Model of an artificial blastula for assessing development toxicity

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Model of an artificial blastula for assessing development toxicity

Version 1.0

Muzika, František; Górecki, Jerzy, 2023, "Model of an artificial blastula for assessing development toxicity", https://doi.org/10.18150/JKFBUW, RepOD, V1

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Description

Dataset to a book chapter on "Cheminformatics - Fundamentals, Recent Advances, New Perspectives and Applications." at IntechOpen.

Abstract:

We are concerned with computer simulations of a ring of twenty coupled CSTRs with glycolytic oscillatory reaction. Each CSTR represents an artificial cell, and the ring can be regarded as an artificial blastula. The cells are coupled to two adjacent CSTRs via the mass exchange of reagents. The glycolytic oscillatory reaction is simulated using the two-variable core model. Our work is focused on the classification of stationary discrete non-uniform concentration patterns (discrete Turing patterns). The control parameters in simulations are autocatalytic and inhibition rate coefficients, as well as the transport rate coefficients. We performed the analysis of stability and bifurcations of stationary states to identify the stationary states. The inflow of reagents into each CSTR was used to initiate a particular pattern. We propose a method to assess the morphogenetic toxicity of any chemical from a database by switching between patterns or between patterns and oscillations. Moreover, we investigated non-uniform patterns that create discrete concentration waves inside the ring of twenty coupled cells, which can trigger gastrulation.

(2023-01)

Subject

Chemistry; Computer and Information Science; Engineering

Keyword

discrete Turing patterns, glycolysis, 2D artificial blastula, cheminformatics, morphogenesis toxicity

License

CC0 Creative Commons Zero 1.0

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		IntechOpenMuzikaf_manuscript_v2.edited.docx MS Word (docx) - 1.6 MB - Feb 3, 2023 - 19 Downloads MD5: 3da6ae298be0033f7c7a903bb4100606 License: CC0 Creative Commons Zero 1.0 manuscript	Download
		description.txt Plain Text - 11.8 KB - Feb 3, 2023 - 14 Downloads MD5: 515c5b82c36889e8548116e3bb5511d3 License: CC0 Creative Commons Zero 1.0 text describing files	Preview Download
		Figure1.svg Unknown - 1.7 MB - Feb 3, 2023 - 17 Downloads MD5: ac03ef735a1363de555262c983bd8fb3 License: CC0 Creative Commons Zero 1.0 Figure 1: The array of N=20 coupled cells taken as a 2D-blastula model: a) regime of uniform oscillations, b) regime of discrete non-uniform patterns, c) regime of uniform oscillations again. Black arrows represent the reagent exchange between cells. Each cell is numbered. Blue arrows represent perturbation leading to a transition to discrete non-uniform pattern from uniform oscillations and vice versa. The applied perturbation is shown in Figure 3.	Download
		Figure2.zip ZIP Archive - 16.7 MB - Feb 3, 2023 - 12 Downloads MD5: b6d0242f51e4555f9d4f9c35ce027330 License: CC0 Creative Commons Zero 1.0 file "Figure2.zip" Contains a list of files to plot a solution diagram of ADP in the first cell for sigma_M =100s-1, kd=0.1 s-1, ny = 1.84 s-1. Red solid curve – stable stationary state, blue dashed curve – unstable stationary state, solid black curve – stable minima and maxima of glycolytic oscillations, dashed black curve – unstable minima and maxima of glycolytic oscillations, Hopf bifurcation points, and branch points are omitted for the purpose of readability of the solution diagram. contains files: "contplt.s" contains data set for stable curves, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents inhibition rate coeffient, column #42 represents an arch (see manual for program CONT), column #43 represents stability sign (-1 is stable, +1 unstable, 0 stability changing bifurcation point). "contplt.u" contains data set for unstable curves, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents inhibition rate coeffient, column #42 represents an arch (see manual for program CONT), column #43 represents stability sign (-1 is stable, +1 unstable, 0 stability changing bifurcation point). "dcontplt.s"contains data set for stable minima and maxima of glycolytic oscillations, column #1 represents sigma_inh, column #2 represents an amplitude, column #3 represents minima, column #4 represents maxima, column #5 represents stability sign(-1 is stable, +1 unstable, 0 stability changing bifurcation point) "dcontplt.u"contains data set for unstable minima and maxima of glycolytic oscillations, column #1 represents sigma_inh, column #2 represents an amplitude, column #3 represents minima, column #4 represents maxima, column #5 represents stability sign(-1 is stable, +1 unstable, 0 stability changing bifurcation point) "bbranch.txt" contains data set for branch points, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents inhibition rate coeffient, column #42 represents an arch (see manual for program CONT), column #43 represents point type sign (6 is branch point, 5 is Hopf bifurcation, 99 is codimension point). "hhopf.txt" contains data set for Hopf bifurcation points, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents inhibition rate coeffient, column #42 represents an arch (see manual for program CONT), column #43 represents point type sign (6 is branch point, 5 is Hopf bifurcation, 99 is codimension point). "mustr.gnu" - file for plotting the solution diagram in Gnuplot	Download
		Figure2.svg Unknown - 1.1 MB - Feb 3, 2023 - 12 Downloads MD5: e9814945a08fdfa628025e68e0cd4c96 License: CC0 Creative Commons Zero 1.0 Figure 2: Solution diagram of ADP in the first cell for Sigma_M =100s-1, kd=0.1 s-1, ny = 1.84 s-1. Red solid curve – stable stationary state, blue dashed curve – unstable stationary state, solid black curve – stable minima and maxima of glycolytic oscillations, dashed black curve – unstable minima and maxima of glycolytic oscillations, Hopf bifurcation points, and branch points are omitted for the purpose of readability of the solution diagram.	Download
		Figure3.zip ZIP Archive - 1.8 MB - Feb 3, 2023 - 9 Downloads MD5: 1c4437715b77fea58b51f80616434b02 License: CC0 Creative Commons Zero 1.0 file "Figure3.zip" Contains a list of files to plot dynamic simulation of transitions in between uniform oscillations and non-uniform discrete patterns, sigma_M= 100 s-1, sigma_inh = 35 s-1, kd = 0.1 s-1 : cotnains files: "contplt.1" Concentrations of ATP and ADP for a) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 4000 seconds. "perturbace.txt" column #1 represents time, column #2 represents ny_1(t), column #3 represents ny_2(t),..., column #21 represents ny_20(t) "mustr.gnu" - file for plotting the solution diagram in Gnuplot	Download
		Figure3.svg Unknown - 457.6 KB - Feb 3, 2023 - 17 Downloads MD5: 76d1ca441059df74d6f106f32bbc29c2 License: CC0 Creative Commons Zero 1.0 Figure 3: Dynamic simulation of transitions in between uniform oscillations and non-uniform discrete patterns, sigma_M= 100 s-1, sigma_inh = 35 s-1, kd = 0.1 s-1 : a) red curve represents ny_1, the green curve represents ny_11, the blue dashed curve represents ny_6; b) red curve represents ny_2, the green curve represents ny_20, the blue dashed curve represents ny_10; c) ADP concentrations in selected cells: red curve - cell #1, green curve - cell #11, blue curve - cell #6 d) ADP concentrations in selected cells: red curve - cell #2, green curve - cell #20, blue curve - cell #10.	Download
		Figure4.zip ZIP Archive - 570.5 KB - Feb 3, 2023 - 12 Downloads MD5: ddddfae5fd58d5c86ea119730c1dae17 License: CC0 Creative Commons Zero 1.0 file "Figure4.zip" Contains a list of files to plot Discrete patterns of the stationary concentrations of ADP in 20 cells of the artificial blastula arranged in the time interval [500 s, 1000 s] for various sets of parameters sigma_M= 100 s-1. a) sigma_inh = 60 s-1, kd = 0.1 s-1, b) sigma_inh = 60 s-1, kd = 0.1 s-1, c) sigma_inh = 26 s-1, kd = 0.1 s-1, d) sigma_inh = 26 s-1, kd = 0.1 s-1, e) sigma_inh = 35 s-1, kd = 0.55 s-1. contains files: "uniform.txt" Stationary concentrations of ATP and ADP in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds in the region of SUSS,odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 1000 seconds. "contplt1.1" Stationary concentrations of ATP and ADP for a) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt2.1" Stationary concentrations of ATP and ADP for b) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt3.1" Stationary concentrations of ATP and ADP for c) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt4.1" Stationary concentrations of ATP and ADP for d) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt5.1" Stationary concentrations of ATP and ADP for e) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "mustr.gnu" - file for plotting the solution diagram in Gnuplot	Download
		Figure4.svg Unknown - 636.7 KB - Feb 3, 2023 - 12 Downloads MD5: b01b91f8ee0a07d90c262d5151b790a1 License: CC0 Creative Commons Zero 1.0 Figure 4: Discrete patterns of the stationary concentrations of ADP in 20 cells of the artificial blastula arranged in the time interval [500 s, 1000 s] for various sets of parameters sigma_M= 100 s-1. a) sigma_inh = 60 s-1, kd = 0.1 s-1, b) sigma_inh = 60 s-1, kd = 0.1 s-1, c) sigma_inh = 26 s-1, kd = 0.1 s-1, d) sigma_inh = 26 s-1, kd = 0.1 s-1, e) sigma_inh = 35 s-1, kd = 0.55 s-1. Each cell is numbered by a green number. The blue dashed line corresponds to ADP concentration in an unstable uniform stationary state. The red lines represent stationary concentrations of ADP in each cell.	Download
		Figure5.zip ZIP Archive - 139.5 KB - Feb 3, 2023 - 18 Downloads MD5: 954046316db349f6be4f10fb45739390 License: CC0 Creative Commons Zero 1.0 file "Figure5.zip" Contains a list of files to plot Discrete patterns of the stationary concentrations of ADP in 20 cells of the artificial blastula arranged in the time interval [500 s, 1000 s] for sigma_M= 100 s-1, sigma_inh = 35 s-1, kd = 0.1 s-1 contains files: "uniform.txt" Stationary concentrations of ATP and ADP in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds in the region of SUSS,odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 1000 seconds. "contplt1.1" Stationary concentrations of ATP and ADP for a) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt2.1" Stationary concentrations of ATP and ADP for b) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt3.1" Stationary concentrations of ATP and ADP for c) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt4.1" Stationary concentrations of ATP and ADP for d) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt5.1" Stationary concentrations of ATP and ADP for e) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt6.1" Stationary concentrations of ATP and ADP for f) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt7.1" Stationary concentrations of ATP and ADP for g) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt8.1" Stationary concentrations of ATP and ADP for h) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "contplt9.1" Stationary concentrations of ATP and ADP for i) in i-th cell in 20 cells of cyclic array arranged in a row in time interval 0-1000 seconds, odd columns represent stationary concentrations of ATP in cells from 1 to 20(last column is column #39), even columns represent stationary concentrations of ADP in cells from 1 to 20(last column is column #40), column #41 represents the time interval from 0 to 10000 seconds. "mustr2.gnu" - file for plotting the solution diagram in Gnuplot	Download

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