Team:Heidelberg/Modeling/Chemotaxis

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<ul class="DropDownMenu" id="MB1-DDM1">
<ul class="DropDownMenu" id="MB1-DDM1">
<li><a href="https://2008.igem.org/Team:Heidelberg/Project"><span><span>Overall Project</span></span></a></li>
<li><a href="https://2008.igem.org/Team:Heidelberg/Project"><span><span>Overall Project</span></span></a></li>
 +
<li><a href="https://2008.igem.org/Team:Heidelberg/Notebook/material"><span><span>Material & Methods</span></span></a>
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Sensing"><span><span>Sensing</span></span></a></li>
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Sensing"><span><span>Sensing</span></span></a></li>
-
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Killing_I"><span><span>Killing I</span></span></a></li>
+
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Killing_I"><span><span>Killing I - Phages</span></span></a></li>
-
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Killing_II"><span><span>Killing II</span></span></a></li>
+
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Killing_II"><span><span>Killing II - Colicin</span></span></a></li>
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Visualization"><span><span>Visualization</span></span></a></li>
<li><a href="https://2008.igem.org/Team:Heidelberg/Project/Visualization"><span><span>Visualization</span></span></a></li>
</ul>
</ul>
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</li>
</li>
<li>
<li>
-
<a href="https://2008.igem.org/Team:Heidelberg/Chemotaxis" style="color: white">Modeling<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
<a href="https://2008.igem.org/Team:Heidelberg/Modeling" style="color: white">Modeling<!--[if gt IE 6]><!--></a><!--<![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<ul class="DropDownMenu" id="MB1-DDM3">
<ul class="DropDownMenu" id="MB1-DDM3">
-
<li><a href="https://2008.igem.org/Team:Heidelberg/Modeling/Chemotaxis"><span><span>Chemotaxis - Killing</span></span></a></li>
+
<li><a href="https://2008.igem.org/Team:Heidelberg/Modeling"><span><span>Overview</span></span></a></li>
-
<li><a href="https://2008.igem.org/Team:Heidelberg/Modeling/Phage"><span><span>Phage Dynamics - model</span></span></a></li>
+
<li><a href="https://2008.igem.org/Team:Heidelberg/Modeling/Chemotaxis"><span><span>Chemotaxis-Colicin</span></span></a></li>
 +
<li><a href="https://2008.igem.org/Team:Heidelberg/Modeling/Phage"><span><span>Phage Dynamics model</span></span></a></li>
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<!--[if lte IE 6]></td></tr></table></a><![endif]-->
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</li>
<li>
<li>
-
<a href="https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Notebook" style="color: white">Notebook<!--[if gt IE 6]><!--></a><!--<![endif]-->
+
<a href="https://2008.igem.org/Team:Heidelberg/Notebook/Overview" style="color: white">Notebook<!--[if gt IE 6]><!--></a><!--<![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
<ul class="DropDownMenu" id="MB1-DDM5">
<ul class="DropDownMenu" id="MB1-DDM5">
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<li><a href="https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Notebook"><span><span>Sensing Group ></span></span><!--[if gt IE 6]><!--></a><!--<![endif]-->
+
<li><a href="https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Notebook"><span><span>Sensing ></span></span><!--[if gt IE 6]><!--></a><!--<![endif]-->
<!--[if lt IE 7]><table border="0" cellpadding="0" cellspacing="0"><tr><td><![endif]-->
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<ul class="SideMenu" id="MB1-DDM2-SM1">
<ul class="SideMenu" id="MB1-DDM2-SM1">
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</li>
</li>
-
<li><a href="https://2008.igem.org/Team:Heidelberg/Notebook/Killing_I/Notebook"><span><span>Killing I ></span></span><!--[if gt IE 6]><!--></a><!--<![endif]-->
+
<li><a href="https://2008.igem.org/Team:Heidelberg/Notebook/Killing_I/Notebook"><span><span>Killing I - Phages ></span></span><!--[if gt IE 6]><!--></a><!--<![endif]-->
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==Chemotaxis - Killing Model==
 
-
in progress...
 
-
<math><$ \int_v=0 ^\infty \frac{dx}{dt} = y$></math>
+
== Chemotaxis - Killing Model ==
 +
Our detailed documentation "Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in ''Escherichia Coli''." includes the following information:
 +
* Introduction into the biological sytem
 +
* Chemotaxis model
 +
* Parameter estimation
 +
* Numerical methods
 +
* Results
 +
* Conclusions
 +
 
 +
You can download the documentation on [[Media:Documentation_Sensing_Colicin.pdf|Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in ''Escherichia Coli'']]. Further we have made a [[Media:Summary.pdf|summary]] of the complete modeling group for non-mathematicians.
 +
 
 +
 
 +
=== Simulation movies ===
 +
Below is a list of simulation movies. Specific parameters can be taken from our documentation. All simulations are in ogg vorbis format (see http://www.vorbis.com for help).
 +
 
 +
* movie 1 ([https://static.igem.org/mediawiki/2008/7/7f/HD_4PDE_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/6/6d/HD_4PDE_2D.ogg '''2D'''])
 +
** 4-PDE system
 +
** killer cells positioned in corner
 +
** prey evenly distributed
 +
* movie 2 ([https://static.igem.org/mediawiki/2008/f/f8/HD_5PDE_a_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/8/8a/HD_5PDE_a_2D.ogg '''2D'''])
 +
** 5-PDE system
 +
** killer cells positioned in corner
 +
** prey evenly distributed
 +
* movie 3 ([https://static.igem.org/mediawiki/2008/2/2f/HD_5PDE_a_0-01AI2_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/1/10/HD_5PDE_a_0-01AI2_2D.ogg '''2D'''])
 +
** 5-PDE system
 +
** killer cells positioned in corner
 +
** prey evenly distributed
 +
** 1/1000 AI-2 production rate
 +
* movie 4 ([https://static.igem.org/mediawiki/2008/1/15/HD_5PDE_a_4-fold-chemotaxis_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/9/9b/HD_5PDE_a_4-fold-chemotaxis_2D.ogg '''2D'''])
 +
** 5-PDE system
 +
** killer cells positioned in corner
 +
** prey evenly distributed
 +
** 8-fold chemotactic activity towards AI-2
 +
* movie 5 ([https://static.igem.org/mediawiki/2008/8/81/HD_5PDE_b_3D.ogg '''3D'''], [https://static.igem.org/mediawiki/2008/1/11/HD_5PDE_b_2D.ogg '''2D'''])
 +
** 5-PDE system
 +
** killer cells evenly distributed
 +
** prey positioned in center

Latest revision as of 22:54, 29 October 2008


Chemotaxis - Killing Model

Our detailed documentation "Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in Escherichia Coli." includes the following information:

  • Introduction into the biological sytem
  • Chemotaxis model
  • Parameter estimation
  • Numerical methods
  • Results
  • Conclusions

You can download the documentation on Spatially Resolved Modeling of Colicin-Induced Killing and Chemotactic Sensing in Escherichia Coli. Further we have made a summary of the complete modeling group for non-mathematicians.


Simulation movies

Below is a list of simulation movies. Specific parameters can be taken from our documentation. All simulations are in ogg vorbis format (see http://www.vorbis.com for help).

  • movie 1 (3D, 2D)
    • 4-PDE system
    • killer cells positioned in corner
    • prey evenly distributed
  • movie 2 (3D, 2D)
    • 5-PDE system
    • killer cells positioned in corner
    • prey evenly distributed
  • movie 3 (3D, 2D)
    • 5-PDE system
    • killer cells positioned in corner
    • prey evenly distributed
    • 1/1000 AI-2 production rate
  • movie 4 (3D, 2D)
    • 5-PDE system
    • killer cells positioned in corner
    • prey evenly distributed
    • 8-fold chemotactic activity towards AI-2
  • movie 5 (3D, 2D)
    • 5-PDE system
    • killer cells evenly distributed
    • prey positioned in center
Retrieved from "http://2008.igem.org/Team:Heidelberg/Modeling/Chemotaxis"