PROGRAM SUMMARY
Title of program:
CA3D
Catalogue identifier:
ADNW
Ref. in CPC:
136(2001)269
Distribution format: tar gzip file
Operating system: Solaris (SunOS 5.6), GNU/Linux, Win32
Number of lines in distributed program, including test data, etc:
2085
Supplementary material:
Pseudocoloured animated images of calcium 2D maps obtained from the
simulation.
Keywords:
Biology, Ion diffusion, Random walk, Buffering, Reaction-diffusion.
Programming language used: Fortran
Computer:
SUN Enterprise 3000 ,
PC Pentium III 450MHz ,
PC Pentium II 350MHz .
Nature of problem:
The buffered diffusion of ions in the sub-membrane domain of cells is
simulated by means of Monte Carlo methods. Two geometries of
submembrane domains are considered. The first, a conical domain,
applies to spherical cells with a locally uniform distribution of
channels while the second, a cylindrical domain, is intended to model
ciliar cells and presynaptic terminals. Other domains can be
implemented in the code with ease. The entry of ions takes place
through discrete entry points (channel pores) which are distributed
over the compartments of the first slice of the domain (base of the cone
or the cylinder). Ions diffuse inside the cell and react with
endogenous or exogenous buffers, mobile or fixed.
Method of solution:
The diffusion of ions and binding molecules is modeled as a 3D random
walk process by moving each individual ion and molecule. The reaction
of ions with the binding molecules is also modeled probabilistically.
Restrictions:
The number of radial grid points is restricted to 100 (diameter 200
points). The depth is limited to 100 grid points. In case the grid
resolution and the sizes of the domain are chosen is such a way that
this limit is surpassed, a warning message is generated and the program
gives the option of continuing the simulation by taking the largest
possible sizes of the domain, maintaining the spatial resolution. The
number of grid points available could be smaller in other (generally
older) computer systems, depending on the RAM available. In all the
systems checked (with a RAM of 64MB or higher) the restrictions on the
number of grid points described above were always within computable
ranges. The dimension of the arrays limit the resolution and size of
the domain of simulation that can be taken into account. In this way,
for domains with a typical size of L, the best resolution achievable is
of the order of L/100.
Typical running time:
Depends on the buffers, grid resolution, unitary current, etc. For
example, for a conical domain of 1 mum radius and 5 mum deep, a calcium
time course lasting 1 ms takes 34 s of CPU time for a resolution of 100
nm and 378 s for a resolution of 50 nm; in both cases a standard
endogenous buffering is considered with the addition of an exogenous
buffer (Fura-2 100 muM). See section "CPU times" for more details.