Team:ETHZ Basel/Modeling

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= Molecular Modeling Overview =
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= Mathematical Modeling Overview =
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In order to support [[Team:ETHZ_Basel/Biology|wet laboratory experiments]] and to create a test bench for the [[Team:ETHZ_Basel/InformationProcessing|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.
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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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== Implementation of molecular models ==
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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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[[Image:ETHZ_Basel_molecular_comb.png|thumb|400px|'''Schematical overview of the devices and change upon light pulse induction.''' LSP? refers to light switch protein, AP to anchor protein, anchor to the plasmid anchor and Che? to the attacked protein of the chemotaxis pathway.]]
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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/directed flagellar movement state ratio.
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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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=== Individual molecular models ===
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* [[Team:ETHZ_Basel/Modeling/Light_Switch|'''Light Switch''']]: both implementation approaches have been modeled:
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In a first step, we implemented individual deterministic molecular models of subdevices.
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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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* [[Team:ETHZ_Basel/Modeling/Light_switch|'''Light switch''']]: based upon the light-sensitive dimerizing Arabidopsis proteins PhyB and PIF3.
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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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* [[Team:ETHZ_Basel/Modeling/Chemotaxis|'''Chemotaxis''']]: two similar models of the chemotaxis receptor pathway.
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* [[Team:ETHZ_Basel/Modeling/Chemotaxis|'''Chemotaxis Pathway''']]: two deterministic molecular models of the chemotaxis pathway.
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* [[Team:ETHZ_Basel/Modeling/Movement|'''Movement''']]: a statistical model of E. coli movement, determined by distribution of input bias.
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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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=== Combined molecular models ===
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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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[[Image:ETHZ_Basel_models_overview_comb.png|thumb|400px|'''Combined models.''' Coupled individual models for the simulation of the whole process and their interfaces.]]
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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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The next step, combination of the individual molecular models to a comprehensive model of E. lemming was achieved in two substeps:
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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|'''Light switch - Chemotaxis''']]: used to provide support for wet laboratory.
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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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* [[Team:ETHZ_Basel/Modeling/Combined|'''Light switch - Chemotaxis - Movement''']]: complete molecular model.
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== Support for wet laboratory ==
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To create the biological implementation of E. lemming, the parts of the core components had to be chosen in an order to improve chances to result in a functioning ensemble. By using the combined molecular models for ''in silico'' evaluation of the best possible parts, it was possible to reduce the amount of different combinations to be tested.
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[[Team:ETHZ_Basel/Modeling/Evaluation|'''Evaluation''']] results have showed, that molecular modeling and experimental biology can collaborate to gain new insight for both perceptions of the problem.
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== Test bench for information processing ==
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[[Image:ETHZ_Basel_models_overview_ip.png|thumb|400px|'''Test bench for information processing.''']]
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In order to create a first test bench for the information processing pipeline, the combined molecular models have been used to create and evaluate the controller. By providing an input port for light pulse and an output port for movement, it was possible to close the loop and simulate the whole system.
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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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