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Team:Edinburgh/modelling(reallifemodelling)
From 2009.igem.org
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<center><img src="https://static.igem.org/mediawiki/2009/8/8b/Formula4.jpg"></center> | <center><img src="https://static.igem.org/mediawiki/2009/8/8b/Formula4.jpg"></center> | ||
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| - | The diffusion coefficient for TNT is 1.18 *10<sup>-6</sup> cm<sup>2</sup> <sup> | + | The diffusion coefficient for TNT is 1.18 *10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup> <sup>4</sup> and the diffusion of Nitrite is 1.9*10<sup>-5</sup> cm<sup>2</sup> s<sup>-1</sup> . |
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This system was coded in both MATLAB and JAVA. MATLAB was used to produce graphs and JAVA was used for the chemotaxis modelling which is described below. | This system was coded in both MATLAB and JAVA. MATLAB was used to produce graphs and JAVA was used for the chemotaxis modelling which is described below. | ||
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| + | The TNT diffusion graph after a year is shown below | ||
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| + | <center><img src="https://static.igem.org/mediawiki/2009/3/30/ModellingFigure1.jpg"></center> | ||
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Revision as of 18:44, 14 October 2009
Modelling - Real Life Modelling
Personal note
Since our system designed to detect landmines it was thought that we should include a visual representation of how the system would operate in real life. It is known that TNT leaks out of the landmine into the soil and we predict that the bacteria will move toward the TNT due to the chemotaxis response of the ribose binding protein which has previously computationally designed TNT receptor1
TNT and Nitrite diffusion has been modelled using a finite difference method which approximates the 2 dimensional time dependent diffusion equation below
where α is the diffusion coefficient, to a numerical solution which can be solved . By splitting the area into a grid M2 by N with a space step of h=1/M (in both the x and y directions) and time step size of k=T/N. This gives a grid of the form
which was set up as a matrix in the program.
An initial concentration of TNT in the field was then set to 107800µg/cm3 and the diffusion of TNT out from this site was calculated from the following equation,
and
The diffusion coefficient for TNT is 1.18 *10-6 cm2 s-1 4 and the diffusion of Nitrite is 1.9*10-5 cm2 s-1 .
This system was coded in both MATLAB and JAVA. MATLAB was used to produce graphs and JAVA was used for the chemotaxis modelling which is described below.
The TNT diffusion graph after a year is shown below
where α is the diffusion coefficient, to a numerical solution which can be solved . By splitting the area into a grid M2 by N with a space step of h=1/M (in both the x and y directions) and time step size of k=T/N. This gives a grid of the form
which was set up as a matrix in the program.
An initial concentration of TNT in the field was then set to 107800µg/cm3 and the diffusion of TNT out from this site was calculated from the following equation,
and
The diffusion coefficient for TNT is 1.18 *10-6 cm2 s-1 4 and the diffusion of Nitrite is 1.9*10-5 cm2 s-1 .
This system was coded in both MATLAB and JAVA. MATLAB was used to produce graphs and JAVA was used for the chemotaxis modelling which is described below.
The TNT diffusion graph after a year is shown below
Edinburgh University iGEM Team 2009
