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  • richardmitnick 2:52 pm on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From Madison: “Sustainable Nanotechnology Center Lands New $20 Million Contract” 

    U Wisconsin

    University of Wisconsin

    Terry Devitt

    Two graduate students working with the Center for Sustainable Nanotechnology examine a vial in a chemistry laboratory

    The Center for Sustainable Nanotechnology, a multi-institutional research center based at the University of Wisconsin-Madison, has inked a new contract with the National Science Foundation (NSF) that will provide nearly $20 million in support over the next five years.

    Directed by UW-Madison chemistry Professor Robert Hamers, the center focuses on the molecular mechanisms by which nanoparticles interact with biological systems.

    Nanotechnology involves the use of materials at the smallest scale, including the manipulation of individual atoms and molecules. Products that use nanoscale materials range from beer bottles and car wax to solar cells and electric and hybrid car batteries. If you read your books on a Kindle, a semiconducting material manufactured at the nanoscale underpins the high-resolution screen.

    While there are already hundreds of products that use nanomaterials in various ways, much remains unknown about how these modern materials and the tiny particles they are composed of interact with the environment and living things.

    “The purpose of the center is to explore how we can make sure these nanotechnologies come to fruition with little or no environmental impact,” explains Hamers. “We’re looking at nanoparticles in emerging technologies.”

    In addition to UW-Madison, scientists from UW-Milwaukee, the University of Minnesota, the University of Illinois, Northwestern University and the Pacific Northwest National Laboratory have been involved in the center’s first phase of research. Joining the center for the next five-year phase are Tuskegee University, Johns Hopkins University, the University of Iowa, Augsburg College, Georgia Tech and the University of Maryland, Baltimore County.

    At UW-Madison, Hamers leads efforts in synthesis and molecular characterization of nanomaterials. Soil science Professor Joel Pedersen and chemistry Professor Qiang Cui lead groups exploring the biological and computational aspects of how nanomaterials affect life.

    Much remains to be learned about how nanoparticles affect the environment and the multitude of organisms — from bacteria to plants, animals and people — that may be exposed to them.

    “Some of the big questions we’re asking are: How is this going to impact bacteria and other organisms in the environment? What do these particles do? How do they interact with organisms?” says Hamers.

    For instance, bacteria, the vast majority of which are beneficial or benign organisms, tend to be “sticky” and nanoparticles might cling to the microorganisms and have unintended biological effects.

    “There are many different mechanisms by which these particles can do things,” Hamers adds. “The challenge is we don’t know what these nanoparticles do if they’re released into the environment.”

    To get at the challenge, Hamers and his UW-Madison colleagues are drilling down to investigate the molecular-level chemical and physical principles that dictate how nanoparticles interact with living things.

    Pedersen’s group, for example, is studying the complexities of how nanoparticles interact with cells and, in particular, their surface membranes.

    “To enter a cell, a nanoparticle has to interact with a membrane,” notes Pedersen. “The simplest thing that can happen is the particle sticks to the cell. But it might cause toxicity or make a hole in the membrane.”

    Pedersen’s group can make model cell membranes in the lab using the same lipids and proteins that are the building blocks of nature’s cells. By exposing the lab-made membranes to nanomaterials now used commercially, Pedersen and his colleagues can see how the membrane-particle interaction unfolds at the molecular level — the scale necessary to begin to understand the biological effects of the particles.

    Such studies, Hamers argues, promise a science-based understanding that can help ensure the technology leaves a minimal environmental footprint by identifying issues before they manifest themselves in the manufacturing, use or recycling of products that contain nanotechnology-inspired materials.

    To help fulfill that part of the mission, the center has established working relationships with several companies to conduct research on materials in the very early stages of development.

    “We’re taking a look-ahead view. We’re trying to get into the technological design cycle,” Hamers says. “The idea is to use scientific understanding to develop a predictive ability to guide technology and guide people who are designing and using these materials.”

    See the full article here.

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    In achievement and prestige, the University of Wisconsin–Madison has long been recognized as one of America’s great universities. A public, land-grant institution, UW–Madison offers a complete spectrum of liberal arts studies, professional programs and student activities. Spanning 936 acres along the southern shore of Lake Mendota, the campus is located in the city of Madison.

  • richardmitnick 2:38 pm on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , Help Conquer Cancer project,   

    From WCG: “Analyzing crystals to help fight cancer” 

    New WCG Logo

    28 Aug 2015
    Help Conquer Cancer research team

    Behind-the-scenes work continues on the Help Conquer Cancer project – the team is analyzing millions of protein crystallization images processed by World Community Grid volunteers, with the hope of finding patterns that will help researchers build better cancer screening tools.

    Dear World Community Grid volunteers:

    We continue to analyze the millions of protein-crystallization images that you processed as part of Help Conquer Cancer (HCC), with the end goal of gaining insight into the crystallization process. In turn, this will enable us to crystalize cancer and other disease-related proteins, determine their structure, function, and design drugs accordingly. We aim to identify non-trivial, interesting and ultimately useful patterns in this large and valuable data set.

    We strive to integrate more detailed data we have received from Hauptman Woodward Institute which will allow us to interpret patterns we are identifying and linking properties of proteins, conditions, and temporal data to specific images that were processed on World Community Grid. Work is ongoing, albeit more slowly at present, as the Post Doctoral Fellow working on the integration and data mining had to take a leave of absence to expand her teaching skills. Christian continues to dedicate some of his time to the HCC project, but also had to expand on the analysis and streamline infrastructure to support our Mapping Cancer Markers project.

    We have been working on some novel analysis angles with a visiting student from Denmark, and a new student is expected to start working on the project in the Fall 2015. We therefore expect to be able to give you more detailed results in the next HCC update, which we will provide in a few months.

    See more detail in the original article.

    See the full article here.

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    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.


    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding


    Computing for Sustainable Water

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation

    IBM – Smarter Planet

  • richardmitnick 2:26 pm on August 31, 2015 Permalink | Reply
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    From PNNL: “Oxygen: Not at All Random” 

    PNNL Lab

    July 2015

    Rejecting random diffusion, oxygen atoms create detailed architectures in uranium dioxide, radically altering our understanding of corrosion

    Oxygen atoms follow a set pattern in corroding uranium dioxide, the primary component of fuel rods in nuclear reactors, not random diffusion. Understanding this pattern opens new doors for controlling corrosion. Image by Cortland Johnson, PNNL.

    Results: Corrosion follows a different path when it comes to uranium dioxide, the primary component of the rods that power nuclear reactors, according to a new study by scientists at the Pacific Northwest National Laboratory, University of Chicago, and the Stanford Synchrotron Radiation Lightsource. In uranium dioxide, the oxygen atoms-key corrosion creators-do not diffuse randomly through the material. Rather, the oxygen atoms settle into the third, sixth, ninth, etc., layers. They space themselves within the layers and alter the structure by causing the layers of uranium atoms above and below to draw closer to the oxygen. The oxygen atoms essentially self-assemble into a highly structured array.

    Why It Matters: Oxygen’s interactions can extensively corrode materials, whether it is a car in a field or a fuel canister in a nuclear reactor. Under certain conditions, oxygen corrodes fuel rods and causes them to swell by more than 30 percent, creating problems during both routine operations and emergency situations. Also, this swelling can be a problem for long-term storage of nuclear waste. The study shows atomic-level changes counter to those shown by the classical diffusion model that states most of the oxygen atoms are near the surface. The new study gives scientists accurate information to understand the start of corrosion, possibly leading to new ways to avoid corrosion-related failures.

    See the full article here.

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    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.


  • richardmitnick 1:53 pm on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From Caltech: “New, Ultrathin Optical Devices Shape Light in Exotic Ways” 

    Caltech Logo

    Ker Than

    Schematic drawing of generation and focusing of radially polarized light by a metasurface. Credit: Dr. Amir Arbabi/Faraon Lab/Caltech

    Caltech engineers have created flat devices capable of manipulating light in ways that are very difficult or impossible to achieve with conventional optical components.

    The new devices are not made of glass, but rather of silicon nanopillars that are precisely arranged into a honeycomb pattern to create a “metasurface” that can control the paths and properties of passing light waves.

    These metasurface devices, described in a paper published online on August 31, 2015, in the journal Nature Nanotechnology, could lead to ultracompact optical systems such as advanced microscopes, displays, sensors, and cameras that can be mass-produced using the same photolithography techniques used to manufacture computer microchips.

    “Currently, optical systems are made one component at a time, and the components are often manually assembled,” says Andrei Faraon (BS ’04), an assistant professor of applied physics and materials science, and the study’s principal investigator. “But this new technology is very similar to the one used to print semiconductor chips onto silicon wafers, so you could conceivably manufacture millions of systems such as microscopes or cameras at a time.”

    Seen under a scanning electron microscope [SEM], the new metasurfaces that the team created resemble a cut forest where only the stumps remain. Each silicon stump, or pillar, has an elliptical cross section, and by carefully varying the diameters of each pillar and rotating them around their axes, the scientists were able to simultaneously manipulate the phase and polarization of passing light. Light is an electromagnetic field, and the field of single-color, or monochromatic, light oscillates at all points in space with the same frequency but varying relative delays, or phases.

    Scanning electron microscope

    Manipulating this relative delay, or phase, influences the degree to which a light ray bends, which in turn influences whether an image is in or out of focus.

    Polarization refers to the trajectory of the oscillations of the electromagnetic field at each point in space. Manipulating the polarization of light is essential for the operation of advanced microscopes, cameras, and displays; the control of polarization also enables simple gadgets such as 3-D glasses and polarized sunglasses.

    “Using our metasurfaces, we have complete control of the polarization and phase of light,” says study first author Amir Arbabi, a senior researcher at Caltech. “We can take any incoming light and shape its phase and polarization profiles arbitrarily and with very high efficiency.”

    While the same goal can be achieved using an arrangement of multiple conventional optical components such as glass lenses, prisms, spatial light modulators, polarizers, and wave plates, these many components lead to much bulkier systems. “If you think of a modern microscope, it has multiple components that have to be carefully assembled inside,” Faraon says. “But with our platform, we can actually make each of these optical components and stack them atop one another very easily using an automated process. Each component is just a millionth of a meter thick, or less than a hundredth of the thickness of a human hair. ”

    In addition to being compact, a metasurface device could manipulate light in novel ways that are very hard and sometimes impossible to do using current setups. For example, the Caltech team showed that one of their metasurfaces can project one image when illuminated by a horizontally polarized beam of light, and a different image when illuminated by a vertically polarized beam. “The two images will appear overlapped under illumination with light polarized at 45 degrees,” Faraon says.

    In another experiment, the team was able to use a metasurface to create a beam with radial polarization, that is, a beam whose polarization is pointing toward the beam axis. Such beams have doughnut-shaped intensity profiles and have applications in superresolution microscopy, laser cutting, and particle acceleration. “You generally would need a large optical setup, consisting of multiple components, to create this effect using conventional instruments,” Arbabi says. “With our setup, we can compress all of the optical components into one device and generate these beams with higher efficiency and more purity.”

    The team is currently working with industrial partners to create metasurfaces for use in commercial devices such as miniature cameras and spectrometers, but a limited number have already been produced for use in optical experiments by collaborating scientists in other disciplines.

    In addition, the Faraon lab current is investigating ways to combine different metasurfaces to create functioning optical systems and to correct for color distortions and other optical aberrations. “Like any optical system, you get distortions,” Faraon said. “That’s why expensive cameras have multiple lenses inside. Right now, we are experimenting with stacking different metasurfaces to correct for these aberrations and achieve novel functionalities.”

    The paper is entitled Dielectric metasurfaces for complete control of phase and polarization with sub wavelength spatial resolution and high transmission. In addition to Faraon and Arbabi, other Caltech coauthors include graduate student Yu Horie and Mahmood Bagheri, a microdevices engineer at JPL. The work was supported by the Caltech/JPL President’s and Director’s Fund and the Defense Advanced Research Projects Agency. Yu Horie was supported by the Department of Energy’s Energy Frontier Research Center program and a Japan Student Services Organization fellowship. The device nanofabrication was performed in the Kavli Nanoscience Institute at Caltech.

    See the full article here.

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
    Caltech buildings

  • richardmitnick 1:34 pm on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From phys.org: “Scientists ‘squeeze’ light one particle at a time” 


    August 31, 2015
    No Writer Credit

    An image from an experiment in the quantum optics laboratory in Cambridge. Laser light was used to excite individual tiny, artificially constructed atoms known as quantum dots, to create “squeezed” single photons. Credit: Mete Atature

    A team of scientists has successfully measured particles of light being “squeezed”, in an experiment that had been written off in physics textbooks as impossible to observe.

    Squeezing is a strange phenomenon of quantum physics. It creates a very specific form of light which is “low-noise” and is potentially useful in technology designed to pick up faint signals, such as the detection of gravitational waves.

    The standard approach to squeezing light involves firing an intense laser beam at a material, usually a non-linear crystal, which produces the desired effect.

    For more than 30 years, however, a theory has existed about another possible technique. This involves exciting a single atom with just a tiny amount of light. The theory states that the light scattered by this atom should, similarly, be squeezed.

    Unfortunately, although the mathematical basis for this method – known as squeezing of resonance fluorescence – was drawn up in 1981, the experiment to observe it was so difficult that one established quantum physics textbook despairingly concludes: “It seems hopeless to measure it”.

    So it has proven – until now. In the journal Nature, a team of physicists report that they have successfully demonstrated the squeezing of individual light particles, or photons, using an artificially constructed atom, known as a semiconductor quantum dot. Thanks to the enhanced optical properties of this system and the technique used to make the measurements, they were able to observe the light as it was scattered, and proved that it had indeed been squeezed.

    Professor Mete Atature, a Fellow of St John’s College at the University of Cambridge, who led the research, said: “It’s one of those cases of a fundamental question that theorists came up with, but which, after years of trying, people basically concluded it is impossible to see for real – if it’s there at all.”

    “We managed to do it because we now have artificial atoms with optical properties that are superior to natural atoms. That meant we were able to reach the necessary conditions to observe this fundamental property of photons and prove that this odd phenomenon of squeezing really exists at the level of a single photon. It’s a very bizarre effect that goes completely against our senses and expectations about what photons should do.”

    The left diagram represents electromagnetic activity associated with light at its lowest possible level, according to the laws of classical physics. On the right, part of the field has been reduced to lower than is technically possible, at the expense of making another part of the field less measurable. This effect is called “squeezing” because of the shape it produces. Credit: Mete Atature

    It begins with the fact that wherever there are light particles, there are also associated electromagnetic fluctuations. This is a sort of static which scientists refer to as “noise”. Typically, the more intense light gets, the higher the noise. Dim the light, and the noise goes down.

    But strangely, at a very fine quantum level, the picture changes. Even in a situation where there is no light, electromagnetic noise still exists. These are called vacuum fluctuations. While classical physics tells us that in the absence of a light source we will be in perfect darkness, quantum mechanics tells us that there is always some of this ambient fluctuation.

    “If you look at a flat surface, it seems smooth and flat, but we know that if you really zoom in to a super-fine level, it probably isn’t perfectly smooth at all,” Atature said. “The same thing is happening with vacuum fluctuations. Once you get into the quantum world, you start to get this fine print. It looks like there are zero photons present, but actually there is just a tiny bit more than nothing.”

    Importantly, these vacuum fluctuations are always present and provide a base limit to the noise of a light field. Even lasers, the most perfect light source known, carry this level of fluctuating noise.

    This is when things get stranger still, however, because, in the right quantum conditions, that base limit of noise can be lowered even further. This lower-than-nothing, or lower-than-vacuum, state is what physicists call squeezing.

    In the Cambridge experiment, the researchers achieved this by shining a faint laser beam on to their artificial atom, the quantum dot. This excited the quantum dot and led to the emission of a stream of individual photons. Although normally, the noise associated with this photonic activity is greater than a vacuum state, when the dot was only excited weakly the noise associated with the light field actually dropped, becoming less than the supposed baseline of vacuum fluctuations.

    Explaining why this happens involves some highly complex quantum physics. At its core, however, is a rule known as Heisenberg’s uncertainty principle. This states that in any situation in which a particle has two linked properties, only one can be measured and the other must be uncertain.

    In the normal world of classical physics, this rule does not apply. If an object is moving, we can measure both its position and momentum, for example, to understand where it is going and how long it is likely to take getting there. The pair of properties – position and momentum – are linked.

    In the strange world of quantum physics, however, the situation changes. Heisenberg states that only one part of a pair can ever be measured, and the other must remain uncertain.

    In the Cambridge experiment, the researchers used that rule to their advantage, creating a tradeoff between what could be measured, and what could not. By scattering faint laser light from the quantum dot, the noise of part of the electromagnetic field was reduced to an extremely precise and low level, below the standard baseline of vacuum fluctuations. This was done at the expense of making other parts of the electromagnetic field less measurable, meaning that it became possible to create a level of noise that was lower-than-nothing, in keeping with Heisenberg’s uncertainty principle, and hence the laws of quantum physics.

    Plotting the uncertainty with which fluctuations in the electromagnetic field could be measured on a graph creates a shape where the uncertainty of one part has been reduced, while the other has been extended. This creates a squashed-looking, or “squeezed” shape, hence the term, “squeezing” light.

    Atature added that the main point of the study was simply to attempt to see this property of single photons, because it had never been seen before. “It’s just the same as wanting to look at Pluto in more detail or establishing that pentaquarks are out there,” he said. “Neither of those things has an obvious application right now, but the point is knowing more than we did before. We do this because we are curious and want to discover new things. That’s the essence of what science is all about.”

    See the full article here.

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    About Phys.org in 100 Words

    Phys.org™ (formerly Physorg.com) is a leading web-based science, research and technology news service which covers a full range of topics. These include physics, earth science, medicine, nanotechnology, electronics, space, biology, chemistry, computer sciences, engineering, mathematics and other sciences and technologies. Launched in 2004, Phys.org’s readership has grown steadily to include 1.75 million scientists, researchers, and engineers every month. Phys.org publishes approximately 100 quality articles every day, offering some of the most comprehensive coverage of sci-tech developments world-wide. Quancast 2009 includes Phys.org in its list of the Global Top 2,000 Websites. Phys.org community members enjoy access to many personalized features such as social networking, a personal home page set-up, RSS/XML feeds, article comments and ranking, the ability to save favorite articles, a daily newsletter, and other options.

  • richardmitnick 10:28 am on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From Forbes: “What Has Quantum Mechanics Ever Done For Us?” 


    Forbes Magazine

    Aug 13, 2015
    Chad Orzel

    Intel Corp. CEO Paul Otellini show off chips on a wafer built on so-called 22-nanometer technology at the Intel Developers’ Forum in San Francisco, Tuesday, Sept. 22, 2009. Those chips are still being developed in Intel’s factories and won’t go into production until 2011. Each chip on the silicon “wafer” Otellini showed off has 2.9 billion transistors. (AP Photo/Paul Sakuma)

    In a different corner of the social media universe, someone left comments on a link to Tuesday’s post about quantum randomness declaring that they weren’t aware of any practical applications of quantum physics. There’s a kind of Life of Brian absurdity to posting this on the Internet, which is a giant world-spanning, life-changing practical application of quantum mechanics. But just to make things a little clearer, here’s a quick look at some of the myriad everyday things that depend on quantum physics for their operation.

    Computers and Smartphones

    At bottom, the entire computer industry is built on quantum mechanics. Modern semiconductor-based electronics rely on the band structure of solid objects. This is fundamentally a quantum phenomenon, depending on the wave nature of electrons, and because we understand that wave nature, we can manipulate the electrical properties of silicon. Mixing in just a tiny fraction of the right other elements changes the band structure and thus the conductivity; we know exactly what to add and how much to use thanks to our detailed understanding of the quantum nature of matter.

    Stacking up layers of silicon doped with different elements allows us to make transistors on the nanometer scale. Millions of these packed together in a single block of material make the computer chips that power all the technological gadgets that are so central to modern life. Desktops, laptops, tablets, smartphones, even small household appliances and kids’ toys are driven by computer chips that simply would not be possible to make without our modern understanding of quantum physics.

    Green LED lights and rows of fibre optic cables are seen feeding into a computer server inside a comms room at an office in London, U.K., on Tuesday, Dec. 23, 2014. Vodafone Group Plc will ask telecommunications regulator Ofcom to guarantee that U.K. wireless carriers, which rely on BT’s fiber network to transmit voice and data traffic across the country, are treated fairly when BT sets prices and connects their broadcasting towers. Photographer: Simon Dawson/Bloomberg

    Unless my grumpy correspondent was posting from the exact server hosting the comment files (which would be really creepy), odds are very good that comment took a path to me that also relies on quantum physics, specifically fiber optic telecommunications. The fibers themselves are pretty classical, but the light sources used to send messages down the fiber optic cables are lasers, which are quantum devices.

    The key physics of the laser is contained in a 1917 paper [Albert] Einstein wrote on the statistics of photons (though the term “photon” was coined later) and their interaction with atoms. This introduces the idea of stimulated emission, where an atom in a high-energy state encountering a photon of the right wavelength is induced to emit a second photon identical to the first. This process is responsible for two of the letters in the word “laser,” originally an acronym for “Light Amplification by Stimulated Emission of Radiation.”

    Any time you use a laser, whether indirectly by making a phone call, directly by scanning a UPC label on your groceries, or frivolously to torment a cat, you’re making practical use of quantum physics.

    Atomic Clocks and GPS

    One of the most common uses of Internet-connected smart phones is to find directions to unfamiliar places, another application that is critically dependent on quantum physics. Smartphone navigation is enabled by the Global Positioning System, a network of satellites each broadcasting the time. The GPS receiver in your phone picks up the signal from multiple clocks, and uses the different arrival times from different satellites to determine your distance from each of those satellites. The computer inside the receiver then does a bit of math to figure out the single point on the surface of the Earth that is that distance from those satellites, and locates you to within a few meters.

    This trilateration relies on the constant speed of light to convert time to distance. Light moves at about a foot per nanosecond, so the timing accuracy of the satellite signals needs to be really good, so each satellite in the GPS constellation contains an ensemble of atomic clocks. These rely on quantum mechanics– the “ticking” of the clock is the oscillation of microwaves driving a transition between two particular quantum states in a cesium atom (or rubidium, in some of the clocks).

    Any time you use your phone to get you from point A to point B, the trip is made possible by quantum physics.

    Magnetic Resonance Imaging

    Leila Wehbe, a Ph.D. student at Carnegie Mellon University in Pittsburgh, talks about an experiment that used brain scans made in this brain-scanning MRI machine on campus, Wednesday, Nov. 26, 2014. Volunteers where scanned as each word of a chapter of “Harry Potter and the Sorcerer’s Stone” was flashed for half a second onto a screen inside the machine. Images showing combinations of data and graphics were collected. (AP Photo/Keith Srakocic)

    The transition used for atomic clocks is a “hyperfine” transition, which comes from a small energy shift depending on how the spin of an electron is oriented relative to the spin of the nucleus of the atom. Those spins are an intrinsically quantum phenomenon (actually, it comes in only when you include special relativity with quantum mechanics), causing the electrons, protons, and neutrons making up ordinary matter behave like tiny magnets.

    This spin is responsible for the fourth and final practical application of quantum physics that I’ll talk about today, namely Magnetic Resonance Imaging (MRI). The central process in an MRI machine is called Nuclear Magnetic Resonance (but “nuclear” is a scary word, so it’s avoided for a consumer medical process), and works by flipping the spins in the nuclei of hydrogen atoms. A clever arrangement of magnetic fields lets doctors measure the concentration of hydrogen appearing in different parts of the body, which in turn distinguishes between a lot of softer tissues that don’t show up well in traditional x-rays.

    So any time you, a loved one, or your favorite professional athlete undergoes an MRI scan, you have quantum physics to thank for their diagnosis and hopefully successful recovery.

    So, while it may sometimes seem like quantum physics is arcane and remote from everyday experience (a self-inflicted problem for physicists, to some degree, as we often over-emphasize the weirder aspects when talking about quantum mechanics), in fact it is absolutely essential to modern life. Semiconductor electronics, lasers, atomic clocks, and magnetic resonance scanners all fundamentally depend on our understanding of the quantum nature of light and matter.

    But, you know, other than computers, smartphones, the Internet, GPS, and MRI, what has quantum physics ever done for us?

    See the full article here.

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  • richardmitnick 9:57 am on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From Cornell: “Antibody-making bacteria promise drug development” 

    Cornell Bloc

    Cornell University

    August 31, 2015
    Anne Ju

    Monoclonal antibodies, proteins that bind to and destroy foreign invaders in our bodies, routinely are used as therapeutic agents to fight a wide range of maladies including breast cancer, leukemia, asthma, arthritis, psoriasis, Crohn’s disease and transplant rejection. Humira, a treatment for arthritis and Crohn’s disease, was among the first lab-engineered antibody drugs.

    A general representation of the method used to produce monoclonal antibodies

    Typically, monoclonal antibodies are manufactured in animal cell lines, such as Chinese hamster ovary (CHO) cells, with long development times that can drive up cost. A team of Cornell chemical engineers and New England Biolabs scientists have devised a shortcut. They’ve done it using an engineered E. coli bacterium that carries machinery for human antibody production and can churn out complex proteins, including many of today’s blockbuster, life-saving antibody drugs, in as little as a week.

    A Nature Communications paper published Aug. 27 details the feat, led by co-senior author Matthew DeLisa, the William L. Lewis Professor of Engineering, and first author Michael-Paul Robinson, a graduate student in the field of chemical engineering. They worked with a team led by co-senior author Mehmet Berkmen, a staff scientist at New England Biolabs.

    The work built on a previously commercialized E. coli strain invented by Berkmen, called “SHuffle,” which could make shorter, simpler proteins such as antibody fragments that had less therapeutic value than their full-sized, monoclonal antibody counterparts. Now, the researchers report producing full-length antibodies using the specially engineered SHuffle bacterium, including ones that fight the avian flu virus, the anthrax pathogen Bacillus anthracis, and a replica of the therapeutic antibody Herceptin that is used to treat breast cancer.

    “We can engineer new antibodies in SHuffle almost as quickly as our bodies can. Customizing an antibody requires only simple edits to the bacterium’s DNA, which opens up a low-effort way to prototype new ideas for future therapeutics,” Berkmen said.

    The SHuffle bacterium harbors genetic modifications that allow it, unlike other bacteria, to assemble antibodies and other human proteins into their natural, functional shape. A unique aspect of the method is the “all-in-one-pot” manner in which the large, complicated antibody molecules are assembled, taking place exclusively in the cytoplasmic compartment of the bacterium.

    This method effectively bypasses some of the key bottlenecks in the multi-compartment biosynthesis inherent to such production hosts as CHO cells. Preliminary experiments indicate the SHuffle-made antibodies could be recognized by the human immune system as robustly as the originals.

    “We think this is going to be a very powerful way of biomanufacturing existing antibodies, or even developing entirely new ones from scratch, that is much faster than current methods,” DeLisa said.

    While immunotherapeutics invented in bacteria may one day become useful medicines, other uses may abound.

    “Many diagnostic tests, such as those performed on tumor biopsies, depend on finely-tuned antibodies,” DeLisa said. “Scientists also depend upon antibodies to make the molecular mechanics of living organisms visible, but sometimes they lack antibodies that work well enough for their experiments.”

    The paper is titled “Efficient expression of full-length antibodies in the cytoplasm of engineered bacteria,” and the work was supported by the National Institutes of Health, the Ford Foundation and the National Science Foundation.

    See the full article here.

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    Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

    Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

    On the Ithaca campus alone nearly 20,000 students representing every state and 120 countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

  • richardmitnick 9:43 am on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , , , Air Pollution   

    From MIT Tech Review: “How Artificial Intelligence Can Fight Air Pollution in China” 

    MIT Technology Review
    M.I.T Technology Review

    August 31, 2015
    Will Knight

    A woman wearing a face mask makes her way along a street in Beijing on January 16, 2014.

    IBM is testing a new way to alleviate Beijing’s choking air pollution with the help of artificial intelligence. The Chinese capital, like many other cities across the country, is surrounded by factories, many fueled by coal, that emit harmful particulates. But pollution levels can vary depending on factors such as industrial activity, traffic congestion, and weather conditions.

    The IBM researchers are testing a computer system capable of learning to predict the severity of air pollution in different parts of the city several days in advance by combining large quantities of data from several different models—an extremely complex computational challenge. The system could eventually offer specific recommendations on how to reduce pollution to an acceptable level—for example, by closing certain factories or temporarily restricting the number of drivers on the road. A comparable system is also being developed for a city in the Hebei province, a badly affected area in the north of the country.

    “We have built a prototype system which is able to generate high-resolution air quality forecasts, 72 hours ahead of time,” says Xiaowei Shen, director of IBM Research China. “Our researchers are currently expanding the capability of the system to provide medium- and long-term (up to 10 days ahead) as well as pollutant source tracking, ‘what-if’ scenario analysis, and decision support on emission reduction actions.”

    The project, dubbed Green Horizon, is an example of how broadly IBM hopes to apply its research on using advanced machine learning to extract insights from huge amounts of data—something the company calls “cognitive computing.” The project also highlights an application of the technology that IBM would like to export to other countries where pollution is a growing problem.

    IBM is currently pushing artificial intelligence in many different industries, from health care to consulting. The cognitive computing effort encompasses natural language processing and statistical techniques originally developed for the Watson computer system, which competed on the game show Jeopardy!, along with many other approaches to machine learning (see “Why IBM Just Bought Millions of Medical Images” and “IBM Pushes Deep Learning with a Watson Upgrade”).

    Predicting pollution is challenging. IBM uses data supplied by the Beijing Environmental Protection Bureau to refine its models, and Shen says the predictions have a resolution of a kilometer and are 30 percent more precise than those derived through conventional approaches. He says the system uses “adaptive machine learning” to determine the best combination of models to use.

    Pollution is a major public health issue in China, accounting for more than a million deaths each year, according to a study conducted by researchers at the University of California, Berkeley. It is also a major subject of public and political debate.

    China has committed to improving air quality 10 percent by 2017 through the Airborne Pollution Prevention and Control Action Plan. This past April, an analysis of 360 Chinese cities by the charity Greenpeace East Asia, based in Beijing, showed that 351 of them had pollution levels exceeding China’s own air quality standards, although levels had improved since the period 12 months before. The average level of airborne particulates measured was more than two and a half times the limit recommended by the World Health Organization.

    See the full article here.


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    The mission of MIT Technology Review is to equip its audiences with the intelligence to understand a world shaped by technology.

  • richardmitnick 9:31 am on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, , Photoactivated localization microscopy   

    From NYT: “Eric Betzig’s Life Over the Microscope” 

    New York Times

    The New York Times

    AUG. 28, 2015
    Claudia Dreifus

    Eric Betzig at the Janelia Research Campus of the Howard Hughes Medical Institute in Ashburn, Va. Credit Drew Angerer for The New York Times

    In October 2014, the Nobel Prize in Chemistry went to three scientists for their work developing a new class of microscopes that may well transform biological research by permitting researchers to observe cellular processes as they happen.

    One of the winners was Eric Betzig, 55, a group leader at the Janelia Research Campus of the Howard Hughes Medical Institute. On Friday, the journal Science published a paper by him and his colleagues describing a microscope powerful enough to observe living cells with unprecedented detail — a goal he and others have spent decades pursuing.

    I spoke with Dr. Betzig recently for three hours at his laboratory and office in Ashburn, Va., and again later by telephone. A condensed and edited version of the conversations follows.

    Q. What makes these microscopes different from those most researchers use in their laboratories today?

    A.The big problem with the standard optical microscope — that’s the one in most biology labs — is that they don’t magnify enough to see individual molecules inside a living cell. You can see a lot of detail, but it’s 100 times too corse for single molecules. With the more sophisticated electron microscope, you can get down to the molecular level. But to do that, you have to bombard your sample with so many electrons that you essentially fry it. This means you can’t see a living process in real time.

    What I and others have been trying to do is create microscopes that can image the building blocks within a cell. The goal is to link the fields of molecular and cellular biology, and thus unravel the mystery of how inanimate molecules come together to create life.

    Are you a biologist by trade?

    You know, I’m not comfortable with labels. I’m trained in physics but don’t think of myself as a physicist. I have a Nobel Prize in Chemistry, but I certainly don’t know any chemistry. I work all the time with biologists, but any biology I have is skin-deep. If there is one way I characterize myself, it’s as an inventor. My father is that, too. He spent his life inventing and making tools for the automotive industry. I grew up around inventors.

    When did the quest to build this microscope begin for you?

    I started working on this in 1982 as a grad student at Cornell. By 1992, I had my own lab at Bell Laboratories. There, I built what’s called a near-field microscope that worked, to a degree. But this instrument was still too difficult, slow and damaging to samples to be useful for biological research on live tissue. I became frustrated and quit both it and Bell Labs in 1994.

    Shortly after that, two experiments I’d done at Bell with this machine sparked the idea that I published in 1995 and that would eventually lead to photoactivated localization microscopy — PALM — 10 years later.

    Photoactivated localization microscopy — PALM

    Ten years? Why did it take that long?

    Well, for one thing, I went through a very depressing period after leaving Bell. My then-wife and I had just had a baby. I stayed home as a house husband, trying to figure out what to do next. Should I go to med school? Become a gourmet chef? I didn’t have any plan except to stop making microscopes.

    Astonishingly, a couple of months after quitting, an insight came to me about how to make the microscope finally work. It came while I was pushing my child’s stroller. The idea involved isolating individual molecules and measuring their distance. I wrote this up in a three-page paper, which would later be noted by the Nobel Committee as one reason for giving me the prize.

    Funny thing about that paper: It wasn’t much cited, probably only a hundred times in 20 years. That tells you something about the value of citations as a metric of impact.

    For the next eight years, I worked in private industry, and I discovered it was even harder to succeed there than in science.

    By 2004, I was in another personal crisis, and I looked up my best friend from the old days at Bell, Harald Hess. Harald had quit Bell a few years after I did. He was now working for a company that made equipment to test disk drives and was feeling unsatisfied. So we began trying to figure things out by taking trips to Yosemite and Joshua Tree and talking about what the hell we wanted to do with our lives.

    I started reading up on all the developments in microscopy of the past decade. And that led to us to building, in Harald’s living room, the microscope I’d envisioned while pushing my baby’s stroller — PALM.

    Were you pleased with what you built?

    To a point. PALM had the limitations I mentioned earlier. By 2008, I became bored and frustrated with it, and started working on other types of microscopes. By then, I was at Howard Hughes and could work on anything that interested me. Here I developed the lattice light sheet microscope, which can image living cells at unprecedented speeds and often with no damage. But its resolution level wasn’t any better than that of conventional microscopes.

    Lattice light sheet microscope

    I also worked on a highly advanced SIM microscope, which was begun by my Janelia colleague Mats Gustafsson, which would allow us to look at a sample in high resolution and at high speed. Mats occupied the office next to mine, and he was — I don’t say this lightly — one of the most brilliant people I’ve met. Unfortunately, he was diagnosed with a brain tumor after falling off his bike on the way to work in 2009, and died in 2011.

    When Mats died, there was still much work to be done to make his high-resolution form of SIM compatible with live imaging. After his death, I inherited much of his instrumentation and a few of his people. Since then, we’ve been working to make his higher-resolution instrument fast and noninvasive enough for live cells.

    We believe we’ve done it. The result is a paper published in Science. We finally have the tool to understand the cell and the dynamics of its full complexity.

    How has the Nobel affected your life?

    It’s disrupted my happy life quite a lot. I hate traveling, and you’re constantly asked to give talks. I’m in a second marriage. I have young children, ages 2 and 5. The emails, the travel have kept me away from the two things I love the most: my family and my work. However, this is a problem of my own making. I’m learning to say “no” more often.

    I mean, I’m a guy who’s always been insecure, O.K.? You do feel more confident. On the other hand, insecurity always made me productive. These days, I sometimes want to slap myself and say: “You gotta keep pushing. This isn’t the end. This is a chapter.”

    See the full article here.

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  • richardmitnick 8:33 am on August 31, 2015 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From COSMOS: “Fighting superbugs with supercomputers” 

    Cosmos Magazine bloc


    31 Aug 2015
    Viviane Richter

    Doctors need new ways to attack the antibiotic-resistant bacterium MRSA, shown here growing on a blood agar plate.Credit: By R Parulan Jr./getty images

    We’re losing the arms race against superbugs. Now with the aid of a supercomputer, Alan Grossfield at the University of Rochester is refining a new battlefield strategy. Instead of attacking their proteins, which bacteria can disguise, the new weapons attack the membrane which is much harder to hide. Grossfield and his team’s findings were published in Biophysical Journal in August.

    In this arms race “the cell membrane is like the final frontier”, says University of Queensland microbiologist Matt Cooper.

    Last year, the UK Review on Antimicrobial Resistance estimated that antibiotic resistant bacteria account for at least 700,000 deaths each year and could grow to 10 million worldwide by 2050. If we want to avoid entering a post-antibiotic era we need new armaments.

    Most antibiotics are designed to latch on to and deactivate a single protein target in the cell. Penicillin, for example, blocks an enzyme bacteria need to hold their cell wall together. However, bacteria can rapidly mutate these protein targets making them unrecognisable to the antibiotics.

    But bacteria are far less able to mutate the structure of their membranes; their basic life chemistry relies on it. So drugs that attack the bacterial membrane should be harder to beat.

    Tree frogs discovered this trick long ago. Their skin contains a host of antimicrobial and antifungal defences – including a group called lipopeptides that slice bacterial membranes, making them leaky. Medicinal chemists are now developing lipopeptides of their own, to be used as antimicrobial drugs. The first, daptomycin, is the only new antibiotic to be approved by the US Food and Drug Administration in the past 15 years.

    Researchers hope to make other lipopeptide drugs that are even more potent that daptomycin. The problem is that human cells also have membranes – so when designing membrane-slicing drugs, it’s important that bacteria remain their sole target. Grossfield looked more closely at one lipopeptide drug in development, already shown to clear bacterial infections in mice, in order to understand how the drug worked.

    Antimicrobial lipopeptides clump together in roughly spherical clusters known as micelles. They float through the bloodstream with their weapons hidden – like a Swiss army knife with all its blades folded away. Only when a clump reaches a target do the blades flip out to pierce the membrane.

    With the help of a supercomputer, Grossfield’s team simulated how the drug responded when stuck to a bacterial and mammalian membrane. This drug’s action takes less than 500th of a second, but the simulations took an entire year of number crunching.

    It turns out the drug has a slight positive charge. Luckily mammalian membranes are neutral, so the drug doesn’t stick. But bacterial membranes are negatively charged. Once stuck, the drug’s “blades” quickly flick out and slice into the membrane. The team found the drug stabbed bacterial membranes 50 orders of magnitude faster than mammalian membranes. “This was really cool,” Grossfield says.

    In this computer simulation, the lipopeptide cluster (green and yellow) sticks to the bacterium’s surface (blue), and then all of a sudden (12 seconds through the video) slices its way into the bacterium’s membrane. Credit: Dejun Lin, University of Rochester Medical Centre

    He also found there’s a sweet spot to the drug’s blade length. If they’re too long, they tend to get jammed in the clump. Too short, and they don’t inflict enough damage to kill the bacterium.

    He hopes his work will help chemists design better lipopeptides in the future: “I hope I can explain to the medicinal chemists what drug properties they should think about.”

    The new drugs will buy us more time, but even this strategy is not likely to last. Some bacteria have already found a defence against daptomycin, first membrane-stabbing drug, which was rolled out in 2003.

    Cooper believes over-prescription of antibiotics is the biggest contributor to resistance. But “attacking the membrane gives us more time”, he says. “We want to find drugs that give us a couple of decades.”

    See the full article here.

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