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  • richardmitnick 8:58 am on June 25, 2019 Permalink | Reply
    Tags: Applied Research & Technology, , Formeric spin-off,   

    From Science and Technology Facilities Council: “UK start-up meets manufacturers’ need for speed in new product innovation” 

    From Science and Technology Facilities Council

    24 June 2019

    Wendy Ellison
    STFC Communications
    Daresbury Laboratory
    Tel: 01925 603232
    Wendy Ellison

    For chemical manufacturing companies, speed to market for developing, testing and improving product formulations is critical against a tough, highly competitive market environment. Access to high performance computing can drastically speed up time-to-market, but is a complex process and can be a daunting task without an in-house specialist.

    Formeric Infographic. (Credit: Formeric)

    Eco-friendly cleaning products and fuels, more sustainable crop protection products and breakthrough personal care products – these are just some of the consumer and industrial goods that will benefit from this capability. Company needs can be very different, but they all have in common the need to understand the ingredients they use as quickly and efficiently as possible.

    Now, UK start-up company Formeric is meeting this need for speed with a revolutionary cloud-based app that puts supercomputing into the hands of manufacturers to develop new products, with no supercomputer specialist required.

    Formeric is a spin out of the world leading expertise and supercomputing technologies of the Hartree Centre, part of the Science and Technology Facilities Council (STFC).


    Located at STFC’s Daresbury Laboratory, at Sci-Tech Daresbury in the Liverpool City Region, the Hartree Centre’s key mission is to transform the UK industry through high performance computing, data analytics and artificial intelligence technologies.

    Daresbury Laboratory at Sci-Tech Daresbury in the Liverpool City Region

    Formeric’s platform application, which connects to the Hartree Centre, enables manufacturers and materials scientists to use the latest high performance and cloud computing technologies to accurately predict the behaviour and structure of different concentrations of liquid compounds. It will also show how they will interact with each other, both in the packaging, throughout shelf-life and in use. It means that a single simulation can be requested in seconds, helping researchers to plan fewer and more focussed experiments, reducing time to market.

    STFC’s Dr Rick Anderson, a founder of Formeric, said: “STFC, through its Scientific Computing Department and Hartree Centre, is well known for its expertise in modelling and simulation that can be used to benefit UK companies competing on an international scale. Formeric has been a few years in the planning since concept, so I’m thrilled that our cloud-based app is now ready to speed up design processes and reduce manufacturing costs. The resulting advances in materials chemistry will bring significant benefits to consumers, the environment and the wider economy.”

    Dr Elizabeth Kirby, Director of Innovation at STFC, said: “Manufacturing companies are seeking to embrace digital technologies more and more in their efforts to deliver increasingly efficient and profitable products in a global market. Formeric can now provide these companies with valuable access to supercomputing capabilities, without the need for the specialist skills, in their efforts to embrace digital transformation. I’m excited that we have harnessed the commercial potential for digital transformation from our innovative research by creating this new business.”

    Daresbury Laboratory is part of the Science and Technology Facilities Council. Further information at the website.

    See the full article here .


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    STFC Hartree Centre

    Helping build a globally competitive, knowledge-based UK economy

    We are a world-leading multi-disciplinary science organisation, and our goal is to deliver economic, societal, scientific and international benefits to the UK and its people – and more broadly to the world. Our strength comes from our distinct but interrelated functions:

    Universities: we support university-based research, innovation and skills development in astronomy, particle physics, nuclear physics, and space science
    Scientific Facilities: we provide access to world-leading, large-scale facilities across a range of physical and life sciences, enabling research, innovation and skills training in these areas
    National Campuses: we work with partners to build National Science and Innovation Campuses based around our National Laboratories to promote academic and industrial collaboration and translation of our research to market through direct interaction with industry
    Inspiring and Involving: we help ensure a future pipeline of skilled and enthusiastic young people by using the excitement of our sciences to encourage wider take-up of STEM subjects in school and future life (science, technology, engineering and mathematics)

    We support an academic community of around 1,700 in particle physics, nuclear physics, and astronomy including space science, who work at more than 50 universities and research institutes in the UK, Europe, Japan and the United States, including a rolling cohort of more than 900 PhD students.

    STFC-funded universities produce physics postgraduates with outstanding high-end scientific, analytic and technical skills who on graduation enjoy almost full employment. Roughly half of our PhD students continue in research, sustaining national capability and creating the bedrock of the UK’s scientific excellence. The remainder – much valued for their numerical, problem solving and project management skills – choose equally important industrial, commercial or government careers.

    Our large-scale scientific facilities in the UK and Europe are used by more than 3,500 users each year, carrying out more than 2,000 experiments and generating around 900 publications. The facilities provide a range of research techniques using neutrons, muons, lasers and x-rays, and high performance computing and complex analysis of large data sets.

    They are used by scientists across a huge variety of science disciplines ranging from the physical and heritage sciences to medicine, biosciences, the environment, energy, and more. These facilities provide a massive productivity boost for UK science, as well as unique capabilities for UK industry.

    Our two Campuses are based around our Rutherford Appleton Laboratory at Harwell in Oxfordshire, and our Daresbury Laboratory in Cheshire – each of which offers a different cluster of technological expertise that underpins and ties together diverse research fields.

    The combination of access to world-class research facilities and scientists, office and laboratory space, business support, and an environment which encourages innovation has proven a compelling combination, attracting start-ups, SMEs and large blue chips such as IBM and Unilever.

    We think our science is awesome – and we know students, teachers and parents think so too. That’s why we run an extensive Public Engagement and science communication programme, ranging from loans to schools of Moon Rocks, funding support for academics to inspire more young people, embedding public engagement in our funded grant programme, and running a series of lectures, travelling exhibitions and visits to our sites across the year.

    Ninety per cent of physics undergraduates say that they were attracted to the course by our sciences, and applications for physics courses are up – despite an overall decline in university enrolment.

  • richardmitnick 11:34 am on June 24, 2019 Permalink | Reply
    Tags: "As countries battle for control of North Pole, Applied Research & Technology, , , science is the ultimate winner",   

    From Science Magazine: “As countries battle for control of North Pole, science is the ultimate winner” 

    From Science Magazine

    Jun. 20, 2019
    Richard Kemeny

    Canadian and U.S. Coast Guard ships worked together to map the Arctic sea floor for continental shelf claims. DVIDSHUB/FLICKR/CC BY 2.0

    A competition for the North Pole heated up last month, as Canada became the third country to claim—based on extensive scientific data—that it should have sovereignty over a large swath of the Arctic Ocean, including the pole. Canada’s bid, submitted to the United Nations’s Commission on the Limits of the Continental Shelf (CLCS) on 23 May, joins competing claims from Russia and Denmark. Like theirs, it is motivated by the prospect of mineral riches: the large oil reserves believed to lie under the Arctic Ocean, which will become more accessible as the polar ice retreats. And all three claims, along with dozens of similar claims in other oceans, rest on extensive seafloor mapping, which has proved to be a boon to science, whatever the outcome for individual countries. The race to obtain control over parts of the sea floor has “dramatically changed our understanding of the oceans,” says marine geophysicist Larry Mayer of the University of New Hampshire in Durham.

    Coastal nations have sovereign rights over an exclusive economic zone (EEZ), extending by definition 200 nautical miles (370 kilometers) out from their coastline. But the 1982 United Nations Convention on the Law of the Sea opened up the possibility of expanding that zone if a country can convince CLCS that its continental shelf extends beyond the EEZ’s limits.

    Most of the 84 submissions so far were driven by the prospect of oil and gas, although advances in deep-sea mining technology have added new reasons to apply. Brazil, for example, filed an application in December 2018 that included the Rio Grande Rise, a deep-ocean mountain range 1500 kilometers southeast of Rio De Janeiro that’s covered in cobalt-rich ferromanganese crusts.

    To make a claim, a country has to submit detailed data on the shape of the sea floor and on its sediment, which is thicker on the shelf than in the deep ocean. The data come from sonar, which reveals seafloor topography, and seismic profiling, which uses low-frequency booms to probe the sediment. Canada’s bid also enlisted ships to conduct high-resolution gravimetry—measurements of gravity anomalies that reveal seafloor structure. Elevated gravity readings are found over higher-density mantle rocks found in oceanic crust, and lower readings over lighter, continental structures. And the bid used analyses of 800 kilograms of rock samples dredged up from the sea floor, whose composition can distinguish continental from ocean crust.

    The studies don’t come cheap; Canada’s 17 Arctic expeditions alone cost more than CA$117 million. But the work by the three countries vying for the Arctic—and that of dozens of others elsewhere in the world—has been a bonanza for oceanography. In the Arctic alone, the mapping has revealed several sunken mountains, previously missed or undetected by older sonar methods. Hundreds of pockmarks found on the Chukchi Cap, a submarine plateau extending out from Alaska, suggest that bursts of previously frozen methane have erupted from the seabed, a phenomenon that could accelerate climate change. And gaps discovered across submarine ridges allow currents to flow from basin to basin, with “important ramifications on the distribution of heat in the Arctic and on overall modeling of climate and ice melting,” Mayer says.

    Who owns the North Pole? Countries can clain the sea floor beyond the 200-nautical-mile (370-kilometer) ex-clusive economic zone (EEZ) if data show it to be an extension of the continental shelf (below). Russia Denmark and Canada have submitted overlapping claims in the Artic Ocean.

    CLCS, composed of 21 scientists in fields such as geology and hydrography who are elected by member states, has accepted 24 of the 28 claims it has finished evaluating, some partially or with caveats; in several cases, it has asked for follow-up submissions with more data. Australia was the first country to succeed, adding 2.5 million square kilometers to its territory in 2008. New Zealand gained undersea territory six times larger than its terrestrial area. But CLCS only judges the merit of each individual scientific claim; it has no authority to decide boundaries when claims overlap. To do that, countries have to turn to diplomatic channels once the science is settled.

    The three claims on the North Pole revolve around the Lomonosov Ridge, an underwater mountain system that runs from Ellesmere Island in Canada’s Qikiqtaaluk region to the New Siberian Islands of Russia, passing the North Pole. Both countries claim the ridge is geologically connected to their continent, whereas Denmark says it is also tied to Greenland, a Danish territory. As the ridge is thought to be continental crust, the territorial extensions could be extensive. (U.S. scientists should finish mapping in the Arctic in about 2 years, says Mayer, who is involved in that effort, but as one of the few countries that hasn’t ratified the Law of the Sea convention, the United States can’t file an official submission.)

    Tensions flared when Russia planted a titanium flag on the sea floor beneath the North Pole in 2007, after CLCS rejected its first claim, saying more data were needed. The Canadian foreign minister at the time likened the move to the land grabs of early European colonizers. Not that the North Pole has any material value: “The oil potential there is zip,” says geologist Henry Dick of the Woods Hole Oceanographic Institution in Massachusetts. “The real fight is over the Amerasian Basin,” Dick says (see map, above) where large amounts of oil are thought to be locked up.

    It will take years, perhaps decades, for CLCS to rule on the overlapping Arctic claims. Whoever wins the scientific contest still faces a diplomatic struggle.

    Denmark, Russia, and Canada have expressed their desire to settle the situation peacefully. “Russia actually has played nice on this and stopped at the North Pole,” rather than extending its claim along the length of the ridge, says Philip Steinberg, a political geographer at Durham University in the United Kingdom. Denmark had no such qualms and put in a claim up to the edge of Russia’s EEZ, “even though there’s no way in hell they’ll get that,” when it comes to the diplomatic discussions, Steinberg says.

    One solution would be to use the equidistance principle, by drawing a median line between the coastlines, as has been done when proposed marine territories overlapped in the past; doing so would mean the North Pole falls to Denmark. There’s also a proposal to make the pole international, like Antarctica, as a sign of peace, says Oran Young, a political scientist at the University of California, Santa Barbara. “It seems a very sensible idea.”

    See the full article here .


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  • richardmitnick 9:37 am on June 24, 2019 Permalink | Reply
    Tags: "Scientists Hit Pay Dirt with New Microbial Research Technique", (BONCAT+FACS-BONCAT Fluorescent Activated Cell Sorting, Applied Research & Technology, BONCAT- short for Bioorthogonal Non-Canonical Amino Acid Tagging, DOE Office of Science' Joint Genome Institute (JGI), ENIGMA- Ecosystems and Networks Integrated with Genes and Molecular Assemblies, , , Most soil microbes won’t grow in cultures in a laboratory, Soils are probably the most diverse microbial communities on the planet   

    From Lawrence Berkeley National Lab: “Scientists Hit Pay Dirt with New Microbial Research Technique” 

    Berkeley Logo

    From Lawrence Berkeley National Lab

    June 24, 2019
    Aliyah Kovner

    A better method for studying microbes in the soil will help scientists understand large-scale environmental cycles.

    Credit: Susan Brand and Marilyn Chung/Berkeley Lab

    Long ago, during the European Renaissance, Leonardo da Vinci wrote that we humans “know more about the movement of celestial bodies than about the soil underfoot.” Five hundred years and innumerable technological and scientific advances later, his sentiment still holds true.

    But that could soon change.

    In a report published in Nature Communications, a team of scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) detailed the first-ever successful use of a technique called BONCAT to isolate active microbes present in a sample of soil – an achievement that could enable a tidal wave of new research.

    “Soils are probably the most diverse microbial communities on the planet,” said Estelle Couradeau, first author of the study. “In every gram of soil, there are billions of cells from tens of thousands of species that, all together, perform important Earth nutrient cycles. They are the backbone of terrestrial ecosystems, and healthy soil microbiomes are key to sustainable agriculture. We now have the tools to see who these species are, but we don’t yet know how they do what they do. This proof-of-concept study shows that BONCAT is an effective tool that we could use to link active microbes to environmental processes.”

    A close look at soil microbiomes

    For the past two years, Couradeau, her co-authors, and many other researchers from around the U.S. have been collaborating in a Berkeley Lab-led scientific focus area called ENIGMA (for Ecosystems and Networks Integrated with Genes and Molecular Assemblies) in order to dig deeper into the inner-workings of soil microbiomes. ENIGMA’s projects are a high priority for biologists and energy and Earth scientists not only because they help fill gaps in our knowledge of how the environment functions, but also because these fundamental insights could help applied scientists more effectively harness microbiomes to improve drought-resistance in crops, remove contaminants from the environment, and sustainably produce fuels and other bioproducts.

    Charles Paradis, now a post-doctoral researcher at Los Alamos National Laboratory, holds a soil core sample taken from the Oak Ridge Field Research Site in Tennessee. The BONCAT+FACS optimization testing reported in the current study used samples such as this one. (Credit: Lance E. King/Y-12 National Security Complex)

    However, because most soil microbes won’t grow in cultures in a laboratory, and because of their truly mind-boggling abundance in their natural habitats, investigating which microbial species do what is incredibly difficult. “There are many barriers to measuring microbial activities and interactions,” said Trent Northen, lead author and director of biotechnology for ENIGMA. “For example, soil microbiomes that remove waste from underground water reservoirs are found hundreds of feet below the surface. And in some ecosystems, up to 95% of the microbes are inactive at any given time.”

    Because direct observation is off the table, microbiologists typically collect environmental samples and rely on indirect approaches such as DNA sequencing to characterize the communities. However, most of the commonly used techniques fail to differentiate active microbes from those that are dormant or from the plethora of free-floating bits of DNA found in soil and sediment.

    Expanding the toolkit

    BONCAT, short for Bioorthogonal Non-Canonical Amino Acid Tagging, was invented by Caltech geneticists in 2006 as a way to isolate newly made proteins in cells. In 2014, Rex Malmstrom, Danielle Goudeau, and others at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility managed by Berkeley Lab, collaborated with Victoria Orphan’s lab at Caltech to adapt BONCAT into a tool that could identify active, symbiotic clusters of dozens to hundreds of marine microbes within ocean sediment. After further refining their approach, called BONCAT Fluorescent Activated Cell Sorting (BONCAT+FACS), they were able to detect individual active microbes.

    A graph representing how the addition of fluorescent tags allows scientists to sort microbial cells. (Estelle Couradeau/Berkeley Lab)

    As the name suggests, BONCAT+FACS allows scientists to sort single-cell organisms based on the presence or absence of fluorescent tagging molecules, which bind to a modified version of the amino acid methionine. When fluid containing the modified methionine is introduced to a sample of microbes, only those that are creating new proteins – the hallmark of activity – will incorporate the modified methionine into cells.

    In addition to being far more streamlined and reliable than previous methods of microbial identification, the entire process takes just a few hours – meaning it can tag active cells even if they are not replicating.

    Given that some soil microbes are notoriously slow-growing, many scientists were immediately interested in applying BONCAT+FACS to terrestrial soils. After three months of experimentation and optimization, the team of ENIGMA and JGI researchers devised a protocol that works smoothly and, most importantly, gives very reproducible results.

    “BONCAT+FACS is a powerful tool that provides a more refined method to determine which microbes are active in a community at any particular time,” said Malmstrom, who is also an author of the current study. “It also opens the door for us to experiment, to assess which cells are active under condition A and which cells become active or inactive when switched to condition B.”

    The next steps

    Moving forward, BONCAT+FACS will be a capability available to researchers who wish to collaborate through the JGI’s user programs. Northen and Malmstrom have already received several proposals from research groups eager to start working with the tool, including groups from Berkeley Lab who hope to use BONCAT to assess how environmental changes stimulate groups of microbes. “With BONCAT, we will be able to get immediate snapshots of how microbiomes react to both normal habitat fluctuations and extreme climate events – such as drought and flood – that are becoming more and more frequent,” said Northen.

    According to Couradeau, the team expects the approach will catalyze a variety of other important and intriguing lines of study, such as improving agricultural land practices, assessing antibiotic susceptibility in unculturable microbes, and investigating the completely unknown roles of Candidatus Dormibacteraeota – a phylum of soil bacteria, found across the world, that appear to remain dormant most of the time.

    Reflecting on how he and his colleagues achieved a goal that many have been pursuing, Malmstrom cited the diversity of scientists within ENIGMA and JGI. “This a true example of team science, because no single person had or will ever have the expertise to do it all.”

    The other researchers involved in this work were Joelle Sasse, Danielle Goudeau, Nandita Nath, Terry Hazen, Ben Bowen, and Romy Chakraborty. The study was funded by a discovery proposal grant awarded to Trent Northen as part of the ENIGMA Science Focus Area. Both ENIGMA and JGI are supported by the DOE Office of Science.

    See the full article here .


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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.

    A U.S. Department of Energy National Laboratory Operated by the University of California.

    University of California Seal

    DOE Seal

  • richardmitnick 10:48 am on June 23, 2019 Permalink | Reply
    Tags: "Boost for space technology essential to keep UK in first place for future of auto industry", Applied Research & Technology, Harwell Science and Innovation campus, Oxfordshire,   

    From UK Space Agency: “Boost for space technology essential to keep UK in first place for future of auto industry” 

    UK Space Agency

    From UK Space Agency

    23 June 2019
    Building the technology to link autonomous vehicles to telecoms satellites means that you will be able to take your car wherever you want to go.

    The UK Space Agency is joining forces with mobile communications giant O2 to develop next generation technology needed for driverless cars.

    The new Darwin programme aims to test seamless highspeed data connections using 5G and satellites. Next generation telecoms satellites will ensure that vehicles stay connected outside of towns and cities which typically have good mobile signals.

    Connected and autonomous vehicles (CAVs) will transform travel with safer, smoother and smarter road journeys through high levels of automation facilitated by being able to communicate with other vehicles and to road infrastructure around them.

    However, they require robust and seamless high-speed data connections to operate their complex systems effectively.

    O2 research shows that CAVs are expected to generate unprecedented levels of data – 4TB per hour – highlighting the need for next generation connectivity.

    Business Secretary Greg Clark said:

    “Our world-beating space and auto industries have a proven track record in driving forward pioneering research, while the UK’s satellite services are constantly enhancing services such as the quality of our communications, healthcare and environmental monitoring.

    This new partnership between Government and industry will build on our world-leading reputation in the development and manufacture of satellites even further, to bring together two of the UK’s great strengths – automotive and space. Putting us at the forefront of the next generation of self-driving cars of tomorrow – a key ambition in our modern Industrial Strategy.”

    Since 2014, the Government has invested significantly into the research and development of CAVs — including £120 million in CAV projects, with a further £68 million coming from industry contributions.

    Catherine Mealing-Jones, Director of Growth, UK Space Agency, said:

    “Autonomous vehicles require robust high-speed mobile data connections to operate effectively, so building the technology to link autonomous vehicles to telecoms satellites means that you will be able to take your car wherever you want to go, not just where there’s decent mobile signal.

    The future of mobility is one of the UK government’s Industrial Strategy Grand Challenges, so I’m delighted to support Project Darwin to ensure that this critical technology is developed in Harwell, bringing expertise, jobs and growth to Britain.”

    This research will be based at the Harwell Science and Innovation Campus, Oxfordshire, and is co-funded through the UK Space Agency’s investment in the European Space Agency’s programme of Advanced Research in Telecommunications Systems (ARTES).

    Harwell Science and Innovation campus, Oxfordshire

    Other partners are Oxford and Glasgow universities, telecoms business O2 Telefonica, Spanish satellite operator Hispasat, and the Darwin Innovation Group Oxford.

    Darwin is developing an ARTES ‘Partner Study’ programme with UK support (first phase £2m) to help define all the different elements needed to deliver the larger programme. The future of mobility is one of the UK government’s Industrial Strategy Grand Challenges. UK Space Agency is working closely with Darwin and O2 to support this ambition in the UK.

    Derek McManus, COO at O2 said:

    “Project Darwin is an important piece of the connected and autonomous vehicle puzzle. The research taking place at Harwell during the next four years will be vital in the creation of new transport ecosystems for the UK public and the the companies that will offer these services. Our approach to this project is part of our wider strategy to collaborate with British businesses, partners and start-ups to unlock the possibilities of 5G for customers and wider UK economy.”

    5G connectivity delivered by converged networks will also support remote and rural enterprise and provide ubiquitous communications, one of the UK Space Agency’s strategic priorities in telecoms.

    Dr Stephan von Delft, University of Glasgow Adam Smith Business School, said:

    “Ecosystems that connect data, technologies and users create opportunities for business model innovation. However, new business models for 5G connected ecosystems will not emerge fully formed. Firms must therefore systematically explore, test and adapt new business models as conditions change. Our research aims to support Project Darwin in this process.”

    Daniela Petrovic, Darwin Innovation Group co-founder said:

    “Our team at Harwell is thrilled to gather key innovation partners like Telefonica, UK Space Agency and ESA, together with a number of start-ups from Oxfordshire with whom we have longstanding relationships, to join forces in this exciting innovation.

    Our aim is that Mobility as a Service (MaaS) developed by project DARWIN will benefit society in multiple ways: by creating new apprenticeships in this newly developing area, informing policies and regulations related to connected and autonomous vehicles, and creating a new industry vertical”.

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The UK Space Agency is responsible for all strategic decisions on the UK civil space programme and provides a clear, single voice for UK space ambitions.

    At the heart of UK efforts to explore and benefit from space, we are responsible for ensuring that the UK retains and grows a strategic capability in space-based systems, technologies, science and applications. We lead the UK’s civil space programme in order to win sustainable economic growth, secure new scientific knowledge and provide benefit to all citizens.

    We work to:

    co-ordinate UK civil space activity
    encourage academic research
    support the UK space industry
    raise the profile of UK space activities at home and abroad
    increase understanding of space science and its practical benefits
    inspire our next generation of UK scientists and engineers
    licence the launch and operation of UK spacecraft
    promote co-operation and participation in the European Space programme

    We’re an executive agency of the Department for Business, Innovation and Skills, made up of about 70 staff based in Swindon, London and the UK Space Gateway in Oxfordshire.

    We are responsible for:

    leading the UK civil space policy and increasing the UK contribution to European initiatives
    building a strong national space capability, including scientific and industrial centres of excellence
    co-ordinating strategic investment across industry and academia
    working to inspire and train a growing, skilled UK workforce of space technologists and scientists
    working on national and international space projects in co-operation with industry and academia
    regulating the UK civil space activities and ensuring we meet international treaty obligations

  • richardmitnick 10:23 am on June 23, 2019 Permalink | Reply
    Tags: Applied Research & Technology, , , Mellanox HDR 200G InfiniBand is powering next-gen supercomputers,   

    From insideHPC: “Mellanox HDR 200G InfiniBand is powering next-gen supercomputers” 

    From insideHPC

    June 23, 2019

    Today Mellanox announced that HDR 200G InfiniBand is powering the next generation of supercomputers world-wide, enabling higher levels of research and scientific discovery. HDR 200G InfiniBand solutions include the ConnectX-6 adapters, Mellanox Quantum switches, LinkX cables and transceivers and software packages. With its highest data throughput, extremely low latency, and smart In-Network Computing acceleration engines, HDR InfiniBand provides world leading performance and scalability for the most demanding compute and data applications.

    HDR 200G InfiniBand introduces new offload and acceleration engines, for delivering leading performance and scalability for high-performance computing, artificial intelligence, cloud, storage, and other applications. InfiniBand, a standards-based interconnect technology, enjoys the continuous development of new capabilities, while maintaining backward and forward software compatibility. InfiniBand is the preferred choice for world leading supercomputers, replacing lower performance or proprietary interconnect options.

    “We are proud to have our HDR InfiniBand solutions accelerate supercomputers around the world, enhance research and discoveries, and advancing Exascale programs,” said Gilad Shainer, senior vice president of marketing at Mellanox Technologies. “InfiniBand continues to gain market share, and be selected by many research, educational and government institutes, weather and climate facilities, and commercial organizations. The technology advantages of InfiniBand make it the interconnect of choice for compute and storage infrastructures.”

    The Texas Advanced Computing Center’s (TACC) Frontera supercomputer, funded by the National Science Foundation, is the fastest supercomputer at any U.S. university and one of the most powerful systems in the world.

    TACC Frontera Dell EMC supercomputer fastest at any university

    Ranked #5 on the June 2019 TOP500 Supercomputers list, Frontera utilizes HDR InfiniBand, and in particular multiple 800-port HDR InfiniBand switches, to deliver unprecedented computing power for science and engineering.

    “HDR InfiniBand enabled us to build a world-leading, 8,000+ node, top 5 supercomputer that will serve our users’ needs for the next several years,” said Dan Stanzione, TACC Executive Director. “We appreciate the deep collaboration with Mellanox and are proud to host one of the fastest supercomputers in the world. We look forward to utilizing the advanced routing capabilities and the In-Network Computing acceleration engines to enhance our users’ research activities and scientific discoveries.”

    Located at the Mississippi State University High Performance Computing Collaboratory, the new HDR InfiniBand-based Orion supercomputer will accelerate the university research, educational and service activities.

    Dell EMC Orion supercomputer at Mississippi State University

    Ranked #62 on the June 2019 TOP500 list, the 1800-node supercomputer leverages the performance advantages of HDR InfiniBand and its application acceleration engines to provide new levels of application performance and scalability.

    “HDR InfiniBand brings us leading performance and the ability to build very scalable and cost efficient supercomputers utilizing its high switch port density and configurable network topology,” said Trey Breckenridge, Director for High Performance Computing at Mississippi State University. “Over 16 years ago MSU became one of the first adopters of the InfiniBand technology in HPC. We are excited to continue that legacy by leveraging the latest InfiniBand technology to enhance the capabilities of our newest HPC system.”

    CSC, the Finnish IT Center for Science, and the Finnish Meteorological Institute Selected HDR 200G InfiniBand to accelerate a multi-phase supercomputer program. The program will serve researchers in Finnish universities and research institutes, enhancing their research into climate science, renewable energy, astrophysics, nanomaterials, and bioscience, among a wide range of exploration activities. The first supercomputer is ranked #166 on the TOP500 list.

    “The new supercomputer will enable our researchers and scientists to leverage the most efficient HPC and AI platform to enhance their competitiveness for years to come,” said Pekka Lehtovuori, Director of services for research at CSC. “The HDR InfiniBand technology, and the Dragonfly+ network topology will provide our users with leading performance and scalability while optimizing our total cost of ownership.”

    Cygnus is the first HDR InfiniBand supercomputer in Japan, located in the Center for Computational Sciences at the University of Tsukuba.

    Cygnus FPGA GPU supercomputer at University of Tsukuba Japan

    Ranked #264 on the TOP500 list, Cygnus leverages HDR InfiniBand to connect CPUs, GPUs and FPGAs together, enabling accelerated research in the areas of astrophysics, particle physics, material science, life, meteorology and artificial intelligence.

    The Center for Development of Advanced Computing (C-DAC) has selected HDR InfiniBand for India’s national supercomputing mission. The C-DAC HDR InfiniBand supercomputer advances India’s research, technology, and product development capabilities.

    “The Center for Development of Advanced Computing (C-DAC), an autonomous R&D institution under the Ministry of Electronics and IT, Government of India with its focus in Advanced Computing is uniquely positioned to establish dependable and secure Exascale Ecosystem offering services in various domains. As our nation embarks upon its most revolutionary phase of Digital Transformation, C-DAC has committed itself to explore and engage in the avant-garde visionary areas excelling beyond in the present areas of research transforming human lives through technological advancement,” said Dr Hemant Darbari, Director General, C-DAC.”

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  • richardmitnick 1:41 pm on June 22, 2019 Permalink | Reply
    Tags: Applied Research & Technology, , LBCO (lanthanum barium copper oxide) was the first high-temperature (high-Tc) superconductor discovered some 33 years ago., ,   

    From Brookhaven National Lab: “Electron (or ‘Hole’) Pairs May Survive Effort to Kill Superconductivity” 

    From Brookhaven National Lab

    June 14, 2019
    Karen McNulty Walsh,
    (631) 344-8350

    Peter Genzer
    (631) 344-3174

    Emergence of unusual metallic state supports role of charge stripes in formation of charge-carrier pairs essential to resistance-free flow of electrical current.

    Showing their stripes: Brookhaven Lab physicists present new evidence that stripes—alternating areas of charge and magnetism in certain copper-oxide materials—are good for forming the charge-carrier pairs needed for electrical current to flow with no resistance. Left to right: Qiang Li, Genda Gu, John Tranquada, Alexei Tsvelik, and Yangmu Li in front of an image of wind-blown ripples in desert sand.

    Scientists seeking to understand the mechanism underlying superconductivity in “stripe-ordered” cuprates—copper-oxide materials with alternating areas of electric charge and magnetism—discovered an unusual metallic state when attempting to turn superconductivity off. They found that under the conditions of their experiment, even after the material loses its ability to carry electrical current with no energy loss, it retains some conductivity—and possibly the electron (or hole) pairs required for its superconducting superpower.

    “This work provides circumstantial evidence that the stripe-ordered arrangement of charges and magnetism is good for forming the charge-carrier pairs required for superconductivity to emerge,” said John Tranquada, a physicist at the U.S. Department of Energy’s Brookhaven National Laboratory.

    Tranquada and his co-authors from Brookhaven Lab and the National High Magnetic Field Laboratory at Florida State University, where some of the work was done, describe their findings in a paper just published in Science Advances. A related paper in the Proceedings of the National Academy of Sciences by co-author Alexei Tsvelik, a theorist at Brookhaven Lab, provides insight into the theoretical underpinnings for the observations.

    This image represents the stripes of magnetism and charge in the cuprate (copper and oxygen) layers of the superconductor LBCO. Gray shading represents the modulation of the charge (“holes,” or electron vacancies), which is maximized in stripes that separate areas of magnetism, indicated by arrows representing alternating magnetic orientations on adjacent copper atoms.

    The scientists were studying a particular formulation of lanthanum barium copper oxide (LBCO) that exhibits an unusual form of superconductivity at a temperature of 40 Kelvin (-233 degrees Celsius). That’s relatively warm in the realm of superconductors. Conventional superconductors must be cooled with liquid helium to temperatures near -273°C (0 Kelvin or absolute zero) to carry current without energy loss. Understanding the mechanism behind such “high-temperature” superconductivity might guide the discovery or strategic design of superconductors that operate at higher temperatures.

    “In principle, such superconductors could improve the electrical power infrastructure with zero-energy-loss power transmission lines,” Tranquada said, “or be used in powerful electromagnets for applications like magnetic resonance imaging (MRI) without the need for costly cooling.”

    The mystery of high-Tc

    LBCO was the first high-temperature (high-Tc) superconductor discovered, some 33 years ago. It consists of layers of copper-oxide separated by layers composed of lanthanum and barium. Barium contributes fewer electrons than lanthanum to the copper-oxide layers, so at a particular ratio, the imbalance leaves vacancies of electrons, known as holes, in the cuprate planes. Those holes can act as charge carriers and pair up, just like electrons, and at temperatures below 30K, current can move through the material with no resistance in three dimensions—both within and between the layers.

    Copper-oxide layers of LBCO (the lanthanum-barium layers would be between these). 3-D superconductivity occurs when current can flow freely in any direction within and between the copper-oxide layers, while 2-D superconductivity exists when current moves freely only within the layers (not perpendicular). The perpendicular orientations of stripe patterns from one layer to the next may be part of what inhibits movement of current between layers.

    An odd characteristic of this material is that, in the copper-oxide layers, at the particular barium concentration, the holes segregate into “stripes” that alternate with areas of magnetic alignment. Since this discovery, in 1995, there has been much debate about the role these stripes play in inducing or inhibiting superconductivity.

    In 2007, Tranquada and his team discovered the most unusual form of superconductivity in this material at the higher temperature of 40K. If they altered the amount of barium to be just under the amount that allowed 3-D superconductivity, they observed 2-D superconductivity—meaning just within the copper-oxide layers but not between them.

    “The superconducting layers seem to decouple from one another,” Tsvelik, the theorist, said. The current can still flow without loss in any direction within the layers, but there is resistivity in the direction perpendicular to the layers. This observation was interpreted as a sign that charge-carrier pairs were forming “pair density waves” with orientations perpendicular to one another in neighboring layers. “That’s why the pairs can’t jump from layer to another. It would be like trying to merge into traffic moving in a perpendicular direction. They can’t merge,” Tsvelik said.

    Superconducting stripes are hard to kill

    In the new experiment, the scientists dove deeper into exploring the origins of the unusual superconductivity in the special formulation of LBCO by trying to destroy it. “Often times we test things by pushing them to failure,” Tranquada said. Their method of destruction was exposing the material to powerful magnetic fields generated at Florida State.

    “As the external field gets bigger, the current in the superconductor grows larger and larger to try to cancel out the magnetic field,” Tranquada explained. “But there’s a limit to the current that can flow without resistance. Finding that limit should tell us something about how strong the superconductor is.”

    A phase diagram of LBCO at different temperatures and magnetic field strengths. Colors represent how resistant the material is to the flow of electrical current, with purple being a superconductor with no resistance. When cooled to near absolute zero with no magnetic field, the material acts as a 3-D superconductor. As the magnetic field strength goes up, 3-D superconductivity disappears, but 2-D superconductivity reappears at higher field strength, then disappears again. At the highest fields, resistance grew, but the material retained some unusual metallic conductivity, which the scientists interpreted as an indication that charge-carrier pairs might persist even after superconductivity is destroyed.

    For example, if the stripes of charge order and magnetism in LBCO are bad for superconductivity, a modest magnetic field should destroy it. “We thought maybe the charge would get frozen in the stripes so that the material would become an insulator,” Tranquada said.

    But the superconductivity turned out to be a lot more robust.

    Using perfect crystals of LBCO grown by Brookhaven physicist Genda Gu, Yangmu Li, a postdoctoral fellow who works in Tranquada’s lab, took measurements of the material’s resistance and conductivity under various conditions at the National High Magnetic Field Laboratory. At a temperature just above absolute zero with no magnetic field present, the material exhibited full, 3-D superconductivity. Keeping the temperature constant, the scientists had to ramp up the external magnetic field significantly to make the 3-D superconductivity disappear. Even more surprising, when they increased the field strength further, the resistance within the copper-oxide planes went down to zero again!

    “We saw the same 2-D superconductivity we’d discovered at 40K,” Tranquada said.

    Ramping up the field further destroyed the 2-D superconductivity, but it never completely destroyed the material’s ability to carry ordinary current.

    “The resistance grew but then leveled off,” Tranquada noted.

    Signs of persistent pairs?

    Additional measurements made under the highest-magnetic-field indicated that the charge-carriers in the material, though no longer superconducting, may still exist as pairs, Tranquada said.

    “The material becomes a metal that no longer deflects the flow of current,” Tsvelik said. “Whenever you have a current in a magnetic field, you would expect some deflection of the charges—electrons or holes—in the direction perpendicular to the current [what scientists call the Hall effect]. But that’s not what happens. There is no deflection.”

    In other words, even after the superconductivity is destroyed, the material keeps one of the key signatures of the “pair density wave” that is characteristic of the superconducting state.

    “My theory relates the presence of the charge-rich stripes with the existence of magnetic moments between them to the formation of the pair density wave state,” Tsvelik said. “The observation of no charge deflection at high field shows that the magnetic field can destroy the coherence needed for superconductivity without necessarily destroying the pair density wave.”

    “Together these observations provide additional evidence that the stripes are good for pairing,” Tranquada said. “We see the 2-D superconductivity reappear at high field and then, at an even higher field, when we lose the 2-D superconductivity, the material doesn’t just become an insulator. There’s still some current flowing. We may have lost coherent motion of pairs between the stripes, but we may still have pairs within the stripes that can move incoherently and give us an unusual metallic behavior.”

    See the full article here .


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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

  • richardmitnick 12:15 pm on June 22, 2019 Permalink | Reply
    Tags: A new crystal built of a spiraling stack of atomically thin germanium sulfide sheets., Applied Research & Technology, Lawrence Berkeley National Laboratory, Such “nanosheets” are usually referred to as “2D materials.", the team took advantage of a crystal defect called a screw dislocation a “mistake” in the orderly crystal structure that gives it a bit of a twisting force., These “inorganic” crystals are built of more far-flung eleThese “inorganic” crystals are built of more far-flung elemenmnts of the periodic table — in this case sulfur and germanium, This is Unlike “organic” DNA which is primarily built of familiar atoms like carbon oxygen and hydrogen,   

    From UC Berkeley: “Crystal with a twist: scientists grow spiraling new material” 

    From UC Berkeley

    June 19, 2019
    Kara Manke

    UC Berkeley and Berkeley Lab researchers created a new crystal built of a spiraling stack of atomically thin germanium sulfide sheets. (UC Berkeley image by Yin Liu)

    With a simple twist of the fingers, one can create a beautiful spiral from a deck of cards. In the same way, scientists at the University of California, Berkeley, and Lawrence Berkeley National Laboratory (Berkeley Lab) have created new inorganic crystals made of stacks of atomically thin sheets that unexpectedly spiral like a nanoscale card deck.

    Their surprising structures, reported in a new study appearing online Wednesday, June 20, in the journal Nature, may yield unique optical, electronic and thermal properties, including superconductivity, the researchers say.

    These helical crystals are made of stacked layers of germanium sulfide, a semiconductor material that, like graphene, readily forms sheets that are only a few atoms or even a single atom thick. Such “nanosheets” are usually referred to as “2D materials.”

    “No one expected 2D materials to grow in such a way. It’s like a surprise gift,” said Jie Yao, an assistant professor of materials science and engineering at UC Berkeley. “We believe that it may bring great opportunities for materials research.”

    While the shape of the crystals may resemble that of DNA, whose helical structure is critical to its job of carrying genetic information, their underlying structure is actually quite different. Unlike “organic” DNA, which is primarily built of familiar atoms like carbon, oxygen and hydrogen, these “inorganic” crystals are built of more far-flung elements of the periodic table — in this case, sulfur and germanium. And while organic molecules often take all sorts of zany shapes, due to unique properties of their primary component, carbon, inorganic molecules tend more toward the straight and narrow.

    To create the twisted structures, the team took advantage of a crystal defect called a screw dislocation, a “mistake” in the orderly crystal structure that gives it a bit of a twisting force. This “Eshelby Twist”, named after scientist John D. Eshelby, has been used to create nanowires that spiral like pine trees. But this study is the first time the Eshelby Twist has been used to make crystals built of stacked 2D layers of an atomically thin semiconductor.

    “Usually, people hate defects in a material — they want to have a perfect crystal,” said Yao, who also serves as a faculty scientist at Berkeley Lab. “But it turns out that, this time, we have to thank the defects. They allowed us to create a natural twist between the material layers.”

    In a major discovery [Nature] last year, scientists reported that graphene becomes superconductive when two atomically thin sheets of the material are stacked and twisted at what’s called a “magic angle.” While other researchers have succeeded at stacking two layers at a time, the new paper provides a recipe for synthesizing stacked structures that are hundreds of thousands or even millions of layers thick in a continuously twisting fashion.

    The helical crystals may yield surprising new properties, like superconductivity. (UC Berkeley image by Yin Liu)

    “We observed the formation of discrete steps in the twisted crystal, which transforms the smoothly twisted crystal to circular staircases, a new phenomenon associated with the Eshelby Twist mechanism,” said Yin Liu, co-first author of the paper and a graduate student in materials science and engineering at UC Berkeley. “It’s quite amazing how interplay of materials could result in many different, beautiful geometries.”

    By adjusting the material synthesis conditions and length, the researchers could change the angle between the layers, creating a twisted structure that is tight, like a spring, or loose, like an uncoiled Slinky. And while the research team demonstrated the technique by growing helical crystals of germanium sulfide, it could likely be used to grow layers of other materials that form similar atomically thin layers.

    “The twisted structure arises from a competition between stored energy and the energy cost of slipping two material layers relative to one another,” said Daryl Chrzan, chair of the Department of Materials Science and Engineering and senior theorist on the paper. “There is no reason to expect that this competition is limited to germanium sulfide, and similar structures should be possible in other 2D material systems.”

    “The twisted behavior of these layered materials, typically with only two layers twisted at different angles, has already showed great potential and attracted a lot of attention from the physics and chemistry communities. Now, it becomes highly intriguing to find out, with all of these twisted layers combined in our new material, if will they show quite different material properties than regular stacking of these materials,” Yao said. “But at this moment, we have very limited understanding of what these properties could be, because this form of material is so new. New opportunities are waiting for us.”

    Other co-first authors of the paper include Su Jung Kim and Haoye Sun of UC Berkeley and Jie Wang of Argonne National Laboratory. Other authors include Fuyi Yang, Zixuan Fang, Ruopeng Zhang, Bo Z. Xu, Michael Wang, Shuren Lin, Kyle B. Tom, Yang Deng, Robert O. Ritchie, Andrew M. Minor and Mary C. Scott of UC Berkeley; Nobumichi Tamura, Xiaohui Song, Qin Yu, John Turner and Emory Chan of Berkeley Lab and Jianguo Wen and Dafei Jin of Argonne National Laboratory.

    Work at Berkeley Lab’s Molecular Foundry and the Advanced Light Source was supported by the U.S. Department of Energy’s Office of Science and Office of Basic Energy Sciences under contract no. DE-AC02-05CH11231. The research was also supported by the U.S. Department of Energy’s Office of Science, Office of Basic Energy Sciences and Materials Sciences and Engineering Division under contract no. DE-AC02-244 05CH11231 within the Electronic Materials Program (KC1201).

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  • richardmitnick 10:17 am on June 22, 2019 Permalink | Reply
    Tags: "Scientists make first high-res movies of proteins forming crystals in a living cell", Applied Research & Technology, “The protein molecules are self-assembling building blocks and they will spontaneously form themselves into crystals No enzyme is required.”, , Microbial cell division, , Single-molecule tracking, , Stimulated emission depletion, Super-resolution fluorescence microscopy   

    From SLAC National Accelerator Lab: “Scientists make first high-res movies of proteins forming crystals in a living cell” 

    From SLAC National Accelerator Lab

    June 21, 2019
    Glennda Chui

    A close-up look at how microbes build their crystalline shells has implications for understanding how cell structures form, preventing disease and developing nanotechnology.

    Scientists have made the first observations of proteins assembling themselves into crystals, one molecule at a time, in a living cell. The method they used to watch this happen – an extremely high-res form of molecular moviemaking ­– could shed light on other important biological processes and help develop nanoscale technologies inspired by nature.

    Led by researchers at Stanford University and the Department of Energy’s SLAC National Accelerator Laboratory, the study was published in Nature Communications today.

    “I’ve been super-excited to watch and track the movements of single molecules as they form this fascinating crystalline shell on the surface of a microbe,” said Stanford professor and study co-author W.E. Moerner, who shared the 2014 Nobel Prize in chemistry for stunning advances in pushing the boundaries of what optical microscopes can see. “We can look on a very fine scale and see the molecules arranging themselves in the shell. It’s the first time we’ve been able to do this.”

    The study focused on a bacterium called Caulobacter crescentus that lives in lakes and streams. It’s one of many microbes that sport a very thin crystalline shell, known as a surface layer or S-layer, made of identical protein building blocks.

    An Illustration shows the cylindrical stalk of the microbe covered in a crystalline protein shell known as an S-layer. (Greg Stewart/SLAC National Accelerator Laboratory)

    This illustration zooms in to show six-sided protein crystal “tiles” forming at top left and far right. (Greg Stewart/SLAC National Accelerator Laboratory)

    Scientists have been trying to figure out what roles these brittle shells play in the lives of their owners and how they come together to smoothly cover a microbe’s curvy surfaces. The research is driven not just by a desire to understand how nature works, but also by the possibility of applying that knowledge to create new types of nanotechnology – for instance, by using the protein shells as scaffolds for building “engineered living materials.” The shells also offer a potential target for drugs aimed at disarming infectious bacteria.

    In this study, the research team used two established techniques that transcend the previous resolution limitations of optical microscopy – super-resolution fluorescence microscopy and single-molecule tracking – to watch individual building blocks move around the surfaces of living bacteria and assemble themselves into a shell. The resulting images and movies revealed how protein building blocks crystallize to form the bacterium’s S-layer coat.

    “It’s like watching a pile of bricks self-assemble into a two-story house,” said Jonathan Herrmann, a PhD student at Stanford and SLAC who along with fellow Stanford PhD students Colin Comerci and Josh Yoon carried out the bulk of the work.

    A still image shows the tracks (red, white and blue lines) of individual protein molecules moving around the surface of a microbe over a period of 60 seconds. One of the molecules has just bound to an existing patch of the shell (bottom), which is labeled with a green fluorescent tag. The microbe is outlined in orange. (Josh Yoon, Colin Comerci, Jonathan Herrmann/Stanford University)

    This high-res movie represents the first observation ever made of protein crystallization by a living cell. It shows single protein molecules (red) roving over the surface of a microbe over the course of two minutes; when they join an existing patch of the microbe’s shell (green) they crystallize like rock candy around a string. The molecules are tagged with fluorescent chemicals to make them visible. (Josh Yoon, Colin Comerci, Jonathan Herrmann/Stanford University)

    Following the glow

    Protein crystals are widespread in nature: in shells that surround many bacteria and almost all of the ancient microbes called Archaea, in the outer shells of viruses and even in the human eye. The bacteria that cause anthrax and salmonella infections have these crystalline shells; so does Clostridium difficile, which causes serious infections of the colon and intestines. A lot of research has been aimed at disrupting these shells to head off infection.

    The bacteria in this study don’t infect healthy people and are well-studied and understood, so they make good research subjects. Scientists know, among other things, that these bacteria can’t thrive without their shells, which are made from protein building blocks called RsaA. But shell assembly takes place at such a tiny scale that it had never been observed before.

    To watch it happen, the researchers stripped microbes of their S-layers and supplied them with synthetic RsaA building blocks labeled with chemicals that fluoresce in bright colors when stimulated with a particular wavelength of light.

    These images show how a super-resolution fluorescence microscopy technique called STED produces much sharper images of microbial shell assembly (right) than a previous technique, confocal microscopy (left). Areas in red are places where the shell is growing: at the ends of the microbial cell, in the pinched middle section where it is preparing to divide and at cracks and defects in the shell. (Colin Comerci, Jonathan Herrmann/Stanford University)

    Then they tracked the glowing building blocks with single-molecule microscopy as they formed a shell that covered the microbe in a hexagonal, tile-like pattern in less than two hours. A technique called stimulated emission depletion (STED) microscopy allowed them to see structural details of the layer as small as 60 to 70 nanometers, or billionths of a meter, across – about one-thousandth the width of a human hair.

    The team discovered that the shell-building didn’t happen the way they thought: The RsaA blocks were not guided into position and joined to the shell by enzymes, which promote most biological reactions. Instead they randomly moved around, found a patch of existing shell and joined it, like rock candy crystallizing around a string dipped in sugar water.

    “The protein molecules are self-assembling building blocks, and they will spontaneously form themselves into crystals,” Herrmann said. “No enzyme is required.”

    An illustration shows how protein building blocks secreted by a microbe (at arrows) travel over its surface until they encounter its growing crystalline shell. There they join one of the six-sided units that tile the microbe’s surface, crystallizing like rock candy around a string. (Greg Stewart/SLAC National Accelerator Laboratory)

    A new way of seeing

    Since the flat crystalline shell can never perfectly fit the constantly changing 3-D shape of the microbe – “It’s not a huge leap to say that if you try to bend the sheet to fit the microbe, you have to break it,” Comerci said – there are always small defects and gaps in coverage, and those places, he said, are where they saw the shell grow.

    “For the first time,” he said, “we were able to watch the S-layer proteins do things on their own.”

    Sketch showing where the microbe’s crystalline shell would be expected to crack, based on the curvature of its surface as it grows and prepares to divide. The predicted cracks and defects are shown here in white. These are places where the crystalline shell tends to grow. (Colin Comerci/Stanford University)

    A closer look at areas where shell growth is occurring. Green areas are existing patches of shell; red areas are new growth at cracks, the ends (poles) of the microbial cell and in the middle, where the microbe is growing and preparing to divide. (Colin Comerci, Jonathan Herrmann/Stanford University)

    This new way of observing shell formation “is opening up a new way to understand and eventually manipulate surface layer structures, both in living organisms and in isolation,” said co-author Soichi Wakatsuki, a professor at SLAC and Stanford who leads the Biological Sciences Division at the lab’s Stanford Synchrotron Radiation Lightsource.


    “Now that we know how they assemble, we can modify their properties so they can do specific types of work, like forming new types of hybrid materials or attacking biomedical problems.”

    The next step, researchers said, is to find out how the crystallization process starts using higher resolution X-ray and electron imaging available at SLAC: How do the very first bits of the shell crystallize without the equivalent of the rock candy string?

    Optical microscopy for this study was carried out at the Moerner lab at Stanford. Researchers from the University of British Columbia and from Professor Lucy Shapiro’s laboratory at Stanford also contributed to this work, which was funded in part by the National Institute of General Medical Sciences and the Chan Zuckerberg Biohub. Work in Wakatsuki’s labs at SLAC and Stanford was partly funded by a Laboratory Directed Research and Development grant from SLAC and by the DOE Office of Biological and Environmental Research. The Stanford Synchrotron Radiation Lightsource is a DOE Office of Science user facility.

    See the full article here .

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  • richardmitnick 1:48 pm on June 21, 2019 Permalink | Reply
    Tags: "Blue Pigment from Engineered Fungi Could Help Turn the Textile Industry Green", A blue pigment called indigoidine, Applied Research & Technology, , , Most indigo used today is synthesized, Opens the door for next-generation bioproduction., Rhodosporidium toruloides, The scientists examined Rhodosporidium toruloide'sNRPS expression capability by inserting a bacterial NRPS into its genome   

    From Lawrence Berkeley National Lab: “Blue Pigment from Engineered Fungi Could Help Turn the Textile Industry Green” 

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    From Lawrence Berkeley National Lab

    June 21, 2019
    Aliyah Kovner

    A new platform for producing blue pigment could provide a sustainable alternative to conventional synthetic dyes and open the door for next-generation bioproduction.

    Lead researcher Aindrila Mukhopadhyay holds a vial of purified indigoidine crystals. (Credit: Marilyn Chung/Berkeley Lab)

    Often, the findings of fundamental scientific research are many steps away from a product that can be immediately brought to the public. But every once in a while, opportunity makes an early appearance.

    Such was the case for a team from the Department of Energy’s Joint BioEnergy Institute (JBEI), whose outside-the-box thinking when investigating microbe-based biomanufacturing led straight to an eco-friendly production platform for a blue pigment called indigoidine. With a similar vividly saturated hue as synthetic indigo, a dye used around the world to color denim and many other items, the team’s fungi-produced indigoidine could provide an alternative to a largely environmentally unfriendly process.

    “Originally extracted from plants, most indigo used today is synthesized,” said lead researcher Aindrila Mukhopadhyay, who directs the Host Engineering team at JBEI. “These processes are efficient and inexpensive, but they often require toxic chemicals and generate a lot of dangerous waste. With our work we now have a way to efficiently produce a blue pigment that uses inexpensive, sustainable carbon sources instead of harsh precursors. And so far, the platform checks many of the boxes in its promise to be scaled-up for commercial markets.”

    Droplets of purified indigoidine, produced by bioengineered fungi, are added to water to showcase the pigment’s rich, saturated hue. (Marilyn Chung/Berkeley Lab)

    Importantly, these commercial markets already have considerable demand for what the scientists hope to supply. After meeting with many key stakeholders in the textile industry, the team found that many companies are eager for more sustainably sourced pigments because customers are increasingly aware of the impacts of conventional dyes. “There seems to be a shift in society toward wanting better processes for creating everyday products,” said Maren Wehrs, a graduate student at JBEI and first author of the paper describing the discovery, now published in Green Chemistry. “That’s exactly what JBEI is trying to do, using tools derived from biological systems – it just so happens that our engineered biological platform worked very well.”

    The story began when the team set out to test how well a hardy fungi species called Rhodosporidium toruloides could express nonribosomal peptide synthetases (NRPSs) – large enzymes that bacteria and fungi use to assemble important compounds. The scientists examined this fungi’s NRPS expression capability by inserting a bacterial NRPS into its genome. They chose an NRPS that converts two amino acid molecules into indigoidine – a blue pigment – to make it easy to tell if the strain engineering had worked. Quite simply, when it did, the culture would turn blue.

    Going into this experiment, indigoidine itself was not the main interest for the team. Instead, they were focused on the larger picture: exploring how the assembly line functionality of these enzymes could be harnessed to create biosynthetic manufacturing pathways for valuable organic compounds, such as biofuels, and assessing whether or not the fungi represented a good host species for the production of these compounds. But when they cultivated their engineered strain, and saw just how blue the culture was, they knew something incredible had happened.

    Aindrila Mukhopadhyay and Maren Wehrs inspect a bioreactor full of their Bluebelle strain at JBEI. (Credit: Marilyn Chung/Berkeley Lab)

    With an average titer of 86 grams of indigoidine per liter of bioreactor culture, the yield of the strain – which they named Bluebelle – is by far the highest that has ever been reported. (Other research groups, including the JBEI team, have synthesized indigoidine using different host microbes.) Adding to the weight of the achievement, the record-breaking yield was obtained from a culture process that uses nutrient and precursor inputs sourced from sustainable plant material. Previous pathways required considerably more expensive inputs yet made about one-tenth the amount of indigoidine.

    Beyond the potential applications of indigoidine, the study succeeded in its original goal of providing a potential production pathway for other NRPSs – something that is much more valuable than any single product. These complex enzymes have multiple subunits that each perform a distinct and predictable action in assembling a compound out of smaller molecules. Scientists at JBEI and beyond are keen to engineer enzymes that use NRPSs’ Lego block-like features to produce advanced bioproducts that are currently hard to make.

    “A big challenge is to get a microbe to efficiently express such enzymes. This host has huge potential to fulfill that need,” said Mukhopadhyay.

    The team’s next steps will be to characterize how indigoidine could be used as a dye and to dig deeper into the capabilities of R. toruloides.

    See the full article here .


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    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 2:08 pm on June 20, 2019 Permalink | Reply
    Tags: "Researchers Call for Personalized Approach to Aging Brain Health", Applied Research & Technology, , ,   

    From University of Arizona: “Researchers Call for Personalized Approach to Aging Brain Health” 

    U Arizona bloc

    From University of Arizona

    June 18, 2019
    Alexis Blue

    UA psychologist Lee Ryan and her collaborators have proposed a precision aging model designed to help researchers better understand and treat age-related cognitive decline on an individual level.

    People are living longer than ever before, but brain health isn’t keeping up. To tackle this critical problem, a team of researchers has proposed a new model for studying age-related cognitive decline – one that’s tailored to the individual.


    There’s no such thing as a one-size-fits-all approach to aging brain health, says Lee Ryan, professor and head of the University of Arizona Department of Psychology. A number of studies have looked at individual risk factors that may contribute to cognitive decline with age, such as chronic stress and cardiovascular disease. However, those factors may affect different people in different ways depending on other variables, such as genetics and lifestyle, Ryan says.

    In a new paper published in the journal Frontiers in Aging Neuroscience, Ryan and her co-authors advocate for a more personalized approach, borrowing principles of precision medicine in an effort to better understand, prevent and treat age-related cognitive decline.

    “Aging is incredibly complex, and most of the research out there was focusing on one aspect of aging at a time,” Ryan said. “What we’re trying to do is take the basic concepts of precision medicine and apply them to understanding aging and the aging brain. Everybody is different and there are different trajectories. Everyone has different risk factors and different environmental contexts, and layered on top of that are individual differences in genetics. You have to really pull all of those things together to predict who is going to age which way. There’s not just one way of aging.”

    Although most older adults – around 85% – will not experience Alzheimer’s disease in their lifetimes, some level of cognitive decline is considered a normal part of aging. The majority of people in their 60s or older experience some cognitive impairment, Ryan said.

    This not only threatens older adults’ quality of life, it also has socioeconomic consequences, amounting to hundreds of billions of dollars in health care and caregiving costs, as well as lost productivity in the workplace, Ryan and her co-authors write.

    The researchers have a lofty goal: to make it possible to maintain brain health throughout the entire adult lifespan, which today in the U.S. is a little over 78 years old on average.

    In their paper, Ryan and her co-authors present a precision aging model meant to be a starting point to guide future research. It focuses primarily on three areas: broad risk categories; brain drivers; and genetic variants. An example of a risk category for age-related cognitive decline is cardiovascular health, which has been consistently linked to brain health. The broader risk category includes within it several individual risk factors, such as obesity, diabetes and hypertension.

    The model then considers brain drivers, or the biological mechanisms through which individual risk factors in a category actually impact the brain. This is an area where existing research is particularly limited, Ryan said.

    Finally, the model looks at genetic variants, which can either increase or decrease a person’s risk for age-related cognitive decline. Despite people’s best efforts to live a healthy lifestyle, genes do factor into the equation and can’t be ignored, Ryan said. For example, there are genes that protect against or make it more likely that a person will get diabetes, sometimes regardless of their dietary choices.

    While the precision aging model is a work in progress, Ryan and her collaborators believe that considering the combination of risk categories, brain drivers and genetic variants is key to better understanding age-related cognitive decline and how to best intervene in different patients.

    Ryan imagines a future in which you can go to your doctor’s office and have all of your health and lifestyle information put into an app that would then help health-care professionals guide you on an individualized path for maintaining brain health across your lifespan. We may not be there yet, but it’s important for research on age-related cognitive decline to continue, as advances in health and technology have the potential to extend the lifespan even further, she said.

    “Kids that are born in this decade probably have a 50% chance of living to 100,” Ryan said. “Our hope is that the research community collectively stops thinking about aging as a single process and recognizes that it is complex and not one-size-fits-all. To really move the research forward you need to take an individualized approach.”

    Ryan is associate director of the Evelyn F. McKnight Brain Institute at the UA, which is one of the foremost universities in the world for researching the aging brain and age-related cognitive changes. Her co-authors on the paper include UA Regents’ Professor of Psychology Carol Barnes, who directs the UA’s Evelyn F. McKnight Brain Institute; UA professors Meredith Hay and Matthias Mehl; and collaborators from the Phoenix-based Translational Genomics Institute, Georgia Institute of Technology, Leonard M. Miller School of Medicine and John Hopkins University.

    See the full article here .

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    The University of Arizona (UA) is a place without limits-where teaching, research, service and innovation merge to improve lives in Arizona and beyond. We aren’t afraid to ask big questions, and find even better answers.

    In 1885, establishing Arizona’s first university in the middle of the Sonoran Desert was a bold move. But our founders were fearless, and we have never lost that spirit. To this day, we’re revolutionizing the fields of space sciences, optics, biosciences, medicine, arts and humanities, business, technology transfer and many others. Since it was founded, the UA has grown to cover more than 380 acres in central Tucson, a rich breeding ground for discovery.

    Where else in the world can you find an astronomical observatory mirror lab under a football stadium?

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    An entire ecosystem under a glass dome? Visit our campus, just once, and you’ll quickly understand why the UA is a university unlike any other.

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