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2014 was a productive year for the Computation Institute, so much so that we can't even fit our entire year in review into a single post. From papers on influenza, climate modeling, whole genome analysis, and autism prevalence to workshops on research data management, urban research, and the science of science, the Computation Institute was active across the University of Chicago and Argonne National Laboratory campuses and beyond, facilitating collaboration between disciplines and applying powerful computational tools to accelerate the pace of science. In this post, we cover January through June of this busy 2014, with the second half of the year coming later this week. Happy Holidays!

Computer simulations that reveal a key mechanism in the replication process of influenza A may help defend against future deadly pandemics.
Treating influenza relies on drugs such as Amantadine that are becoming less and less effective due to viral evolution. But University of Chicago and Computation Institute scientists have published computational results that may give drug designers the insight they need to develop the next generation of effective influenza treatment.

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On March 20th, our third Inside The Discovery Cloud event focused on Particles to Cosmos, featuring two researchers who design complex computer models to research vastly different scales. John Grime, of the Center for Multiscale Theory and Simulation, studies microsocopic viruses and proteins smaller many times smaller than a cell. Katrin Heitmann, a CI Senior Fellow at Argonne, studies the expansion of the universe, running the largest cosmological simulations ever performed on Argonne's Mira supercomputer.​ In the first talk, Grime takes us through the creation of coarse-grained models which make it possible to perform previously impossible simulations for chemistry, biology, and materials science.

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A day after the Royal Swedish Academy of Sciences celebrated a computation-enabled discovery 50 years in the making for the Nobel Prize in Physics, the prize committee chose to honor pioneers in another vibrant computational field with the Prize in Chemistry. On Wednesday, Martin Karplus, Michael Levitt, and Arieh Warshel received the chemistry prize for their contributions to the field of computational chemistry, developing software that allowed researchers to run simulations that incorporated both classical and quantum physics. The work created a modern environment where "​chemists now spend as much time in front of their computers as they do among test tubes" according to the Nobel Committee's materials. ​The CI's Center for Multiscale Theory and Simulation is one such place where the work of Karplus, Levitt and Warshel has been expanded to offer new insights in chemistry and biology. 

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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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Computer graphics have greatly expanded the possibilities of cinema.

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Monoclonal 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.

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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.