Abstract:
:Simple computation can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous-time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it. We conclude by introducing example mechanisms that can implement such circuits experimentally and discuss their individual strengths and weaknesses.
journal_name
ACS Synth Bioljournal_title
ACS synthetic biologyauthors
Boemo MA,Lucas AE,Turberfield AJ,Cardelli Ldoi
10.1021/acssynbio.5b00275subject
Has Abstractpub_date
2016-08-19 00:00:00pages
878-84issue
8issn
2161-5063journal_volume
5pub_type
杂志文章abstract::A major force shaping form and patterns in biology is based in the presence of amplification mechanisms able to generate ordered, large-scale spatial structures out of local interactions and random initial conditions. Turing patterns are one of the best known candidates for such ordering dynamics, and their existence ...
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journal_title:ACS synthetic biology
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journal_title:ACS synthetic biology
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