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Improved two-regime method for spatial stochastic simulations of cellular signaling

Author(s):

A. Martinez Gomez
Conference/Journal:

Semester Thesis, HS 13 (10286)
Abstract:

Signaling in the cell transmits external signals received at the surface by receptors to the nucleus inside of the cell, where respective genes are regulated in response to the signal. In addition to the spatial component also noise due to low particle number has to be included in the simulation. Two simulation regimes are well-used for such simulations, namely (1) particle-based simulations that track every molecule on its diffusive path through the cell and (2) compartment-based simulations that only keep track of the number of molecules in sub-compartments defined by a spatial discretization of the cell volume. While particle-based simulations have a higher accuracy and resolution of the process than compartmentbased methods, they are also computationally more demanding. Therefore Two- Regime Methods have been developed to combine the resolution of the particle-based regime with the performance advantage of the compartment-based method. The project investigated improved methods to couple both regimes, especially by increasing the inherent spatial resolution of the compartment-based simulation method. This improved the boundary conditions between the two regimes, and smoothened the effect of the interface compared to the original model.

Year:

2013
Type of Publication:

(13)Semester/Bachelor Thesis
Supervisor:

M. Klann

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% Autogenerated BibTeX entry
@PhdThesis { Xxx:2013:IFA_4539
}
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