Archive for the ‘CMTS’ Category


By Kevin Jiang, University of Chicago Medicine

Just 12 molecules of water cause the long post-activation recovery period required by potassium ion channels before they can function again. Using molecular simulations that modeled a potassium channel and its immediate cellular environment, atom for atom, University of Chicago scientists have revealed this new mechanism in the function of a nearly universal biological structure, with implications ranging from fundamental biology to the design of pharmaceuticals. Their findings were published online July 28 in Nature.

“Our research clarifies the nature of this previously mysterious inactivation state. This gives us better understanding of fundamental biology and should improve the rational design of drugs, which often target the inactivated state of channels” said Benoît Roux, PhD, professor of biochemistry and molecular biology at the University of Chicago and senior fellow at the Computation Institute.

Potassium channels, present in the cells of virtually living organisms, are core components in bioelectricity generation and cellular communication. Required for functions such as neural firing and muscle contraction, they serve as common targets in pharmaceutical development.


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CGI for Science

An image from a model of how endophilin sculpts membrane vesicles into a network of tubules. (Mijo Simunovic/CMTS)

An image from a model of how endophilin sculpts membrane vesicles into a network of tubules. (Mijo Simunovic/CMTS)

Computer graphics have greatly expanded the possibilities of cinema. Special effects using CGI (computer-generated imagery) today enable directors to shoot scenes that were once considered impossible or impractical, from interstellar combat to apocalyptic action sequences to fantastical digital characters that realistically interact with human actors.

In science, computer graphics are also creating sights that have never been seen before. But where movie special effects artists are realizing the vision of a screenwriter and director, scientific computer models are inspiring new discoveries by revealing a restless molecular world we cannot yet see with the naked eye.

Using computers to peer into this hidden universe was the theme of CI faculty and senior fellow Gregory Voth‘s Chicago Council on Science and Technology talk last week, titled Molecular Modeling: A Window to the Biochemical World. Scientists at Voth’s Center for Multiscale Theory and Simulation use computers to recreate real-world physics and produce awe-inspiring, intricate images, pushing the frontiers of discovery one femtosecond and nanometer at a time.

[Some of those images, including the one above by Mijo Simunovic, were on display as a “Science as Art” gallery, which you can view in a slideshow here.]

“The computer simulation allows us to make a movie, if you will, but it’s a movie describing what the laws of physics tells us,” Voth said. “It’s not a movie where we tell the computer we want this figure to run and shoot this figure. We don’t know what’s going happen. We know the equations, we feed them in [to a supercomputer], and we solve those equations…and we can reach scales we never dreamed of reaching before.”


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A few weeks ago, we urged readers to vote in the Bloomberg Mayors Challenge for the City of Chicago’s entry, a collaboration with the Urban Center for Computation and Data called the SmartData Platform. This week, the project received good news as it was chosen for a $1 million grant from Bloomberg Philanthropies to launch the project, one of five proposals to receive funding from the original pool of 305 applications. The SmartData platform will put city datasets — like those that can found on the city’s data portal — to work in making the city run more effectively and efficiently, and the UrbanCCD will help provide the computational expertise and tools to extract the maximum potential from the data. The new open-source platform is considered the next iteration of the WindyGrid system currently used internally by the city, which was discussed by Chicago’s Chief Data Officer Brett Goldstein at the recent Urban Sciences Research Coordination Network workshop.

Chicago and the other Bloomberg winners were covered by the New York Times, the Chicago Sun-Times, Crain’s Chicago Business, NBC Chicago, ABC Chicago, The Atlantic Cities,


The security at Argonne National Laboratory will be even tighter than usual today as President Barack Obama visits to deliver a speech on the subjects of energy and climate change. The Presidential visit comes just months after the announcement of the Argonne “Battery Hub,” a $155 million project that’s part of the national Joint Center for Energy Storage Research. But President Obama’s speech will also come at a time where national laboratories such as Argonne face budget cuts due to the federal sequestration.  If you want to see what the President says about these pressing topics, tune into White House Live at 1:30 p.m. Central time.


Next month will feature a lot of exciting CI-affiliated events. On April 3rd, Senior Fellow Gregory Voth will deliver a lunchtime talk in downtown Chicago on “Molecular Modeling: A Window to the Biochemical World” (register here). The 2013 edition of the GlobusWorld meeting runs from April 16-18 at Argonne, and registration for the conference and hotel rooms is currently open. Finally, the Computation Institute will host the inaugural Day of the Beagle symposium on April 23rd, celebrating the groundbreaking biology and medicine research performed on the Beagle supercomputer in its first year of operation.

The first supercomputer in the country of Jordan was built with somewhat unusual components: the processors from Playstation 3 video game consoles. As the article discusses, it follows a US Air Force supercomputer in using video game parts for high-performance computing.

Two visions of the future of computing received attention in recent weeks. A special issue of Science put the spotlight on quantum computing and recent experiments that move it closer to real-world application, and a feature on the new Nova Next website speculated on how synthetic biology could someday create computers made up of biological components.

“The Internet of Things” is catching on as a tech/computing buzzword, and in this video for the business news site Quartz, Robert Mawrey of ioBridge uses a fresh cup of coffee to explain why might soon want our appliances to send and receive tweets.

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cmts-mabMonoclonal antibodies are increasingly popular therapies for diseases such as cancer, arthritis and multiple sclerosis. They are also very expensive, due in part to the requirement that they are given intravenously at high concentrations to achieve their therapeutic benefits. Attempts to redesign the therapies to allow for easier and cheaper subcutaneous delivery have been stymied by the tendency of the antibodies to clump together, producing an unusably viscous solution. While experimental studies have identified some of the reasons for this viscosity, fully understanding these protein-protein interactions requires zooming in to a scale that’s currently beyond the ability of experiments.

Enter computational modeling, which can help scientists determine why some antibodies aggregate and others don’t, pointing the way to designing better treatments. While a postdoctoral scholar with the Center for Multiscale Theory and Simulation, Anuj Chaudhri worked with CMTS director Gregory Voth and scientists Dan Zarraga, Steve Shire and Tom Patapoff from the Late & Early Stage Pharmaceutical Development teams at Genentech to construct a model of what exactly happens when you put a lot of these antibodies into close proximity. The work was published by The Journal of Physical Chemistry.

“For high concentration proteins, not many experimental methods are available to get a deeper understanding of the fundamental interactions involved,” Chaudhri said. “This is where computation comes in. Using theoretical and computational methods, we can model the problem step by step by putting each piece together.”


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Using laboratory experiments, scientists have learned a great deal about our world at the molecular and cellular scale. But when modern techniques reach their limit, the baton can be passed to computer simulations and theory to fill in the gaps. The Center for Multiscale Theory and Simulation, directed by CI Senior Fellow Gregory Voth, uses these methods for research on biological systems to reveal the inner workings of cells, build better materials and design more effective drugs. To describe the potential of bringing theoretical chemistry and multiscale computer simulations to bear on biology, the CMTS produced this video featuring Voth, Marissa Saunders, and John Grime (whose work on HIV was previously featured on ScaleOut). Enjoy the video below:

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How HIV Builds its Suit of Armor

(L to R) The coarse-grained model of the viral capsid; Example results of lattice assembly simulations; Simulation detail showing the characteristic hexagonal lattice structure. (Image by John Grime)

At the molecular level, science is often a series of snapshots. With the most advanced imaging techniques, researchers can magnify targets over a million times, allowing them to examine structures as small as an Ångstrom. But in order to achieve this incredible resolution, most techniques require their targets to be fixed in place, reducing the dramatic, flowing motions of molecules to a series of before and after pictures.

To fill in the gaps, computational scientists such as those at the Center for Multiscale Theory and Simulation (CMTS), develop models that use these still images and the laws of physics to predict the movement of a molecule from point A to point B. In the case of a virus such as HIV, filling in those blanks could reveal potential weaknesses to exploit as new drug targets. In a new paper for Biophysical Journal, CMTS researchers John Grime and Gregory Voth simulated the intermediate steps of a critical moment for HIV: when it assembles a “suit of armor” for its genes.


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