TY - GEN
T1 - Synchronous sequential computation with molecular reactions
AU - Jiang, Hua
AU - Riedel, Marc
AU - Parhi, Keshab
PY - 2011
Y1 - 2011
N2 - Just as electronic systems implement computation in terms of voltage (energy per unit charge), molecular systems compute in terms of chemical concentrations (molecules per unit volume). Prior work has established mechanisms for implementing logical and arithmetic functions including addition, multiplication, exponentiation, and logarithms with molecular reactions. In this paper, we present a general methodology for implementing synchronous sequential computation. We generate a four-phase clock signal through robust, sustained chemical oscillations. We implement memory elements by transferring concentrations between molecular types in alternating phases of the clock. We illustrate our design methodology with examples: a binary counter as well as a four-point, two-parallel FFT. We validate our designs through ODE simulations of mass-action chemical kinetics. We are exploring DNA-based computation via strand displacement as a possible experimental chassis.
AB - Just as electronic systems implement computation in terms of voltage (energy per unit charge), molecular systems compute in terms of chemical concentrations (molecules per unit volume). Prior work has established mechanisms for implementing logical and arithmetic functions including addition, multiplication, exponentiation, and logarithms with molecular reactions. In this paper, we present a general methodology for implementing synchronous sequential computation. We generate a four-phase clock signal through robust, sustained chemical oscillations. We implement memory elements by transferring concentrations between molecular types in alternating phases of the clock. We illustrate our design methodology with examples: a binary counter as well as a four-point, two-parallel FFT. We validate our designs through ODE simulations of mass-action chemical kinetics. We are exploring DNA-based computation via strand displacement as a possible experimental chassis.
KW - Computational Biology
KW - Digital Design
KW - Molecular Computation
KW - Sequential Logic
KW - Synchronous Logic
KW - Synthetic Biology
UR - http://www.scopus.com/inward/record.url?scp=80052652330&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=80052652330&partnerID=8YFLogxK
U2 - 10.1145/2024724.2024911
DO - 10.1145/2024724.2024911
M3 - Conference contribution
AN - SCOPUS:80052652330
SN - 9781450306362
T3 - Proceedings - Design Automation Conference
SP - 836
EP - 841
BT - 2011 48th ACM/EDAC/IEEE Design Automation Conference, DAC 2011
PB - Institute of Electrical and Electronics Engineers Inc.
ER -