Information Technology Reference
In-Depth Information
2.2 Tool Description
At cellular scales, a finite number of molecules interact in complex spaces defined
by cell and organelle membranes. In order to simulate stochastic cellular events
(movements, interactions, diverse reactions) with spatial realism at reasonable
computational cost, specific numerical techniques should be employed [3,18].
Using these optimization techniques in conjunction with Monte Carlo reaction
probabilities, it is nowadays possible to study biological systems considering their
evolution during a wide range of time from milliseconds to minutes [11].
The standard approximation for reaction-diffusion systems ignores the dis-
crete nature of the reactants and the stochastic character of their interactions.
Techniques based on the chemical master equation, such as the Gillespie algo-
rithm [20], assume that at each instant the particles are uniformly distributed
in space.
(a)
Experimental setup
(b)
Detection of labeled molecules
(c)
Fluorescence intensity time trace
(d)
Autocorrelation function
Fig. 2.
Representation of a confocal or two photon microscope Fluorescence Correlation
Spectroscopy measurements
In order to take into account both the full spatial distribution of the com-
ponents and the stochastic character of their interactions, a technique based on
Brownian dynamics is used. The MCell simulation package [11,19,18] is based
