Posts Tagged Models

Network-Sculpting in 3D

Not only the WWW, but also the roots of Linux date back about 20 years. (What the heck was going on back then?)
Happy birthday, little Penguin! It has waddled a long way, found many friends and has grown up considerably.

(see the Linux Foundation pages for more info, and I’ll spare you the historic details of my first install of a kernel with a version nr.<1.0). Besides that much of the internet rests on Linux, what’s that got to do with 3D and networks? Read the rest of this entry »

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DREAM – RECOMB

The 6th Annual DREAM on Reverse Engineering Challenges, the 7th Annual RECOMB Satellite on Systems Biology, and the 8th Annual RECOMB Satellite on Regulatory Genomics will be held jointly at the IDIBELL institute (Barcelona) on October 14-19, 2011. The meeting will start at 9am on Friday October 14, 2011, and run till 6pm on Wednesday October 19, 2011 (October 14: DREAM; October 16-17: Systems Biology; October 18-19: Regulatory Genomics).
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Everything and Nothing


The pictures of the anisotropy of the cosmic microwave background radiation have been fascinating me since looking deeper into the relative spatial distribution of residue contacts in proteins and complexes.  Now here is a beautifully produced documentary by the BBC that takes you to the edge of the universe and everyting else we know about – well – mostly nothing :
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Lively Molecules in a Crowded Cytoplasm

cytoplasm model at the end of a Brownian dynamics simulation performed with the ‘full’ energy model

Proteins are not static entities – since we live at about 300 degrees above absolute zero there is constant Brownian motion. However, looking at deposited X-Ray structures, one might get the impression that the structures are rigidly sitting in vacuum – nothing could be further from the truth! I like the analogy with early photography :

Photography, ca. 1893

because the photoplates were not that sensitive, long exposure times were necessary. Hence people had to hold very, very still for several minutes in order to get a decent picture. Photographers had special setups and chairs with neckbraces to keep the poor subject in place. This apparatus is the analogy to a protein crystal – it keeps the proteins in place, floppy and moving parts will not show up on the resulting electron-density maps.
The photographs of our great-grandfathers leave us with the impression that they were very stiff people, largely devoid of any humour. That’s probably not true, but how happy and lively would you look if you had to sit still for quite some time in your best outfit with your head squeezed onto some weird mechanical contraption? The same holds true for proteins. Read the rest of this entry »

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