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  • richardmitnick 7:23 am on September 27, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , Killing Superbugs with Star-Shaped Polymers instead of Antibiotics, , Shu Lam, U Melbourne   

    From University of Melbourne via Science Alert: Women in STEM – “Killing Superbugs with Star-Shaped Polymers instead of Antibiotics” Shu Lam 


    University of Melbourne


    Science Alert

    The science world is freaking out over this 25-year-old’s answer to antibiotic resistance

    26 SEP 2016

    Could this be the end of superbugs?

    Shu Lam

    A 25-year-old student has just come up with a way to fight drug-resistant superbugs without antibiotics.

    The new approach has so far only been tested in the lab and on mice, but it could offer a potential solution to antibiotic resistance, which is now getting so bad that the United Nations recently declared it a “fundamental threat” to global health.

    Antibiotic-resistant bacteria already kill around 700,000 people each year, but a recent study suggests that number could rise to around 10 million by 2050.

    In addition to common hospital superbug, methicillin-resistant Staphylococcus aureus (MRSA), scientists are now also concerned that gonorrhoea is about to become resistant to all remaining drugs.

    But Shu Lam, a 25-year-old PhD student at the University of Melbourne in Australia, has developed a star-shaped polymer that can kill six different superbug strains without antibiotics, simply by ripping apart their cell walls.

    “We’ve discovered that [the polymers] actually target the bacteria and kill it in multiple ways,” Lam told Nicola Smith from The Telegraph. “One method is by physically disrupting or breaking apart the cell wall of the bacteria. This creates a lot of stress on the bacteria and causes it to start killing itself.”

    The research has been published in Nature Microbiology, and according to Smith, it’s already being hailed by scientists in the field as “a breakthrough that could change the face of modern medicine”.

    Before we get too carried away, it’s still very early days. So far, Lam has only tested her star-shaped polymers on six strains of drug-resistant bacteria in the lab, and on one superbug in live mice.

    But in all experiments, they’ve been able to kill their targeted bacteria – and generation after generation don’t seem to develop resistance to the polymers.

    The polymers – which they call SNAPPs, or structurally nanoengineered antimicrobial peptide polymers – work by directly attacking, penetrating, and then destabilising the cell membrane of bacteria.

    Unlike antibiotics, which ‘poison’ bacteria, and can also affect healthy cells in the area, the SNAPPs that Lam has designed are so large that they don’t seem to affect healthy cells at all.

    “With this polymerised peptide we are talking the difference in scale between a mouse and an elephant,” Lam’s supervisor, Greg Qiao, told Marcus Strom from the Sydney Morning Herald. “The large peptide molecules can’t enter the [healthy] cells.”

    You can see the SNAPPs (green) surrounding and ripping apart bacterial cells below:


    While the results are positive so far, it’s too early to get excited about what this could mean for humans, says Cyrille Boyer from the University of New South Wales in Australia, who wasn’t involved in the research.

    “The main advantage seems to be they can kill bacteria more effectively and selectively [than other peptides]” Boyer told Strom, before adding that the team is a long way off clinical applications.

    But what’s awesome about the new project is that, while other teams are looking for new antibiotics, Lam has found a completely different approach. And it could make all the different in the coming ‘post-antibiotic world’.

    That’s what she’s hoping, anyway.

    “For a time, I had to come in at 4am in the morning to look after my mice and my cells,” she told The Telegraph. “I wanted to be involved in some kind of research that would help solve problems … I really hope that the polymers we are trying to develop here could eventually be a solution.”

    See the full article here .


    The University of Melbourne (informally Melbourne University) is an Australian public research university located in Melbourne, Victoria. Founded in 1853, it is Australia’s second oldest university and the oldest in Victoria. Times Higher Education ranks Melbourne as 33rd in the world, while the Academic Ranking of World Universities places Melbourne 44th in the world (both first in Australia).

    Melbourne’s main campus is located in Parkville, an inner suburb north of the Melbourne central business district, with several other campuses located across Victoria. Melbourne is a sandstone university and a member of the Group of Eight, Universitas 21 and the Association of Pacific Rim Universities. Since 1872 various residential colleges have become affiliated with the university. There are 12 colleges located on the main campus and in nearby suburbs offering academic, sporting and cultural programs alongside accommodation for Melbourne students and faculty.

    Melbourne comprises 11 separate academic units and is associated with numerous institutes and research centres, including the Walter and Eliza Hall Institute of Medical Research, Florey Institute of Neuroscience and Mental Health, the Melbourne Institute of Applied Economic and Social Research and the Grattan Institute. Amongst Melbourne’s 15 graduate schools the Melbourne Business School, the Melbourne Law School and the Melbourne Medical School are particularly well regarded.

    Four Australian prime ministers and five governors-general have graduated from Melbourne. Nine Nobel laureates have been students or faculty, the most of any Australian university

  • richardmitnick 4:59 pm on September 26, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , ,   

    From BNL: “Crystalline Fault Lines Provide Pathway for Solar Cell Current” 

    Brookhaven Lab

    September 26, 2016
    Karen McNulty Walsh
    (631) 344-8350
    Peter Genzer
    (631) 344-3174

    New tomographic AFM imaging technique reveals that microstructural defects, generally thought to be detrimental, actually improve conductivity in cadmium telluride solar cells.

    CFN staff scientist Lihua Zhang places a sample in the transmission electron microscope.

    A team of scientists studying solar cells made from cadmium telluride, a promising alternative to silicon, has discovered that microscopic “fault lines” within and between crystals of the material act as conductive pathways that ease the flow of electric current. This research—conducted at the University of Connecticut and the U.S. Department of Energy’s Brookhaven National Laboratory, and described in the journal Nature Energy—may help explain how a common processing technique turns cadmium telluride into an excellent material for transforming sunlight into electricity, and suggests a strategy for engineering more efficient solar devices that surpass the performance of silicon.

    “If you look at semiconductors like silicon, defects in the crystals are usually bad,” said co-author Eric Stach, a physicist at Brookhaven Lab’s Center for Functional Nanomaterials (CFN). As Stach explained, misplaced atoms or slight shifts in their alignment often act as traps for the particles that carry electric current—negatively charged electrons or the positively charged “holes” left behind when electrons are knocked loose by photons of sunlight, making them more mobile. The idea behind solar cells is to separate the positive and negative charges and run them through a circuit so the current can be used to power houses, satellites, or even cities. Defects interrupt this flow of charges and keep the solar cell from being as efficient as it could be.

    But in the case of cadmium telluride, the scientists found that boundaries between individual crystals and “planar defects”—fault-like misalignments in the arrangement of atoms—create pathways for conductivity, not traps.

    These CTAFM images show a cadmium telluride solar cell from the top (above) and side profile (bottom) with bright spots representing areas of higher electron conductivity. The images reveal that the conductive pathways coincide with crystal grain boundaries. Credit: University of Connecticut.

    Members of Bryan Huey’s group at the Institute of Materials Science at the University of Connecticut were the first to notice the surprising connection. In an effort to understand the effects of a chloride solution treatment that greatly enhances cadmium telluride’s conductive properties, Justin Luria and Yasemin Kutes studied solar cells before and after treatment. But they did so in a unique way.

    Several groups around the world had looked at the surfaces of such solar cells before, often with a tool known as a conducting atomic force microscope. The microscope has a fine probe many times sharper than the head of a pin that scans across the material’s surface to track the topographic features—the hills and valleys of the surface structure—while simultaneously measuring location-specific conductivity. Scientists use this technique to explore how the surface features relate to solar cell performance at the nanoscale.

    But no one had devised a way to make measurements beneath the surface, the most important part of the solar cell. This is where the UConn team made an important breakthrough. They used an approach developed and perfected by Kutes and Luria over the last two years to acquire hundreds of sequential images, each time intentionally removing a nanoscale layer of the material, so they could scan through the entire thickness of the sample. They then used these layer-by-layer images to build up a three-dimensional, high-resolution ‘tomographic’ map of the solar cell—somewhat like a computed tomography (CT) brain scan.

    Assembling the layer-by-layer CTAFM scans into a side-profile video file reveals the relationship between conductivity and planar defects throughout the entire thickness of the cadmium telluride crystal, including how the defects appear to line up to form continuous pathways of conductivity.Credit: University of Connecticut.

    “Everyone using these microscopes basically takes pictures of the ‘ground,’ and interprets what is beneath,” Huey said. “It may look like there’s a cave, or a rock shelf, or a building foundation down there. But we can only really know once we carefully dig, like archeologists, keeping track of exactly what we find every step of the way—though, of course, at a much, much smaller scale.”

    The resulting CT-AFM maps uniquely revealed current flowing most freely along the crystal boundaries and fault-like defects in the cadmium telluride solar cells. The samples that had been treated with the chloride solution had more defects overall, a higher density of these defects, and what appeared to be a high degree of connectivity among them, while the untreated samples had few defects, no evidence of connectivity, and much lower conductivity.

    Huey’s team suspected that the defects were so-called planar defects, usually caused by shifts in atomic alignments or stacking arrangements within the crystals. But the CTAFM system is not designed to reveal such atomic-scale structural details. To get that information, the UConn team turned to Stach, head of the electron microscopy group at the CFN, a DOE Office of Science User Facility.

    “Having previously shared ideas with Eric, it was a natural extension of our discovery to work with his group,” Huey said.

    Said Stach, “This is the exact type of problem the CFN is set up to handle, providing expertise and equipment that university researchers may not have to help drive science from hypothesis to discovery.”

    CFN staff physicist Lihua Zhang used a transmission electron microscope (TEM) and UConn’s results as a guide to meticulously study how atomic scale features of chloride-treated cadmium telluride related to the conductivity maps. The TEM images revealed the atomic structure of the defects, confirming that they were due to specific changes in the stacking sequence of atoms in the material. The images also showed clearly that these planar defects connected different grains in the crystal, leading to high-conductivity pathways for the movement of electrons and holes.

    “When we looked at the regions with good conductivity, the planar defects linked from one crystal grain to another, forming continuous pathways of conductance through the entire thickness of the material,” said Zhang. “So the regions that had the best conductivity were the ones that had a high degree of connectivity among these defects.”

    These transmission electron microscopy images taken at Brookhaven’s CFN reveals how the stacking pattern of individual atoms (bright spots) shifts. The images confirmed that the bright spots of high conductivity observed with CTAFM imaging at UConn occurred at the interfaces between two different atomic alignments (left) and that these “planar defects” were continuous between individual crystals, creating pathways of conductivity (right). The labels WZ and ZB refer to the two atomic stacking sequences “wurtzite” and “zinc blende,” which are the two types of crystal structures cadmium telluride can form. No image credit.

    The authors say it’s possible that the chloride treatment helps to create the connectivity, not just more defects, but that more research is needed to definitively determine the most significant effects of the chloride solution treatment.

    In any case, Stach says that combining the CTAFM technique and electron microscopy, yields a “clear winner” in the search for more efficient, cost-competitive alternatives to silicon solar cells, which have nearly reached their limit for efficiency.

    “There is already a billion-dollar-a-year industry making cadmium telluride solar cells, and lots of work exploring other alternatives to silicon. But all of these alternatives, because of their crystal structure, have a higher tendency to form defects,” he said. “This work gives us a systematic method we can use to understand if the defects are good or bad in terms of conductivity. It can also be used to explore the effects of different processing methods or chemicals to control how defects form. In the case of cadmium telluride, we may want to find ways to make more of these defects, or look for other materials in which defects improve performance.”

    This research was supported by the DOE Office of Energy Efficiency and Renewable Energy (EERE)—including its Sunshot Program—and the DOE Office of Science. The cadmium telluride samples were provided by Andrew Moore of Colorado State University.

    The University of Connecticut’s Institute of Materials Science serves as the heart of materials science research at the University of Connecticut, with a mission of supporting materials research and industry throughout Connecticut and the Northeast. It houses the research labs of more than 30 core faculty, with an overall membership of 120 UConn faculty whose work benefits from the available facilities and expertise.

    See the full article here .

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    BNL Campus

    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 4:34 pm on September 26, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , Neutron capture   

    From MSU: “Solving a heavy-duty mystery” 

    Michigan State Bloc

    Michigan State University

    Sept. 26, 2016
    Tom Oswald
    Sean Liddick

    To determine how the universe’s heavy elements – gold, silver and many others – came about, a team of international researchers is studying both the largest and smallest things known to us – stars and atoms.

    The team, led by scientists from Michigan State University, is providing critical data to computer models of what are known as stellar events – supernovas and neutron stars mergers, to be exact.

    By matching the computer models with real observations of these cataclysmic events, it could help answer one of astronomy’s most puzzling questions.

    A supernova is a star that, in its old age, collapses and then catastrophically explodes under its own weight; a neutron-star merger occurs when two of these small yet incredibly massive stars come together and spew out huge amounts of stellar debris.

    By conducting experiments in MSU’s National Superconducting Cyclotron Laboratory, the researchers were able to come a bit closer to determining what actually goes on during these stellar events, an important step in determining how heavy elements were formed.

    A technician works on equipment at the National Superconducting Cyclotron Laboratory at Michigan State University.

    What the researchers were looking at, at the atomic-sized level, is something called neutron capture. This is when an atom latches onto a neutron, increasing its mass number and helping it attain “heavy” status.

    The heavy elements produced in these processes have atomic numbers greater than 26. The atomic number is the number of protons in the nucleus of an atom.

    “What we’re trying to do is infer, or re-create, the probability of neutron capture, because it’s almost impossible to measure directly,” said Sean Liddick, an MSU associate professor with appointments in chemistry and the NSCL. “We want to match the theoretical models to the stellar observations.”

    Using a telescope, the observational astronomers were able to determine the amount of heavy elements in that spectrum. “Then,” said Liddick, “what you would like to be able to do is compare that to a theoretical prediction for what happens during these explosive events.

    “What we’re doing is trying to remove some of the uncertainty and build a better theoretical model.”

    The research is published in the journal Physical Review Letters. Liddick said this research is a harbinger of the work that will be done at the Facility for Rare Isotope Beams, currently under construction at MSU.

    “We’re laying the groundwork that will be significantly extended by the broader reach provided by FRIB,” he said.

    MSU is establishing FRIB as a new scientific user facility for the Office of Nuclear Physics in the U.S. Department of Energy Office of Science.

    Under construction on campus and operated by MSU, FRIB will enable scientists to make discoveries about the properties of rare isotopes in order to better understand the physics of nuclei, nuclear astrophysics, fundamental interactions, and applications for society, including in medicine, homeland security and industry.

    See the full article here .

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    Michigan State Campus

    Michigan State University (MSU) is a public research university located in East Lansing, Michigan, United States. MSU was founded in 1855 and became the nation’s first land-grant institution under the Morrill Act of 1862, serving as a model for future land-grant universities.

    MSU pioneered the studies of packaging, hospitality business, plant biology, supply chain management, and telecommunication. U.S. News & World Report ranks several MSU graduate programs in the nation’s top 10, including industrial and organizational psychology, osteopathic medicine, and veterinary medicine, and identifies its graduate programs in elementary education, secondary education, and nuclear physics as the best in the country. MSU has been labeled one of the “Public Ivies,” a publicly funded university considered as providing a quality of education comparable to those of the Ivy League.

    Following the introduction of the Morrill Act, the college became coeducational and expanded its curriculum beyond agriculture. Today, MSU is the seventh-largest university in the United States (in terms of enrollment), with over 49,000 students and 2,950 faculty members. There are approximately 532,000 living MSU alumni worldwide.

  • richardmitnick 3:49 pm on September 26, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , Researchers unlock coveted bond connection   

    From Princeton: “Researchers unlock coveted bond connection” 

    Princeton University
    Princeton University

    September 23 2016
    Tien Nguyen

    Researchers at Princeton University have introduced a long-awaited reaction capable of forming sp3-sp3 bonds whose presence increases a molecule’s complexity and its chances for clinical success as a drug candidate.

    Published in Nature, the study detailed a mild and general method to couple sp3 carbon atoms – carbon centers defined by that fact that only single bonds connect them to their neighbors. Until now, this coveted reaction had resisted chemists’ efforts, even eluding transition metal catalysis, a powerful field that has enabled a staggering range of coupling reactions over the past 50 years.

    General schematic of metallophotoredox catalyzed sp3-sp3 couplings

    “The reaction is a very unique way of approaching how you would join molecules together, and broadly expands the types of carbons you can connect,” said David MacMillan, the James S. McDonnell Distinguished University, Professor of Chemistry and corresponding author on the work.

    Their method revolves around the cooperation of two catalysts, a light-activated iridium catalyst and a nickel-based catalyst. Coined metallaphotoredox catalysis, this process circumvents roadblocks, such as undesired side reactions and an inability to form key intermediates, which had plagued other transition metal mediated attempts. Also, in contrast to previous, specialized versions of the reaction, the researchers’ strategy doesn’t require high temperatures, harsh basic compounds or additional zinc-based molecules.

    The reaction succeeds by enlisting the two catalysts to bring together the molecules forming either side of the final sp3-sp3 bond. The light-activated iridium catalyst converts the commercially available starting compound known as a carboxylic acid into a ready partner. This intermediate is intercepted by the nickel catalyst, which can then incorporate the other chemical partner, called an alkyl halide. Finally, the nickel catalyst excises itself from the compound, releasing the desired product and resetting the cycle.

    The team demonstrated the reaction’s generality as it proceeded smoothly with array of structurally diverse partners. Using this method, they also constructed the antiplatelet drug tirofiban in two steps from simple starting materials using their sp3-sp3 coupling reaction and another metallaphotoredox method recently developed in their lab. This example showcased the utility of their program for drug discovery though it holds potential for other industries as well.

    “That’s what we really care about – inventing reactions that people will use,” MacMillan said. “We really want to do things that are enabling to people all around the world who care about making molecules.”

    See the full article here .

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    Princeton University Campus

    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

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  • richardmitnick 8:41 am on September 26, 2016 Permalink | Reply
    Tags: Applied Research & Technology, Controllable light-emitting materials to advance light sensing and nano-medicine, , , Tokyo Tech   

    From Tokyo Tech: “Controllable light-emitting materials to advance light sensing and nano-medicine” 


    Tokyo Institute of Technology

    September 26, 2016
    No writer credit found

    Luminous bismuth: controllable light-emitting materials having the potential to advance high-intensity, light sensing and nano-medicine

    Scientists at Tokyo Tech have developed an approach to control the photoluminescence and solid-state emission of bismuth complexes by complexation with phenylazomethine dendrimers. This research
    [journal: Angewandte Chemie International Edition] not only sheds light on the structure of a rare, luminescent bismuth complex, but will also be used to advance the potential applications of luminous dendrimers, especially in light harvesting, sensing, electronics, photonics, and nano-medicine.

    Precise control of the photoluminescence, or light emission from matter after the absorption of photons, plays a considerable role in the advancement of various optical materials. Modification of the emission intensity, rather than the wavelength, presents a challenge for materials scientists, and simple strategies that can be used to control the intensity of phosphors are desired.

    The assembly of photoluminescent components within dendrimers, a class of synthetic polymers with branching, tree-like structures, may be a suitable method for controlling the emission intensity. However, the use of dendrimers as nano-capsules suffers from several drawbacks such as quenched luminescence due to high local concentrations of the phosphors, and controlling the number of phosphors within the dendrimer skeleton is difficult.

    To address these challenges, a group of scientists led by Kimihisa Yamamoto from the Laboratory for Chemistry and Life Science at Tokyo Institute of Technology developed luminous dendrimers with finely tunable optical properties using dendritic polyphenylazomethines (DPAs). Due to the electron donating ability of the phenylazomethines, the assembly of the metal ions could be controlled in a radial and stepwise fashion. The semi-rigid structure of the DPAs also allowed for the optical properties of the metal complexes to be maintained by preventing intermolecular electronic interactions. Thus, by careful selection of the ligand, the typical issues encountered with encapsulation of phosphors by dendrimers were overcome, and a new method to control emission intensity was achieved. In addition, the luminescence of the bismuth complexes could be switched on and off by the addition of a Lewis base or by redox control, owing to the reversible coordination bonds within the complexes. As such, Prof. Yamamoto and co-workers showed that the phenylazomethine-bismuth complexes are a new class of stimuli-responsive materials.

    Prof. Yamamoto and co-workers formed rare and functional photoluminescent dendrimers containing specific numbers of bismuth ions. The stimuli-responsive optical properties of the bismuth complexes, including the tunable emission intensity, are expected to be useful for the generation of novel sensors and optical standards. The results not only shed light on the structures of the novel bismuth complexes, but will also facilitate the future design of novel functional phosphors, which may have far-reaching applications in a variety of fields.

    Figure. Luminous phenylazomethine-bismuth complexes were precisely assembled in the dendrimer. The emission intensity of one molecular dendrimer could be controlled by the number of bismuth units. The dendrimer skeleton enabled solid-state emission and optical switching induced by chemical and electronic stimuli. No image credit.

    See the full article here .

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    Tokyo Tech is the top national university for science and technology in Japan with a history spanning more than 130 years. Of the approximately 10,000 students at the Ookayama, Suzukakedai, and Tamachi Campuses, half are in their bachelor’s degree program while the other half are in master’s and doctoral degree programs. International students number 1,200. There are 1,200 faculty and 600 administrative and technical staff members.

    In the 21st century, the role of science and technology universities has become increasingly important. Tokyo Tech continues to develop global leaders in the fields of science and technology, and contributes to the betterment of society through its research, focusing on solutions to global issues. The Institute’s long-term goal is to become the world’s leading science and technology university.

  • richardmitnick 8:16 am on September 26, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From Niels Bohr Institute: “Effective reflection of light for quantum technology” 

    Niels Bohr Institute bloc

    Niels Bohr Institute

    23 September 2016
    No writer credit found

    Quantum Technology: Light usually spreads out in all directions and when the light hits an object, it is reflected and is scattered even more. So light is normally quite uncontrollable. But researchers want to be able to control light all the way down to the atomic level in order to develop future quantum technologies. Researchers at the Niels Bohr Institute have therefore developed a new method where they create a very strong interaction between light and atoms, which means that the light can be controlled and reflected on a glass fiber. The results are published in the scientific journal, Physical Review Letters [link is below].

    The experiments are carried out in a glass chamber with an ultra thin optical glass fiber stretched across it. The optical glass fiber has a diameter of 500 nanometers – that is 1000 times smaller than the diameter of a strand of hair. In the glass chamber there is also a gas of caesium atoms, which is cooled down to 50 micro-degrees Kelvin, which is almost absolute zero at minus 273 degrees Celsius. Due to the ultracold temperature, the caesium atoms are almost motionless and they are held close to the surface of the glass fiber. Using laser light, the researchers can push the individual atoms a bit so that they are evenly spaced along the surface of the glass fiber.

    Mirror effect. “We now send laser light through the glass fiber. The light has a particular wavelength and when the fiber is thinner than the wavelength of the light, the light moves along the surface of the fiber, where the atoms sit in a row. When the light hits the first atom, a strong interaction is created between the light and the atom and the atom moves with the light wave. With the atom’s precise distance, which matches the wavelength of the light, you get a backwards reflection of the light,” explains Jürgen Appel, associate professor in the research group Quantop at the Niels Bohr Institute at the University of Copenhagen.

    He explains that it is this backward reflection that is so important. When the light hits the next atom in the row the same thing happens – and the next, and the next. For every time the light hits an atom, a small part of the light is reflected and sent backwards.
    “We have managed to divert more than 10 percent of the light. With only 1000 atoms, an interaction is created that is just as strong as a glass plate with billions of atoms. We have created a mirror that effectively reflects light and we can even turn it on and off,” says Jürgen Appel.

    Such an on/off mirror based on just a few atoms can be used to improve the interaction between individual atoms and the fiber-guided light and it can be developed to improve entangled quantum states in connection with captured atomic systems for future quantum technology.

    Link to the article in Physical Review Letters: http://physics.aps.org/articles/v9/109

    See the full article here .

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    Niels Bohr Institute Campus

    The Niels Bohr Institute (Danish: Niels Bohr Institutet) is a research institute of the University of Copenhagen. The research of the institute spans astronomy, geophysics, nanotechnology, particle physics, quantum mechanics and biophysics.

    The Institute was founded in 1921, as the Institute for Theoretical Physics of the University of Copenhagen, by the Danish theoretical physicist Niels Bohr, who had been on the staff of the University of Copenhagen since 1914, and who had been lobbying for its creation since his appointment as professor in 1916. On the 80th anniversary of Niels Bohr’s birth – October 7, 1965 – the Institute officially became The Niels Bohr Institute.[1] Much of its original funding came from the charitable foundation of the Carlsberg brewery, and later from the Rockefeller Foundation.[2]

    During the 1920s, and 1930s, the Institute was the center of the developing disciplines of atomic physics and quantum physics. Physicists from across Europe (and sometimes further abroad) often visited the Institute to confer with Bohr on new theories and discoveries. The Copenhagen interpretation of quantum mechanics is named after work done at the Institute during this time.

    On January 1, 1993 the institute was fused with the Astronomic Observatory, the Ørsted Laboratory and the Geophysical Institute. The new resulting institute retained the name Niels Bohr Institute.

  • richardmitnick 7:29 am on September 26, 2016 Permalink | Reply
    Tags: Applied Research & Technology, Bragg reflection, , , , world’s most ethereal mirrors – made of just 1000 or 2000 atoms   

    From COSMOS: “Physicists build mirrors from just 1,000 atoms” 

    Cosmos Magazine bloc


    26 September 2016
    Cathal O’Connell

    A conceptual drawing of how optical circuits may look in future computers. RICHARD KAIL/Getty Images

    Mirror, mirror in mid-air. Two independent teams of physicists have created the world’s most ethereal mirrors – made of just 1,000 or 2,000 atoms suspended in a vacuum.

    The mirrors are held in space like beads on a string. By controlling the spacing between the atoms, the physicists could make the strings reflect up to 75% of the light shone on them.

    The reflectivity can be switched rapidly on or off, just by applying a few bursts of light – so the new mirrors could be useful for controllably bouncing light around optical circuits. And because the atoms interact with one another as well as the light, the set-up might be useful for linking quantum bits (or “qubits”) together in a quantum computer.

    The mirrors were created by two independent groups, one in France and the other in Denmark. Both are described in the current issue of Physical Review Letters.

    In a regular mirror, such as a polished metal surface, light is reflected because it interacts with the cloud of unattached electrons floating free in the metal, causing them to wobble. These wobbling electrons then re-emit the light. (These electrons are also the reason metals conduct electricity, so that’s the connection between shininess and conductivity.)

    But the new mirrors use something called Bragg reflection, which is a bit different.

    As Australia-born British physicist William Lawrence Bragg discovered in 1912, light waves scattering off layers in a crystal are reinforced at certain angles – those where neighbouring light waves return in lock step.

    Building on this work, just three years later, Bragg and his dad, William Henry Bragg, won the Nobel Prize for physics for using X-rays to figure out the structure of crystals. This kicked off the whole field of X-ray crystallography – instrumental a few decades later in unravelling the double helix structure of DNA.

    But when the spacing between the crystal layers is just right, the scattering angle is 90 degrees and so the crystal strongly reflects the light back where it came from – a special case known as Bragg reflection.

    A schematic showing a Bragg diffraction – the usual scattering of light that occurs when two beams with identical wavelength and phase approach a crystalline solid and are scattered off two different atoms within it. The lower beam traverses an extra length of 2dsinθ. But when the angle θ of the light hitting the surface is 90°, the light is reflected straight back the way it came – a Bragg reflection. WIKIMEDIA COMMONS

    Whereas regular mirrors can reflect any visible wavelength (that’s why mirrors appear to have no “colour” of their own), a Bragg mirror only reflects one wavelength. So don’t expect to see yourself in one.

    But that’s no limitation for communications technology, or optical circuits, which involve shuttling around light of a single wavelength.

    In 2011, a German team managed to turn a cloud of cold atoms into a Bragg mirror. They crisscrossed beams of lasers to arrange the atoms of the cloud into a lattice with just the right spacing. Although they achieved 80% reflection, they needed 10 million atoms to do it.

    Now two teams have dramatically reduced the number of atoms needed to make a useful mirror. Instead of simply shining a beam of light into a cloud of atoms (as the German group did), the teams transmit light along microscopically thin optical fibres. Atoms precisely positioned next to the fibre do the reflecting.

    When light travels along very thin optical fibres, some of the light spills out forming a so-called evanescent field – you can picture the field as a glowing halo around the fibre.

    Because the light is intensely confined in this halo, the interaction with any nearby atoms is very strong. This means only 1,000 or so atoms are needed to achieve a reflection, versus tens of millions for the cloud situation.

    The groups created their strings of single atoms by holding them in place using a laser beam running parallel to the fibre, and just a few hundred nanometres away, via the optical tweezers effect.

    Each string was evenly spaced with atoms every few hundred nanometres and was about one millimetre long.

    The physicists then sent another beam of light along the fibre – and this one interacted with the string of atoms through the halo of its evanescent field. When the spacing between the atoms was tuned just right, the Bragg condition applied – and much of the light was reflected back along the fibre in the opposite direction.

    The Danish team could reflect about 10% of the light using a string of 1,300 caesium atoms. While the French team reflected 75% using 2,000 atoms, also of caesium. The increased reflectivity achieved by the French group was not just a factor of more atoms in a row, they also had better control over the positions of their atoms.

    The mirror could be rapidly disassembled and reassembled simply by knocking the atoms out of their ordered state, and then replacing them. This mirror switching mechanism could be very useful for making optical switches in light-based circuitry.

    Red light sent through an optical fibre is visible in the fibre segment that is just a few hundred nanometres in diameter in this Danish experiment. J. Appel / University of Copenhagen

    The atoms also interact with one another via the light field, and over quite a long range. This kind of interaction could be used to simulate less tangible quantum interactions, or even for linking quantum bits (or “qubits”) together in quantum computers.

    All these applications will need stronger interactions between the light and the atoms – in effect a reflectivity much closer to 100%.

    Both teams have some tricks up their sleeves to achieve this, such as using longer sections of very thin fibre, or by reshaping the surface of the fibre to increase the interaction.

    As Wolfgang Ketterle, a physicist in quantum optics at the Massachusetts Institute of Technology told the American Physical Society, these works represent “a major advance in engineering and controlling how atoms scatter light”.

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  • richardmitnick 7:04 am on September 26, 2016 Permalink | Reply
    Tags: Applied Research & Technology, Australian Centre for Quantum Computation and Communication Technology, , Michelle Simmons, , ,   

    From COSMOS: Women in STEM – “Michelle Simmons: a quantum queen” 

    Cosmos Magazine bloc


    26 September 2016
    Elizabeth Finkel

    Michelle Simmons is using a scanning tunnelling microscope (pictured behind her) to build silicon-based quantum devices atom by atom. Nic Walker / Fairfax Syndication

    Building a quantum computer is not for the faint-hearted. These blazingly fast machines could revolutionise computing by ripping through big data, improving everything from tracking financial markets to weather forecasting. But the technology requires shrinking computer bits to the size of an atom.

    And unlike the robust bits of your laptop, quantum bits or qubits are weird and fragile. Trying to corral them is like trying to harness a flock of butterflies.

    And then there is the competition: IBM, Google and Microsoft are all in the race.

    None of this fazes physicist Michelle Simmons. She is confident the team she leads – the Australian Centre for Quantum Computation and Communication Technology – can deliver the most reliable type of quantum computer ever emerge victorious. In their machine, the quixotic qubit is made of stable silicon.

    “I’m not out there to recreate Intel, but I honestly believe our devices will win in the long term,” she says. “They are the most reproducible ones that are out there.”

    Simmons’ audacity is paying off.

    This year the Australian Centre garnered A$45 million from the federal government and businesses. Backing the “space race of the century”, telecommunications company Telstra and the Commonwealth Bank each put in A$10 million; the federal government, A$25 million.

    The boost should allow the Australian team to shrink their timeline for building a 10-qubit processor from 10 to five years.

    They need to work fast: using different types of qubits, MIT and IBM already have a five-qubit processor, Google’s has nine, and Canadian company D-wave controversially boasts 1,000. The Australian team may be behind, but Simmons believes they will win the distance race.

    And she is not the only one.

    “I think in the long term, for any number of reasons silicon will be the winner,” says electrical engineer John Randall, president of Texas-based Zyvex labs, an atomic-scale manufacturing company. “Australia can be a big player.”

    The way Simmons sees it, she is tracking a path not unlike the one that conventional computers followed. It took about a decade to advance from the first transistor bit in 1947 to the first silicon chip. The Australian group achieved the first qubit in 2010; if they get to 10 bits in five years, they will be well on track.

    Simmons’ team is used to her blithe confidence. “Michelle is just mapping it out step by step,” says lab head Tony Raeside as he takes me on a tour through two floors of glass-walled, state-of-the-art rooms of the fabrication centre at University of New South Wales (UNSW). Some of the rooms are brand new – the first fruits of the new funds. The big contraptions, like steel monsters in glass enclosures, are scanning tunnelling electron microscopes (STMs). Like a blind person’s fingers scanning braille, their fine tips detect the contours of individual atoms.

    These finely tuned electron microscopes allow skilled operators like Simmons to fulfil a vision imagined 30 years ago by Nobel prize-winning physicist Richard Feynman: to sculpt matter atom by atom. They are also the key to making the silicon qubit.

    Many remain sceptical about the promise of quantum computing. But things are changing. Two years ago, Simmons was invited to give a tutorial at a satellite conference of the International Electronic Devices Meeting, the premier gathering for the electronics field. The organisers vetted every word of her talk to make sure it didn’t contain anything too mind-bending. They needn’t have worried. Her talk was a hit, and last December, they invited her back to give the keynote lecture.

    Simmons has always had an audacious streak. She tells a story about how, as an eight-year-old, she sat silently week after week watching her father, a high-ranking policeman in London, play chess with her elder brother. One day she asked her father if she could play. Her father reluctantly acquiesced and played without paying much attention – until she took his first pawn. By then it was too late. She checkmated him.

    Simmons’ mother was a bank manager, and her grandparents included diplomats and members of the military. She describes her family as “take-responsibility kind of people”. The family DNA also includes a sense of adventure. Her father would always tell her, “don’t take the easy route. Do the most challenging thing”.

    I am sitting opposite Simmons, now 49, in the Quad café on a sunny wintry day at UNSW. She has rushed in for a snatched lunch and is clad in her signature look of casual black, draped across her tall, solid frame. Her hair is short and practical; she wears no jewellery or make-up. There is a soft, gentle femininity about her. As we talk, I wait for a glimpse of the iron fist that must surely reside inside the velvet glove. Leading a team of brilliant physicists bent on world domination must take some doing.

    It was by popular demand that in 2010, 11 years after joining the group, Simmons became their leader, overseeing the entire consortium of 180 researchers from UNSW, University of Queensland, University of Melbourne, Griffith University and Australian National University. The UNSW headquarters hosts four scientific teams, each with its own research leader: Andrew Dzurak, Sven Rogge, Andrea Morello and Simmons. Like mountaineers navigating a maze of crevasses and cliffs, they are trying different paths but are united in their push to scale the peak of silicon-based computing. (See figure.)

    Cosmos Magazine / UNSW

    “The strength of our centre is that we have three parallel pathways marching forwards. Of course, we all love our own children, but we a have respect and regard for the others,” says Dzurak. Leadership here requires the ability to rally and unify the team while belaying your own rope.

    Simmons revels in the different strengths and perspectives of her colleagues. “Physicists have very unique ways of seeing the world,” she says. She also enjoys pushing them out of their comfort zones and seeing them scale new heights. The key to her leadership is her clarity of purpose. “I could always see the obvious way to go forward,” she says. There is the eight-year-old anticipating all the moves ahead. Only today, she is navigating her way through the chessboard of quantum computing.

    Qubits may be weird, but the day-to-day work of building one is very down to earth. The process starts with a commercial computer chip, a pure silicon crystal wafer about 3 millimetres by 10 millimetres, which is placed inside the ultra-high vacuum chamber of the STM. A trickle of hydrogen gas is bled into the chamber, coating the surface of the wafer with a mask of hydrogen one atom thick. Guided by a scan of the atomic landscape, the tip of the microscope probe becomes a nanoscale etching pen. By varying its voltage, it can be used to poke a single hole through the hydrogen mask or scratch out a line of millions of atoms.

    When phosphene gas seeps in, one phosphate atom will parachute into the hole to become the qubit, while others will fill the long scratch to become the wire that measures the qubit’s signal. Next, the crystal wafer is heated to 350 °C for one minute to bond the phosphate atoms. Then the crystal is coaxed to grow over its new components by sprinkling it with a light soot of silicon atoms – a technique known as epitaxy.

    Simmons pioneered this two-day, 25-step manufacturing technique. “Her ability to position atoms with this accuracy is unique,” says Klaus Ensslin, who heads the nanophysics lab at the Swiss research institute ETH in Zurich. Learning to master it is tough; typically it takes a student a half a year.

    Richard Feynman proposed a basic model for a quantum computer in 1982. The Caltech physicist had been part of the tail end of the quantum mechanics revolution that revealed how strange the universe was at the atomic scale. An electron or the nucleus of an atom has a magnetic orientation called “spin” and can exist in one of two spin states: up or down.

    But in the quantum world, the spins can also exist in these states at the same time. This phenomenon is termed “superposition”. Even more mind-bending, two electrons could influence each others’ spin even if they were at opposite ends of the universe. They were said to be “entangled”. Einstein referred to it as “spooky action at a distance”.

    It was these two properties, superposition and entanglement, that led Feynman to speculate that a quantum computer would be able to perform a massive number of calculations in parallel.

    The bits of a classical computer have a value of either 1 or 0 (because they either pass current or not). But a qubit would also have the value of 1 or 0 simultaneously. The long and short of this quantum logic is that hundreds of qubits are predicted to have the same crunching power as billions of classical bits.

    When it comes to problems that stump modern computers, such as finding the prime factors of huge numbers (the basis of encryption) or finding the optimum path between destinations from billions of possible ones, quantum computers would ace it. That’s why banks and companies that deal with vast databases are so keen on the technology.

    But for two decades, quantum computing remained stuck on the drawing board. Computing requires that calculations are done many times to correct errors. But that’s a problem for quantum computers because each time you read the result you influence it.

    In 1995 several people, including Peter Shor at Bell Labs in the US, figured out how to solve the error correction problem. Shor had also written an algorithm for a quantum computer to factorise prime numbers. Galvanised by the possibilities, labs around the world dove in to try to build a quantum computer. For qubits, MIT used ions trapped in a vacuum; IBM used tiny loops of superconducting metal; others tried quantum dots of gallium arsenide.

    The Australians tried something entirely different: silicon.

    Leading different routes to a silicon-based quantum computer (left to right): UNSW’s Sven Rogge, Andrea Morello, Michelle Simmons and Andrew Dzurak. UNSW

    There is an obvious question to be asked. If silicon really is the clear winner for reliable quantum computing, then why did Australia end up with it, and not MIT or IBM?

    Three things seem to have conspired to make Australia the germination ground: good timing, a core group of visionary physicists, and the exceptionally receptive environment of UNSW.

    Australian physicist Bob Clark founded the group in the late 1990s after returning from Oxford where he had helped pioneer low-dimensional physics. Advances in fabricating silicon and gallium arsenide crystals for the semiconductor industry, using extremely low temperatures and strong magnetic fields, were revealing remarkable new states of matter. So-called “electron gases” with novel behaviours lay between the layers of the crystals. Nobel prizes were awarded for those discoveries.

    To continue the work at UNSW, Clark established a silicon nanofabrication facility and the National Magnet Lab. His reputation attracted bright young physicists from around the world, including Andrew Dzurak, an Australian who had completed a PhD at Cambridge.

    Around 1996, Bruce Kane, a junior scientist from Bell Labs in the US arrived to work on the low-dimensional physics of gallium arsenide crystals. Clark also suggested that he try working with silicon.

    Months later, Kane appeared in Clark’s office bearing a hard-back notebook filled with calculations. In his spare time at UNSW, Kane had worked out a design for the basic elements of a quantum computer.

    Kane’s idea was entirely different from the other approaches in play. He conceived a way to make a qubit using the computer industry’s standard materials. Kane’s qubit would be a single phosphorous atom embedded in a silicon crystal. Because the phosphorous atom is very close in size to the silicon atom, it should cause minimal disturbance to the silicon crystal. Pure silicon, whose atomic nuclei have zero spin, would provide a noiseless background against which to read the spin of the phosphorous nucleus.

    By the time Kane was scribbling in his notebook, it was clear that noise was a limitation of other types of qubits; it was interfering with the ability of the qubit to hold its signal long enough to do some processing – its so-called “coherence” time. While other systems had coherence times of a 1,000th of a second or less, in theory silicon would provide the qubits with entire seconds to carry out its processing.

    Clark stayed up all night reading Kane’s paper. By morning it was clear to him this was a work of genius. It was also clear to him that he would move heaven and earth to bring the idea to fruition. The team filed a patent and published a paper in Nature in 1998. Physicists read it and were enthralled. But there weren’t many who were eager to give it a try.

    Manipulating single atoms to build the qubit was only the start. No-one knew how to read the spin signal of a single electron or nucleus; the available technologies read signals from a million of them.

    “It was a theory on paper but I never thought it would work,” recalls Ensslin.

    But there was one person who did. She was just a junior scientist at Cambridge, but she had a reputation as a world leader in fabricating quantum electronic devices. Dzurak, her former Cambridge colleague, had already regaled her with tales of sunny Sydney skies and the blues of Bondi Beach. In 1999, Simmons joined the budding group of UNSW visionaries.

    A chilled chamber cools the silicon qubits to 0.02 degrees above absolute zero, which allows information to be read and written onto them. Marcus Enno

    When Simmons arrived at UNSW, she was no stranger to daunting problems.

    She encountered one of the first as a 16-year‑old at a rough inner London comprehensive school. In her final two years, the school decided to road-test “independent learning”; it was so independent her class had no chemistry teacher. Most of her classmates failed the year. But Simmons unpacked boxes with the textbooks and chemistry experiments and figured out a DIY chemistry course. It was an experience that forged her signature trait: self-reliance. “ I still believe the best way you learn is by yourself,” she says.

    Years later, that self-reliance got her a dream collaboration with NASA while still working on her PhD. “I love everything space,” she says. Simmons was to test the potential of perfectly symmetrical 3-D crystals grown on the space shuttle to advance solar cell technology.

    But tragedy struck. In 1988, her supervisor, who was fond of taking a weekend swim between two bays in Northeast England, didn’t make it to the second bay. Simmons thought of moving on to another university but her supervisor’s wife entreated her to continue her husband’s work. She stayed. But then the space crystals didn’t cooperate – what came back on the shuttle was a sludge. Seeking help from other Durham professors, she took a different tack. It required combining cadmium sulphide and cadmium telluride – an unusual combination of a cubic and hexagonal crystal. The resultant material was superior to silicon, achieving a record efficiency for solar cells at that time.

    Her success took her to Cambridge, where her modest project was to build the world’s fastest transistor using crystals of gallium arsenide. Known as “the material of the future”, unlike silicon, it could be fabricated as a single crystal, not just in a horizontal layer but also the vertical layer, offering the possibility of 3-D computer chips.

    Simmons became a master fabricator. Even so, she struggled. Out of 10 chips, they all behaved differently. She could not see how the gallium arsenide crystal could ever be useful on an industrial scale or how it could deliver reproducible results as a qubit.

    But when Simmons read Kane’s paper, she sniffed a game-changer. And so when the call from UNSW came, she enthusiastically accepted. It was a place, she recalls, where “peoples’ eyes didn’t glaze over” at crazy ideas.

    Physicists say there is no way to underestimate the difficulty of what Simmons and the group have achieved so far. “All of our Australian friends are pioneers. They pushed this [silicon-based] technology when we gave up,” says Ensslin. But, he adds, “Michelle is truly courageous. She pushed through with amazing tenacity for 10 years”.

    Somehow, Simmons manages to have a life beyond work. She is the mother of three children, aged eight, 11 and 12. Her husband also has a high-powered career as an academic consultant. Her husband’s family makes it all possible, she says. Each time she gave birth, she moved into her husband’s family home for a couple of weeks. Now her kids are older, with different needs. “They are all terrific, but it doesn’t get any easier,” she says. The relentless travel is difficult, but “they believe what I am doing is important”, she adds.

    Her unwavering dedication has not gone unnoticed by the scientific community. Simmons has won a string of Australian and international awards. Last May, she received the prestigious Feynman prize. The judges credited her with creating “the new field of atomic electronics”.

    But Simmons spends little of her own time fabricating atomic electronics now. Her energies are directed towards leading the team’s ascent.

    There’s still a long distance to travel from two qubits to 10. And the pressure to deliver over the next five years is huge.

    Simmons is undaunted. Ever the policeman’s daughter, she remains focused, driven by a sense of responsibility and unafraid to face a challenge. “All my life, I’ve always thought, ‘well this is another little problem, this is what we’ve got to do’ and I’ve always wanted to get on with it,” she says. “It’s all working the way Bruce Kane imagined. That’s what gives me that audacity.”

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  • richardmitnick 7:36 am on September 24, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , Research at Princeton   

    From Research at Princeton: “New method identifies protein-protein interactions on basis of sequence alone (PNAS)” 

    Princeton University
    Princeton University

    September 23, 2016
    Catherine Zandonella, Office of the Dean for Research

    Researchers can now identify which proteins will interact just by looking at their sequences. Pictured are surface representations of a histidine kinase dimer (HK, top) and a response regulator (RR, bottom), two proteins that interact with each other to carry out cellular signaling functions. (Image based on work by Casino, et. al. credit: Bitbol et. al 2016/PNAS.)

    Genomic sequencing has provided an enormous amount of new information, but researchers haven’t always been able to use that data to understand living systems.

    Now a group of researchers has used mathematical analysis to figure out whether two proteins interact with each other, just by looking at their sequences and without having to train their computer model using any known examples. The research, which was published online today in the journal Proceedings of the National Academy of Sciences, is a significant step forward because protein-protein interactions underlie a multitude of biological processes, from how bacteria sense their surroundings to how enzymes turn our food into cellular energy.

    “We hadn’t dreamed we’d be able to address this,” said Ned Wingreen, Princeton University‘s Howard A. Prior Professor in the Life Sciences, and a professor of molecular biology and the Lewis-Sigler Institute for Integrative Genomics, and a senior co-author of the study with Lucy Colwell of the University of Cambridge. “We can now figure out which protein families interact with which other protein families, just by looking at their sequences,” he said.

    Although researchers have been able to use genomic analysis to obtain the sequences of amino acids that make up proteins, until now there has been no way to use those sequences to accurately predict protein-protein interactions. The main roadblock was that each cell can contain many similar copies of the same protein, called paralogs, and it wasn’t possible to predict which paralog from one protein family would interact with which paralog from another protein family. Instead, scientists have had to conduct extensive laboratory experiments involving sorting through protein paralogs one by one to see which ones stick.

    In the current paper, the researchers use a mathematical procedure, or algorithm, to examine the possible interactions among paralogs and identify pairs of proteins that interact. The method was able to correctly predict 93% of the protein-protein paralog pairs that were present in a dataset of more than 20,000 known paired protein sequences, without being first provided any examples of correct pairs.

    Interactions between proteins happen when two proteins come into physical contact and stick together via weak bonds. They may do this to form part of a larger piece of machinery used in cellular metabolism. Or two proteins might interact to pass a signal from the exterior of the cell to the DNA, to enable a bacterial organism to react to its environment.

    When two proteins come together, some amino acids on one chain stick to the amino acids on the other chain. Each site on the chain contains one of 20 possible amino acids, yielding a very large number of possible amino-acid pairings. But not all such pairings are equally probable, because proteins that interact tend to evolve together over time, causing their sequences to be correlated.

    The algorithm takes advantage of this correlation. It starts with two protein families, each with multiple paralogs in any given organism. The algorithm then pairs protein paralogs randomly within each organism and asks, do particular pairs of amino acids, one on each of the proteins, occur much more or less frequently than chance? Then using this information it asks, given an amino acid in a particular location on the first protein, which amino acids are especially favored at a particular location on the second protein, a technique known as direct coupling analysis. The algorithm in turn uses this information to calculate the strengths of interactions, or “interaction energies,” for all possible protein paralog pairs, and ranks them. It eliminates the unlikely pairings and then runs again using only the top most likely protein pairs.

    The most challenging part of identifying protein-protein pairs arises from the fact that proteins fold and kink into complicated shapes that bring amino acids in proximity to others that are not close by in sequence, and that amino-acids may be correlated with each other via chains of interactions, not just when they are neighbors in 3D. The direct coupling analysis works surprisingly well at finding the true underlying couplings that occur between neighbors.

    The work on the algorithm was initiated by Wingreen and Robert Dwyer, who earned his Ph.D. in the Department of Molecular Biology at Princeton in 2014, and was continued by first author Anne-Florence Bitbol, who was a postdoctoral researcher in the Lewis-Sigler Institute for Integrative Genomics and the Department of Physics at Princeton and is now a CNRS researcher at Universite Pierre et Marie Curie – Paris 6. Bitbol was advised by Wingreen and Colwell, an expert in this kind of analysis who joined the collaboration while a member at the Institute for Advanced Study in Princeton, NJ, and is now a lecturer in chemistry at the University of Cambridge.

    The researchers thought that the algorithm would only work accurately if it first “learned” what makes a good protein-protein pair by studying ones discovered in experiments. This required that the researchers give the algorithm some known protein pairs, or “gold standards,” against which to compare new sequences. The team used two well-studied families of proteins, histidine kinases and response regulators, which interact as part of a signaling system in bacteria.

    But known examples are often scarce, and there are tens of millions of undiscovered protein-protein interactions in cells. So the team decided to see if they could reduce the amount of training they gave the algorithm. They gradually lowered the number of known histidine kinase-response regulator pairs that they fed into the algorithm, and were surprised to find that the algorithm continued to work. Finally, they ran the algorithm without giving it any such training pairs, and it still predicted new pairs with 93 percent accuracy.

    “The fact that we didn’t need a gold standard was a big surprise,” Wingreen said.

    Upon further exploration, Wingreen and colleagues figured out that their algorithm’s good performance was due to the fact that true protein-protein interactions are relatively rare. There are many pairings that simply don’t work, and the algorithm quickly learned not to include them in future attempts. In other words, there is only a small number of distinctive ways that protein-protein interactions can happen, and a vast number of ways that they cannot happen. Moreover, the few successful pairings were found to repeat with little variation across many organisms. This it turns out, makes it relatively easy for the algorithm to reliably sort interactions from non-interactions.

    Wingreen compared this observation – that correct pairs are more similar to one another than incorrect pairs are to each other – to the opening line of Leo Tolstoy’s Anna Karenina, which states, “All happy families are alike; each unhappy family is unhappy in its own way.”

    The work was done using protein sequences from bacteria, and the researchers are now extending the technique to other organisms.

    The approach has the potential to enhance the systematic study of biology, Wingreen said. “We know that living organisms are based on networks of interacting proteins,” he said. “Finally we can begin to use sequence data to explore these networks.”

    The research was supported in part by the National Institutes of Health (Grant R01-GM082938) and the National Science Foundation (Grant PHY–1305525).

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  • richardmitnick 11:22 am on September 23, 2016 Permalink | Reply
    Tags: Applied Research & Technology, Fermions, , ,   

    From Research at Princeton: “Unconventional quasiparticles predicted in conventional crystals” 

    Princeton University
    Princeton University

    July 22, 2016 [Just appeared in social media.]
    No writer credit found

    Two electronic states known as Fermi arcs, localized on the surface of a material, stem out of the projection of a 3-fold degenerate bulk new fermion. This new fermion is a cousin of the Weyl fermion discovered last year in another class of topological semimetals. The new fermion has a spin-1, a reflection of the 3- fold degeneracy, unlike the spin-½ that the recently discovered Weyl fermions have. No image credit.

    An international team of researchers has predicted the existence of several previously unknown types of quantum particles in materials. The particles — which belong to the class of particles known as fermions — can be distinguished by several intrinsic properties, such as their responses to applied magnetic and electric fields. In several cases, fermions in the interior of the material show their presence on the surface via the appearance of electron states called Fermi arcs, which link the different types of fermion states in the material’s bulk.

    The research, published online this week in the journal Science, was conducted by a team at Princeton University in collaboration with researchers at the Donostia International Physics Center (DIPC) in Spain and the Max Planck Institute for Chemical Physics of Solids in Germany. The investigators propose that many of the materials hosting the new types of fermions are “protected metals,” which are metals that do not allow, in most circumstances, an insulating state to develop. This research represents the newest avenue in the physics of “topological materials,” an area of science that has already fundamentally changed the way researchers see and interpret states of matter.

    The team at Princeton included Barry Bradlyn and Jennifer Cano, both associate research scholars at the Princeton Center for Theoretical Science; Zhijun Wang, a postdoctoral research associate in the Department of Physics, Robert Cava, the Russell Wellman Moore Professor of Chemistry; and B. Andrei Bernevig, associate professor of physics. The research team also included Maia Vergniory, a postdoctoral research fellow at DIPC, and Claudia Felser, a professor of physics and chemistry and director of the Max Planck Institute for Chemical Physics of Solids.

    For the past century, gapless fermions, which are quantum particles with no energy gap between their highest filled and lowest unfilled states, were thought to come in three varieties: Dirac, Majorana and Weyl. Condensed matter physics, which pioneers the study of quantum phases of matter, has become fertile ground for the discovery of these fermions in different materials through experiments conducted in crystals. These experiments enable researchers to explore exotic particles using relatively inexpensive laboratory equipment rather than large particle accelerators.

    In the past four years, all three varieties of gapless fermions have been theoretically predicted and experimentally observed in different types of crystalline materials grown in laboratories around the world. The Weyl fermion was thought to be last of the group of predicted quasiparticles in nature. Research published earlier this year in the journal Nature (Wang et al., doi:10.1038/nature17410) has shown, however, that this is not the case, with the discovery of a bulk insulator which hosts an exotic surface fermion.

    In the current paper, the team predicted and classified the possible exotic fermions that can appear in the bulk of materials. The energy of these fermions can be characterized as a function of their momentum into so-called energy bands, or branches. Unlike the Weyl and Dirac fermions, which, roughly speaking, exhibit an energy spectrum with 2- and 4-fold branches of allowed energy states, the new fermions can exhibit 3-, 6- and 8-fold branches. The 3-, 6-, or 8-fold branches meet up at points – called degeneracy points – in the Brillouin zone, which is the parameter space where the fermion momentum takes its values.

    “Symmetries are essential to keep the fermions well-defined, as well as to uncover their physical properties,” Bradlyn said. “Locally, by inspecting the physics close to the degeneracy points, one can think of them as new particles, but this is only part of the story,” he said.

    Cano added, “The new fermions know about the global topology of the material. Crucially, they connect to other points in the Brillouin zone in nontrivial ways.”

    During the search for materials exhibiting the new fermions, the team uncovered a fundamentally new and systematic way of finding metals in nature. Until now, searching for metals involved performing detailed calculations of the electronic states of matter.

    “The presence of the new fermions allows for a much easier way to determine whether a given system is a protected metal or not, in some cases without the need to do a detailed calculation,” Wang said.

    Verginory added, “One can just count the number of electrons of a crystal, and figure out, based on symmetry, if a new fermion exists within observable range.”

    The researchers suggest that this is because the new fermions require multiple electronic states to meet in energy: The 8-branch fermion requires the presence of 8 electronic states. As such, a system with only 4 electrons can only occupy half of those states and cannot be insulating, thereby creating a protected metal.

    “The interplay between symmetry, topology and material science hinted by the presence of the new fermions is likely to play a more fundamental role in our future understanding of topological materials – both semimetals and insulators,” Cava said.

    Felser added, “We all envision a future for quantum physical chemistry where one can write down the formula of a material, look at both the symmetries of the crystal lattice and at the valence orbitals of each element, and, without a calculation, be able to tell whether the material is a topological insulator or a protected metal.”

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    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

    Princeton Shield

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