IDEAS home Printed from https://ideas.repec.org/a/eee/apmaco/v348y2019icp425-436.html
   My bibliography  Save this article

Most probable dynamics of a genetic regulatory network under stable Lévy noise

Author

Listed:
  • Chen, Xiaoli
  • Wu, Fengyan
  • Duan, Jinqiao
  • Kurths, Jürgen
  • Li, Xiaofan

Abstract

Numerous studies have demonstrated the important role of noise in the dynamical behaviour of a complex system. The most probable trajectories of nonlinear systems under the influence of Gaussian noise have recently been studied already. However, there has been only a few works that examine how most probable trajectories in the two-dimensional system (MeKS network) are influenced under non-Gaussian stable Lévy noise. Therefore, we discuss the most probable trajectories of a two-dimensional model depicting the competence behaviour in B. subtilis under the influence of stable Lévy noise. On the basis of the Fokker-Planck equation, we describe the noise-induced most probable trajectories of the MeKS network from the low ComK protein concentration (vegetative state) to the high ComK protein concentration (competence state) under stable Lévy noise. We demonstrate choices of the non-Gaussianity index α and the noise intensity ϵ which generate the ComK protein escape from the low concentration to the high concentration. We also reveal the optimal combination of both parameters α and ϵ making the tipping time shortest. Moreover, we find that different initial concentrations around the low ComK protein concentration evolve to a metastable state, and provide the optimal α and ϵ such that the distance between the deterministic competence state and the metastable state is smallest.

Suggested Citation

  • Chen, Xiaoli & Wu, Fengyan & Duan, Jinqiao & Kurths, Jürgen & Li, Xiaofan, 2019. "Most probable dynamics of a genetic regulatory network under stable Lévy noise," Applied Mathematics and Computation, Elsevier, vol. 348(C), pages 425-436.
  • Handle: RePEc:eee:apmaco:v:348:y:2019:i:c:p:425-436
    DOI: 10.1016/j.amc.2018.12.005
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0096300318310464
    Download Restriction: Full text for ScienceDirect subscribers only

    File URL: https://libkey.io/10.1016/j.amc.2018.12.005?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. David M Holloway & Alexander V Spirov, 2017. "Transcriptional bursting in Drosophila development: Stochastic dynamics of eve stripe 2 expression," PLOS ONE, Public Library of Science, vol. 12(4), pages 1-24, April.
    2. Niraj Kumar & Abhyudai Singh & Rahul V Kulkarni, 2015. "Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models," PLOS Computational Biology, Public Library of Science, vol. 11(10), pages 1-22, October.
    3. Gao, Ting & Duan, Jinqiao & Li, Xiaofan, 2016. "Fokker–Planck equations for stochastic dynamical systems with symmetric Lévy motions," Applied Mathematics and Computation, Elsevier, vol. 278(C), pages 1-20.
    4. Gürol M. Süel & Jordi Garcia-Ojalvo & Louisa M. Liberman & Michael B. Elowitz, 2006. "An excitable gene regulatory circuit induces transient cellular differentiation," Nature, Nature, vol. 440(7083), pages 545-550, March.
    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. Han, Ping & Xu, Wei & Wang, Liang & Zhang, Hongxia & Ma, Shichao, 2020. "Most probable dynamics of the tumor growth model with immune surveillance under cross-correlated noises," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 547(C).
    2. Han, Ping & Xu, Wei & Wang, Liang & Ma, Shichao, 2020. "The most probable response of some prototypical stochastic nonlinear dynamical systems," Chaos, Solitons & Fractals, Elsevier, vol. 132(C).
    3. Han, Ping & Wang, Liang & Xu, Wei & Zhang, Hongxia & Ren, Zhicong, 2021. "The stochastic P-bifurcation analysis of the impact system via the most probable response," Chaos, Solitons & Fractals, Elsevier, vol. 144(C).
    4. Yang, Anji & Wang, Hao & Yuan, Sanling, 2023. "Tipping time in a stochastic Leslie predator–prey model," Chaos, Solitons & Fractals, Elsevier, vol. 171(C).
    5. Han, Ping & Xu, Wei & Zhang, Hongxia & Wang, Liang, 2022. "Most probable trajectories in the delayed tumor growth model excited by a multiplicative non-Gaussian noise," Chaos, Solitons & Fractals, Elsevier, vol. 156(C).
    6. Song, Yi & Xu, Wei, 2021. "Asymmetric Lévy noise changed stability in a gene transcriptional regulatory system," Chaos, Solitons & Fractals, Elsevier, vol. 151(C).
    7. Hao, Mengli & Jia, Wantao & Wang, Liang & Li, Fuxiao, 2022. "Most probable trajectory of a tumor model with immune response subjected to asymmetric Lévy noise," Chaos, Solitons & Fractals, Elsevier, vol. 165(P1).

    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. Karin Münch & Richard Münch & Rebekka Biedendieck & Dieter Jahn & Johannes Müller, 2019. "Evolutionary model for the unequal segregation of high copy plasmids," PLOS Computational Biology, Public Library of Science, vol. 15(3), pages 1-17, March.
    2. Payne, Joshua L., 2016. "No tradeoff between versatility and robustness in gene circuit motifs," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 449(C), pages 192-199.
    3. Singh, Abhyudai & Vahdat, Zahra & Xu, Zikai, 2019. "Time-triggered stochastic hybrid systems with two timer-dependent resets," OSF Preprints u8fzg, Center for Open Science.
    4. Muir Morrison & Manuel Razo-Mejia & Rob Phillips, 2021. "Reconciling kinetic and thermodynamic models of bacterial transcription," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-30, January.
    5. Margaritis Voliotis & Philipp Thomas & Ramon Grima & Clive G Bowsher, 2016. "Stochastic Simulation of Biomolecular Networks in Dynamic Environments," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-18, June.
    6. Yu, Haiyan & Liu, Quansheng & Bi, Yuanhong, 2023. "Lévy noise-induced phase transition in p53 gene regulatory network near bifurcation points," Chaos, Solitons & Fractals, Elsevier, vol. 166(C).
    7. Tesfay, Daniel & Wei, Pingyuan & Zheng, Yayun & Duan, Jinqiao & Kurths, Jürgen, 2020. "Transitions between metastable states in a simplified model for the thermohaline circulation under random fluctuations," Applied Mathematics and Computation, Elsevier, vol. 369(C).
    8. Song, Yi & Xu, Wei, 2021. "Asymmetric Lévy noise changed stability in a gene transcriptional regulatory system," Chaos, Solitons & Fractals, Elsevier, vol. 151(C).
    9. 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.
    10. Mohammad Soltani & Cesar A Vargas-Garcia & Duarte Antunes & Abhyudai Singh, 2016. "Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-23, August.
    11. Matthieu Wyart & David Botstein & Ned S Wingreen, 2010. "Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data," PLOS Computational Biology, Public Library of Science, vol. 6(11), pages 1-14, November.
    12. Sandra H Dandach & Mustafa Khammash, 2010. "Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach," PLOS Computational Biology, Public Library of Science, vol. 6(11), pages 1-11, November.
    13. Ruoyu Luo & Lin Ye & Chenyang Tao & Kankan Wang, 2013. "Simulation of E. coli Gene Regulation including Overlapping Cell Cycles, Growth, Division, Time Delays and Noise," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-10, April.
    14. Hao, Mengli & Jia, Wantao & Wang, Liang & Li, Fuxiao, 2022. "Most probable trajectory of a tumor model with immune response subjected to asymmetric Lévy noise," Chaos, Solitons & Fractals, Elsevier, vol. 165(P1).
    15. Kazunari Mouri & Yasushi Sako, 2013. "Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-15, November.
    16. Greg J Stephens & Bethany Johnson-Kerner & William Bialek & William S Ryu, 2008. "Dimensionality and Dynamics in the Behavior of C. elegans," PLOS Computational Biology, Public Library of Science, vol. 4(4), pages 1-10, April.
    17. Miles Miller & Marc Hafner & Eduardo Sontag & Noah Davidsohn & Sairam Subramanian & Priscilla E M Purnick & Douglas Lauffenburger & Ron Weiss, 2012. "Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-18, July.
    18. Youtao Lu & Jaehee Lee & Jifen Li & Srinivasa Rao Allu & Jinhui Wang & HyunBum Kim & Kevin L. Bullaughey & Stephen A. Fisher & C. Erik Nordgren & Jean G. Rosario & Stewart A. Anderson & Alexandra V. U, 2023. "CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    19. Cabrera Fernández, Juan Luis & Herrera-Almarza, Gioconda C. & Gutiérrez M., Esther D., 2018. "Chromosome progression and mitotic times behavior are mimicked by an stochastic unstable dynamics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 512(C), pages 1121-1127.
    20. Zhao, Na & Liu, Haihong & Yan, Fang, 2020. "Oscillation dynamics of MeKS core module containing positive and negative feedback loops with time delay," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 538(C).

    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:apmaco:v:348:y:2019:i:c:p:425-436. 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: https://www.journals.elsevier.com/applied-mathematics-and-computation .

    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.