A cybernetic modeling framework for analysis of metabolic systems

Computers and Chemical Engineering

Volumn 29, Issue 3, 2005, Pages 487-498

  Namjoshi, Abhijit Anand ^a   Ramkrishna, Doraiswami ^a  

^a Purdue University   (United States)

Author keywords

Cybernetic modeling; Metabolic systems; Modeling framework

Indexed keywords

BACTERIA; BIOMEDICAL ENGINEERING; BIOSYNTHESIS; CELLS; CYBERNETICS; ENZYMES; GENES; METABOLITES; RNA;

ALLOSTERIC PROCESSES; BACTERIAL GROWTH; ENZYME SYNTHESIS; METABOLIC SYSTEMS;

METABOLISM;

ENZYME; MESSENGER RNA;

CHEMICAL ENGINEERING;

BACTERIAL GROWTH; BIOMASS; BIOTECHNOLOGY; CYBERNETICS; ENZYME ACTIVITY; ENZYME SYNTHESIS; GENETIC ALGORITHM; MATHEMATICAL MODEL; METABOLIC ENGINEERING; METABOLITE; REVIEW; THEORETICAL MODEL;

EID: 15744374803     PISSN: 00981354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compchemeng.2004.08.011     Document Type: Article

References (21)

1. A.F. Europa, A. Gambhir, P.C. Fu, and W.S. Hu Multiple steady states with distinct cellular metabolism in continuous culture of mammalian cells Biotechnology and Bioengineering 67 1 2000 25 34
2. C.A. Floudas Deterministic global optimization: Theory, algorithms and applications 2000 Kluwer Academic Publishers
3. C.A. Floudas, and P.M. Pardalos Optimization in computational chemistry and molecular biology: Local and global approaches 2000 Kluwer Academic Publishers
4. D.E. Goldberg Genetic algorithms in search, optimization and machine learning 1989 Addison-Wesley Pub. Co.
5. A. Gupta, J. Varner, and C.D. Maranas Large-scale inference of the transcriptional regulation of Bacillus subtilis Computers and Chemical Engineering 29 2005 565 576
6. J.H. Holland Adaptation in natural and artificial systems: An introductory analysis with applications to biology, control, and artificial intelligence 1975 University of Michigan Press Ann Arbor
7. D.S. Kompala, D. Ramkrishna, N.B. Jansen, and G.T. Tsao Investigation of bacterial growth on mixed substrates: Experimental evaluation of cybernetic models Biotechnology and Bioengineering 28 1986 1044 1055
8. Namjoshi, A. A. (2003, May). A mathematical investigation of the consequences of metabolic regulation in complex pathways: The cybernetic approach. Ph.D. Thesis, Purdue University, West Lafayette, IN 47907, USA.
9. A.A. Namjoshi, W.-S. Hu, and D. Ramkrishna Unveiling steady state multiplicity in hybridoma cultures: The cybernetic approach Biotechnology and Bioengineering 81 1 2003 80 91
10. A.A. Namjoshi, A. Kienle, and D. Ramkrishna Steady-state multiplicity in bioreactors: Bifurcation analysis of cybernetic models Chemical Engineering Science, ISCRE-17 58 2003 793 800 [special issue]
11. A.A. Namjoshi, and D. Ramkrishna Multiplicity and stability of steady states in continuous bioreactors. Dissection of cybernetic models Chemical Engineering Science 56 2001 5593 5607
12. R. Ramakrishna, D. Ramkrishna, and A.E. Konopka Cybernetic modeling of growth in mixed, substitutable substrate environments: Preferential and simultaneous utilization Biotechnology and Bioengineering 52 1 1996 141 151
13. Ramkrishna, D. (1982). Foundations of biochemical engineering: Kinetics and thermodynamics in biological systems. A cybernetic perspective of microbial growth (pp. 161-178). Washington, DC: American Chemical Society.
14. Straight, J. V., & Ramkrishna, D. (1990). Regulation of complex growth dynamics - substitutable and complementary processes, Abstracts of Papers of The American Chemical Society, 200, 4-BIOT.
15. A. Sundaram, P. Ghosh, J.M. Caruthers, and V. Venkatasubramanian Design of fuel additives using neural networks and evolutionary algorithms AIChE Journal 47 6 2001 1387 1406
16. J. Varner, and D. Ramkrishna Application of cybernetic models to metabolic engineering: Investigation of storage pathways Biotechnology and Bioengineering 58 2-3 1998 282 291
17. J. Varner, and D. Ramkrishna Metabolic engineering from a cybernetic perspective: 1, theoretical preliminaries Biotechnology Progress 15 1999 407 425
18. J. Varner, and D. Ramkrishna Metabolic engineering from a cybernetic perspective: 2, qualitative investigation of nodal architectures and their response to genetic perturbation Biotechnology Progress 15 1999 426 438
19. J.D. Varner Large-scale prediction of phenotype: Concept Biotechnology and Bioengineering 69 6 2000 664 678
20. V. Venkatasubramanian, K. Chan, and J.M. Caruthers Computer aided molecular design using genetic algorithms Computers and Chemical Engineering 18 9 1994 833 844
21. M.K.S. Yeung, J. Tegner, and J.J. Collins Reverse engineering gene networks using singular value decomposition and robust regression Proceedings of the National Academy of Sciences of the United States of America 99 9 2002 6163 6168