THERMAL SCIENCE

International Scientific Journal

Shuqiang Wang

,

Yanyan Shen

,

Jinxing Hu

,

Ning Li

,

Dewei Zeng

DYNAMIC ANALYSIS OF BIOCHEMICAL NETWORK USING COMPLEX NETWORK METHOD

ABSTRACT
In this study, the stochastic biochemical reaction model is proposed based on the law of mass action and complex network theory. The dynamics of biochemical reaction system is presented as a set of non-linear differential equations and analyzed at the molecular-scale. Given the initial state and the evolution rules of the biochemical reaction system, the system can achieve homeostasis. Compared with random graph, the biochemical reaction network has larger information capacity and is more efficient in information transmission. This is consistent with theory of evolution.
KEYWORDS
biochemical reaction channels, network homeostasis, complex network, dynamical analysis
PAPER SUBMITTED: 2015-02-11
PAPER REVISED: 2015-03-25
PAPER ACCEPTED: 2015-05-08
PUBLISHED ONLINE: 2015-10-25
DOI REFERENCE: https://doi.org/10.2298/TSCI1504249W
CITATION EXPORT: view in browser or download as text file
THERMAL SCIENCE YEAR 2015, VOLUME 19, ISSUE Issue 4, PAGES [1249 - 1253]
REFERENCES
  1. Strogatz, S. H., Exploring Complex Networks, Nature, 410 (2001), 6825, pp. 268-276
  2. Newman, M. J., The Structure and Function of Complex Networks, Siam Review, 45 (2003), 2, pp. 167- 256
  3. Albert, R., Barabasi, A. L., Statistical Mechanics of Complex Networks, Rev. Mod. Phys., 74 (2002), 1, pp. 49-97
  4. Wang, X. F., Chen, G., Complex Networks: Small-World, Scale-Free and Beyond, Circuits and Systems Magazine, IEEE, 3 (2003), 1, pp. 6-20
  5. Costa, L. F., et al., Characterization of Complex Networks: A Survey of Measurements, Advances in Physics, 56 (2007), 1, pp. 167-242
  6. Boccaletti, S., et al., Complex Networks: Structure and Dynamics, Physics Reports, 424 (2006), 4-5, pp. 175-308
  7. Bollobas, B., Random Graphs, Academic Press, London, UK, 1985
  8. Dorogovtsev, S. N., Goltsev, A. V., Critical Phenomena in Complex Networks, Rev. Mod. Phys., 80 (2008), Oct., pp. 1275-1335
  9. Watts, D. J., Strogatz, S. H., Collective Dynamics of ‘Small-World' Networks, Nature, 393 (1998), June, pp. 440-442
  10. Albert, L. B., Reka, A., Emergence of Scaling in Random Networks, Science, 286 (1999), 5439, pp. 509- 512
  11. Bhalla, U. S., Iyengar, R., Emergent Properties of Networks of Biological Signaling Pathways, Science, 283 (1999), 5400, pp. 381-387
  12. Lu, X. J., et al., Data-Driven Robust Design for a Curing Oven, IEEE Trans. on Components, Packaging and Manufacturing Technology, 4 (2014), 8, pp. 1366-1373
  13. Lu, X. J., et al., A Process/Shape-Decomposition Modeling Method for Deformation Force Estimation in Complex Forging Processes, International Journal of Mechanical Sciences, 90 (2015), Jan., pp. 190-199
  14. Newman, M. E. J., The Structure of Scientific Collaboration Networks, Proceedings of the National Academy of Sciences, 98 (2001), 2, pp. 404-409
  15. Faloutsos, M., et al., On Power-Law Relationships of the Internet Topology, Computer Communication Review, 29 (1999), 4, pp. 251-262
  16. Milo, R., et al., Network Motifs: Simple Building Blocks of Complex Networks, Science, 298 (2002), 5594, pp. 824-827
  17. Jeong, H., et al., The Large-Scale Organization of Metabolic Networks, Nature, 407 (2000), Oct., pp. 651-654
  18. Guelzim, N. et al., Topological and Causal Structure of the Yeast Transcriptional Regulatory Network, Nat. Genet., 31 (2002), 1, pp. 60-63
  19. Oltvai, Z. N., Barabasi, A. L., Systems Biology. Life's Complexity Pyramid, Science, 298 (2002), 5594, pp. 763-764
  20. Guggenheim, E. A., Textbook Errors IX: More About the Laws of Reaction Rates and of Equilibrium, Journal of Chemical Education, 33 (1956), 11, pp. 544-545
  21. Cai, X., Exact Stochastic Simulation of Coupled Chemical Reactions with Delays, Journal of Chemical Physics, 126 (2007), 12, 124108
  22. Gillespie, D. T., Exact Stochastic Simulation of Coupled Chemical Reactions, Journal of Computational Physics, 81 (1977), 25, pp. 2340-2361
  23. Cai, X., Wen, J., Efficient Exact and K-Skip Methods for Stochastic Simulation of Coupled Chemical Reactions, Journal of Chemical Physics, 131 (2009), 6, 064108
  24. Ramaswamy, R., Sbalzarini, I. F., A Partial-Propensity Formulation of the Stochastic Simulation Algorithm for Chemical Reaction Networks with Delays, Journal of Chemical Physics, 134 (2011), 1, 014106
  25. Ramaswamy, R., Sbalzarini, I. F., A Partial-Propensity Variant of the Composition-Rejection Stochastic Simulation Algorithm for Chemical Reaction Networks, Journal of Chemical Physics, 132 (2010), 4, 044102
  26. Wenzhe, M., et al., Defining Network Typologies that Can Achieve Biochemical Adaptation, Cell, 138 (2009), 4, pp. 760-773
PDF VERSION [DOWNLOAD]
DYNAMIC ANALYSIS OF BIOCHEMICAL NETWORK USING COMPLEX NETWORK METHOD

© 2024 Society of Thermal Engineers of Serbia. Published by the Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, Belgrade, Serbia. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International licence