Solving Hard Computational Problems by In Silico Molecular Catalysis
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ABSTRACT:
This paper is centered on the introduction of the basic ideas of simulated catalytic reactions. We designed a distributed stochastic algorithm that simulates reaction systems wherein the molecular species are being represented either by a human genomic contig panel, a Hamiltonian cycle, or an aircraft landing schedule. We created a chemical universe governed by reactions that can alter genomic sequences, re-order Hamiltonian cycles, or reschedule an aircraft landing program. We considered molecular masses as metrics of goodness of solutions such as radiation hybrid (RH) vector similarities, costs of Hamiltonian cycles, and penalty costs for landing an aircraft before and after target landing times. Tested by solving in tandem with deterministic algorithms, this novel method was demonstrated to have superior processing rate for combinatronics of finding the minima RH vector similarities of genomic data, minima costs in Hamiltonian cycles of the traveling salesman, and minima costs for landing aircraft before or after target landing times.
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