Towards the modeling of cell communication and computation using the shape algebra of biopolymers*

One of the critical components of the mechanisms of cell communication and cell computing has been postulated to be spaceand time-organized teleonomic (or goaldirected) shape changes of biopolymers that are driven by exergonic chemical reactions catalyzed by biopolymer shape changes themselves. The generalized Franck-Condon principle resolves the apparent paradox arising when a coupling is attempted between endergonic biopolymer shape changes and the exergonic chemical reactions that are catalyzed by biopolymer shape changes themselves. The agents that induce shape changes in biopolymers are referred to as shape changers, and conformons, defined in 1972-1985 as sequence-specific conformational strains resident in biopolymers, have been identified as shape changers of biopolymers. Given a set of spaceand timeorganized teleonomic shape changes of biopolymers driven by shape changers, conformons, all of the functions of the cell can be accounted for in molecular terms at least in principle. To convert a conceptual model of the cell into a computer model of cell communication and cell computation, it is necessary to encode the conceptual model into a formal model represented in terms of an algebraic language. To this end, we used the process algebra developed by R. Milner et al in order to construct what is here referred to as “shape algebra” that is capable of describing complex and mobile patterns of interactions that occur among biomolecules inside the cell, including proteins and DNA, leading to cell functions.