Modeling

Because the biodegradable hydrogel used to carry our EcnB peptide has several tunable properties including rate of biodegradation and internal concentration of EcnB, we decided to model the flow of the peptide in order to better understand what properties we want in the gel. Our model was divided into two parts to represent the two different environments the EcnB peptide will travel through - inside a fish and contained inside the flavocide hydrogel. Both parts were designed using COMSOL Multiphysics software.

Part 1: Necessary concentrations of EcnB in the fish
Working backwards, we know the necessary concentration for EcnB to be effective against Flavobacterium. We used this to find the necessary concentration of EcnB in the bloodstream.

We modelled the convection, diffusion, and degradation of the peptide first through blood vessels, then muscle tissue, and finally the skin of an “ideal” 2D fish. While properties for the peptide and fish are not exactly known, we estimated the values based on similar known constants [cite the Parameters sheet’s sources?].

Tweaking the initial concentration parameters in the bloodstream, we were able to find a target concentration in the blood for a necessary concentration range on the skin. The target concentration of EcnB on the skin was bounded by the minimum effective concentration against Flavobacterium and the toxic concentration of EcnB in the fish.

Part 2: Properties of the hydrogel
Now assuming all of the peptide within the gel is transferred into the fish, we tried to find what our ideal gel degradation rate and peptide concentration would be.

We decided on a 3D model for this part because the fish tag has some odd geometries and isn’t actually symmetric. As before, we tweaked the initial EcnB concentration within the gel, as well as the gel degradation rate, until we found our target values for the resultant concentration within the fish.