Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

doi:10.1088/1674-1056/20/12/128703

中国物理B ›› 2011, Vol. 20 ›› Issue (12): 128703-128703.doi: 10.1088/1674-1056/20/12/128703

Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

刘圣君¹, 王祺¹, 刘波¹, 晏世伟², Fumihiko Sakata³

(1)College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China; (2)College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China;Beijing Radiation Centre, Beijing 100875, China; (3)Institute of Applied Beam Science, Graduate School of Science and Technology, Ibaraki University, Mito 310-8512, Japan

收稿日期:2011-02-26 修回日期:2011-06-12 出版日期:2011-12-15 发布日期:2011-12-15
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 10975019), the Foundation of the Ministry of Personnel of China for Returned Scholars (Grant No. MOP2006138), and the Fundamental Research Funds for the Central Universities.

Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

Liu Sheng-Jun(刘圣君)^a), Wang Qi(王祺)^a), Liu Bo(刘波)^a), Yan Shi-Wei(晏世伟)^a)b)†, and Fumihiko Sakata^c)

^a College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China; ^b Beijing Radiation Centre, Beijing 100875, China; ^c Institute of Applied Beam Science, Graduate School of Science and Technology, Ibaraki University, Mito 310-8512, Japan

Received:2011-02-26 Revised:2011-06-12 Online:2011-12-15 Published:2011-12-15
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 10975019), the Foundation of the Ministry of Personnel of China for Returned Scholars (Grant No. MOP2006138), and the Fundamental Research Funds for the Central Universities.

摘要/Abstract

摘要： With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation. We systematically analyse the effects of time delays, the feedback mechanism, and biological stochasticity on the power spectra. It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator. Delay-induced stochastic resonance can be expected, which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations. Through the analysis of the power spectrum, a new approach is proposed to estimate the oscillation period.

关键词: biological stochasticity, time delay, oscillation and resonance, network motif

Abstract: With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation. We systematically analyse the effects of time delays, the feedback mechanism, and biological stochasticity on the power spectra. It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator. Delay-induced stochastic resonance can be expected, which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations. Through the analysis of the power spectrum, a new approach is proposed to estimate the oscillation period.

Key words: biological stochasticity, time delay, oscillation and resonance, network motif

中图分类号: (Noise in biological systems)

87.18.Tt

05.40.-a (Fluctuation phenomena, random processes, noise, and Brownian motion) 87.16.dj (Dynamics and fluctuations)

刘圣君, 王祺, 刘波, 晏世伟, Fumihiko Sakata. Noise transmission and delay-induced stochastic oscillations in biochemical network motifs[J]. 中国物理B, 2011, 20(12): 128703-128703.

Liu Sheng-Jun(刘圣君), Wang Qi(王祺), Liu Bo(刘波), Yan Shi-Wei(晏世伟), and Fumihiko Sakata . Noise transmission and delay-induced stochastic oscillations in biochemical network motifs[J]. Chin. Phys. B, 2011, 20(12): 128703-128703.

参考文献 54

[1]	Bundschuh R, Hayot F and Jayaprakash C 2003 it Biophys. J. 84 1606
[2]	Tanase-Nicola S, Warren P B and ten Wolde P R 2006 Phys. Rev. Lett. 97 068102
[3]	Tyson J J, Chen K C and Novak B 2003 Curr. Opin. Cell Biol. 15 221
[4]	Alon U 2007 Nat. Rev. Genet. 8 450
[5]	Kierzek A M, Zaim J and Zielenkiewicz P 2001 J. Biol. Chem. 276 8165
[6]	Shahrezaei V and Swain P S 2008 Curr. Opin. Biotechnol. 8 369
[7]	Kaufmann B B and Oudenaarden A V 2007 Curr. Opin. Genet. Dev. 17 107
[8]	Swain P S and Longtin A 2006 Chaos 16 026101
[9]	Scott M, Ingalls B and Kaern M 2006 Chaos 16 026107
[10]	Swain P S, Elowitz M B and Siggia E D 2002 Proc. Natl. Acad. Sci. bf 99 12795
[11]	Kepler T B and Elston T C 2001 Biophys. J. 81 3116
[12]	Paulsson J 2004 Nature 427 415
[13]	Shibata T and Fujimoto K 2005 Proc. Natl. Acad. Sci. bf 102 331
[14]	Strogatz S H 1998 Nature 394 316
[15]	Hirata H, Yoshiura S, Ohtsuka T, Bessho Y, Harada T, Yoshikawa K and Kageyama R 2002 Science 298 840
[16]	Bar-Or R L, Maya R, Segel L A, Alon U, Levine A J and Oren M 2000 Proc. Natl. Acad. Sci. 97 11250
[17]	Frank T D, Beek P J and Friedrich R 2003 Phys. Rev. E 68 021912
[18]	Ohira T and Yamane T 2000 Phys. Rev. E 61 1247
[19]	Zhu R and Salahub D 2008 FEBS Lett. 582 2905
[20]	Bratsun D, Volfson D, Tsimring L S and Hasty J 2005 Proc. Natl. Acad. Sci. 102 14593
[21]	Monk N A M 2003 Curr. Biol. 13 1409
[22]	Yan S 2007 J. Bio. Syst. 35 123
[23]	Lewis J 2003 Curr. Biol. 13 1398
[24]	Xia J F and Jia Y 2010 Chin. Phys. B 19 040506
[25]	Ren H P, Li W C and Liu D 2010 Chin. Phys. B 19 030511
[26]	Long F, Du L C and Mei D C 2009 Chin. Phys. B 18 4738
[27]	Heldin C H, Lennartsson J and Hellberg C 2008 Eur. J. Hum. Genet. 16 769
[28]	Detwiler P B, Ramanathan S, Sengupta A and Shraiman B I 2000 Biophys. J. 79 2801
[29]	Oltvai Z N and Barab'asi Z L 2002 Science 298 763
[30]	To T L and Maheshri N 2010 Science 327 1142
[31]	Samoilov M, Plyasunov S and Arkin A P 2005 Proc. Natl. Acad. Sci. 102 2310
[32]	Tian T, Burrage K, Burrage P M and Carletti M 2007 J. Comput. Appl. Math. 205 696
[33]	Gillespie D T 1977 J. Chem. Phys. 81 2340
[34]	van Kampen N G 1992 Stochastic Processes in Physics and Chemistry (Amsterdam: North-Holland)
[35]	Barrio M, Burrage K, Leier A and Tian T 2006 PLOS Comput. Biol. 2 117
[36]	Warren P B, Nicola S T and Ten Wolde P R 2006 J. Chem. Phys. 125 144904
[37]	McDonnell M D and Abbott D 2009 PLOS Comput. Biol. 5 e1000348
[38]	Du L C and Mei D C 2009 Chin. Phys. B 18 946
[39]	Jia Z L 2010 Chin. Phys. B 19 020504
[40]	Li H, Hou Z and Xin H 2005 Phys. Rev. E 71 061916
[41]	Boland R P, Galla T and McKane A J 2008 J. Stat. Mech. P09001
[42]	Wang M 2006 Molecular Biology (Beijing: Science Press)
[43]	Weaver R F 2002 Molecular Biology 4th edn. (New York: McGraw-Hill)
[44]	Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P 2002 Molecular Biology of the Cell (New York: Garland Science)
[45]	Bentley D 2002 Curr. Opin. Cell Biol. 14 336
[46]	Simpson M L, Cox C D and Sayler G S 2003 Proc. Natl. Acad. Sci. 100 4554
[47]	Dong G Q and McMillen D R 2008 Phys. Rev. E 77 021908
[48]	Verdugo A and Rand R 2008 Commun. Nonlinear Sci. Numer. Simul. 13 235
[49]	Mann M and Jensen O N 2003 Nat. Biotechnol. 21 255
[50]	Nishii K, Yamanaka I, Yasuda M, Kiyohara Y B, Kitayama Y, Kondo T and Yagita K 2006 Neurosci. Lett. 401 44 30
[51]	Nalivaeva N N and Turner A J J 2001 Proteomics 1 735
[52]	Fox R F 1991 Phys. Rev. A 43 2649
[53]	Reid B G and Flynn G C 1997 Biochem. 36 6786
[54]	Falcke M 2003 Biophys. J. 84 42

Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

Noise transmission and delay-induced stochastic oscillations in biochemical network motifs

PDF (PC)

赞

可视化

摘要/Abstract

引用本文

使用本文

参考文献 54

相关文章 15

Metrics

本文评价

推荐阅读 0

[1]	Zhan-Hong Guo(郭展宏), Zhi-Jun Li(李志军), Meng-Jiao Wang(王梦蛟), and Ming-Lin Ma(马铭磷). Hopf bifurcation and phase synchronization in memristor-coupled Hindmarsh-Rose and FitzHugh-Nagumo neurons with two time delays[J]. 中国物理B, 2023, 32(3): 38701-038701.
[2]	Xuan Ma(马璇), Yaya Zhao(赵鸭鸭), Yafeng Wang(王亚峰), Yueling Chen(陈月玲), and Hengtong Wang(王恒通). Effect of autaptic delay signal on spike-timing precision of single neuron[J]. 中国物理B, 2023, 32(3): 38703-038703.
[3]	Xiaoming Liang(梁晓明), Chao Fang(方超), Xiyun Zhang(张希昀), and Huaping Lü(吕华平). Influence of coupling asymmetry on signal amplification in a three-node motif[J]. 中国物理B, 2023, 32(1): 10504-010504.
[4]	Xun-Qin Huo(火勋琴), Wei-Feng Yang(杨玮枫), Wen-Hui Dong(董文卉), Fa-Cheng Jin(金发成), Xi-Wang Liu(刘希望), Hong-Dan Zhang(张宏丹), and Xiao-Hong Song(宋晓红). Review on typical applications and computational optimizations based on semiclassical methods in strong-field physics[J]. 中国物理B, 2022, 31(3): 33101-033101.
[5]	Changbao Deng(邓长宝), Weinuo Jiang(蒋未诺), and Shihong Wang(王世红). Inferring interactions of time-delayed dynamic networks by random state variable resetting[J]. 中国物理B, 2022, 31(3): 30502-030502.
[6]	Wenjie Yang(杨文杰). Bifurcation and dynamics in double-delayed Chua circuits with periodic perturbation[J]. 中国物理B, 2022, 31(2): 20201-020201.
[7]	Guan Wang(王冠), Zhixia Ding(丁芝侠), Sai Li(李赛), Le Yang(杨乐), and Rui Jiao(焦睿). Finite-time Mittag—Leffler synchronization of fractional-order complex-valued memristive neural networks with time delay[J]. 中国物理B, 2022, 31(10): 100201-100201.
[8]	Ben Cao(曹奔), Huaguang Gu(古华光), and Yuye Li(李玉叶). Delayed excitatory self-feedback-induced negative responses of complex neuronal bursting patterns[J]. 中国物理B, 2021, 30(5): 50502-050502.
[9]	Guoyuan Qi(齐国元) and Zimou Wang(王子谋). Modeling and dynamics of double Hindmarsh-Rose neuron with memristor-based magnetic coupling and time delay[J]. 中国物理B, 2021, 30(12): 120516-120516.
[10]	Weilin Ren(任卫林), Rongjun Cheng(程荣军), and Hongxia Ge(葛红霞). Stabilization strategy of a car-following model with multiple time delays of the drivers[J]. 中国物理B, 2021, 30(12): 120506-120506.
[11]	黄玉娇, 袁孝焰, 杨旭华, 龙海霞, 肖杰. Multiple Lagrange stability and Lyapunov asymptotical stability of delayed fractional-order Cohen-Grossberg neural networks[J]. 中国物理B, 2020, 29(2): 20703-020703.
[12]	魏长立, 赵曦. Validity of extracting photoionization time delay from the first moment of streaking spectrogram[J]. 中国物理B, 2019, 28(1): 13201-013201.
[13]	钱郁, 高红艳, 姚成贵, 崔晓华, 马军. Synchronization performance in time-delayed random networks induced by diversity in system parameter[J]. 中国物理B, 2018, 27(10): 108902-108902.
[14]	杨增强, 叶地发, 傅立斌. Attosecond transient absorption spectroscopy: Comparative study based on three-level modeling[J]. 中国物理B, 2018, 27(1): 13301-013301.
[15]	王莉芳, 仇康, 贾亚. Effects of time delays in a mathematical bone model[J]. 中国物理B, 2017, 26(3): 30503-030503.