Optimization of Enzymatic Biochemical Logic for Noise Reduction and Scalability: How Many Biocomputing Gates Can Be Interconnected in a Circuit?

We report an experimental evaluation of the "input-output surface" for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic variables appropriate for analysis of Boolean logic for scalability. In order to minimize "analog" noise, we consider a theoretical approach for determining an optimal set for the process parameters to minimize "analog" noise amplification for gate concatenation. We establish that under optimized conditions, presently studied biochemical gates can be concatenated for up to order 10 processing steps. Beyond that, new paradigms for avoiding noise build-up will have to be developed. We offer a general discussion of the ideas and possible future challenges for both experimental and theoretical research for advancing scalable biochemical computing

Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate

We consider a realization of the XOR logic gate in a process biocatalyzed by an enzyme (here horseradish peroxidase: HRP), the function of which can be inhibited by a substrate (hydrogen peroxide for HRP), when the latter is inputted at large enough concentrations. A model is developed for describing such systems in an approach suitable for evaluation of the analog noise amplification properties of the gate. The obtained data are fitted for gate quality evaluation within the developed model, and we discuss aspects of devising XOR gates for functioning in "biocomputing" systems utilizing biomolecules for information processing

All optical full adder based on intramolecular electronic energy transfer in the rhodamine-azulene bichromophoric system

peer reviewedCharge and electronic energy transfer (ET and EET) are well-studied examples whereby different molecules can signal their state from one (the donor, D) to the other (the acceptor, A). The electronic energy transfer from the donor (Rh) to the acceptor (Az) is used to build an all-optical full adder on a newly synthesized bichromophoric molecule Rh-Az. The results are supported and interpreted by a full kinetic simulation. It is found that the optimal design for the implementation of the full adder relies in an essential way on the intramolecular transfer of information from the donor to the acceptor moiety. However, it is not the case that the donor and the acceptor each act as a half adder