A new channel coding algorithm based on phosphorylation/dephosphorylation-proteins and GTPases

Jian-Qin Liu; Hidefumi  Sawai

1st International ICST Conference on Bio Inspired Models of Network, Information and Computing Systems

Research Article

A new channel coding algorithm based on phosphorylation/dephosphorylation-proteins and GTPases

Cite: BibTeX Plain Text

@INPROCEEDINGS{10.1145/1315843.1315853,
    author={Jian-Qin Liu and Hidefumi  Sawai},
    title={A new channel coding algorithm based on phosphorylation/dephosphorylation-proteins and GTPases},
    proceedings={1st International ICST Conference on Bio Inspired Models of Network, Information and Computing Systems},
    publisher={ACM},
    proceedings_a={BIONETICS},
    year={2006},
    month={12},
    keywords={Molecular communication; nano-scale biologically engineered systems; biological computing},
    doi={10.1145/1315843.1315853}
}

Jian-Qin Liu
Hidefumi Sawai
Year: 2006
A new channel coding algorithm based on phosphorylation/dephosphorylation-proteins and GTPases
BIONETICS
ACM
DOI: 10.1145/1315843.1315853

Jian-Qin Liu¹^,*, Hidefumi Sawai²^,*

1: Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology, 588-2, Iwaoka, Nishi-ku, Kobe, Hyogo, 651-2492, Japan
2: Kobe Advanced ICT Research Center National Institute of Information and Communications Technology, 588-2, Iwaoka, Nishi-ku, Kobe, Hyogo, 651-2492, Japan

*Contact email: liu@nict.go.jp, sawai@nict.go.jp

Abstract

Although molecular signaling of phosphorylation/dephosphorylation-proteins and GTPases has been extensively studied in molecular biology, it is still an open problem as to how information be coded in these molecules for molecular communication. In this paper, we propose a new channel coding algorithm based on signaling pathways in cells, extending our previous work on source codes to channel codes. The time complexity of the encoding/decoding algorithm we proposed is O(Qxm+Lx(P+ζ)) where Q refers to the number of the elements in the set of information vectors, m refers to the length of GTPase codeword, L refers to the number of the GTPase groups, P is the number of phosphorylation/dephosphorylation-proteins, ζ refers to the number of GTPases that are embedded in X'-codeword. This result shows the algorithm is theoretically realistic because the encoding/decoding process in a linear order time complexity is efficient. This benefits the studies on engineered cell communication in terms of information theory.

Keywords: Molecular communication; nano-scale biologically engineered systems; biological computing

Published: 2006-12-13
Publisher: ACM

: http://dx.doi.org/10.1145/1315843.1315853