Team:Valencia Biocampus/Modeling

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Revision as of 13:30, 13 August 2013

Modeling

The main goal in our modelling project is to predict accurately the behaviour of our system in several issues, from the mounting of bacteria on C. elegans to the performance of our worms reaching the place of interest. In order to do that, we use several modelling techniques.

Biobricks modeling

Modeling of the biobricks performance

Chemotaxis

In first place, we model C. elegans behaviour in absence of chemoatractant and bacteria. When no chemotactic source is present, C. elegans moves randomly. This behaviour can be modeled as a random walk (Berg,1993) and can be simulated in several steps using a programming language as Matlab. The equations of this model are the following:

Add equations

Simulations were performed in Matlab, proceeding as described in (Pierce-Shimomura et al., 1999). We developed our own script based on the article, obtaining similar results.

Add simulations

However, we are interested in the movement of the nematode in a gradient of a chemoatractant. In presence of a chemotactic source,C. elegans moves in a similiar fashion as E. coli (Bangmann, 2006), a mechanism called the pirouette model (Pierce-Shimomura et al., 1999). Following this model, we run

Bangmann CI (2006) Chemosensation in C. elegans. Wormbook
Berg HC (1993) Random walks in biology. Princeton, NJ: Princeton UP.
Pierce-Shimomura JT, Morse TM, Lockery SR (1999) The Fundamental Role of Pirouettes in C. elegans Chemotaxis. The journal of Neuroscience, 19(21):9557-9569

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 == Chemotaxis ==
-The movement of <i>C. elegans</i> in presence of a chemoatractant in order to carry our bacteria to that source is the main issue in our project, so we consider modeling this aspect of the project. Several layers show up that must be modeled in different ways. In our approach, we describe mathematically each layer, from simpler to the most complex.
-<br>
 <br>In first place, we model <i>C. elegans</i> behaviour in absence of chemoatractant and bacteria. When no chemotactic source is present, <i>C. elegans</i> moves randomly. This behaviour can be modeled as a random walk (Berg,1993) and can be simulated in several steps using a programming language as <i>Matlab</i>. The equations of this model are the following:
 <br>