#81302 Overall Influence

American chemist

Gregory A. Voth is a theoretical chemist and Haig P. Papazian Distinguished Service Professor of Chemistry at the University of Chicago. He is also a Professor of the James Franck Institute and the Institute for Biophysical Dynamics.

Source: Wikipedia- A multiscale coarse-graining method for biomolecular systems.
- Unique spatial heterogeneity in ionic liquids.
- Flexible simple point-charge water model with improved liquid-state properties.
- Ionic liquids.
- Fluid particle accelerations in fully developed turbulence
- The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.
- On the Structure and Dynamics of Ionic Liquids
- Coarse-Graining of Condensed Phase and Biomolecular Systems
- Multiscale coarse graining of liquid-state systems.
- The computer simulation of proton transport in water
- Unique spatial heterogeneity in ionic liquids.
- Flexible simple point-charge water model with improved liquid-state properties.
- Ionic liquids.
- Fluid particle accelerations in fully developed turbulence
- The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.
- On the Structure and Dynamics of Ionic Liquids
- Coarse-Graining of Condensed Phase and Biomolecular Systems
- Multiscale coarse graining of liquid-state systems.
- The computer simulation of proton transport in water
- Rigorous formulation of quantum transition state theory and its dynamical corrections
- Measurement of particle accelerations in fully developed turbulence
- Multiscale modeling of biomolecular systems: in serial and in parallel.
- The formulation of quantum statistical mechanics based on the Feynman path centroid density. II. Dynamical properties
- Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals
- Coarse-graining methods for computational biology.
- Molecular dynamics simulation of nanostructural organization in ionic liquid/water mixtures.
- Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.
- Tail aggregation and domain diffusion in ionic liquids.
- Multistate Empirical Valence Bond Model for Proton Transport in Water
- Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals. III. Comparison with Born–Oppenheimer dynamics
- Molecular Dynamics Simulation of Ionic Liquids: The Effect of Electronic Polarizability
- Computer simulation of proton solvation and transport in aqueous and biomolecular systems.
- The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.
- The quantum dynamics of an excess proton in water
- Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals. II. Generalizations based on mass-weighting, idempotency, energy conservation and choice of initial conditions
- The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics
- Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations.
- Special pair dance and partner selection: elementary steps in proton transport in liquid water.
- Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.
- Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.
- A second generation multistate empirical valence bond model for proton transport in aqueous systems
- Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations
- Further developments in the local-orbital density-functional-theory tight-binding method
- A derivation of centroid molecular dynamics and other approximate time evolution methods for path integral centroid variables
- A bond-order analysis of the mechanism for hydrated proton mobility in liquid water.
- The curious case of the hydrated proton.
- Structural Basis of Membrane Bending by the N-BAR Protein Endophilin
- The hydrated proton at the water liquid/vapor interface
- A new perspective on quantum time correlation functions
- The formulation of quantum statistical mechanics based on the Feynman path centroid density. III. Phase space formalism and analysis of centroid molecular dynamics
- Experimental measurements of stretching fields in fluid mixing.
- Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis.
- Coarse-grained modeling of the actin filament derived from atomistic-scale simulations.
- An improved multistate empirical valence bond model for aqueous proton solvation and transport.
- When Physics Takes Over: BAR Proteins and Membrane Curvature.
- A quantum model for water: Equilibrium and dynamical properties
- Well-tempered metadynamics converges asymptotically.
- The vibrational spectrum of the hydrated proton: Comparison of experiment, simulation, and normal mode analysis
- Anisotropic Particles in Turbulence
- Path integral centroid variables and the formulation of their exact real time dynamics
- Lagrangian acceleration measurements at large Reynolds numbers
- Modeling real dynamics in the coarse-grained representation of condensed phase systems.
- An accurate and simple quantum model for liquid water.
- Promoting transparency and reproducibility in enhanced molecular simulations
- The formation and dynamics of proton wires in channel environments.
- Coarse-grained peptide modeling using a systematic multiscale approach.
- Mechanism of membrane curvature sensing by amphipathic helix containing proteins.
- Molecular dynamics simulations of imidazolium-based ionic liquid/water mixtures: Alkyl side chain length and anion effects
- The properties of water: insights from quantum simulations.
- Multiscale coarse-graining and structural correlations: connections to liquid-state theory.
- Structure of the liquid-vacuum interface of room-temperature ionic liquids: a molecular dynamics study.
- Multiscale coarse-graining of ionic liquids.
- The mechanism of proton exclusion in aquaporin channels
- Rotation rate of rods in turbulent fluid flow.
- Friction Mediates Scission of Tubular Membranes Scaffolded by BAR Proteins
- Quantum effects in liquid water from an ab initio-based polarizable force field.
- The Mechanism of Hydrated Proton Transport in Water
- Atomic crystal and molecular dynamics simulation structures of human carbonic anhydrase II: insights into the proton transfer mechanism.
- Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion.
- A systematic methodology for defining coarse-grained sites in large biomolecules.
- Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers.
- Coarse-grained free energy functions for studying protein conformational changes: a double-well network model.
- The properties of ion-water clusters. I. The protonated 21-water cluster.
- Probing selected morphological models of hydrated Nafion using large-scale molecular dynamics simulations.
- Mechanism of fast proton transport along one-dimensional water chains confined in carbon nanotubes.
- Systematic multiscale parameterization of heterogeneous elastic network models of proteins.
- Multiscale Coarse-Graining of the Protein Energy Landscape
- Nucleotide-dependent conformational states of actin
- Linear aggregation of proteins on the membrane as a prelude to membrane remodeling
- Applications of higher order composite factorization schemes in imaginary time path integral simulations
- Mechanistic insights into cobalt(ii/iii)-catalyzed C–H oxidation: a combined theoretical and experimental study
- PROTON TRANSFER IN THE ENZYME CARBONIC ANHYDRASE : AN AB INITIO STUDY
- Hydroxide Solvation and Transport in Anion Exchange Membranes.
- Path‐Integral Centroid Methods in Quantum Statistical Mechanics and Dynamics
- The Theory of Ultra-Coarse-Graining. 1. General Principles.
- A comparative study of imaginary time path integral based methods for quantum dynamics.
- Membrane tension controls the assembly of curvature-generating proteins
- Infrared spectroscopy and hydrogen-bond dynamics of liquid water from centroid molecular dynamics with an ab initio-based force field.
- Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation.
- The formulation of quantum statistical mechanics based on the Feynman path centroid density. V. Quantum instantaneous normal mode theory of liquids
- Proton solvation and transport in hydrated nafion.
- Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane nafion.
- The 2018 biomembrane curvature and remodeling roadmap
- Proton transport behavior through the influenza A M2 channel: insights from molecular simulation.
- Bridging microscopic and mesoscopic simulations of lipid bilayers.
- Mechanism and Determinants of Amphipathic Helix-Containing Protein Targeting to Lipid Droplets.
- Atomistic Modeling of the Electrode–Electrolyte Interface in Li-Ion Energy Storage Systems: Electrolyte Structuring
- The theory of electron transfer reactions: what may be missing?
- Effective force coarse-graining.
- A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor.
- Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach
- Systematic coarse-graining of a multicomponent lipid bilayer.
- Car–Parrinello molecular dynamics simulation of liquid water: New results
- The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials.
- Time correlation function and path integral analysis of quantum rate constants
- Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation.
- Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations.
- Systematic multiscale simulation of membrane protein systems.
- The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures.
- Internal granular dynamics, shear-induced crystallization, and compaction steps.
- Coarse-graining of multiprotein assemblies.
- Calculation of solvent free energies for heterogeneous electron transfer at the water–metal interface: Classical versus quantum behavior
- Molecular dynamics simulation of proton transport through the influenza A virus M2 channel.
- Hydrated excess proton at water-hydrophobic interfaces.
- Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining.
- Actin filament remodeling by actin depolymerization factor/cofilin
- The Multiscale Coarse‐Graining Method
- How curvature-generating proteins build scaffolds on membrane nanotubes
- Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited.
- A Feynman path centroid dynamics approach for the computation of time correlation functions involving nonlinear operators
- A Multiscale Coarse-Graining Study of the Liquid/Vacuum Interface of Room-Temperature Ionic Liquids with Alkyl Substituents of Different Lengths
- Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.
- Simple reversible molecular dynamics algorithms for Nosé-Hoover chain dynamics
- Nanostructural organization in acetonitrile/ionic liquid mixtures: molecular dynamics simulations and optical Kerr effect spectroscopy.
- Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane.
- A centroid molecular dynamics study of liquid para-hydrogen and ortho-deuterium.
- Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.
- Peptide folding using multiscale coarse-grained models.
- Mixing rates and symmetry breaking in two-dimensional chaotic flow
- Quantum-mechanical reaction rate constants from centroid molecular dynamics simulations
- Solvent-free lipid bilayer model using multiscale coarse-graining.
- A unified framework for quantum activated rate processes. I. General theory
- Elucidation of the proton transport mechanism in human carbonic anhydrase II.
- Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.
- Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling.
- A novel method for simulating quantum dissipative systems
- Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway.
- On the amphiphilic behavior of the hydrated proton: an ab initio molecular dynamics study
- Semiclassical approximations to quantum dynamical time correlation functions
- New insights into BAR domain-induced membrane remodeling.
- Shape-dependence of particle rotation in isotropic turbulence
- Coupling field theory with continuum mechanics: a simulation of domain formation in giant unilamellar vesicles.
- Protein-mediated transformation of lipid vesicles into tubular networks.
- Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly
- Coarse-grained modeling of the self-association of therapeutic monoclonal antibodies.
- A Feynman Path Integral Formulation of Quantum Mechanical Transition State Theory
- Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations
- Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel.
- Multiscale coarse-graining of monosaccharides.
- Ab initio molecular dynamics simulation of the Cu(110)–water interface
- Alignment of vorticity and rods with Lagrangian fluid stretching in turbulence
- Kinetics of proton migration in liquid water.
- Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data.
- Ab initio molecular dynamics simulation of the Ag(111)-water interface
- Pseudopotentials for centroid molecular dynamics: Application to self-diffusion in liquid para-hydrogen
- Charge delocalization in proton channels, I: the aquaporin channels and proton blockage.
- Fascin- and α-Actinin-Bundled Networks Contain Intrinsic Structural Features that Drive Protein Sorting
- A linear-scaling self-consistent generalization of the multistate empirical valence bond method for multiple excess protons in aqueous systems.
- Feynman path integral approach for studying intramolecular effects in proton-transfer reactions
- Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster.
- The multiscale challenge for biomolecular systems: coarse-grained modeling
- On the representability problem and the physical meaning of coarse-grained models.
- KINETIC MONTE CARLO–MOLECULAR DYNAMICS APPROACH TO MODEL SOOT INCEPTION
- A path integral study of electronic polarization and nonlinear coupling effects in condensed phase proton transfer reactions
- Exact exchange in ab initio molecular dynamics: An efficient plane-wave based algorithm
- Ab Initio Calculations of Reactive Pathways for α-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (α-HMX)
- The role of amino acid sequence in the self-association of therapeutic monoclonal antibodies: insights from coarse-grained modeling.
- The properties of ion-water clusters. II. Solvation structures of Na+, Cl-, and H+ clusters as a function of temperature.
- Vibrational energy relaxation of Si-H stretching modes on the H/Si(111)1×1 surface
- Semiclassical molecular dynamics computation of spontaneous light emission in the condensed phase: Resonance Raman spectra
- Multiscale computer simulation of the immature HIV-1 virion.
- Gating of the mechanosensitive channel protein MscL: the interplay of membrane and protein.
- A theory for adiabatic bond breaking electron transfer reactions at metal electrodes
- Insights into the mechanism of proton transport in cytochrome c oxidase.
- Enhancement of proton conductance by mutations of the selectivity filter of aquaporin-1.
- Molecular Dynamics Simulations of Proton Transport in 3M and Nafion Perfluorosulfonic Acid Membranes
- A coarse-grained model for double-helix molecules in solution: spontaneous helix formation and equilibrium properties.
- Hybrid coarse-graining approach for lipid bilayers at large length and time scales.
- A theory for the activated barrier crossing rate constant in systems influenced by space and time dependent friction
- Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method.
- Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales.
- Quantum time correlation functions and classical coherence
- The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations.
- Early stages of the HIV-1 capsid protein lattice formation.
- A Failure of Continuum Theory: Temperature Dependence of the Solvent Reorganization Energy of Electron Transfer in Highly Polar Solvents
- Fitting coarse-grained distribution functions through an iterative force-matching method.
- Transferable Coarse-Grained Models for Ionic Liquids.
- Hydrated Excess Protons Can Create Their Own Water Wires
- Infrared Spectrum of the Hydrated Proton in Water.
- A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models.
- Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel
- Modeling the free energy surfaces of electron transfer in condensed phases
- Classical and Quantum Simulation of Electron Transfer Through a Polypeptide
- A unified framework for quantum activated rate processes. II. The nonadiabatic limit
- The highly excited C–H stretching states of CHD3, CHT3, and CH3D
- Classical molecular dynamics simulation of the photoinduced electron transfer dynamics of plastocyanin.
- Molecular dynamics simulation of the energetic room-temperature ionic liquid, 1-hydroxyethyl-4-amino-1,2,4-triazolium nitrate (HEATN).
- Ab initio molecular dynamics: Propagating the density matrix with gaussian orbitals. IV. Formal analysis of the deviations from born‐oppenheimer dynamics
- Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface.
- Measurements of the coupling between the tumbling of rods and the velocity gradient tensor in turbulence
- Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence.
- Rotation and alignment of rods in two-dimensional chaotic flow
- Structure and dynamics of the actin filament.
- A computer simulation study of the hydrated proton in a synthetic proton channel.
- Structure of hydrated Na-Nafion polymer membranes.
- Chemical rescue of enzymes: proton transfer in mutants of human carbonic anhydrase II.
- Intrinsic bending and structural rearrangement of tubulin dimer: molecular dynamics simulations and coarse-grained analysis.
- Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations.
- Mechanisms of passive ion permeation through lipid bilayers: insights from simulations.
- A Multi-State Empirical Valence Bond Model for Weak Acid Dissociation in Aqueous Solution†
- Emerging methods for multiscale simulation of biomolecular systems
- A quantitative assessment of the accuracy of centroid molecular dynamics for the calculation of the infrared spectrum of liquid water.
- Membrane binding by the endophilin N-BAR domain.
- Properties of hydrated excess protons near phospholipid bilayers.
- Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks
- Analytic expression for the transmission coefficient in quantum mechanical transition state theory
- Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials.
- A computer simulation model for proton transport in liquid imidazole.
- Interfacing continuum and molecular dynamics: An application to lipid bilayers
- Optimal number of coarse-grained sites in different components of large biomolecular complexes.
- Unraveling the Mystery of ATP Hydrolysis in Actin Filaments
- Mesoscale Simulation of Proton Transport in Proton Exchange Membranes
- Structure and dynamics of hydronium in the ion channel gramicidin A.
- An electrochemically and thermally switchable donor-acceptor [c2]daisy chain rotaxane.
- Intricate role of water in proton transport through cytochrome c oxidase.
- Multiscale reactive molecular dynamics.
- Molecular mechanism of membrane binding of the GRP1 PH domain.
- Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain
- Protons may leak through pure lipid bilayers via a concerted mechanism.
- Nanostructural organization in carbon disulfide∕ionic liquid mixtures: molecular dynamics simulations and optical Kerr effect spectroscopy.
- Ordered clusters and dynamical states of particles in a vibrated fluid.
- Coupling field theory with mesoscopic dynamical simulations of multicomponent lipid bilayers.
- Quantum effects and the excess proton in water
- Molecular dynamics simulations of polyglutamine aggregation using solvent-free multiscale coarse-grained models.
- Electronic Structure Calculation of the Structures and Energies of the Three Pure Polymorphic Forms of Crystalline HMX
- Mechanoregulated inhibition of formin facilitates contractile actomyosin ring assembly
- A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles.
- A computer simulation study of free energy curves in heterogeneous electron transfer
- Intrinsic bending of microtubule protofilaments.
- Membrane docking geometry and target lipid stoichiometry of membrane-bound PKCα C2 domain: a combined molecular dynamics and experimental study.
- A multistate empirical valence bond description of protonatable amino acids.
- Orientational dynamics of water in the nafion polymer electrolyte membrane and its relationship to proton transport.
- Proton transport pathway in the ClC Cl-/H+ antiporter.
- A relationship between centroid dynamics and path integral quantum transition state theory
- Hyper-parallel algorithms for centroid molecular dynamics: application to liquid para-hydrogen
- Measurements of the solid-body rotation of anisotropic particles in 3D turbulence
- Calculating the bulk modulus for a lipid bilayer with nonequilibrium molecular dynamics simulation.
- Acid activation mechanism of the influenza A M2 proton channel
- Preferred orientations of His64 in human carbonic anhydrase II.
- Multi-scale modeling of phase separation in mixed lipid bilayers.
- Using cavitation to measure statistics of low-pressure events in large-Reynolds-number turbulence
- A Computationally Efficient Treatment of Polarizable Electrochemical Cells Held at a Constant Potential
- Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane.
- The F-actin bundler α-actinin Ain1 is tailored for ring assembly and constriction during cytokinesis in fission yeast
- Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation.
- Proton Transport Mechanism of Perfluorosulfonic Acid Membranes
- Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology.
- Atom-Centered Density Matrix Propagation (ADMP): Generalizations Using Bohmian Mechanics †
- Multiscale simulation of transmembrane proteins.
- Nature of lithium trapping sites in the quantum solids para‐hydrogen and ortho‐deuterium
- The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation.
- Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport.
- ELECTRON TRANSFER ACROSS THE ELECTRODE/ELECTROLYTE INTERFACE : INFLUENCE OF REDOX ION MOBILITY AND COUNTERIONS
- Proton conduction in exchange membranes across multiple length scales.
- Manifestations of spatially dependent friction in classical activated rate processes
- Electrochemical Bond-Breaking Reactions: A Comparison of Large Scale Simulation Results with Analytical Theory
- Lamellipodium is a myosin-independent mechanosensor
- The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials.
- Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis.
- Studies on the influence of nonlinearity in classical activated rate processes
- On the Feynman path centroid density for Bose-Einstein and Fermi-Dirac statistics
- Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane
- An analysis of hydrated proton diffusion in ab initio molecular dynamics.
- Application of the SCC-DFTB method to hydroxide water clusters and aqueous hydroxide solutions.
- Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.
- Simulating accidental fires and explosions
- Effects of Polymer Morphology on Proton Solvation and Transport in Proton-Exchange Membranes
- Quantum Effects Strongly Influence the Surface Premelting of Ice
- Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data.
- Fast centroid molecular dynamics: a force-matching approach for the predetermination of the effective centroid forces.
- A Bayesian statistics approach to multiscale coarse graining.
- Molecular origins of cofilin-linked changes in actin filament mechanics.
- Comparison between actin filament models: coarse-graining reveals essential differences.
- Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton.
- Inertial range scaling in rotations of long rods in turbulence.
- Calculation of quantum activation free energies for proton transfer reactions in polar solvents
- Proton movement and coupling in the POT family of peptide transporters
- Molecular dynamics simulations of human carbonic anhydrase II: Insight into experimental results and the role of solvation
- The Computation of Electron Transfer Rates: The Nonadiabatic Instanton Solution.
- Discovering crystals using shape matching and machine learning
- Proton transport pathways in [NiFe]-hydrogenase.
- Designing free energy surfaces that match experimental data with metadynamics.
- The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems.
- A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics.
- Critical comparison of approximate and accurate quantum-mechanical calculations of rate constants for a model activated reaction in solution
- Acceleration statistics of neutrally buoyant spherical particles in intense turbulence.
- Are many-body electronic polarization effects important in liquid water?
- Quantum Dynamical Simulation of the Energy Relaxation Rate of the CN- Ion in Water
- A solid-solid phase transition in carbon dioxide at high pressures and intermediate temperatures.
- Reconstructing atomistic detail for coarse-grained models with resolution exchange.
- Quantum Properties of the Excess Proton in Liquid Water
- Mesoscopic lateral diffusion in lipid bilayers.
- Multiscale simulation of protein mediated membrane remodeling.
- A computational study of the closed and open states of the influenza a M2 proton channel.
- Modeling physical systems by effective harmonic oscillators: The optimized quadratic approximation
- Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation.
- Actin Filament Strain Promotes Severing and Cofilin Dissociation.
- Computer Simulation of Proton Solvation and Transport in Aqueous and Biomolecular Systems
- An improved Polarflex water model
- Coarse-graining provides insights on the essential nature of heterogeneity in actin filaments.
- Water molecules in the nucleotide binding cleft of actin: effects on subunit conformation and implications for ATP hydrolysis.
- Single-Molecule Studies Reveal a Hidden Key Step in the Activation Mechanism of Membrane-Bound Protein Kinase C-α
- Quantum molecular dynamics and spectral simulation of a boron impurity in solid para-hydrogen
- Stretching and mixing of non-Newtonian fluids in time-periodic flows
- A perturbation theory for solvation thermodynamics: Dipolar-quadrupolar liquids
- The relative roles of acetylene and aromatic precursors during soot particle inception
- Loss of the F-BAR protein CIP4 reduces platelet production by impairing membrane-cytoskeleton remodeling.
- Interfacing molecular dynamics and macro-scale simulations for lipid bilayer vesicles.
- The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States.
- Path integral calculation of hydrogen diffusion rates on metal surfaces
- A theory for treating spatially‐dependent friction in classical activated rate processes
- A Multistate Empirical Valence Bond Approach to a Polarizable and Flexible Water Model
- Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter.
- Diffusion mechanisms in smectic ionic liquid crystals: insights from coarse-grained MD simulations
- Nonlinear vibrational dynamics of a neon atom in fullerene (C60)
- The isotope substitution effect on the hydrated proton
- A theory for adiabatic electron transfer processes across the semiconductor/electrolyte interface
- Feynman path centroid dynamics for Fermi–Dirac statistics
- Path integral formulation of centroid dynamics for systems obeying Bose–Einstein statistics
- The Theory of Ultra Coarse-graining
- Two-dimensional granular Poiseuille flow on an incline: multiple dynamical regimes.
- Nucleotide-dependent lateral and longitudinal interactions in microtubules.
- Conformational switching between protein substates studied with 2D IR vibrational echo spectroscopy and molecular dynamics simulations.
- Free energy profiles for H+ conduction in the D-pathway of Cytochrome c Oxidase: a study of the wild type and N98D mutant enzymes.
- Unusual "amphiphilic" association of hydrated protons in strong acid solution.
- A silicon strip detector system for high resolution particle tracking in turbulence
- Semiclassical theory of Fermi resonance between stretching and bending modes in polyatomic molecules
- A new perspective on the coarse-grained dynamics of fluids.
- Structure and dynamics of concentrated hydrochloric acid solutions.
- Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins
- Classical And Quantum Transition State Theory For The Diffusion Of Helium In Silica Sodalite
- A three-dimensional potential energy surface for dissociative adsorption and associative desorption at metal electrodes
- A multi-state empirical valence bond model for acid base chemistry in aqueous solution
- Extending the range and physical accuracy of coarse-grained models: Order parameter dependent interactions.
- Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.
- Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II.
- IR spectral assignments for the hydrated excess proton in liquid water.
- A theory for time correlation functions in liquids
- Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations.
- Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits
- Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations.
- Proton transport in carbonic anhydrase: Insights from molecular simulation.
- The semiclassical calculation of nonadiabatic tunneling rates
- Advances in coarse-grained modeling of macromolecular complexes.
- Delocalization and stretch-bend mixing of the HOH bend in liquid water.
- Unraveling the role of the protein environment for [FeFe]-hydrogenase: a new application of coarse-graining.
- Extension of path integral quantum transition state theory to the case of nonadiabatic activated dynamics
- Systematic coarse graining of biomolecular and soft-matter systems
- Key structural features of the actin filament Arp2/3 complex branch junction revealed by molecular simulation.
- A Centroid Molecular Dynamics Approach for Nonadiabatic Dynamical Processes in Condensed Phases: the Spin-Boson Case†
- Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel.
- Exploring the behaviour of the hydrated excess proton at hydrophobic interfaces.
- Transition-Tempered Metadynamics Is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes.
- Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules.
- Effects of nonuniversal large scales on conditional structure functions in turbulence
- Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase
- Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics
- A theory for the thermally activated rate constant in systems with spatially dependent friction
- Reconstructing protein remodeled membranes in molecular detail from mesoscopic models.
- Adiabatically reduced coupled equations for intramolecular dynamics calculations
- An effective barrier model for describing quantum mechanical activated rate processes in condensed phases
- Proton Solvation and Transport in Realistic Proton Exchange Membrane Morphologies
- Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling
- Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction
- Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 1. Charge Transfer Reactions
- Vibrational energy redistribution across a heavy atom
- Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems.
- Coarse-graining of proteins based on elastic network models
- Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics
- Extending the fluctuation theorem to describe reaction coordinates.
- A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion
- The quantum vibrational dynamics of Cl−(H2O)n clusters
- Water under the BAR.
- Large-scale computer simulation of an electrochemical bond-breaking reaction
- Mesoscale Study of Proton Transport in Proton Exchange Membranes: Role of Morphology
- Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex.
- A theory for electron transfer between an electrode and a multilevel acceptor/donor species in an electrolyte solution
- Interactions of Protein Kinase C-α C1A and C1B Domains with Membranes: A Combined Computational and Experimental Study
- Solvent Free Ionic Solution Models from Multiscale Coarse-Graining.
- Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding
- Persistent Subdiffusive Proton Transport in Perfluorosulfonic Acid Membranes.
- Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase
- A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models.
- Computational studies of proton transport through the M2 channel
- Extending a spectrin repeat unit. I: linear force-extension response.
- Phosphomimetic S3D cofilin binds but only weakly severs actin filaments
- Amphiphilic character of the hydrated proton in methanol-water solutions.
- Signatures of non-universal large scales in conditional structure functions from various turbulent flows
- A first-principles simulation of the semiconductor/water interface
- Measurements of the steady streaming flow around oscillating spheres using three dimensional particle tracking velocimetry
- Computer simulation of electron transfer processes across the electrode|electrolyte interface: a treatment of solvent and electrode polarizability
- A path integral Einstein model for characterizing the equilibrium states of low temperature solids
- Interfacing molecular dynamics with continuum dynamics in computer simulation: Toward an application to biological membranes
- Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems
- Dynamic force matching: Construction of dynamic coarse-grained models with realistic short time dynamics and accurate long time dynamics.
- Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems
- Exploration of transferability in multiscale coarse-grained peptide models.
- Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity.
- The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter
- Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments.
- Mesoscopic modeling of bacterial flagellar microhydrodynamics.
- Centroid molecular dynamics: A quantum dynamics method suitable for the parallel computer
- Reaction‐coordinate‐dependent friction in classical activated barrier crossing dynamics: When it matters and when it doesn’t
- The Properties of Water: Insights from Quantum Simulations
- Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants.
- Calculation of electron spin resonance linewidths for hydrogen atom impurities in solid para‐hydrogen
- Disks aligned in a turbulent channel
- The computer simulation of proton transport in biomolecular systems.
- Autoinhibition of endophilin in solution via interdomain interactions.
- The coupled proton transport in the ClC-ec1 Cl(-)/H(+) antiporter.
- Organizing membrane-curving proteins: the emerging dynamical picture.
- Electrostatic interactions between the Bni1p Formin FH2 domain and actin influence actin filament nucleation.
- Real-time image compression for high-speed particle tracking.
- Coarse-graining in interaction space: an analytical approximation for the effective short-ranged electrostatics.
- Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility.
- LITHIUM IMPURITY RECOMBINATION IN SOLID PARA-HYDROGEN : A PATH INTEGRAL QUANTUM TRANSITION STATE THEORY STUDY
- “Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly”
- Quantum and classical energy transfer between ligands of a heavy metal atom
- Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability.
- Effects of fluctuating energy input on the small scales in turbulence
- Preferential Rotation of Chiral Dipoles in Isotropic Turbulence.
- A theory for electron transfer across the electrode/electrolyte interface involving more than one redox ion
- ISOTOPE EFFECTS IN ELECTRON TRANSFER ACROSS THE ELECTRODE-ELECTROLYTE INTERFACE : A MEASURE OF SOLVENT MODE QUANTIZATION
- The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites.
- Probing the molecular-scale lipid bilayer response to shear flow using nonequilibrium molecular dynamics.
- Simulation of Proton Transport in Proton Exchange Membranes with Reactive Molecular Dynamics
- An effective Golden Rule decay rate expression for quasidissipative IVR processes
- Mixed Resolution Modeling of Interactions in Condensed-Phase Systems.
- Nucleotide regulation of the structure and dynamics of G-actin.
- Extending a spectrin repeat unit. II: rupture behavior.
- Multiscale Kinetic Modeling Reveals an Ensemble of Cl–/H+ Exchange Pathways in ClC-ec1 Antiporter
- Nonlinear quantum time correlation functions from centroid molecular dynamics and the maximum entropy method.
- Insights into the transport of aqueous quaternary ammonium cations: a combined experimental and computational study.
- First‐principles molecular dynamics study of surface vibrations and vibrational mode coupling on the H/Si(111)1×1 surface
- A Theory of Electron Transfer and Steady-State Optical Spectra of Chromophores with Varying Electronic Polarizability
- Quantum Molecular Dynamics Simulations of Low-Temperature High Energy Density Matter: Solid p-H2/Li and p-H2/B
- TRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid
- Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations.
- Unusual hydrophobic interactions in acidic aqueous solutions.
- Expanding the view of proton pumping in cytochrome c oxidase through computer simulation.
- Potential Energy Surfaces for Chemical Reactions: An Analytical Representation from Coarse Grained Data with an Application to Proton Transfer in Water
- A Modification of Path Integral Quantum Transition State Theory for Asymmetric and Metastable Potentials
- Chapter 7 Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior
- Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia cross-linker fascin
- Inertial torques and a symmetry breaking orientational transition in the sedimentation of slender fibres
- A computer simulation method for studying the ablation of polymer surfaces by ultraviolet laser radiation
- Long-Range Organization of Membrane-Curving Proteins
- Effect of membrane environment on proton permeation through gramicidin A channels.
- Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data.
- Ab initio molecular dynamics simulation of the H/InP(100)–water interface
- Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II
- Proton transport under external applied voltage.
- Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation
- Experimental measurements of the collapse of a two-dimensional granular gas under gravity.
- Proton Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel.
- Minimizing memory as an objective for coarse-graining.
- Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase.
- Spatial heterogeneity in ionic liquids
- Mechanical and kinetic factors drive sorting of F-actin cross-linkers on bundles
- Molecular modeling and assignment of IR spectra of the hydrated excess proton in isotopically dilute water.
- Gating mechanisms during actin filament elongation by formins
- Stretching fields and mixing near the transition to nonperiodic two-dimensional flow.
- The Multiscale Coarse- Graining Method: A Systematic Approach to Coarse-Graining
- On the Feynman path centroid density as a phase space distribution in quantum statistical mechanics
- Ion mixing, hydration, and transport in aqueous ionic systems.
- Failure and strengthening of granular slopes under horizontal vibration.
- Simulation of Biomolecular Systems at Multiple Length and Time Scales
- The mesoscopic membrane with proteins (MesM-P) model.
- Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules.
- Ion Transport through Ultrathin Electrolyte under Applied Voltages.
- Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain.
- On the use of Feynman–Hibbs effective potentials to calculate quantum mechanical free energies of activation
- Molecular and thermodynamic insights into the conformational transitions of Hsp90.
- Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes
- Reorganization Parameters of Electronic Transitions in Electronically Delocalized Systems. 2. Optical Spectra
- A partial averaging strategy for low temperature Fourier path integral Monte Carlo calculations
- Vibrational energy relaxation dynamics of C–H stretching modes on the hydrogen‐terminated H/C(111)1×1 surface
- Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models.
- Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux
- On the relationship of classical resonances to the quantum mechanics of coupled oscillator systems
- Highly Coarse-Grained Representations of Transmembrane Proteins
- A Multi-scale Computational Approach for Nanoparticle Growth in Combustion Environments
- Plastic Deformation and Fragmentation of Strained Actin Filaments.
- Quasidissipative intramolecular dynamics: An adiabatically reduced coupled equations approach
- Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
- A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission
- Massively parallel linear-scaling algorithm in an ab initio local-orbital total-energy method
- Evaluation of nonlinear quantum time correlation functions within the centroid dynamics formulation.
- Semiclassical Dressed State Theory for the Vibrational Excitation of a Morse Oscillator by Radiation
- Introduction: Coarse-Graining in Molecular Modeling and Simulation.
- A Multiscale Description of Biomolecular Active Matter: The Chemistry Underlying Many Life Processes.
- Predicting the Sensitivity of Multiscale Coarse-Grained Models to their Underlying Fine-Grained Model Parameters.
- Extracting turbulent spectral transfer from under-resolved velocity fields
- Coarse-graining away electronic structure: a rigorous route to accurate condensed phase interaction potentials
- The computer simulation of correlated electron transfer across the electrode/electrolyte interface involving multiple redox species
- Lagrangian acceleration measurements in turbulence at large Reynolds numbers
- Measurements of the steady streaming flow around oscillating spheres using 3 D particle tracking velocimetry
- Multiscale simulations reveal key features of the proton pumping mechanism in cytochrome c oxidase
- Multiscale simulations of protein-facilitated membrane remodeling.
- Quantum theory of multiscale coarse-graining.
- On the origin of proton mobility suppression in aqueous solutions of amphiphiles.
- Coarse-Grained Directed Simulation.
- Multiscale model of integrin adhesion assembly
- A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals.
- Path Integral Coarse-Graining Replica Exchange Method for Enhanced Sampling.
- Design of Energetic Ionic Liquids
- Effect of active-site mutation at Asn67 on the proton transfer mechanism of human carbonic anhydrase II.
- Coarse-Grained Simulation of Full-Length Integrin Activation.
- Infrared laser-induced chaos and conformational disorder in a model polymer crystal: Melting vs ablation
- Multiconfigurational Coarse-Grained Molecular Dynamics
- Superposition State Molecular Dynamics.
- Microtubule Simulations Provide Insight into the Molecular Mechanism Underlying Dynamic Instability.
- Numerical approaches for computing nonadiabatic electron transfer rate constants
- Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water
- Response to “Comment on ‘A centroid molecular dynamics study of liquid para-hydrogen and ortho-deuterium’ ” [J. Chem. Phys. 122, 057101 (2005)]
- Quantum and classical simulations of an excess proton in water
- New Developments in the Theoretical Description of Charge‐Transfer Reactions in Condensed Phases
- Effect of Solvent on Semiconductor Surface Electronic States: A First-Principles Study.
- A Feynman Path Integral Approach for Calculating Quantum Rate Constants in Complex Systems
- Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining.
- The dynamic stress responses to area change in planar lipid bilayer membranes.
- Rotational dynamics of rod particles in fluid flows
- Iteratively determined effective Hamiltonians for the adiabatically reduced coupled equations approach to intramolecular dynamics calculations
- Temperature and Phase Transferable Bottom-up Coarse-Grained Models.
- Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data.
- Scale-dependent alignment, tumbling and stretching of slender rods in isotropic turbulence
- Using deformable particles for single particle measurements of velocity gradient tensors
- Approximate coupled equations for multiphoton processes induced by one or more lasers
- A multiscale coarse-grained model of the SARS-CoV-2 virion
- Hydrated Proton Structure and Diffusion at Platinum Surfaces
- Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding.
- Coarse-graining involving virtual sites: Centers of symmetry coarse-graining.
- Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem.
- Methods for Measuring the Orientation and Rotation Rate of 3D-printed Particles in Turbulence.
- Passive directors in turbulence
- The dependence of the potential of mean force on the solvent friction: Consequences for condensed phase activated rate theories
- Multiscale simulation of actin filaments and actin-associated proteins
- Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems.
- Response to “Comment on ‘Simple reversible molecular dynamics algorithms for Nosé–Hoover chain dynamics’ ” [J. Chem. Phys. 110, 3623 (1999)]
- Erratum: “Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited” [J. Chem. Phys. 123, 044505 (2005)]
- Lipid-composition mediated forces can stabilize tubular assemblies of I-BAR proteins.
- Efficient Multistate Reactive Molecular Dynamics Approach Based on Short-Range Effective Potentials.
- Visualization of collisional substructure in granular shock waves.
- Computer Simulation of Electrochemical Processes
- Combining the semiclassical initial value representation with centroid dynamics
- An efficient and accurate implementation of centroid molecular dynamics using a Gaussian approximation.
- Simulations of granular gravitational collapse.
- Integral equation calculation of solvent activation free energies for electron- and proton-transfer reactions
- A semiclassical reactive flux method for the calculation of condensed phase activated rate constants
- A variational model for the thermodynamical and structural properties of impurities in low temperature solids
- A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission
- Aqueous solutions and their interfaces.
- Path integral molecular dynamics simulation of solid para-hydrogen with an aluminum impurity
- Can quantum transition state theory be defined as an exact t = 0+ limit?
- The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter
- Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale
- Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate (IP6)
- Erratum: “A unified framework for quantum activated rate processes. II. The nonadiabatic limit” [J. Chem. Phys. 106, 1769 (1997)]
- New and notable: key new insights into membrane targeting by proteins.
- Feynman path centroid methods for condensed phase quantum dynamics
- Supercharged Assembly: A Broad-Spectrum Mechanism of Action for Drugs that Undermine Controlled HIV-1 Viral Capsid Formation
- Feynman Path Centroid Dynamics
- Non-uniqueness of quantum transition state theory and general dividing surfaces in the path integral space.
- Orientation statistics of non-spherical particles sedimenting in turbulence
- Orientation patterns of non-spherical particles in turbulence
- Correction to “Proton Solvation and Transport in Hydrated Nafion”
- Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).
- Multiscale Simulation of Hydroxide Solvation and Transport in Anion Exchange Membranes
- A THEORY FOR THE QUANTUM ACTIVATED RATE CONSTANT IN DISSIPATIVE SYSTEMS
- Modeling condensed-phase chemistry through molecular dynamics simulation
- Signatures of non-universal large scales in conditional structure functions from eight different turbulent flows
- A TIME-SCALE PROBLEM FOR THE FORMATION OF SOOT PRECURSORS IN PREMIXED FLAMES
- Exceptionally low charge trapping enables highly efficient organic bulk heterojunction solar cells
- Cover Picture: Nanostructural Organization in Acetonitrile/Ionic Liquid Mixtures: Molecular Dynamics Simulations and Optical Kerr Effect Spectroscopy (ChemPhysChem 7/2012)
- Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization.
- Role of solvation structure in the shuttling of the hydrated excess proton
- Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover
- Self-consistent harmonic theory of solvation in glassy systems: Classical solvation
- Designing Alkaline Exchange Membranes from Scratch
- Precision Measurements of Stretching and Compression in Fluid Mixing
- Compatible observable decompositions for coarse-grained representations of real molecular systems.
- Anisotropic Motions of Fibrils Dictated by Their Orientations in the Lamella: A Coarse-Grained Model of a Plant Cell Wall.
- Computer Simulations of Proton Transport Through the M2 Channel of the Influenza A Virus
- Reactive Coarse-grained Molecular Dynamics.
- Erratum: “A relationship between centroid dynamics and path integral quantum transition state theory” [J. Chem. Phys. 112, 8747 (2000)]
- Correction to The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States.
- Water Assisted Proton Transport in Confined Nanochannels
- Unraveling the Mystery of ATP Hydrolysis in Actin Filaments
- A Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water.
- Extending parallel scalability of LAMMPS and multiscale reactive molecular simulations
- Systematic Coarse-Graining of Biomolecular Systems
- Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation
- Emergent scar lines in chaotic advection of passive directors
- The Origin of Coupled Chloride and Proton Transport in a Cl−/H+ Antiporter
- Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6)
- Coarse-grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding the Origins of a MARTINI Hangover
- Vibrational energy relaxation dynamics of SiH stretching modes on stepped H/Si(111) 1×1 surfaces
- Charge-Transfer Dynamics in Blue Copper Proteins: Experiment and Simulation
- Entropic Forces Drive Clustering and Spatial Localization of Influenza A M2 During Viral Budding
- Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2
- Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics
- Molecular Dynamics Simulations of Hydroxide Solvation and Transport in Anionic Exchange Membranes
- WORKSHOP ON TIME-DEPENDENT QUANTUM MOLECULAR DYNAMICS
- Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments.
- Molecular Origins of the Barriers to Proton Transport in Acidic Aqueous Solutions.
- Progress towards Robust Anion Exchange Membranes for Fuel Cell Applications
- A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.
- Multiscale Molecular Simulations at the Petascale (Parallelization of Reactive Force Field Model for Blue Gene/Q)
- Submission PDF Entropic Forces Drive Clustering and Spatial Localization of Influenza A M 2 During Viral Budding
- Exploration of the flow field around an oscillating sphere using 3D particle tracking velocimetry
- Structural basis for polarized elongation of actin filaments
- Molecular Dynamics Simulations of Proton Transport in 3 M and Na fi on Per fl uorosulfonic Acid Membranes
- Binding mechanism of the matrix domain of HIV-1 gag on lipid membranes
- Development of an All-Atom/Coarse Grain, Mixed Resolution Model for Proteins and their Environment
- Special Issue on Free Energy.
- Fundamental Studies of Alkaline Exchange Membranes towards Optimization in a Fuel Cell Environment
- Author response: Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks
- Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia crosslinker fascin
- Erratum: A solid-solid phase transition in carbon dioxide at high pressures and intermediate temperatures (Nature Communications (2013) 4 (2647) DOI 10.1038/ncomms3647)
- Using Cavitation as a Probe of Low-Pressure Filaments in Turbulence
- OKE Spectroscopy and Molecular Dynamics Simulations of Nonpolar and Polar Molecules in Ionic Liquids
- Membrane-mediated forces can stabilize tubular assemblies of I-Bar proteins
- Experimental and Theoretical Probing of Molecular Dynamics at Catalytic and Ionic Liquid Interfaces
- Corrigendum: A solid-solid phase transition in carbon dioxide at high pressures and intermediate temperatures.
- Binding Mechanism of the Matrix Domain of HIV-1 Gag on Lipid Membranes
- Actin Filament Nucleation is Influenced by Electrostatic Interactions with the Bni1p Formin FH2 Domain
- Measurements of Accelerations of Large Neutrally-buoyant Particles in Intense Turbulence
- Alignment of Disks with Lagrangian Stretching in Turbulence
- Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics
- New Insights into the Conformational Activation of Full-Length Integrin
- Structural basis of fast- and slow-severing actin–cofilactin boundaries
- Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles.
- Mechanical and kinetic factors drive sorting of F-actin crosslinkers on bundles
- Structural basis for polarized elongation of actin filaments
- Invited) Thin Robust Anion Exchange Membranes for Fuel Cell Applications
- Local conformational dynamics regulating transport properties of a Cl−/H+ antiporter
- S 1 Supplementary Information Effective Force Coarse-Graining
- Effects of Particle Size on Acceleration Measurements in Intense Turbulence
- Friction Mediates Scission of Membrane Nanotubes Scaffolded by BAR Proteins
- Multiscale Simulation of Multiprotein Assemblies: The Challenges of Ultra-Coarse-Graining
- Coarse-Grained Analysis and Modeling of Nucleotide-Dependent Changes in F-Actin
- Understanding Ionic Liquids Through Atomistic and Coarse-Grained Molecular Dynamics Simulations
- Density Functional Theory-based Quantum Mechanics/Coarse-grained Molecular Mechanics: Theory and Implementation.
- Voth Lightning Talk Slide NSF-SSE OAC-1740211
- Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis.
- The orientation field of fibers advected by a two-dimensional chaotic flow
- Insights into the cooperative nature of ATP hydrolysis in actin filaments
- Technologies for Developing Predictive Atomistic and Coarse-Grained Force Fields for Ionic Liquid Property Prediction
- Orientations of High-Concentration Fibers in Turbulence
- Experimental measurements of time dependent structure in shock waves and gravitational‐collapse of a granular gas
- Integrin Catch Bond Kinetics Mediate Mechanosensing during Cell Spreading
- What correlations between velocity differences and velocity sums tell us about small scale universality
- Molecular dynamics of synthetic ion channels in a lipid membrane
- Design Principles for Functionalized Surfaces
- NANO HIGHLIGHT Nano Carbon Particles in the Atmosphere: Formation and Transformation NSF NIRT Grant EEC030443
- Semiclassical Reactive Flux Method for the Calculation ONR N 00014-92-J-1243 of Condensed Phase Activated Rate Constants
- 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.
- Where Do We Get the Helium We Use
- Modeling the Cooperativity of Tropomyosin Binding to Actin Filaments
- The lamellipodium is a myosin independent mechanosensor
- Exploring Protein Conformational Change Using The Double Well Network Model
- Author response: Binding mechanism of the matrix domain of HIV-1 gag on lipid membranes
- Measurements of the Motion and Orientation of Rods in 2D Chaotic flow
- What Coordinate Best Describes the Affinity of the Hydrated Excess Proton for the Air-Water Interface?
- 1 Spatial Heterogeneity in Ionic Liquids
- The Role of Intermolecular Interactions in the Polymerization of Actin by Formins
- Cholesterol Alters the Orientation and Activity of the Influenza Virus M2 Amphipathic Helix in the Membrane
- Inverse Coarse-Graining: A New Tool for Molecular Design
- Using machine learning to drive computational discovery in self-organizing material systems
- Ultra-coarse-grained (UCG) models for biomolecular simulations
- Workstation Cluster For High Energy Density Matter Simulations
- Synthesis, Characterization, and Simulation of Four-Armed Megamolecules.
- Simultaneous measurements of velocity gradients and rod rotation in 3D turbulence
- Coarse-Grained Molecular Dynamics Simulations of TRIM5α Self-Assembly and Restriction of HIV
- Single particle measurements of material line stretching in turbulence: Experiments
- Visualizing Orientation Fields of Fibers Advected in Turbulent and Chaotic Flows
- Design of Energetic Ionic Liquids (Challenge Project C2H) (Preprint)
- Lipid-Lipid and Lipid-Protein Interactions of the Matrix Domain of HIV-Gag at the Viral Assembly Site
- Can quantum transition state theory be defined as a t=0+ limit?
- If Water Boils at 100[degrees]c, How Can a Glass Full of Water Evaporate at Room Temperature? - Why Do Glaciers Look Blue? - How Many Substances, Besides Water, Are Less Dense in Their Solid State Than in Their Liquid State?
- Design of Energetic Ionic Liquids
- Quantum Mechanical Calculations of Tunneling Rates in Condensed Phase Systems
- Endophilin N-BAR Domains-induced Membrane Remodeling Revealed by Molecular Dynamics Simulations
- Preservation of HIV-1 Gag helical bundle symmetry by bevirimat is central to maturation inhibition
- New Materials Design
- Measurements of inertial range scaling in rotations of rigid particles in turbulence
- Quantifying the Effects of Large Scale Intermittency in Turbulence
- Measurements of Inertial Torques on Sedimenting Fibers
- Simulation of proton exchange at the mineral water interface
- Fluctuations in the energy input determine Kolmogorov constants in turbulence
- Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport.
- Experimental And Theoretical Study Of Charge-transfer Dynamics In Biue Copper Proteins
- Integrin-Based Mechanosensing is Mediated by Conformational Activation
- Coarse-Grained Simulations of Membrane Remodeling by Bar Domains
- Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale.
- Experimental measurements of flow topology in chaotic mixing
- Size effects in the turbulent tumbling of thin rods and large particles
- CHSSI: Scalable Software for Bridging Atomistic and Continuum Simulations
- Exploring the Morphological Landscape of Self-Assembled Hiv-1 Proteins from a Coarse-Grained Perspective
- Third generation multi-state empircal valence bond model for bulk water Molecular dynamics simulations of multiple protons in bulk water
- Measuring the orientation and rotation rate of 3D printed particles in turbulent flow
- Computer Simulations of Proton Channels
- Theoretical Studies of Intramolecular Dynamics and Energy Redistribution
- Computational Model of Integrin Clustering in Response to Actin Turnover
- Conformational Transitions of Heat Shock Proteins: The Case of Hsp90
- Multiscale Simulation of Protein Assemblies
- Final Report: Computer Simulation of Proton Transport in Fuel Cell Membranes
- Understanding the Role of RNA in Driving the Clustering of HIV Gag Molecules using Coarse-Grained Molecular Dynamics Models
- Computer Simulation of Proton Transport in Fuel Cell Membranes
- Reshaping Biological Membranes: From Molecular Interactions to Macroscopic Mechanics
- Simulations of N-BAR Protein Interactions with Membranes.
- How Shape, Flexibility, and Crowding affect Curvature Sensing and Generation by Generic Scaffolding Proteins
- Molecular Dynamics of Bond-Braking Electron-Transfer Reactions at Metal-Liquid Interfaces
- Design of Energetic Ionic Liquids (Preprint)
- Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as substrates for proteolytic maturation
- Designing a Robust Micromixer Based on Fluid Stretching
- Proton Solvation and Transport in Aqueous Environments
- Mechanical and Kinetic Factors Drive Sorting of Actin Crosslinkers
- Rotation rate of rods in turbulent flow
- Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining.
- Unraveling N-BAR Domain Initiated Membrane Remodeling
- Quantum Simulations of Low Temperature High Energy Density Matter
- Understanding the Essential Nature of the Hydrated Excess Proton Through Simulation and Interpretation of Recent Spectroscopic Experiments
- Systematic Coarse-graining and Multiscale Modeling of Soft Matter [PowerPoint Submission]
- Quaternary Phosphonium Based Hydroxide Exchange Membranes: Synthesis, MEA Performance, and Hydroxide Transport Studies
- Multi-Scale Simulation of High Energy Density Ionic Liquids
- Multiscale model of integrin adhesion assembly
- Activation of Integrin: A Multiscale Computational Study
- Highly parallel proton transport simulations on Blue Gene/Q
- Quantum Rate Theory: A Path Integral Centroid Perspective
- S 1 Supporting information for : Pd ( II ) and Ni ( II ) complexes featuring a “ phosphasalen ” ligand : synthesis and DFT study
- Mesoscale Simulations of Hydroxide Transport in Polymeric Anion Exchange Membranes
- Reactive Molecular Dynamics Simulations of Proton Exchange Membranes
- Membrane Remodeling By N-bar Domains At All Scales: Theory And Simulation Of The Ensemble Effect
- Reynolds number scaling of Lagrangian accelerations
- The role of protein interactions in HIV-1 Capsid Shape and Stability: A Multiscale Analysis
- A Computational Cluster for Multiscale Simulations of Ionic Liquids
- Quantum Dynamical Simulations of Charge Transport and Energy Relaxation in the Condensed Phase
- Experimental measurements of the collapse of a 2D granular gas under gravity
- \textbf{Creating a Community to Strengthen the Broader Impacts of Condensed Matter Physics Research}
- Proton Transport Pathways in [NiFe]-Hydrogenase B
- Gravitational-Inelastic Collapse of a Granular Gas
- Real-time Image Compression for Lagrangian Particle Tracking
- Mechanism of Proton Transport in Proton Exchange Membranes: Insights from Computer Simulation
- Computational Modeling of Ena/VASP Interacting with Actin Filament to Understand its Processivity
- Computer Simulations of Low Temperature High Energy Density Materials
- Molecular Dynamics Simulation of the ENTH Domain on Lipid Bilayer
- The Internal Structure and Velocity Distribution of a Granular Shock
- Rotations of long, inertialess rods in turbulence
- Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT
- Simultaneous measurements of velocity gradients and tumbling motion of rods in 3D turbulence
- Quantum Simulation of Heterogeneous Electron Transfer Free Energies at the Water-Metal Interface
- Publisher’s Note: “Ab initio molecular dynamics simulation of the H/InP(100)–water interface” [J. Chem. Phys. 117, 872 (2002)]
- Defense Technical Information Center Compilation Part Notice ADP 023774 TITLE : Design of Energetic Ionic Liquids
- DoD High Performance Computing Challenge Project
- Theoretical Studies of the Dynamics of Condensed Phase High Energy Density Materials.
- Measurements of Anisotropy in Turbulence using SO(3) decomposition
- Effects of Large Scale Intermittency on Small Scale Turbulence
- Measuring the effects of large scale intermittency on the small scales of turbulent flows
- Molecular Dynamics Simulation of Excess Proton Solvation and Transport in Polymer Electrolyte Membranes
- Two point correlations between velocity sums and differences in turbulence
- What is coarse-graining and can it be done rigorously ?
- Computational Model of RGD-Containing Computational Model of RGD-Containing Peptides and Their Effects on Integrin Binding
- PROOF COPY 509037JCP Modeling the free energy surfaces of electron transfer
- Measuring anisotropy as a function of scale in turbulence using 3D particle tracking
- Systematic Coarse-graining of Molecular Dynamics Simulations
- Immature HIV-1 Lattice Assembly Dynamics are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane
- Organization of I-BAR Proteins on Tubular and Vesicular Membranes
- Multiscale Simulation of Proton Exchange Membranes
- Coarse-graining of many-body path integrals: Theory and numerical approximations.
- Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis
- F eb 2 00 2 O rdered clusters and dynam icalstates ofparticles in a vibrated uid
- Multiscale Kinetic Modeling of a Cl - /H + Antiporter: Integrating Simulation and Experiment to Characterize A Complex Ion Exchange Process
- Modeling Protein-Lipid Interactions during Viral Assembly of SARS-CoV-2
- Modulating the Chemical Transport Properties of the CLC Antiporter via Alternative Anion Flux and Mutation
- Proton Transport Through Channels: Insights and Surprises from Molecular Simulation
- Measurements of orientation, sedimentation, and dispersal of ramified particles in isotropic turbulence
- Lagrangian Stretching and the Dynamics of Anisotropic Particles in Turbulence
- Molecular Origins of Cofilin-Linked Changes in Actin Filament Mechanics
- Formin Cdc12's specific actin assembly properties are tailored for cytokinesis in fission yeast.
- Molecular Simulations of Proton and Hydroxide Transport in Fuel Cell Membranes
- Gating Mechanisms during Actin Filament Elongation by Formins
- Chaotic Mixing of Viscoelastic Flows [1]
- Selective Targeting of Lipid Droplets by Proteins
- Lord Kelvin's isotropic helicoid
- A Quantitative Paradigm for Water Assisted Proton Transport Through Proteins and Other Confined Spaces
- PNAS Plus Significance Statements
- Scar lines and topological singularities in the orientation field of fibers advected in fluid flows
- Coarse-Grained and Atomistic Simulations of the Mature HIV Capsid and Related Restriction Factors
- Specific Cation Binding Stiffens Actin Filaments by Adhering D-Loops to Adjacent Monomers
- Protein aggregation and protein-membrane interactions of the matrix (MA) domain of HIV-1 Gag protein
- Systematically Defining Coarse-Grained Representations of Large Biomolecular Complexes
- Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid Membranes
- 3D Particle Tracking in Turbulent Flows using Real-time Image Compression
- Models of Heterogenous Actin Filaments
- The Mechanism of Action for Drugs that Undermine HIV-1 Viral Capsid Formation and Activity: Insights from Large-Scale Coarse-Grained Simulations
- CONDENSED-PHASE CHEMISTRY THROUGH MOLECULAR DYNAMICS SIMULATION
- Nano Carbon Particles in the Atmosphere: Formation and Transformation
- Atomistic Simulations of Hydroxide Solvation and Transport in Anionic Exchange Membranes with Benzyltrimethylammoinum Cations
- Effects of Inhomogeneity and Large Scale Intermittency on Small Scale Turbulence
- Simulating Protein-Mediated Membrane Remodeling at Multiple Scales
- Computer Simulation of Excess Proton Solvation and Transport
- Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core
- Clustering Instability of Fiber Suspensions in Turbulent Shear Flows
- Statistics of Lagrangian Variables in High Reynolds Number Turbulence
- Inertial Range Scaling of Rotation Rates of Particles in Turbulence
- Measuring anisotropy of conditional structure functions in turbulence using real-time image compression
- Author response: Gating mechanisms during actin filament elongation by formins
- All-Atom Simulation and Coarse-Grained Analysis of the Rigor Actomyosin System
- Computational Studies in Molecular Geochemistry and Biogeochemistry
- Relating Molecular Interactions with N-BAR Domains to the Mesoscopic Nature of Membrane Remodeling
- The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water.
- Multiscale Simulation of Proteins at the Membrane-Cytoskeleton Interface
- Free Energy Calculations along Complex Proton Transport Pathways
- Computer for AB Initio Molecular Dynamics Simulations
- Shaping and scission of membranes with BAR domain proteins
- Membrane Curvature - the Assembler of Proteins
- Rotation rate of tracer and long rods in turbulence
- Chloride Enhances Fluoride Transport in Anion Exchange Membranes
- Modeling Synthesized Protein Megamolecules: Structure, Dynamics, and Functions
- Editorial overview: COSB biophysical and computational methods.
- Measuring the effects of finite length of rods on rotation rate in turbulent flow
- Accelerations of Finite Size Particles in Turbulence
- Mechanism of Protein Targeting to Lipid Droplets
- Systematic Coarse-Graining of Peptides to Understand their Effective Molecular Interactions
- Simulation Reveals Fundamental Behavior of the Actin Filament and Arp2/3 Branch Junction
- Lagrangian Measurements of Vorticity and the Rotational Dyanmics of Anisotropic Particles in Turbulence
- Scalable Software for Quantum Molecular Dynamics
- Molecular motors work with protein scaffolds to drive fission of membrane tubules.
- Measurements of Deformations of Fibers and Multi-armed Particles in Fluid Flows
- Measuring the rotation rate of rod-shaped particles in 3D turbulence
- Preferential sampling of Lagrangian velocity gradients by tumbling rods in turbulence
- Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites.
- Experimental measurement of the stress tensor in a granular gas
- Chaotic mixing of polymer solutions: Transport, local flow analysis, and time reversibility
- Alignment and rotation of anisotropic particles in complex flows
- Precision 3D measurements of the flow around oscillating spheres

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