Module locking in biochemical synthesis

Brian Fett, Marc D. Riedel

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

7 Scopus citations

Abstract

We are developing a framework for computation with biochemical reactions with a focus on synthesizing specific logical functionality, a task analogous to technology-independent logic synthesis. Our method synthesizes biochemical reactions that compute output quantities of molecular types as a function of input quantities, either deterministically or probabilistically. An important constraint is the timing, captured in the relative rates of the biochemical reactions: all the outputs of a given phase must be produced before the next phase can begin consuming them as inputs. To achieve this synchronization, the reaction rates must sometimes be separated by orders of magnitude: some much faster than others, some much slower. This might be costly or infeasible given a specific library of biochemical reactions. In this paper, we describe a novel mechanism for locking the computation of biochemical modules - analogous to handshaking mechanisms in asynchronous circuit design. With locking, our method synthesizes robust computation that is nearly rate independent, requiring at most two speeds ("fast" and "slow"). The trade-off is with respect to the size of the solution: more reactions are needed. We characterize this trade-off for inter-and intra-module locking in general and for a variety of specific modules that we have designed. In particular, we discuss locking in detail for a stochastic module that implements probabilistic computation, producing different combinations of molecular types according to specified probability distributions.

Original languageEnglish (US)
Title of host publication2008 IEEE/ACM International Conference on Computer-Aided Design Digest of Technical Papers, ICCAD 2008
Pages758-764
Number of pages7
DOIs
StatePublished - 2008
Event2008 International Conference on Computer-Aided Design, ICCAD - San Jose, CA, United States
Duration: Nov 10 2008Nov 13 2008

Publication series

NameIEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD
ISSN (Print)1092-3152

Other

Other2008 International Conference on Computer-Aided Design, ICCAD
Country/TerritoryUnited States
CitySan Jose, CA
Period11/10/0811/13/08

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