Synthesizing Stochasticity in Biochemical Systems

Fett, Brian and Bruck, Jehoshua and Riedel, Marc D. (2007) Synthesizing Stochasticity in Biochemical Systems. Technical Report. California Institute of Technology, Pasadena, CA. [CaltechPARADISE:2007.ETR081]

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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.

EPrint Type:	Monograph (Technical Report)
Additional Information:	This work is supported in part by the “Alpha Project” at the Center for Genomic Experimentation and Computation, an NIH Center of Excellence (grant no. P50 HG02370). Also available from http://www.paradise.caltech.edu/papers/etr081.pdf
Uncontrolled Keywords:	Synthetic biology, Computational Biology, Synthesis, Biochemical Reactions, Stochasticity, Markov processes, Random processes
Subjects:	All Records
ID Code:	115
Deposited By:	Caltech Library System
Deposited On:	19 February 2008
Record Number:	CaltechPARADISE:2007.ETR081
Official Persistent URL:	http://resolver.caltech.edu/CaltechPARADISE:2007.ETR081
Usage Policy:	You are granted permission for individual, educational, research and non-commercial reproduction, distribution, display and performance of this work in any format.

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