Team:ETHZ Basel/Modeling

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== Implementation of molecular models ==
== Implementation of molecular models ==
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[[Image:Modeling_overview.png|thumb|400px|'''Combined models.''' Coupled individual models for the simulation of the whole process and their interfaces.]]
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[[Image:Modeling_overview_molecular.png|thumb|400px|'''Schematical overview of the devices.''' ]]
The core component of E. lemming is the fusion of one light-sensitive protein (LSP?) to a protein of the chemotaxis pathway (Che?). Upon change of wavelength of light pulses, this component will dimerize with the corresponding light-sensitive protein (LSP?'), which is linked to an anchor protein, bound to an anchor (plasmid). The result is a change of the spatial localization of Che? and perturbation of the chemotaxis pathway, which ultimately leads to a different tumbling/straight run ratio.
The core component of E. lemming is the fusion of one light-sensitive protein (LSP?) to a protein of the chemotaxis pathway (Che?). Upon change of wavelength of light pulses, this component will dimerize with the corresponding light-sensitive protein (LSP?'), which is linked to an anchor protein, bound to an anchor (plasmid). The result is a change of the spatial localization of Che? and perturbation of the chemotaxis pathway, which ultimately leads to a different tumbling/straight run ratio.
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E. lemming, aims to modify the chemotaxis property of E.coli such that, instead of response to a chemical attractant or repellent, the bacterium responds to a light stimulus. Furthermore, this light sensitivity is used to control E.coli’s movement by deciding, at any given time, which type of motion the bacterium will adopt (tumbling or straight run). This leads to a controllable E.coli, which can move to a defined direction, as a result of the combination of tumbling and straight run. The bacteria in the experiment are imaged and, by image processing, the position of a single tracked cell is inferred. By activating a light switch, the user decides whether the bacterium should continue running or should change direction.
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[[Image:Modeling_overview.png|thumb|400px|'''Combined models.''' Coupled individual models for the simulation of the whole process and their interfaces.]]
In the theory world, the steps we are following in mindlessly driving E.coli to our pre - defined target are the following:   
In the theory world, the steps we are following in mindlessly driving E.coli to our pre - defined target are the following:   

Revision as of 12:16, 22 September 2010

Molecular Modeling Overview

In order to support wet laboratory experiments and to create a test bench for the information processing part, a molecular model of E. lemming was created. This goal was achieved by implementing and combining deterministic molecular models of the individual parts.

Implementation of molecular models

Schematical overview of the devices.

The core component of E. lemming is the fusion of one light-sensitive protein (LSP?) to a protein of the chemotaxis pathway (Che?). Upon change of wavelength of light pulses, this component will dimerize with the corresponding light-sensitive protein (LSP?'), which is linked to an anchor protein, bound to an anchor (plasmid). The result is a change of the spatial localization of Che? and perturbation of the chemotaxis pathway, which ultimately leads to a different tumbling/straight run ratio.

Combined models. Coupled individual models for the simulation of the whole process and their interfaces.

In the theory world, the steps we are following in mindlessly driving E.coli to our pre - defined target are the following:

• deterministic (ODE) & stochastic models of the chemotaxis pathway (documented from the literature)
• model of the movement of E.coli (built on the information of the pathway derived from the molecular models)
• control algorithms ( built on the user’s desire to play around with E.coli)
• image tracking & image processing algorithms
• java applications/movies of the E.Lemming (the fun part)

Support for wet laboratory

Test bench for information processing

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