Team:St Andrews/project/modelling/model 3/spatial

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University of St Andrews iGEM 2010

Welcome!

University of St Andrews iGEM 2010

Our first year at iGEM!

Spatialality

Previous models contained no element of spatiality whatsoever, so in order to improve on this we decided on a fixed volume in which our simulations would take place.

Implementation

A new variable was created called 'Volume' which was given a value of 10¹² ml³ which was chosen as it is the typical volume of a standard laboratory petri dish. Furthermore, any additional HSL which is produced by cells spreads immediately through the entire volume, such that it is diluted to fill the volume. There is no distinction between the internal and external volume however, so it is as if the cells do not posses cells membranes, but are more like areas of the total volume in which certain chemicals are found.

An example of where the volume variable is used is in the differential equation for HSL:

dy[1] = ( (y[9] * kConvHSL * y[6])  / Volume ) - ( 2 * kAssHSLLuxR * y[1] * y[7] ) + ( ( y[9] * 2 * kDissHSLLuxR * y[2] ) / Volume ) 
        - (kDegHSL * y[1] ) + ( (y[9] * kDegHSL * y[2]) /  Volume ) + ( (2 * kDegLuxR  * y[2]) / Volume ) ;