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Team:BCCS-Bristol/Modelling/BSIM/Results
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=BSim Demonstration: Outline= | =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 | * Generating an Octree | ||
* Simple diffusion | * Simple diffusion | ||
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=Generating an Octree= | =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. | |
| - | + | ||
<center><html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Uoh1mCADghI?fs=1&hl=en_US&rel=0&hd=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Uoh1mCADghI?fs=1&hl=en_US&rel=0&hd=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html></center> | <center><html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Uoh1mCADghI?fs=1&hl=en_US&rel=0&hd=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/Uoh1mCADghI?fs=1&hl=en_US&rel=0&hd=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html></center> | ||
=Simple Diffusion= | =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. | ||
<center><html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/fn76xu4aB4U?fs=1&hl=en_US&rel=0&hd=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/fn76xu4aB4U?fs=1&hl=en_US&rel=0&hd=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html></center> | <center><html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/fn76xu4aB4U?fs=1&hl=en_US&rel=0&hd=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/fn76xu4aB4U?fs=1&hl=en_US&rel=0&hd=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html></center> | ||
=Motility in a Gel Matrix= | =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. | ||
<center><html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/7ourSYT8Oug?fs=1&hl=en_US&rel=0&hd=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/7ourSYT8Oug?fs=1&hl=en_US&rel=0&hd=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html></center> | <center><html><object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/7ourSYT8Oug?fs=1&hl=en_US&rel=0&hd=1"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/7ourSYT8Oug?fs=1&hl=en_US&rel=0&hd=1" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="344"></embed></object></html></center> | ||
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==Tracking 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''' | ||
https://static.igem.org/mediawiki/2010/0/04/Dense_paths_average_and_error.png | https://static.igem.org/mediawiki/2010/0/04/Dense_paths_average_and_error.png | ||
| + | |||
| + | '''Degratded Gel Matrix''' | ||
| + | |||
| + | https://static.igem.org/mediawiki/2010/6/63/Less_dense_paths_average_and_error.png | ||
Revision as of 16:17, 25 October 2010
iGEM 2010
Contents |
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
Degratded Gel Matrix
