Binary Counting with Chemical Reactions Aleksandra Kharam, Hua Jiang, Marc Riedel, and Keshab Parhi Electrical and Computer Engineering University of Minnesota.

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Presentation transcript:

Binary Counting with Chemical Reactions Aleksandra Kharam, Hua Jiang, Marc Riedel, and Keshab Parhi Electrical and Computer Engineering University of Minnesota

Signal 10, 2, 12, 8, 4, 8, 10, 2, … 5, 6, 7, 10, 6, 6, 9, 6, … inputoutput Electronics Chemical Reactions Molecular computations In ElectronicsIn Chemistry Input Output

Modeled by Ordinary Differential Equations: inputoutput ac Playing by The Rules + k b cba

Principles of Binary Counting ZYX

ZYX Intuitive Model

Algorithm ` X inj ZYX 0 0 0

Prereactants and Absence Indicators Molecular Type X Absence indicator a x

Prereactants and Absence Indicators Molecular Type X Absence indicator a x Prereactant X p Prereactant for the next type Y p

Modified Algorithm

Three-Phase Synchronization But how do we know that a group of molecules is absent ? R r

Basic AlgorithmThree-Phase Synchronization

Final Design

Simulation Results

zx Mapping to Experimental Chassis Auxiliary Complexes Reactants Products * D. Soloveichik et al: “DNA as a Universal Substrate for Chemical Kinetics.” PNAS, Mar 2010

Conclusion Robustness: - the design is rate independent. Future and related work: - generalizing to n-bit counter; - borrowing idea from digital logic (edge triggered clock ); - computing variety of functions

Questions? Thanks to PSB organizers, NSF, BICB, and UROP NSF CAREER Award # NSF EAGER Grant # Biomedical Informatics & Computational Biology UMN / Mayo Clinic / IBM

Some additional slides

Synchronization

Three-Phase Synchronization