophys J. 2017 ;112.
. Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
Adiabatically Reduced Coupled Equations for Intramolecular Dynamics Calculations. The Journal of Chemical Physics. 1986 ;84:2254-2261.
. 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.
Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Curr. Opin. Struct. Biol. 2018 ;52:119–126.
. Adversarial-Residual-Coarse-Graining: Applying Machine Learning Theory to Systematic Molecular Coarse-Graining. J. Chem. Phys. 2019 ;151(12):124110.
. Allostery of Actin Filaments: Molecular Dynamics Simulations and Coarse-grained Analysis. Proc Natl Acad Sci U S A. 2005 ;102:13111-6.
. On the Amphiphilic Behavior of the Hydrated Proton: An Ab Initio Molecular Dynamics Study. Int. J. Mass. Spec. 2005 ;241:197-204.
. Amphiphilic Character of the Hydrated Proton in Methanol−Water Solutions. J Phys Chem B. 2006 ;110:7085-9.
. An Analysis of Hydrated Proton Diffusion in Ab Initio Molecular Dynamics. J. Chem. Phys. 2015 ;142(014104):1-13.
. Analytic Expression for the Transmission Coefficient in Quantum Mechanical Transition State Theory. Chem. Phys. Lett. 1990 ;170:289-296.
. Anisotropic Motions of Fibrils Dictated by Their Orientations in the Lamella: A Coarse-Grained Model of a Plant Cell Wall. J. Phys. Chem. B. 2020 ;124(17):3527–3539.
. Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions. J. Phys. Chem. B . 2013 ;117:5165-5179.
. Applications Of Higher Order Composite Factorization Schemes In Imaginary Time Path Integral Simulations. J. Chem. Phys. 2001 ;115:7832-7842.
. Approximate Coupled Equations for Multiphoton Processes Induced by One or More Lasers. Chem. Phys. Lett. 1986 ;129:315-320.
. Aqueous Solutions and their Interfaces. J. Phys. Chem. B. 2009 ;113:3997.
. Are Many-body Electronic Polarization Effects Important in Liquid Water?. J Chem Phys. 2007 ;126:124505.
. Atom-centered Density Matrix Propagation (ADMP): Generalizations using Bohmian Mechanics. J. Phys. Chem. 2003 ;107:7269-7277.
. Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II: Insights into the Proton Transfer Mechanism. Biochemistry. 2007 ;46:2930-7.
. Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6). Sci. Adv. 2020 ;6(36).
. Atomistic and Coarse-grained Analysis of Double Spectrin Repeat Units: the Molecular Origins of Flexibility. J Mol Biol. 2007 ;365:523-34.
. Atomistic Modeling of the Electrode-Electrolyte Interface in Li-ion Energy Storage Systems: Electrolyte Structuring. J. Phys. Chem. C. 2013 ;17.
. Autoinhibition of Endophilin in Solution via Inter-domain Interactions. Biophys. J. 2013 ;104:396-403.
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