Passivity analysis of discrete-time genetic regulatory networks with reaction-diffusion coupling and delay-dependent stability criteria

Yongwei Yang , Yang Yu , Chunyun Xu , Chengye Zou

Electronic Research Archive ›› 2025, Vol. 33 ›› Issue (5) : 3111 -3134.

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Electronic Research Archive ›› 2025, Vol. 33 ›› Issue (5) :3111 -3134. DOI: 10.3934/era.2025136
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Passivity analysis of discrete-time genetic regulatory networks with reaction-diffusion coupling and delay-dependent stability criteria
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Abstract

Gene regulatory networks (GRNs) play a crucial role in biological processes, with their dynamic behaviors heavily influenced by the spatial organization of genes. In particular, reaction- diffusion mechanisms govern the coupling between adjacent spatial locations in continuous time GRNs. However, traditional models often ignore the spatial coupling and reaction-diffusion properties of these networks, especially in discrete-time settings. In order to solve this problem, a new discrete- time gene regulatory network model is proposed in this paper, which explicitly considers the mutual coupling between adjacent spatial positions. To ensure the passivity of the proposed model, delay- dependent stability criteria are established by constructing appropriate Lyapunov-Krasovskii functions formulated in terms of linear matrix inequalities. To showcase the effectiveness and validity of this approach, a numerical example is presented in this paper. The results reveal that the model accurately captures the spatial coupling and reaction-diffusion nature of gene regulatory networks in discrete time settings.

Keywords

discrete-time genetic regulatory networks / dirichlet boundary / reaction-diffusion / linear matrix inequalities

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Yongwei Yang, Yang Yu, Chunyun Xu, Chengye Zou. Passivity analysis of discrete-time genetic regulatory networks with reaction-diffusion coupling and delay-dependent stability criteria. Electronic Research Archive, 2025, 33 (5) : 3111-3134 DOI:10.3934/era.2025136

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References

[1]

J. Hasty, D. McMillen, F. Isaacs, J. J. Collins, Computational studies of gene regulatory networks: in numero molecular biology, Nat. Rev. Genet., 2 (2001), 268-279. https://doi.org/10.1038/35066056

[2]

N. Bernaola, M. Michiels, P. Larrañaga, C. Bielza, Learning massive interpretable gene regulatory networks of the human brain by merging Bayesian networks, PloS Comput. Biol., 19 (2023), 1011443. https://doi.org/10.1371/journal.pcbi.1011443

[3]

J. Musilova, Z. Vafek, B. L. Puniya, R. Zimmer, T. Helikar, K. Sedlar, Augusta: From RNA-Seq to gene regulatory networks and Boolean models, Comput. Struct. Biotechnol. J., 23 (2024), 783-790. https://doi.org/10.1016/j.csbj.2024.01.013

[4]

G. Karlebach, P. N. Robinson, Computing minimal Boolean models of gene regulatory networks, J. Comput. Biol., 31 (2024), 117-127. https://doi.org/10.1089/cmb.2023.0122

[5]

I. Hossai, V. Fanfani, J. Fischer, J. Quackenbush, R. Burkholz, Biologically informed NeuralODEs for genome-wide regulatory dynamics, Genome Biol., 25 (2024), 127. https://doi.org/10.1186/s13059-024-03264-0

[6]

X. She, L. Wang, Y. Zhang, Finite-time stability of genetic regulatory networks with nondifferential delays, IEEE Trans. Circuits Syst. II: Express Briefs, 70 (2023), 2107-2111. https://doi.org/10.1109/TCSII.2022.3233797

[7]

T. Zhang, Y. Li, Exponential Euler scheme of multi-delay Caputo-Fabrizio fractional-order differential equations, Appl. Math. Lett., 124 (2022), 107709. https://doi.org/10.1016/j.aml.2021.107709

[8]

A. Polynikis, S. J. Hogan, M. D. Bernardo, Comparing different ODE modelling approaches for gene regulatory networks, J. Theor. Biol., 261 (2009), 511-530. https://doi.org/10.1016/j.jtbi.2009.07.040

[9]

M. Kchaou, G. Narayanan, M. S. Ali, S. Sanober, G. Rajchakit, B. Priya, Finite-time Mittag-Leffler synchronization of delayed fractional-order discrete-time complex-valued genetic regulatory networks: Decomposition and direct approaches, Inf. Sci., 664 (2024), 120337. https://doi.org/10.1016/j.ins.2024.120337

[10]

K. Xie, C. Zhang, S. Lee, Y. Liu, C. Zhai, Sector bound-dependent matrix-separation-based inequality and its application to stability analysis of discrete-time delayed genetic regulatory networks, IEEE Trans. Circuits Syst. II: Express Briefs, 71 (2024), 3785-3789. https://doi.org/10.1109/TCSII.2024.3367777

[11]

K. Mathiyalagan, R. Sakthivel, Robust stabilization and H∞ control for discrete-time stochastic genetic regulatory networks with time delays , Can. J. Phys., 90 (2012), 939-953. https://doi.org/10.1139/p2012-088

[12]

Q. Li, H. Q. Wei, D. Hua, J. Wang, J. Yang, Stabilization of semi-Markovian jumping uncertain complex-valued networks with time-varying delay: A sliding-mode control approach, Neural Process Lett., 56 (2024), 111. https://doi.org/10.1007/s11063-024-11585-1

[13]

G. Narayanan, M. S. Ali, H. Alsulami, T. Saeed, B. Ahmad Synchronization of T-S fuzzy fractional-order discrete-time complex-valued molecular models of mRNA and protein in regulatory mechanisms with leakage effects, Neural Process Lett., 55 (2023), 3305-3331. https://doi.org/10.1007/s11063-022-11010-5

[14]

H. Wei, K. Zhang, M. Zhang, Q. Li, J. Wang, Dissipative synchronization of Semi-Markovian jumping delayed neural networks under random deception attacks: An event-triggered impulsive control strategy, J. Franklin Inst., 361 (2024), 106835. https://doi.org/10.1016/j.jfranklin.2024.106835

[15]

S. Pandiselvi, R. Raja, J. Cao, G. Rajchakit, B. Ahmad, Approximation of state variables for discrete-time stochastic genetic regulatory networks with leakage, distributed, and probabilistic measurement delays: A robust stability problem, Adv. Differ. Equations, 2018 (2018), 123. https://doi.org/10.1186/s13662-018-1569-z

[16]

Y. Zhao, H. Wu, Fixed/Prescribed stability criterions of stochastic system with time-delay, AIMS Math., 9 (2024), 14425-14453. https://doi.org/10.3934/math.2024701

[17]

T. Zhang, Z. Li, Switching clusters’ synchronization for discrete space-time complex dynamical networks via boundary feedback controls, Pattern Recognit., 143 (2023), 109763. https://doi.org/10.1016/j.patcog.2023.109763

[18]

R. Liang, J. Wang, PD control for passivity of coupled reaction-diffusion neural networks with multiple state couplings or spatial diffusion couplings, Neurocomputing, 489 (2022), 558-569. https://doi.org/10.1016/j.neucom.2021.12.070

[19]

P. U. Avila, T. Padvitski, A. C. Leote, H. Chen, J. Saez-Rodriguez, M. Kann, et al., Gene regulatory networks in disease and ageing, Nat. Rev. Nephrol., 20 (2024), 616-633. https://doi.org/10.1038/s41581-024-00849-7

[20]

P. Jothiappan, M. Kalidass, Robust passivity analysis of stochastic genetic regulatory networks with Levy noise, Int. J. Control Autom. Syst., 20 (2022), 3241-3251. https://doi.org/10.1007/s12555-021-0552-8

[21]

Y. Qin, F. Li, J. Wang, H. Shen, Extended dissipative synchronization of reaction-diffusion genetic regulatory networks based on sampled-data control, Neural Process Lett., 55 (2023), 3169-3183. https://doi.org/10.1007/s11063-022-11003-4

[22]

X. Song, X. Li, S. Song, C. K. Ahn, State observer design of coupled genetic regulatory networks with Reaction-diffusion terms via time-space sampled-data communications, IEEE/ACM Trans. Comput. Biol. Bioinf., 19 (2022), 3704-3714. https://doi.org/10.1109/TCBB.2021.3114405

[23]

Y. Zhang, H. Liu, H. Yan, J. Zhou, Oscillatory behaviors in genetic regulatory networks mediated by microRNA with time delays and reaction-diffusion terms, IEEE Trans. Nanobiosci., 16 (2017), 166-176. https://doi.org/10.1109/TNB.2017.2675446

[24]

C. Ma, Q. Zeng, L. Zhang, Y. Zhu, Passivity and passification for Markov jump genetic regulatory networks with time-varying delays, Neurocomputing, 136 (2014), 321-326. https://doi.org/10.1016/j.neucom.2013.12.028

[25]

X. Zhang, Y. Han, L. Wu, Y. Wang, State estimation for delayed genetic regulatory networks with reaction-diffusion terms, IEEE Trans. Neural Networks Learn. Syst., 29 (2018), 299-309. https://doi.org/10.1109/TNNLS.2016.2618899

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