Team:Exeter/Modelling

Introduction

We aim to produce a model of system that predicts the optical properties of our bacteria (output) as a function of incident light (input). The purpose of this model is to numerically characterize our bio-bricks for future use.

The Team

We are Exeter iGEM's dry team. Together we are responsible for the creation and development of a working model of our system and other various tasks

Angus Laurenson Physics

Callum Vincent Physics

Henri Laakso Electrical Engineering

The Model

The model is divided into three independant biological pathways. One for each light sensor; Red, Green and Blue. The chemistry of each is described by a set of rules whose rates are experimentally or theoretically determined. The three pathways are combined to form the final model.

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

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.