Diffusion Visualization - Jonathan Johannes

PHYS 210 PROJECTS --> here

Hey y'all,

My avenue of interest in physics led me to my (intended) major of biophysics. Therefore I'd like my project to be something related to the physics of biological systems such as:

1. a molecular dynamics (MD) simulator of the diffusion/movement of a specified particle in solution. I'm not sure how difficult this would be, because there are a lot of factors involved such as electrostatics, thermal energies and a whole load of things. But maybe an approximate model could be made. You might be able to adapt RASMOL or some such molecule-visualization program to show a molecule in solution being pelted by the surrounding water molecules, a sort of movie of the Brownian motion effects for which Einstein got his PhD. I think the problem would be getting the sources to work from; most of these really gorgeous visualization programs are proprietary and cost $$$$. Google '"Open Source" RASMOL' and see what comes up, if anything. But even a simple version of Brownian motion animation would be a nice Project if you write it yourself. -- Jess 14:54, 20 September 2008 (PDT)

or

2. a protein folding "predictor." This project would have to be very simplified with only the barebones and basic proteins, because the best and the brightest in the field still don't know how proteins fold. But it would be neat to compute and incorporate hydrophobic and hydrophilic interactions. You might want to talk to Steve Plotkin about this; he does cool stuff with protein folding etc. My impression is that this is 'way too hard, but that's because I am totally ignorant of how it's done; maybe there are simple parts that can be done in the available time. For instance (now that I think about it) you could treat each "pivot point" in a protein molecule as a sort of random walk in angles, let all the pivots shift at random and see if some general configurations are more likely than others; this would be sort of equivalent to finding configurations of maximum entropy, which is where things tend to end up. -- Jess 14:54, 20 September 2008 (PDT)

Those are my ideas now, if something else comes up I will update the page

Hello, it's Shauna Maybe it would be of interest to model the function of chaperones in protein folding. Either of the two current views: acting as force generated motors to pull the unfolded polypeptide through translocation pore or diffusion. I think the first view would be fun to model!! Target sites at N-terminus etc.Just an idea! Cheers

So I think I've made up my mind and will do a simple MD simulation where I'll approximate the trajectory of a solute within solution. And if possible will make a visualization of it with "OpenRasmol"! Should be fun!

I've just looked into a programming language/environment called Processing, it looks neat, not too sure of anything about it on top of that. I was wondering if anyone had any input on it?