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From 2010.igem.org

Geometric Modelling

Implementation

Octrees

BSim carries out its simulations in a three dimensional space, this is necessary for many simulations involving populations of bacteria and modelling their interactions. In figure 1, for example, you can see an example of bacteria emitting and merging with vesicles in three dimensions. They are modelled as being in water, with a periodic boundary conditions (meaning that if you go out of the top of the box you re-appear at the bottom). This creates a continuous domain, which is fine for modelling the conditions inside a test tube where the environment is large enough compared to the items being modelled that it is effectively infinite.

Some of the modelling questions that we want to answer in this project pertain to environments that are of the same scale as the bacteria. One important question is how E. coli move inside the micro-structure of the gellan beads gel matrix (figure 2). This is important as it will determine how much of the E. coli escapes the bead environment over time. Another question that could be answered via accurate modelling of surfaces in BSim would be how exactly nitrate diffuses from the soil contact area of the bead and into the micro-structure of the gellan bead. This would provide an insight into how homogeneous the nitrate concentrations inside the bead are.

Depreciated links:

Team:BCCS-Bristol/Modelling/BSIM/Geometric_Modelling/Meshes

Team:BCCS-Bristol/Modelling/BSIM/Geometric_Modelling/Chemical_Fields