Publications
] . Acidic Conditions Impact Hydrophobe Transfer Across the Oil-Water Interface in Unusual Ways. J. Phys. Chem. B. Submitted .
. Organization of Upstream ESCRT Machinery at the HIV-1 Budding Site. Biophys. J. Submitted .
. Proton Dissociation and Delocalization Under Stepwise Hydration of Zeolite HZSM-5. J. Am. Chem. Soc. Submitted .
. Solvated Excess Proton as the Active Site in Methanol Dehydration: Beyond the Hydrated Hydronium Ion. Submitted .
The Structural Basis of Phosphatidylinositol Remodeling and Identification of Inhibitors of Human MBOAT7. Nat. Struct. Mol. Biol. Submitted .
. Using Classifiers to Understand Coarse-grained Models and Their Fidelity with the Underlying All-Atom Systems. J. Chem. Phys. Submitted .
. The Role of Conformational Change and Key Glutamic Acid Residues in the ClC-ec1 Antiporter. Biophys. J. In Press .
. Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins. Nat. Chem. In Press .
. Utilizing Machine Learning to Greatly Expand the Range and Accuracy of Bottom-Up Coarse-Grained Models through Virtual Particles. J. Chem. Theory Comput. In Press .
. Critical Mechanistic Features of HIV-1 Viral Capsid Assembly. Sci. Adv. 2023 ;9(1):eadd7434.
. How Does Electronic Polarizability or Scaled-Charge Affect the Interfacial Properties of Room Temperature Ionic Liquids?. J. Phys. Chem. B. 2023 ;127(5):1264–1275.
. Statistical Mechanical Design Principles for Coarse-grained Interactions Across Different Conformational Free Energy Surfaces. J. Phys. Chem. Lett. 2023 ;14(6):1354–1362.
. Understanding Dynamics in Coarse-Grained Models: I. Universal Excess Entropy Scaling Relationship. J. Chem. Phys. 2023 ;158(3):034103.
. Understanding Dynamics in Coarse-Grained Models: II. Coarse-Grained Diffusion Modeled Using Hard Sphere Theory. J. Chem. Phys. 2023 ;158(3):034104.
. 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.
Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions. Sci. Adv. 2022 ;8(41):eabp8677.
. Bottom-up Coarse-Graining: Principles and Perspectives. J. Chem. Theory Comput. 2022 ;18(10):5759–5791.
. Centroid Molecular Dynamics Can Be Greatly Accelerated through Neural Network Learned Centroid Forces Derived from Path Integral Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(10):5856–5863.
. Coarse-Graining of Imaginary Time Feynman Path Integrals: Inclusion of Intramolecular Interactions and Bottom-up Force-Matching. J. Phys. Chem. A. 2022 ;126(35):6004–6019.
. Computational Studies of Lipid Droplets. J. Phys. Chem. B. 2022 ;126(11):2145–2154.
. Cooperative Multivalent Receptor Binding Promotes Exposure of the SARS-CoV-2 Fusion Machinery Core. Nat. Commun. 2022 ;13:1002.
. Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins. J. Phys. Chem. B. 2022 ;126(49):10452–10459.
. Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly Towards Kinetically-Trapped Morphologies. J. Am. Chem. Soc. 2022 ;144(23):10417–10428.
. Ion Permeation, Selectivity, and Electronic Polarization in Fluoride Channels. Biophys. J. 2022 ;121(7):1336–1347.
. Key Factors Governing Initial Stages of Lipid Droplet Formation. J. Phys. Chem. B. 2022 ;126(2):453–462.
. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior. J. Am. Chem. Soc. 2022 ;144(2):776–776.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat. Commun. 2022 ;13:5879.
. Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys. J. 2022 ;121(12):2266–2278.
. Seipin Transmembrane Segments Critically Function in Triglyceride Nucleation and Droplet Budding from the Membrane. eLife. 2022 ;11:e75808.
. 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.
. Strain and Crack Propagation of HIV-1 Capsids During Uncoating. Proc. Nat. Acad. Sci. USA. 2022 ;119(10):e2117781119.
. Structure of SARS-CoV-2 M protein in lipid nanodiscs. eLife. 2022 ;11:e81702.
. Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics. J. Chem. Theory Comput. 2022 ;18(2):599–604.
. Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory. J. Phys. Chem. B. 2021 ;125(37):10471–10480 .
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.
. Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover. J. Chem. Theory Comput. 2021 ;17(2):1170–1180.
. Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments. J. Phys. Chem. B. 2021 ;17(3):1900–1913.
. Constructing Many-body Mesoscopic Models of Fluids from Bottom-up Coarse-graining. J. Chem. Phys. 2021 ;154(8):084122.
. Formin Cdc12’s Specific Actin Assembly Properties are Tailored for Cytokinesis in Fission Yeast. Mol. Biol. Cell. 2021 ;120(15):2984–2997.
. The Hopping Mechanism of the Hydrated Excess Proton and Its Contribution to Proton Diffusion in Water. J. Chem. Phys. 2021 ;154(19):194506.
. 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.
. 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.
. Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins. Biophys. J. 2021 ;120(1):46–54.
. Molecular Interactions of the M and E Integral Membrane Proteins of SARS-CoV-2. Faraday Discuss. 2021 ;232:49–67 .
. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. Biophys. J. 2021 ;120(6):1097–1104.
. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-body Projected Water (BUMPer). I. General Theory and Model. J. Chem. Phys. 2021 ;154(4):044104.
. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-Body Projected Water (BUMPer). II. Temperature Transferability and Structural Properties at Low Temperature. J. Chem. Phys. 2021 ;154(4):044105.
. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis. J. Phys. Chem. B. 2021 ;125(25):6872–6888.
. Preservation of HIV-1 Gag Helical Bundle Symmetry by Bevirimat is Central to Maturation Inhibition. J. Am. Chem. Soc. 2021 ;143(45):19137−19148 .
. A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces. Proc. Natl. Acad. Sci. USA. 2021 ;118(49 ):e2113141118.
. Resolving the Structural Debate for the Hydrated Excess Proton in Water. J. Am. Chem. Soc. 2021 ;143(44):18672−18683.
. Structural Asymmetry in Fast- And Slow-Severing Actin-Cofilactin Boundaries. J. Biol. Chem. 2021 ;296:100337.
. Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites. J. Am. Chem. Soc. 2021 ;143(27):10203–10213.
. Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6). Sci. Adv. 2020 ;6(36).
. Binding Mechanism of the Matrix Domain of HIV-1 Gag to Lipid Membranes. eLife. 2020 ;9.
. Cholesterol Alters the Membrane Orientation and Activity of the Influenza Virus M2 Amphipathic Helix. J. Phys. Chem. B. 2020 ;124(31):6738–6747 .
. Density Functional Theory-based Quantum Mechanics/Coarse-grained Molecular Mechanics: Theory and Implementation. J. Chem. Theory Comput. 2020 ;16(10):6329–6342.
. Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics. J. Am. Chem. Soc. 2020 ;142(41):17425–17433.
. Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles. Phys. Chem. Chem. Phys. 2020 ;22(19):10753–10763.
. Local conformational dynamics regulating transport properties of a Cl–/H+ antiporter. J. Comput. Chem. 2020 ;41(6):513–519 .
. Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability. Biophys. J. 2020 ;118(12):2938–2951.
. Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water. J. Chem. Theory. Comput. 2020 ;16(9):5675–5684 .
. Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions. J. Phys. Chem. B. 2020 ;124(40):8868–8876.
. Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale. Biophys. J. 2020 ;119(5):1033–1040.
. Reactive Coarse-grained Molecular Dynamics. J. Chem. Theory. Comput. 2020 ;16(4):2541−2549.
. Structural Basis for Polarized Elongation of Actin Filaments. Proc. Natl. Acad. Sci. USA. 2020 ;117(48):30458–30464.
. Temperature and Phase Transferable Bottom-up Coarse-Grained Models. J. Chem. Theory Comput. 2020 ;16(11):6823–6842.
. TRIM5α Self-Assembly and Compartmentalization of the HIV-1 Viral Capsid. Nat. Commun. 2020 ;11:1307.
. Water Assisted Proton Transport in Confined Nanochannels. J. Phys. Chem. C. 2020 ;124(29):16186−16201.
. What Coordinate Best Describes the Affinity of the Hydrated Excess Proton for the Air-Water Interface?. J. Phys. Chem. B. 2020 ;124(24):5039–5046.
. Adversarial-Residual-Coarse-Graining: Applying Machine Learning Theory to Systematic Molecular Coarse-Graining. J. Chem. Phys. 2019 ;151(12):124110.
. Coarse-Grained Simulation of Full-Length Integrin Activation. Biophys. J. 2019 ;116(6):1000–1010 .
. Coarse-Graining Involving Virtual Sites: Centers of Symmetry Coarse-Graining. J. Chem. Phys. 2019 ;150(15):154103.
. Coarse-graining of many-body path integrals: Theory and numerical approximations. J. Chem. Phys. 2019 ;150(24):244103.
. Compatible Observable Decompositions for Coarse-grained Representations of Real Molecular Systems. J. Chem. Phys. 2019 ;151(13):134115.
. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J. Am. Chem. Soc. 2019 ;141(34):13421–13433.
. 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.
. Mechanical and Kinetic Factors Drive Sorting of F-actin Crosslinkers on Bundles. Proc. Natl. Acad. Sci. USA. 2019 ;116(13):16192–16197.
. Multiconfigurational Coarse-Grained Molecular Dynamics. J. Chem. Theory Comput. 2019 ;15(5):3306–3315.
. Multiscale model of integrin adhesion assembly. PLoS Comput. Biol. 2019 ;15(6):e1007077.
. 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.
. Plastic Deformation and Fragmentation of Strained Actin Filaments. Biophys. J. 2019 ;117(3):453–463.
. Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel. J. Am. Chem. Soc. 2019 ;141(29):11667–11676.
. Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites. J. Chem. Theory Comput. 2019 ;15(3):2087–2100.
. Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes. Biophys. J. 2019 ;117(3):553–562.
. Advances In Coarse-Grained Modeling of Bio-Macromolecular Complexes. Curr. Opin. Struct. Biol. 2018 ;52:119–126.
. Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding. Proc. Natl. Acad. Sci. USA. 2018 ;115(37):E8595–E8603.
. Gating mechanisms during actin filament elongation by formins. eLife. 2018 ;7:e37342.
. Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments. Biophys. J. 2018 ;115(18):1589–1602.
. The Lamellipodia is a Myosin Independent Mechanosensor. Proc. Nat. Acad. Sci. USA. 2018 ;115(11):2646–2651.
. Mechanism of Targeting of Amphipathic Helix-Containing Proteins to Lipid Droplets. Dev. Cell. 2018 ;44(1):73–86.
. Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models. J. Chem. Phys. 2018 ;149(4):044104.
. Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants. J. Chem. Phys. 2018 ;149(7):072310.
. Multiscale Kinetic Modeling Reveals Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter. J. Am. Chem. Soc. 2018 ;140(5):1793–1804.
. Multiscale Simulation of Actin Filaments and Actin-Associated Proteins. Biophys. Rev. 2018 ;10(6):1521–1535.
. Organizing Membrane-Curving Proteins: The Emerging Dynamical Picture. Curr. Opin. Struct. Biol. 2018 ;51:99–105 .
. Quantum Mechanics/Coarse-Grained Molecular Mechanics (QM/CG-MM). J. Chem. Phys. 2018 ;148(1):014102.
. Quantum Theory of Multiscale Coarse-graining. J. Chem. Phys. 2018 ;148(10):102335.
. Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding. J. Chem. Theory Comput. 2018 ;14(12):6159–6174.
. Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems. J. Chem. Theory Comput. 2018 ;14(4):2180–2197.
Proton Movement and Coupling in the POT Family of Peptide Transporters. Proc. Nat. Acad. Sci. USA . 2017 ;114(13182).
. Interactions of Protein Kinase C-α C1A and C1B Domains with Membranes: A Combined Computational and Experimental Study. J. Am. Chem. Soc. 2014 ;136(33):11757–11766.
. Path Integral Coarse-graining Replica Exchange Method for Enhanced Sampling. J. Chem. Theor. Comp. 2014 ;10 (9 ):3634–3640.
. Solvent-Free Highly Coarse-Grained Models for Charged Lipid Systems. J. Chem. Theor. Comp. . 2014 ;(10):4730-4744.
. Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-The-Fly Transition Barrier Estimation. J. Chem. Theor. Comp. 2014 .
. Unraveling the Mystery of ATP Hydrolysis in Actin Filaments. J. Am. Chem. Soc. . 2014 ;136(37):13053–13058.
. Coarse-Graining of Condensed Phase and Biomolecular Systems. Boca Raton, FL: CRC Press/Taylor and Francis Group; 2009.