Virtual DNA simulator and protocol design by GA

摘要

Many algorithms and protocols for DNA computing have been proposed so far, but most of them remain mere proposals and their feasibility has not yet been verified. Even in cases when in vitro experiments are possible, it is desirable to verify the feasibility in advance. We developed a simulator to aid those who design algorithms and protocols for DNA computing. In this simulator, abstract sequences instead of real DNA sequences are used to represent molecules in order to increase efficiency of simulations. It consists of two main parts, one for finding reactions among existing molecules and generating new ones, and the other for numerically solving differential equations to calculate the concentration of each molecule. The two parts rely on each other. In particular, the former avoids a combinatorial explosion by setting a threshold on concentrations of molecules that can take part in reactions. Some simulation results are also presented: computation of Boolean circuits, formation of DNA tiles and simulation of polymerase chain reaction (PCR). As for PCR, we also tried to find good protocols for PCR amplification using Genetic Algorithm (GA).