Abstract
Two new molecular algorithms are presented that are
designed for the improvement of efficiency and
reliability of DNA computing. The first algorithm
introduces an evolutionary cycle to guide chemical
reactions of DNA molecules. The second molecular
algorithm extends the first one by adding another
evolutionary loop for optimizing encodings of the
problem instance. Just as genetic programming is a
method for programming conventional computers by means
of natural evolution, our approach, which might be
called molecular programming, provides a method for
programming biocomputers by means of artificial
evolution. Simulations have been performed with the
Hamiltonian path problem to verify the positive effect
of the presented molecular algorithms on the
reliability and efficiency of DNA computing.
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