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Team:Exeter/Modelling
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| - | We aim to produce a model that predicts how the optical properties of our bacteria change in response to incident light. The model is composed of a red, green and a blue light activated pathway. The chemistry of each pathway is described by a set of rules. The rates of which are experimentally or theoretically determined. The purpose of the model is to numerically characterize our bio-bricks for future use. | + | We aim to produce a model that predicts how the optical properties of our bacteria change in response to incident light. The model is composed of a red, green and a blue light activated pathway. The chemistry of each pathway is described by a set of rules. The rates of which are experimentally or theoretically determined. The purpose of the model is to numerically characterize our bio-bricks for future use and to help us create the first colour coliroid. |
<!-- The model will focus on the rates of the reactions in our pathways and how light interacts with both the sensors and pigments. The final model will predict what colour and tone a bacteria will be given light exposure. --> | <!-- The model will focus on the rates of the reactions in our pathways and how light interacts with both the sensors and pigments. The final model will predict what colour and tone a bacteria will be given light exposure. --> | ||
Revision as of 10:55, 9 September 2013
Contents |
Introduction
We aim to produce a model that predicts how the optical properties of our bacteria change in response to incident light. The model is composed of a red, green and a blue light activated pathway. The chemistry of each pathway is described by a set of rules. The rates of which are experimentally or theoretically determined. The purpose of the model is to numerically characterize our bio-bricks for future use and to help us create the first colour coliroid.
The Team
 Physics |
 Physics |
 Electrical Engineering |
Modelling Software
The majority of our modelling efforts will be focused on creating a system of rules for the protein interaction programming language [http://www.kappalanguage.org/ Kappa]. Using Kappa we will be able to create a [http://en.wikipedia.org/wiki/Stochastic stochastic] model, which will take experimentally determined reaction rates and provide an accurate prediction of the bacteria's reaction to light exposure.
Assumptions
Due to the complexity of biological systems our model will include but not be limited to the following assumptions:
- Classical elastic mechanics
- Bacteria contain a homogeneous mix of components
- All constituents move with brownian motion
- Bacteria are identical
- Bacteria evenly distributed across surface
- Bacteria do not interact
- Only pathway specific species are rate limiting
With many thanks to our sponsors:
