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Irregular oscillations and symmetry breaking in a ring of coupled cells with yeast extract

Version 1.0

Muzika, František; Valent, Ivan, 2022, "Irregular oscillations and symmetry breaking in a ring of coupled cells with yeast extract", https://doi.org/10.18150/GB24WE, RepOD, V1

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Abstract:

Our work is focused on finding discrete non-uniform stationary states applicable for chemical computing and oscillations in a ring of coupled cells with glycolytic oscillatory reaction and equal transport rates for all chemical species. The cells (cuvettes) are fed by the Select Yeast Extract Y1625 and D-glucose solution, both enhanced by NaHCO3. The ring of coupled cells is formed by the two cuvettes and two capillaries. The mutual mass exchange is realized via reciprocal peristaltic pumping. The dynamic states of both cuvettes are measured by UV-Vis spectrophotometers at absorbance level of NADH (340 nm). We report an observation of in-phase, anti-phase, and phase-shifted glycolytic oscillations and transitions between uniform oscillations and chimera-like states occurring from an in-phase oscillatory system.

We also performed an analysis of stability and bifurcations of stationary states in a model of twenty coupled cells in a cyclic array using the core model of glycolysis. Cells 1 and 11 represent main flow reactors (CSTRs) in the model with a much higher volume than cells 2-10 and 12-20, which approximate the capillaries mediating mass exchange between cells 1 and 11 as a cascade of small CSTRs. A bifurcation diagram in a plane of an inhibition rate coefficient (sigma_

inh) and a transport rate coefficient (kd) is used to show the parameter region of occurrence of discrete non-uniform stationary states. We describe and mathematically simulate the mechanism of switching between them, establishing a chemical computing technique (working as AND/NOR logic gate). The ring of twenty coupled cells offers the same logic functions as two coupled cells.

(2022-12-11)
Subject
Chemistry; Computer and Information Science; Engineering
Keyword

glycolysis, discrete non-uniform patterns, multistability, oscillations, chimera death, amplitude death, chemical computing

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descritption.txt
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Fig_2_data.txt
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Experimental absorbance at 340 nm vs. time recordings in both cuvettes. a)column #1(time)/column #2(absorbance)-cell 1//column #3(time)/column #4(absorbance)-cell 2 T1 = 47.6°C, T2 = 48.7°C, CyeatsEx0 = 7.5 g·l-1, Cglu0 = 440mM, CNaHCO3_0 = 200 mM, input/output flow rate = 0.013 ml·s-1, coupling flow rate 0.01 ml·s-1, b) column #5(time)/column #6(absorbance)-cell 1//column #7(time)/column #8(absorbance)-cell 2 T1= 49.2°C, T2= 49.5°C, CyeatsEx0=7.5 g·l-1, Cglu0 = 440 mM, CNaHCO3_0=200 mM, input/output flow rate = 0.013 ml·s-1, coupling flow rate 0.01 ml·s-1, c) column #9(time)/column #10(absorbance)-cell 1//column #11(time)/column #12(absorbance)-cell 2 T1 = T2 = 45°C, CyeatsEx0 = 8.33 g·l-1, Cglu0 = 440 mM, CNaHCO3_0 = 200 mM, input/output flow rate = 0.013 ml·s-1, coupling flow rate 0.033 ml·s-1.
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