Genetic Networks Described in Stochastic Pi Machine (SPiM)
Programming Language: Compositional Design |
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Freiburg University, Baden-Wuerttemberg, Germany |
| *Corresponding author: |
Dr. Andrew Kuznetsov,
Freiburg University, Germany |
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Received September 29, 2009; Accepted October 29, 2009; Published
October 29, 2009 |
Citation:
Kuznetsov A (2009) VMD: Genetic Networks Described in Stochastic Pi Machine (SPiM) Programming Language: Compositional Design. J Comput Sci Syst Biol 2: 272-282. doi:10.4172/jcsb.1000042 |
Copyright: © 2009 Kuznetsov A. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium,
provided the original author and source are credited. |
| Abstract |
| If biological objects are created by natural selection, why are
they composed of discrete modules? What has been the nature
of mutations since the Darwinian epoch? This paper presents
examples of genetic circuits in terms of stochastic π-calculus; a
new mathematical language for nanosystems. The author used a
constructor of five elements such as decay, null gate, gene product,
and negative and positive gates. These primitives were applied
to design genetic switches, oscillators, feedforward and
feedback loops, pulse generators, memory elements, and combinatorial
logics. The behaviors of those circuits were investigated – functions, such as oscillations or a spontaneous pulse generation were performed simply, flip-flops between stable
states occurred in the noisy environment. The modular essence
of π-calculus and the following up features of Stochastic Pi
Machine (SPiM) programming language allowed us to change
the topology of networks that resembled a gene exchange in
nature. Other types of mutations were considered as variations
in parameters. Perturbations modified system behavior in unpredictable
ways that generated diversity for a possible future
design by selection of appropriative variants. |
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