(Q39399462)

11 September 2017

Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information (English)

1 reference

11 September 2017

1 reference

Christopher P Calderon

series ordinal

1

1 reference

11 September 2017

Lorant Janosi

series ordinal

2

1 reference

11 September 2017

Ioan Kosztin

series ordinal

3

1 reference

11 September 2017

language of work or name

English

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publication date

1 April 2009

1 reference

Journal of Chemical Physics

11 September 2017

1 reference

11 September 2017

130

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11 September 2017

14

1 reference

11 September 2017

144908

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Quantifying DNA melting transitions using single-molecule force spectroscopy

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Towards biomedical applications for nucleic acid nanodevices

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Single-molecule experiments in vitro and in silico

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Theoretical and computational models of biological ion channels

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Role of protein flexibility in ion permeation: a case study in gramicidin A.

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Nanoscale hydrodynamics: enhanced flow in carbon nanotubes

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Scalable molecular dynamics with NAMD

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Calculating potentials of mean force from steered molecular dynamics simulations

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Gating gramicidin channels in lipid bilayers: reaction coordinates and the mechanism of dissociation

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Energetics of ion conduction through the gramicidin channel

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Ten years of tension: single-molecule DNA mechanics

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Mechanical design of proteins studied by single-molecule force spectroscopy and protein engineering.

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Sequence-dependent mechanics of single DNA molecules.

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Kramers' diffusion theory applied to gating kinetics of voltage-dependent ion channels

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Optimal prediction of underresolved dynamics

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Reconstructing potential energy functions from simulated force-induced unbinding processes

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

VMD: visual molecular dynamics

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Extracting Kinetic and Stationary Distribution Information from Short MD Trajectories via a Collection of Surrogate Diffusion Models

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Quantifying multiscale noise sources in single-molecule time series

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Comment on "Free energy simulations of single and double ion occupancy in gramicidin A" [J. Chem. Phys. 126, 105103 (2007)].

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Approximating nonequilibrium processes using a collection of surrogate diffusion models.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

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

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Direct measurements of base stacking interactions in DNA by single-molecule atomic-force spectroscopy.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Extending the fluctuation theorem to describe reaction coordinates.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Dynamic coupling between coordinates in a model for biomolecular isomerization.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Coarse-grained kinetic computations for rare events: application to micelle formation.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Generalized Langevin equation with fractional Gaussian noise: subdiffusion within a single protein molecule.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

A molecular dynamics study of gating in dioxolane-linked gramicidin A channels

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2832035

Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach

21 August 2018

1 reference

Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems

21 January 2018

1 reference

Ca2+ dynamics in a population of smooth muscle cells: modeling the recruitment and synchronization

21 January 2018

1 reference

Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations

21 January 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

The Nonequilibrium Thermodynamics of Small Systems

21 January 2018

1 reference

On the use of local diffusion models for path ensemble averaging in potential of mean force computations

21 January 2018

1 reference

Vibrational excitation of CF4by electron impact: a computational analysis

21 January 2018

1 reference

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

21 January 2018

1 reference

12 December 2020

Structural biology. Dynamic visions of enzymatic reactions

1 reference

12 December 2020

Free energy simulations of single and double ion occupancy in gramicidin A

1 reference

12 December 2020

Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimators

1 reference

12 December 2020

Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling

1 reference

12 December 2020

Experimental free energy surface reconstruction from single-molecule force spectroscopy using Jarzynski's equality

1 reference

12 December 2020

Optimized free energies from bidirectional single-molecule force spectroscopy

1 reference

12 December 2020

Rare events and the convergence of exponentially averaged work values

1 reference

12 December 2020

Molecular dynamics simulations of gramicidin A in a lipid bilayer: from structure-function relations to force fields

1 reference

12 December 2020

Mechanics of binding of a single integration-host-factor protein to DNA

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3106225

1 reference

11 September 2017

1 reference

11 September 2017

PubMed publication ID

19368472

1 reference