Team:ETH Zurich/Modeling

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Revision as of 02:08, 22 September 2011

Can you feel the smoke tonight?

Modeling Overview
We created a computational model of our system in order to check whether our ideas might work in reality. We investigated questions such as for which range of acetaldehyde input we get a GFP band from the band-pass filter, or what the most suitable channel dimensions are in silico. Only afterwards we started with the actual experimental channel design.

Roundup

Most of the modeling was done in Matlab. The 3D diffusion models were implemented using COMSOL.

Our goal was to create a large, spatiotemporal 3D reaction-diffusion model not only reliably reproducing the molecular dynamics of a single cell, but also the population dynamics arising from the intra-cell communication with acetaldehyde, xylene and AHL. Since the gradients of these signaling molecules are not only sensed, but also created by the SmoColi cells in a cooperative manner, a single cell model alone would not have been able to fully capture the dynamics of the microfluidic cellular sensor device.

Nevertheless, we started our modeling efforts in designing a single cell model based on ordinary differential equations. Although this single cell model can not answer any questions regarding the formation of the acetaldehyde, xylene and AHL gradients, it can be reliably used to predict if the sensor, band-pass filter and alarm system works, given that there is a gradient of the signaling molecules.

In parallel to this effort we created a three dimensional dynamic reaction-diffusion model using the mechanical engineering software platform COMSOL. Different to the single cell model, this model can not provide any answers regarding the dynamics inside each cell. However, it can give information on if a gradient of acetaldehyde or xylene can be obtained, given that the degradation rate of these molecules per cell does not depend on the state of the rest of the synthetic network.

With these two separate models most of the questions regarding biological implementation and channel design could already be answered. However, the AHL alarm system depends neither only on the inter-cellular, nor only on the extra-cellular state of the overall network, but on both. Therefore, we combined both models in a final step to create a three dimensional, temporal, molecular reaction diffusion model, which can reliably reproduce all important characteristics of our SmoColi smoke-detector.

These modeling efforts were not only valuable in the decision process on how to construct the overall network, but also played a crucial role in the construction process of our microfluidic device.

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 == Roundup==
 [[File:ETH codeExample.png|350px|left|thumb|Most of the modeling was done in Matlab. The 3D diffusion models were implemented using COMSOL.]]
-Our goal was to create a large, spatiotemporal 3D reaction-diffusion model not only reliably reproducing the molecular dynamics of a single cell, but also the population dynamics arising from the intra-cell communication with acetaldehyde, xylene and AHL. Since the gradients of the signaling molecules are not only sensed, but also created by the SmoColi cells in a cooperative manner, a single cell model alone would not have been able to fully capture the dynamics of the microfluidic cellular sensor device.
+Our goal was to create a large, spatiotemporal 3D reaction-diffusion model not only reliably reproducing the molecular dynamics of a single cell, but also the population dynamics arising from the intra-cell communication with acetaldehyde, xylene and AHL. Since the gradients of these signaling molecules are not only sensed, but also created by the SmoColi cells in a cooperative manner, a single cell model alone would not have been able to fully capture the dynamics of the microfluidic cellular sensor device.
-Most of the model equations and parameters we took from existing literature, which is supported by biological data. For some of them, we had to make assumptions or small adjustments, so that they meet the biological conditions under which we create our system in the lab.
+Nevertheless, we started our modeling efforts in designing a single cell model based on ordinary differential equations. Although this single cell model can not answer any questions regarding the formation of the acetaldehyde, xylene and AHL gradients, it can be reliably used to predict if the sensor, band-pass filter and alarm system works, given that there is a gradient of the signaling molecules.
-First, we simulated the '''[[Team:ETH_Zurich/Modeling/SingleCell|single cell model]]''' in MATLAB to see whether every module (sensor, band detector, filter) works properly. Most of the parameter manipulations and fine tuning of the system were done on the single sell model.
+In parallel to this effort we created a three dimensional dynamic reaction-diffusion model using the mechanical engineering software platform COMSOL. Different to the single cell model, this model can not provide any answers regarding the dynamics inside each cell. However, it can give information on if a gradient of acetaldehyde or xylene can be obtained, given that the degradation rate of these molecules per cell does not depend on the state of the rest of the synthetic network.
-Then, we used the COMSOL software to simulate diffusion of the toxic molecules to see whether a realistic gradient could be created '''[[Team:ETH_Zurich/Modeling/Microfluidics|(diffusion model)]]'''. This is the point when we started to get some feeling about the channel dimensions.
+With these two separate models most of the questions regarding biological implementation and channel design could already be answered. However, the AHL alarm system depends neither only on the inter-cellular, nor only on the extra-cellular state of the overall network, but on both. Therefore, we combined both models in a final step to create a three dimensional, temporal, molecular reaction diffusion model, which can reliably reproduce all important characteristics of our SmoColi smoke-detector.
-At the end, we combined the single cell model with the diffusion model to get the '''[[Team:ETH_Zurich/Modeling/Combined| final (reaction-diffusion) model]]''' in COMSOL. By visualizing the diffusion and the movement of the GFP band, we saw that our system can actually work in practice.
+These modeling efforts were not only valuable in the decision process on how to construct the overall network, but also played a crucial role in the construction process of our microfluidic device.
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