Name
Abstract | ||
|---|---|---|
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. Two
approaches for simulation are available: threshold and stochastic. The simulator 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 for the threshold approach, the former avoids a combinatorial explosion by setting a threshold
on concentrations of molecules that can take part in reactions. In addition, the stochastic approach is also available for
simulations which are hard by the threshold approach. Some simulation results by the approaches are also presented: computation
of Boolean circuits, whiplash PCR, formation of DNA tiles and polymerase chain reaction (PCR). We also integrate simulating
DNA computation and fitting parameters by the genetic algorithm (GA), where simulation results are used as evaluation functions
for the genetic algorithm. The integration is applied to find good protocols for PCR amplification. A trial to refine the
reaction model for hybridization is also described before the final discussion on the simulator. |
Year | DOI | Venue |
|---|---|---|
2001 | 10.1007/s005000000062 | Soft Comput. |
Keywords | Field | DocType |
dna sequence,differential equation,polymerase chain reaction,boolean circuits,genetic algorithm,evaluation function,dna computing | Computer science,Theoretical computer science,Artificial intelligence,Combinatorial explosion,Genetic algorithm,Computation,Differential equation,Mathematical optimization,Boolean circuit,Simulation,Algorithm,DNA,Machine learning,DNA computing | Journal |
Volume | Issue | Citations |
5 | 1 | 5 |
PageRank | References | Authors |
0.49 | 0 | 3 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Akio Nishikawa | 1 | 53 | 7.01 |
| Masayuki Yamamura | 2 | 242 | 37.62 |
| Masami Hagiya | 3 | 649 | 102.85 |