A random walk modelling approach for passive metabolic pathways in gram-negative bacteria

Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06

Volumn , Issue , 2006, Pages 217-224

  Mazloom, Amin R ^a   Basu, Kalyan ^a   Das, Sajal K ^a  

^a UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL INTELLIGENCE; BACTERIA; BACTERIOLOGY; BIOCOMMUNICATIONS; BIOINFORMATICS; CELLS; CHLORINE COMPOUNDS; CYTOLOGY; ENZYMES; FOOD ADDITIVES; INFORMATION SCIENCE; INTELLIGENT CONTROL; MARKOV PROCESSES; MINE FLOODING; RANDOM PROCESSES; SEMICONDUCTOR DOPING;

ABSTRACT MODELING; COMPUTATIONAL BIOLOGY; COMPUTATIONAL INTELLIGENCE; CURRENT MODELING; DIFFUSION PROCESSES; GRAM-NEGATIVE BACTERIA; IN-VIVO; KINETIC RATE LAWS; KINETIC RATES; LINEAR TIME; METABOLIC PATHWAYS; NUMERICA L RESULTS; PASSIVE DIFFUSION; PHOSPHO-TRANSFER; PHOSPHOENOL PYRUVATE; RANDOM ENVIRONMENTS; RANDOM WALKS;

COMPUTATIONAL COMPLEXITY;

EID: 50249166510     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CIBCB.2006.330993     Document Type: Conference Paper

References (21)

1. T. C. Meng, S. Somani and P. Dhar, "Modeling and simulation of biological systems with stochasticity", J. In Silico Biology, vol. 4, p. 0024, 2004.
2. M. A. Gibson and J. Bruck, "Efficient exact stochastic simulation of chemical systems with many species and many channels", J. Phys. Chem., Vol. 104, 2000, p. 1876-1889.
3. M. Firth, "Stochastic Simulation of Cell signaling Pathways", Ph. D. thesis, University of Cambridge, Cambridge UK, 1998.
4. K. Basu, P. Ghosh, S. Ghosh, S. K. Das, S. Dafler, "iSimBioSys: A Discrete Event Simulation Platform for 'in silico' Study of Biological Systems", IEEE 39th Annual Simulation Symposium, 2006.
5. S. O. Nelson, B. J. Scholte and P. W.Postma, "Phsphoenolpyruvate: Sugar Phsophotrasferase System Mediated Regulation fo Carbohydrate Metabolism in Salmonalla Typhimutium", J. Bacteriology Vol. 50, May 1982, p. 604-615.
6. B. Alberts, D. Bray J. Lewis, M. Raff, K. Roberts and J. D. Watson, "Molecular Biology of the Cell Third Edition", Garland Publishing Inc., New York, 1994.
7. G. Gottschalk, "Bacterial Metabolism Second Edition", Springer Velrag, Series in Microbiology, New York, 1986, ISBN 3-540-96153-4.
8. H. P. Leeuwen and W. Koster, "Physicochemical Kinetics and Transport at Bioinformatics", IUPAC Series on Analytical and Physical Chemistry of Environmental Systems Vol. 9 , John Wiley , England , 2004, ISBN 0-471-49845-9.
9. H. J. Rogers, "Bacterial Cell Structure", American Society of Microbilogy, Van Nostrand ReinHold, London, 1983.
10. F. C. Neidhart, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter and H. E. Umbargar, "Escherichia Coli and Salmonella Tyhpimutium Cellular and Molecular Biology Vol. I", American Socienty of Mirobiology, Washinton DC, 1987.
11. J. M. Rohwer, N. D. Meadowi, S. Rosemani, H. V. Westerhoff and P. W. Postma, "Understanding Glucose Transport by the Bacterial Phosphoenolpyruvate:Glycose Phosphotransferase System on the Basis of Kinetic Measurements in Vitro", J. Biol. Chemistry, Vol. 275, No. 45, Nov. 2000, pp. 3490934921.
12. H. C. Berg, "Random Walks in Biology", Princeton university Press, Prinston, NJ, 1983, ISBN 0-691-08245-6.
13. J. Van Der Vlag, R. Van'T Hof, K. Van Dam and P. W. Postma, "Control of glucose metabolism by the enzymes of the glucose phosphotransferase system in Salmonella typhimurium", Eur. J. Biochem. 230, 1995, p. 170-182.
14. C. Fall, E. Marland, J Wagner and J. Tyson, "Computational Cell Biology", Interdisciplinary Applied Mathematics, SpringerVerlag, New York, 2002, ISBN 0-387-95369-8.
15. A. H. Romano, S. J. Eberhard, S. L. Dingle, AND T. D. McDowell "Distribution of the Phosphoenolpyruvate: Glucose Phosphotransferase System in Bacteria", J.J. Bacteriology, Nov. 1970, p. 808-813.
16. E. W. Weisstein,"Spherical Cap.", From MathWorld - A Wolfram Web Resource, http://mathworld.wolfram.com/SphericalCap.html
17. I. M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I. T. Paulsen, M. Peralta-Gil and P. D. Karp, "EcoCyc: a comprehensive database resource for Escherichia coli", Nucleic Acids Research, Vol. 33, 2005, Database issue D334-D337.
18. S. Sundararaj, A. Guo, B. Habibi-Nazhad, M. Rouani, P. Stothard, M. Ellison,and D. S. Wishart "The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli", Nucleic Acids Res. Vol 32, Jan 2004, Database issue D293.D295.
19. T. E. Barman, F. Travers, "The rapid-flow-quench method in the study of fast reactions in biochemistry: extension to subzero conditions", Methods Biochem Anal, 1985;31:159.
20. J.B. Stock, E.B. Waygood, N.D. Meadow, P.W. Postma and S. Roseman, "Sugar transport by the bacterial phosphotransferase system. The glucose receptors of the Salmonella typhimurium phosphotransferase system", J. Biol. Chem., Vol. 257, Issue 23, 14543-14552, 12, 1982.
21. G J Ruijter, G van Meurs, M A Verwey, P W Postma, and K van Dam, "Analysis of mutations that uncouple transport from phosphorylation in enzyme IIGlc of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system", J Bacteriol. 1992 May; 174(9): 28432850.