The slow-scale linear noise approximation: an accurate, reduced stochastic description of biochemical networks under timescale separation conditions.

BMC Systems Biology
Philipp ThomasRamon Grima

Abstract

It is well known that the deterministic dynamics of biochemical reaction networks can be more easily studied if timescale separation conditions are invoked (the quasi-steady-state assumption). In this case the deterministic dynamics of a large network of elementary reactions are well described by the dynamics of a smaller network of effective reactions. Each of the latter represents a group of elementary reactions in the large network and has associated with it an effective macroscopic rate law. A popular method to achieve model reduction in the presence of intrinsic noise consists of using the effective macroscopic rate laws to heuristically deduce effective probabilities for the effective reactions which then enables simulation via the stochastic simulation algorithm (SSA). The validity of this heuristic SSA method is a priori doubtful because the reaction probabilities for the SSA have only been rigorously derived from microscopic physics arguments for elementary reactions. We here obtain, by rigorous means and in closed-form, a reduced linear Langevin equation description of the stochastic dynamics of monostable biochemical networks in conditions characterized by small intrinsic noise and timescale separation. The slow-scal...Continue Reading

References

Mar 1, 1968·European Journal of Biochemistry·E E Sel'kov
Jun 13, 2000·Nature·A Becskei, L Serrano
Dec 2, 2000·Nature Biotechnology·B SchwikowskiS Fields
Apr 23, 2002·Nature Genetics·Ertugrul M OzbudakAlexander van Oudenaarden
Nov 15, 2002·Nature·Christopher V RaoAdam P Arkin
Oct 17, 2003·Nature·Sina GhaemmaghamiJonathan S Weissman
Jan 30, 2004·Nature·Johan Paulsson
Jan 11, 2005·The Journal of Chemical Physics·Yang CaoLinda R Petzold
Aug 11, 2005·Physical Review Letters·A J McKane, T J Newman
May 23, 2006·Nature Genetics·Arren Bar-EvenNaama Barkai
Oct 14, 2006·Annual Review of Physical Chemistry·Daniel T Gillespie
Sep 11, 2007·The Journal of Chemical Physics·Ethan A MastnyJames B Rawlings
Oct 25, 2007·PloS One·Etay ZivChris H Wiggins
Feb 29, 2008·BMC Genomics·Yasushi IshihamaDmitrij Frishman
Oct 31, 2008·Nature Reviews. Molecular Cell Biology·Béla Novák, John J Tyson
Nov 8, 2008·Proceedings of the National Academy of Sciences of the United States of America·Vahid Shahrezaei, Peter S Swain
Oct 21, 2009·BMC Bioinformatics·Michał KomorowskiDavid A Rand
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·María Rodríguez MartínezItay Furman
Nov 16, 2010·IET Systems Biology·M Maienschein-ClineA R Dinner
Dec 4, 2010·Journal of Theoretical Biology·Chetan D PahlajaniMustafa Khammash
Jan 26, 2011·IET Systems Biology·K R SanftL R Petzold
Jul 1, 2011·Molecular BioSystems·E GiampieriP Lió
Jul 21, 2011·Physical Review Letters·Michael AssafZaida Luthey-Schulten
Dec 21, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ramon Grima
Dec 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Philipp ThomasArthur V Straube
Dec 1, 2002·Journal of Biological Physics·D GonzeA Goldbeter

❮ Previous
Next ❯

Citations

Apr 4, 2014·Journal of the Royal Society, Interface·Andre LeierTatiana T Marquez-Lago
Mar 22, 2013·The Journal of Chemical Physics·Manuel BarrioTatiana T Marquez-Lago
May 9, 2014·The Journal of Chemical Physics·Maria BrunaMatthew J Smith
Apr 3, 2015·Journal of Mathematical Biology·Nikola PopovićPeter S Swain
Dec 10, 2015·The Journal of Chemical Physics·Stephen SmithRamon Grima
Sep 12, 2015·IEEE Transactions on Biomedical Circuits and Systems·Thomas P Prescott, Antonis Papachristodoulou
Nov 26, 2015·BMC Systems Biology·Jae Kyoung KimMatthew R Bennett
Sep 27, 2014·IET Systems Biology·Siavash GhavamiMichael Linnebacher
Aug 8, 2014·Biophysical Journal·Jae Kyoung KimMatthew R Bennett
Mar 31, 2015·Biostatistics·Kirsty L HeyBärbel Finkenstädt
Apr 12, 2015·Biophysical Journal·Andrey A DovzhenokChristian I Hong
Apr 29, 2014·Journal of Theoretical Biology·Jason Lloyd-PriceAndre S Ribeiro
Jun 2, 2016·PLoS Computational Biology·Margaritis VoliotisClive G Bowsher
Feb 23, 2019·PloS One·Stefan VetLendert Gelens
Nov 1, 2016·Bulletin of Mathematical Biology·David F Anderson, Simon L Cotter
Jul 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Stephen Smith, Vahid Shahrezaei
Feb 14, 2019·Bulletin of Mathematical Biology·Bin XuAlexandra Jilkine
Apr 9, 2019·Journal of the Royal Society, Interface·Fabrizio Pucci, Marianne Rooman
Sep 7, 2020·The Journal of Chemical Physics·Wuyue YangLiu Hong
Jun 15, 2016·Physical Review. E·Stephen Smith, Ramon Grima
Aug 19, 2018·Nature Communications·Zhixing Cao, Ramon Grima
Sep 4, 2020·PLoS Computational Biology·Ignasius JoanitoChao-Ping Hsu
Jun 25, 2020·Physical Review. E·Md Sorique Aziz Momin, Ayan Biswas
Jan 5, 2017·The Journal of Chemical Physics·M Navarro JimenezO M Knio
Feb 23, 2018·PLoS Computational Biology·Edgar Herrera-DelgadoPeter Sollich
Jun 6, 2017·PLoS Computational Biology·Jae Kyoung Kim, Eduardo D Sontag
Jul 2, 2019·Frontiers in Genetics·Pavel LoskotLyudmila Mihaylova
Jul 17, 2020·The Journal of Chemical Physics·Barbara BraviPeter Sollich
Mar 3, 2020·The Journal of Chemical Physics·Chen Jia, Ramon Grima
Nov 7, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jiajun Zhang, Tianshou Zhou
Mar 4, 2014·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ramon Grima
Dec 12, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Philipp ThomasArthur V Straube
Oct 23, 2020·PLoS Computational Biology·Jae Kyoung Kim, John J Tyson
Nov 4, 2020·The Journal of Chemical Physics·James HolehouseRamon Grima

❮ Previous
Next ❯

Software Mentioned

hLNA
ssLNA
QSSA

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

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Philipp ThomasArthur V Straube
Proceedings of the National Academy of Sciences of the United States of America
Matthew ScottBrian Ingalls
© 2021 Meta ULC. All rights reserved