Joining the Atomic Ballet

Danceroom spectroscopy meets molecular dynamics simulation

Colored atoms bounce off one another on a vast wall at the Stanford Art Gallery on the Stanford University campus. But when visitors approach, their energy avatars appear on the wall and the atoms react: Sparkly blue ones accumulate inside the avatars while others bounce off them, scattering and gathering in response to their tilting, dancing bodies.  

 

This is Danceroom Spectroscopy (dS), an immersive, interactive simulation that David Glowacki, PhD, a Stanford visiting scholar and Royal Society research fellow, produced in collaboration with more than 40 scientists and artists.

 

Xbox 360 Kinect cameras capture gallery visitors’ 3-D images and convert them into an energy landscape embedded in a quantum simulation of an atomic liquid. The system rotates through hundreds of different atomic simulation setups, each with different physical properties and visual effects. And the soundscape changes too, in response to participant-generated waves and ripples in the atomic bath. It’s all running as close to real-time as it can (just a 17 millisecond delay), harnessing the power of more than 5000 GPU cores on a computer that, Glowacki says, “is pushing the limits of what interactive computing can do.”

Using Danceroom Spectroscopy (dS), human avatars push or pull a simulated 10-alanine peptide molecule into various conformations. Above right: A dancer performs with dS. Photos by Paul Blakemore courtesy of Danceroom Spectroscopy.
Taking advantage of that power, Glowacki recently used dS for more scientific purposes: a molecular dynamics (MD) simulation of the 10-alanine peptide embedded in 10,000 water molecules. The work was reported during a Faraday Discussions meeting in March 2014. In ordinary MD simulations, Glowacki says, “it can take a long time to simulate the rare events you really care about.” Using hand manipulations of 10-alanine, experts and novices were able to accelerate the rare events by three to four orders of magnitude.
Someday soon, Glowacki hopes to investigate whether dS has any potential as a crowd-sourced platform for mapping conformations in proteins and other molecules—enabling the video game generation to help advance biomedical science.



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