Revision as of 17:29, 23 October 2011

Team IGEM Paris 2011

Modeling

Overview

Our modeling was organized around two main questions:

Can we explain the transfer through nanotubes?
What will be the behaviour of our constructs and how will it impact our experimental designs?

In order to aswer the first question, we investigated the physical properties of cell membrane and passive diffusion to comprehend how the transfer could occur. Our models show that transfer through the nanotubes, wether it is through passive diffusion or the so-called assisted diffusion, is happening too quickly to be accurately measured through fluorescent microscopy. Our conclusion was that our designs would not allow us to see which process is dominant during the transfer. However, knowing the time scale of the transfer allowed us to move on to the models of our genetic networks without having to create a complicated model of diffusion through the tubes. These models are entirely new ones. They were done using Java for passive diffusion and Matlab for assisted diffusion.

The second question was a crucial step in the design of our experiments. We showed that some designs might not work as well as others (ComS system for instance) and evaluated the response time of our constructs. With these estimations, were able to prepare a protocol for our microscopic experiments. The models are an improvement of Uri Alon's approach in An Introduction to Systems Biology: Design Principles of Biological Circuits. Matlab was used for solving the differential equations.

Answering those two questions was a major milestone of our project. We needed to know what to expect in order to design our experiments properly and to know what kind of restults we should obtain. We discovered that nanotube transfer is too fast compared to genetic response to allow us to measure its time span correctly. We also saw which of our designs were the most likely to give us clear results and which could prove troublesome to test.

You can find more about our models below.

Modeling in our project

	What is modeling in synthetic biology? You can find here an introduction to our methods and the general idea behind most models in gene network.
	Our assumptions Because of the specificities of our project, we had to adapt the "classic" model to better represent our current situation. On top of that we made and justified a few other hypotheses detailed in this section.
	Modeling our designs Models predicting the behaviour of our designs are detailled in this section.
	Passive diffusion in nanotubes We investigate here the hypothesis of passive diffusion through nanotubes.
	Assisted diffusion We propose here a model explaining how diffusion through nanotubes could be "assisted" by the tension differential between cell walls.