A New Approach to Computing Equilibrium State of Combinatorial Hybridization Reaction Systems

Satoshi Kobayashi

1st International ICST Workshop on Computing and Communications from Biological Systems: Theory and Applications

Research Article

A New Approach to Computing Equilibrium State of Combinatorial Hybridization Reaction Systems

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@INPROCEEDINGS{10.4108/ICST.BIONETICS2007.2376,
    author={Satoshi Kobayashi},
    title={A New Approach to Computing Equilibrium State of Combinatorial Hybridization Reaction Systems},
    proceedings={1st International ICST Workshop on Computing and Communications from Biological Systems: Theory and Applications},
    proceedings_a={CCBS},
    year={2008},
    month={8},
    keywords={DNA   RNA   convex programming   equilibrium   hypergraphs   molecular computing   secondary structure   symmetry   tile assembly},
    doi={10.4108/ICST.BIONETICS2007.2376}
}

Satoshi Kobayashi
Year: 2008
A New Approach to Computing Equilibrium State of Combinatorial Hybridization Reaction Systems
CCBS
IEEE
DOI: 10.4108/ICST.BIONETICS2007.2376

Satoshi Kobayashi¹^,*

1: Dept. of Computer Science, Univ. of Electro-Communications 1-5-1, Chofugaoka, Chofu, Tokyo 182-8585, JAPAN

*Contact email: satoshi@cs.uec.ac.jp

Abstract

This paper provides a new approach to the efficient analysis of equilibrium state of a combinatorial Hybridization Reaction System (HRS, for short) in which exponentially many assemblies of molecules are generated from a set of molecules. The proposed framewok provides a method to overcome the combinatorial explosion problem of resultant assemblies. The key idea exists in the locality of HRSs. The goal of this paper is to present a general theory for the efficient computation of equilibrium states

Keywords: DNA RNA convex programming equilibrium hypergraphs molecular computing secondary structure symmetry tile assembly

Published: 2008-08-29
Modified: 2011-07-07

: http://dx.doi.org/10.4108/ICST.BIONETICS2007.2376