Semantics of a DNA Strand Displacement Model

Photograph of Kathy Gray

Kathy Gray

(Swansea)

DNA strand displacement techniques have significant promise in the fields of medicine, bioengineering, and other biological sciences. Additionally, DNA strands can be used to create biological circuits (as opposed to digital circuits) including standard boolean logic gates, and Turing machines. However a major challenge in the construction of devices comprised of DNA has been to enable sound automated analysis of high-level designs for complex structures.

In collaboration with the MSR Biology research group, we have been addressing these problems with a programming language and modeling tool to specify DNA circuits, simulate their chemical reactions, and analyze the designs. This talk presents the operational semantics for our language, which models the chemical reactions involved in DNA strand displacement circuits. We will begin with the basic reductions and structures, as well as present new techniques for encoding modularity and scalability.

No knowledge of biology is expected.
Thursday 1st March 2012, 14:00
Robert Recorde Room
Department of Computer Science