Publications
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. Elucidating the Molecular Mechanism of CO2 Capture by Amino Acid Ionic Liquids. J. Am. Chem. Soc. Submitted .
. Gaussian Representation of Coarse-Grained Interactions of Liquids: Theory, Parametrization, and Transferability. J. Mol. Liq. Submitted .
. OpenMSCG: A Software Tool for Multiscale Coarse-graining. J. Phys. Chem. B. 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 .
. Dynamics of Upstream ESCRT Organization at the HIV-1 Budding Site. Biophys. J. In Press .
. Transient Water Wires Mediate Selective Proton Conduction in Designed Channel Proteins. Nat. Chem. In Press .
. Unveiling the Catalytic Mechanism of GTP Hydrolysis in Microtubules. Proc. Natl. Acad. Sci. U.S.A. In Press .
. Using Classifiers to Understand Coarse-grained Models and Their Fidelity with the Underlying All-Atom Systems. J. Chem. Phys. 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 .
. Acidic Conditions Impact Hydrophobe Transfer Across the Oil-Water Interface in Unusual Ways. J. Phys. Chem. B. 2023 ;127(17):3911–3918.
. 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.
. The Role of Conformational Change and Key Glutamic Acid Residues in the ClC-ec1 Antiporter. Biophys. J. 2023 ;122(6):1068–1085.
. Statistical Mechanical Design Principles for Coarse-grained Interactions Across Different Conformational Free Energy Surfaces. J. Phys. Chem. Lett. 2023 ;14(6):1354–1362.
. Structure and Function of Lipid Droplet Assembly Complexes. Curr. Opin. Struct. Biol. 2023 ;80:102606.
. 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.
Synthesis, Characterization and Simulation of Four-Armed Megamolecules. Biomacromolecules. 2021 ;22(6):2363–2372.
. 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.
. 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.
A Helical Assembly of Human ESCRT-I Scaffolds Reverse-Topology Membrane Scission. Nat. Struct. Mol. Biol. 2020 ;27(6):570–580.
. 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.
. Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability. J. Phys. Chem. Lett. 2019 ;10(16):4549–4557.
. 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.
. Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux. J Am. Chem. Soc. 2018 ;140(48):16535–16543.
. 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.
. Actin Filament Strain Promotes Severing and Cofilin Dissociation. Biophys J. 2017 ;112.
. Coarse-Grained Directed Simulation. J. Chem. Theory Comput. 2017 .
. Competition Between Tropomyosin, Fimbrin, and ADF/Cofilin Drive Their Sorting to Distinct Actin Filament Networks. eLife. 2017 ;6.
. Delocalization and Stretch-Bend Mixing of the HOH Bend in Liquid Water. J. Chem. Phys. 2017 ;147(084503).
. Development of Reactive Force Fields Using Ab Initio Molecular Dynamics Simulation Minimally Biased to Experimental Data. J. Chem. Phys. 2017 .
. Extending the Range and Physical Accuracy of Coarse-grained Models: Order Parameter Dependent Interactions. J. Chem. Phys. 2017 .
. Highly Coarse-grained Representations of Transmembrane Proteins. J. Chem. Theory Comput. 2017 ;13.
. 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 .
. Improved Ab Initio Molecular Dynamics by Minimally Biasing with Experimental Data. J. Chem. Phys. 2017 ;146.
. IR Spectral Assignments for the Hydrated Excess Proton in Liquid Water. J. Chem. Phys. 2017 ;146.
. Lipid Membrane Mediates Long-Range Interactions Between Linear Filaments of Membrane-Curving Proteins. ACS Cen. Sci. 2017 ;3:1246-1253 .
. Mechanosensitive Inhibition of Formin Facilitates Contractile Actomyosin Ring Assembly. Nat. Comm. 2017 ;8 (703).
. The Mesoscopic Membrane with Proteins Model (MesM-P). J. Chem. Phys. 2017 ;147.
. A Multiscale Description of Biological Active Matter: The Chemistry Underlying Many Life Processes. Acc. Chem. Res. 2017 ;50.
. Non-Uniqueness of Quantum Transition State Theory and General Dividing Surfaces in the Path Integral Space. J. Chem. Phys. 2017 ;146.
Phosphomimetic S3D-Cofilin Binds But Does Not Sever Actin Filaments. J. Biol. Chem. 2017 ;292:19565-19579 .
Proton Movement and Coupling in the POT Family of Peptide Transporters. Proc. Nat. Acad. Sci. USA . 2017 ;114(13182).
. Reactive Molecular Dynamics Models from Ab Initio Molecular Dynamics Data Using Relative Entropy Minimization. Chem. Phys. Lett. 2017 ;683.
. Role of Solvation Structure in the Shuttling of the Hydrated Excess Proton. J. Chem. Sci. 2017 ;129.
. Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics. J. Chem. Theory Comput. 2017 ;13.
. The Theory of Ultra-Coarse-Graining. 3. Coarse-grained Sites with Rapid Local Equilibrium of Internal States. J. Chem. Theory Comput. 2017 ;13.
. Understanding the Essential Proton Pumping Kinetic Gates and Decoupling Mutations in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA . 2017 ;114.
. Acid Activation Mechanism of the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2016 .
. Can Quantum Transition State Theory be Defined as a t = 0+ Limit?. J. Chem. Phys. 2016 ;144(084110):1-12.
. Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits. J. Phys. Chem. B. 2016 ;120(20).
. Coarse-grained Simulation Reveals Key Features of HIV-1 Capsid Self-Assembly. Nat. Comm. 2016 ;7(1156):1-11.
. Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins. J. Chem. Theory Comp. . 2016 ;12:879-891.
. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J. Phys. Chem. B. 2016 :8389−8404 .
. A Direct Method for Incorporating Experimental Data into Multiscale Coarse-grained Models. J Chem Theory Comp. 2016 ;12(5):2144-2153.
. 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.
. The F-Actin Bundler α-Actinin Ain1 is Tailored for Ring Assembly and Constriction during Cytokinesis in Fission Yeast. Mol Biol Cell. 2016 ;27(11):1821-1833.
. Fascin and α-Actinin-bundled Networks Contain Intrinsic Structural Features That Drive Protein Sorting. Current Biology. 2016 ;26(20):2697–2706.
. How Curvature-Generating Proteins Build Scaffolds on Membrane Nanotubes. Proc. Nat. Acad. Sci. USA. 2016 .
. Hydroxide Solvation and Transport in Anion Exchange Membranes. J. Am. Chem. Soc. 2016 ;138(3):991-1000.
. Molecular Modeling and Assignment of IR Spectra of the Hydrated Excess Proton in Isotopically Dilute Water. J. Chem. Phys. . 2016 .
. Multiscale Simulations of Protein Facilitated Membrane Remodeling. J. Struct. Biol. 2016 .
. Multiscale Simulations Reveal Key Features of the Proton Pumping Mechanism in Cytochrome c Oxidase. Proc. Nat. Acad. Sci. USA. 2016 ;(113):7420-7425.
. Multiscale Simulations Reveal the Proton Transport Mechanism in the ClC-ec1 Antiporter. Biophys. J. 2016 ;110(6):1334–1345.
. The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter. J. Am. Chem. Soc. . 2016 .
. Proton Solvation and Transport in Realistic Proton Exchange Membrane Morphologies. J. Phys. Chem. C. 2016 ;120(6):3176–3186.
. On the Representability Problem and the Physical Meaning of Coarse-Grained Models. J. Chem. Phys. 2016 ;145(044108):1-12.
. Role of Pre-Solvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport. J. Phys. Chem. B . 2016 ;120(8):1793–1804.
. Simulation of Proton Transport in Proton Exchange Membranes with Reactive Molecular Dynamics. Fuel Cells. 2016 ;0000:1-9.
. Transition-Tempered Metadynamics is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes. J. Chem. Theory Comp. . 2016 .
. An Analysis of Hydrated Proton Diffusion in Ab Initio Molecular Dynamics. J. Chem. Phys. 2015 ;142(014104):1-13.
. Designing Free Energy Surfaces that Match Experimental Data with Metadynamics. J. Chem. Theor. Comp. 2015 ;11.
. Dynamic Force Matching: A Method for Constructing Dynamical Coarse-Grained Models with Realistic Time Dependence. J. Chem. Phys. 2015 ;142(154104):1-21.
. Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure. 2015 ;23.
. Exploring Valleys Without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction. J. Chem. Theory Comp. 2015 .
. Hydrated Excess Protons Can Create Their Own Water Wires. J. Phys. Chem. B. 2015 ;(119).
. Hydrated Proton Structure and Diffusion at Platinum Surfaces. J. Phys. Chem. C. 2015 ;119:7516-7521.
. Ion Mixing, Hydration, and Transport in Aqueous Ionic Systems. J. Chem. Phys. 2015 ;142(184905):1-7.
. Ion Transport through Ultra-Thin Electrolyte under Applied Voltages. J. Phys. Chem. B. 2015 ;119:7516-7521.
. Membrane Tension Controls the Assembly of Curvature-Generating Proteins. Nature Communications. 2015 ;6(7219):1-8.
. Mesoscale Study of Proton Transport in Proton Exchange Membranes: Role of Morphology. J. Phys. Chem. C. 2015 ;119:1753-1762.
. The Multiscale Coarse-Graining Method. XI. Accurate Interactions Based on the Centers of Charge of Coarse-Grained Sites. J. Chem. Phys. 2015 ;143(243116):1-11.
. Predicting the Sensitivity of Multiscale Coarse-grained Models to their Underlying Fine-grained Model Parameters. J. Chem. Theory Comp. . 2015 ;11:3547-3560.
. Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface. J. Am. Chem. Soc. 2015 ;137(39):12610-12616.
. A Reductionist Perspective on Quantum Statistical Mechanics: Coarse-Graining of Path Integrals. J. Chem. Phys. 2015 ;143(094104):1-10.
. When Physics Takes Over: BAR Proteins and Membrane Curvature. Trends Cell Biol. 2015 .
. Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J. Chem. Theor. Comp. 2014 ;10(1):451–462.
. Can the Ring Polymer Molecular Dynamics Method be Interpreted as Real Time Quantum Dynamics?. J. Chem. Phys. 2014 ;140:1-11.
. Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems. J. Phys. Chem. C. 2014 ;118:845-853.
. Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data. J. Chem. Theor. Comp. 2014 ;10(8):3023–3030.
. An Electrochemically and Thermally Switchable Donor-Acceptor [c2]Daisy Chain Rotaxane. Angewandte Chemie. 2014 ;53:1953-1958.
. Electron Transfer Activation of a Second Water Channel for Proton Transport in [FeFe]-Hydrogenase. J. Chem. Phys. 2014 ;141(22D527):1-9.
. Highly Scalable and Memory Efficient Ultra-coarse-grained Molecular Dynamics Simulations. J. Chem. Theor. Comp. 2014 ;10:423-431.
. Insights into the Transport of Aqueous Quaternary Ammonium Cations: A Combined Experimental and Computational Study. J. Phys. Chem. B. 2014 ;118:1363-1372.
. 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.
. Multiscale Simulation Reveals a Multifaceted Mechanism of Proton Permeation through the Influenza A M2 Proton Channel. Proc. Nat. Acad. Sci. USA. 2014 ;111:9396-9401.
. Nucleotide Regulation of the Structure and Dynamics of G-actin. Biophys. J. 2014 ;106:1710-1720.
. Path Integral Coarse-graining Replica Exchange Method for Enhanced Sampling. J. Chem. Theor. Comp. 2014 ;10 (9 ):3634–3640.
. Persistent Sub-diffusive Proton Transport in Perfluorosulfonic Acid Membranes. J. Phys. Chem. Lett. . 2014 ;(5(17):3037–3042.
. The Proton Transport Mechanism of Perfluorosulfonic Acid Membranes. J. Phys. Chem. C. 2014 ;118(31):17436–17445.
. Proton Transport Under External Applied Voltage. J. Phys. Chem. B. 2014 .
. Single Molecule Studies Reveal A Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C alpha. Biochemistry. 2014 ;53:1697-1713.
. Solvent-Free Highly Coarse-Grained Models for Charged Lipid Systems. J. Chem. Theor. Comp. . 2014 ;(10):4730-4744.
. The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation. J. Chem. Theory Comp. . 2014 ;10:5265-5275.
. 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.
. Well-tempered Metadynamics Converges Asymptotically. Phys. Rev. Lett. 2014 ;112:1-6.
. Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions. J. Phys. Chem. B . 2013 ;117:5165-5179.
. 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.
. Coarse-graining Methods for Computational Biology. Annu. Rev. Biophysics. 2013 ;42:73-93.
. Coarse-Graining of Proteins Based on Elastic Network Models. Chem. Phys. 2013 ;422:165-174.
. Diffusion Mechanisms in Smectic Ionic Liquid Crystals: Insights from Coarse-grained MD Simulations. Soft Matter. 2013 ;9:5716-5725.
. Discovering Crystals Using Shape Matching and Machine Learning. Soft Matter. 2013 ;9:8552.
. Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain. Biophys. J. 2013 ;105(7):1624-1634.
. Exploring the Behavior of the Hydrated Excess Proton at Hydrophobic Interfaces. Faraday Discussions. 2013 .
. Fitting coarse-grained distribution functions through an iterative force-matching method. J. Chem. Phys. 2013 ;139:1-10.
. A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models. J. Chem. Theor. Comp. 2013 ;9:750-765.
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