Difference between revisions of "Team:DTU-Denmark/Model"

 
(25 intermediate revisions by 5 users not shown)
Line 1: Line 1:
 
{{DTU-Denmark}}
 
{{DTU-Denmark}}
 +
{{DTU-Denmark/Styling}}
 
{{DTU-Denmark/footercss}}
 
{{DTU-Denmark/footercss}}
 +
 
<html>
 
<html>
  
−
<div style="position: relative; top: 0; right: 0;z-index: 0;width:100%; left: 0;opacity: 1; overflow: hidden;
+
<div class="toppercontainer">
−
    padding: 0;">
+
 
<img src="https://static.igem.org/mediawiki/2018/6/6a/T--DTU-Denmark--toppermodel.jpg" style="max-width: 100%; object-fit: cover; width:100%;" >
 
<img src="https://static.igem.org/mediawiki/2018/6/6a/T--DTU-Denmark--toppermodel.jpg" style="max-width: 100%; object-fit: cover; width:100%;" >
−
<div style="position: absolute;
+
<div class="headlinecontainer"><h1>Modeling</h1></div>
−
    top: 40%;
+
−
    left: 50%;
+
−
 
+
−
transform: translate(-50%, -50%);
+
−
    color:#fff;font-size:470%;"><h1>Modeling</h1></div>
+
 
</div>
 
</div>
  
  
 +
 +
<script type="text/x-mathjax-config">
 +
MathJax.Hub.Config({
 +
  tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}
 +
});
 +
</script>
 
<script src="https://2018.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
 
<script src="https://2018.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
 
</script>
 
</script>
Line 26: Line 28:
  
 
<div class="interlabspace">
 
<div class="interlabspace">
−
<p>
+
<p style="text-align:justify">
−
Modelling in the biological sciences provides a great tool for investigating and predicting outcomes based on a multiple of parameters. <br><br>
+
Modeling in the biological sciences provides a great tool for investigating and predicting outcomes based on a variety of different parameters. <br><br>
  
−
From studying the fungal behaviour in details to the structural behaviour of the mycelium-based structures, we’ve been applying four different approaches to solve some of the problems and increase our understanding of the processes involved in the project. <br><br>
+
From studying the fungal behavior in details to the structural behavior of the mycelium-based structures, we have been applying four different approaches to solve some of the problems and increase our understanding of the processes involved in the project. <br><br>
  
−
The whole idea of basing structures on fungal mycelium relies on the growth and the optimization of the basic physical and mechanical properties of the fungus. We have therefore developed two different approaches to simulating the biomass growth; a detailed model following the location of hyphae and locations [LINK TO SECTION] and another one involving applying a system of partial differential equations (PDE) that models the biomass movement [LINK TO SECTION].<br><br>
+
The whole idea of basing structures on fungal mycelium relies on the growth and the optimization of the basic physical and mechanical properties of the fungus. We have therefore developed two different approaches to simulating the biomass growth; a detailed model following the location of <a href="https://2018.igem.org/Team:DTU-Denmark/GrowthModelling">hyphae and locations</a> and another one involving applying a system of partial differential equations (PDE) that models <a href="https://2018.igem.org/Team:DTU-Denmark/GrowthModelling">the biomass movement</a>.<br><br>
  
−
When you change the characteristics of the mycelium, the structural properties will most likely also be influenced. The study of this have therefore been carried out by both designing the building [LINK TO SECTION] and testing out whether the mycelium can withstand the pressure needed [LINK TO SECTION].
+
When you change the characteristics of the mycelium, the structural properties will most likely also be influenced. The study of this has therefore been carried out by <a href="https://2018.igem.org/Team:DTU-Denmark/DesignOfExperiments">designing the building materials</a>, testing the designs and testing out whether the <a href="https://2018.igem.org/Team:DTU-Denmark/StructuralIntegrity">mycelium can withstand the pressure needed</a>.
 
</p>
 
</p>
  
 
</div>
 
</div>
−
 
−
 
 
<div class="interlabspace">
 
<div class="interlabspace">
−
<h2>Under the lens</h2>
+
<div class="col-xs-4" style="padding:3px;">
−
<p>
+
<p style="text-align:center;"> <a href="https://2018.igem.org/Team:DTU-Denmark/GrowthModelling"><img class="hoverimg" src="https://static.igem.org/mediawiki/2018/8/8d/T--DTU-Denmark--model1-overview.jpg" style="max-width: 100%;" title="Growth Modeling"> </a>
−
Filamentous fungi have a very characteristic growth pattern on solid medium, as they appear as a large network of interwoven filaments [link to figure of fungi network] [3]. If we can accurately predict how a fungus will grow over time, it will allow us to determine the optimal growth conditions to gain the best end product. Therefore, we have investigated how the fungal morphology changes over time at two level of details.
+
−
 
+
−
</p>
+
−
 
+
 
</div>
 
</div>
−
 
+
<div class="col-xs-4" style="padding:3px;">
−
 
+
<p style="text-align:center;"> <a href="https://2018.igem.org/Team:DTU-Denmark/DesignOfExperiments"><img class="hoverimg" src="https://static.igem.org/mediawiki/2018/d/da/T--DTU-Denmark--model3-overview.jpg" style="max-width: 100%;" title="Design of Experiments"> </a>
−
<div class="interlabspace">
+
</div>
−
<h2>Microscopic view</h2>
+
<div class="col-xs-4" style="padding:3px;">
−
<p>
+
<p style="text-align:center;"> <a href="https://2018.igem.org/Team:DTU-Denmark/StructuralIntegrity"><img class="hoverimg" src="https://static.igem.org/mediawiki/2018/3/3d/T--DTU-Denmark--model2-overview.jpg" style="max-width: 100%;" title="Structural Integrity"> </a>
−
One of our models focuses on the morphology at the hyphal level by simulating the movement of hyphal tips, branching rates, extension rates and the density levels during a growth period in two dimensions. All of the code scripts can be found on our <a href="https://github.com/BioBuilders2018/mycelium-simulations" target="_blank">GitHub repository.</a><br><br>
+
−
 
+
−
The mycelium of a fungi consists of many interwoven hyphae, and the density depends on how many filaments there are in the location. In figure 1 below, it is possible to see microscopic pictures of fungal mycelium. Three different levels of zoom illustrate how the network looks, where it can be observed how they interlink and how a fungal filament can branch into more.
+
−
</p>
+
−
<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/f/fc/T--DTU-Denmark--model-1.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 1: </b> - Snapshots of mycelium development of Aspergillus oryzae. These are representative microscopic images of how a network of intertwined hyphal filaments could look in a microscope.</p></figcaption>
+
−
</p>
+
−
 
+
−
 
+
−
 
+
 
</div>
 
</div>
−
 
−
 
−
 
−
 
−
<div class="interlabspace">
 
−
<h3>Simulation of the mycelium development</h3>
 
−
<p>
 
−
Fungal growth is initiated by $n$ number of spores, and a branch will start to extend from each of the spores added to the space. Following along one of these branches originating from a single spore, the hyphae will grow in a direction $\theta$ with a tip extension $r_{tip, i}$. A branching event, in which a new branch is formed from the first branch, can occur with a probability $q$.
 
−
 
−
Tip extension rate is calculated by using the equation below, which considers growth kinetics for the fungi and the amount of substrate available. It essentially outputs the accelerated growth dependent on the amount of substrate available, where the accelerated growth equation depends on fungal kinetics and branch lengths [1, 3].
 
−
\begin{equation}
 
−
r_{tip, i} = \bigg(k_{tip,1} + k_{tip,2}\cdot \frac{l_{br,i}}{l_{br, i} + K_t}\bigg)\cdot\bigg(\frac{S}{S+K_s}\bigg)
 
−
\end{equation}
 
−
$k_{tip,1}$ is the initial tip extension rate of the branch and $k_{tip,2}$ is the difference between the maximum extension rate and $k_{tip,1}$ [1, 3]. The length of branch $i$ described by $l_{br,i}. $S$ is the substrate concentration and $K_S$ corresponds to the substrate concentration to reach half of the maximum growth level [4].
 
−
 
−
As the starting coordinates of this simulation are $(x_0, y_0)$  and end coordinates $(x, y)$, the length of branch $i$ can be calculated as the distance between two points:
 
−
\begin{equation}
 
−
l_{br, i} = \sqrt{(x-x_0)^2 + (y-y_0)^2}
 
−
\end{equation}
 
−
 
−
By dividing the growth area into a grid of $w\cdot h$ areas, it is possible to investigate the uptake of substrate, hyphal movement and the development of biomass through the simulation.
 
−
 
−
</p>
 
−
 
−
 
−
 
 
</div>
 
</div>
−
 
−
 
−
 
−
 
  
 
</div>
 
</div>
Line 120: Line 77:
 
<a href="https://2018.igem.org/Team:DTU-Denmark/Description">Project description</a>
 
<a href="https://2018.igem.org/Team:DTU-Denmark/Description">Project description</a>
 
&bull;
 
&bull;
−
                       <a href="https://2018.igem.org/Team:DTU-Denmark/Model">Modelling</a>
+
                       <a href="https://2018.igem.org/Team:DTU-Denmark/Model">Modeling</a>
 
&bull;
 
&bull;
 
<a href="https://2018.igem.org/Team:DTU-Denmark/Parts">Parts overview</a>
 
<a href="https://2018.igem.org/Team:DTU-Denmark/Parts">Parts overview</a>

Latest revision as of 01:56, 18 October 2018

Modeling

Modeling in the biological sciences provides a great tool for investigating and predicting outcomes based on a variety of different parameters.

From studying the fungal behavior in details to the structural behavior of the mycelium-based structures, we have been applying four different approaches to solve some of the problems and increase our understanding of the processes involved in the project.

The whole idea of basing structures on fungal mycelium relies on the growth and the optimization of the basic physical and mechanical properties of the fungus. We have therefore developed two different approaches to simulating the biomass growth; a detailed model following the location of hyphae and locations and another one involving applying a system of partial differential equations (PDE) that models the biomass movement.

When you change the characteristics of the mycelium, the structural properties will most likely also be influenced. The study of this has therefore been carried out by designing the building materials, testing the designs and testing out whether the mycelium can withstand the pressure needed.