Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation

The Journal of Chemical Physics
Radek ErbanTimothy C Elston

Abstract

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long ...Continue Reading

References

Feb 5, 2000·Nature·T S GardnerJ J Collins
Apr 3, 2001·Nature Reviews. Genetics·J HastyJ J Collins
Nov 15, 2002·Nature·Jeff HastyJ J Collins
Jun 1, 2004·Physical Review Letters·Mikko HaatajaIoannis G Kevrekidis
Jan 11, 2005·The Journal of Chemical Physics·Yang CaoLinda R Petzold
Mar 3, 2005·The Journal of Chemical Physics·Dmitry I KopelevichIoannis G Kevrekidis
Mar 3, 2005·The Journal of Chemical Physics·Howard Salis, Yiannis Kaznessis
Mar 15, 2005·FEBS Letters·Thomas Schlitt, Alvis Brazma
May 11, 2005·Nature Reviews. Genetics·Mads KaernJames J Collins
Oct 4, 2005·Physical Review Letters·Saravanapriyan SriramanGerhard Hummer
Dec 3, 2005·The Journal of Chemical Physics·Weinan EEric Vanden-Eijnden

❮ Previous
Next ❯

Citations

Feb 3, 2007·Journal of Mathematical Biology·Radek Erban, Hans G Othmer
Apr 2, 2009·Proceedings of the National Academy of Sciences of the United States of America·Christian A YatesDavid J T Sumpter
Oct 16, 2007·Bioinformatics·T FournierN Mermod
Jan 25, 2007·Annual Review of Biophysics and Biomolecular Structure·Eric L Haseltine, Frances H Arnold
Sep 15, 2011·The Journal of Chemical Physics·Simon L CotterRadek Erban
Jun 17, 2008·The Journal of Chemical Physics·Aryeh WarmflashAaron R Dinner
Dec 10, 2008·The Journal of Chemical Physics·Yueheng LanGaregin A Papoian
Dec 6, 2006·The Journal of Chemical Physics·Liang QiaoIoannis G Kevrekidis
Apr 28, 2007·The Journal of Chemical Physics·Radek ErbanIoannis G Kevrekidis
Aug 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Amit SingerRonald R Coifman
Apr 3, 2015·Journal of Mathematical Biology·Nikola PopovićPeter S Swain
Sep 8, 2010·Journal of Theoretical Biology·Nikolai W F BodeA Jamie Wood
Dec 10, 2015·The Journal of Chemical Physics·Stephen SmithRamon Grima
May 1, 2007·Biophysical Journal·Martin Hemberg, Mauricio Barahona
Dec 17, 2014·Computational and Structural Biotechnology Journal·Tamás Székely, Kevin Burrage
Feb 13, 2017·Journal of Theoretical Biology·Oren Rimer, Gil Ariel
Oct 11, 2016·Faraday Discussions·Wei ZhangChristof Schütte
Sep 15, 2017·IEEE Transactions on Neural Networks and Learning Systems·Yurong LiuFuad E Alsaadi
Mar 15, 2019·Mathematical Medicine and Biology : a Journal of the IMA·Pavol Bokes, John R King
Aug 7, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M PinedaR Imbihl
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Hanshuang ChenYijing Yan
Dec 22, 2015·Integrative Biology : Quantitative Biosciences From Nano to Macro·Le-Zhi WangXiao Wang
Jan 24, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Yongzheng SunRadek Erban
Dec 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Louise DysonAlan J McKane
Jan 3, 2019·Chaos·Chuansheng ShenJürgen Kurths
Jul 30, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Chuansheng ShenHouwen Xin
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Christian A YatesPhilip K Maini
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Carlos EscuderoPhilip K Maini
Mar 16, 2021·Journal of the Royal Society, Interface·Jack D HywoodMaté Biro
Aug 30, 2014·Physical Review Letters·Mingyang LuEshel Ben-Jacob

❮ 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

Proceedings of the National Academy of Sciences of the United States of America
H H McAdams, Adam P Arkin
Proceedings of the National Academy of Sciences of the United States of America
M Thattai, A van Oudenaarden
© 2021 Meta ULC. All rights reserved