易鸣分享 http://blog.sciencenet.cn/u/yiming123 对生物网络的建模和模拟以及动力学分析非常感兴趣

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个人科研积累小结:生物网络数学建模和动力学分析

已有 6271 次阅读 2011-4-13 13:32 |系统分类:科研笔记| 科学院, 研究所, 数学建模, 动力学, 神经元

易鸣,中国科学院武汉物理与数学研究所副研究员。

http://www.researcherid.com/rid/B-5383-2011



 
   统计物理专业出生,自2001年起一直从事生物系统随机动力学的研究,在基因调控网络以及神经网络的随机理论和应用上积累了一定的基础,主要包括:研究了随机噪声对于果蝇的单细胞昼夜生理节律振子的影响。当节律振子只被外部光噪声驱动时,发现外噪声可以诱导相干共振现象(Phys. Rev. E 72,012902 (2005));当内噪声和外噪声同时驱动系统时,我们发现外噪声在一定的噪声强度范围能够促进“内噪声相干共振”,这是随机噪声起积极作用的一个典型例子(Phys. Rev. E 73,041923 (2006));依据一个大肠杆菌质粒体的拷贝数控制模型,理论研究发现:在一定的参数范围内,增加信号分子的噪声强度会减少质粒体分子的噪声强度,推导得到了这种噪声降低效应发生的临界条件(Phys. Rev. E 77,022902 (2008));研究了单个双稳的神经元在加性以及乘性噪声作用下分别诱导相干共振过程中的不同动力学机制(Phys. Rev. E 77, 061905 (2008));探讨了一个多层前馈型神经元网络模型,通过数值模拟发现,高斯白噪声在第一层激发产生不规则的神经触发行为,经过该多层神经元网络后,神经元的电兴奋会慢慢变得同步,进一步分析了网络连接结构对于同步触发的影响(Phys. Rev. E 81,061924 (2010));研究了小世界神经网络中神经元的同步动力学,发现时间延迟以及神经差异性能够诱导网络同步性质发生丰富的转变,通过时空斑图以及同步指标定性以及定量的阐述了同步转变的机制(Phys. Rev. E 83, 046207 (2011) )。
   近四年来,重点研究信号转导网络的数学建模和动力学分析,在研究酶的反应扩散体系方面取得了如下工作:基于离散的固定步长随机行走蒙特卡洛数值模拟研究了微观条件下的米氏动力学,得到了单酶条件下的酶催化速率,并探讨了扩散速率的变化对于米氏曲线的影响(Physica A 389,3791 (2010)),同时研究了多酶的MAPK级联模块中支架蛋白对于信号放大的影响,发现慢的去磷酸化情形下,支架蛋白的结合有利于信号放大,而支架蛋白的数目则抑制了信号放大;快的去磷酸化情形下,支架蛋白的结合削弱了信号放大。这些定性的结论都在真实的生物体系中被观察到(Biophys. Chem. 147, 130 (2010));基于常规的整数阶“反应扩散方程”,建立了MAPK信号级联从细胞膜到细胞质空间的反应扩散模型,研究发现MAPK级联处于超灵敏、磷酸化环局部双稳、级联全局双稳以及振荡等四种不同的操作模式下时,活性激酶的空间分布以及药剂依赖关系具有非常不同的响应特点(Phys. Biol. (2011)接收待发表),其次,我们提出了一个整合的生物网络模型,将钙离子振荡模块、GTPase环模块以及MAPK级联模块依次结合起来,研究了振荡的钙信号对于MAPK活性的影响,动力学分析表明:MAPK模块合适的操作模式以及GTPase环模块合理的参数取值对于重现实验现象是十分关键的(Biophys. Chem. 157 (2011) 33)。
 
文章列表
 
1. Delay and diversity-induced synchronization  transitions in a small-world neuronal network,
Jun Tang, Jun Ma, Ming Yi, Hui Xia, and Xianqing Yang,
Physical Review E.  83, (2011) 046207
 
2.  Spatial distribution and dose response for different operation modes in a reaction-diffusion model of MAPK cascade,
Qi Zhao, Ming Yi*, Yan Liu,
Physical Biology.  (2011) accepted for publication.
 
3. A theoretical modeling for frequency modulations of Ca2+ signal on activation of MAPK cascade,
Ming Yi* and Qi Zhao,
Biophysical Chemistry. 157 (2011) 33

4.  Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion
Author(s): Yi, M; Liu, QA
Source: Physica a-Statistical Mechanics and Its Applications Volume: 389 Issue: 18 Pages: 3791-3803 Published: 2010

5. Propagation of firing rate by synchronization and coherence of firing pattern in a feed-forward multilayer neural network
Author(s): Yi, M; Yang, LJ
Source: Physical Review E Volume: 81 Issue: 6 Published: 2010

6. Theoretical study for regulatory property of scaffold protein on MAPK cascade: A qualitative modeling
Author(s): Yi, M; Xia, KL; Zhan, M
Source: Biophysical Chemistry Volume: 147 Issue: 3 Pages: 130-139 Published: 2010

7.  A constructive role of internal noise on coherence resonance induced by external noise in a calcium oscillation system
Author(s): Yu, G; Yi, M; Jia, Y; et al.
Source: Chaos Solitons & Fractals Volume: 41 Issue: 1 Pages: 273-283 Published: 2009

8.  Cooperative effects of noise and coupling on stochastic dynamics of a membrane-bulk coupling model
Author(s): Tang, J; Jia, Y; Yi, M
Source: Communications in Theoretical Physics Volume: 51 Issue: 3 Pages: 455-459 Published: 2009

9.  Information propagation from IP3 to target protein: A combined model for encoding and decoding of Ca2+ signal
Author(s): Zhao, Q; Yi, M; Xia, KL; et al.
Source: Physica a-Statistical Mechanics and Its Applications Volume: 388 Issue: 19 Pages: 4105-4114 Published: 2009

10.  Suppression of spiral wave and turbulence by using amplitude restriction of variable in a local square area
Author(s): Ma, J; Jia, Y; Yi, M; et al.
Source: Chaos Solitons & Fractals Volume: 41 Issue: 3 Pages: 1331-1339 Published: 2009

11. Theoretical Study on Drift of Ca2+ Spiral Waves Controlled by Electric Field
Author(s): Tang, J; Jia, Y; Ma, J; et al.
Source: Communications in Theoretical Physics Volume: 51 Issue: 5 Pages: 941-946 Published: 2009

12.  Control of spiral wave and turbulence in the time-varied reaction-diffusion system
Author(s): Ma, J; Jin, WY; Yi, M; et al.
Source: Acta Physica Sinica Volume: 57 Issue: 5 Pages: 2832-2841 Published: 2008

13. Coupling effect of ion channel clusters on calcium signalling
Author(s): Tang, J; Jia, Y; Yi, M; et al.
Source: Chinese Physics Letters Volume: 25 Issue: 3 Pages: 1149-1152 Published: 2008

14.  Critical condition for the occurrence of a noise-reduction effect
Author(s): Yi, M; Jia, Y; Ma, J; et al.
Source: Physical Review E Volume: 77 Issue: 2 Published: 2008

15. Evolution of spiral wave and pattern formation in a vortical polarized electric field
Author(s): Ma, J; Yi, M; Li, BW; et al.
Source: Chinese Physics B Volume: 17 Issue: 7 Pages: 2438-2445 Published: 2008

16.  Multiplicative-noise-induced coherence resonance via two different mechanisms in bistable neural models
Author(s): Tang, J; Jia, Y; Yi, M; et al.
Source: Physical Review E Volume: 77 Issue: 6 Published: 2008

17.  Numerical study of IP3-dependent Ca2+ spiral waves in Xenopus oocytes
Author(s): Tang, J; Jia, Y; Ma, J; et al.
Source: Epl Volume: 83 Issue: 6 Published: 2008

18.  RyR channels and glucose-regulated pancreatic beta-cells
Author(s): Zhan, X; Yang, L; Yi, M; et al.
Source: European Biophysics Journal With Biophysics Letters Volume: 37 Issue: 6 Pages: 773-782 Published: 2008

19.  Stabilization of pattern in complex Ginzburg-Landau equation with spatial perturbation scheme
Author(s): Ma, J; Yi, M; Zhang, LP; et al.
Source: Communications in Theoretical Physics Volume: 49 Issue: 6 Pages: 1541-1546 Published: 2008

20. Title: Suppression of spiral wave in modified Orengonator model
Author(s): Ma, J; Jin, WY; Yi, M; et al.
Source: Communications in Theoretical Physics Volume: 50 Issue: 2 Pages: 403-410 Published: 2008

21. Title: Theoretical study of mesoscopic stochastic mechanism and effects of finite size on cell cycle of fission yeast
Author(s): Yi, M; Jia, Y; Tang, J; et al.
Source: Physica a-Statistical Mechanics and Its Applications Volume: 387 Issue: 1 Pages: 323-334 Published: 2008

22. Title: A coarse estimation of cell size region from a mesoscopic stochastic cell cycle model
Author(s): Yi, M; Jia, Y; Liu, Q; et al.
Source: Chinese Physics Letters Volume: 24 Issue: 7 Pages: 1829-1832 Published: JUL 2007

23. Title: Enhancement of internal-noise coherence resonance by modulation of external noise in a circadian oscillator
Author(s): Yi, M; Jia, Y; Liu, Q; et al.
Source: Physical Review E Volume: 73 Issue: 4 Published: APR 2006

24. Title: Light-noise-induced suprathreshold circadian oscillations and coherent resonance in Drosophila
Author(s): Yi, M; Jia, Y
Source: Physical Review E Volume: 72 Issue: 1 Published: JUL 2005

==========================================================================

 
25. Lijian Yang, Ya Jia, Ming Yi,The effects of electrical coupling on the temporal coding of neural signal in noisy Hodgkin-Huxley neuron ensemble International Conference on Natural Computation.10, 819(2010)(EI).
 
26. Ming Yi, Guang Yu, Jun Tang, Jun Ma, Ya Jia, Effects of structural diversity and fluctuations on synchronization of coupled circadian oscillators, International Journal of Biomedical Soft Computing and Human Sciences. 14, (2009) 67.
 
27. Spatiotemporal stochastic resonance in a bistable FitzHugh-Nagumo ring with phase-repulsive coupling
Qi Zhao Ming Yi* Chenggui Yao    EPJB 2011  in revise


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