Optimization of enzymatic biochemical logic for noise reduction and scalability: how many biocomputing gates can be interconnected in a circuit?

The Journal of Physical Chemistry. B
Vladimir PrivmanEvgeny Katz

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.

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Citations

May 14, 2010·Analytical and Bioanalytical Chemistry·Joseph Wang, Evgeny Katz
Oct 8, 2008·Journal of Materials Science. Materials in Medicine·Marcos PitaEvgeny Katz
Dec 25, 2008·Journal of the American Chemical Society·Liron AmirEvgeny Katz
Dec 31, 2008·Journal of the American Chemical Society·Marina PrivmanEvgeny Katz
Aug 14, 2009·Journal of the American Chemical Society·Tsz Kin TamEvgeny Katz
Jun 13, 2012·Nature Reviews. Genetics·Yaakov Benenson
Mar 5, 2009·Chemical Communications : Chem Comm·A Prasanna de SilvaBoontana Wannalerse
Jun 30, 2009·Molecular BioSystems·Yaakov Benenson
Apr 10, 2010·Chemical Communications : Chem Comm·Jan HalámekEvgeny Katz
Jul 22, 2010·Nanoscale·Sylwia GawedaKonrad Szaciłowski
Jan 25, 2011·Physical Chemistry Chemical Physics : PCCP·Marcos PitaEvgeny Katz
Jul 23, 2009·Bioelectrochemistry·Xuemei WangMarcos Pita
Jun 16, 2009·Biosensors & Bioelectronics·Kalayil Manian ManeshJoseph Wang
Mar 25, 2009·Chembiochem : a European Journal of Chemical Biology·Jian ZhouEvgeny Katz
Jan 1, 2013·Computational and Structural Biotechnology Journal·Gerd Hg Moe-Behrens
Dec 22, 2009·Chemical Communications : Chem Comm·Valeriya BychkovaEvgeny Katz
Jan 13, 2015·Chemical Communications : Chem Comm·Evgeny Katz, Sergiy Minko
May 6, 2016·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Nataliia GuzEvgeny Katz
Jul 20, 2016·Angewandte Chemie·Yulia V Gerasimova, Dmitry M Kolpashchikov
Jun 5, 2013·The Journal of Physical Chemistry. B·Vladimir PrivmanEvgeny Katz
Oct 27, 2012·The Journal of Physical Chemistry. B·Sergii Domanskyi, Vladimir Privman
Jul 19, 2012·The Journal of Physical Chemistry. B·Oleksandr ZavalovEvgeny Katz
Aug 3, 2013·The Journal of Physical Chemistry. B·Saira BakshiEvgeny Katz
Apr 27, 2010·Chemical Society Reviews·Evgeny Katz, Vladimir Privman
Oct 26, 2018·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Evgeny Katz
Jun 13, 2020·Sensors·Melisa Del BarrioMarcos Pita
Dec 3, 2016·Analytical and Bioanalytical Chemistry·Evgeny KatzMichael J Schöning
Dec 14, 2018·Natural Computing·Yiyu XiangBaojun Wang
Mar 31, 2010·The Journal of Physical Chemistry. B·Mary A ArugulaEvgeny Katz
Aug 12, 2009·The Journal of Physical Chemistry. B·Guinevere StrackEvgeny Katz
Apr 10, 2009·The Journal of Physical Chemistry. B·Vladimir PrivmanEvgeny Katz
Jul 9, 2009·The Journal of Physical Chemistry. B·Dmitriy MelnikovEvgeny Katz
Sep 3, 2010·The Journal of Physical Chemistry. B·Dmitriy MelnikovEvgeny Katz
Oct 5, 2010·The Journal of Physical Chemistry. B·Vladimir PrivmanEvgeny Katz
Oct 21, 2010·The Journal of Physical Chemistry. B·Vladimir PrivmanEvgeny Katz

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