(Q37407010)

20 August 2017

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages (English)

1 reference

20 August 2017

David D L Minh

1

1 reference

20 August 2017

John D Chodera

series ordinal

2

1 reference

20 August 2017

language of work or name

English

0 references

publication date

1 October 2009

1 reference

Journal of Chemical Physics

20 August 2017

1 reference

20 August 2017

131

1 reference

20 August 2017

13

1 reference

20 August 2017

134110

1 reference

Density-dependent analysis of nonequilibrium paths improves free energy estimates

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Far-from-equilibrium measurements of thermodynamic length

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Statistically optimal analysis of samples from multiple equilibrium states

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Exact low-force kinetics from high-force single-molecule unfolding events

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Free energy surfaces from single-molecule force spectroscopy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Equilibrium free energy estimates based on nonequilibrium work relations and extended dynamics.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Computing the optimal protocol for finite-time processes in stochastic thermodynamics.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Entropy-energy decomposition from nonequilibrium work trajectories.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Annealed importance sampling of peptides.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Multidimensional potentials of mean force from biased experiments along a single coordinate

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Optimal finite-time processes in stochastic thermodynamics.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Free-energy reconstruction from experiments performed under different biasing programs.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Optimal estimates of free energies from multistate nonequilibrium work data.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Theory of a systematic computational error in free energy differences.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

Nonequilibrium Equality for Free Energy Differences

2 September 2018

1 reference

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

21 January 2018

1 reference

Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems

21 January 2018

1 reference

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

Optimally combining sampling techniques for Monte Carlo rendering

21 January 2018

1 reference

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

1 reference

Recovery of free energy branches in single molecule experiments

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2771048

A theory of statistical models for Monte Carlo integration

2 October 2018

1 reference

Calculation of relative free energy via indirect pathways

21 January 2018

1 reference

Optimized Monte Carlo data analysis

21 January 2018

1 reference

12 December 2020

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

1 reference

12 December 2020

Single-ensemble nonequilibrium path-sampling estimates of free energy differences

1 reference

12 December 2020

Rare events and the convergence of exponentially averaged work values

1 reference

12 December 2020

Optimized free energies from bidirectional single-molecule force spectroscopy

1 reference

12 December 2020

Optimal protocols for minimal work processes in underdamped stochastic thermodynamics

1 reference

12 December 2020

Efficient extraction of free energy profiles from nonequilibrium experiments

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3242285

1 reference

20 August 2017

0 references

1 reference

20 August 2017

PubMed publication ID

19814546

1 reference