Team:Evry/pop scale

From 2013.igem.org

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This model is based on a cellular automaton algorithm : both the bacteria and the enterobactins are cellular automaton.  
This model is based on a cellular automaton algorithm : both the bacteria and the enterobactins are cellular automaton.  
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     <b>Figure 1 : </b> Influence graph.
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The <a href="#Fig1">Figure 1</a> is a graph representing the influence between the system's variables. <br/>
The <a href="#Fig1">Figure 1</a> is a graph representing the influence between the system's variables. <br/>

Revision as of 03:41, 29 October 2013

Iron coli project

Introduction

The Enterobactin production model showed us that our bacteria take too much time to produce enterobactins, which disables the flush strategy.
In response, we changed the strategy, by delivering a gel that would block the bacteria in the jejunum.
This model is thus very similar to the flush treatment model, except for the longer time scale, and the computational method.

Goal

This model was made to check if our first strategy was viable. It aims to answer the following question:
"Is it possible to chelate a significant amount of iron with a flush strategy?"

Assumptions

  • No regulation of the patient's iron absorption
  • Constant iron flow in the intestine
  • Homogeneous fluid
  • The bacterial natural absorption is insignificant compared to the chelation
  • The patient ingests 20mg of iron per day (Guideline Daily Amounts)

Materials and methods

This model is based on a cellular automaton algorithm : both the bacteria and the enterobactins are cellular automaton.

Absorption
Figure 1 : Influence graph.

The Figure 1 is a graph representing the influence between the system's variables.

Absorption
Figure 2 : Graph of bacteria automaton.
Pgrowth Division Probability
Pdeath Death probability
age variable rate of bacteria ageing

The Figure 2 represents the bacteriial automaton. It has two functions : the division and the ennterobactin production.
The bacteria produces enterobactins. This production is ruled by an activator. This activator is a step functionn (from 0 to 1) with a Ka threshold, fixed thanks to the sensor model:

The enterobactins chelate iron. For this automoton, we have one rule : One Enterobactin atom can chelate one Iron molecule
Still, the automaton is ruled by an encounter probability: .

Results

Absorption
Figure 3 : Iron dissolved in jejunum.
Absorption
Figure 4 : Iron absorbed by the body.

Parameter values

Description Value Unit Reference
Iron absorption rate by the body 0.2 s-1
Iron pulse value 4.5.10-9 mol-1
Sact 10**-9 m Duodenum length [3]

Models and scripts

This model was made using the Python language. You can download the python script here.

References: