Practical guide to replica exchange transition interface sampling and forward flux sampling

Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook

(2021) Peter G. Bolhuis et al.   Advanced Theory and Simulations

Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook

(2020) Sarwar Hussain et al.   JOURNAL OF CHEMICAL PHYSICS

Automatic error control during forward flux sampling of rare events in master equation models

(2020) Max C. Klein et al.   JOURNAL OF CHEMICAL PHYSICS

Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics

(2020) Ron Elber   Annual Review of Biophysics

Identification of a multi-dimensional reaction coordinate for crystal nucleation in Ni3Al

(2020) Yanyan Liang et al.   JOURNAL OF CHEMICAL PHYSICS

Role of pre-ordered liquid in the selection mechanism of crystal polymorphs during nucleation

(2020) Sarath Menon et al.   JOURNAL OF CHEMICAL PHYSICS

Forward Flux Sampling of Polymer Desorption Paths from a Solid Surface into Dilute Solution

(2020) Kyle J. Huston et al.   Polymers

Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis

(2019) Brian M. Bonk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PyRETIS 2: An improbability drive for rare events

(2019) Enrico Riccardi et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Forward flux sampling calculation of homogeneous nucleation rates from aqueous NaCl solutions

(2018) Hao Jiang et al.   JOURNAL OF CHEMICAL PHYSICS

Forward-flux sampling with jumpy order parameters

(2018) Amir Haji-Akbari   JOURNAL OF CHEMICAL PHYSICS

Local initiation conditions for water autoionization

(2018) Mahmoud Moqadam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics

(2018) David W. H. Swenson et al.   Journal of Chemical Theory and Computation

OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes

(2018) David W. H. Swenson et al.   Journal of Chemical Theory and Computation

Maximum Likelihood Analysis of Reaction Coordinates during Solidification in Ni

(2018) Grisell Díaz Leines et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Atomistic insight into the non-classical nucleation mechanism during solidification in Ni

(2017) Grisell Díaz Leines et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleation mechanism of clathrate hydrates of water-soluble guest molecules

(2017) Ryan S. DeFever et al.   JOURNAL OF CHEMICAL PHYSICS

PyRETIS: A well-done, medium-sized python library for rare events

(2017) Anders Lervik et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Fast Decorrelating Monte Carlo Moves for Efficient Path Sampling

(2017) Enrico Riccardi et al.   Journal of Physical Chemistry Letters

A one-way shooting algorithm for transition path sampling of asymmetric barriers

(2016) Z. Faidon Brotzakis et al.   JOURNAL OF CHEMICAL PHYSICS

Ordering effects of conjugate thermal fields in simulations of molecular liquids: Carbon dioxide and water

(2016) Harro R. Dittmar et al.   JOURNAL OF CHEMICAL PHYSICS

Practical and conceptual path sampling issues

(2015) P. G. Bolhuis et al.   European Physical Journal-Special Topics

Exact milestoning

(2015) Juan M. Bello-Rivas et al.   JOURNAL OF CHEMICAL PHYSICS

Easy Transition Path Sampling Methods: Flexible-Length Aimless Shooting and Permutation Shooting

(2015) Ryan Gotchy Mullen et al.   Journal of Chemical Theory and Computation

Direct calculation of ice homogeneous nucleation rate for a molecular model of water

(2015) Amir Haji-Akbari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two-component order parameter for quantifying clathrate hydrate nucleation and growth

(2014) Brian C. Barnes et al.   JOURNAL OF CHEMICAL PHYSICS

Probing Methane Hydrate Nucleation through the Forward Flux Sampling Method

(2014) Yuanfei Bi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automatic, optimized interface placement in forward flux sampling simulations

(2013) Kai Kratzer et al.   JOURNAL OF CHEMICAL PHYSICS

A variant of importance splitting for rare event estimation

(2011) Michael Amrein et al.   ACM Transactions on Modeling and Computer Simulation

On the Relation Between Projections of the Reweighted Path Ensemble

(2011) Peter G. Bolhuis et al.   JOURNAL OF STATISTICAL PHYSICS

The reweighted path ensemble

(2010) Jutta Rogal et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetics and mechanism of the unfolding native-to-loop transition of Trp-cage in explicit solvent via optimized forward flux sampling simulations

(2010) Camilo Velez-Vega et al.   JOURNAL OF CHEMICAL PHYSICS

The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures

(2010) Bin W. Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleation Pathways of Clathrate Hydrates: Effect of Guest Size and Solubility

(2010) Liam C. Jacobson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics

(2010) Baron Peters   MOLECULAR SIMULATION

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

(2009) Camilo Velez-Vega et al.   JOURNAL OF CHEMICAL PHYSICS

Nucleation of tetrahedral solids: A molecular dynamics study of supercooled liquid silicon

(2009) Tianshu Li et al.   JOURNAL OF CHEMICAL PHYSICS

Transition path sampling and forward flux sampling. Applications to biological systems

(2009) Fernando A Escobedo et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Development of an interatomic potential for the Ni-Al system

(2009) G.P. Purja Pun et al.   PHILOSOPHICAL MAGAZINE

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

(2008) Jarek Juraszek et al.   BIOPHYSICAL JOURNAL

Precision shooting: Sampling long transition pathways

(2008) Michael Grünwald et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2008) Ernesto E. Borrero et al.   JOURNAL OF CHEMICAL PHYSICS

Rare events via multiple reaction channels sampled by path replica exchange

(2008) Peter G. Bolhuis   JOURNAL OF CHEMICAL PHYSICS

Accurate determination of crystal structures based on averaged local bond order parameters

(2008) Wolfgang Lechner et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

(2008) Jerry B. Abrams et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Modeled As an Intermediate Element between Carbon and Silicon†

(2008) Valeria Molinero et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS