TY - GEN
T1 - Digital signal processing with biomolecular reactions
AU - Jiang, Hua
AU - Riedel, Marc D.
AU - Parhi, Keshab K.
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
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U2 - 10.1109/SIPS.2010.5624796
DO - 10.1109/SIPS.2010.5624796
M3 - Conference contribution
AN - SCOPUS:84874741239
SN - 9781424489336
T3 - IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation
SP - 237
EP - 242
BT - IEEE Workshop on Signal Processing Systems, SiPS: Design and Implementation
T2 - 2010 IEEE Workshop on Signal Processing Systems, SiPS 2010
Y2 - 6 October 2010 through 8 October 2010
ER -