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In this video, I describe my class project for a Biomolecular Modeling course I took at UIC in the Summer of 2008.

Open source simulation and visualization tools, both developed at UIUC, were used for this project.

NAMD was used to computationally generate the model.
VMD was used to visualize the model.

The protein was simulated in the water cloud, first, but I removed the water for the "pulling and refolding" simulation, to clarify and speed it up. The water cloud model shown in the video doesn't actually have any dynamics; it just spins around rigidly as a static model.

A few seconds of simulation footage for the protein molecule in the water cloud was generated but it isn't enough be very interesting. That simulation was just used to obtain a more realistic model. It could have been loaded into the visualization to see the protein in its supercooled crystaline state relax in the warm water bath. The models that are downloaded from the PDB (Protein Data Bank) aren't quite true to the protein's natural state because of the low tempurature crystaline state that the protein needs to be in to allow its atomic coordinates to be ascertained. The crystal structures are close but there are some slight deviations. Perhaps that video can be posted soon.

I wrote my own simulation tool but it isn't ready for market yet. It doesn't do molecular dynamics, yet, but instead, performs statistical fluid dynamics using a reaction table in an adaptable mesh. I am still planning on incorporating molecular dynamics to update the reaction table. This seems to be necessary since all sorts of extremes in pressure, temperature and reagent concentrations occur in the microscale localities, which no preconceived reaction table is likely to effectively cover.

Once we figure out which genes play which roles in which diseases, we can not only neutralize their protein products to cure the diseases, but we can also engineer in-vitro firtilization processe to screen for and select sperm and egg that don't have those genes in them.

As far as overpopulating our planet is concerned, well, we just need more planets to populate, so we can give this one a rest for a little while. There are plenty of underpopulated planets within our reach; they just need a little tlc; they're fixer-upper planets.

I think disease is a terribly slow and inefficient sorter/strengthener of genetic information. I think microarrays, micropipettes, ultracentrifuges, robots and supercomputers and much better at sorting and strengthening human dna. Yeah, I think that living longer would be good for the planet, in fact. I think that people drive around in cars and throw things into incinerators and landfills because they think that they won't be around to have to deal with the long term effects. If that whole life-is-short mindset is biochemically extracted, people might start thinking a few hundred years ahead a bit more frequently.

Furthermore, the major obstacle preventing humans from inhabiting other planets and interplanetary space is the high levels of cancer causing ionizing radiation in low atmospheric pressure environments. If cancer genes were more controllable more people could leave planet Earth, further reducing its population.

Evolution is the macroscopic manifestation of a genetic algorithm spontaneously self-programmed with a fitness landscape oriented toward harnessing solar radiation by way of photosynthesis and combustion of its byproducts.

Sassy is my faithful canine companion.

A body of research has suggested that interactions with therapy dogs can increase oxytocin (bonding) and dopamine (happiness), while lowering cortisol (stress)

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the balloon valvuloplasty operation that will save her congenitally misformed heart!

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