4.5 Review

Forward flux sampling for rare event simulations

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

Hydrodynamic effects on the translocation rate of a polymer through a pore

Juan P. Hernandez-Ortiz et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol

Camilo Velez-Vega et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Evaluating nucleation rates in direct simulations

Guram Chkonia et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Nonequilibrium umbrella sampling in spaces of many order parameters

Alex Dickson et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Markovian milestoning with Voronoi tessellations

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Simulating the Kinetics and Thermodynamics of Transitions via Forward Flux/Umbrella Sampling

Ernesto E. Borrero et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Chemistry, Physical

Homogeneous Bubble Nucleation Driven by Local Hot Spots: A Molecular Dynamics Study

Zun-Jing Wang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Physics, Fluids & Plasmas

Statistical physics of a model binary genetic switch with linear feedback

Paolo Visco et al.

PHYSICAL REVIEW E (2009)

Article Multidisciplinary Sciences

DNA looping provides stability and robustness to the bacteriophage λ switch

Marco J. Morelli et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Biophysics

Reaction coordinates for the flipping of genetic switches

Marco J. Morelli et al.

BIOPHYSICAL JOURNAL (2008)

Review Biochemistry & Molecular Biology

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Arjun Raj et al.

Article Computer Science, Interdisciplinary Applications

Efficient path sampling on multiple reaction channels

Titus S. van Erp

COMPUTER PHYSICS COMMUNICATIONS (2008)

Article Chemistry, Physical

Nucleation in the presence of slow microscopic dynamics

Richard P. Sear

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Multiple state transition path sampling

Jutta Rogal et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch

Marco J. Morelli et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes

Ernesto E. Borrero et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Rare events via multiple reaction channels sampled by path replica exchange

Peter G. Bolhuis

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Homogeneous nucleation under shear in a two-dimensional Ising model: Cluster growth, coalescence, and breakup

Rosalind J. Allen et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

The rate constant of polymer reversal inside a pore

Lei Huang et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

On the assumptions underlying milestoning

Eric Vanden-Eijnden et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

Two-step vapor-crystal nucleation close below triple point

J. A. van Meel et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Review Chemistry, Physical

State-of-the-art models for the phase diagram of carbon and diamond nucleation

L. M. Ghiringhelli et al.

MOLECULAR PHYSICS (2008)

Article Physics, Multidisciplinary

Exact solution of a model DNA-inversion genetic switch with orientational control

Paolo Visco et al.

PHYSICAL REVIEW LETTERS (2008)

Article

Nucleation in a Sheared Ising Model: Effects of External Field

Rosalind J. Allen et al.

PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT (2008)

Article Chemistry, Physical

Reaction coordinates and transition pathways of rare events via forward flux sampling

Ernesto E. Borrero et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Umbrella sampling for nonequilibrium processes

Aryeh Warmflash et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Molecular simulations of droplet coalescence in oil/water/surfactant systems

Live Rekvig et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling

Chantal Valeriani et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Physics, Multidisciplinary

Local structure of liquid carbon controls diamond nucleation

L. M. Ghiringhelli et al.

PHYSICAL REVIEW LETTERS (2007)

Article Physics, Multidisciplinary

Evidence for out-of-equilibrium crystal nucleation in suspensions of oppositely charged colloids

Eduardo Sanz et al.

PHYSICAL REVIEW LETTERS (2007)

Article Chemistry, Physical

Extensions to the likelihood maximization approach for finding reaction coordinates

Baron Peters et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Physics, Multidisciplinary

Reaction rate calculation by parallel path swapping

Titus S. van Erp

PHYSICAL REVIEW LETTERS (2007)

Article Chemistry, Physical

Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide

Anthony M. A. West et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

New method to analyze simulations of activated processes

Jan Wedekind et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Physics, Multidisciplinary

Probing rare physical trajectories with Lyapunov weighted dynamics

Julien Tailleur et al.

NATURE PHYSICS (2007)

Article Materials Science, Multidisciplinary

Competitive nucleation and the Ostwald rule in a generalized Potts model with multiple metastable phases

David P. Sanders et al.

PHYSICAL REVIEW B (2007)

Article Physics, Multidisciplinary

Kinetic accessibility of buried DNA sites in nucleosomes

Wolfram Möbius et al.

PHYSICAL REVIEW LETTERS (2006)

Article Chemistry, Physical

Folding kinetics of a lattice protein via a forward flux sampling approach

Ernesto E. Borrero et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Physics, Multidisciplinary

Freezing of a Lennard-Jones fluid: From nucleation to spinodal regime

Federica Trudu et al.

PHYSICAL REVIEW LETTERS (2006)

Article Physics, Multidisciplinary

Heterogeneous nucleation in and out of pores

Amanda J. Page et al.

PHYSICAL REVIEW LETTERS (2006)

Article Chemistry, Physical

Obtaining reaction coordinates by likelihood maximization

Baron Peters et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

Forward flux sampling-type schemes for simulating rare events: Efficiency analysis

Rosalind J. Allen et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

Order-parameter-based Monte Carlo simulation of crystallization

M Chopra et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

Heterogeneous and homogeneous nucleation compared: Rapid nucleation on microscopic impurities

RP Sear

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Chemistry, Physical

Simulating rare events in equilibrium or nonequilibrium stochastic systems

RJ Allen et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Physics, Multidisciplinary

Interplay between structure and size in a critical crystal nucleus

D Moroni et al.

PHYSICAL REVIEW LETTERS (2005)

Article Chemistry, Physical

Rate of homogeneous crystal nucleation in molten NaCl

C Valeriani et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Multidisciplinary Sciences

Reaction coordinates and rates from transition paths

RB Best et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Computer Science, Interdisciplinary Applications

Elaborating transition interface sampling methods

TS van Erp et al.

JOURNAL OF COMPUTATIONAL PHYSICS (2005)

Article Physics, Fluids & Plasmas

Simultaneous computation of free energies and kinetics of rare events

D Moroni et al.

PHYSICAL REVIEW E (2005)

Article Chemistry, Physical

Automatic method for identifying reaction coordinates in complex systems

A Ma et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Chemistry, Physical

Chemical models of genetic toggle switches

PB Warren et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Chemistry, Physical

Finite temperature string method for the study of rare events

E Weinan et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2005)

Article Physics, Multidisciplinary

Sampling rare switching events in biochemical networks

RJ Allen et al.

PHYSICAL REVIEW LETTERS (2005)

Article Physics, Multidisciplinary

Enhancement of the stability of genetic switches by overlapping upstream regulatory domains

PB Warren et al.

PHYSICAL REVIEW LETTERS (2004)

Article Chemistry, Physical

Rate constants for diffusive processes by partial path sampling

D Moroni et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Chemistry, Physical

From transition paths to transition states and rate coefficients

G Hummer

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Multidisciplinary Sciences

Speed-up of Monte Carlo simulations by sampling of rejected states

D Frenkel

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Chemistry, Physical

Computing time scales from reaction coordinates by milestoning

AK Faradjian et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Chemistry, Multidisciplinary

Nucleation of hexagonal ice (Ih) in liquid water

R Radhakrishnan et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Article Chemistry, Physical

A novel path sampling method for the calculation of rate constants

TS van Erp et al.

JOURNAL OF CHEMICAL PHYSICS (2003)

Article Materials Science, Multidisciplinary

String method for the study of rare events

E Weinan et al.

PHYSICAL REVIEW B (2002)

Article Telecommunications

Analysis of RESTART simulation:: Theoretical basis and sensitivity study

M Villén-Altamirano et al.

EUROPEAN TRANSACTIONS ON TELECOMMUNICATIONS (2002)

Article Multidisciplinary Sciences

Drying-induced hydrophobic polymer collapse

PR ten Wolde et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Physics, Fluids & Plasmas

Efficient transition path sampling for nonequilibrium stochastic dynamics

GE Crooks et al.

PHYSICAL REVIEW E (2001)

Article Multidisciplinary Sciences

Reaction coordinates of biomolecular isomerization

PG Bolhuis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)