Is there an alternative open source software to COMSOL for modeling drug delivery/neuroregeneration?

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Samantha Kamath

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Dec 14, 2017, 8:46:50 AM12/14/17
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Hi! For school, I am required to complete a research project. My current focus is on using tissue-engineered nerve guide conduits to treat peripheral nerve injury--specifically, mathematically modeling drug delivery systems within the conduit to determine their effects on neurogenesis. This mathematical modeling approach has been used in slightly different scenarios with COMSOL Multiphysics software. However, COMSOL is expensive; does anybody know of an open source alternative to COMSOL that allows for a similar approach?

Gordana Ostojic

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Dec 14, 2017, 10:33:12 AM12/14/17
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Cory J. Geesaman

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Dec 14, 2017, 10:35:23 AM12/14/17
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Nathan McCorkle

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Dec 14, 2017, 11:37:10 PM12/14/17
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Over many years, I have been trying to slowly learn about fluid
dynamics and CFD and hoping to stick to open-source tools. I am
interested in nanofluidics and electrophoresis modelling.

Here are some links I collected, but have not repeated yet:
https://en.wikiversity.org/wiki/CAD_to_FEniCS_example
https://fenicsproject.org/pub/tutorial/html/._ftut1009.html#ftut1:NS

A list of software:
https://cfdandheattransfer.wordpress.com/category/cfd-softwares/

I have a Python library to programmatically create 3D objects using BRL-CAD:
https://github.com/nmz787/python-brlcad-tcl
which can export to at least:
STL and image-slices (for i.e. lithography masks)

-Nathan

Skyler Gordon

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Dec 15, 2017, 1:08:29 AM12/15/17
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Hello,

Interesting project you’ve chosen. Could you elaborate on what you mean by conduit?

If it’s what I think it is: a small pathway that will deliver the drug to the specific locations at a desired rate, then I’ll also assume that it has to be permeable at some point. But that will depend on if it is end point (just a tube that provides the medicine) or a semi-permeable membrane that will slowly deliver the drug.

End point would be easier, since you could just have a constant influx of medicine in one spot and attempt to model the diffusion of it in the skin using some sort of Stokes-Einstein diffusion equation where the ‘tissue’ has some average diffusion constant. You would have to convert it to a spherical coordinate system with a little bit of calculus (or you could just look up the right answer) but it’s certainly possible.

The semi-permeable version is a little more elegant, giving a more full delivery of the medicine using only a single ‘conduit’, but the concentration of the medicine will decrease over time. Luckily that should be an easy variable to integrate into your system. This version would require converting to a cylindrical coordinate system, but like I said before: the information is already out there. Constructing it, may be more difficult.

Not sure if I helped.

-SG
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