TY - GEN
T1 - Functional analysis of large-scale DNA strand displacement circuits
AU - Yordanov, Boyan
AU - Wintersteiger, Christoph M.
AU - Hamadi, Youssef
AU - Phillips, Andrew
AU - Kugler, Hillel
PY - 2013
Y1 - 2013
N2 - We present a method for the analysis of functional properties of large-scale DNA strand displacement (DSD) circuits based on Satisfiability Modulo Theories that enables us to prove the functional correctness of DNA circuit designs for arbitrary inputs, and provides significantly improved scalability and expressivity over existing methods. We implement this method as an extension to the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root circuit, together with the components used for its construction. We show that our method successfully verifies that certain designs function as required and identifies erroneous computations in others, even when millions of copies of a circuit are interacting with each other in parallel. Our method is also applicable in the verification of properties for more general chemical reaction networks.
AB - We present a method for the analysis of functional properties of large-scale DNA strand displacement (DSD) circuits based on Satisfiability Modulo Theories that enables us to prove the functional correctness of DNA circuit designs for arbitrary inputs, and provides significantly improved scalability and expressivity over existing methods. We implement this method as an extension to the Visual DSD tool, and use it to formalize the behavior of a 4-bit square root circuit, together with the components used for its construction. We show that our method successfully verifies that certain designs function as required and identifies erroneous computations in others, even when millions of copies of a circuit are interacting with each other in parallel. Our method is also applicable in the verification of properties for more general chemical reaction networks.
UR - http://www.scopus.com/inward/record.url?scp=84888333101&partnerID=8YFLogxK
U2 - 10.1007/978-3-319-01928-4_14
DO - 10.1007/978-3-319-01928-4_14
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AN - SCOPUS:84888333101
SN - 9783319019277
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 189
EP - 203
BT - DNA Computing and Molecular Programming - 19th International Conference, DNA 2013, Proceedings
T2 - 19th International Conference on DNA Computing and Molecular Programming, DNA 2013
Y2 - 22 September 2013 through 27 September 2013
ER -