TY - GEN
T1 - Module locking in biochemical synthesis
AU - Fett, Brian
AU - Riedel, Marc D.
PY - 2008
Y1 - 2008
N2 - 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.
AB - 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.
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U2 - 10.1109/ICCAD.2008.4681661
DO - 10.1109/ICCAD.2008.4681661
M3 - Conference contribution
AN - SCOPUS:57849133481
SN - 9781424428205
T3 - IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD
SP - 758
EP - 764
BT - 2008 IEEE/ACM International Conference on Computer-Aided Design Digest of Technical Papers, ICCAD 2008
T2 - 2008 International Conference on Computer-Aided Design, ICCAD
Y2 - 10 November 2008 through 13 November 2008
ER -