Discrete-time signal processing (2nd ed.)
Discrete-time signal processing (2nd ed.)
Computational methods for stochastic biological systems
Computational methods for stochastic biological systems
Synthesizing stochasticity in biochemical systems
Proceedings of the 44th annual Design Automation Conference
Module locking in biochemical synthesis
Proceedings of the 2008 IEEE/ACM International Conference on Computer-Aided Design
Synchronous sequential computation with molecular reactions
Proceedings of the 48th Design Automation Conference
Compiling program control flows into biochemical reactions
Proceedings of the International Conference on Computer-Aided Design
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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. 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, the proposed 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.