Posts Tagged Dynamics

ATP Synthase movie

The proton driven turbine cranking out ATP – beautifully animated.
More background info at

shared by Rajini Rao via google+.

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The Joy of Stats

Visualisation is right at the heart of my own work, too […]
and I know, having the data is not enough.
I have to show it in ways people both enjoy and understand.

Hans Rosling’s TED talks have been a shining and influential example to many (including myself, I hope) – here is him condensing the development of the last 200 years around the globe into an engaging presentation in just under 4 minutes.

Hans Rosling’s 200 Countries, 200 Years, 4 Minutes – The Joy of Stats – BBC Four – shared by Hyun P. via the group Wolfson College, Cambridge on LinkedIn.

More links and the full (1h) documentary on BBC Four are available here and on the Open University website. Also, there is an interview and a best-of video on

“I kid you not, statistics is now the sexiest subject on the planet” says Hans Rosling – I guess the title is a (not so subtle) reference to the 1972 book from Dr. Alex Comfort.

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Visualizing Social Network Dynamics

Honestly, I am still coming to grips with some features of google+, but it’s gaining on me. Thanks to suggestions there, I came across this visualisation :

This video visualizes 5 hours of posts, comments, and likes on Google Plus condensed in to 4 minutes.

I think the way dynamical aspects of the network are highlighted is quite impressive and could be useful in the context of biomolecular networks as well:

More details explaining what’s going on are available on the youtube-page (click the youtube-logo in the lower right of the video). There you can switch from 360p to HD (up to 1080p) and watch it in full screen mode, which allows to clearly read the text and labels that pop up. A nice description is in “Take That, Google: Interactive Google+ Stream Visualizer Launching as Chrome Extension” – it is also mentioned among “The 65 Stories TechCrunch Didn’t Cover in November (But LAUNCH Did)” on (surprise!) LAUNCH.

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Molecular Animations Galore

To continue with examples in communicating “what is it all good for”: the University of British Columbia’s former “iCapture Centre” (now James Hogg Research Centre) has done a great piece on linking Asthma treatment with the underlying genetic and molecular mechanisms. (Here is Part1 and Part2)

The animations were realised by Arkitek Studios and they made a science-demoReel available.

They did some impressive work for nature on RNAi:

This series of three animations was created for Nature Reviews Genetics in 2004, built originally to live on Nature’s site temporarily, perhaps a month or so.
Seven years later, with millions of hits, it has proven to be one of the most popular things Nature has ever had on its site.
Plans are in the works to revisit the piece, since much has been learned about RNAi in the interrim. Look for the new RNAi animation by the end of 2011.

Looking forward to it!
There is also a “Nature Education Scitable“, something on Cadherin,
Stem Cells – “What are they?”, GPCR proteins, and Large Scale Biology (Human Protein Index). Enjoy!

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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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Speeding through the CLOUD

video tutorial to set up your HPC environment in less than 10 minutes.

Along the lines of Cloud and High Performance Computing (HPC) Amazon pushes its web-services into research applications : “With Amazon Web Services businesses and researchers can easily fulfill their high performance computational requirements with the added benefit of ad-hoc provisioning and pay-as-you-go pricing.” The image above has a link to the tutorial on setting up a HPC environment in less than 10 minutes – demonstrating the setup of a 7-node virtual cluster and running a molecular dynamics simulation with CHARMM.

NVIDIA unveiled the Tesla M2090 GPU this week. Equipped with 512 CUDA parallel processing cores, it delivers 665 GigaFLOPS of peak double-precision performance and 178 GB/sec memory bandwidth...

Similarly, the power of current many-core (>500 cores!) general-purpose graphics processing units (gpGPUs) can be awesome, of course the code has to be adjusted to take full advantage of the architecture. The release of the CUDA Toolkit 4.0 (Common Universal Device Architecture) in April simplified parallel programming already
and foreshadowed future CPU-GPU architectures. Think yesterdays beowulf-cluster shrunk to a single card that fits into your desktop machine. Depending on the application, GPUs seems to pack at least 10x the punch of a comparable CPU, for Amber this factor seems to be about 20x. NVidia has a test-drive of Amber available … Simulators, start your engines! Also there are a couple of standard Bioinformatics applications readily available for GPUs. Just last week, they announced “New NVIDIA Tesla GPU Smashes World Record in Scientific Computation“. Allegedly, this was achieved on only 4(!) GPUs – that fits into a midi-tower under the desk. Imagine if you’d stuff a full-height 19inch rack with these beasts – you’d not quite get to something like the Nebulae or Tianhe1A but definitely would land somewhere among the TOP500 Supercomputers in the world.

And finally in this category, also Googles App-Engine (GAE) is developing nicely, although I haven’t yet found a bioinformatics-related pet-project that would motivate me to test it more thoroughly. “App Engine enables your application to scale automatically without worrying about managing machines.“. Yep, that’s the spirit.

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