Allows the user to specify display interval, store interval, simulation duration, number of simulations, reaction volume, molarity or complex per Reaction volume ratio and the algorithm type.

Display Interval:

The time interval each event displayed on the console.

Store Interval:

The time interval storage of the simulation result on the file.

Simulation Duration:

The total length of simulation time.

Number of Simulations:

The number of stochastic simulation is run.

Reaction Volume:

Volume of the container in which the reactions take place.

Molarity:

The unit of concentration. This unit by default is one molar.

UNIT = Molar
u = micro molar
n = nanomolar

Complex/Reaction Volume:

The number of molecules of a complex (eg. Proteins) that corresponds to one unit of concentration.

Algorithm Type:

One of the four different algorithm types can be used to run the simulation.

1. Direct Gillespie (D.T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics 22 (1976) 403-434)
2. Firth/Bray (StochSim : http://info.anat.cam.ac.uk/groups/comp-cell/StochSim.html)
3. Fricke-Wendt-Gillespie (T. Fricke and D. Wendt, The Markoff automaton a new algorithm for simulating the time-evolution of large stochastic dynamic systems, Int. J. Mod. Phys. C, 6, 277-306, 1995.
4. Gibson-Gillespie (M. A. Gibson and J. Bruck, Efficient exact stochastic simulation of chemical systems with many species and many channels, J. Phys. Chem. A 104 (2000) 1876-1889.)

Optimize Time:

This option is available if Firth/Bray algorithm is chosen. For this algorithm time increment may not be as specified by the user if more than one reaction could occur during the given time step. Optimizing the time increment results in use of the largest time step where only one event can take place at each time step.

Ternary Reactions:

Under Construction

Time Increment:

Time increment needs to be specified when the Firth/Bray algorithm is chosen. This determines the length of each simulated iteration.

Maximum Complexes:

The maximum number of all molecules of complexes (or proteins) that can be present during the simulation.

Display Type:

Simulation results can be presented as Concentration, Molecule Number averages and 3D relative frequency. Note: 3D relative frequency also gives molecular number averages)