Approaching mathematical model of the immune network based DNA Strand Displacement system. 2013

Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
Department of Micro-Nano Systems Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan. Electronic address: rizki@robo.mein.nagoya-u.ac.jp.

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.

UI MeSH Term Description Entries
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D008962 Models, Theoretical Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment. Experimental Model,Experimental Models,Mathematical Model,Model, Experimental,Models (Theoretical),Models, Experimental,Models, Theoretic,Theoretical Study,Mathematical Models,Model (Theoretical),Model, Mathematical,Model, Theoretical,Models, Mathematical,Studies, Theoretical,Study, Theoretical,Theoretical Model,Theoretical Models,Theoretical Studies
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D003658 Decision Making, Computer-Assisted Use of an interactive computer system designed to assist the physician or other health professional in choosing between certain relationships or variables for the purpose of making a diagnostic or therapeutic decision. Computer-Assisted Decision Making,Medical Decision Making, Computer-Assisted,Computer Assisted Decision Making,Decision Making, Computer Assisted,Medical Decision Making, Computer Assisted
D004277 DNA, Single-Stranded A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle. Single-Stranded DNA,DNA, Single Stranded,Single Stranded DNA
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D018448 Models, Immunological Theoretical representations that simulate the behavior or activity of immune system, processes, or phenomena. They include the use of mathematical equations, computers, and other electrical equipment. Immunological Models,Immunologic Model,Model, Immunologic,Immunologic Models,Immunological Model,Model, Immunological,Models, Immunologic
D039301 Computers, Molecular Computers whose input, output and state transitions are carried out by biochemical interactions and reactions. DNA Computers,RNA Computers,DNA Computation,Molecular Computation,RNA Computation,Computation, DNA,Computation, Molecular,Computation, RNA,Computations, DNA,Computations, Molecular,Computations, RNA,Computer, DNA,Computer, Molecular,Computer, RNA,Computers, DNA,Computers, RNA,DNA Computations,DNA Computer,Molecular Computations,Molecular Computer,Molecular Computers,RNA Computations,RNA Computer

Related Publications

Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
January 2021, IEEE transactions on nanobioscience,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
January 2022, IEEE/ACM transactions on computational biology and bioinformatics,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
July 2011, Nature,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
January 2022, IEEE/ACM transactions on computational biology and bioinformatics,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
January 2014, Bio Systems,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
June 2021, Chemphyschem : a European journal of chemical physics and physical chemistry,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
September 2021, ACS synthetic biology,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
April 2021, ACS applied materials & interfaces,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
August 2017, ACS omega,
Rizki Mardian, and Kosuke Sekiyama, and Toshio Fukuda
August 2020, Angewandte Chemie (International ed. in English),
Copied contents to your clipboard!