Efficient and exact sampling of transition path ensembles on Markovian networks

The Journal of Chemical Physics
Daniel J Sharpe, David J Wales

Abstract

The problem of flickering trajectories in standard kinetic Monte Carlo (kMC) simulations prohibits sampling of the transition path ensembles (TPEs) on Markovian networks representing many slow dynamical processes of interest. In the present contribution, we overcome this problem using knowledge of the metastable macrostates, determined by an unsupervised community detection algorithm, to perform enhanced sampling kMC simulations. We implement two accelerated kMC methods to simulate the nonequilibrium stochastic dynamics on arbitrary Markovian networks, namely, weighted ensemble (WE) sampling and kinetic path sampling (kPS). WE-kMC utilizes resampling in pathway space to maintain an ensemble of representative trajectories covering the state space, and kPS utilizes graph transformation to simplify the description of an escape trajectory from a trapping energy basin. Both methods sample individual trajectories governed by the linear master equation with the correct statistical frequency. We demonstrate that they allow for efficient estimation of the time-dependent occupation probability distributions for the metastable macrostates, and of TPE statistics, such as committor functions and first passage time distributions. kPS is part...Continue Reading

References

Jan 7, 1997·Proceedings of the National Academy of Sciences of the United States of America·R Zwanzig
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·A RojnuckarinS Subramaniam
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Nov 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Wei CaiVasily V Bulatov
Mar 15, 2003·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·J D MuñozS J Mitchell
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nancy M AmatoGuang Song
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mehmet Serkan ApaydinChris Varma
Jul 21, 2004·The Journal of Chemical Physics·David A Evans, David J Wales
Jul 23, 2004·The Journal of Chemical Physics·Anton K Faradjian, Ron Elber
Aug 18, 2004·Journal of Molecular Biology·Francesco Rao, Amedeo Caflisch
Dec 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Daan Frenkel
Jan 11, 2005·The Journal of Chemical Physics·Abhijit ChatterjeeMarkos A Katsoulakis
Feb 9, 2005·Physical Review Letters·Rosalind J AllenPieter Rein Ten Wolde
Mar 4, 2005·The Journal of Chemical Physics·Maurice de KoningVasily V Bulatov
May 28, 2005·The Journal of Chemical Physics·John Goutsias
Dec 3, 2005·The Journal of Chemical Physics·Weinan EEric Vanden-Eijnden
Jan 21, 2006·The Journal of Chemical Physics·Rosalind J AllenPieter Rein ten Wolde
Feb 8, 2006·The Journal of Chemical Physics·Brian Munsky, Mustafa Khammash
May 30, 2006·The Journal of Chemical Physics·Rosalind J AllenPieter Rein ten Wolde
Jun 28, 2006·The Journal of Physical Chemistry. B·Sergei V Krivov, Martin Karplus
Jun 29, 2006·Physical Review Letters·Sean X Sun
Jul 11, 2006·The Journal of Chemical Physics·Semen A Trygubenko, David J Wales
Jul 21, 2006·The Journal of Physical Chemistry. B·Ao Ma, Aaron R Dinner
Oct 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·J Juraszek, P G Bolhuis
Oct 14, 2006·Annual Review of Physical Chemistry·Daniel T Gillespie
Feb 3, 2007·Proceedings of the National Academy of Sciences of the United States of America·D GfellerF Rao
Mar 3, 2007·The Journal of Chemical Physics·Bin W ZhangDaniel M Zuckerman
Apr 28, 2007·The Journal of Chemical Physics·Frank NoéJeremy C Smith
Sep 4, 2007·The Journal of Chemical Physics·Georgios C Boulougouris, Doros N Theodorou
Sep 18, 2007·The Journal of Chemical Physics·Ben Harland, Sean X Sun
Sep 25, 2007·The Journal of Chemical Physics·Chantal ValerianiPieter Rein ten Wolde
Oct 24, 2007·The Journal of Chemical Physics·Aryeh WarmflashAaron R Dinner
Nov 6, 2007·The Journal of Chemical Physics·Ernesto E Borrero, Fernando A Escobedo
Nov 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Bin W ZhangDaniel M Zuckerman
Feb 1, 2008·The Journal of Physical Chemistry. B·Nicolae-Viorel Buchete, Gerhard Hummer
Apr 2, 2008·Current Opinion in Structural Biology·Frank Noé, Stefan Fischer
Jun 3, 2008·The Journal of Chemical Physics·Alexander SlepoySteven J Plimpton
Nov 27, 2008·Proceedings of the National Academy of Sciences of the United States of America·Daniel SchultzPeter G Wolynes
Dec 3, 2008·The Journal of Chemical Physics·Lijun Xu, Graeme Henkelman
Feb 26, 2009·The Journal of Chemical Physics·Alex DicksonAaron R Dinner
Aug 7, 2009·The Journal of Chemical Physics·Eric Vanden-Eijnden, Maddalena Venturoli

❮ Previous
Next ❯

Citations

Oct 10, 2020·The Journal of Chemical Physics·Thomas D SwinburneDavid J Wales
Jan 1, 2021·The Journal of Chemical Physics·Deepti KannanDavid J Wales
Jul 18, 2021·Physical Review. E·Daniel J Sharpe, David J Wales
Nov 4, 2020·Journal of Chemical Theory and Computation·Daniel NagelGerhard Stock

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.