A dynamical computation universality, which is dealt with in the paper, employs an architecture-less collison-based approache. Autonomous signals travel in a uniform space and perform computation by colliding with other travelling signals. Truth-values are represented by either absence or presence of information quanta or by various states of the quanta. Three key stones might be put in a basis of collision-based computing: proof of universality of Game of Life via collision of glider streams [1], construction of billiard ball model in the context of the conservative logic [2] and development of a concept of computation in cellular automata with soliton-like patterns [3]. These ideas are evolved to a theory of dynamical computing in excitable lattices, which is developed in [4].

The paper explores material basis of dynamical universal computing in non-linear media and varieties of collision based gates. The interactions of mobile self-localizations in DNA molecules, monomolecular arrays of Scheibe aggregates and tubulin arrays of microtubules are discussed in the context of existence and morphonomy of collision-based logical gates.

The first part of the paper deals with breather collision-based gates that can be implemented in a DNA molecule. Basing on numerical results of [5] we construct a catalogue of logical gates that are realized in collisions between breathers and impurities in the DNA molecule. The findings are discussed in the context of particle machines [6] and filtrons [7]. In the second part we speculate about collisions of excitons in monomolecular arrays of Scheibe aggregates [8]. We also set up analogies between cellular automata models of excitable media [4] and excitable monomolecular arrays. The third part of the paper discovers a possibility for collision-based computing in microtubules, where quanta of information are represented by either finite groups of antialigned dipoles [9] or solitons [10].

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^{*}Corresponding Address:
Andrew Adamatzky
Intelligent Autonomous Systems Lab
University of the West of England
DuPont Building, Frenchay Campus, Coldharbour Lane
Bristol, BS16 1QY United Kingdom
E-mail: Andrew.Adamatzky@uwe.ac.uk
Web: http://www.ias.uwe.ac.uk/~a-adamat/