Discrete Turing patterns in coupled reaction cells in a cyclic array

Muzika, František; Schreiberová, Lenka; Schreiber, Igor

doi:10.1007/s11144-016-1004-y

Cited by 11 publications

(12 citation statements)

References 62 publications

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“…We identified coexisting discrete Turing patterns in linear arrays of two and three coupled cells (Muzika and Schreiber, 2013;Muzika et al, 2014) and applied targeted perturbations to perform basic logical functions. In our experimental research, we substituted membrane by a reciprocal peristaltic pumping to form a cyclic array of four coupled subsystems where the reaction of yeast extract and Dglucose took place (Muzika et al, 2016). In agreement with our theoretical predictions we found coexistence of discrete Turing patterns with uniform oscillations and were able to apply specific perturbations, inducing transition between discrete Turing patterns and uniform oscillations.…”

Section: Introductionsupporting

confidence: 80%

“…In vivo experiments have shown that the addition of hydrocarbonate increased motility of sperm cells (Hereng et al, 2014) due to increased ATP-pool levels. We observed and used the same effect to increase activity of phosphofructokinase in our experimental research of discrete Turing patterns (Muzika et al, 2016). Phosphofructokinase can be inhibited by addition of: (1) ATP by up to 95%, (2) citrate by up to 60%, (3) PEP by up to 50%, (4) fructose 6-phosphate by up to 70%, and (5) phosphoglycerate by up to 60% (Mediavilla et al, 2007).…”

Section: Modelmentioning

confidence: 82%

“…More complicated gates [switch gate, Fredkin gate, half bit adder, half bit subtractor ] can be constructed using three or more interconnected microfluidic devices, where the result is read from cuvette as collected solution from the microfluidic devices as a concentration of NADH and ABTS or ferricyanide/ferrocyanide. These techniques are somewhat closer to measuring metabolites, mainly NADH metabolically connected to ATP/ADP through glycolytic reaction chain as in our experimental system (Muzika et al, 2016), where the level of NADH concentrations is not the result of triggering one cascade of enzymes in microfluidic devices over another cascade of enzymes, but it is the result of transitions between non-uniform spatiotemporal patterns caused by synergy of enzymatic reactions and diffusion.…”

Section: Discussionmentioning

confidence: 95%

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Advanced Chemical Computing Using Discrete Turing Patterns in Arrays of Coupled Cells

2020

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We examine dynamical switching among discrete Turing patterns that enable chemical computing performed by mass-coupled reaction cells arranged as arrays with various topological configurations: three coupled cells in a cyclic array, four coupled cells in a linear array, four coupled cells in a cyclic array, and four coupled cells in a branched array. Each cell is operating as a continuous stirred tank reactor, within which the glycolytic reaction takes place, represented by a skeleton inhibitor-activator model where ADP plays the role of activator and ATP is the inhibitor. The mass coupling between cells is assumed to be operating in three possible transport regimes: (i) equal transport coefficients of the inhibitor and activator (ii) slightly faster transport of the activator, and (iii) strongly faster transport of the inhibitor. Each cellular array is characterized by two pairs of tunable parameters, the rate coefficients of the autocatalytic and inhibitory steps, and the transport coefficients of the coupling. Using stability and bifurcation analysis we identified conditions for occurrence of discrete Turing patterns associated with non-uniform stationary states. We found stable symmetric and/or asymmetric discrete Turing patterns coexisting with stable uniform periodic oscillations. To switch from one of the coexisting stable regimes to another we use carefully targeted perturbations, which allows us to build systems of logic gates specific to each topological type of the array, which in turn enables to perform advanced modes of chemical computing. By combining chemical computing techniques in the arrays with glycolytic excitable channels, we propose a cellular assemblage design for advanced chemical computing.

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Section: Introductionsupporting

confidence: 80%

Section: Modelmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 95%

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Advanced Chemical Computing Using Discrete Turing Patterns in Arrays of Coupled Cells

2020

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“…The networks of chemical oscillators can be formed in different ways. One can use individual continuously stirred chemical reactors (CSTRs) and link them by pumps ensuring the flow of reagents [ 29 , 30 ]. Alternatively, networks of oscillators can be formed by touching droplets containing a water solution of reagents of an oscillatory BZ reaction stabilized by lipids dissolved in the surrounding oil phase.…”

Section: Resultsmentioning

confidence: 99%

Applications of Information Theory Methods for Evolutionary Optimization of Chemical Computers

Górecki

2020

Entropy

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It is commonly believed that information processing in living organisms is based on chemical reactions. However, the human achievements in constructing chemical information processing devices demonstrate that it is difficult to design such devices using the bottom-up strategy. Here I discuss the alternative top-down design of a network of chemical oscillators that performs a selected computing task. As an example, I consider a simple network of interacting chemical oscillators that operates as a comparator of two real numbers. The information on which of the two numbers is larger is coded in the number of excitations observed on oscillators forming the network. The parameters of the network are optimized to perform this function with the maximum accuracy. I discuss how information theory methods can be applied to obtain the optimum computing structure.

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“…Glycolytic oscillations were explored by Muzika et al [8] and Turing patterns were found in coupled reaction cells in a cyclic array. It was shown experimentally that transitions between Turing patterns and uniform oscillations are possible.…”

mentioning

confidence: 99%

Editorial

Čupić¹

2016

Reac Kinet Mech Cat

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Discrete Turing patterns in coupled reaction cells in a cyclic array

Cited by 11 publications

References 62 publications

Advanced Chemical Computing Using Discrete Turing Patterns in Arrays of Coupled Cells

Advanced Chemical Computing Using Discrete Turing Patterns in Arrays of Coupled Cells

Applications of Information Theory Methods for Evolutionary Optimization of Chemical Computers

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