Team:Calgary/Model



MODELLING OVERVIEW


While inside our respective quarantine hovels, we were desperate to understand the system that we were creating. Through model, we sought to propel our project from a series of zoom sessions brainstorms into something potentially viable. For this to be achievable, we had to compartmentalize our project into various subsections. From this compartmentalization, we were able to identify areas that were better suited for human practices verification and where modelling may serve as our looking glass. This led us to four main modelling paths that influenced our design and how we built Oviita. The paths can be seen below. For more in-depth information on the models, and the impact they had on our project, please click on the icons.

ENDOGLUCANASE

For the first cellulase in our cellulose-degradation pathway, we looked into how our modifications would impact the dynamics and structure of the protein. This was achieved through the use of molecular dynamics, and our in-house GausHaus measuring software. Not only did this provide us with confidence in the efficacy of the modified proteins, but it also offered a great way to test and improve GausHaus.

CELLOBIOHYDROLASE-1

For the second cellulase in our cellulose-degradation pathway, we interrogated how different protonation states change the dynamics of the modified protein. This was conducted through the use of ProteinPrepare by playmolecule, molecular dynamic simulations, and linear regression. This modelling influenced the design of our FAB and LAB, as well as our assessment of acceptable growing conditions.

RANDLE CELL TESTING DEVICE

For our testing device, we had to first build an understanding of the electrical phenomena involved before we could have any hope of properly quantifying vitamin A levels in the blood. These models changed how we approached the sensor scheme and how we designed the hardware.

BIOREACTOR

With regards to the growth of our yeast, we needed to develop an understanding of what conditions and punishment it could handle. Therefore, we developed beta carotene production curves to understand production with varying conditions. We also wanted to understand how oxygen moves in the system and how we could optimize our bioreactors to give our yeast the best shot at success in the field.



Through the subprojects above, we were able to breathe life into Oviita without the physical use of a lab. From our protein engineering models, for example, we built confidence in our system’s field efficacy. These models were then able to directly influence the design and sequencing of our parts. When we encountered issues surrounding cultivation of Y. lipolytica , and whether or not it could handle certain growth conditions, we addressed our concerns through metabolic flux models. These models also greatly influenced the design and implementation strategies of our bioreactor.

When our HP work brought to light the difficulties in detecting vitamin A deficiency, we developed another subproject where we designed a detection system to quantify vitamin A levels in the blood. To ensure the viability of this detection system, known as the Randle Cell Testing Device, we performed extensive modelling.

Ultimately, modelling was the gateway through which Oviita was built to be physically sustainable. Combined with the efforts of our human practices work and preliminary lab findings, we have built confidence in Oviita’s potential to go from ideation to sustainable implementation.