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On trajectories of a system modeling evolution of genetic networks


  • Received: 31 August 2022 Revised: 26 October 2022 Accepted: 03 November 2022 Published: 17 November 2022
  • A system of ordinary differential equations is considered, which arises in the modeling of genetic networks and artificial neural networks. Any point in phase space corresponds to a state of a network. Trajectories, which start at some initial point, represent future states. Any trajectory tends to an attractor, which can be a stable equilibrium, limit cycle or something else. It is of practical importance to answer the question of whether a trajectory exists which connects two points, or two regions of phase space. Some classical results in the theory of boundary value problems can provide an answer. Some problems cannot be answered and require the elaboration of new approaches. We consider both the classical approach and specific tasks which are related to the features of the system and the modeling object.

    Citation: Inna Samuilik, Felix Sadyrbaev. On trajectories of a system modeling evolution of genetic networks[J]. Mathematical Biosciences and Engineering, 2023, 20(2): 2232-2242. doi: 10.3934/mbe.2023104

    Related Papers:

  • A system of ordinary differential equations is considered, which arises in the modeling of genetic networks and artificial neural networks. Any point in phase space corresponds to a state of a network. Trajectories, which start at some initial point, represent future states. Any trajectory tends to an attractor, which can be a stable equilibrium, limit cycle or something else. It is of practical importance to answer the question of whether a trajectory exists which connects two points, or two regions of phase space. Some classical results in the theory of boundary value problems can provide an answer. Some problems cannot be answered and require the elaboration of new approaches. We consider both the classical approach and specific tasks which are related to the features of the system and the modeling object.



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    [1] J. C. Sprott, Elegant Chaos: Algebraically Simple Chaotic Flows, World Scientific, Singapore, 2010.
    [2] K. Funahashi, Y. Nakamura, Approximation of dynamical systems by continuous time recurrent neural networks, Neural Networks, 6 (1993), 801–806. https://doi.org/10.1016/S0893-6080(05)80125-X doi: 10.1016/S0893-6080(05)80125-X
    [3] F. M. Alakwaa, Modeling of gene regulatory networks: A literature review, J. Comput. Syst. Biol., 1 (2014), 67–103.
    [4] F. Sadyrbaev, I. Samuilik, V. Sengileyev, On modelling of genetic regulatory networks, WSEAS Trans. Electron., 12 (2021), 73–80.
    [5] H. D. Jong, Modeling and simulation of genetic regulatory systems: A literature review, J. Comput. Biol., 9 (2002), 67–103. https://doi.org/10.1089/10665270252833208 doi: 10.1089/10665270252833208
    [6] T. Schlitt, Approaches to modeling gene regulatory networks: A gentle introduction, in Silico Systems Biology, (2013), 13–35. https://doi.org/10.1007/978-1-62703-450-0_2
    [7] N. Vijesh, S. K. Chakrabarti, J. Sreekumar, Modeling of gene regulatory networks: A review, J. Biomed. Sci. Eng., 6 (2013), 223–231. http://dx.doi.org/10.4236/jbise.2013.62A027 doi: 10.4236/jbise.2013.62A027
    [8] I. Samuilik, F. Sadyrbaev, V. Sengileyev, Examples of periodic biological oscillators: Transition to a six-dimensional system, WSEAS Trans. Comput. Res., 10 (2022), 49–54. https://doi.org/10.37394/232018.2022.10.7 doi: 10.37394/232018.2022.10.7
    [9] H. R. Wilson, J. D. Cowan, Excitatory and inhibitory interactions in localized populations of model neurons, Biophys. J., 12 (1972), 1–24. https://doi.org/10.1016/S0006-3495(72)86068-5 doi: 10.1016/S0006-3495(72)86068-5
    [10] V. W. Noonburg, Differential Equations: From Calculus to Dynamical Systems, 2nd edition, American Mathematical Society, 2019.
    [11] Y. Koizumi, T. Miyamura, S. Arakawa, E. Oki, K. Shiomoto, M. Murata, Adaptive virtual network topology control based on attractor selection, J. Lightwave Technol., 28 (2010), 1720–1731. https://doi.org/10.1109/JLT.2010.2048412 doi: 10.1109/JLT.2010.2048412
    [12] L. Z. Wang, R. Q. Su, Z. G. Huang, X. Wang, W. X. Wang, C. Grebogi, et al., A geometrical approach to control and controllability of nonlinear dynamical networks, Nat. Commun., 7 (2016), 11323. http://doi.org/10.1038/ncomms11323 doi: 10.1038/ncomms11323
    [13] S. P. Cornelius, W. L. Kath, A. E. Motter, Realistic control of network dynamic, Nat. Commun., 4 (2013), 1942. https://doi.org/10.1038/ncomms2939 doi: 10.1038/ncomms2939
    [14] D. K. Arrowsmith, C. M. Place, Dynamical Systems: Differential Equations, Maps and Chaotic Behavior, Chapman and Hall/CRC, London, 1992.
    [15] S. Bernfeld, V. Lakshmikantham, An Introduction to Nonlinear Boundary Value Problems, Academic Press, New York, 1974.
    [16] R. Conti, Equazioni differenziali ordinarie quasilineari concondizioni lineari, Ann. Mat. Pura Appl., 57 (1962) 49–61. https://doi.org/10.1007/BF02417726 doi: 10.1007/BF02417726
    [17] L. Perko, Differential Equations and Dynamical Systems, 3rd Edition, Springer, New York, 2001.
    [18] M Sandri, Numerical calculation of Lyapunov exponents, Math. J., 6 (1996), 78–84.
    [19] A. Das, A. B. Roy, P. Das, Chaos in a three dimensional neural network, Appl. Math. Model., 24 (2000), 511–522. https://doi.org/10.1016/S0307-904X(99)00046-3 doi: 10.1016/S0307-904X(99)00046-3
    [20] I. Samuilik, F. Sadyrbaev, Modelling three dimensional gene regulatory networks, WSEAS Trans. Syst. Control, 12 (2021), 73–80. https://doi.org/doi:10.37394/232017.2021.12.10 doi: 10.37394/232017.2021.12.10
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