Experiments with a universe for molecular modelling of biological processes

A computer simulation program and results of preliminary simulations of an abstract two-dimensional universe are presented, in which biological and physical processes can be modelled at the molecular level. Two types of permanent elements (atoms) occupy squares of the universe: called 0 and 1. Atoms sharing a common square form a particle, with properties determined by its component atoms. Atoms, particles, and complexes of particles move and collide according to rules like those of classical mechanics. At a higher level of organization, the string of atoms in a particle is viewed as a program, whose execution can affect the space around the particle. The computer program (written in Turbo-Pascal language) can simulate the evolution of the universe starting from any given initial configuration of the particles. Three examples of simulations, showing the development of ordered spatial structures from initial sets of randomly distributed particles, illustrate the universe's potential in modelling various molecular processes.