Based on simulation model formal specification, the abstract simulation algorithm is given and SCSL virtual machine, which is capable of automatically interpreting and executing simulation model represented by SCSL, is designed.
Figure 6a, b shows the volume of the catalytic cavity during a specific portion of the simulation, represented by the frame index, and the root mean square fluctuation (RMSF) per residue, respectively.
In order to have readable results we set δ f u = 0. 25 1 - 1 L and δ u f = 0. 0 21 + 0. 28 1 L. With these values we obtain, for L = 3, the curves given in the graphs (c) and (d) of Figure 3 (which approximate the stochastic simulations represented in the same figure by graphs (a) and (b)).
The results from the Brutus simulations are represented by the data points, for each of the four sets of initial conditions: Plummer equal mass (black bullets), Plummer with different masses (red triangles), cold Plummer equal mass (blue squares) and cold Plummer with different masses (green stars).
Simulations are represented by solid (MSD scenario) or dotted (MD scenario) lines, in green color for N = 10 in Figure 1, and blue color for N = 50 in Figure 2, as in the remaining figures.
We furthermore investigated the responsiveness of the system predicted by the model with respect to the total amount of stimulus provided (Epo tot ), which in our simulations is represented by the product Epo tot = Epo tr · T Epo (Sup. Mat. A4 contains further explanations [see Additional file 1]). Figure 6 shows our results, which condense the information depicted in Figure 5.
Any participant of simulation is represented by agents.
Thus, the data from each replicate simulation was represented by a single data point for each age class.
Each individual in the simulation is represented by a network composed of components inherited from two parents.
The population in each simulation is represented by three numbers, corresponding to the abundance of each of the three alleles.
