COLLISION-BASED COMPUTING IN BIOPOLYMERS AND THEIR AUTOMATA MODELS

Abstract

In collision-based computing, quanta of information are represented by autonomous mobile signals. The signals travel in a uniform architectureless medium. They collide to each other. Assuming the presence or abscence of a signal represent truth or falsity values of logical variable, we can consider logical functions are calculated at the sites of signals' collision. Physically, the signals are localized compact disturbances of medium's characteristics. In this paper, we extensively exploit results published in Refs. 1–7. We consider three types of localizations: breathers in one-dimensional arrays of DNA molecules, excitons and groups of antialigned dipoles in two-dimensional arrays of Scheibe aggregates and microtubules respectively. Several forms of logical gates are extracted from published results on numerical simulation of breathers and excitons. In cellular automata models, we study interactions of the localizations with each other. We show what kinds of logical gates can be realized in such interactions. Parallels between physical and discrete automata models are provided.