Multivariate moment closure techniques for stochastic kinetic models

The Journal of Chemical Physics
Eszter LakatosMichael P H Stumpf

Abstract

Stochastic effects dominate many chemical and biochemical processes. Their analysis, however, can be computationally prohibitively expensive and a range of approximation schemes have been proposed to lighten the computational burden. These, notably the increasingly popular linear noise approximation and the more general moment expansion methods, perform well for many dynamical regimes, especially linear systems. At higher levels of nonlinearity, it comes to an interplay between the nonlinearities and the stochastic dynamics, which is much harder to capture correctly by such approximations to the true stochastic processes. Moment-closure approaches promise to address this problem by capturing higher-order terms of the temporally evolving probability distribution. Here, we develop a set of multivariate moment-closures that allows us to describe the stochastic dynamics of nonlinear systems. Multivariate closure captures the way that correlations between different molecular species, induced by the reaction dynamics, interact with stochastic effects. We use multivariate Gaussian, gamma, and lognormal closure and illustrate their use in the context of two models that have proved challenging to the previous attempts at approximating s...Continue Reading

References

Feb 13, 2004·Bioinformatics·Thomas R KiehlMelvin K Simmons
May 17, 2005·Bulletin of Mathematical Biology·Isthrinayagy KrishnarajahGavin Gibson
Jun 15, 2006·Molecular Systems Biology·Naama Geva-ZatorskyUri Alon
Feb 16, 2007·Mathematical Biosciences·Isthrinayagy KrishnarajahGavin Gibson
Apr 20, 2007·Bulletin of Mathematical Biology·Abhyudai Singh, João Pedro Hespanha
Feb 20, 2008·PLoS Computational Biology·Joshua F ApgarBruce Tidor
Sep 23, 2008·Mathematical Biosciences·Kamil Erguler, Michael P H Stumpf
Jan 14, 2009·Nature Reviews. Genetics·Darren J Wilkinson
Jan 22, 2009·IET Systems Biology·C S Gillespie
Feb 11, 2009·Journal of the Royal Society, Interface·Tina ToniMichael P H Stumpf
Apr 10, 2009·The Journal of Chemical Physics·Chang Hyeong LeePilwon Kim
Jun 9, 2009·Journal of Theoretical Biology·Mukhtar Ullah, Olaf Wolkenhauer
Oct 21, 2009·BMC Bioinformatics·Michał KomorowskiDavid A Rand
Nov 6, 2009·Molecular Systems Biology·Brian MunskyMustafa Khammash
Feb 23, 2011·Mathematical Biosciences·Peter MilnerDarren J Wilkinson
May 10, 2011·Proceedings of the National Academy of Sciences of the United States of America·Michał KomorowskiMichael P H Stumpf
Aug 31, 2011·Proceedings of the National Academy of Sciences of the United States of America·Chris P BarnesMichael P H Stumpf
Feb 6, 2013·PLoS Computational Biology·Juliane LiepeMichael P H Stumpf
Apr 13, 2013·Current Opinion in Biotechnology·Paul KirkMichael P H Stumpf
Apr 23, 2013·Biophysical Journal·Michał KomorowskiMichael P H Stumpf
May 10, 2013·The Journal of Chemical Physics·Angelique AleMichael P H Stumpf
Aug 14, 2013·Proceedings of the National Academy of Sciences of the United States of America·Patrick Smadbeck, Yiannis N Kaznessis
Dec 11, 2013·Statistical Applications in Genetics and Molecular Biology·Dennis PrangleNigel P French
May 14, 2014·Statistical Applications in Genetics and Molecular Biology·Iain G Johnston
Jun 13, 2014·PLoS Computational Biology·Daniel SilkMichael P H Stumpf
Sep 1, 2014·The Journal of Chemical Physics·David SchnoerrRamon Grima
Dec 10, 2014·Methods in Molecular Biology·Patrick Smadbeck, Yiannis N Kaznessis
Feb 27, 2015·Statistical Applications in Genetics and Molecular Biology·Jamie OwenColin S Gillespie
May 17, 2015·The Journal of Chemical Physics·Patrick Smadbeck, Yiannis N Kaznessis
Sep 1, 2000·The Journal of Animal Ecology·Matt J Keeling

❮ Previous
Next ❯

Citations

Nov 17, 2015·The Journal of Chemical Physics·David SchnoerrRamon Grima
May 7, 2016·Bioinformatics·Sisi FanMichael P H Stumpf
Sep 9, 2016·Journal of the Royal Society, Interface·Lirong HuangHeinz Koeppl
Jul 1, 2017·Physical Biology·Khem Raj GhusingaAbhyudai Singh
Nov 21, 2017·PLoS Computational Biology·David J PriceOlivier Restif
Sep 8, 2017·Royal Society Open Science·Eszter Lakatos, Michael P H Stumpf
Jan 13, 2018·Journal of the Royal Society, Interface·Yuta Sakurai, Yutaka Hori
Mar 18, 2017·Reports on Progress in Physics·Markus F Weber, Erwin Frey
Sep 9, 2017·Bioinformatics·Dennis PischelRobert J Flassig
Aug 19, 2018·Nature Communications·Zhixing Cao, Ramon Grima
Jul 2, 2019·Frontiers in Genetics·Pavel LoskotLyudmila Mihaylova
Mar 29, 2020·Physical Review Letters·Lucy HamMichael P H Stumpf
Sep 2, 2020·Proceedings of the National Academy of Sciences of the United States of America·Lorenzo Duso, Christoph Zechner
Jan 8, 2018·The Journal of Chemical Physics·Leo Bronstein, Heinz Koeppl
Jul 22, 2019·The Journal of Chemical Physics·Juan KuntzMauricio Barahona
Dec 17, 2020·Journal of the Royal Society, Interface·Alexander P BrowningMatthew J Simpson
Nov 21, 2020·Physical Review. E·Yan-Mei Kang, Ruo-Nan Liu
Jun 26, 2021·Bioinformatics·Augustinas Sukys, Ramon Grima
Aug 4, 2021·Journal of the Royal Society, Interface·Tamara Kurdyaeva, Andreas Milias-Argeitis
Aug 13, 2021·PloS One·Abhyudai Singh

❮ 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.

Related Papers

The Journal of Chemical Physics
Angelique AleMichael P H Stumpf
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Tiago RamalhoTorsten A Ensslin
© 2021 Meta ULC. All rights reserved