Automatic molecular design using evolutionary techniques

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Abstract
Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The individual molecules in a population are then evolved towards greater fitness by randomly combining parts of the better existing molecules to create new molecules. These new molecules then replace some of the less fit molecules in the population. We apply a unique genetic crossover operator to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Most prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph-representable systems such as circuits, transportation networks, metabolic pathways, and computer networks.

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