title: Optimization of enzymatic biochemical logic for noise reduction and scalability: how many biocomputing gates can be interconnected in a circuit?
abstract: 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 buildup 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.
authors: Department of Chemistry and Biomolecular Science and Department of Physics, Clarkson University, Potsdam, New York 13699, USA.
authors: Vladimir
authors: V
authors: Privman
authors: Guinevere
authors: G
authors: Strack
authors: Dmitry
authors: D
authors: Solenov
authors: Marcos
authors: M
authors: Pita
authors: Evgeny
authors: E
authors: Katz
mesh_terms: D002384:Catalysis; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D008962:Models, Theoretical
chemical_list: D004798:Enzymes; D004247:DNA