My current research interest is centered around building the model of the living cell on both the conceptual and computational levels. The conceptual model of the cell known as the Bhopalator was formulated about 20 years ago [1,2] and has been applied to toxicology [3,4] and pharmacology [5]. There are two major theories supporting the Bhopalator model of the cell – i) the conformon theory of molecular machines and motors [6,7], and ii) the cell language theory of intracellular molecular interactions [8,9,10]. These two theories have recently been integrated into a single theory called Molecular Information Theory [11].

In the coming decades, the conceptual theoretical model of the cell and its associated theories of molecular and cell biology are expected to play a major role in cell biology and related fields including toxicology, particularly in the field of the microarray technology (for an introductory review, see [12]). The massive digital data that have been, and are being continuously, generated by this revolutionary technique invented in 1995 may not be interpretable without equally powerful conceptual models of the living cell itself, just as the massive atomic spectral data that had accumulated in physics throughout the 19 th century could not be interpreted correctly until Bohr formulated his model of the atom in 1913 [11]. Our preliminary analysis of the yeast cell cycle microarray data reported by M. Eisen's group at the Stanford University suggests that, due to the instability of mRNA levels, only about 30% of the data reflects the rates of gene expression and the rest may not be directly related to the gene expression process per se [13].

References :

[1] Ji, S. (1985). The Bhopalator—A Molecular Model of the Living Cell Based on the Concepts of Conformons and Dissipative Structures. J. Theoret. Biol . 116 :399-426.

[2] Ji, S. (2002). The Bhopalator: An Information/Energy Dual Model of the Living Cell (II). Fundamenta Informaticae 49 (1-3):147-165.

[3] Ji, S. (1987). A General Theory of Chemical Cytotoxicity Based on the Molecualr Model of the Living Cell, the Bhopalator. Arch. Toxicol. 60 :95-102.

[4] Ji, S. (1997). A Cell Linguistic Analysis of Apoptosis. Comments Toxicology 5 (6):571-585.

[5] Ji, S. (2000-2004). Theoretical Aspects of Pharmacology, an elective course taught at the Ernest Mario School of Pharmacy, Rutgers University, Piscataway, N.J. Some lecture notes in Power Points are available here.

[6] Ji, S. (1974). A General Theory of ATP Synthesis and Utilization. Ann. N.Y. Acad. Sci. 227 :211-226.

[7] Ji, S. and Ciobanu, G. (2003). Conformon-driven biopolymer shape changes in cell modeling. BioSystems 70 :165-181.

[8] Ji, S. (1997). Isomorphism between cell and human languages: molecular biological, bioinformatic and linguistic implications. BioSystems 44 :17-39.

[9] Ji, S. (1999). Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics. Ann. N.Y. Acad. Sci. 870 :411-417.

[10] Ji, S. (2002). Microsemiotics of DNA. Semiotica 138 (1/4):15-42.

[11] Ji, S. (2004). Molecular Information Theory: Solving the Mysteries of DNA. In : Modeling in Molecular Biology (Ciobanu, G., and Rozenberg, G., eds.), Natural Computing Series, Springer, Berlin. Pp. 141-150.

[12] Watson, S. J., and Akil, H. (1999). Gene Chips and Arrays Revealed: A Primer on Their Power and Their Uses. Biol. Psychiatry 45 :533-543.

[13] Ji, S., J. Eom, and Miura, R. (2004). Kinetic Model-Based Analysis of Microarray Data. The 7 th International Meeting of the Microarray Gene Expression Data Society , The University of Toronto, Toronto, September 8-10. Abstract submitted.