Networks of relations
Module locking in biochemical synthesis
Proceedings of the 2008 IEEE/ACM International Conference on Computer-Aided Design
On the expressibility of stochastic switching circuits
ISIT'09 Proceedings of the 2009 IEEE international conference on Symposium on Information Theory - Volume 3
A synthesis flow for digital signal processing with biomolecular reactions
Proceedings of the International Conference on Computer-Aided Design
Compiling program control flows into biochemical reactions
Proceedings of the International Conference on Computer-Aided Design
Digital logic with molecular reactions
Proceedings of the International Conference on Computer-Aided Design
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Randomness is inherent to biochemistry: at each instant, the sequence of reactions that fires is a matter of chance. Some biological systems exploit such randomness, choosing between different outcomes stochastically - in effect, hedging their bets with a portfolio of responses for different environmental conditions. In this paper, we discuss techniques for synthesizing such stochastic behavior in engineered biochemical systems. We propose a general method for designing a set of biochemical reactions that produces different combinations of molecular types according to a specified probability distribution. The response is precise and robust to perturbations. Furthermore, it is programmable: the probability distribution is a function of the quantities of input types. The method is modular and extensible. We discuss strategies for implementing various functional dependencies: linear, logarithmic, exponential, etc. This work has potential applications in domains such as biochemical sensing, drug production, and disease treatment. Moreover, it provides a framework for analyzing and characterizing the stochastic dynamics in natural biochemical systems such as the lysis/lysogeny switch of the lambda bacteriophage.