Radek Erban, S. Jonathan Chapman, Philip K. Maini, "A practical guide to stochastic simulations of reaction-diffusion processes", available as http://arxiv.org/abs/0704.1908, 2007

The most recent version of the manuscript can be downloaded here: pdf file

Computer codes which were used to compute the illustrative results from this paper can be downloaded below. Computations from Sections 2, 3 and (partially) 5 were done in Matlab. A Matlab file "FigureX.m" plots the corresponding Figure X in the paper. Computations from Section 4 and Figure 5.4 were done in Fortran 90. A Fortran 90 code "FortranFigureX.f90" stores the computed data in the corresponding data file "FigureX.dat" which is plotted (visualized) in Matlab using the Matlab file "FigureX.m". All codes were successfully tested on both, Unix and MS Windows, versions of Matlab. Comments and suggestions can be sent to my e-mail.

Section 2

Figure 2.1: Figure2_1a.m, Figure2_1b.m (Matlab files)
Figure 2.2: Figure2_2a.m, Figure2_2b.m (Matlab files)
Figure 2.3: Figure2_3.m (Matlab file)
Figure 2.4: Figure2_4.m (Matlab file)

Section 3

Figure 3.1: Figure3_1.m (Matlab file)
Figure 3.2: Figure3_2a.m, Figure3_2b.m (Matlab files)
Figure 3.3: Figure3_3a.m, Figure3_3b.m (Matlab files)

Section 4

Figure 4.1: Figure4_1.m (Matlab file), dataFigure4_1.dat (data file), FortranFigure4_1.f90 (Fortran 90 file)
Figure 4.2: Figure4_2.m (Matlab file), dataFigure4_2.dat (data file), FortranFigure4_2.f90 (Fortran 90 file)
Figure 4.3: Figure4_3.m (Matlab file), dataFigure4_3.dat (data file), FortranFigure4_3.f90 (Fortran 90 file)

Section 5

Figure 5.1: Figure5_1a.m, Figure5_1b.m (Matlab files)
Figure 5.2: Figure5_2.m (Matlab file)
Figure 5.3: Figure5_3.m (Matlab file)
Figure 5.4: Figure5_4.m (Matlab file), dataFigure5_4.dat (data file), FortranFigure5_4.f90 (Fortran 90 file)

Back to my homepage