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  • richardmitnick 12:15 pm on December 5, 2019 Permalink | Reply
    Tags: "These overlooked global diseases take a turn under the microscope", Applied Research & Technology, , Hookworm, Leishmaniasis, , ,   

    From Penn Today: “These overlooked global diseases take a turn under the microscope” 

    From Penn Today

    December 4, 2019
    Katherine Unger Baillie, Writer
    Eric Sucar, Photographer

    In rural areas of Nigeria, such as this small fishing village in the north, children are at risk of infection with hookworm as well as other parasites. De’Broski Herbert of the School of Veterinary Medicine is embarking on a study of the disease in Nigerian schoolchildren. (Image: De’Broski Herbert)

    Most people don’t die from tropical diseases like hookworm, schistosomiasis, or even malaria. But these understudied diseases, often caused by parasites, rob people of health in sometimes insidious ways.

    For example, schistosomiasis is a disease caused by a waterborne, snail-transmitted parasite, and it’s the research focus of the School of Veterinary Medicine’s Robert Greenberg.

    Schistosomiasis, a disease caused by parasitic flatworms, has long been a research focus for Penn Vet’s Robert Greenberg. (Image: John Donges/Penn Vet)

    “It’s not necessarily a death sentence, though there are fatalities” says Greenberg, a research associate professor of pathobiology. “But you get anemia, children get stunted in terms of growth and cognitive abilities. It’s a disease that keeps people in poverty.”

    Such diseases, by and large, receive less financial support and, as a result, far less scientific attention than those that more often afflict residents of wealthier nations, such as diabetes and heart disease.

    Penn Vet researchers, however, have committed attention to these diseases, which, taken as a whole, affect billions around the globe. Their work benefits from the niche strengths of the school, specifically in immunology and host-pathogen interactions.

    “At the Vet School, a third of our funding supports infectious disease research,” says Phillip Scott, vice dean for research and academic resources and a professor of microbiology and immunology in the Department of Pathobiology. “That’s pretty amazing, given that the School is also awarded funding for regenerative medicine, for cancer, and for a variety of other areas.”

    That strength is seen in the research portfolios of some of the more senior faculty, such as Christopher Hunter’s work on toxoplasmosis, James “Sparky” Lok’s studies of Strongyloides, Carolina Lopez’s investigations of lung infections, and Bruce Freedman and Ron Harty’s efforts against Ebola and other hemorrhagic viral diseases. It has attracted newer faculty members, like cryptosporidium expert Boris Striepen, to Penn Vet.

    Parasitology professor James Lok’s studies of the development and basic biology of parasites, particularly the roundworm
    Strongyloides, have implications for finding new drug candidates. Veterinary schools have traditionally been strongholds of parasitology research, and Penn Vet is no exception. (Image: Eric Sucar)

    Raising awareness

    Penn Vet’s De’Broski Herbert, for example, an associate professor of pathobiology, had held prior positions at Cincinnati Children’s Hospital and the University of California, San Francisco. He had felt called to work on hookworm, a parasite he first learned of growing up in the South from his great-grandmother, who warned him about walking around barefoot because of the risk of contracting the parasite. But at the medical centers where he worked, he shifted gears away from studying the parasite itself, instead focusing on related research in asthma and allergy.

    As part of his hookworm research in Nigeria, Herbert (left), speaking with Babatunde Adewale of the Nigerian Institute for Medical Research, hopes to study the impacts of infection on the microbiome, the immune system, and more. (Image: Courtesy of De’Broski Herbert)

    “Here, our veterinary students are likely to encounter parasites in their patients, so working directly on the parasite is easier to justify,” Herbert says.

    This spring, Herbert traveled to Nigeria where, working with partners at the Nigerian Institute for Medical Research, he launched a study of hookworm in 300 school-aged children in five sites around the northern and central portions of the country.

    “The goal is to first establish what the prevalence of the disease really is and draw attention to that,” Herbert says. “And secondly, this is a place where the World Health Organization is going in and doing mass treatments, so I’m also interested in learning something very novel about the association between the microbiome, tissue repair, immune suppression, and metabolism in these children in Nigeria.”

    Pairing basic and translational science

    Those insights could lead to treatments, but they will also likely shed new light on the basic science of how hookworms affect their host. This pairing of basic and applied work is characteristic of Penn Vet scientists. In Scott’s lab, for instance, which has long pursued studies of the tropical disease leishmaniasis, advances in basic science have unfurled alongside insights that stand to reshape treatment of this parasitic infection which, in its cutaneous form, can cause serious and chronic skin ulcers.

    “When I was a postdoc at NIH, there’s something my boss used to say that I still use in my talks,” says Scott. “He said, ‘Leishmaniasis has done more for immunology than immunology has done for leishmaniasis.’ And you could substitute parasitology for leishmaniasis and it would be much the same quote.

    The Leishmania parasite (in red), transmitted by a sandfly, can cause painful, disfiguring ulcers. Immunologist Phillip Scott and collaborators including Daniel Beiting have worked to understand the immune response to infection and better tailor treatment for those affected. (Image: Courtesy of Phillip Scott)

    “What I think is exciting right now,” he adds, “is that that’s going to change.”

    As part of this contribution toward advancements against parasitic disease, Scott has traveled regularly to a leishmaniasis clinic in Brazil to obtain samples for his research and, back at Penn, has paired up with dermatology and microbiome experts such as Elizabeth Grice in the Perelman School of Medicine, and Dan Beiting from Penn Vet’s Center for Host-Microbial Interactions to break new ground.

    No vaccine exists for leishmaniasis and current therapies fail a substantial percentage of the time. But recent publications from Scott’s lab have revealed new information about how the disease and existing treatments work and when to predict when they don’t. At the same time, Scott and colleagues’ research into the immunology of the infection has identified ways that FDA-approved drugs could be leveraged to alleviate the most severe forms of leishmaniasis.

    New diagnostics

    A major hurdle to matching appropriate therapies with neglected disease comes at one of the earliest stages of medical intervention: diagnostics. Researchers at Penn Vet are employing innovative techniques to fill these unmet needs. Robert Greenberg is one who has crossed disciplinary boundaries to do so.

    In a partnership between Greenberg and Haim Bau of Penn’s School of Engineering and Applied Science, the scientists are working to craft an improved diagnostic test for schistosomes, which can lead to schistosomiasis, causing anemia, tissue fibrosis and lesions, malnutrition, learning difficulties, and, depending on the parasite species, bladder cancer and heightened HIV risk.

    Greenberg has studied the ion channels that govern key biological functions in schistosomes to potentially develop drug targets that paralyze and kill the organisms. And by adapting insights from other researchers about additional parasitic-specific targets, he’s helping Bau train his microfluidic, portable diagnostic system on schistosomes to one day help clinicians make point-of-care diagnoses and issue timely treatment for infected patients.

    “The current diagnostics are pretty terrible,” Greenberg says. “We’re looking at some new approaches now that should give us a much earlier, more sensitive, and more specific diagnosis for individual patients that might be able to detect other coinfections simultaneously.”

    At Penn Vet’s New Bolton Center, Marie-Eve Fecteau and Ray Sweeney are also taking part in the design of a 21st-century solution to diagnostics of an insidious and challenging disease, in this case, a disease that takes a particular toll on livestock: paratuberculosis, or Johne’s disease. Caused by the bacterium Mycobacterium avium paratuberculosis, the condition affects ruminants such as cows and goats and drastically decreases their weight and milk production.

    Infectious diseases take a toll on livestock as well, indirectly impacting human health and livelihoods. Large animal veterinarians Marie-Eve Fecteau and Raymond Sweeney are making progress on a stall-side diagnostic system that could quickly identify calves infected with paratuberculosis, halting the spread of infection. (Image: Louisa Shepard)

    “Ruminants are a very important part of survival and livelihood in developing countries,” says Fecteau, an associate professor of food animal medicine and surgery. “Families may rely on only one or two cows to provide for their nutritional needs or income, and if that cow is affected by Johne’s, that’s a serious problem.”

    Paratuberculosis has been shown to be endemic in parts of India and elsewhere in Asia and is also a burden for U.S. farms, where 70% of dairy herds test positive for the infection. Separating infected animals from the herd is a key step to stem the spread, but the bacteria have proved difficult to grow in the lab, making diagnosis challenging.

    Fecteau and Sweeney, the Mark Whittier & Lila Griswold Allam Professor at Penn Vet, are hoping to change that, working with Beiting and biotechnology firm Biomeme to develop a “lab in a fanny pack,” as they call it: A stall-side diagnostic test that relies on PCR to identify infected animals from stool samples within hours.

    “This is the kind of technology that could be extremely valuable for use in areas where sophisticated technology is harder to come by,” says Sweeney.

    Stopping disease where it starts

    Elsewhere at Penn Vet, researchers are approaching globally significant diseases by focusing on the vector. In the insectary that is part of Michael Povelones’s lab, he and his team test methods to stop disease-transmission cycles within mosquitoes.

    The tens of thousands of mosquitoes in Michael Povelones’s insectary enable new insights into how the disease vectors defend themselves against infection. (Image: Rebecca Elias Abboud)

    In the work, which relies on disrupting the way that mosquitoes interact with or respond immunologically to the pathogens they pass on, Povelones, an assistant professor of pathobiology, has explored everything from dengue to Zika to heart worm to elephantiasis, and his discoveries have implications for targeting a much longer list of diseases. In a recent study, Povelones and colleagues developed a new model system for studying the transmission of diseases caused by kinetoplastids, a group of parasites that includes the causative agents of Chagas disease and leishmaniasis.

    “We think this could be a model for a number of important neglected diseases,” Povelones says.

    In the latest of his team’s work finding ways to activate mosquitoes’ immune system to prevent pathogen transmission, they’ve identified a strategy that both blocks heartworm and the parasite that causes elephantiasis.

    “These two diseases have very different behavior once they’re in the mosquito, so we’re still figuring out why this seems to work for both,” says Povelones. “But we’re very encouraged that it does.”

    Using these types of creative approaches is a common thread across the Vet School, and the researchers’ efforts and successes seem to be multiplying. To continue accelerating progress, the School is developing a plan to harness these strengths, working with existing entities such as the Center for Host-Microbial Interactions internally and cross-school units such as the Institute for Immunology.

    “We are a key part of the biomedical community at Penn and bring a valuable veterinary component to the table in confronting diseases of poverty,” says Scott.

    See the full article here .


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    Academic life at Penn is unparalleled, with 100 countries and every U.S. state represented in one of the Ivy League’s most diverse student bodies. Consistently ranked among the top 10 universities in the country, Penn enrolls 10,000 undergraduate students and welcomes an additional 10,000 students to our world-renowned graduate and professional schools.

    Penn’s award-winning educators and scholars encourage students to pursue inquiry and discovery, follow their passions, and address the world’s most challenging problems through an interdisciplinary approach.

  • richardmitnick 1:04 pm on December 4, 2019 Permalink | Reply
    Tags: Applied Research & Technology, , , "A new algorithm trains AI to avoid bad behaviors", “Seldonian algorithm”   

    From Stanford University Engineering: “A new algorithm trains AI to avoid bad behaviors” 

    From Stanford University Engineering

    November 22, 2019
    Tom Abate

    In a society where AI powers important decision-making, how do we minimize undesirable outcomes? | Illustration by Sarah Rieke

    Artificial intelligence has moved into the commercial mainstream thanks to the growing prowess of machine learning algorithms that enable computers to train themselves to do things like drive cars, control robots or automate decision-making.

    But as AI starts handling sensitive tasks, such as helping pick which prisoners get bail, policy makers are insisting that computer scientists offer assurances that automated systems have been designed to minimize, if not completely avoid, unwanted outcomes such as excessive risk or racial and gender bias.

    A team led by researchers at Stanford and the University of Massachusetts Amherst published a paper Nov. 22 in Science suggesting how to provide such assurances. The paper outlines a new technique that translates a fuzzy goal, such as avoiding gender bias, into the precise mathematical criteria that would allow a machine-learning algorithm to train an AI application to avoid that behavior.

    “We want to advance AI that respects the values of its human users and justifies the trust we place in autonomous systems,” said Emma Brunskill, an assistant professor of computer science at Stanford and senior author of the paper.

    Avoiding misbehavior

    The work is premised on the notion that if “unsafe” or “unfair” outcomes or behaviors can be defined mathematically, then it should be possible to create algorithms that can learn from data on how to avoid these unwanted results with high confidence. The researchers also wanted to develop a set of techniques that would make it easy for users to specify what sorts of unwanted behavior they want to constrain and enable machine learning designers to predict with confidence that a system trained using past data can be relied upon when it is applied in real-world circumstances.

    “We show how the designers of machine learning algorithms can make it easier for people who want to build AI into their products and services to describe unwanted outcomes or behaviors that the AI system will avoid with high-probability,” said Philip Thomas, an assistant professor of computer science at the University of Massachusetts Amherst and first author of the paper.

    Fairness and safety

    The researchers tested their approach by trying to improve the fairness of algorithms that predict GPAs of college students based on exam results, a common practice that can result in gender bias. Using an experimental dataset, they gave their algorithm mathematical instructions to avoid developing a predictive method that systematically overestimated or underestimated GPAs for one gender. With these instructions, the algorithm identified a better way to predict student GPAs with much less systematic gender bias than existing methods. Prior methods struggled in this regard either because they had no fairness filter built-in or because algorithms developed to achieve fairness were too limited in scope.

    The group developed another algorithm and used it to balance safety and performance in an automated insulin pump. Such pumps must decide how big or small a dose of insulin to give a patient at mealtimes. Ideally, the pump delivers just enough insulin to keep blood sugar levels steady. Too little insulin allows blood sugar levels to rise, leading to short term discomforts such as nausea, and elevated risk of long-term complications including cardiovascular disease. Too much and blood sugar crashes — a potentially deadly outcome.

    Machine learning can help by identifying subtle patterns in an individual’s blood sugar responses to doses, but existing methods don’t make it easy for doctors to specify outcomes that automated dosing algorithms should avoid, like low blood sugar crashes. Using a blood glucose simulator, Brunskill and Thomas showed how pumps could be trained to identify dosing tailored for that person — avoiding complications from over- or under-dosing. Though the group isn’t ready to test this algorithm on real people, it points to an AI approach that might eventually improve quality of life for diabetics.

    In their Science paper, Brunskill and Thomas use the term “Seldonian algorithm” to define their approach, a reference to Hari Seldon, a character invented by science fiction author Isaac Asimov, who once proclaimed three laws of robotics beginning with the injunction that “A robot may not injure a human being or, through inaction, allow a human being to come to harm.”

    While acknowledging that the field is still far from guaranteeing the three laws, Thomas said this Seldonian framework will make it easier for machine learning designers to build behavior-avoidance instructions into all sorts of algorithms, in a way that can enable them to assess the probability that trained systems will function properly in the real world.

    Brunskill said this proposed framework builds on the efforts that many computer scientists are making to strike a balance between creating powerful algorithms and developing methods to ensure that their trustworthiness.

    “Thinking about how we can create algorithms that best respect values like safety and fairness is essential as society increasingly relies on AI,” Brunskill said.

    The paper also had co-authors from the University of Massachusetts Amherst and the Universidade Federal do Rio Grande do Sol.

    This work was supported in part by Adobe, the National Science Foundation and the Institute of Educational Science.

    See the full article here .


    Please help promote STEM in your local schools.

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    Stanford Engineering has been at the forefront of innovation for nearly a century, creating pivotal technologies that have transformed the worlds of information technology, communications, health care, energy, business and beyond.

    The school’s faculty, students and alumni have established thousands of companies and laid the technological and business foundations for Silicon Valley. Today, the school educates leaders who will make an impact on global problems and seeks to define what the future of engineering will look like.

    Our mission is to seek solutions to important global problems and educate leaders who will make the world a better place by using the power of engineering principles, techniques and systems. We believe it is essential to educate engineers who possess not only deep technical excellence, but the creativity, cultural awareness and entrepreneurial skills that come from exposure to the liberal arts, business, medicine and other disciplines that are an integral part of the Stanford experience.

    Our key goals are to:

    Conduct curiosity-driven and problem-driven research that generates new knowledge and produces discoveries that provide the foundations for future engineered systems
    Deliver world-class, research-based education to students and broad-based training to leaders in academia, industry and society
    Drive technology transfer to Silicon Valley and beyond with deeply and broadly educated people and transformative ideas that will improve our society and our world.

    The Future of Engineering

    The engineering school of the future will look very different from what it looks like today. So, in 2015, we brought together a wide range of stakeholders, including mid-career faculty, students and staff, to address two fundamental questions: In what areas can the School of Engineering make significant world‐changing impact, and how should the school be configured to address the major opportunities and challenges of the future?

    One key output of the process is a set of 10 broad, aspirational questions on areas where the School of Engineering would like to have an impact in 20 years. The committee also returned with a series of recommendations that outlined actions across three key areas — research, education and culture — where the school can deploy resources and create the conditions for Stanford Engineering to have significant impact on those challenges.

    Stanford University

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

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  • richardmitnick 12:19 pm on December 4, 2019 Permalink | Reply
    Tags: "Freeze Frame: Scientists Capture Atomic-Scale Snapshots of Artificial Proteins", Applied Research & Technology, , cryo-EM-Cryogenic electron microscopy,   

    From Lawrence Berkeley National Lab: “Freeze Frame: Scientists Capture Atomic-Scale Snapshots of Artificial Proteins” 

    Berkeley Logo

    From Lawrence Berkeley National Lab

    December 4, 2019
    Theresa Duque
    (510) 495-2418

    Berkeley Lab scientists adapt microscopy technique to build and image peptoid nanosheets with unprecedented atomic precision.

    Berkeley Lab scientists employed cryogenic electron microscopy (cryo-EM) to reveal the atomic structure of peptoid nanosheets. Their use of cryo-EM allowed them to visualize distinct bromine atoms (magenta) in the peptoid’s side chains. (Credit: Berkeley Lab)

    Protein-like molecules called “polypeptoids” (or “peptoids,” for short) have great promise as precision building blocks for creating a variety of designer nanomaterials, like flexible nanosheets – ultrathin, atomic-scale 2D materials. They could advance a number of applications – such as synthetic, disease-specific antibodies and self-repairing membranes or tissue – at a low cost.

    To understand how to make these applications a reality, however, scientists need a way to zoom in on a peptoid’s atomic structure. In the field of materials science, researchers typically use electron microscopes to reach atomic resolution, but soft materials like peptoids would disintegrate under the harsh glare of an electron beam.

    Now, scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have adapted a technique that enlists the power of electrons to visualize a soft material’s atomic structure while keeping it intact.

    Nitash Balsara (clockwise from left), Nan Li, David Prendergast, Xi Jiang, Ronald Zuckermann, and Sunting Xuan used cryogenic electron microscopy to atomically engineer and image a peptoid crystal. (Credit: Marilyn Sargent/Berkeley Lab)

    Their study, published in the journal Proceedings of the National Academy of Sciences, demonstrates for the first time how cryo-EM (cryogenic electron microscopy), a Nobel Prize-winning technique originally designed to image proteins in solution, can be used to image atomic changes in a synthetic soft material. Their findings have implications for the synthesis of 2D materials for a wide variety of applications.

    “All materials we touch function because of the way atoms are arranged in the material. But we don’t have that knowledge for peptoids because unlike proteins, the atomic structure of many soft synthetic materials is messy and hard to predict,” said Nitash Balsara, a senior faculty scientist in Berkeley Lab’s Materials Sciences Division, and professor of chemical engineering at UC Berkeley, who co-led the study. “And if you don’t know where the atoms are, you’re flying blind. Our use of cryo-EM for the imaging of peptoids will set a clear path for the design and synthesis of soft materials at the atomic scale.”

    Taking a close look at soft materials

    For the last 13 years, Balsara has been leading an effort to image soft materials at the atomic scale through Berkeley Lab’s Soft Matter Electron Microscopy Program. For the current study, he joined forces with Ronald Zuckermann, a senior scientist in Berkeley Lab’s Molecular Foundry who first discovered peptoids almost 30 years ago in his search for new polymers –materials made of long, repeating chains of small molecular units called “monomers” – for targeted drug therapies.

    “This study comes out of many years of research here at Berkeley Lab. To make a material and see the atoms – it’s the dream of my career,” said Zuckermann, who co-led the study with Balsara.

    Ronald Zuckermann holding a 3D model of a peptoid structure imaged with cryo-EM at Berkeley Lab’s Molecular Foundry. (Credit: Marilyn Sargent/Berkeley Lab)

    Unlike most synthetic polymers, peptoids can be made to have a precise sequence of monomer units, a common trait in biological polymers, such as proteins and DNA.

    And like natural proteins, peptoids can grow or self-assemble into distinct shapes for specific functions – such as helices, fibers, nanotubes, or thin and flat nanosheets.

    But unlike proteins, the molecular structure of peptoids is typically amorphous and unpredictable – like a pile of wet noodles. And untangling such an unpredictable structure has long been an obstacle for materials scientists.

    Pinning down peptoids with cryo-EM

    So the researchers turned to cryo-EM, which flash-freezes the peptoids at a temperature of around 80 kelvins (or minus 316 degrees Fahrenheit) in microseconds. The ultracold temperature of cryo-EM locks in the structure of the sheet and also prevents the electrons from destroying the sample.

    To protect soft materials, cryo-EM uses fewer electrons than conventional electron microscopy, resulting in ghostly black-and-white images. To better document what’s going on at the atomic level, hundreds of these images are taken. Sophisticated mathematical tools combine these images to make more detailed atomic-scale pictures.

    Short peptoid polymer chains (green) stacked in a nanosheet crystal lattice are overlaid on a cryo-EM image (grayscale image). Bromine atoms on the peptoid side chains are shown in magenta. (Credit: Berkeley Lab)

    For the study, the researchers fabricated nanosheets in solution from short peptoid polymers made of a chain of six hydrophobic monomers known as “aromatics,” connected to four hydrophilic polyether monomers. The hydrophilic or “water-loving” monomers are attracted to the water in the solution, while the hydrophobic or “water-hating” monomers avoid the water, orienting the molecules to form crystalline nanosheets that are only one-molecule thick (around 3 nanometers, or 3 billionths of a meter).

    Lead author Sunting Xuan, a postdoctoral researcher in the Materials Sciences Division, synthesized the peptoid nanosheets and used X-ray scattering techniques at Berkeley Lab’s Advanced Light Source (ALS) to characterize their molecular structure.


    The ALS produces light in a variety of wavelengths to enable studies of samples’ nanoscale structure and chemistry, among other properties.

    Xi Jiang, a project scientist in the Materials Sciences Division, captured the high-quality images and developed the algorithms necessary to achieve atomic resolution in the peptoid imaging.

    Xi Jiang shown with the cryogenic transmission electron microscope at UC Berkeley’s Donner Lab. (Credit: Marilyn Sargent/Berkeley Lab)

    David Prendergast, senior staff scientist and interim director of the Molecular Foundry, modeled atomic substitutions in the peptoids, and Nan Li, a postdoctoral researcher at the Molecular Foundry, performed molecular dynamics simulations to establish an atomic-scale model of the nanosheet.

    At the heart of the team’s discovery was their ability to rapidly iterate between materials synthesis and atomic imaging. The precision of peptoid synthesis, coupled with the researchers’ ability to directly image the placement of atoms using cryo-EM, allowed them to engineer the peptoid at the atomic level. To their surprise, when they created several new variations of the peptoid monomer sequence, the atomic structure of the nanosheet changed in a very orderly way.

    For example, when one additional bromine atom was added to each aromatic ring, the shape of each peptoid molecule remained unchanged yet the space between rows increased by just enough to accommodate the additional bromine atoms.

    Furthermore, when four additional variants of the peptoid nanosheet structure were imaged, the researchers noticed a remarkable uniformity across their atomic structure, and that the nanosheets shared the same shape of peptoid molecules. This allowed them to predictably engineer the nanosheet structure, Zuckermann said.

    “To have so much control at the atomic scale in soft materials was completely unexpected,” said Balsara, because it was assumed that only proteins could form defined shapes when you have a specific sequence of monomers – in their case, amino acids.

    A team approach to new materials

    For close to four decades, Berkeley Lab has pushed the boundaries of electron microscopy into fields of science once considered impossible to explore with an electron beam. Pioneering work by scientists at Berkeley Lab also played a key role in the 2017 Nobel Prize in chemistry, which honored the development of cryo-EM.

    “Most people would say it’s not possible to develop a technique that can position and see individual atoms in a soft material,” said Balsara. “The only way to solve hard problems like this is to team up with experts across scientific disciplines. At Berkeley Lab, we work as a team.”

    Zuckermann added that the current study proves that the cryo-EM technique could be applied to a wide range of common polymers and other industrial soft materials, and could lead to a new class of soft nanomaterials that fold into protein-like structures with protein-like functions.

    “This work sets the stage for materials scientists to tackle the challenge of making artificial proteins a reality,” he said, adding that their study also positions the team to work on solving a diversity of exciting problems, and to “raise people’s awareness that they, too, can begin to look at the atomic structure of their soft materials using these cryo-EM techniques.”

    Researchers from Berkeley Lab, UC Berkeley, and UC Irvine participated in the work.

    This work was supported by the DOE Office of Science through the Soft Matter Electron Microscopy Program.

    The Molecular Foundry, which specializes in nanoscale science, and the Advanced Light Source are DOE Office of Science user facilities.

    See the full article here .


    Please help promote STEM in your local schools.

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    Bringing Science Solutions to the World
    In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

    Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the UC Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

    Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a UC Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.

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  • richardmitnick 1:57 pm on December 3, 2019 Permalink | Reply
    Tags: "When laser beams meet plasma- New data addresses gap in fusion research", Applied Research & Technology, , , ,   

    From University of Rochester: “When laser beams meet plasma- New data addresses gap in fusion research” 

    From University of Rochester

    December 2, 2019
    Lindsey Valich

    Researchers used the Omega Laser Facility at the Rochester’s Laboratory for Laser Energetics to make highly detailed measurements of laser-heated plasmas. (University photo / J. Adam Fenster)

    New research from the University of Rochester will enhance the accuracy of computer models used in simulations of laser-driven implosions. The research, published in the journal Nature Physics, addresses one of the challenges in scientists’ longstanding quest to achieve fusion.

    In laser-driven inertial confinement fusion (ICF) experiments, such as the experiments conducted at the University of Rochester’s Laboratory for Laser Energetics (LLE), short beams consisting of intense pulses of light—pulses lasting mere billionths of a second—deliver energy to heat and compress a target of hydrogen fuel cells. Ideally, this process would release more energy than was used to heat the system.

    Laser-driven ICF experiments require that many laser beams propagate through a plasma—a hot soup of free moving electrons and ions—to deposit their radiation energy precisely at their intended target. But, as the beams do so, they interact with the plasma in ways that can complicate the intended result.

    “ICF necessarily generates environments in which many laser beams overlap in a hot plasma surrounding the target, and it has been recognized for many years that the laser beams can interact and exchange energy,” says David Turnbull, an LLE scientist and the first author of the paper.

    To accurately model this interaction, scientists need to know exactly how the energy from the laser beam interacts with the plasma. While researchers have offered theories about the ways in which laser beams alter a plasma, none has ever before been demonstrated experimentally.

    Now, researchers at the LLE, along with their colleagues at Lawrence Livermore National Laboratory in California and the Centre National de la Recherche Scientifique in France, have directly demonstrated for the first time how laser beams modify the conditions of the underlying plasma, in turn affecting the transfer of energy in fusion experiments.

    “The results are a great demonstration of the innovation at the Laboratory and the importance of building a solid understanding of laser-plasma instabilities for the national fusion program,” says Michael Campbell, the director of the LLE.

    Using supercomputers to model fusion

    I asked U Rochester to tell me the supercomputers used in this work.
    Statement from U Rochester:

    “Hi Richard,
    This was experimental research that was conducted using the Omega laser facility at the University of Rochester’s Laboratory for Laser Energetics. The researchers used a novel high-power laser beam with a tunable wavelength to study the energy transfer between laser beams while simultaneously measuring the plasma conditions. This research was not conducted using supercomputers, but, rather, the experiments were designed to gather data that will be input into computer models to improve the predictive capabilities of models used in supercomputer simulations of inertial confinement fusion (ICF) experiments.”

    Researchers often use supercomputers to study the implosions involved in fusion experiments. It is important, therefore, that these computer models accurately depict the physical processes involved, including the exchange of energy from the laser beams to the plasma and eventually to the target.

    For the past decade, researchers have used computer models describing the mutual laser beam interaction involved in laser-driven fusion experiments. However, the models have generally assumed that the energy from the laser beams interacts in a type of equilibrium known as Maxwellian distribution—an equilibrium one would expect in the exchange when no lasers are present.

    “But, of course, lasers are present,” says Dustin Froula, a senior scientist at the LLE.

    Froula notes that scientists predicted almost 40 years ago that lasers alter the underlying plasma conditions in important ways. In 1980, a theory was presented that predicted these non-Maxwellian distribution functions in laser plasmas due to the preferential heating of slow electrons by the laser beams. In subsequent years, Rochester graduate Bedros Afeyan ’89 (PhD) predicted that the effect of these non-Maxwellian electron distribution functions would change how laser energy is transferred between beams.

    But lacking experimental evidence to verify that prediction, researchers did not account for it in their simulations.

    Turnbull, Froula, and physics and astronomy graduate student Avram Milder conducted experiments at the Omega Laser Facility at the LLE to make highly detailed measurements of the laser-heated plasmas. The results of these experiments show for the first time that the distribution of electron energies in a plasma is affected by their interaction with the laser radiation and can no longer be accurately described by prevailing models.

    The new research not only validates a longstanding theory, but it also shows that laser-plasma interaction strongly modifies the transfer of energy.

    “New inline models that better account for the underlying plasma conditions are currently under development, which should improve the predictive capability of integrated implosion simulations,” Turnbull says.

    This research is based upon work supported by the US Department of Energy National Nuclear Security Administration and the New York State Energy Research and Development Authority.

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    U Rochester Campus

    The University of Rochester is one of the country’s top-tier research universities. Our 158 buildings house more than 200 academic majors, more than 2,000 faculty and instructional staff, and some 10,500 students—approximately half of whom are women.

    Learning at the University of Rochester is also on a very personal scale. Rochester remains one of the smallest and most collegiate among top research universities, with smaller classes, a low 10:1 student to teacher ratio, and increased interactions with faculty.

  • richardmitnick 12:53 pm on December 3, 2019 Permalink | Reply
    Tags: "A Deep-Sea Magma Monster Gets a Body Scan", Applied Research & Technology, , ,   

    From The New York Times: “A Deep-Sea Magma Monster Gets a Body Scan” 

    New York Times

    From The New York Times

    Scientists set sail on a perilous expedition to create the first internal 3D images of Axial Seamount, an underwater volcano deep in the Pacific Ocean.

    The caldera and rift zones of the Axial Seamount off the coast of Oregon, depicted as a computer generated 3D oblique view using seafloor bathymetry. The red zone is the shallowest area, and the blues and purples are as much as 2 miles deep.Credit Susan Merle, Oregon State University, CIMRS

    Dec. 3, 2019
    Robin George Andrews

    This summer, the 235-foot research vessel Marcus G. Langseth set out into the ocean off the Pacific Northwest. Trailing the ship were four electronic serpents, each five miles in length. These cables were adorned with scientific instruments able to peer into the beating heart of a monster a mile below the waves: Axial Seamount, a volcanic mountain.

    The ship’s crew had one overriding imperative: Do not let the cables get tangled.

    If they did, “it’s game over,” said Sam Mitchell, a submarine volcanologist who joined the voyage.

    The ship belongs to the National Science Foundation, and is operated by Columbia University’s Lamont-Doherty Earth Observatory. Scientists aboard spent 33 days in July and August hoping to create 3D maps of the magmatic ponds and pathways in an individual, active submarine volcano for the very first time. If the researchers succeeded, they would provide a view of a hyperactive volcano that had never been seen.

    Charting Axial’s internal anatomy also would improve scientists’ understanding of underwater volcanoes all over the world, most of which still lie waiting to be discovered in the gloomy depths.
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    The ship had to be steered carefully and couldn’t be stopped abruptly, or else those cables could settle, drift and become entangled, like earphones getting twisted in your pocket, only with profoundly expensive consequences.

    Retrieving an air-gun array on the stern of the Marcus G. Langseth research vessel in Pacific northwest waters this summer.Credit Sam Mitchell

    Toward the end of the Langseth’s month at sea, what seemed like a nightmare began when one of the cables broke. Scientists deep within the hull of the ship, in a room full of screens that recorded the data streaming in, saw several monitors turn black. The cable’s GPS data indicated it was definitely not where it was supposed to be.

    For all the scientists knew, it could be lost at sea, gone forever.

    Compared to expeditions to volcanoes on land, those like the Marcus G. Langseth’s take years to prepare and have “several more zeros” added to their price tags, said Dr. Mitchell. Losing an entire family of probes and sensors to the Pacific would have been a stressful and costly accident.

    “You get one shot to do these expeditions,” he said.

    All eyes on Axial

    The volcano’s base would cover the entire city of Austin, Tex., said Adrien Arnulf, a seismologist at the University of Texas at Austin, the expedition’s principal investigator.

    It is far from the world’s largest volcano, but the walls of the horseshoe-shaped caldron at Axial’s peak are as high as the pillars of the Golden Gate Bridge. The volcano’s main magma reservoir is two-thirds of the length of Manhattan, the same width, and taller than any building in the city.

    Axial is also, volcanologically speaking, no shrinking violet.

    Over geological time, a stationary mantle plume below the shifting Pacific tectonic plate has created a 1,120-mile-long line of submarine volcanoes, known as the Cobb-Eickelberg seamount chain. Axial, the youngest member of the chain, is currently sitting atop that hot spot.

    The volcano also sits astride the mid-ocean ridge separating the Pacific plate to the west and the Juan de Fuca plate to the east. These plates are moving apart. Ridges like this are the birthplace of oceanic crust; molten rock rises from deep within the Earth to the seafloor, creating profuse volcanic activity.

    Marine technicians and protected species observers kept an eye on monitors in the main lab aboard the Langseth.Credit Sam Mitchell

    This dual power of the plume and the moving ridge helps make Axial the most active submarine volcano in the region. It was erupting long before humans spotted it. So far, three eruptions — in 1998, 2011 and 2015 — have been documented as they occurred.

    Axial is remote and deep enough that it is vanishingly unlikely to ever cause anyone harm, said Ken Rubin, a volcanologist at the University of Hawaii at Manoa. But a better comprehension of Axial will help blunt hazards at other volcanoes that do pose risks. These include Hawaii’s Kilauea volcano, a veritable lava factory near plenty of people, and Anak Krakatau in Indonesia, which has shown how volcanoes growing out of the sea can trigger deadly mega-tsunamis.

    Axial’s hyperactivity and proximity to the mainland make it one of the most comprehensively researched and monitored submarine volcanoes in the world. It has been stared at by ships, visited up close by humans in submersibles and autonomous robot divers, and since late 2014, continuously monitored by an underwater observatory network known as the Cabled Array.

    The devil’s in the details

    Axial’s surface has been thoroughly studied, but what lies beneath remains far more ambiguous, said Annie Kell, a seismologist at the University of Nevada, Reno, who was part of the research effort.

    The only way to make sense of what happens when a volcano erupts is to peer inside. Earlier seismic scanning and listening to geological tremors have produced 2D cross-sections of parts of Axial, pinpointing key features like its faults, conduits, and primary and smaller magma reservoirs.

    Like physicians, volcanologists would be better placed to understand Axial if all of its volcanic organs, magmatic veins and geological bones could be precisely imaged and placed in true 3D — which is easier said than done.

    On-board technicians and Michelle Lee, a student at the Lamont-Doherty Earth Observatory of Columbia University, center, kept records of instruments being added onto the cables during deployment of the 3D seismic array.Credit Steffen Saustrup

    Giving a land volcano a geological CT scan these days is relatively routine. Not so for underwater volcanoes. Their inaccessibility means that only part of the East Pacific Rise, a section of another mid-ocean ridge, has been subjected to the type of seismic scrutiny that Axial’s insides are getting, said Dr. Rubin.

    Key to the mission was a collection of pneumatic air guns, whose barrages of pressurized air created acoustic pulses. These pulses bounced around inside Axial before coming back to one of the many receivers on those cables, each of them drifting far from the ship’s own noise so as to obtain accurate readings.

    Those waves migrate through the subsurface differently depending on the properties of the rock they encounter. This behavior allows scientists to work out what is present within Axial, as well as how molten or solid each of its magmatic organs are. And with the Marcus G. Langseth’s more expansive and heavily equipped array of sensors, scientists would get their 3D view into an active submarine seamount for the first time.

    Praying to Poseidon

    As the vessel orbited above Axial, 50 scientists, students, technicians and crew members made sure everything was going according to plan. “It’s a small city, in a way,” said Dr. Arnulf.

    Data streamed in, but scientists had to take shifts watching the screens to make sure that it continued uninterrupted. It was a bit like a less thrilling version of watching the screens of green code in “The Matrix.”

    “You barely see the sun, because you’re often in the hull of the boat,” said Dr. Arnulf. Spacing out was to be expected from time to time.

    Everyone played their parts, but luck wasn’t always on their side. That snapped cable, perhaps caused by the tremendous physical strain it and the other components of the ship’s sensors were often under, provided an unwelcome dose of jeopardy.

    “That was a very, very tense day,” Dr. Mitchell added.

    Victoire Lucas, a student at Université de Bretagne Occidentale in France, kept an eye on the spools being used to deploy cables in the ship’s stern.Credit Sam Mitchell

    Fortunately, the cable was found clinging on, somehow still attached to the ship. Because it could not be repaired at sea, the team had to finish the mission with just three cables.

    At another point, the engine decided to throw a fit, requiring the team to power down the entire ship and spend the next 18 hours or so carefully reeling the four 55-ton cables back onto the vessel. The engine was fixed within an hour, but unspooling the lines again required another day. That stole two days from the cruise.

    Dr. Kell, choosing to stay back on land with her children, gave mission support to the Langseth and shared the crew’s moments of technological peril. With these sorts of expeditions, so much is on the line that, she said, “you have to channel an inner peace, even though your nerves are like, oh my gosh, this is all about to go out the window!”

    Dr. Arnulf was more nonchalant. “I don’t think I’ve ever been on a cruise where everything goes smoothly,” he said. “You’re always losing instruments.”

    For most of the students, it was the first time at sea, so it was important to keep them entertained, said Dr. Mitchell.

    Plenty of bets were wagered on ludicrous things, like how many eggs were brought on board (2,880) or how many springs were in a single air gun (24). Between shifts, people completed theses, wrote papers, read books. Dr. Arnulf, training for extreme sporting events on land, spent a fair amount of time in the gym.

    Curiosity killed the cruise

    Technical hitches weren’t all the team had to worry about. Local wildlife, such as fin whales, dolphins, sharks and sunfish had the potential to scupper the expedition.

    Officers on deck kept an eye out for aquatic interlopers while using hydrophones to listen underwater. Marine mammals are dependent on acoustic communications, so if any got within 3,300 feet of the ship, the booming seismic equipment had to be shut down.

    “You are basically creating a sound in the ocean every 15 seconds, and it’s a big sound,” said Dr. Mitchell.

    Younger critters triggered a shutdown of all the equipment if they were seen at any distance. To an infant blue whale, the pulses made by the ship’s array would be like screams in its ear.

    Those officers, understandably, had a lot of science-stopping power. Many things could jeopardize the mission, but Dr. Mitchell said it was surreal to think that half a decade of preparation could be nixed by a persistently curious baby whale refusing to leave the ship’s side.

    Stitching together a masterpiece

    An early 3D view of Axial and its magma reservoirs.

    Despite a few moments of chaos, the voyage achieved its objective. With the expedition concluded, scientists are now digging into all of the Langseth’s seismic slices and stitching all the data together to form a proper 3D view of Axial’s guts.

    It is already clear that the Langseth’s data has game-changing potential.

    The roofs of the primary and secondary magma chambers can be clearly seen in three dimensions. Their complexities are becoming clear: multiple horizontal wafers of magma, known as sills, streak through the subsurface. A previously discovered field of hydrothermal vents, some as high as buildings, has been found sitting above a newly identified third magma cache.

    As they learn more about what the crew of the Langseth found, scientists stand to better understand other volcanoes, particularly those hidden beneath the sea. “A significant fraction of Earth’s volcanism happens at places like Axial,” said Dr. Rubin, referring to the mid-ocean ridges, which collectively represent a spine of volcanism stretching about 40,000 miles around the world.

    But it won’t be a breeze to finish this work. Years of processing and analysis lies ahead.

    “There really is both a science and an art to processing and interpreting seismic data,” said Jackie Caplan-Auerbach, a seismologist and volcanologist at Western Washington University. Compared to 2D profiles, “3D seismic data is an order of magnitude more challenging.”

    The mission’s data might also help scientists better understand why Axial seems to be breathing.

    When magma is rising to the surface, volcanoes tend to inflate, and Axial is no exception. Using a special arrangement of pressure sensors beneath the waves, Dr. Chadwick and his colleagues found that “if Axial’s not erupting, it’s reinflating.”

    The sensor cables extended at sea.Credit Sam Mitchell

    Right after one eruption ends, the volcano immediately begins refueling for the next one, getting to roughly the same level each time before it blows its top.

    This rhythm allowed these scientists to predict the timing of its two most recent eruptions with ever-increasing precision. “It seems fairly well behaved, at least so far,” said Dr. Chadwick.

    The next eruption is predicted to be in 2020 or 2021. Whether or not scientists achieve this forecasting hat trick, these cycles of inflation and eruption will make more sense as Axial’s magma caches come into focus.

    Surface deformation is one of the main ways in which volcanoes of all kinds are monitored, from Washington State’s explosive Mount St. Helens to Hawaii’s effusive Mauna Loa. With a more holistic model of Axial and its balloon-like behavior, scientists may better understand or identify the precursors of eruptions at these volcanoes, too.

    Dr. Arnulf said that members of the public can ask how an expedition to a volcano far from anyone benefits society in terms of financial gain or hazard mitigation. But, he said, anyone raising these questions might as well ask why astronomers bother studying the stars.

    For him and his colleagues, gazing into the Hadean labyrinths of a restless underwater volcano holds another, more visceral appeal.

    “It’s freaking awesome,” he said.

    See the full article here .


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  • richardmitnick 4:11 pm on December 2, 2019 Permalink | Reply
    Tags: "Scientist travels to the end of the world to change the world", Applied Research & Technology, Clothilde Langlais, , , Our oceans are a support system for us all. They influence our climate and provide food for billions of people and are a meaningful part of Aussie culture.,   

    From CSIROscope: Women in STEM-“Scientist travels to the end of the world, to change the world” Clothilde Langlais 

    CSIRO bloc

    From CSIROscope

    2 December 2019
    Natalie Kikken

    Flying the CSIRO flag: Clothilde Langlais is proud to be part of the Homeward Bound cohort for 2019.

    Our oceans are a support system for us all. They influence our climate, provide food for billions of people, and are a meaningful part of Aussie culture.

    But we don’t have to tell that to Clothilde Langlais, one of our leading physical oceanographers. Her passion is how our oceans connect with our climate system, and she’s been delivering some impressive science in this space for the last 15 years.

    Clothilde is currently in one of the most remote parts of the world – Antarctica – to champion women in STEM and build on her climate change knowledge.

    Connecting climate, oceans and people

    Clothilde would be a great asset on any trivia team for questions related to our oceans.

    “Did you know our oceans absorb more than 90 per cent of the excess heat trapped on Earth caused by human-made greenhouse gases? And that our oceans absorb almost 40 per cent of the human-made carbon from the atmosphere? This can impact ocean circulation and our climate,” Clothilde explained.

    She looked at how carbon and heat are soaked up from the atmosphere and stored deep in the Southern Ocean. Now she’s researching the impacts of that on one of Australia’s most valued marine assets – the Great Barrier Reef. She’s also exploring ways to reduce the effects and help the reef adapt to a changing climate.

    “As an oceanographer, I am focused on the pressing challenges facing our coasts. These include warming, sea-level rise, change in circulation, the shifting of habitats, coral bleaching, and ocean acidification. I’ve also researched how climate projections could create change in our marine environment including eddies (circular currents), the Southern Ocean and El Nino.”

    Clothilde really is a walking encyclopedia on ocean science.

    Women in STEM cheerleader

    Building on her scientific career, Clothilde wants to bring her science and knowledge to the wider community. And she is, by taking part in the Homeward Bound leadership program for women in STEM.

    Clothilde will be joining close to 100 women for a voyage to Antarctica (including six of our own scientists). They’ll develop professional and personal skills and build an international network with female leaders in science.

    “Through my science, I want to make a difference. I want to change the world,” she tells us.

    “I am proud to participate in the growing knowledge around climate change. And I want to bring this knowledge far and wide. I want to bring my science to life through visualisation and storytelling, while increasing the presence of women in STEM. Homeward Bound will help me do that, by helping me raising my voice and vision for a brighter future.”

    Behold Mother Nature

    Through Clothilde’s career, she has seen differences in the progress of male and female scientists.

    “There has been variation in the level of opportunities, support and trust in ideas. And being caring was not considered a popular leadership attribute. But things are changing. I am gaining confidence, connecting with other female leaders and creating a strategic path for my science.”

    Clothilde is pleased to be meeting Mother Nature in its wildest and most majestic form. But she recognises that Antarctica is also vulnerable.

    “Science gives us an understanding of why things are the way they are and how our planet works. It also helps us to plan for the future.”

    “I’m excited that my science and participation in Homeward Bound will influence female scientists all around the world to help shape decisions for our planet.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    SKA/ASKAP radio telescope at the Murchison Radio-astronomy Observatory (MRO) in Mid West region of Western Australia

    So what can we expect these new radio projects to discover? We have no idea, but history tells us that they are almost certain to deliver some major surprises.

    Making these new discoveries may not be so simple. Gone are the days when astronomers could just notice something odd as they browse their tables and graphs.

    Nowadays, astronomers are more likely to be distilling their answers from carefully-posed queries to databases containing petabytes of data. Human brains are just not up to the job of making unexpected discoveries in these circumstances, and instead we will need to develop “learning machines” to help us discover the unexpected.

    With the right tools and careful insight, who knows what we might find.

    CSIRO campus

    CSIRO, the Commonwealth Scientific and Industrial Research Organisation, is Australia’s national science agency and one of the largest and most diverse research agencies in the world.

  • richardmitnick 3:53 pm on December 2, 2019 Permalink | Reply
    Tags: "Mysterious Tectonic Fault Zone Detected Off The Coast of California", Applied Research & Technology, Cables could monitor earthquakes across long stretches of land and sea., Recording underwater earthquakes., Researchers discovered a new fault system underwater., , ,   

    From UC Berkeley and Rice University via Science Alert: “Mysterious Tectonic Fault Zone Detected Off The Coast of California” 

    From UC Berkeley


    Rice U bloc

    Rice University



    Science Alert

    2 DEC 2019

    Monterey Bay. (N.J. Lindsey)

    Nearly 3,000 feet (900 metres) below the surface of Monterey Bay, a network of deep sea cables helps scientists to study marine life.

    Spanning 32 miles (51 kilometres) across the floor of the Pacific Ocean, the cables record sounds like the high-pitched squeal of a dolphin or the deep moans of a humpback whale. They also capture the emission of light from undersea organisms like poisonous algae.

    But a team of researchers from Rice University and the University of California, Berkeley, have discovered another use for the network: recording underwater earthquakes.

    Last year, the researchers conducted a four-day experiment using 12 miles (19 kilometres) of the cable network to study the motion of the seafloor. The results of that experiment appear in a new paper in the journal Science published on November 28.

    Deep sea cables that connect the internet. (TeleGeography)

    The researchers reveal that they detected a 3.5-magnitude earthquake in Gilroy, a city in Northern California, in March 2018. They also discovered a new fault system at the bottom of the ocean. The technology could eventually help them map fault lines in areas where scientists know very little about seismic activity on the ocean floor.

    “It’s kind of like streetlamps shining light on an area of the seafloor,” Nate Lindsey, the paper’s lead author, told Business Insider. “There’s a lot of potential to go and do this in an area where it makes a difference.”

    Researchers discovered a new fault system underwater

    Before the researchers conducted their experiment at sea, they tested their technology on land using underground fibre-optic cables from the US Department of Energy, which funded the project. The cables stretch 13,000 miles (20,000 kilometres) below ground in Sacramento, California, but the researchers only used 14 miles for their experiment.

    To start, they attached a device to the end of the cables that shoots out bursts of light. When the ground moves, it places a strain on the cables that scatters the light and sends it hurtling back toward the device. These light waves can be measured to determine the magnitude of an earthquake.

    After six months of experimenting on land, the researchers moved their technology underwater. They partnered with the Monterey Accelerated Research System (MARS), which operates a network of undersea fibre-optic cables.

    Every year, the cables need to be taken offline for maintenance, giving the researchers a brief window to test their technology.

    For their experiment, the researchers used a portion of the cables that stretches from Moss Landing, a small fishing village off the coast of Monterey Bay, to Soquel Canyon, an offshore marine protected area.

    MARS cable in Monterey Bay with pink portion used for sensing. (Lindsey et al., Science, 2019)

    By installing their device at the end of the undersea cables, the researchers were able to monitor shifts and fractures at the bottom of the ocean. This led to the discovery of a new underwater fault system in the Pacific Ocean in-between two major fault lines, the San Gregorio and the San Andreas, which run parallel to each other.

    Lindsey said the fault system is likely “much, much smaller” and “minor” compared to the San Andreas – which scientists have pinpointed as the likely source of the next major California earthquake.

    But he said his technology could ultimately be used to identify larger fault lines in unexplored areas like offshore Taiwan.

    Cables could monitor earthquakes across long stretches of land and sea.

    Since most of Earth’s surface – around 70 percent – is covered in water, scientists don’t have many ways to measure offshore earthquakes.

    Jonathan Ajo-Franklin, a geophysics professor at Rice University who worked on the experiment, said systems like the one from MARS – which are tethered to the shore by a cable – are so rare that you could count them on one hand. He estimated that just three or four operate at one time on the West Coast.

    “In every case, it’s limited scope in terms of the length of the experiment and it’s high cost,” Lindsey said. The MARS observatory, for instance, cost around US$13.5 million.

    Monterey Accelerated Research System’s underwater observatory. (MBARI, 2009)

    But Lindsey still thinks cable networks are the best way to study underwater seismic activity. Other ocean researchers share his enthusiasm.

    John Collins, a senior researcher at the Woods Hole Oceanographic Institution who didn’t work on the study, called the technique “very promising”. Bruce Howe, a physical oceanographer at the University of Hawaii, also thought the system could provide useful data.

    “It’s based on good physics, so I think it will pan out,” Howe, who also wasn’t involved in the study, told Business Insider.

    On land, traditional earthquake sensors typically measure the speed of the ground motion at a single point. But fibre-optic cables allow researchers to take multiple measurements across a long path.

    “For every metre of cable, you’re measuring a stretch of tens of nanometres or even smaller,” Ajo-Franklin said. That’s about the width of a human hair.

    The MARS system, for instance, can record measurements at 10,000 locations, meaning it has the same capacity as 10,000 individual motion sensors. That gives researchers lots of data points for studying how earthquakes rattle across the ocean.

    When the 3.5-magnitude earthquake struck Gilroy last year, the researchers were able to record the tremors of the ocean waves – a tool that might eventually help with the early detection of tsunamis.

    “The nice thing about recording that earthquake was not necessarily locating it,” Ajo-Franklin said.

    “When you have densely sampled locations, you can do a lot more with the earthquake’s wavefield to allow you to build pictures of what’s on the ground.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Rice U campus

    In his 1912 inaugural address, Rice University president Edgar Odell Lovett set forth an ambitious vision for a great research university in Houston, Texas; one dedicated to excellence across the range of human endeavor. With this bold beginning in mind, and with Rice’s centennial approaching, it is time to ask again what we aspire to in a dynamic and shrinking world in which education and the production of knowledge will play an even greater role. What shall our vision be for Rice as we prepare for its second century, and how ought we to advance over the next decade?

    This was the fundamental question posed in the Call to Conversation, a document released to the Rice community in summer 2005. The Call to Conversation asked us to reexamine many aspects of our enterprise, from our fundamental mission and aspirations to the manner in which we define and achieve excellence. It identified the pressures of a constantly changing and increasingly competitive landscape; it asked us to assess honestly Rice’s comparative strengths and weaknesses; and it called on us to define strategic priorities for the future, an effort that will be a focus of the next phase of this process.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

    UC Berkeley Seal

  • richardmitnick 1:00 pm on December 2, 2019 Permalink | Reply
    Tags: "Heating by cooling", Applied Research & Technology, , Magnetic fusion research, ,   

    From MIT News: “Heating by cooling” Pablo Rodriguez-Fernandez 

    MIT News

    From MIT News

    November 27, 2019
    Paul Rivenberg | Plasma Science and Fusion Center

    Pablo Rodriguez-Fernandez resolves a fusion paradox to receive Del Favero Prize.

    For his prize-winning thesis, Pablo Rodriguez-Fernandez examined data from MIT’s Alcator C-Mod tokamak (background). Photo: Paul Rivenberg/PSFC

    The field of magnetic fusion research has mysteries to spare. How to confine turbulent plasma fuel in a donut-shaped vacuum chamber, making it hot and dense enough for fusion to take place, has generated questions — and answers — for decades.

    As a graduate student under the direction of Department of Nuclear Science and Engineering Professor Anne White, Pablo Rodriguez-Fernandez PhD ’19 became intrigued by a fusion research mystery that had remained unsolved for 20 years. His novel observations and subsequent modeling helped provide the answer, earning him the Del Favero Prize.

    The focus of his thesis is plasma turbulence, and how heat is transported from the hot core to the edge of the plasma in a tokamak. Experiments over 20 years have shown that, in certain circumstances, cooling the edge of the plasma results in the core becoming hotter.

    “When you cool the edge of the plasma by injecting impurities, what every standard theory and intuition would tell you is that a cold pulse propagates in, so that eventually the core temperature will drop as well. But what we observed is that, in certain conditions when we drop the temperature of the edge, the core got hotter. It’s sort of heating by cooling.”

    The counterintuitive observation was not supported by any existing theory for plasma behavior.

    “The fact that our theory cannot explain something that happens so often in experiments makes us question those models,” Rodriquez-Fernandez says. “Should we trust them to predict what will happen in future fusion devices?”

    These models were the basis for predicting performance in the Plasma Science and Fusion Center’s Alcator C-Mod tokamak, which is no longer in operation. They are currently used for ITER, the next-generation machine being constructed in France, and SPARC, the tokamak the PSFC is pursuing with Commonwealth Fusion Systems.

    ITER Tokamak in Saint-Paul-lès-Durance, which is in southern France

    MIT SPARC fusion reactor tokamak

    To solve the mystery, Rodriguez-Fernandez learned complex coding that would allow him to run simulations of the edge-cooling experiments. When he manually cooled the edge in his early simulations, however, his models failed to reproduce the core heating observed in the actual experiments.

    Carefully studying data from Alcator C-Mod experiments, Rodriguez-Fernandez realized that the impurities injected to cool the plasma perturb not only the temperature, but every parameter, including the density.

    Alcator C-Mod tokamak at MIT, no longer in operation

    “We are perturbing the density because we are introducing more particles into the plasma. I was looking at the Alcator C-Mod data and I was seeing all the time these bumps in density. People have been disregarding them forever.”

    With new density perturbations to introduce into his simulation, he was able to simulate the core heating that had been observed in so many experiments around the world for more than two decades. These findings became the basis for an article in Physical Review Letters (PRL).

    To strengthen his thesis, Rodriguez-Fernandez wanted to use the same model to predict the response to edge cooling in a very different tokamak — DIII-D in San Diego, California. At the time, this tokamak did not have the capability to run such an experiment, but the MIT team, led by Research Scientist Nathan Howard, installed a new laser ablation system for injecting impurities and cold pulses into the machine. The subsequent experiments run on DIII-D showed the predictions to be accurate.

    DOE DIII-D Tokamak, in San Diego, California

    “This was further support that my answer to the mystery and my predictive simulations were correct,” says Rodriguez-Fernandez. “The fact that we can reproduce core heating by edge cooling in a simulation, and for more than one tokamak, means that we can understand the physics behind the phenomenon. And what is more important, it gives us confidence that the models we have for C-Mod and SPARC are not wrong.”

    Rodriquez-Fernandez notes the excellent collegial environment at the PSFC, as well as a strong external collaboration network. His collaborators include Gary Staebler at General Atomics, home to DIII-D, who authored the Trapped Gyro-Landau Fluid transport model used for his simulations; Princeton Plasma Physics Laboratory researchers Brian Grierson and Xingqiu Yuan, who are experts at a modeling tool called TRANSP that was invaluable to his work; and Clemente Angioni at the Max-Planck Institute for Plasma Physics in Garching, Germany, whose experiments on the ASDEX Upgrade tokamak supported the findings from the PRL article.

    Now a postdoc at the PSFC, Rodriguez-Fernandez devotes half of his time to SPARC and half to DIII-D and ASDEX Upgrade.

    ASDEX, Max Planck Institute for Plasma Physics

    With all these projects, he is using the simulations from his PhD thesis to develop techniques for predicting and optimizing tokamak performance.

    The postdoc admits that the timing of his thesis could not have been better, just as the SPARC project was ramping up. He quickly joined the team that is designing the device and working on the physics basis.

    As part of the Dec. 5 ceremony where Rodriguez Fernandez will receive the Del Favero Thesis Prize, he will discuss his how his thesis research is connected to his current work on predicting SPARC performance. Established in 2014 with a generous gift from alum James Del Favero SM ’84, the prize is awarded annually to a PhD graduate in NSE whose thesis is judged to have made the most innovative advance in the field of nuclear science and engineering.

    “It’s very exciting,” he says. “The SPARC project really drives me. I see a future here for me, and for fusion.”

    This research is supported by the U.S. Department of Energy Office of Fusion Energy Sciences.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    MIT Seal

    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

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  • richardmitnick 11:47 am on December 2, 2019 Permalink | Reply
    Tags: Applied Research & Technology, , X-ray laser, ,   

    From SLAC National Accelerator Lab: “SLAC scientists invent a way to see attosecond electron motions with an X-ray laser” 

    From SLAC National Accelerator Lab

    December 2, 2019
    Manuel Gnida
    (650) 926-2632

    Called XLEAP, the new method will provide sharp views of electrons in chemical processes that take place in billionths of a billionth of a second and drive crucial aspects of life.

    Researchers at the Department of Energy’s SLAC National Accelerator Laboratory have invented a way to observe the movements of electrons with powerful X-ray laser bursts just 280 attoseconds, or billionths of a billionth of a second, long.

    A SLAC-led team has invented a method, called XLEAP, that generates powerful low-energy X-ray laser pulses that are only 280 attoseconds, or billionths of a billionth of a second, long and that can reveal for the first time the fastest motions of electrons that drive chemistry. This illustration shows how the scientists use a series of magnets to transform an electron bunch (blue shape at left) at SLAC’s Linac Coherent Light Source into a narrow current spike (blue shape at right), which then produces a very intense attosecond X-ray flash (yellow). (Greg Stewart/SLAC National Accelerator Laboratory)


    The technology, called X-ray laser-enhanced attosecond pulse generation (XLEAP), is a big advance that scientists have been working toward for years, and it paves the way for breakthrough studies of how electrons speeding around molecules initiate crucial processes in biology, chemistry, materials science and more.

    The team presented their method today in an article in Nature Photonics.

    “Until now, we could precisely observe the motions of atomic nuclei, but the much faster electron motions that actually drive chemical reactions were blurred out,” said SLAC scientist James Cryan, one of the paper’s lead authors and an investigator with the Stanford PULSE Institute, a joint institute of SLAC and Stanford University. “With this advance, we’ll be able to use an X-ray laser to see how electrons move around and how that sets the stage for the chemistry that follows. It pushes the frontiers of ultrafast science.”

    Studies on these timescales could reveal, for example, how the absorption of light during photosynthesis almost instantaneously pushes electrons around and initiates a cascade of much slower events that ultimately generate oxygen.

    “With XLEAP we can create X-ray pulses with just the right energy that are more than a million times brighter than attosecond pulses of similar energy before,” said SLAC scientist Agostino Marinelli, XLEAP project lead and one of the paper’s lead authors. “It’ll let us do so many things people have always wanted to do with an X-ray laser – and now also on attosecond timescales.”

    A leap for ultrafast X-ray science

    One attosecond is an incredibly short period of time – two attoseconds is to a second as one second is to the age of the universe. In recent years, scientists have made a lot of progress in creating attosecond X-ray pulses. However, these pulses were either too weak or they didn’t have the right energy to home in on speedy electron motions.

    Over the past three years, Marinelli and his colleagues have been figuring out how an X-ray laser method suggested 14 years ago [Physical Review Accelerators and Beams] could be used to generate pulses with the right properties – an effort that resulted in XLEAP.

    In experiments carried out just before crews began work on a major upgrade of SLAC’s Linac Coherent Lightsource (LCLS) X-ray laser, the XLEAP team demonstrated that they can produce precisely timed pairs of attosecond X-ray pulses that can set electrons in motion and then record those movements. These snapshots can be strung together into stop-action movies.

    Linda Young, an expert in X-ray science at DOE’s Argonne National Laboratory and the University of Chicago who was not involved in the study, said, “XLEAP is a truly great advance. Its attosecond X-ray pulses of unprecedented intensity and flexibility are a breakthrough tool to observe and control electron motion at individual atomic sites in complex systems.”

    X-ray lasers like LCLS routinely generate light flashes that last a few millionths of a billionth of a second, or femtoseconds. The process starts with creating a beam of electrons, which are bundled into short bunches and sent through a linear particle accelerator, where they gain energy. Travelling at almost the speed of light, they pass through a magnet known as an undulator, where some of their energy is converted into X-ray bursts.

    The shorter and brighter the electron bunches, the shorter the X-ray bursts they create, so one approach for making attosecond X-ray pulses is to compress the electrons into smaller and smaller bunches with high peak brightness. XLEAP is a clever way to do just that.

    Making attosecond X-ray laser pulses

    At LCLS, the team inserted two sets of magnets in front of the undulator that allowed them to mold each electron bunch into the required shape: an intense, narrow spike containing electrons with a broad range of energies.

    Schematic of the XLEAP experiment at SLAC’s Linac Coherent Light Source (LCLS) X-ray laser. LCLS sends bunches of high-energy electrons (green) through an undulator magnet, where electron energy gets converted into extremely bright X-ray pulses (blue) of a few femtoseconds, or millionths of a billionth of a second. In the XLEAP configuration, electron bunches pass two additional sets of magnets (wiggler and chicane) that shape each electron bunch into an intense, narrow spike containing electrons with a broad range of energies. The spikes then produce attosecond X-ray pulses in the undulator. The XLEAP team also developed a customized pulse analyzer (right) to measure the extremely short pulse lengths. (Greg Stewart/SLAC National Accelerator Laboratory)

    “When we send these spikes, which have pulse lengths of about a femtosecond, through the undulator, they produce X-ray pulses that are much shorter than that,” said Joseph Duris, a SLAC staff scientist and paper co-first-author. The pulses are also extremely powerful, he said, with some of them reaching half a terawatt peak power.

    To measure these incredibly short X-ray pulses, the scientists designed a special device in which the X-rays shoot through a gas and strip off some of its electrons, creating an electron cloud. Circularly polarized light from an infrared laser interacts with the cloud and gives the electrons a kick. Because of the light’s particular polarization, some of the electrons end up moving faster than others.

    “The technique works similar to another idea implemented at LCLS, which maps time onto angles like the arms of a clock,” said Siqi Li, a paper co-first-author and recent Stanford PhD. “It allows us to measure the distribution of the electron speeds and directions, and from that we can calculate the X-ray pulse length.”

    Next, the XLEAP team will further optimize their method, which could lead to even more intense and possibly shorter pulses. They are also preparing for LCLS-II, the upgrade of LCLS that will fire up to a million X-ray pulses per second – 8,000 times faster than before. This will allow researchers to do experiments they have long dreamed of, such as studies of individual molecules and their behavior on nature’s fastest timescales.

    The XLEAP team included researchers from SLAC; Stanford University; Imperial College, UK; Max Planck Institute for Quantum Optics, Ludwig-Maximilians University Munich, Kassel University, Technical University Dortmund and Technical University Munich in Germany; and DOE’s Argonne National Laboratory. Large portions of this project were funded by the DOE Office of Science and through DOE’s Laboratory Directed Research and Development (LDRD) program. LCLS is a DOE Office of Science user facility.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition


    SLAC/LCLS II projected view

    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

  • richardmitnick 4:23 pm on December 1, 2019 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From European Space Agency – United space in Europe: “Space is key to monitoring ocean acidification” 

    ESA Space For Europe Banner

    From European Space Agency – United space in Europe

    United space in Europe

    ESA’s Ocean SODA

    This week, the UN World Meteorological Organization announced that concentrations of greenhouse gases in the atmosphere have reached yet another high. This ongoing trend is not only heating up the planet, but also affecting the chemical composition of our oceans. Until recently, it has been difficult to monitor ‘ocean acidification’, but scientists are exploring new ways to combine information from different sources, including from ESA’s SMOS mission, to shed new light on this major environmental concern.

    As the amount of atmospheric carbon dioxide continues to rise, our oceans are playing an increasingly important role in absorbing some of this excess. In fact, it was reported recently that the global ocean annually draws down about a third of the carbon released into the atmosphere by human activities.

    While this long-term absorption means that the planet isn’t as hot as it would be otherwise, the process is causing the ocean’s carbonate chemistry to change: seawater is becoming less alkaline – a process commonly known as ocean acidification.

    In turn, this is altering bio-geo-chemical cycles and having a detrimental effect on ocean life.

    Sea butterfly

    Ocean acidification is altering bio-geo-chemical cycles and having a detrimental effect on ocean life. Pteropods, tiny marine snails known as ‘sea butterflies’, are an example of a particularly vulnerable species, where shell damage has been observed already in portions of the Arctic and Southern Ocean. Pteropods are hugely important in the polar food web, serving as a key food source for important fisheries species, such as salmon and cod.

    Pteropods, tiny marine snails known as ‘sea butterflies’, are an example of a particularly vulnerable species, where shell damage has been observed already in portions of the Arctic and Southern Ocean. Pteropods are hugely important in the polar food web, serving as a key food source for important fisheries species, such as salmon and cod.

    With the damaging effects of ocean acidification already becoming evident, it is vital that the current shift in pH is monitored closely. Covering over 70% of Earth’s surface, ocean wellbeing also has a bearing on the health and balance of the rest of the planet.

    Recent advances in data capture have included state-of-the-art pH instruments on ships and floats, but we can gain a global view by taking measurements from space. However, at present there aren’t any spaceborne sensors that can measure pH directly.

    The use of satellites has not yet been thoroughly explored as an option for routinely observing ocean surface chemistry, but a paper published recently in Remote Sensing of Environment describes how scientists are testing new ways of merging different datasets to estimate and ultimately monitor ocean acidification.

    The changing chemistry of our oceans
    As carbon dioxide builds up in the atmosphere, increasing amounts of carbon are entering the world’s oceans, which is changing the chemical balance of seawater and leading to ocean acidification. Marine chemistry can be studied using four parameters: partial pressure of carbon dioxide in the water; dissolved inorganic carbon; alkalinity; potential of hydrogen (pH). Two of these parameters, along with measurements of salinity and temperature, allow us to understand the complete carbon chemistry of the ocean. Salinity and temperature can be detected from space by their effect on electromagnetic emissions from the ocean surface. ESA’s SMOS mission provides information on ocean salinity – a key piece of the puzzle.

    The animation above illustrates how marine chemistry can be studied using four parameters: partial pressure of carbon dioxide in the water, dissolved inorganic carbon, alkalinity and pH. Any two of these parameters, along with measurements of salinity and temperature, allow us to understand the complete carbon chemistry of the ocean.

    ESA’s SMOS mission and NASA’s Aquarius mission, which both provide information on ocean salinity, have been key to the research. The work was made possible through access to thousands of collated and quality controlled measurements collected by the international community from ships and research campaigns.


    NASA Aquarius

    Lead author, Peter Land, from the Plymouth Marine Laboratory, UK, said, “The advent of salinity measurements from space, pioneered by SMOS, has opened up the exciting possibility of continuously monitoring the ocean carbonate chemistry, identifying areas most at risk, and helping us to understand this threat to our oceans.”

    Jamie Shutler, from the University of Exeter, UK, added, “We were able to carry out this research through ESA’s Earth Observation Science for Society programme. We hope that the view from space can be used to help understand how ocean acidification is likely affecting our fisheries and marine ecosystems, on which we rely for food, health and tourism.”

    This work is now being continued within the ESA’s Ocean SODA project as part of the ESA Ocean Science Cluster.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The European Space Agency (ESA), established in 1975, is an intergovernmental organization dedicated to the exploration of space, currently with 19 member states. Headquartered in Paris, ESA has a staff of more than 2,000. ESA’s space flight program includes human spaceflight, mainly through the participation in the International Space Station program, the launch and operations of unmanned exploration missions to other planets and the Moon, Earth observation, science, telecommunication as well as maintaining a major spaceport, the Guiana Space Centre at Kourou, French Guiana, and designing launch vehicles. ESA science missions are based at ESTEC in Noordwijk, Netherlands, Earth Observation missions at ESRIN in Frascati, Italy, ESA Mission Control (ESOC) is in Darmstadt, Germany, the European Astronaut Centre (EAC) that trains astronauts for future missions is situated in Cologne, Germany, and the European Space Astronomy Centre is located in Villanueva de la Cañada, Spain.

    ESA50 Logo large

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