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Researchers in the group of Professor Tom Jones (MSI Fellow; Astronomy) are engaged in a long-term, unique, and highly successful study of the dynamics of diffuse, conducting media in astrophysical environments and their roles in mediating the acceleration and propagation of high-energy charged particles (so-called “cosmic rays”). The group has developed codes that combine high-performance, highly scalable, multidimensional magnetohydrodyamics (MHD) algorithms with uniquely efficient treatments of diffusive transport of cosmic rays.
In the image above, the left side illustrates results from an innovative MHD simulation carried out in November by Pete Mendygral and Tom Jones on MSI's Itasca supercomputer. The right side shows radio (pink) and X-ray (blue) astronomical observations of the astrophysical system that the simulation was intended to model (image credit: NASA and the National Radio Astronomy Observatory). The simulation modeled the dynamics of two pairs of supersonic, magnetized plasma jets. The jets were generated from sources that were orbiting each other while being subjected to a strong, supersonic cross wind. This simulation, which took roughly 10,000 CPU hours to complete, is the first of its kind. It was possible to set up, test, and execute the simulation over a span of three days prior to a symposium because of excellent HPC support from MSI. The underlying science is described below.The jets represent highly supersonic outflows from massive black holes at the centers of a pair of merging galaxies that are components of a pair of merging clusters of galaxies. As the black holes swallow nearby matter some of the energy released drives fast jets along the spin axes of the black holes. These are details of ongoing construction in the universe. On the biggest scales, clusters of galaxies spanning millions of light years fall together due to mutual gravity and collide to form bigger clusters over a time span of a few billion years. Some of the individual galaxies within those clusters also fall together, collide and merge together over time spans of a few hundred million years. Astronomers have established that all galaxies have massive black holes anchoring their centers. As two galaxies merge, gravitational effects cause their individual black holes to merge as well, also over a span of about 100 million years. Although cluster mergers are long lived enough to make them easy to find, it is much rarer to witness the faster merger of two massive black holes. But there are examples, including the very interesting pair of black holes in the galaxy cluster known as Abell 400, which is about 300 million light years from Earth. In this case two galaxies and their black holes are bound into an orbit about 20,000 light years apart and just beginning their inward spiral towards a merger. Each black hole, as it turns out is making plasma jets, so both are easy to find. The orbital motions of the black holes is causing the jets to become intertwined. At this point in the cluster merger the hot atmosphere of the clusters (revealed by X-rays) is "sloshing" in the gravitational well of the combined system. In effect the two merging galaxies are sitting in a very strong wind, which is blowing away the radio jets.
Work by Dr. Mendygral that involved a large data transfer was featured in a previous Research Spotlight.
MSI honored the retirement of the University of Minnesota Vice President for Research (VPR), Tim Mulcahy, with a special event on October 29, 2012. VP Mulcahy will be retiring from the University on December 31.
MSI came under the Office of the VPR in July 2008, and VP Mulcahy has been a staunch supporter of MSI’s mission during the past four years. He was instrumental in the procurement of Itasca, the Institute’s flagship supercomputer, and he has been a force in MSI’s expansion into new areas of research support, such as the University-wide informatics effort.
Also, on a day in 2011 that MSI staff will never forget, VP Mulcahy performed a song set to “La Donna e Mobile,” while dressed in full Renaissance costume. This event was a prize from VP Mulcahy to MSI for “highest increase in participation” among OVPR units in the 2011 Community Fund Drive.
The MSI retirement event for VP Mulcahy included a video game on the LMVL’s interactive screen, where he was asked to select various humorous options for his retirement. He was also presented with a paperweight that included a processor from Itasca and a musical card with an excerpt from his 2011 musical performance for MSI.
The MSI staff are grateful for VP Mulcahy’s support and we wish him well in his retirement.
Scientists are now using computers to help discover new drugs. Researchers at the University’s Center for Drug Design are in the forefront of these efforts. Professor Yuk Sham and his research group are studying the molecular recognition process of how molecules selectively associate with one another. Understanding the specific interactions involved is important for identifying and designing new drugs that can inhibit the normal function of viral proteins and stop the proliferation of viruses.
HIV/AIDS is an incurable disease. With the continuing emergence of drug resistance, it is extremely important to continue developing new drugs for the long-term management of the HIV/AIDS patients. Dr. Sham and his group, working closely with other members of the Center for Drug Design, use MSI high-performance computing clusters to develop accurate structural models to better understand these interactions to design a better inhibitor for the discovery and development of new antiviral drugs. The image above shows the structural model of HIV integrase developed by Professor Sham's research group. It is an essential viral enzyme that incorporates the HIV genome into human DNA. Effective inhibition of this enzyme is one of the validated approaches for the effective treatment of HIV/AIDS.
Dr. Sham’s group has also created videos describing the drug-development process against HIV/AIDS. They can be seen on YouTube:
"Targeting HIV Replication” (3:02 min)
"Making of an AIDS Drug” (2:26 min)
Protein kinase A (PKA) is involved in many cellular events and its activity can be tweaked and compartmentalized through mirystoylation of its N-terminus. (Mirystoylation is a type of protein modification that plays a role in directing and anchoring proteins to membranes and, thus, is involved with cellular regulation, signal transduction, and apoptosis.)
Research Associate Dr. Alessandro Cembran, who works with MSI PIs Professor Gianluigi Veglia (Biochemistry, Molecular Biology, and Biophysics) and Professor Jiali Gao (MSI Fellow, Chemistry), presented a poster at the 2012 MSI Research Exhibition about research he, Professors Veglia and Gao, and Research Associate Dr. Larry Masterson performed concerning PKA. The PKA catalytic subunit (PKA-C) mediates the transfer of the γ-phosphate group from ATP to threonine or serine residues. PKA activity must be tightly controlled in time and space, and myristoylation of its N-terminus is a regulatory mechanism that is not yet fully understood. The research presented in the poster investigated the short- and long-range structural and dynamical effects of PKA-C N-myristoylation through a combined experimental and computational approach. The group uses MSI resources to perform structural modeling and molecular dynamics simulations of cardiac proteins in their native lipid environment.
The results showed that myristoylation induces changes in structure and dynamics of the residues surrounding the myristoyl group, as well as long range perturbations involving catalytically relevant residues.
The image above shows the structure of the myristoylated kinase. Highlighted in the box is the allosteric link, responsible for the transmission of the allosteric signal from the myristoyl group to the active site. On the right, distance matrix analysis allows to identify regions in close contact.
MSI, with the support of the University of Minnesota’s NTS (Network and Telecommunication Services), has recently deployed a system to take advantage of the ten-gigabit network known as the Northern Lights GigaPoP network. With this system in place, MSI was able to help Peter J. Mendygral, a post-doctoral member of MSI principal investigator Tom Jones’s research group and employee of Cray, with some important work. Pete needed to transfer about seven terabytes of data in less than two days. He was able to do this successfully by utilizing MSI’s high-performance TeraScala storage system to store his remote data and using Globus GridFTP software to effect the transfer. Pete sat down with a MSI staffer to talk about his research, experience with MSI, and how MSI resources have helped him succeed.
MSI: What type of research are you doing?
Pete: My research is in astrophysics. I study magnetohydrodynamics, which means fluid dynamics simulations of ionized plasma with magnetic fields and their effects. I also study what we understand to exist in galaxy clusters, which are the largest gravitationally bound systems in the universe. So, specifically what I look at are the interactions between outflows of supermassive black holes that we believe exist at the centers of some of the large galaxies in these galaxy clusters. Within these galaxies are black holes that emit jets, supersonic jets. On a very large scale, they can have an enormous influence on the evolution of the clusters as well as the individual galaxies and stars.
MSI: What resources previously and currently have you utilized here at MSI?
Pete: Primarily we’ve run these simulations of jets and galaxy clusters on Itasca. I’ve also focused on other more specific phenomena, like the build-up of magnetic fields in galaxy clusters and the creation and evolution of cosmic ray particles. We have also done some smaller, kind of one-off type of things mainly for verifying the codes that I have written. Collaborators and I have done simulations of solar wind, galactic super bubbles, and giant bubbles created in galaxies by supernovas. My primary focus has been on the outflows of black holes and galaxy clusters, in terms of the simulations I have run on MSI systems. In addition, I use the LMVL systems a lot for my movie creations. In the LMVL I do a lot of stereo renderings because it really gives me an edge in understanding what’s going on inside a simulation. Seeing that third dimension is critical for understanding these simulations.
MSI: How has your use of the Northern Lights GigaPoP network in coordination with MSI systems and our high-performance TeraScala storage system enhanced your capabilities as a researcher?
Pete: I did my simulation this particular time on the Kraken system [the image above is from that simulation] at the National Institute for Computational Science (NISC) in Tennessee and it produced around seven terabytes of data. It’s often taken for granted in high-performance computing that you can produce your calculation relatively quickly, but then you come across the problem of dealing with this enormous dataset, especially when you run your simulation at a non-local site. So getting it in-house for analysis and creating movies become difficult challenges. The traditional route would be to send a secured copy via remote access (i.e. the ‘scp’ command), but this process would have taken at least 90 days. In this particular instance I had a conference coming up in a couple of weeks and I needed the data as soon as possible. So, 90 days was not going to work for me. The other option was to try to coordinate someone on the other end filling up a large number of hard drives and manually mailing them to me. That would require a large personnel cost and, best-case scenario, it would have still taken about two weeks. So what MSI’s Jeff McDonald and David Porter did for me was set up an MSI hardware interface with the Northern Lights GigaPoP network and I was able to move the entire dataset in less than two days. Because of this I was able to start working on my data immediately. This is an absolutely critical ability to have.
With the ever-changing needs of our users, MSI is proud to be able to help meet their challenges and to support researchers like Pete Mendygral in his pursuit of cutting edge research.