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2016 ; 632
(ä): 43-73
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A strand graph semantics for DNA-based computation
#MMPMID27293306
Petersen RL
; Lakin MR
; Phillips A
Theor Comput Sci
2016[Jun]; 632
(ä): 43-73
PMID27293306
show ga
DNA nanotechnology is a promising approach for engineering computation at the
nanoscale, with potential applications in biofabrication and intelligent
nanomedicine. DNA strand displacement is a general strategy for implementing a
broad range of nanoscale computations, including any computation that can be
expressed as a chemical reaction network. Modelling and analysis of DNA strand
displacement systems is an important part of the design process, prior to
experimental realisation. As experimental techniques improve, it is important for
modelling languages to keep pace with the complexity of structures that can be
realised experimentally. In this paper we present a process calculus for
modelling DNA strand displacement computations involving rich secondary
structures, including DNA branches and loops. We prove that our calculus is also
sufficiently expressive to model previous work on non-branching structures, and
propose a mapping from our calculus to a canonical strand graph representation,
in which vertices represent DNA strands, ordered sites represent domains, and
edges between sites represent bonds between domains. We define interactions
between strands by means of strand graph rewriting, and prove the correspondence
between the process calculus and strand graph behaviours. Finally, we propose a
mapping from strand graphs to an efficient implementation, which we use to
perform modelling and simulation of DNA strand displacement systems with rich
secondary structure.
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