Team:BCCS-Bristol/Modelling/BSIM/Geometric Modelling

From 2010.igem.org

(Difference between revisions)
Line 20: Line 20:
the items being modelled that it is effectively infinite.
the items being modelled that it is effectively infinite.
-
 
+
[[Image:BsimVesicle.png|thumbnail|right||Figure 1]]
-
[[Image:BsimVesicle.png|400px|vesiculation]]
+
Some of the modelling questions that we want to answer in this project pertain to environments
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
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. This is important as it will determine how much of the E. coli
+
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
-
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
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
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.
homogeneous the nitrate concentrations inside the bead are.
-
https://static.igem.org/mediawiki/2010/6/61/Depth0.png
+
 
 +
 
 +
[[Image:Depth0.png|thumbnail|right|Figure 2]]

Revision as of 10:13, 26 October 2010

Geometric Modelling

Why did we decide ot extend BSIM in this way? How did we do it (overview)? What other areas can we look at with this tech (microfluidics etc)?

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

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

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


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.

Figure 1

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.


Figure 2