Search filters

List of works by Gregory A. Voth

A Bayesian statistics approach to multiscale coarse graining

scientific article published in December 2008

A Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles

scientific article

A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models

scientific article

A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models

scientific article

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

scientific article published on 02 October 2020

A Multiscale Description of Biomolecular Active Matter: The Chemistry Underlying Many Life Processes

scientific article published on March 2017

A comparative study of imaginary time path integral based methods for quantum dynamics

scientific article published in April 2006

A computational study of the closed and open states of the influenza a M2 proton channel

scientific article

A computer simulation model for proton transport in liquid imidazole

scientific article published in April 2009

A computer simulation study of the hydrated proton in a synthetic proton channel

scientific article

A derivation of centroid molecular dynamics and other approximate time evolution methods for path integral centroid variables

article

A multistate empirical valence bond description of protonatable amino acids

scientific article published in January 2006

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

scientific article published on 01 January 2021

A quantitative assessment of the accuracy of centroid molecular dynamics for the calculation of the infrared spectrum of liquid water.

scientific article published in January 2010

A reductionist perspective on quantum statistical mechanics: Coarse-graining of path integrals

scientific article published in September 2015

A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor

scientific article published on December 2009

A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics

scientific article published in February 2006

A solid-solid phase transition in carbon dioxide at high pressures and intermediate temperatures.

scientific article published in January 2013

A systematic methodology for defining coarse-grained sites in large biomolecules

scientific article published on 29 August 2008

A theory for the thermally activated rate constant in systems with spatially dependent friction

scientific article published in May 1993

Ab Initio Calculations of Reactive Pathways for α-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (α-HMX)

article

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

scientific article published in 2001

Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals. III. Comparison with Born–Oppenheimer dynamics

scientific article published on 15 November 2002

Ab initio molecular dynamics: Propagating the density matrix with gaussian orbitals. IV. Formal analysis of the deviations from born-oppenheimer dynamics

scientific article published in December 2002

Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited

scientific article published in July 2005

Ab initiomolecular dynamics: Propagating the density matrix with Gaussian orbitals

scientific article published on 8 June 2001

Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory

scientific article published on 14 September 2021

Accurate p<i>K</i><sub>a</sub> Calculations in Proteins with Reactive Molecular Dynamics Provide Physical Insight Into the Electrostatic Origins of Their Values

scientific article published in 2022

Actin Filament Strain Promotes Severing and Cofilin Dissociation

scientific article published in June 2017

Actin filament remodeling by actin depolymerization factor/cofilin

scientific article

Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining

scientific article published on 01 September 2019

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis

scientific article

An analysis of hydrated proton diffusion in ab initio molecular dynamics

scientific article published in January 2015

Application of the SCC-DFTB method to hydroxide water clusters and aqueous hydroxide solutions

scientific article published on 22 April 2013

Atom-Centered Density Matrix Propagation (ADMP): Generalizations Using Bohmian Mechanics†

scientific article published in September 2003

Atomic crystal and molecular dynamics simulation structures of human carbonic anhydrase II: insights into the proton transfer mechanism

scientific article

Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6)

scientific article published on 16 September 2020

Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility

scientific article published on 6 October 2006

Autoinhibition of endophilin in solution via interdomain interactions

scientific article published in January 2013

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel

scientific article

Bottom-up Coarse-Graining: Principles and Perspectives

scientific article published in 2022

Bridging microscopic and mesoscopic simulations of lipid bilayers

scientific article

Calculating the bulk modulus for a lipid bilayer with nonequilibrium molecular dynamics simulation

scientific article

Can quantum transition state theory be defined as an exact t = 0+ limit? ⬇️

scientific article published in February 2016

Cations Stiffen Actin Filaments by Adhering a Key Structural Element to Adjacent Subunits

scientific article published on 04 May 2016

Centroid Molecular Dynamics Can Be Greatly Accelerated through Neural Network Learned Centroid Forces Derived from Path Integral Molecular Dynamics

scientific article published in 2022

Charge delocalization in proton channels, I: the aquaporin channels and proton blockage

scientific article

Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity

scientific article

Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II ⬇️

scientific article published on March 31, 2011

Chloride Enhances Fluoride Mobility in Anion Exchange Membrane/Polycationic Systems

article

Coarse-Grained Directed Simulation

scientific article published on 11 August 2017

Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover

scientific article published on 21 January 2021

Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies ⬇️

scientific article published on 06 July 2012

Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data

scientific article published on 23 August 2010

Coarse-Graining of Imaginary Time Feynman Path Integrals: Inclusion of Intramolecular Interactions and Bottom-up Force-Matching

scientific article published in 2022

Coarse-grained free energy functions for studying protein conformational changes: a double-well network model

scientific article

Coarse-grained modeling of the actin filament derived from atomistic-scale simulations

scientific article

Coarse-grained peptide modeling using a systematic multiscale approach

scientific article published on 30 March 2007

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

scientific article

Coarse-graining in interaction space: a systematic approach for replacing long-range electrostatics with short-range potentials

scientific article published on 27 March 2008

Coarse-graining involving virtual sites: Centers of symmetry coarse-graining

scientific article published on 01 April 2019

Coarse-graining methods for computational biology

scientific article published on 28 February 2013

Coarse-graining of many-body path integrals: Theory and numerical approximations

scientific article published on 01 June 2019

Coarse-graining of multiprotein assemblies ⬇️

scientific article published on January 23, 2012

Coarse-graining provides insights on the essential nature of heterogeneity in actin filaments

scientific article

Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data

scientific article

Compatible observable decompositions for coarse-grained representations of real molecular systems

scientific article published on 01 October 2019

Competition between Tropomyosin, Fimbrin, and ADF/Cofilin drives their sorting to distinct actin filament networks

scientific article published on 10 March 2017

Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments

scientific article published on 18 February 2021

Computational studies of proton transport through the M2 channel

scientific article

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

scientific article

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins

scientific article published on 6 January 2016

Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway

scientific article

Computer simulation of proton solvation and transport in aqueous and biomolecular systems

scientific article

Conformational Switching between Protein Substates Studied with 2D IR Vibrational Echo Spectroscopy and Molecular Dynamics Simulations ⬇️

scientific article published on December 3, 2010

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

scientific article published on 22 February 2022

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

preprint published on 7 June 2021

Correction to The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States

scientific article published on 06 March 2018

Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.

scientific article

Coupling field theory with continuum mechanics: a simulation of domain formation in giant unilamellar vesicles

scientific article

Coupling field theory with mesoscopic dynamical simulations of multicomponent lipid bilayers

scientific article

Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton

scientific article published on 23 September 2010

Defining coarse-grained representations of large biomolecules and biomolecular complexes from elastic network models.

scientific article

Delocalization and stretch-bend mixing of the HOH bend in liquid water.

scientific article published in August 2017

Designing Alkaline Exchange Membranes from Scratch

Designing free energy surfaces that match experimental data with metadynamics

scientific article

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

scientific article

Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations

scholarly article

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules

scientific article published on 16 August 2019

Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

scientific article published on April 2015

Dynamic force matching: Construction of dynamic coarse-grained models with realistic short time dynamics and accurate long time dynamics

scientific article

Early Stages of the HIV-1 Capsid Protein Lattice Formation ⬇️

scientific article published on October 16, 2012

Effect of active-site mutation at Asn67 on the proton transfer mechanism of human carbonic anhydrase II.

scientific article published on August 2009

Effect of membrane environment on proton permeation through gramicidin A channels

scientific article

Effective force coarse-graining

scientific article published on 12 February 2009

Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method

scientific article published in April 2005

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching

scientific article published in June 2004

Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain

scientific article published on October 2013

Efficient Multistate Reactive Molecular Dynamics Approach Based on Short-Range Effective Potentials

scientific article published in October 2010

Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

scientific article

Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining.

scientific article published on 27 January 2010

Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase

scientific article published in December 2014

Electrostatic interactions between the Bni1p Formin FH2 domain and actin influence actin filament nucleation

scientific article

Elucidation of the proton transport mechanism in human carbonic anhydrase II.

scientific article published on June 2009

Enhancement of Proton Conductance by Mutations of the Selectivity Filter of Aquaporin-1 ⬇️

scientific article published on January 28, 2011

Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding

article published in the Proceedings of the National Academy of Sciences of the United States of America

Evaluation of nonlinear quantum time correlation functions within the centroid dynamics formulation

scientific article published in September 2006

Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules

scientific article

Expanding the view of proton pumping in cytochrome c oxidase through computer simulation ⬇️

scientific article published on December 8, 2011

Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction

scientific article

Exploring the behaviour of the hydrated excess proton at hydrophobic interfaces

scientific article published in January 2013

Extending a spectrin repeat unit. I: linear force-extension response

scientific article

Extending a spectrin repeat unit. II: rupture behavior

scientific article

Extending the fluctuation theorem to describe reaction coordinates

scientific article published in February 2007

Extending the range and physical accuracy of coarse-grained models: Order parameter dependent interactions.

scientific article published in July 2017

Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations

scientific article published on 9 May 2008

Fitting coarse-grained distribution functions through an iterative force-matching method.

scientific article

Flexible simple point-charge water model with improved liquid-state properties

scientific article

Further developments in the local-orbital density-functional-theory tight-binding method

scientific article

Gating mechanisms during actin filament elongation by formins

scientific article published on 23 July 2018

Gating of the mechanosensitive channel protein MscL: the interplay of membrane and protein

scientific article

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

scientific article

Highly Coarse-Grained Representations of Transmembrane Proteins.

scientific article published on 02 January 2017

Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations

scientific article published on January 2014

Hybrid Ab-Initio/Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-Centered Density Matrix Propagation (ADMP) Approach

scientific article published in April 2004

Hybrid coarse-graining approach for lipid bilayers at large length and time scales

scientific article published on April 2009

Hydrated Excess Protons Can Create Their Own Water Wires

scientific article published on 12 November 2014

Hydroxide Solvation and Transport in Anion Exchange Membranes

scientific article published on 30 December 2015

IR spectral assignments for the hydrated excess proton in liquid water.

scientific article

Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation

scientific article published on 01 January 2021

Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane

scientific article published on 7 November 2017

Infrared Spectrum of the Hydrated Proton in Water

scientific article published on 23 December 2010

Infrared spectroscopy and hydrogen-bond dynamics of liquid water from centroid molecular dynamics with an ab initio-based force field

scientific article published in October 2009

Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments

Insights into the mechanism of proton transport in cytochrome c oxidase

scientific article

Interactions of protein kinase C-α C1A and C1B domains with membranes: a combined computational and experimental study

scientific article

Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles

scientific article published on 10 March 2020

Interfacing molecular dynamics and macro-scale simulations for lipid bilayer vesicles

scientific article

Intricate Role of Water in Proton Transport through Cytochrome c Oxidase ⬇️

scientific article published on October 21, 2010

Intrinsic bending and structural rearrangement of tubulin dimer: molecular dynamics simulations and coarse-grained analysis

scientific article

Intrinsic bending of microtubule protofilaments

scientific article published in March 2011

Ion Transport through Ultrathin Electrolyte under Applied Voltages

scientific article published on 14 January 2015

Ion mixing, hydration, and transport in aqueous ionic systems

scientific article published in May 2015

Ionic Liquids

Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation ⬇️

scientific article published on December 17, 2011

Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis

scientific article published on 3 October 2011

Kinetics of proton migration in liquid water

scientific article published in January 2010

Lamellipodium is a myosin-independent mechanosensor

scientific article published on 27 February 2018

Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.

scientific article

Linear aggregation of proteins on the membrane as a prelude to membrane remodeling

scientific article

Local conformational dynamics regulating transport properties of a Cl- /H+ antiporter

scientific article published on 21 October 2019

Long-Range Organization of Membrane-Curving Proteins

scientific article published on 21 November 2017

Loss of the F-BAR protein CIP4 reduces platelet production by impairing membrane-cytoskeleton remodeling

scientific article

Massively parallel linear-scaling algorithm in an ab initio local-orbital total-energy method

Mechanism and Determinants of Amphipathic Helix-Containing Protein Targeting to Lipid Droplets

scientific article published on 8 January 2018

Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins ⬇️

scientific article published on March 2, 2011

Mechanisms of passive ion permeation through lipid bilayers: insights from simulations

scientific article

Mechanoregulated inhibition of formin facilitates contractile actomyosin ring assembly

scientific article published on 26 September 2017

Membrane Curvature - the Assembler of Proteins

Membrane binding and self-association of the epsin N-terminal homology domain

scientific article published on 24 August 2012

Membrane binding by the endophilin N-BAR domain

scientific article

Membrane docking geometry and target lipid stoichiometry of membrane-bound PKCα C2 domain: a combined molecular dynamics and experimental study

scientific article published on 24 July 2010

Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation

scientific article published on 26 February 2007

Membrane tension controls the assembly of curvature-generating proteins

scientific article

Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models

scientific article published on 01 July 2018

Mesoscopic lateral diffusion in lipid bilayers

scientific article

Mesoscopic modeling of bacterial flagellar microhydrodynamics

scientific article

Minimizing memory as an objective for coarse-graining

scientific article published in March 2013

Mixed Resolution Modeling of Interactions in Condensed-Phase Systems

scientific article

Modeling real dynamics in the coarse-grained representation of condensed phase systems

scientific article published in October 2006

Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux

scientific article published on 27 November 2018

Molecular Dynamics Simulations of Proton Transport in 3M and Nafion Perfluorosulfonic Acid Membranes

article

Molecular and Thermodynamic Insights into the Conformational Transitions of Hsp90 ⬇️

scientific article published on July 17, 2012

Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex

scientific article published on 19 September 2008

Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane

scientific article

Molecular dynamics simulation of proton transport through the influenza A virus M2 channel

scientific article

Molecular dynamics simulation of the energetic room-temperature ionic liquid, 1-hydroxyethyl-4-amino-1,2,4-triazolium nitrate (HEATN).

scientific article

Molecular mechanism of membrane binding of the GRP1 PH domain

scientific article

Molecular modeling and assignment of IR spectra of the hydrated excess proton in isotopically dilute water.

scientific article

Molecular origins of cofilin-linked changes in actin filament mechanics

scientific article published on 24 January 2013

Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants

scientific article published on 01 August 2018

Multi-scale modeling of phase separation in mixed lipid bilayers

scientific article

Multi-state Approach to Chemical Reactivity in Fragment Based Quantum Chemistry Calculations

scientific article published on 28 August 2013

Multiconfigurational Coarse-Grained Molecular Dynamics

scientific article published on 02 April 2019

Multiscale Kinetic Modeling Reveals an Ensemble of Cl-/H+ Exchange Pathways in ClC-ec1 Antiporter

scientific article published on 14 January 2018

Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter

scientific article published on March 2016

Multiscale coarse graining of liquid-state systems

Multiscale coarse-graining and structural correlations: connections to liquid-state theory

scientific article published on 30 March 2007

Multiscale coarse-graining of ionic liquids

scientific article published in March 2006

Multiscale coarse-graining of monosaccharides

scientific article published on 13 September 2007

Multiscale coarse-graining of the protein energy landscape

scientific article

Multiscale computer simulation of the immature HIV-1 virion ⬇️

scientific article published on November 3, 2010

Multiscale model of integrin adhesion assembly.

scientific article published on 4 June 2019

Multiscale modeling of biomolecular systems: in serial and in parallel

scientific article published on 23 March 2007

Multiscale reactive molecular dynamics ⬇️

scientific article published on December 14, 2012

Multiscale simulation of actin filaments and actin-associated proteins

scientific article published on 31 October 2018

Multiscale simulation of protein mediated membrane remodeling

scientific article

Multiscale simulation of transmembrane proteins.

scientific article

Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel

scientific article

Multiscale simulations of protein-facilitated membrane remodeling

scientific article published on 17 June 2016

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

scientific article

New and notable: key new insights into membrane targeting by proteins

scientific article published on February 2013

New insights into BAR domain-induced membrane remodeling

scientific article published on September 2009

Non-uniqueness of quantum transition state theory and general dividing surfaces in the path integral space.

scientific article

Nonlinear quantum time correlation functions from centroid molecular dynamics and the maximum entropy method

scientific article published in November 2008

Nucleotide regulation of the structure and dynamics of G-actin

scientific article

Nucleotide-dependent conformational states of actin

scholarly article

Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation

scientific article published on 19 June 2019

On the amphiphilic behavior of the hydrated proton: an ab initio molecular dynamics study

scientific article published in March 2005

On the origin of proton mobility suppression in aqueous solutions of amphiphiles

scientific article published on 22 July 2013

On the representability problem and the physical meaning of coarse-grained models

scientific article published in July 2016

Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes ⬇️

scientific article published on February 14, 2012

Organizing membrane-curving proteins: the emerging dynamical picture

scientific article published on 30 March 2018

Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II.

scientific article published on 31 July 2008

Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel

scientific article

Path Integral Coarse-Graining Replica Exchange Method for Enhanced Sampling

scientific article published in September 2014

Persistent Subdiffusive Proton Transport in Perfluorosulfonic Acid Membranes

scientific article published on 22 August 2014

Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis

scientific article published on 17 June 2021

Predicting the Sensitivity of Multiscale Coarse-Grained Models to their Underlying Fine-Grained Model Parameters

scientific article published on 13 July 2015

Preferred orientations of His64 in human carbonic anhydrase II

scientific article published on 24 February 2007

Probing selected morphological models of hydrated Nafion using large-scale molecular dynamics simulations

scientific article

Protein-mediated transformation of lipid vesicles into tubular networks

scientific article published on August 2013

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

scientific article

Proton conduction in exchange membranes across multiple length scales

scientific article

Proton movement and coupling in the POT family of peptide transporters

scientific article published on 27 November 2017

Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations

scientific article published on 13 April 2007

Proton transport behavior through the influenza A M2 channel: insights from molecular simulation

scientific article

Proton transport in carbonic anhydrase: Insights from molecular simulation

scientific article

Proton transport pathway in the ClC Cl-/H+ antiporter

scientific article published on July 2009

Proton transport under external applied voltage

scientific article published on 22 April 2014

Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel

scientific article published on 12 July 2019

Protons may leak through pure lipid bilayers via a concerted mechanism

scientific article

Quantum mechanics/coarse-grained molecular mechanics (QM/CG-MM).

scientific article published in January 2018

Quantum theory of multiscale coarse-graining

scientific article published in March 2018

Reactive Coarse-Grained Molecular Dynamics

scientific article published on 10 March 2020

Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization

scientific article published on 22 April 2017

Reconstructing atomistic detail for coarse-grained models with resolution exchange

scientific article

Reconstructing protein remodeled membranes in molecular detail from mesoscopic models ⬇️

scientific article published on April 18, 2011

Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation

scientific article

Reshaping Biological Membranes: From Molecular Interactions to Macroscopic Mechanics

Role of protein interactions in defining HIV-1 viral capsid shape and stability: a coarse-grained analysis

scientific article

Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane

scientific article published on 18 May 2022

Semiclassical approximations to quantum dynamical time correlation functions

Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics

scientific article

Single-molecule studies reveal a hidden key step in the activation mechanism of membrane-bound protein kinase C-α

scientific article

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes

scientific article published in January 2007

Solvent Free Ionic Solution Models from Multiscale Coarse-Graining

scientific article published on 27 November 2012

Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems

scientific article

Solvent-free lipid bilayer model using multiscale coarse-graining

scientific article published on April 2009

Special Issue on Free Energy

scientific article published in July 2014

Special pair dance and partner selection: elementary steps in proton transport in liquid water

scientific article

Static and Dynamic Correlations in Water: Comparison of Classical Ab Initio Molecular Dynamics at Elevated Temperature with Path Integral Simulations at Ambient Temperature

scientific article published on 09 March 2022

Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster

scientific article published on 20 February 2007

Strain and rupture of HIV-1 capsids during uncoating

scientific article published on 01 March 2022

Structural Basis of Membrane Bending by the N-BAR Protein Endophilin ⬇️

scientific article published on March 30, 2012

Structural basis for polarized elongation of actin filaments

scientific article published on 16 November 2020

Structure and dynamics of concentrated hydrochloric acid solutions

scientific article published in July 2010

Structure and dynamics of the actin filament

scientific article

Structure of hydrated Na-Nafion polymer membranes

scientific article published in December 2005

Structure of the liquid-vacuum interface of room-temperature ionic liquids: a molecular dynamics study

scientific article published in February 2006

Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites

scientific article published on 15 February 2019

Systematic coarse-graining of a multicomponent lipid bilayer

scientific article published on February 2009

Systematic multiscale parameterization of heterogeneous elastic network models of proteins

scientific article published on 25 July 2008

Systematic multiscale simulation of membrane protein systems

scientific article

The 2018 biomembrane curvature and remodeling roadmap

scientific article published on 20 July 2018

The Coupled Proton Transport in the ClC-ec1 Cl−/H+ Antiporter ⬇️

scientific article published on November 15, 2011

The Curious Case of the Hydrated Proton ⬇️

scientific article published on August 22, 2011

The Hydrated Proton at the Water Liquid/Vapor Interface

scientific article published in September 2004

The Origin of Coupled Chloride and Proton Transport in a Cl(-)/H(+) Antiporter

scientific article (publication date: 16 November 2016)

The Theory of Ultra-Coarse-Graining. 1. General Principles

scientific article published on 10 April 2013

The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation

scientific article published in December 2014

The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Rapid Local Equilibrium of Internal States

scientific article published on 23 January 2017

The computer simulation of proton transport in biomolecular systems

scientific article

The dynamic stress responses to area change in planar lipid bilayer membranes

scientific article

The formulation of quantum statistical mechanics based on the Feynman path centroid density. I. Equilibrium properties

The formulation of quantum statistical mechanics based on the Feynman path centroid density. II. Dynamical properties

The mechanism of proton exclusion in aquaporin channels

scientific article published in May 2004

The mesoscopic membrane with proteins (MesM-P) model

scientific article published in July 2017

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

scientific article published on June 2008

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

scientific article published on June 2008

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

scientific article published on July 2009

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials

scientific article published in April 2010

The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials

scientific article published in June 2011

The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems ⬇️

scientific article published on May 21, 2012

The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites

scientific article published in December 2015

The properties of ion-water clusters. I. The protonated 21-water cluster

scientific article

The properties of ion-water clusters. II. Solvation structures of Na+, Cl-, and H+ clusters as a function of temperature

scientific article

The role of amino acid sequence in the self-association of therapeutic monoclonal antibodies: insights from coarse-grained modeling

scientific article published on 25 January 2013

The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations

scientific article published in May 2010

The theory of electron transfer reactions: what may be missing?

scientific article published on 01 June 2003

Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem

scientific article published in September 2007

Transition-Tempered Metadynamics Is a Promising Tool for Studying the Permeation of Drug-like Molecules through Membranes

scientific article published on 6 September 2016

Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation

scientific article published in September 2014

Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding

article

Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems

scientific article published on 26 February 2018

Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability

scientific article published on 30 July 2019

Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations

scientific article published on 13 October 2007

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase

scientific article published on 23 May 2017

Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling

scientific article published on January 2013

Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling

scholarly article

Unraveling the mystery of ATP hydrolysis in actin filaments

scientific article

Unraveling the role of the protein environment for [FeFe]-hydrogenase: a new application of coarse-graining

scientific article published on 4 April 2013

Unusual "amphiphilic" association of hydrated protons in strong acid solution

scientific article published on 15 February 2008

Unusual hydrophobic interactions in acidic aqueous solutions.

scientific article published in May 2009

Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface

scientific article published on 01 September 2021

Using Machine Learning to Greatly Accelerate Path Integral <i>Ab Initio</i> Molecular Dynamics

scientific article published on 04 January 2022

Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis ⬇️

scientific article published on August 12, 2011

Water under the BAR ⬇️

scientific article published on September 22, 2010

Well-tempered metadynamics converges asymptotically

scientific article published on 18 June 2014

When Physics Takes Over: BAR Proteins and Membrane Curvature

scientific article

Paulina is supported by:

About Paulina

Help