Matrix representation of cell structure, functional processes and evolution: Part V of a general theory

Abstract

The purpose of this paper is to formulate a compact analytical representation of cell structure, functional processes and evolution. In this formulation, the individual molecular structures are represented by their force-field surfaces. Complementary active sites on these surfaces permit molecular interactions. In cells, these interactions are further regulated by barrier systems in time, space, specificity, and energy. In terms of these parameters, evolution can be represented (modeled) as a random walk in a multi-dimensional space, subject to constraints. In this paper, the various parameters are integrated into a single compact matrix (stack) representation (a three index array). Cell life cycle and functional processes can be represented as a sequence of quantized, time-dependent changes in the representation matrix, subject to specified constraints. Cell evolution can be modeled by generating allowed matrix combinations. This theoretical approach has applications in: (1) ordering and interpreting experimental findings into the matrix representation. Missing matrix elements can be predicted, to be confirmed experimentally; (2) theoretical analysis and prediction of cell regulatory processes and the possible pathological failures; (3) theoretical derivation of the possible biological structures and functional processes, modeling possible pathways of cell and molecular evolution in terms of the matrix representation.