IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v416y2014icp461-466.html
   My bibliography  Save this article

Switch dynamics for stochastic model of genetic toggle switch

Author

Listed:
  • Xu, Yong
  • Zhu, Ya-nan
  • Shen, Jianwei
  • Su, Jianbin

Abstract

Recently, more and more biological experiments have indicated that noise plays an important role in bistable systems, such as the case of the bimodal population distribution in the genetic toggle switch. In this paper, we further verify that noises in degradation rates can indeed induce switching in the genetic toggle switch. Meanwhile, we apply the theory of mean first passage time (MFPT) in high dimensional system to the above stochastic model. According to our assumption, the high order finite difference method is used to compute the MFPT (that the average time switching from one steady state to the other) and we find that the relationship between the MFPT and noise intensity is negative correlation. The result is also verified through another numerical simulation method.

Suggested Citation

  • Xu, Yong & Zhu, Ya-nan & Shen, Jianwei & Su, Jianbin, 2014. "Switch dynamics for stochastic model of genetic toggle switch," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 416(C), pages 461-466.
  • Handle: RePEc:eee:phsmap:v:416:y:2014:i:c:p:461-466
    DOI: 10.1016/j.physa.2014.08.042
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437114007274
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

    File URL: https://libkey.io/10.1016/j.physa.2014.08.042?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. William J. Blake & Mads KÆrn & Charles R. Cantor & J. J. Collins, 2003. "Noise in eukaryotic gene expression," Nature, Nature, vol. 422(6932), pages 633-637, April.
    2. David Frigola & Laura Casanellas & José M Sancho & Marta Ibañes, 2012. "Asymmetric Stochastic Switching Driven by Intrinsic Molecular Noise," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-7, February.
    3. Ertugrul M. Ozbudak & Mukund Thattai & Han N. Lim & Boris I. Shraiman & Alexander van Oudenaarden, 2004. "Multistability in the lactose utilization network of Escherichia coli," Nature, Nature, vol. 427(6976), pages 737-740, February.
    4. Timothy S. Gardner & Charles R. Cantor & James J. Collins, 2000. "Construction of a genetic toggle switch in Escherichia coli," Nature, Nature, vol. 403(6767), pages 339-342, January.
    5. Thomas B. Kepler & Timothy C. Elston, 2001. "Stochasticity in Transcriptional Regulation: Origins, Consequences and Mathematical Representations," Working Papers 01-06-033, Santa Fe Institute.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Wu, Juan & Xu, Yong & Ma, Shaojuan, 2019. "Realizing the transformation of logic gates in a genetic toggle system under Lévy noise," Chaos, Solitons & Fractals, Elsevier, vol. 119(C), pages 171-179.
    2. Xu, Yong & Wu, Juan & Du, Lin & Yang, Hui, 2016. "Stochastic resonance in a genetic toggle model with harmonic excitation and Lévy noise," Chaos, Solitons & Fractals, Elsevier, vol. 92(C), pages 91-100.
    3. Liu, Yuting & Shan, Meijing & Lian, Xinze & Wang, Weiming, 2016. "Stochastic extinction and persistence of a parasite–host epidemiological model," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 462(C), pages 586-602.
    4. Lingling Li & Jianwei Shen, 2017. "Bifurcations and Dynamics of the Rb-E2F Pathway Involving miR449," Complexity, Hindawi, vol. 2017, pages 1-20, October.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Tobias May & Lee Eccleston & Sabrina Herrmann & Hansjörg Hauser & Jorge Goncalves & Dagmar Wirth, 2008. "Bimodal and Hysteretic Expression in Mammalian Cells from a Synthetic Gene Circuit," PLOS ONE, Public Library of Science, vol. 3(6), pages 1-7, June.
    2. Carl Song & Hilary Phenix & Vida Abedi & Matthew Scott & Brian P Ingalls & Mads Kærn & Theodore J Perkins, 2010. "Estimating the Stochastic Bifurcation Structure of Cellular Networks," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-11, March.
    3. Tomas Tokar & Jozef Ulicny, 2013. "The Mathematical Model of the Bcl-2 Family Mediated MOMP Regulation Can Perform a Non-Trivial Pattern Recognition," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-8, December.
    4. Keun-Young Kim & Jin Wang, 2007. "Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch," PLOS Computational Biology, Public Library of Science, vol. 3(3), pages 1-13, March.
    5. Marc S Sherman & Barak A Cohen, 2014. "A Computational Framework for Analyzing Stochasticity in Gene Expression," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-13, May.
    6. Chen, Aimin & Tian, Tianhai & Chen, Yiren & Zhou, Tianshou, 2022. "Stochastic analysis of a complex gene-expression model," Chaos, Solitons & Fractals, Elsevier, vol. 160(C).
    7. Zhou, Peipei & Cai, Shuiming & Liu, Zengrong & Chen, Luonan & Wang, Ruiqi, 2013. "Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems," Chaos, Solitons & Fractals, Elsevier, vol. 50(C), pages 115-126.
    8. Zachary R Fox & Brian Munsky, 2019. "The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments," PLOS Computational Biology, Public Library of Science, vol. 15(1), pages 1-23, January.
    9. Arjun Raj & Charles S Peskin & Daniel Tranchina & Diana Y Vargas & Sanjay Tyagi, 2006. "Stochastic mRNA Synthesis in Mammalian Cells," PLOS Biology, Public Library of Science, vol. 4(10), pages 1-13, September.
    10. Graham Rockwell & Nicholas J Guido & George M Church, 2013. "Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective," PLOS Computational Biology, Public Library of Science, vol. 9(1), pages 1-15, January.
    11. Ioannis G Aviziotis & Michail E Kavousanakis & Andreas G Boudouvis, 2015. "Effect of Intrinsic Noise on the Phenotype of Cell Populations Featuring Solution Multiplicity: An Artificial lac Operon Network Paradigm," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-27, July.
    12. Shintaro Nagata & Macoto Kikuchi, 2020. "Emergence of cooperative bistability and robustness of gene regulatory networks," PLOS Computational Biology, Public Library of Science, vol. 16(6), pages 1-24, June.
    13. Benjamin B Kaufmann & Qiong Yang & Jerome T Mettetal & Alexander van Oudenaarden, 2007. "Heritable Stochastic Switching Revealed by Single-Cell Genealogy," PLOS Biology, Public Library of Science, vol. 5(9), pages 1-8, September.
    14. Avraham E Mayo & Yaakov Setty & Seagull Shavit & Alon Zaslaver & Uri Alon, 2006. "Plasticity of the cis-Regulatory Input Function of a Gene," PLOS Biology, Public Library of Science, vol. 4(4), pages 1-1, March.
    15. Najme Khorasani & Mehdi Sadeghi & Abbas Nowzari-Dalini, 2020. "A computational model of stem cell molecular mechanism to maintain tissue homeostasis," PLOS ONE, Public Library of Science, vol. 15(7), pages 1-25, July.
    16. Stefano Ciliberti & Olivier C Martin & Andreas Wagner, 2007. "Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology," PLOS Computational Biology, Public Library of Science, vol. 3(2), pages 1-10, February.
    17. Liu, Pei & Ning, Li Juan, 2016. "Transitions induced by cross-correlated bounded noises and time delay in a genotype selection model," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 441(C), pages 32-39.
    18. Marc Weber & Javier Buceta, 2013. "Stochastic Stabilization of Phenotypic States: The Genetic Bistable Switch as a Case Study," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-8, September.
    19. Kazunari Mouri & Jose C Nacher & Tatsuya Akutsu, 2009. "A Mathematical Model for the Detection Mechanism of DNA Double-Strand Breaks Depending on Autophosphorylation of ATM," PLOS ONE, Public Library of Science, vol. 4(4), pages 1-14, April.
    20. Lai, Qiang & Norouzi, Benyamin & Liu, Feng, 2018. "Dynamic analysis, circuit realization, control design and image encryption application of an extended Lü system with coexisting attractors," Chaos, Solitons & Fractals, Elsevier, vol. 114(C), pages 230-245.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:416:y:2014:i:c:p:461-466. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.