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Molecular Dynamics simulation of folding

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Views: 380

Tags: folding, protein, proteomics
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Comment by Vincent Granville on March 16, 2008 at 2:51pm
Thanks Theodore for this nice video. I wish I could find the time to produce a few hundreds image of my score distribution (see www.analyticbridge.com/photo/photo/show?id=2004291%3APhoto%3A72 ), with birth and death of these clusters, continuous change in size of these clusters (size = number of observations), and gradual change in color (color = severity of the problem).

Then put this together into a nice video. Are you aware of videos showing simulated statistical birth and death processes the way I describe it?

Thank you,
Vincent
Comment by Theodore Omtzigt on March 16, 2008 at 5:17pm
I have not come across any dynamic statistical process visualizations, but now you have made me aware I can poke around. The number of folks that can cross the divide between a scientific or mathematical discipline and the artistic/animation discipline are far and few between. There is a dude at UC Davis, Kwan-Liu Ma that is absolutely fantastic. http://www.idav.ucdavis.edu/ That SciDAC community is where I hang out.
Comment by Vincent Granville on March 16, 2008 at 9:38pm
Thanks Theodore. You are a very impressive guy. You are probably one of 2-3 people in the whole world who can cross the divide between scientific/mathematics, artistic/animation AND business acumen/marketing.
Comment by Rao on March 18, 2008 at 10:51pm
Theodre, Videos are superb. so much inspiring. It would be good if you provide more details around creating and software used.. etc..
Thanks
Rao
Comment by Theodore Omtzigt on March 19, 2008 at 9:49am
Ah, that is a very rich question. There is a reason why so few animations are made: the software universe for this is either rediculously expensive or totally inept for scientific visualization/animation.

The videos that I posted are all created by custom software that is more or less integrated with the solver. This means it is a one-off and impossible to reuse.

For pure animation of virtual worlds, I am a big fan of Blender (www.blender.org). In addition to the animation package being full features the BlenderNation is full of great artists that can help. The problem here is that these are mostly artists so you need to speak their language.

For scientific visualization there are three packages that I use ever so often: ParaView by KitWare, VisIt from Lawrence Livermore Labs, and MayaVi (folks that I interact with sometimes send me MayaVi files). It appears that ParaView is the old favorite, but VisIt is quickly becoming the new favorite particularly for those folks that use clusters a lot.

Stillwater is trying to adapt Blender to become a better scientific visualization package for exactly the reason that we haven't found a package that can combine animation with visualization and we believe that both are needed for a comprehensive story telling of scientific phenomena. However, that will be a long term activity so don't hold your breadth, :-(

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