TY - GEN
T1 - Automatic design of DNA logic gates based on kinetic simulation
AU - Kawamata, Ibuki
AU - Tanaka, Fumiaki
AU - Hagiya, Masami
PY - 2009/12/11
Y1 - 2009/12/11
N2 - Recently, DNA logic gates and DNA machines have been developed using only a simple complementary base pairing of DNA, that is, hybridization and branch migration. Because such reaction systems have been designed by trial and error, it has been difficult to design a complex system and to correctly verify the reaction. The purpose of this research is to develop a method for automatically searching and designing DNA logic gates based on a kinetic simulation. Since the solution space that should be searched is quite large, a simulated-annealing method is used to search for a highly evaluated system from many candidates and find a semi-optimal one. A simulator based on a kinetic model is developed, which calculates the time change of concentrations of abstracted DNA molecules. An evaluation function, in which the evaluation value rises when the logic gate works correctly, is also designed. The effectiveness of the proposed method is evaluated experimentally with an AND gate, which is designed automatically.
AB - Recently, DNA logic gates and DNA machines have been developed using only a simple complementary base pairing of DNA, that is, hybridization and branch migration. Because such reaction systems have been designed by trial and error, it has been difficult to design a complex system and to correctly verify the reaction. The purpose of this research is to develop a method for automatically searching and designing DNA logic gates based on a kinetic simulation. Since the solution space that should be searched is quite large, a simulated-annealing method is used to search for a highly evaluated system from many candidates and find a semi-optimal one. A simulator based on a kinetic model is developed, which calculates the time change of concentrations of abstracted DNA molecules. An evaluation function, in which the evaluation value rises when the logic gate works correctly, is also designed. The effectiveness of the proposed method is evaluated experimentally with an AND gate, which is designed automatically.
UR - http://www.scopus.com/inward/record.url?scp=71449124315&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=71449124315&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-10604-0_9
DO - 10.1007/978-3-642-10604-0_9
M3 - Conference contribution
AN - SCOPUS:71449124315
SN - 364210603X
SN - 9783642106033
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 88
EP - 96
BT - DNA Computing and Molecular Programming - 15th International Conference, DNA 15, Revised Selected Papers
T2 - 15th International Conference on DNA Computing and Molecular Programming, DNA 15
Y2 - 8 June 2009 through 11 June 2009
ER -