Application of lumping analysis in modelling the living systems - A trade-off between simplicity and model quality

Chemical and Biochemical Engineering Quarterly

Volumn 20, Issue 4, 2006, Pages 353-373

  Maria, G ^a  

^a UNIVERSITY POLITEHNICA OF BUCHAREST   (Romania)

Author keywords

Dynamic models; Genetic regulatory networks; Lumping analysis; Modules

Indexed keywords

BIOCHEMISTRY; CELLS; CHEMICAL ENGINEERING; COMPUTER SIMULATION; DRUG PRODUCTS; GENETIC ENGINEERING;

CELL STRUCTURES; DYNAMIC MODELS; GENETIC REGULATORY NETWORKS; LUMPING ANALYSIS;

LIVING SYSTEMS STUDIES;

EID: 33846599311     PISSN: 03529568     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (53)

1. Maria, G., Chemical and Biochemical Engineering Quarterly 19 (2005a) 213.
2. Maria, G., Chemical and Biochemical Engineering Quarterly 18 (2004) 195.
3. Gorban, A. N., Karlin, I. V., Zinovyev, A. Y., Physica A 333 (2004) 106.
4. Tomlin, A. S., Turanyi, T., Pilling, M. J., Mathematical tools for the construction, investigation and reduction of combustion mechanisms, in: Pilling, M. J., Hancock, G. (Eds.), Low temperature combustion and autoignition, Elsevier, Amsterdam, 1997, p. 293-437.
5. Vajda, S., Rabitz, H., Walter, E., Lecourtier, Y., Chem. Eng. Commun. 83 (1989) 191.
6. Connors, K. A., Chemical kinetics: The study of reaction rates in solution, VCH Publ, New York, 1990.
7. Turanyi, T., J. Mathematical Chemistry 5 (1990) 203.
8. Lei, F., Jorgensen, S. B., J. Biotech. 88 (2001) 223.
9. Vajda, S., Valko, P., Turanyi, T., Int. J. Chem. Kinetics 17 (1985) 55.
10. Malinowski, E. R., Factor analysis in chemistry, Wiley, New York, 1991.
11. Maria, G., Canadian J. Chem. Eng. 67 (1989) 825.
12. Maria, G., Rippin, D. W. T., (1993) Chem. Eng. Sci. 48 (1993) 3855.
13. Le Roux, C., Antonio, G., Joulia, X., Récents Progrès en Génie des Procedés (Grenoble) 7 (1993) 43.
14. Maria, G., Muntean, O., Chem. Eng. Sci. 42 (1987) 1451.
15. Marquardt, D. W., Technom. 12 (1970) 591.
16. Bard, Y., Nonlinear parameter estimation, Academic Press, New York, 1974.
17. Heinrich, R., Schuster, S., The regulation of cellular systems, Chapman & Hall, New York, 1996.
18. Turanyi, T., Tomlin, A. S., Pilling, M. J., J. Phys. Chem. 97 (1993) 163.
19. Wei, J., Kuo, J. C. W., Ind. & Eng. Chem. Fundam. 8 (1969) 114.
20. Li, G., Rabitz, H., Chem. Eng. Sci. 45 (1990) 977.
21. Li, G., Rabitz, H., Chem. Eng. Sci. 46 (1991a) 583.
22. Li, G., Rabitz, H., Chem. Eng. Sci. 46 (1991b) 95.
23. Li, G., Rabitz, H., Toth, J., Chem. Eng. Sci. 49 (1994) 343.
24. Iordache, O., Maria, G., Pop, G., Ind. & Eng. Chem. Research 27 (1988) 2218.
25. Gabaldon, T., Huynen, M. A., Cell Mol Life Sci 61 (2004) 930.
26. Yang, Q., Lindahl, P., Morgan, J., J. theor. Biol. 222 (2003) 407.
27. Sewell, C., Morgan, J., Lindahl, P., J. theor. Biol. 215 (2002) 151.
28. Maria, G., Chemical and Biochemical Engineering Quarterly 17 (2003) 99.
29. Tsuchiya, M., Ross, J., J. Phys. Chem. A 105 (2001) 4052.
30. Morgan, J. J., Surovtsev, I. V., Lindahl, P. A., Theor. Biology 231 (2004) 581.
31. Zhang, W., Tichy, S., Perez, L., Maria, G., Lindahl, P., Simanek, E., Journal of American Chemical Society 125 (2003) 5086.
32. Maria, G., Chemical Engineering Science 60 (2005b) 1709.
33. Wallwork, S. C., Grant, D. J. W., Physical Chemistry, Longman, London, 1977.
34. Styczynski, M. P., Stephanopoulos, G., Computers & Chemical Engineering 29 (2005) 519.
35. Zak, D. E., Vadigepalli, R., Gonye, G. E., Doyle III, F. J., Schwaber, J. S., Ogunnaike, B. A., Computers & Chemical Engineering 29 (2005) 547.
36. Salis, H., Kaznessis, Y., Computers & Chemical Engineering 29 (2005) 577.
37. Kaznessis, Y.N., Chemical Engineering Science 61 (2006) 940.
38. Angeli, D., Ferrell, J. E. Jr., Sontag, E. D., Proceedings of the National Academy of Sciences of the USA 101 (2004) 1822.
39. Kholodenko, B. N., Kiyatkin, A., Bruggeman, F. J., Sontag, E., Westerhoff, H. V., Hoek, J. B., Proceedings of the National Academy of Sciences of the USA 99 (2002) 12841.
40. Savageau, M. A., Math. Biosciences 180 (2002) 237.
41. Voit, E. O., IEE Proc. Syst. Biol. 152 (2005) 207.
42. Ofiteru, D. I., Optimal control strategies for bioprocesses, PhD Thessis, University Politehnica of Bucharest (Romania), 2006.
43. Hlavacek, W. S., Savageau, M. A., J. Mol. Biol. 266 (1997) 538.
44. Van Someren, E. P., Wessels, L. F. A., Backer, E., Reinders, M. J. T., Signal Processing 83 (2003) 763.
45. Schwache, J. H., Voit, E. O., Theoretical Biology and Medical Modelling 1 (2004) 1.
46. Silva, M. R., Bioinformatics tools for the visualization and structural analysis of metabolic networks, PhD Thesis, TU Braunschweig (Germany), 2006.
47. Ma, H. W., Zhao, X. M., Yuan, Y. J., Zeng, A. P., Bioinformatics 20 (2004) 1870.
48. Ma, H. W., Kumar, B., Ditges, U., Gunzer, F., Buer, J., Zeng, A. P., Nucleic Acids Research 32 (2004) 6643.
49. He, F., Zeng, A. P., BMC Bioinformatics 69 (2006) 1.
50. Chang, Y. J., Sahinidis, N. V., Computers & Chemical Engineering 29 (2005) 467.
51. Adrover, A., Cerbelli, S., Giona, M., Int. J. Bifurcation and Chaos 12 (2002) 353.
52. Kaper, H. G., Kaper, T. J., Physica D 165 (2002) 66.
53. Kutznetsov, Y. A., Elements of applied bifurcation theory, Springer-Verlag, Berlin, 1998.