Abstract
There are two basic approaches used to develop the so called genetic algorithms: the deterministic approach, and the second one is the stochastic approach, with algorithms that add randomness to the model. The stochastic model is based on multiple reactions of molecules that can occur in spatially homogenous system, a situation that is characteristic to the natural biological cells. The randomness is a must to have a simulation model behavior that corresponds to the real phenomena. To each simulation model, another problem is to add the feedback reactions that brings the cell model closer to a real one. A cell model built on those principles is describe. The original contribution of this paper is to establish the basic principles that proved to work with that specific cell model.
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References
H. Kitano System Biology: a brief overview. Science. Vol. 295. March 2002
Garrett, R.H., Grisham, C.M. 1999: Biochemistry (Second Edition). Pacific Grove, CA: Thomson Brooks/Cole.
Setubal, J., Meidanis, J. 1997: Introduction to Computational Molecular Biology. Pacific Grove, CA: Thomson Brooks/Cole. ISBN 0-534-95262-3.
Krane, D.E., Raymer, M. L 2002: Fundamental Concepts of Bioinformatics. San Francisco: Benjamin Cummings.
Gillespie, D. T. 1977: Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry, Vol. 81. No25.
M. M. Domach, S.K. Leung, R.E. Cahn, G.G. Cocks, and M.L. Shuler (Computer Model for Glucose-Limited Growth of a Single Cell of Escherichia Coli B/r-A. Biotechnology and Bioengineering, Vol. 26, Issue 3, Pages 203-216. 1984
(J.J. Tyson – Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl. Acad. Sci. USA, Vol. 88, pp. 7328-7332, August 1991).
(Samuel T. Browning and Michael L. Shuler – Towards the Development of a Minimal Cell Model by Generalization of a Model of Escherichia Coli: Use of Dimensionless Rate Parameters. Biotechnology and Bioengineering, Vol. 76, Issue 3, November 2001)
[M.E. Csete, J.C. Doyle – Reverse Engineering of Biological Complexity. Science, Vol. 295, March 2002].
Bănică, M., Coteţiu, R. 2006: Dynamical Optimization of the Tip Relief Parameters for an Involute Spurs Gearing with Impose Center Based on Computer Simulation, 7th International Conference “Automation in Production Planning and Manufacturing”, Zilina, Slovakia, May, pag. 11-16.
Chira, F., Bănică, M, Coteţiu, R. 2008: Optimization of the asymmetric gear design for some different mono-objective function using genetic algorithms, Proceedings of 9th International Scientific Conference “New ways in manufacturing technologies 2008”, ISBN 978-80-553-0044-3, pp. 379-386, 19.-21.6., Presov, Slovakia.
Tudose, L., Pop, D. 2002: Proiectare optimala cu Algoritmi Genetici. Editura MEDIAMIRA, Cluj-Napoca Foy, B.D. 2005: Simulating the Interactions of Genes, Proteins, and Metabolites in Cell-Like Entities. Final Technical Report. Wright State University.
Stoicovici, D.I. 2004: Design and optimization of the chemical sensing capability of a theoretical biological cell using a stochastic simulation. Master Thesis, Wright State University.
Foy, B., Specification of Molecular complexes in Cell Simulations. International Conference on System Biology, Stockholm, Sweden, 2002.
Stoicovici D, Banica M, Ungureanu M, Chira F, Crăciun I: Establishing the Parameter Behavior at a Simulation Program Based On a Stochastic Approach. SCIENTIFIC BULLETIN, Serie C, Fascicle: Mechanics, Tribology, Machine Manufacturing Technology ISSN 1224-3264, Volume 2013 No. XXVII.
E-CELL on http://www.e-cell.org/about/
Virtual Cell on http://www.nrcam.uchc.edu/index.html?current=one
Bio-Spice on http://biospice.sourceforge.net/
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Stoicovici, D., Cotetiu, A., Banica, M., Ungureanu, M., Craciun, I. (2017). Principles to Build a Stochastic Model for a Minimal Biological Cell with Built-in Feedback Reaction Capabilities. In: Vlad, S., Roman, N. (eds) International Conference on Advancements of Medicine and Health Care through Technology; 12th - 15th October 2016, Cluj-Napoca, Romania. IFMBE Proceedings, vol 59. Springer, Cham. https://doi.org/10.1007/978-3-319-52875-5_73
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DOI: https://doi.org/10.1007/978-3-319-52875-5_73
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