Modelling is a key part of synthetic biology. Some experiments take too long, are far too expensive, or the information required just can’t be found via lab work. This is where modelling comes in. We take information from the biologist, construct a theoretical framework, and then feed back to people in the lab about what they should do.
In our project we have come up with a number of models, ranging from cell division to equilibrium reactions.
Click on the images below to explore more.
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Binding Affinity Modelling
A big problem biologists encounter is the uncertainty of binding especially in our design where zinc fingers bind to their sites. Therefore it is important to come up with a model which can calculate the number of cell and zinc finger binding sites required for a given output. This page discusses this and shows a program designed to dictate concentrations for the biologists to use.
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DNA Beading Model
Once we had a method of calculating the concentration of cells needed we had to model the number of cells required to make a certain shape. We also needed to invent a novel approach to creating 2D shapes using cells, this page discusses binding them to a longer string of DNA to form a pattern.
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DNA Origami Glue Modelling
After the inherent problems and issues found from using the first model of 2D shapes we came up with a second, which discusses the use of DNA as an oligonucleotide adhesive to create 2D and 3D structures and shapes.
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Cell Growth Interactions
The previous model works but would change over time as the cells grow. To combat this we came up with a model to shows cell growth which could then be used to come up with starting pattern for the previous model so that the interactions remain contant over time.
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Tetrahedron Construction
The previous model of using DNA as a glue could create 3D shapes but would need vast amounts of unique zinc fingers. This wasn't possible with our time frame so we came up with a model which could create a 3D structure from the minimum amount of unique DNA using tetrahedrons as a base to build from. Cells would then be bound to the outside.
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Cube Construction
The tetrahedron construction model could only create sphere shaped 3D structures. The cells that bound to the outside couldn't be controlled as well as we hoped so we came up with a new model that could. This page discusses the use of cube shaped DNA to create a shape where the cells bonded to the outside could be chosen.
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3D Lithography
Once we had an idea of how we could create small shapes using cells we wanted a quick overview how larger objects could be made. This discusses the different possibilities of the creation of 3D structures and shapes in a general sense, using different forms of bio-printng.
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NTNU Collab
We dcided to get help for some of the modelling and NTNU were kind enough to oblige. This model deals with calculating bonding and binding affinities.