13th International Conference on Membrane Computing - MTA Sztaki

T. Ahmed, G. DeLancy, A. Paun
purpose of this study we will instead assume some ux functions and use the
MetaPlab tool, Simulation Plugin 2, in an eort to derive the ux-dynamics
without needing to resort to a microscopic analysis of the MP systems.
Substance Initial Concentration Molar Weight(gram)
A 100 1
B 100 1
C 0.02 1
Table 1. Description of substances of our MP-model for case study
Reactions Flux regulation maps
R 0:A−→ 2A F 0: 0.000002 * A * B * C
R 1:A−→ B F 1: 0.00003 * B * C
R 2:A−→ C F 2: 0.00004 * C * A
R 3:B−→ λ F 3: 0.0005 * B
R 4:C−→ λ F 4: 0.007 * C
Table 2. Reactions and Flux regulation functions for our model to case study.
Table 2 shows the assumed reactions and corresponding ux regulation maps.
These functions are then used along with the initial concentrations and molar
weights in MetaPlab to construct a model to be used to help us ll out any
other missing relevant information to be derived from what we know about our
substances that we will need to successfully run Simulation Plugin 2. Worth
noting is that the mappings show the inputs and outputs in moles. Reactions
R3 and R4 have inputs of substances B and C respectively, but neither produce
any outputs that are used in the model. This explains both their lack of a known
output (it is irrelevant to our research) and their positions on the model.
A model was constructed using MetaPlab where R0, R1, R2, R3, and R4 were
designated as our reactions; A, B, and C, our substances; and F0, F1, F2, F3,
and F4 our ux regulation maps. For the construction of this model we have no
data about the time series, but do know that we can use MetaPlab to generate
a time series based on the ux functions we have assumed. The mappings to
and from the various nodes on the model represent the functions that regulate
moving from one node to another. For instance, we can see from the table above
that F0 is dependent on the values from substances A, B, and C and as such
there are mappings from A, B, and C to F0. Likewise, we can tell that R2 takes
one mole of substance A and converts it into one mole of substance C. The I/O
gates show where a reaction's products leave the model.
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