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Team:ETHZ Basel/Modeling/Combined
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[[Image:ETHZ_Basel_models_overview_comb.png|thumb|400px|'''Combined model.''' Coupled individual models for the simulation of the whole process and their interfaces.]] | [[Image:ETHZ_Basel_models_overview_comb.png|thumb|400px|'''Combined model.''' Coupled individual models for the simulation of the whole process and their interfaces.]] | ||
| - | == | + | == Light switch - Chemotaxis == |
[[Image:ETHZ_Basel_chemotactical_network.png|thumb|400px|'''Schematical overview on the chemotactical pathway.''' MCPs refers to the membrane receptor proteins and Che are the intracellular chemotactical proteins.]] | [[Image:ETHZ_Basel_chemotactical_network.png|thumb|400px|'''Schematical overview on the chemotactical pathway.''' MCPs refers to the membrane receptor proteins and Che are the intracellular chemotactical proteins.]] | ||
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All of these assumptions will lead to a decrease of tumbling / directed movement ratio upon red light induction and an increase of corresponding far-red light induction. | All of these assumptions will lead to a decrease of tumbling / directed movement ratio upon red light induction and an increase of corresponding far-red light induction. | ||
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| + | == Chemotaxis - Movement == | ||
== Challenges == | == Challenges == | ||
Revision as of 12:56, 12 October 2010
Combined Model
Interface
To combine light switch, chemotaxis and movement models, interfaces were defined. The combination was achieved in two steps:
- First, the deterministic light switch and chemotaxis models were combined by assuming a complete removal of a selected Che protein species by the light switch. The interface was defined as the concentration ([LSP-Che]) of this linked device.
- Second, the probabilistic movement model was combined with the light switch - chemotaxis model. To combine this models, the bias of CheYp was used to be the input parameter of the movement model; determining the probability of straight run / tumbling.
Light switch - Chemotaxis
The following assumptions have been made according to the molecular mechanism to link the light switch and chemotaxis models:
Upon red light pulse induction, the two light-sensitive proteins dimerize and thus the coupled Che protein is spatially dislocated. This means,
- CheR is not able to methylate the MCPs anymore,
- CheY can't be phosphorylated and interact with the motor anymore; nevertheless, it still can be dephosphorylated.
Since CheB and CheZ regulate the chemotactic receptor pathway inverse compared to CheR and CheY, they repress tumbling
- CheB is not able to demethylate the MCPs and can't be phosphorylated anymore, but still can be dephosphorylated,
- CheZ can't dephosphorylate CheY anymore (This assumption is very unsteady, since CheY is not strictly located).
All of these assumptions will lead to a decrease of tumbling / directed movement ratio upon red light induction and an increase of corresponding far-red light induction.
Chemotaxis - Movement
Challenges
The combination of the deterministic and probabilistic models was the biggest challenge in combining the models. The problem of different step-size could be solved by combination via Simulink and independent numerical integration of the two model types.
<<< Movement model: How was it combined? Please write this here. >>>
