Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications

Privman, Vladimir; Domanskyi, Sergii; Mailloux, Shay; Holade, Yaovi; Katz, Evgeny

doi:10.1021/jp508224y

Cited by 24 publications

(19 citation statements)

References 87 publications

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“…Here, we develop a model, using rate equations that are typically used to model different chemical and biochemical processes, [16][17][18][19][20] to describe cellular dynamics during viral infection.…”

Section: Introductionmentioning

confidence: 99%

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

Domanskyi

Schilling

Gorshkov

et al. 2016

The Journal of Chemical Physics

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We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of "stiff" equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

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Section: Introductionmentioning

confidence: 99%

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

Domanskyi

Schilling

Gorshkov

et al. 2016

The Journal of Chemical Physics

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“…Thetime-dependent outputs were studied experimentally and modeled theoretically for some multistep biocatalytic reactions applied for logic operations. [27] Also the time-dependent dissolution of the alginate thin-film and concomitant release of loaded substances were reported recently. [28] Thepresent system includes anumber of processes with complex kinetics (biocatalytic cascades,e lectric potential formation, reductive dissolution of alginate, OP1 release and finally DNAr eactions).…”

Section: Methodsmentioning

confidence: 89%

Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems

et al. 2015

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Molecular computing based on enzymes or nucleic acids has attracted a great deal of attention due to the perspectives of controlling living systems in the way we control electronic computers. Enzyme-based computational systems can respond to a great variety of small molecule inputs. They have the advantage of signal amplification and highly specific recognition. DNA computing systems are most often controlled by oligonucleotide inputs/outputs and are capable of sophisticated computing as well as controlling gene expressions. Here, we developed an interface that enables communication of otherwise incompatible nucleic-acid and enzymecomputational systems. The enzymatic system processes small molecules as inputs and produces NADH as an output. The NADH output triggers electrochemical release of an oligonucleotide, which is accepted by a DNA computational system as an input. This interface is universal because the enzymatic and DNA computing systems are independent of each other in composition and complexity.Modern silicon-based analog/digital computer technology has been one of the most successful and influential transformative developments in recent history. At the same time, natural biological molecules (e.g., nucleic acids and proteins) are organized in complex communicating networks responsible for growth of all living creatures through metabolism and reproduction. It was suggested that application of the well-developed computational approach to biological molecules may open new chapters in understanding biological signaling, neuron communication, [1] and cancer development, [2] as well as in improving diagnosis of infectious diseases and genetic disorders.[3] Indeed, biomolecular information processing has been an active research field [4] in the general framework of chemical [5] unconventional computing. [6] In this research area, DNA computing [4a-e] and enzyme-based computing [7] have received exceptional attention. DNA computing is believed to be a potential alternative to electronic computers [8] for some computational tasks, due to the advantage of massive parallel data processing, [9] a straightforward design of relatively complex circuits, [10] and affordability. Among the most obvious applications of DNA-based logic circuits is the analysis of genetic alterations that can be transformed into clinical testing of infectious and genetic diseases. [2, 3] Despite advances in the development of in vitro selection, functional DNAs are still limited in the diversity and efficiency of catalytic reactions and are inferior to proteins in terms of affinity and diversity of ligands that DNA can recognize. [11,12] At the same time, enzymes are proven to be selective and sensitive receptors; they are known as the best catalysts, enabling rate enhancement up to 10 17 fold in comparison with uncatalyzed reactions.[13] However, enzyme-based computing was experimentally limited to the systems mimicking operation of only a few concatenated logic gates, [7] and the network complexity was restricted by enzym...

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“…Such “filtering” by added chemical or biocatalytic reactions can yield high‐quality AND gates by modifying the typical convex chemical reaction, Equation (1), response . Other, more complicated approaches to get high‐quality AND gates by using the properties of biocatalytic enzymatic reactions have also been explored . We note that another useful property of enzyme‐catalyzed processes is their high selectivity and specificity towards specific analytes as substrates.…”

Section: Introductionmentioning

confidence: 99%

“…[27,28,30,[42][43][44][45][46][47] Other,m ore complicated approaches to get high-quality AND gatesb yu sing the properties of biocatalytic enzymatic reactions have also been explored. [48,49] We note that another useful property of enzyme-catalyzed processesi st heir high selectivity and specificity towards specific analytes as substrates.…”

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confidence: 99%

Design of High Quality Chemical XOR Gates with Noise Reduction

2017

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We describe a chemical XOR gate design that realizes gate‐response function with filtering properties. Such gate‐response function is flat (has small gradients) at and in the vicinity of all the four binary‐input logic points, resulting in analog noise suppression. The gate functioning involves cross‐reaction of the inputs represented by pairs of chemicals to produce a practically zero output when both are present and nearly equal. This cross‐reaction processing step is also designed to result in filtering at low output intensities by canceling out the inputs if one of the latter has low intensity compared with the other. The remaining inputs, which were not reacted away, are processed to produce the output XOR signal by chemical steps that result in filtering at large output signal intensities. We analyze the tradeoff resulting from filtering, which involves loss of signal intensity. We also discuss practical aspects of realizations of such XOR gates.

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Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications

Cited by 24 publications

References 87 publications

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems

Design of High Quality Chemical XOR Gates with Noise Reduction

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