Digital signal processing with biomolecular reactions

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

1 Scopus citations

Abstract

We present a methodology for implementing digital signal processing (DSP) operations such as filtering with biomolecular reactions. From a DSP specification, we demonstrate how to synthesize biomolecular reactions that produce time-varying output quantities of molecules as a function of time-varying input quantities. Unlike all previous schemes for biomolecular computation, ours produces designs that are dependent only on coarse rate categories for the reactions ("fast" and "slow"). Given such categories, the computation is exact and independent of the specific reaction rates. We implement DSP operations through a self-timed "handshaking" protocol that transfers quantities between molecular types based on the absence of other types. Our scheme is efficient: both the number of molecular types and the number of reactions grow linearly with the size of the DSP specification. We illustrate our methodology with the design of a simple moving-average filter as well as a more complex biquad filter. We validate our designs through transient stochastic simulations of the chemical kinetics. Although conceptual for the time being, our methodology has potential applications in domains of synthetic biology such as biochemical sensing and drug delivery. We are exploring DNA-based computation via strand displacement as a possible experimental chassis.

Original languageEnglish (US)
Title of host publicationIEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation
Pages237-242
Number of pages6
DOIs
StatePublished - 2010
Event2010 IEEE Workshop on Signal Processing Systems, SiPS 2010 - San Francisco, CA, United States
Duration: Oct 6 2010Oct 8 2010

Publication series

NameIEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation
ISSN (Print)1520-6130

Other

Other2010 IEEE Workshop on Signal Processing Systems, SiPS 2010
CountryUnited States
CitySan Francisco, CA
Period10/6/1010/8/10

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