Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems

Table 1

List of rules defining reaction and diffusion processes. (𝑥,𝑦) are the compartment’s coordinates, 𝑛∈{−1,0,1}, and 𝑧∈{1,2,3,4}.

Process	Rule
Activation of G1 mediated by F1	G1 + F1 →G1^+
Dissociation of F1 from G1	G1^+ → G1 + F1
Activation of G2 mediated by F1	G2 + F1 → G2^+
Dissociation of F1 from G1	G2^+ → G2 + F2
Inhibition of G1 mediated by F2	G1 + F2 → G1^−
Dissociation of F2 from G1	G1^− → G1 + F2
Inhibition of G2 mediated by F2	G2 + F2 → G2^−
Dissociation of F2 from G2	G2^− → G2 + F2
Activation of G1 mediated by F3	G1 + F3 → G1^+
Dissociation of G1 from F3	G1^+ → G1 + F3
Inhibition of G2 mediated by F3	G2 + F3 → G2^−
Dissociation of F3 from G2	G2^− → G2 + F3
Inhibition of G1 mediated by F4	G1 + F4 → G1^−
Dissociation of G1 from F4	G1^− → G1 + F4
Activation of G2 mediated by F4	G2 + F4 →G2^+
Dissociation of F4 from G2	G2^+ → G2 + F4
Diffusion from (𝑥,𝑦) to (𝑥+𝑛𝑥, 𝑦+𝑛𝑦)	F𝑧^𝑥,𝑦→F𝑧^𝑥+𝑛𝑥,𝑦+𝑛𝑦