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Team:ETHZ Basel/Modeling
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[[Image:ETHZ_Basel_molecular_comb.png|thumb|400px|'''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.]] | [[Image:ETHZ_Basel_molecular_comb.png|thumb|400px|'''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. The implementation | + | A complex mathematical model of E. lemming from both literature inspired and self developed submodels was created. The final implementation combines deterministic molecular models of the [[Team:ETHZ_Basel/Modeling/Chemotaxis| chemotaxis pathway]], the [[Team:ETHZ_Basel/Modeling/Light_Switch| light switch]] and a probabilistic model for the [[Team:ETHZ_Basel/Modeling/Movement| bacterial movement]] in one model. |
This model was used to reduce [[Team:ETHZ_Basel/Biology|wet laboratory experiments]] by identify molecular targets and to create a simulative test bench for the [[Team:ETHZ_Basel/InformationProcessing|information processing]] algorithms. | This model was used to reduce [[Team:ETHZ_Basel/Biology|wet laboratory experiments]] by identify molecular targets and to create a simulative test bench for the [[Team:ETHZ_Basel/InformationProcessing|information processing]] algorithms. | ||
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== Model implementation == | == Model implementation == | ||
| - | === | + | === Submodels === |
| + | Submodels individual processes | ||
| + | |||
In a first step, we implemented individual deterministic molecular models for the subdevices and a stochastic mathematical model of the bacterial movement. | In a first step, we implemented individual deterministic molecular models for the subdevices and a stochastic mathematical model of the bacterial movement. | ||
* [[Team:ETHZ_Basel/Modeling/Light_Switch|'''Light Switch''']]: based on the light-sensitive dimerizing Arabidopsis proteins PhyB and PIF3. | * [[Team:ETHZ_Basel/Modeling/Light_Switch|'''Light Switch''']]: based on the light-sensitive dimerizing Arabidopsis proteins PhyB and PIF3. | ||
Revision as of 11:45, 26 October 2010
Mathematical Modeling Overview
A complex mathematical model of E. lemming from both literature inspired and self developed submodels was created. The final implementation combines deterministic molecular models of the chemotaxis pathway, the light switch and a probabilistic model for the bacterial movement in one model.
This model was used to reduce wet laboratory experiments by identify molecular targets and to create a simulative test bench for the information processing algorithms.
Model implementation
Submodels
Submodels individual processes
In a first step, we implemented individual deterministic molecular models for the subdevices and a stochastic mathematical model of the bacterial movement.
- Light Switch: based on the light-sensitive dimerizing Arabidopsis proteins PhyB and PIF3.
- Chemotaxis Pathway: two similar models of the chemotactic receptor pathway.
- Bacterial Movement: a probabilistic model of E. coli movement, determined by distribution of input bias.
Combined mathematical models
The next step, combining the individual models to a comprehensive and more complex model of E. lemming was achieved in two substeps:
- Light switch - Chemotaxis: used to insights for wet laboratory and information processing.
- Chemotaxis - Movement: complete model of E. lemming.
Experimental Design
Insights for wet laboratory
Since the design of E.lemming implies the existence of many possible biological combinations of the fundamental parts, the first steps in the modeling of our system were directed towards reducing the actual number of combinations implemented in the wetlab. Furthermore, by using the combined molecular models for in silico evaluation of the best possible devices, we derived theoretical results on choosing the biological parts which maximize the chance of a functional final ensemble.
Wet laboratory evaluation results have showed that molecular modeling and experimental biology can interwork to gain new insight on both aspects of our project.
Insights for information processing
In order to adjust the controller to have optimal light pulse rates, the combined molecular model has been used to determine the corresponding time constants.
Information processing evaluation results provide further information on how this task has been accomplished.
Test bench for information processing
In order to create a first test bench for the information processing pipeline, the combined model has been used to set up and evaluate the controller.
By providing input ports for the actual and the desired movement direction of the bacterium and boolean output ports for both light pulses (red light/far red light), it was possible to time - dependently control the E. lemming and close the loop in simulating the overall network.
