Computational Evolution of a Model Polymer that Folds to a Specified Target

A method is described for folding polymers to specific target conformations. The approach uses a fast but approximate dynamics algorithm, coupled with a genetic algorithm that is used to evolve the large number of free parameters needed. The dynamics algorithm uses a state transition matrix approach. At each time step, the distances between pairs of atoms are adjusted by shifting them from Dij to D ij+Sij where Sij is an element of the state transition matrix S. Atom pairs that are attractive have S ij <0 and pairs that are repulsive have S ij >0. The atomic movement is carried out by gradient minimizing the molecular mechanics energy of the molecule subject to harmonic distance constraints. The method is applied to a simple test case, a 19 atom 2-D polymer. The paper also shows that the S matrices can correctly fold a limited variety of initial conformations that differ from the one used during the evolution phase.