Intelligent models of the quantitative behavior of microbial systems

Food and Bioprocess Technology

Volumn 2, Issue 2, 2009, Pages 122-137

  Patnaik, Pratap R ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

AI models; Cellular intelligence; Hybrid systems; Mechanistic models; Microbial cultures; Quantitative behavior

Indexed keywords

AI MODELS; CELLULAR INTELLIGENCE; MECHANISTIC MODELS; MICROBIAL CULTURES; QUANTITATIVE BEHAVIOR;

CELL CULTURE; CELLULAR NEURAL NETWORKS; ELECTRIC GROUNDING; EXPERT SYSTEMS; HYBRID COMPUTERS; INTELLIGENT SYSTEMS;

HYBRID SYSTEMS;

EID: 65249118792     PISSN: 19355130     EISSN: 19355149     Source Type: Journal    
DOI: 10.1007/s11947-008-0112-8     Document Type: Review

References (90)

1. Altenberg, L. (1995). The schema theorem and Price's theorem. In D. Whitley, & M. Vose (Eds.), Foundations of genetic algorithms 3 (pp. 23-49). San Francisco, USA: Morgan Kaufmann.
2. W. Babel J. U. Ackerman U. Breuer 2001 Physiology, regulations, and limits of the synthesis of poly (3HB) Advances in Biochemical Engineering, Biotechnology 71 125 157
3. J. A. Baeza E. C. Ferreira J. Laufuente 2000 Knowledge-based supervision and control of waste-water treatment plant: A real-time application Water Science and Technology 41 129 137 (Pubitemid 30629406)
4. P. M. Bapat D. Das S. V. Sohoni P. P. Wangikar 2006 Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterranei S699, a case study Microbial Cell Factories 5 32
5. W. M. Barnett 1992 Knowledge-based expert system applications in waste treatment operation and control ISA Transactions 31 53 60
6. M. Cakmakci 2007 Adaptive neuro-fuzzy modeling of anaerobic digestion of primary sedimentation sludge Bioprocess and Biosystems Engineering 30 349 357 (Pubitemid 350092699)
7. L. Z. Chen S. K. Nguang X. M. Li X. D. Chen 2004 Soft sensors for on-line biomass measurements Bioprocess and Biosystems Engineering 26 191 195 (Pubitemid 38657145)
8. V. C. P. Chen D. K. Rollins 2000 Issues regarding artificial neural network modeling for reactors and fermenters Bioprocess and Biosystems Engineering 22 85 93 (Pubitemid 30097252)
9. W. B. Z. Chu A. Constantinides 1998 Modeling, optimization and computer control of the cephalosporin C fermentation process Biotechnology and Bioengineering 32 277 288
10. G. Cybenko 1989 Approximation by superpositions of a sigmoidal function Mathematics of Control, Signals and Systems 2 303 314
11. K. Deb A. Pratap S. Agarwal T. Meyarivan 2002 A fast and elitist multi-objective genetic algorithm: NSGA-II IEEE Transactions on Evolutionary Computation 6 182 197 (Pubitemid 34555372)
12. K. Desai Y. Badhe S. S. Tambe B. D. Kulkarni 2006 Soft-sensor development for fed-batch bioreactors using support vector regression Biochemical Engineering Journal 27 225 239 (Pubitemid 41531666)
13. P. Dhurjati D. Ramkrishna M. C. Flickinger G. T. Tsao 1985 A cybernetic view of microbial growth: modeling microbes as optimal strategists Biotechnology and Bioengineering 27 1 9 (Pubitemid 15144379)
14. P. Doshi R. Rengaswamy K. V. Venkatesh 1997 Modelling of microbial growth for sequential utilization in a multi-substrate environment Process Biochemistry 32 643 650 (Pubitemid 27494589)
15. Fuzzy logic toolbox. User's guide. MathWorks: Natick, MD, USA. Ch.2.
16. K. G. Gadkar I. J. Doyle III T. J. Crowley J. D. Varner 2003 Cybernetic model predictive control of a continuous bioreactor with cell recycle Biotechnology Progress 19 1487 1497 (Pubitemid 37250039)
17. K. G. Gadkar S. Mehra J. Gomes 2005 On-line adaptation of neural networks for bioprocess control Computers & Chemical Engineering 29 1047 1057 (Pubitemid 40417821)
18. Gall, R. A. B., & Patry, G. (1989). Knowledge-based system for the diagnosis of an activated sludge plant. In G. Patry, & D. Chapman (Eds.), Dynamic modeling and expert systems in wastewater engineering (pp. 193-240). London: Lewis.
19. V. Galvanauskas R. Simutis A. Lubbert 2004 Hybrid process models for process optimization, monitoring and control Bioprocess and Biosystems Engineering 26 393 400
20. 2 signals from a bioreactor gas outflow using a committee of constructive neural networks Bioprocess and Biosystems Engineering 31 101 109
21. Goldberg, D. E. (1989). Genetic algorithms in search, optimization and machine learning. Addison-Wesley: New York.
22. M. J. Guardia A. Gambhir A. F. Europa D. Ramkrishna W. S. Hu 2000 Cybernetic modeling and regulation of metabolic pathways in multiple steady states of hybridoma cells Biotechnology Progress 16 847 853
23. T. Hanai A. Katayama H. Honda T. Kobayashi 1997 Automatic fuzzy modeling for Ginjo sake brewing process using fuzzy neural networks Journal of Chemical Engineering of Japan 30 94 100 (Pubitemid 127603440)
24. T. Hanai T. Nishida E. Ohkusu H. Honda T. Kobayashi 1995 Experimental fermentation of Ginjo sake with two fuzzy controls Seibutsu-kogaku Jpn 73 283 289
25. Hartley, S. J. (1998). Concurrent programming: The java programming language. Oxford University Press: New York.
26. Hassoun, M. H. (1995). Fundamentals of artificial neural networks. MIT: Cambridge, U.S.A.
27. B. J. Hodgson C. N. Taylor M. Ushio J. R. Leigh T. Kalganova F. Baganz 2004 Intelligent monitoring of bioprocesses: a comparison of structured and unstructured approaches Bioprocess and Biosystems Engineering 26 353 359
28. Holland, J. H. (1975). Adaptation in natural and artificial systems. University of Michigan: Ann Arbor, MI, USA.
29. J. I. Horiuchi 2002 Fuzzy modeling and control of biological processes Journal of Bioscience and Bioengineering 94 574 578 (Pubitemid 36132557)
30. K. Hornik M. Stinchcombe H. White 1990 Multilayer feedforward networks are universal approximators Neural Networks 2 359 366
31. V. L. Huong J. Votruba I. Stuchl 1994 Bioengineering analysis of incomplete data for waste water treatment by fuzzy expert system Collection of Czechoslovak Chemical Communications 59 595 602
32. Isidori, A. (1999). Nonlinear control systems. Springer: New York.
33. S. James R. Legge H. Budman 2000 On-line estimation in bioreactors: a review Reviews in Chemical Engineering 14 311 340 (Pubitemid 32046720)
34. S. James R. Legge H. Budman 2002 Comparative study of black box and hybrid estimation methods in fed-batch fermentation Journal of Process Control 12 113 121
35. J. S. R. Jang 1993 ANFIS: adaptive-network-based fuzzy inference systems IEEE Transactions on Man and Cybernetics 23 665 685
36. Jang, J. S. R., Sun, C. T., & Mizutani, E. (1997). Neuro-fuzzy and soft computing: A computational approach to learning and machine intelligence. Prentice-Hall: London.
37. S. Khanna A. K. Srivastava 2005 A simple structured mathematical model for biopolymer (PHB) production Biotechnology Progress 21 830 838 (Pubitemid 40772288)
38. B. M. Kim S. W. Kim D. R. Yang 2003 Cybernetic modeling of the cephalosporin C fermentation process by Cephalosporium acremomiun Biotechnology Letters 25 611 616 (Pubitemid 36536563)
39. M. Kishimoto T. Omasa Y. Katakura K. Suga K. Okumura 2000 Efficient production of desulfurizing cells with the aid of an expert system Biochemical Engineering Journal 5 143 147 (Pubitemid 30327016)
40. D. S. Kompala D. Ramkrishna J. B. Jansen G. T. Tsao 1986 Investigation of bacterial growth on multiple substrates: experimental evaluation of cybernetic models Biotechnology and Bioengineering 28 1044 1055 (Pubitemid 16588537)
41. Korb, K. B., & Nicholson, A. E. (2004). Bayesian artificial intelligence. CRC: Baton Rouge.
42. S. Y. Lee H. C. Lim J. J. Hong 1997 Application of nonsingular transformation to on-line optimal control of poly-β-hydroxybutyrate fermentation Journal of Biotechnology 55 135 150 (Pubitemid 27339259)
43. F. C. Lee G. P. Rangaiah A. K. Ray 2007 Multi-objective optimization of an industrial penicillin V bioreactor train using non-dominated sorting genetic algorithm Biotechnology and Bioengineering 98 586 598 (Pubitemid 47556127)
44. T. M. Leib C. J. Pereira J. Villadsen 2001 Bioreactors: a chemical engineering perspective Chemical Engineering Science 56 5485 5497 (Pubitemid 32978616)
45. U. Lendenmann T. Egli 1998 Kinetic models for the growth of Escherichia coli with mixtures of sugars under carbon-limited conditions Biotechnology and Bioengineering 59 98 107 (Pubitemid 28232334)
46. G. Liden 2001 Understanding the bioreactor Bioprocess and Biosystems Engineering 24 273 279 (Pubitemid 34117838)
47. C. -F. Mandenius 2004 Recent developments in the monitoring, modeling and control of biological production systems Bioprocess and Biosystems Engineering 26 347 351
48. MathWorks (1995-1998). Matlab 5.3. MathWorks: Natick, MD, USA.
49. M. Matsumara T. Imanaka T. Yoshida H. Taguchi 1981 Modeling of cephalosporin C production and application to fed-batch culture Journal of Fermentation Technology 59 115 123
50. J. M. Modak H. C. Lim 1989 Feedback optimization of fed-batch fermentation Biotechnology and Bioengineering 30 528 540 (Pubitemid 17657480)
51. J. Monod 1949 The growth of bacterial cultures Annual Reviews of Microbiology 3 371 394
52. J. -G. Na Y. K. Chang B. H. Chung H. C. Lim 2002 Adaptive optimization of fed-batch culture of yeast by using genetic algorithms Bioprocess and Biosystems Engineering 24 299 308
53. K. Nakano R. Katsu K. Tada M. Matsumara 2000 Production of highly concentrated xylitol by Candida magnoliae under microaerobic condition by simple fuzzy control Journal of Bioscience and Bioengineering 89 372 376 (Pubitemid 30318039)
54. A. Namjoshi A. Kienle D. Ramkrishna 2003 Steady-state multiplicity in bioreactors: bifurcation analysis of cybernetic models Chemical Engineering Science 58 793 800 (Pubitemid 36310123)
55. A. Narang A. Konopka D. Ramkrishna 1997 The dynamics of microbial growth on mixtures of substrates in batch reactors Journal of Theoretical Biology 184 301 317 (Pubitemid 27096272)
56. E. R. Nucci R. G. Silva T. C. Gomes R. C. Giordano A. J. G. Cruz 2005 A fuzzy logic algorithm for identification of the harvesting threshold during PGA production by Bacillus megaterium Brazilian Journal of Chemical Engineering 22 521 527
57. T. Ohshiro Y. Izumi 1999 Microbial desulfurization of organic sulfur compounds in petroleum Bioscience, Biotechnology and Biochemistry 63 1 9 (Pubitemid 129555229)
58. P. A. Paraskevas I. S. Pantelakis T. D. Lekkas 1999 An advanced integrated expert system for wastewater treatment plants control Knowledge-Based Systems 12 355 361 (Pubitemid 30524126)
59. Y. S. Park Z. P. Shi S. Shiba C. Cayuela S. Iijima T. Kobayashi 1993 Application of fuzzy reasoning on control of glucose and ethanol concentrations in baker's yeast culture Applied Microbiology and Biotechnology 38 649 655 (Pubitemid 23054276)
60. Patnaik, P. R. (1998). Neural network applications to fermentation processes. In G. Subramanian (Ed.), Bioseparation and Bioprocessing, Vol. I, Ch.14. Wiley-VCH: Weinheim, Germany.
61. P. R. Patnaik 2000 Are microbes intelligent beings? An assessment of cybernetic modeling Biotechnology Advances 18 267 288 (Pubitemid 30600073)
62. P. R. Patnaik 2001 A simulation study of dynamic neural filtering and control of a fed-batch bioreactor under nonideal conditions Chemical Engineering Journal 84 533 541 (Pubitemid 34057336)
63. P. R. Patnaik 2001 Microbial metabolism as an evolutionary response: the cybernetic approach to modeling Critical Reviews in Biotechnology 21 155 175 (Pubitemid 32948325)
64. P. R. Patnaik 2001 Further enhancement of fed-batch strepokinase yield in the presence of inflow noise by coupled neural networks Process Biochemistry 37 145 151 (Pubitemid 32880523)
65. P. R. Patnaik 2002 Can imperfections help to improve bioreactor performance? Trends in Biotechnology 20 135 137 (Pubitemid 34242848)
66. P. R. Patnaik 2003 Oscillatory metabolism of Saccharomyces cerevisiae: an overview of mechanisms and models Biotechnology Advances 21 183 192 (Pubitemid 36516656)
67. P. R. Patnaik 2003 Effect of fluid dispersion on cybernetic control of microbial growth on substitutable substrates Bioprocess and Biosystems Engineering 25 315 321 (Pubitemid 36384735)
68. P. R. Patnaik 2003 An integrated hybrid neural system for noise filtering, simulation and control of a fed-batch recombinant fermentation Biochemical Engineering Journal 15 165 175 (Pubitemid 36834545)
69. P. R. Patnaik 2005 Process analysis in a disturbed environment during oscillatory metabolism of Saccharomyces ceresiae Indian Journal of Biotechnology 4 201 208 (Pubitemid 40780286)
70. P. R. Patnaik 2005 Neural network designs for poly-β-hydroxybutyrate production optimization under simulated industrial conditions Biotechnology Letters 27 409 415 (Pubitemid 40572971)
71. P. R. Patnaik 2006 External, extrinsic and intrinsic noise in cellular systems: analogies and implications for protein synthesis Biotechnology and Molecular Biology Reviews 1 123 129
72. P. R. Patnaik 2006 Hybrid filtering to rescue stable oscillations from noise-induced chaos in continuous cultures of budding yeast FEMS Yeast Research 6 129 138
73. A. Punal J. Rodriguez A. Franco E. F. Carrasco E. Roca J. M. Lema 2001 Advanced monitoring and control of anaerobic wastewater treatment plants: diagnosis and supervision by a fuzzy-based expert system Water Science and Technology 43 191 198 (Pubitemid 32479268)
74. Ramkrishna, D. (1982). A cybernetic perspective of microbial growth. In E. Papoutsakis, G. N. Stephanopoulos, & H. W. Blanch (Eds.), Foundations of Biochemical Engineering. Kinetics and Thermodynamics in Biological Systems (pp. 161-178), American Chemical Society: Washington DC.
75. D. Ramkrishna 2003 On modeling of bioreactors for control Journal of Process Control 13 581 589
76. O. Roeva T. Pencheva B. Hitzmann S. Tzonkov 2004 A genetic algorithms based approach for identification of Escherichia coli fed-batch fermentation Bioautomation 1 30 41
77. Russell, S., & Norvig, P. (2002). Artificial intelligence: A modern approach. NJ: Prentice-Hall.
78. K. San G. Stephanopoulos 1989 Optimization of fed-batch penicillin fermentation: a case of singular optimal control with state constraints Biotechnology and Bioengineering 34 72 78 (Pubitemid 19139889)
79. D. Sarkar J. M. Modak 2003 Optimization of fed-batch bioreactors using genetic algorithms Chemical Engineering Science 58 2283 2296 (Pubitemid 36705060)
80. Z. Shi K. Shimizu 1992 Neuro-fuzzy control of bioreactor systems with pattern recognition Journal of Fermentation and Bioengineering 74 39 45
81. S. Shiba Y. Nishida Y. S. Park S. Iijima T. Kobayashi 1994 Improvement of clone α-amylase gene expression in fed-batch culture of recombinant Saccharomyces cerevisiae by regulating both glucose and ethanol concentrations using a fuzzy contoller Biotechnology and Bioengineering 44 1055 1063 (Pubitemid 2156896)
82. S. Shioya K. Shimizu T. Yoshida 1999 Knowledge-based design and operation of bioprocess systems Journal of Bioscience and Bioengineering 87 261 266 (Pubitemid 29189948)
83. B. Sonnleiter 2000 Instrumentation of biotechnological processes Advances in Biochemical Engineering Biotechnology 66 1 64
84. J. V. Straight D. Ramkrishna 1994 Cybernetic modeling and regulation of metabolic pathways. Growth on complementary nutrients Biotechnology Progress 10 574 587
85. K. Suenari Y. Tsuchiya Y. Teshima J. Koizumi S. Nagai 1990 Performance of sake mash brewing with fuzzy control Hakkokogaku (Japanese) 68 131 136
86. Y. Tsuchiya J. Koizumi K. Suenari Y. Teshima S. Nagai 1990 Concentrations of fuzzy rules and a fuzzy simulation based on the control technique of Hiroshima Toji (experts) Hakkokogaku (Japanese) 68 123 129
87. I. ul-Haq H. Mukhtar 2006 Fuzzy logic control of bioreactor for enhanced biosynthesis of alkaline protease by an alkalophilic strain of Bacillus subtilis Current Microbiology 52 149 152 (Pubitemid 43260450)
88. J. Varner D. Ramkrishna 1998 Application of cybernetic models to metabolic engineering: Investigation of storage pathways Biotechnology and Bioengineering 58 282 291 (Pubitemid 28136389)
89. T. C. Zangirolami C. L. Johansen J. Nielsen S. B. Jorgensen 1997 Simulation of penicillin production in fed-batch cultivations using a morphologically structured model Biotechnology and Bioengineering 56 593 604 (Pubitemid 27505970)
90. K. Zuo H. -P. Cheng S. -C. Wu T. Wu 2006 A hybrid model combining hydrodynamic and biological effects for production of bacterial cellulose with a pilot plant airlift reactor Biochemical Engineering Journal 29 81 90