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

 
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Modelling in the biological sciences provides a great tool for investigating and predicting outcomes based on a multiple of parameters. <br><br>
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Modeling in the biological sciences provides a great tool for investigating and predicting outcomes based on a variety of different parameters. <br><br>
  
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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>
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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>
  
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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>
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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>
  
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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].
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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>.
 
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<h2>Under the lens</h2>
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<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>
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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.
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<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>
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<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>
 
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<h2>Microscopic view</h2>
 
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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>
 
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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.
 
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<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>
 
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<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>
 
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                       <a href="https://2018.igem.org/Team:DTU-Denmark/Model">Modelling</a>
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                       <a href="https://2018.igem.org/Team:DTU-Denmark/Model">Modeling</a>
 
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<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.