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From 2010.igem.org

Contents 1 BSim Demonstration: Outline 2 Generating an Octree 3 Simple Diffusion 4 Motility in a Gel Matrix 4.1 Tracking Movement

BSim Demonstration: Outline

We have demonstrated some of the new features of BSim by modeling the interaction of agrEcoli with their bead's gel matrix.

• Generating an Octree
• Simple diffusion
• Motility in a Gel Matrix
• Tracking Movement

Generating an Octree

Video to visualize how the chemical field generated as the mesh is recursively subdivided into an octree data structure. The mesh in this example is a zoomed in gel strand, measuring approximately 20um across.

Simple Diffusion

Simple illustration of chemical field diffusing through two different media, the aqueous environment surrounding the gel strand and the gel itself. The source of the chemical is a contact at the bottom of the simulation volume. The agrEcoli bacteria are shown changing color as concentration changes to represent expression of rfp/gfp ratio.

Motility in a Gel Matrix

Two simulations look at how motile agrEcoli move through a volume of the bead. The average pore diameter is 15um. In the first simulation the gel is hole, in the second the bonds between sugars have broken down creating a less coherent gel. Using BSim we tracked the movement of the agrEcoli to see how this affected their movement.

Tracking Movement

As an illustration of the fact that one can take quantitative data out of BSim rather than just visualizations we've calculated the average distance moved by a sample of agrEcoli in the two gels. It is greater in the intact gel matrix, one might speculate that this is because the continuous voids in this gel offer less opportunity for the bacteria to become tangled in the gel.

Whole Gel Matrix

Degraded Gel Matrix