Simulation Approach for Timing Analysis of Genetic Logic Circuits

Constructing
genetic logic circuits is an application of synthetic
biology in which parts of the DNA of a living cell are engineered
to perform a dedicated Boolean function triggered by an appropriate
concentration of certain proteins or by different genetic components.
These logic circuits work in a manner similar to electronic logic
circuits, but they are much more stochastic and hence much harder
to characterize. In this article, we introduce an approach to analyze
the threshold value and timing of genetic logic circuits. We show
how this approach can be used to analyze the timing behavior of single
and cascaded genetic logic circuits. We further analyze the timing
sensitivity of circuits by varying the degradation rates and concentrations.
Our approach can be used not only to characterize the timing behavior
but also to analyze the timing constraints of cascaded genetic logic
circuits, a capability that we believe will be important for design
automation in synthetic biology.