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  • richardmitnick 12:54 pm on October 30, 2018 Permalink | Reply
    Tags: , , Illinois Quantum Information Science and Technology Center, IQUIST, Quantum information science and engineering, U Illinois   

    From University of Illinois: “New center to accelerate quantum information science and engineering” 

    U Illinois bloc

    From University of Illinois

    Oct 29, 2018

    Robin Kaler, associate chancellor for public affairs

    IQUIST will bring together Illinois’ physicists, engineers, computer scientists and many others to develop new paradigms in quantum information science and technology.
    Photo by L. Brian Stauffer

    The University of Illinois at Urbana-Champaign is making a $15 million investment in the emerging area of quantum information science and engineering, a field poised to revolutionize computing, communication, security, measurement and sensing by utilizing the unique and powerful capabilities of quantum mechanics.

    The centerpiece of the campus effort will be the formation of the Illinois Quantum Information Science and Technology Center. This will include a major hiring initiative to expand the number of quantum science experts at Illinois across multiple departments throughout the College of Engineering and the campus. The center will also enable the development of a focused program to educate the next-generation quantum workforce. The investment will also include state-of-the-art equipment for the fabrication of quantum materials and devices.

    The center will bring together Illinois’ physicists, engineers, computer scientists and many others to develop new paradigms in quantum information science and technology. They will discover and develop novel quantum algorithms, materials and devices. One of the center’s key projects will be the construction of a multi-node quantum testbed, enabling researchers to explore and implement new ideas for distributed quantum processing and applications of quantum networks. This work will continue the legacy of the contributions of the University of Illinois to the digital information revolution.

    “Quantum science and technology researchers are bold, and they face immense and difficult challenges – like any trailblazer,” said Rashid Bashir, who will become dean of Illinois’ College of Engineering on Nov. 1. “IQUIST will serve as the launching pad of innovations in quantum science and engineering. Building on our past and our current strengths, our scientists and engineers will lead the quantum information revolution to develop a new paradigm in computing and information processing.”

    With IQUIST, the College of Engineering will also launch new educational initiatives to train the future leaders of quantum scientists and engineers at the graduate and undergraduate levels. “The New York Times reported on the lack of quantum science and technology talent just last week. It’s crucial, as one of the largest and best engineering and physics programs in the country, to address both the technical and research challenges and the educational and workforce challenges that we face,” Provost Andreas Cangellaris said.

    IQUIST will foster and expand collaborations with industry, national labs and other academic institutions, such as the University of Chicago, Argonne National Laboratory and Fermilab. As a participant in the Discovery Partners Institute’s Illinois Innovation Network, IQUIST will contribute to strengthening Illinois’ economy through high-tech workforce and next-generation technology development.

    “Our campus has a legacy of groundbreaking contributions to fundamental science and the development of technologies that have shaped society over the past century, including the first automatic computer, magnetic resonance imaging, light-emitting diodes and the first modern internet browser. Not to mention the first computer built and owned by an educational institution,” Chancellor Robert Jones said. “Today, we are pleased to announce near-term concrete actions that will advance this critical area of national need and importance.”

    See the full article here .


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    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

  • richardmitnick 8:04 am on May 3, 2018 Permalink | Reply
    Tags: , , , U Illinois,   

    From University of Illinois via EarthSky: “Ample warning for supervolcanos?” 

    U Illinois bloc

    University of Illinois


    May 3, 2018
    Eleanor Imster

    llinois geology professor Patricia Gregg, right, and graduate student Haley Cabaniss have developed the first quantitative model that could help predict supervolcano eruptions.
    Photo by L. Brian Stauffer

    A supervolcano is a large volcano that has had an eruption of magnitude 8, which is the largest value on the Volcanic Explosivity Index (VEI). This means the volume of deposits for that eruption is greater than 240 cubic miles (1,000 cubic km). No image credit.

    No need to panic about an imminent supervolcano eruption, not from the Yellowstone supervolcano or another other similar system around the globe. That’s according to a new study published in the peer-reviewed journal Geophysical Research Letters on April 19, 2018. The study says that geological signs pointing to a catastrophic supervolcano eruption would be clear far in advance.

    Scientists had thought that these huge volcanoes gradually built up more and more molten rock until the pressure got to be too much. But they are now realizing that much of the period between eruptions — as much as a million years — is probably quiet. To help understand how to forecast supervolcano eruptions, a team of geologists quantified the effects of tectonic stress on the rocks that house these sleeping giants.

    Geologist Patricia Gregg of University of Illinois is a co-author on the study. She explained in a statement:

    “Supervolcanos tend to occur in areas of significant tectonic stress, where plates are moving toward, past or away from each other.”

    Haley Cabaniss, a PhD student at University of Illinois, is the study’s first author. Her work focuses on computer modeling of 3-D magma reservoirs of volcanos, in order to determine the how systems fail and ultimately. She explained how the models used in this study showed that tectonic stress does have a profound effect on the stability of supervolcanoes, but that these stresses aren’t the only factor to cause an eruption. She said:

    “Any tectonic stress will help destabilize rock and trigger eruptions, just on slightly different timescales. The remarkable thing we found is that the timing seems to depend not only on tectonic stress, but also on whether magma is being actively supplied to the volcano.”

    The researchers found that, in any given tectonic setting, the magma reservoirs inside supervolcanoes appear to remain stable for hundreds to thousands of years while new magma is being actively suppled to the system. Gregg said:

    “We were initially surprised by this very short timeframe of hundreds to thousands of years. But it is important to realize that supervolcanoes can lay dormant for a very long time, sometimes a million years or more. In other words, they may remain stable, doing almost nothing for 999,000 years, then start a period of rejuvenation leading to a large-scale eruption.”

    The researchers unexpectedly found that their models could help forecast supervolcano eruption timing and inform experts on what to expect, geologically, well before an eruption. Gregg acknowledged that people tend to panic whenever they hear that Yellowstone or, say, the Taupo Volcanic Zone in New Zealand, experience any change in seismic or geyser activity.

    Bay of Plenty, North Island, New Zealand, from the Bay of Plenty coast to Mounts Tongariro, Ngauruhoe, and Ruapehu (at bottom of picture). Also shows Lake Taupo and the Rotorua Lakes. This scene was acquired by the Moderate Resolution Imaging Spectroradiometer (MODIS), flying aboard NASA’s Terra satellite, on October 23, 2002.BayofPlentyA2002296.jpg

    NASA/Terra satellite

    But she said this new research suggests that the precursors to catastrophic eruption will be far greater and long-lasting than anything yet documented. She said:

    “When new magma starts to rejuvenate a supervolcano system, we can expect to see massive uplift, faulting and earthquake activity, far greater than the meter-scale events we have seen in recent time. We are talking on the range of tens to hundreds of meters of uplift. Even then, our models predict that the system would inflate for hundreds to thousands of years before we witness catastrophic eruption.”

    Cabaniss added:

    “It is also important to note that our research suggests that the whole rejuvenation-to-eruption process will take place over several or more human lifetimes. Our models indicate that there should be plenty of warning.”

    Bottom line: Before a supervolcano erupts, many warning signs will appear first, says a new study.

    See the full article here .

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    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

  • richardmitnick 11:44 am on December 11, 2017 Permalink | Reply
    Tags: , , excitonium, Excitonium is a condensate—it exhibits macroscopic quantum phenomena like a superconductor or superfluid or insulating electronic crystal, M-EELS-momentum-resolved electron energy-loss spectroscopy, , Physicists excited by discovery of new form of matter, U Illinois   

    From University of Illinois via phys.org: “Physicists excited by discovery of new form of matter, excitonium” 

    U Illinois bloc

    University of Illinois


    December 8, 2017
    Siv Schwink

    Artist’s depiction of the collective excitons of an excitonic solid. These excitations can be thought of as propagating domain walls (yellow) in an otherwise ordered solid exciton background (blue). Credit: Peter Abbamonte, U. of I. Department of Physics and Frederick Seitz Materials Research Laboratory

    Excitonium has a team of researchers at the University of Illinois at Urbana-Champaign… well… excited! Professor of Physics Peter Abbamonte and graduate students Anshul Kogar and Mindy Rak, with input from colleagues at Illinois, University of California, Berkeley, and University of Amsterdam, have proven the existence of this enigmatic new form of matter, which has perplexed scientists since it was first theorized almost 50 years ago.

    The team studied non-doped crystals of the oft-analyzed transition metal dichalcogenide titanium diselenide (1T-TiSe2) and reproduced their surprising results five times on different cleaved crystals. University of Amsterdam Professor of Physics Jasper van Wezel provided crucial theoretical interpretation of the experimental results.

    So what exactly is excitonium?

    Excitonium is a condensate—it exhibits macroscopic quantum phenomena, like a superconductor, or superfluid, or insulating electronic crystal. It’s made up of excitons, particles that are formed in a very strange quantum mechanical pairing, namely that of an escaped electron and the hole it left behind.

    It defies reason, but it turns out that when an electron, seated at the edge of a crowded-with-electrons valence band in a semiconductor, gets excited and jumps over the energy gap to the otherwise empty conduction band, it leaves behind a “hole” in the valence band. That hole behaves as though it were a particle with positive charge, and it attracts the escaped electron. When the escaped electron with its negative charge, pairs up with the hole, the two remarkably form a composite particle, a boson—an exciton.

    In point of fact, the hole’s particle-like attributes are attributable to the collective behavior of the surrounding crowd of electrons. But that understanding makes the pairing no less strange and wonderful.

    Why has excitonium taken 50 years to be discovered in real materials?

    Until now, scientists have not had the experimental tools to positively distinguish whether what looked like excitonium wasn’t in fact a Peierls phase. Though it’s completely unrelated to exciton formation, Peierls phases and exciton condensation share the same symmetry and similar observables—a superlattice and the opening of a single-particle energy gap.

    The relationship between energy and momentum for the excitonic collective mode observed with M-EELS. Credit: Peter Abbamonte, U. of I. Department of Physics and Frederick Seitz Materials Research Laboratory

    Abbamonte and his team were able to overcome that challenge by using a novel technique they developed called momentum-resolved electron energy-loss spectroscopy (M-EELS). M-EELS is more sensitive to valence band excitations than inelastic X-ray or neutron scattering techniques. Kogar retrofit an EEL spectrometer, which on its own could measure only the trajectory of an electron, giving how much energy and momentum it lost, with a goniometer, which allows the team to measure very precisely an electron’s momentum in real space.

    With their new technique, the group was able for the first time to measure collective excitations of the low-energy bosonic particles, the paired electrons and holes, regardless of their momentum. More specifically, the team achieved the first-ever observation in any material of the precursor to exciton condensation, a soft plasmon phase that emerged as the material approached its critical temperature of 190 Kelvin. This soft plasmon phase is “smoking gun” proof of exciton condensation in a three-dimensional solid and the first-ever definitive evidence for the discovery of excitonium.

    “This result is of cosmic significance,” affirms Abbamonte. “Ever since the term ‘excitonium’ was coined in the 1960s by Harvard theoretical physicist Bert Halperin, physicists have sought to demonstrate its existence. Theorists have debated whether it would be an insulator, a perfect conductor, or a superfluid—with some convincing arguments on all sides. Since the 1970s, many experimentalists have published evidence of the existence of excitonium, but their findings weren’t definitive proof and could equally have been explained by a conventional structural phase transition.”

    Rak recalls the moment, working in the Abbamonte laboratory, when she first understood the magnitude of these findings: “I remember Anshul being very excited about the results of our first measurements on TiSe2. We were standing at a whiteboard in the lab as he explained to me that we had just measured something that no one had seen before: a soft plasmon.”

    U of I Professor of Physics Peter Abbamonte (center) works with graduate students Anshul Kogar (right) and Mindy Rak (left) in his laboratory at the Frederick Seitz Materials Research Laboratory. Credit: L. Brian Stauffer, University of Illinois at Urbana-Champaign.

    “The excitement generated by this discovery remained with us throughout the entire project,” she continues. “The work we did on TiSe2 allowed me to see the unique promise our M-EELS technique holds for advancing our knowledge of the physical properties of materials and has motivated my continued research on TiSe2.”

    Kogar admits, discovering excitonium was not the original motivation for the research—the team had set out to test their new M-EELS method on a crystal that was readily available—grown at Illinois by former graduate student Young Il Joe, now of NIST. But he emphasizes, not coincidentally, excitonium was a major interest:

    “This discovery was serendipitous. But Peter and I had had a conversation about 5 or 6 years ago addressing exactly this topic of the soft electronic mode, though in a different context, the Wigner crystal instability. So although we didn’t immediately get at why it was occurring in TiSe2, we did know that it was an important result—and one that had been brewing in our minds for a few years.”

    The team’s findings are published in the December 8, 2017 issue of the journal Science in the article, “Signatures of exciton condensation in a transition metal dichalcogenide.”

    This fundamental research holds great promise for unlocking further quantum mechanical mysteries: after all, the study of macroscopic quantum phenomena is what has shaped our understanding of quantum mechanics. It could also shed light on the metal-insulator transition in band solids, in which exciton condensation is believed to play a part. Beyond that, possible technological applications of excitonium are purely speculative.

    See the full article here .

    Please help promote STEM in your local schools.

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    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

  • richardmitnick 2:10 pm on August 30, 2017 Permalink | Reply
    Tags: , , , Dealing with massive data, , U Illinois   

    From ANL: “Big Bang – The Movie” 

    Argonne Lab
    News from Argonne National Laboratory

    August 24, 2017
    Jared Sagoff
    Austin Keating

    If you have ever had to wait those agonizing minutes in front of a computer for a movie or large file to load, you’ll likely sympathize with the plight of cosmologists at the U.S. Department of Energy’s (DOE) Argonne National Laboratory. But instead of watching TV dramas, they are trying to transfer, as fast and as accurately as possible, the huge amounts of data that make up movies of the universe – computationally demanding and highly intricate simulations of how our cosmos evolved after the Big Bang.

    In a new approach to enable scientific breakthroughs, researchers linked together supercomputers at the Argonne Leadership Computing Facility (ALCF) and at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign (UI). This link enabled scientists to transfer massive amounts of data and to run two different types of demanding computations in a coordinated fashion – referred to technically as a workflow.

    What distinguishes the new work from typical workflows is the scale of the computation, the associated data generation and transfer and the scale and complexity of the final analysis. Researchers also tapped the unique capabilities of each supercomputer: They performed cosmological simulations on the ALCF’s Mira supercomputer, and then sent huge quantities of data to UI’s Blue Waters, which is better suited to perform the required data analysis tasks because of its processing power and memory balance.

    ANL ALCF MIRA IBM Blue Gene Q supercomputer at the Argonne Leadership Computing Facility

    U Illinois Blue Waters Cray supercomputer

    For cosmology, observations of the sky and computational simulations go hand in hand, as each informs the other. Cosmological surveys are becoming ever more complex as telescopes reach deeper into space and time, mapping out the distributions of galaxies at farther and farther distances, at earlier epochs of the evolution of the universe.

    The very nature of cosmology precludes carrying out controlled lab experiments, so scientists rely instead on simulations to provide a unique way to create a virtual cosmological laboratory. “The simulations that we run are a backbone for the different kinds of science that can be done experimentally, such as the large-scale experiments at different telescope facilities around the world,” said Argonne cosmologist Katrin Heitmann. “We talk about building the ‘universe in the lab,’ and simulations are a huge component of that.”

    Not just any computer is up to the immense challenge of generating and dealing with datasets that can exceed many petabytes a day, according to Heitmann. “You really need high-performance supercomputers that are capable of not only capturing the dynamics of trillions of different particles, but also doing exhaustive analysis on the simulated data,” she said. “And sometimes, it’s advantageous to run the simulation and do the analysis on different machines.”

    Typically, cosmological simulations can only output a fraction of the frames of the computational movie as it is running because of data storage restrictions. In this case, Argonne sent every data frame to NCSA as soon it was generated, allowing Heitmann and her team to greatly reduce the storage demands on the ALCF file system. “You want to keep as much data around as possible,” Heitmann said. “In order to do that, you need a whole computational ecosystem to come together: the fast data transfer, having a good place to ultimately store that data and being able to automate the whole process.”

    In particular, Argonne transferred the data produced immediately to Blue Waters for analysis. The first challenge was to set up the transfer to sustain the bandwidth of one petabyte per day.

    Once Blue Waters performed the first pass of data analysis, it reduced the raw data – with high fidelity – into a manageable size. At that point, researchers sent the data to a distributed repository at Argonne, the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Cosmologists can access and further analyze the data through a system built by researchers in Argonne’s Mathematics and Computer Science Division in collaboration with Argonne’s High Energy Physics Division.

    Argonne and University of Illinois built one such central repository on the Supercomputing ’16 conference exhibition floor in November 2016, with memory units supplied by DDN Storage. The data moved over 1,400 miles to the conference’s SciNet network. The link between the computers used high-speed networking through the Department of Energy’s Energy Science Network (ESnet). Researchers sought, in part, to take full advantage of the fast SciNET infrastructure to do real science; typically it is used for demonstrations of technology rather than solving real scientific problems.

    “External data movement at high speeds significantly impacts a supercomputer’s performance,” said Brandon George, systems engineer at DDN Storage. “Our solution addresses that issue by building a self-contained data transfer node with its own high-performance storage that takes in a supercomputer’s results and the responsibility for subsequent data transfers of said results, leaving supercomputer resources free to do their work more efficiently.”

    The full experiment ran successfully for 24 hours without interruption and led to a valuable new cosmological data set that Heitmann and other researchers started to analyze on the SC16 show floor.

    Argonne senior computer scientist Franck Cappello, who led the effort, likened the software workflow that the team developed to accomplish these goals to an orchestra. In this “orchestra,” Cappello said, the software connects individual sections, or computational resources, to make a richer, more complex sound.

    He added that his collaborators hope to improve the performance of the software to make the production and analysis of extreme-scale scientific data more accessible. “The SWIFT workflow environment and the Globus file transfer service were critical technologies to provide the effective and reliable orchestration and the communication performance that were required by the experiment,” Cappello said.

    “The idea is to have data centers like we have for the commercial cloud. They will hold scientific data and will allow many more people to access and analyze this data, and develop a better understanding of what they’re investigating,” said Cappello, who also holds an affiliate position at NCSA and serves as director of the international Joint Laboratory on Extreme Scale Computing, based in Illinois. “In this case, the focus was cosmology and the universe. But this approach can aid scientists in other fields in reaching their data just as well.”

    Argonne computer scientist Rajkumar Kettimuthu and David Wheeler, lead network engineer at NCSA, were instrumental in establishing the configuration that actually reached this performance. Maxine Brown from University of Illinois provided the Sage environment to display the analysis result at extreme resolution. Justin Wozniak from Argonne developed the whole workflow environment using SWIFT to orchestrate and perform all operations.

    The Argonne Leadership Computing Facility, the Oak Ridge Leadership Computing Facility, the Energy Science Network and the National Energy Research Scientific Computing Center are DOE Office of Science User Facilities. Blue Waters is the largest leadership-class supercomputer funded by the National Science Foundation. Part of this work was funded by DOE’s Office of Science.

    The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign provides supercomputing and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students, and collaborators from around the globe use advanced digital resources to address research grand challenges for the benefit of science and society. NCSA has been advancing one third of the Fortune 50 for more than 30 years by bringing industry, researchers, and students together to solve grand challenges at rapid speed and scale.

    See the full article here .

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    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

  • richardmitnick 4:39 pm on January 22, 2017 Permalink | Reply
    Tags: , Bacterium Staphylococcus aureus, Better understanding the bacteria’s defenses, , Newcastle University in the U.K., Team discovers how bacteria exploit a chink in the body’s armor, U Illinois   

    From U Illinois: “Team discovers how bacteria exploit a chink in the body’s armor” 

    U Illinois bloc

    University of Illinois

    Jan 19, 2017
    Steph Adams

    U. of I. microbiology professor Thomas Kehl-Fie, graduate student Yuritzi Garcia and their colleagues made a key discovery about how a potentially dangerous pathogen defeats the human immune system. Photo by Steph Adams

    Staphylococcus aureus, in yellow, interacts with a human white blood cell. Photo courtesy the National Institute of Allergy and Infectious Disease

    Scientists have discovered how a unique bacterial enzyme can blunt the body’s key weapons in its fight against infection.

    Researchers at the University of Illinois at Urbana-Champaign and Newcastle University in the U.K. are investigating how infectious microbes can survive attacks by the body’s immune system. By better understanding the bacteria’s defenses, new strategies can be developed to cure infections that are currently resistant to treatments, the researchers said.

    The study, reported in the journal PLOS Pathogens, focused on the bacterium Staphylococcus aureus, which is found on approximately half of the population. While it usually safely coexists with healthy individuals, S. aureus has the ability to infect nearly the entire body; in its most pathogenic form, the bacterium is the so-called “superbug” methicillin-resistant S. aureus, or MRSA.

    The human body uses a diverse array of weapons to fight off bacteria like S. aureus. “Our immune system is very effective and prevents the majority of microbes we encounter from causing infections,” said U. of I. microbiology professor Thomas Kehl-Fie, who led the study with Kevin Waldron, of Newcastle University. “But pathogens such as S. aureus have developed ways to subvert the immune response.”

    S. aureus can overcome one of the body’s key defenses, nutritional immunity, which prevents bacteria from obtaining critical nutrients. It starves S. aureus of manganese, a metal needed by the bacterial enzyme superoxide dismutase, or SOD. This enzyme functions as a shield, minimizing the damage from another weapon in the body’s arsenal, the oxidative burst. Together, the two host weapons usually function as a one-two punch, with nutritional immunity weakening the bacteria’s shields, enabling the oxidative burst to kill the bacterium.

    S. aureus is particularly adept at causing devastating infections. Differing from other closely related species, S. aureus possesses two SOD enzymes. The team discovered that the second SOD enhances the ability of S. aureus to resist nutritional immunity and cause disease.

    “This realization was both exciting and perplexing, as both SODs were thought to utilize manganese and therefore should be inactivated by manganese starvation,” Kehl-Fie said.

    The most prevalent family of SODs, to which both of the S. aureus enzymes belong, has long been thought to come in two varieties: those that are dependent on manganese for function and those that use iron.

    Newcastle University researchers, from left, Emma Tarrant, Kevin Waldron and Anna Barwinska-Sendra collaborated on a new study of bacterial defenses.
    Photo courtesy Newcastle University

    In light of their findings, the team tested whether the second staphylococcal SOD was dependent on iron. To their surprise, they discovered that the enzyme was able to use either metal. While the existence of these cambialistic SODs, capable of using both iron and manganese, was proposed decades ago, the existence of this type of enzyme was largely dismissed as a quirk of chemistry, unimportant in real biological systems. The team’s findings dispel this notion, demonstrating that cambialistic SODs critically contribute to infection.

    The team found that, when starved of manganese by the body, S. aureus activated the cambialistic SOD with iron instead of manganese, ensuring its critical bacterial defensive barrier was maintained.

    “The cambialistic SOD plays a key role in this bacterium’s ability to evade the immune defense,” Waldron said. “Importantly, we suspect similar enzymes may be present in other pathogenic bacteria. Therefore, it could be possible to target this system with drugs for future antibacterial therapies.”

    The emergence and spread of antibiotic-resistant bacteria, such as MRSA, make such infections increasingly difficult, if not impossible, to treat.

    This has prompted leading health organizations, such as the Centers for Disease Control and Prevention and the World Health Organization, to issue an urgent call for new approaches to combat the threat of antibiotic resistance

    See the full article here .

    Please help promote STEM in your local schools.

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    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

  • richardmitnick 8:45 am on December 7, 2016 Permalink | Reply
    Tags: , , Researchers discover hot hydrogen atoms in Earth's upper atmosphere, U Illinois   

    From U Illinois: “Researchers discover hot hydrogen atoms in Earth’s upper atmosphere” 

    U Illinois bloc

    University of Illinois

    No writer credit found

    A schematic diagram of the Global Ultraviolet Imager observational geometry. The TIMED satellite is orbiting at 625 km and viewing in the anti-sunward limb direction. No image credit.


    A team of University of Illinois researchers has discovered the existence of hot atomic hydrogen (H) atoms in an upper layer of Earth’s atmosphere known as the thermosphere. This finding, which the authors report today in Nature Communications, significantly changes current understanding of the H distribution and its interaction with other atmospheric constituents.

    Because H atoms are very light, they can easily overcome a planet’s gravitational force and permanently escape into interplanetary space. The ongoing atmospheric escape of H atoms is one reason why Earth’s sister planet, Mars, has lost the majority of its water. In addition, H atoms play a critical role in the physics governing the Earth’s upper atmosphere and also serve as an important shield for societies’ technological assets, such as the numerous satellites in low earth orbit, against the harsh space environment.

    Lara Waldrop

    “Hot H atoms had been theorized to exist at very high altitudes, above several thousand kilometers, but our discovery that they exist as low as 250 kilometers was truly surprising,” said ECE ILLINOIS Assistant Professor Lara Waldrop, principle investigator of the project. Waldrop is also affiliated with the Coordinated Science Lab at Illinois. “This result suggests that current atmospheric models are missing some key physics that impacts many different studies, ranging from atmospheric escape to the thermal structure of the upper atmosphere.”

    The discovery was enabled by the development of new numerical techniques and their application to years’ worth of remote sensing measurements acquired by NASA’s Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED) satellite. “Classical assumptions about upper atmospheric physics didn’t allow for the presence of hot H atoms at these heights,” recalled Dr. Jianqi Qin, the ECE ILLINOIS research scientist who developed the data analysis technique.

    Dr. Jianqi Qin

    “Once we changed our approach to avoid this unphysical assumption, we were able to correctly interpret the data for the first time.”

    Atomic hydrogen efficiently scatters ultraviolet radiation emitted by the sun, and the amount of scattered light sensitively depends on the amount of H atoms that are present in the atmosphere. As a result, remote observations of the scattered H emission, such as those made by NASA’s TIMED satellite, can be used to probe the abundance and spatial distribution of this key atmospheric constituent. In order to extract information about the upper atmosphere from such measurements, one needs to calculate exactly how the solar photons are scattered, which falls into Qin’s unique expertise.

    Under support from the National Science Foundation and NASA, the researchers developed a model of the radiative transfer of the scattered emission along with a new analysis technique that incorporated a transition region between the lower and upper extents of the H distribution. “It turns out that the new model fits the measurements perfectly,” said Qin. “Our analysis of the TIMED data led to the counter-intuitive finding that the temperature of the H atoms in the thermosphere increases significantly with declining solar activity, in contrast to the ambient atmospheric temperature, which decreases with declining solar activity.”

    Their results also show that the presence of such hot H atoms in the thermosphere significantly affects the distribution of the H atoms throughout the entire atmosphere. The origin of such hot H atoms, previously thought not to be able to exist in the thermosphere, is still a mystery. “We know that there must be a source of hot H atoms, either in the local thermosphere or in more distant layers of the atmosphere, but we do not have a solid answer yet,” said Waldrop.

    Qin added, “We will definitely keep working on this puzzle, because knowledge about the H density distribution is critical to the investigation of our atmospheric system as well as its response to space weather, which affects many space-based technologies that are so important for our modern society.”

    See the full article here .

    Please help promote STEM in your local schools.

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    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

  • richardmitnick 11:58 am on May 19, 2016 Permalink | Reply
    Tags: , , U Illinois   

    From U Illinois: “Scientists discover the evolutionary link between protein structure and function” 

    U Illinois bloc

    University of Illinois

    May 18, 2016
    Lauren Quinn

    Heme protein showing loops in orange near the bottom

    Proteins are more than a dietary requirement. This diverse set of molecules powers nearly all of the cellular operations in a living organism. Scientists may know the structure of a protein or its function, but haven’t always been able to link the two.

    “The big problem in biology is the question of how a protein does what it does. We think the answer rests in protein evolution,” says University of Illinois professor and bioinformatician Gustavo Caetano-Anollés.

    Geologists have found remnants of life preserved in rock billions of years old. In some cases, preservation of microbes and tissues has been so good that microscopic cellular structures that were once associated with specific proteins, can be detected. This geological record gives scientists a hidden connection to the evolutionary history of protein structures over incredibly long time periods. But, until now, it hasn’t always been possible to link function with those structures to know how proteins were behaving in cells billions of years ago, compared with today.

    “For the first time, we have traced evolution onto a biological network,” Caetano-Anollés notes.

    Caetano-Anollés and graduate students Fayez Aziz and Kelsey Caetano-Anollés used networks to investigate the linkage between protein structure and molecular function. They built a timeline of protein structures spanning 3.8 billion years across the geological record, but needed a way to connect the structures with their functions. To do that, they looked at the genetic makeup of hundreds of organisms.

    “It turns out that there are little snippets in our genes that are incredibly conserved over time,” Caetano-Anollés says. “And not just in human genomes. When we look at higher organisms, such as plants, fungi and animals, as well as bacteria, archaea, and viruses, the same snippets are always there. We see them over and over again.”

    The research team found that these tiny gene segments tell proteins to produce “loops,” which are the tiniest structural units in a protein. When loops come together, they create active sites, or molecular pockets, which give proteins their function. For example, hemoglobin, the protein that carries oxygen in blood, has two loops which create the active site that binds oxygen. The loops combine to create larger protein structures called domains.

    Remarkably, the new study shows that loops have been repeatedly recruited to perform new functions and that the process has been active and ongoing since the beginning of life.

    “This recruitment is important for understanding biological diversity,” Caetano-Anollés says.

    One important aspect of the study relates to the actual linkage between domain structure and functional loops. The researchers found that this linkage is characterized by an unanticipated property that unfolds in time, an “emergent” property known as hierarchical modularity.

    “Loops are cohesive modules, as are domains, proteins, cells, organs, and bodies.” Caetano-Anollés explains. “We are all made of cohesive modules, including our human bodies. That’s hierarchical modularity: the building of small cohesive parts into larger and increasingly complex wholes.”

    Hierarchical modularity also exists in manmade networks, such as the internet. For example, each router represents a “node” that pushes information to different computers. When millions of computers interact with each other online, larger and more complex entities emerge. Caetano-Anollés suggests that the evolution of manmade networks could be mapped in the same way as the evolution of biological networks.

    “From a computer science point of view, few people have been exploring how to track networks in time. Imagine exploring how the internet grows and changes when new routers are added, are disconnected, or network with each other. It’s a daunting task because there are millions of routers to track and internet communication can be highly dynamic. In our study, we are showcasing how you can do it with a very small network,” Caetano-Anollés explains.

    The methods developed by Caetano-Anollés and his team now have the potential to explain how change is capable of structuring systems as varied as the internet, social networks, or the collective of all proteins in an organism.

    The article, The early history and emergence of molecular functions and modular scale-free network behavior, is published in Scientific Reports. M. Fayez Aziz and Kelsey Caetano-Anollés, also from the University of Illinois, co-authored the report. Full text of the article can be found at: http://www.nature.com/articles/srep25058.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

  • richardmitnick 8:57 am on October 16, 2015 Permalink | Reply
    Tags: , , , U Illinois   

    From U Illinois: “COMPASS method points researchers to protein structures” 

    U Illinois bloc

    University of Illinois

    Oct 9, 2015
    Liz Ahlberg

    Graduate student Joseph Courtney and chemistry professor Chad Rienstra developed a method to quickly and reliably determine a protein’s intricately folded structure. Photo by L. Brian Stauffer

    Searching for the precise, complexly folded three-dimensional structure of a protein can be like hacking through a jungle without a map: a long, intensive process with uncertain direction. University of Illinois researchers developed a new approach, dubbed COMPASS, that points directly to a protein’s likely structure using a combination of advanced molecular spectroscopy techniques, predictive protein-folding algorithms and image recognition software.

    Led by U. of I. chemistry professor Chad Rienstra, the team published its results in the journal Structure.

    “We’ve taken a process that would take months and brought it down to hours,” said Joseph Courtney, an Illinois graduate student and first author of the paper. “We expect this to not only accelerate the rate at which we can study proteins, but also increase its repeatability and the reliability of the results.”

    Proteins carry out functions within the cell, and those functions are determined by the proteins’ precise structures – the way they fold and twist into an intricate three-dimensional shape.

    “Many diseases are caused by a protein that’s not acting correctly, or there is too much of it. If you can understand what the proteins look like, you can study how they work, and you can help design drugs and treatments for those diseases,” Courtney said. “A major benefit is that if you can design a drug to perfectly fit a single protein, that cuts down on side effects, because it won’t interact with other molecules.”

    One key method for determining a protein’s share is a technique called X-ray crystallography. However, many medically interesting proteins – for example, the fibrils that characterize Parkinson’s disease – do not form crystals, so researchers have turned to more advanced spectroscopic techniques. Those techniques require months to years of intensive data collection and analysis, taking numerous readings and measurements of the protein’s spectrum.

    The Illinois team saw an opportunity to take advantage of recent advances in structure prediction algorithms, computational models that generate numerous possible ways a protein could fold based on its sequence.

    “The major shortcoming of those modeling approaches is that they never know if they’re right,” Rienstra said. “It’s great to have models, but it still leaves thousands of possibilities. We need some type of experimental data to determine which is the right one.”

    For COMPASS, the researchers rely on a single spectrum measurement using a spectroscopic technique called nuclear magnetic resonance, which gives a molecular “fingerprint” – no two protein structures have the same spectrum.

    The COMPASS platform looks at the possible structures generated by the predictive models, projects a spectrum for each one, and uses advanced image-recognition software to compare each projected spectrum with the spectrum collected from the experimental sample.

    “We call it COMPASS because we’re using a magnetic field to hopefully point us in the right direction of which protein structure is the right one out of all these options,“ Rienstra said.

    The researchers compared COMPASS results of 15 proteins to the structure information determined from traditional methods, and found that COMPASS was successful in correctly determining the proteins’ structures.

    The researchers hope that other chemists will adopt the COMPASS method. One advantage, Rienstra said, is that a chemist does not have to be an expert to use COMPASS, as the results from the algorithms are automatic, objective and repeatable.

    Rienstra’s group plans to use COMPASS in biomedical applications, hoping to study proteins that have thus far eluded researchers because of structural complexity and scarcity of samples.

    “We already have collaborators sending us samples to compare,” Rienstra said. “We’re working to compare the samples of a protein from Parkinson’s disease patients with the sample we study in the lab, to see if it’s the same in their brains as it is when we make it in the lab. That’s a very important question to address. The samples are very small and the signals are weak, but we can get one spectrum and see if the structures match. This would be impossible with traditional approaches because we would need brain samples a hundred times larger, and you just can’t do that with human patients.”

    “The normal bottleneck of collecting and analyzing the data is now completely gone,” Courtney said. “What would be an entire thesis project for a graduate student can now be reduced to a day. And as the prediction algorithms get better, COMPASS will be able to take advantage of those advances to help find even more difficult protein structures.”

    The National Institutes of Health supported this work.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    U Illinois campus

    The University of Illinois at Urbana-Champaign community of students, scholars, and alumni is changing the world.

    With our land-grant heritage as a foundation, we pioneer innovative research that tackles global problems and expands the human experience. Our transformative learning experiences, in and out of the classroom, are designed to produce alumni who desire to make a significant, societal impact.

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