Rare switching events in non-stationary systems

The Journal of Chemical Physics
Nils B Becker, Pieter Rein ten Wolde

Abstract

Physical systems with many degrees of freedom can often be understood in terms of transitions between a small number of metastable states. For time-homogeneous systems with short-term memory these transitions are fully characterized by a set of rate constants. We consider the question how to extend such a coarse-grained description to non-stationary systems and to systems with finite memory. We identify the physical regimes in which time-dependent rates are meaningful, and state microscopic expressions that can be used to measure both externally time-dependent and history-dependent rates in microscopic simulations. Our description can be used to generalize Markov state models to time-dependent Markovian or non-Markovian systems.

References

Apr 25, 2002·Annual Review of Physical Chemistry·Peter G BolhuisPhillip L Geissler
Aug 11, 2005·Physical Review Letters·Yuhai Tu, G Grinstein
Sep 17, 2005·The Journal of Chemical Physics·YounJoon JungDavid Chandler
Jan 21, 2006·The Journal of Chemical Physics·Rosalind J AllenPieter Rein ten Wolde
Feb 21, 2006·Physical Review Letters·Ekaterina A KorobkovaPhilippe Cluzel
Sep 13, 2006·The Journal of Chemical Physics·Philipp MetznerEric Vanden-Eijnden
Aug 7, 2009·The Journal of Chemical Physics·Eric Vanden-Eijnden, Maddalena Venturoli
Oct 2, 2009·Physical Review Letters·J ProstJ M R Parrondo
Nov 6, 2009·Molecular Systems Biology·Siebe B van AlbadaPieter Rein ten Wolde
May 10, 2011·The Journal of Chemical Physics·Jan-Hendrik PrinzFrank Noé
May 16, 2012·The Journal of Chemical Physics·Nils B BeckerPieter Rein ten Wolde

❮ Previous
Next ❯

Citations

May 16, 2012·The Journal of Chemical Physics·Nils B BeckerPieter Rein ten Wolde
Sep 11, 2012·The Journal of Chemical Physics·Nathan Eidelson, Baron Peters
Sep 28, 2013·The Journal of Chemical Physics·Rory M DonovanDaniel M Zuckerman
Aug 9, 2016·The European Physical Journal. E, Soft Matter·S Jungblut, C Dellago
Jan 24, 2020·The Journal of Chemical Physics·Max C Klein, Elijah Roberts
Jul 17, 2020·The Journal of Chemical Physics·Daniel J Sharpe, David J Wales
Jul 13, 2017·Biophysical Journal·Joris PaijmansPieter Rein Ten Wolde
May 20, 2021·Physical Review. E·Gianmaria Falasco, Massimiliano Esposito

❮ Previous
Next ❯

Software Mentioned

langle cdots
hspace
qquad

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.

Related Papers

The Journal of Chemical Physics
Nils B BeckerPieter Rein ten Wolde
Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Alison OrdBruce E Hobbs
© 2021 Meta ULC. All rights reserved