Synthesizing stochasticity in biochemical systems

Brian Fett, Jehoshua Bruck, Marc D. Riedel

Research output: Chapter in Book/Report/Conference proceedingConference contribution

18 Scopus citations

Abstract

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.

Original languageEnglish (US)
Title of host publication2007 44th ACM/IEEE Design Automation Conference, DAC'07
Pages640-645
Number of pages6
DOIs
StatePublished - 2007
Event2007 44th ACM/IEEE Design Automation Conference, DAC'07 - San Diego, CA, United States
Duration: Jun 4 2007Jun 8 2007

Publication series

NameProceedings - Design Automation Conference
ISSN (Print)0738-100X

Other

Other2007 44th ACM/IEEE Design Automation Conference, DAC'07
CountryUnited States
CitySan Diego, CA
Period6/4/076/8/07

Keywords

  • Biochemical reactions
  • Computational biology
  • Markov processes
  • Random processes
  • Stochasticity
  • Synthesis
  • Synthetic biology

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