Team:ETHZ Basel/Modeling

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= E. Lemming @ ETHZ – Modeling Overview =
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= Mathematical Modeling Overview =
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[[Image:ETHZ_Basel_molecular_comb.png|thumb|400px|'''Figure 1: schematical overview of the modeled processes in E. lemming.''' LSP refers to light switch protein, AP to anchor protein, and Che to the attacked protein of the chemotaxis pathway.]]
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A complex mathematical model of E. lemming from both literature inspired and self developed submodels was created that covers the processes displayed in Figure 1.
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ETHZ’s project, E-Lemming, aims to modify the chemotaxis property of E.coli such that, instead of response to a chemical attractant/repellent, the bacterium responds to a light stimulus (phototaxis). Furthermore, this light sensitivity is used to control E.coli’s movement by deciding, at any given time, which type of motion will our ‘Lemming – in – disguise’ adopt (tumbling or straight run). This leads to a controllable E.coli, which can follow any pre – defined spatial path/maze/game, as a result of the combination of tumbling and going straight. The bacterium colony is 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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In a first step, existing models for the individual processes of E. lemming have been identified by literature research, implemented, corrected and adapted to our needs. Where we could not rely on established models, we started modeling on our own and calibrated the model with regard to available literature knowledge.
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<br><br>
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In the theory world, the steps we are following in mindlessly driving E.coli to our pre - defined target are the following: 
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• deterministic (ODE) & stochastic models of the chemotaxis pathway (documented from the literature)<br>
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* [[Team:ETHZ_Basel/Modeling/Light_Switch|'''Light Switch''']]: both implementation approaches have been modeled:
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• model of the movement of E.coli (built on the information of the pathway derived from the molecular models) <br> 
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** [[Team:ETHZ_Basel/Modeling/Light_Switch#Modeling_of_the_light_switch:_PhyB.2FPIF3|'''PhyB/PIF3''']]: a deterministic molecular model based on the light-sensitive dimerizing Arabidopsis proteins PhyB and PIF3.
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• control algorithms ( built on the user’s desire to play around with E.coli)<br>
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** [[Team:ETHZ_Basel/Modeling/Light_Switch#Modeling_of_the_PhyB.2FPIF3_light_switch#Archeal_light_receptor|'''Archeal Light Receptor''']]: a deterministic molecular model based on the archeal light receptor.
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• image tracking & image processing algorithms<br>
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* [[Team:ETHZ_Basel/Modeling/Chemotaxis|'''Chemotaxis Pathway''']]: two deterministic molecular models of the chemotaxis pathway.
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• java applications/movies of the E.Lemming (the fun part)<br>
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* [[Team:ETHZ_Basel/Modeling/Movement|'''Bacterial Movement''']]: a self developed stochastic model of ''E. coli'' movement on basis of the CheYp bias.
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== Model coupling ==
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In a second part, we combined the submodels stepwise to more comprehensive models that we could use to address different important questions to:
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* [[Team:ETHZ_Basel/Modeling/Combined#PhyB.2FPIF3_light_switch_-_Chemotaxis |'''PhyB/PIF3 light switch - Chemotaxis''']]: this model was used to reduce [[Team:ETHZ_Basel/Biology|wet laboratory experiments]] by identification molecular targets by [[Team:ETHZ_Basel/Modeling/Experimental_Design|experimental design]].
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[[Image:Modeling_overview.png|center|600px|Coupled models for the simulation of the whole process and their interfaces.]]
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* [[Team:ETHZ_Basel/Modeling/Combined#Archeal_light_receptor_-_Chemotaxis |'''Archeal light receptor - Chemotaxis''']]: this model was combined identically to the one above.
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* [[Team:ETHZ_Basel/Modeling/Combined#Chemotaxis_-_Movement |'''Chemotaxis - Movement''']]: complete model of E. lemming as a simulative test bench for the [[Team:ETHZ_Basel/InformationProcessing/Controller|controller]] design and as a brick of the comprehensive simulation of [[Team:ETHZ_Basel/InformationProcessing|information processing]].
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Besides the ''in vivo'' setup allowing the steering of a single ''Escherichia coli'' cell, the whole setup will be modeled. This allows us the testing of the cell detection & tracking as well as the design of the control algorithm in order to start verifying the different biological constructs and to record the successful control of bacterial movement.
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== Timetable ==
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A rough overview about the timetable
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[[Image:timetable.png|center|600px|Timetable of the modeling subgroup.]]
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will be accompanied with status updates from the project responsibles:
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[[Image:status_explained.png|center|600px|Status update scheme.]]
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The individual signs are saved in our wiki space and can be accessed as images with the following name scheme: <br>
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percentagecolour.png <br> <br>
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percentage: 25, 50, 75, 100 <br>
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colour: '''g'''reen, '''o'''range, '''r'''ed <br>
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e.g. 50% in red -> filename 50r.png <br>
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Please embed it with Image:75g.png|none
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[[Image:75g.png|none|50% completed and ok.]]
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== Responsibilities ==
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The responsibilities of the ongoing tasks and their documentation on this page are as follows: <br> <br>
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• receptor models: George <br>
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• cell detection & tracking: Thanuja <br>
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• microscope setup: Moritz <br>
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• movement model: Simona <br>
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• coordination and troubleshooting: Christoph <br>
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== Questions ==
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[[Team:ETHZ_Basel/Modeling/Questions]]
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Latest revision as of 19:09, 27 October 2010

Mathematical Modeling Overview

Figure 1: schematical overview of the modeled processes in E. lemming. LSP refers to light switch protein, AP to anchor protein, and Che to the attacked protein of the chemotaxis pathway.

A complex mathematical model of E. lemming from both literature inspired and self developed submodels was created that covers the processes displayed in Figure 1.

In a first step, existing models for the individual processes of E. lemming have been identified by literature research, implemented, corrected and adapted to our needs. Where we could not rely on established models, we started modeling on our own and calibrated the model with regard to available literature knowledge.

  • Light Switch: both implementation approaches have been modeled:
    • PhyB/PIF3: a deterministic molecular model based on the light-sensitive dimerizing Arabidopsis proteins PhyB and PIF3.
    • Archeal Light Receptor: a deterministic molecular model based on the archeal light receptor.
  • Chemotaxis Pathway: two deterministic molecular models of the chemotaxis pathway.
  • Bacterial Movement: a self developed stochastic model of E. coli movement on basis of the CheYp bias.

In a second part, we combined the submodels stepwise to more comprehensive models that we could use to address different important questions to:

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