Team:Imperial College London/Modelling
From 2010.igem.org
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<li>Split TEV protease (<i>orange on diagrams below</i>), is an inactive, split form of TEV mounted on coiled coils. It can be activated again by coiled coils being cleaved by another active TEV.</li> | <li>Split TEV protease (<i>orange on diagrams below</i>), is an inactive, split form of TEV mounted on coiled coils. It can be activated again by coiled coils being cleaved by another active TEV.</li> | ||
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<li>The chemical and enzymatic reactions are modelled according to the Law of Mass Action.</li> | <li>The chemical and enzymatic reactions are modelled according to the Law of Mass Action.</li> | ||
<li>Model assumes that the modelled system is innert within bacterial body or that reaction with outher species within bacterium is neglible. For example, TEV protease is supposed to be unsuccessful in cleaving other molecules due to its specifity.</li> | <li>Model assumes that the modelled system is innert within bacterial body or that reaction with outher species within bacterium is neglible. For example, TEV protease is supposed to be unsuccessful in cleaving other molecules due to its specifity.</li> | ||
- | <li>Due to carefully chosen cell concentrations, the diffusion of free AIPs could be neglected.</li> | + | <li>Due to carefully chosen cell concentrations, the diffusion of free AIPs could be neglected. However, that restricts the model to the considered cell concentrations only.</li> |
<li>Receptor activation threshold was defined by 1 specific value as opposed to considering intermediate states between fully "off" and "on".</li> | <li>Receptor activation threshold was defined by 1 specific value as opposed to considering intermediate states between fully "off" and "on".</li> | ||
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Revision as of 20:30, 13 October 2010
Temporary sub-menu: Dry Lab Diary; Surface Protein Model; Output Amplification Model;Wet-Dry Lab Interaction |
Introduction to modelling |
In the process of designing our construct two major questions arose which could be answered by computer modelling:
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Results & Conclusions | ||||
Output Amplification Model
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Quick overview of models | |||||||||
Output Amplification Model Goals: This model was mainly developed in order to determine whether simple production is better than 1- or 2-step amplification. Further goals, contained estimation of the speed of modelled response.Elements of the system:
The aim of this model is to determine the concentration of Schistosoma elastase or TEV protease that should be added to bacteria to trigger the response. It is also attempted to model how long it takes for the protease or elastase to cleave enough peptides. Elements of the system:
Major assumptions:
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