title: Approaching mathematical model of the immune network based DNA Strand Displacement system.
abstract: One biggest obstacle in molecular programming is that there is still no direct method to compile any existed mathematical model into biochemical reaction in order to solve a computational problem. In this paper, the implementation of DNA Strand Displacement system based on nature-inspired computation is observed. By using the Immune Network Theory and Chemical Reaction Network, the compilation of DNA-based operation is defined and the formulation of its mathematical model is derived. Furthermore, the implementation on this system is compared with the conventional implementation by using silicon-based programming. From the obtained results, we can see a positive correlation between both. One possible application from this DNA-based model is for a decision making scheme of intelligent computer or molecular robot.
authors.affiliation: Department of Micro-Nano Systems Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan. Electronic address: rizki@robo.mein.nagoya-u.ac.jp.
authors.forename: Rizki
authors.initials: R
authors.lastname: Mardian
authors.forename: Kosuke
authors.initials: K
authors.lastname: Sekiyama
authors.forename: Toshio
authors.initials: T
authors.lastname: Fukuda
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D039301:Computers, Molecular / Q000639:trends*; D004277:DNA, Single-Stranded / Q000378:metabolism; D003658:Decision Making, Computer-Assisted; D008956:Models, Chemical; D018448:Models, Immunological; D008962:Models, Theoretical
chemical_list: D004277:DNA, Single-Stranded
keywords: Chemical Reaction Network; DNA Strand Displacement; Immune Network Theory; Mathematical model; Molecular programming