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  • richardmitnick 3:47 pm on August 30, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , kISMET,   

    From SURF: “kISMET taps into vast heat resources” 

    SURF logo
    Sanford Underground levels

    Sanford Underground Research facility

    August 30, 2016
    Constance Walter

    1
    Each kISMET drill hole is photographed and logged by lowering an optical televiewer. Credit: Matthew Kapust

    On the 4850 Level of Sanford Lab, scientists with kISMET (permeability (k) and Induced Seismicity Management for Energy Technologies) drilled and cored five 50-meter deep boreholes. Led by Curtis Oldenburg and Patrick Dobson of Lawrence Berkeley National Lab, the team is trying to better understand the relationship between the rock fabric and fracturing as a way to tap into and use the earth’s heat as an energy resource.

    “We hope to develop permeability enhancement techniques that can improve our ability to extract heat from geothermal reservoirs,” Oldenburg said. “The best way to engineer permeability is to fracture the rock.” These engineered geothermal systems are call Enhanced Geothermal Systems, or EGS.

    At about 4,000 miles below the surface, the Earth’s temperature is nearly that of the sun’s surface—9,932 degrees Fahrenheit. Closer to the surface, temperatures are dramatically cooler, but remain warm enough to be a potential source of renewable energy. According to the Department of Energy (DOE), EGS technology has the potential to access these vast resources of heat as a way to meet the energy needs of the United States.

    After drilling the boreholes, the kISMET team lowered an optical televiewer into each hole. A camera takes continuous photos of the borehole walls, which helps the scientists determine intervals to target for fracturing. Other tools are “parked” inside the boreholes to record and monitor several things.

    “Primarily, we want to understand the effects of the stress state, rock fabric and existing fractures in the rock,” Oldenburg said. The stress state controls the orientation and development of fractures, both natural and man made, while rock fabric refers to the non-isotropic character of the rock. The rock at Sanford Lab tends to have a fairly strong fabric, Oldenburg added, making it cleave, or split, along one plane.

    To create fractures within the borehole, scientists injected water at 4,000 psi. The key to extracting geothermal energy, Oldenburg said, is to create just the right amount of permeability to capture the heat—too much and the water won’t heat up during the flow from injection to production wells.

    “Our kISMET project will help inform how to develop EGS sites,” Oldenburg said.

    But the team is also looking to better understand seismicity within deep crystalline rock. “Induced seismicity, or fracturing, has become a serious issue in some parts of the country,” Oldenburg said. He credits that to the disposal water that is produced.

    “Through our highly controlled water injection experiments, we will be able to improve our ability to detect and locate microseismicity in deep crystalline rock.”

    See the full article here .

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    About us.
    The Sanford Underground Research Facility in Lead, South Dakota, advances our understanding of the universe by providing laboratory space deep underground, where sensitive physics experiments can be shielded from cosmic radiation. Researchers at the Sanford Lab explore some of the most challenging questions facing 21st century physics, such as the origin of matter, the nature of dark matter and the properties of neutrinos. The facility also hosts experiments in other disciplines—including geology, biology and engineering.

    The Sanford Lab is located at the former Homestake gold mine, which was a physics landmark long before being converted into a dedicated science facility. Nuclear chemist Ray Davis earned a share of the Nobel Prize for Physics in 2002 for a solar neutrino experiment he installed 4,850 feet underground in the mine.

    Homestake closed in 2003, but the company donated the property to South Dakota in 2006 for use as an underground laboratory. That same year, philanthropist T. Denny Sanford donated $70 million to the project. The South Dakota Legislature also created the South Dakota Science and Technology Authority to operate the lab. The state Legislature has committed more than $40 million in state funds to the project, and South Dakota also obtained a $10 million Community Development Block Grant to help rehabilitate the facility.

    In 2007, after the National Science Foundation named Homestake as the preferred site for a proposed national Deep Underground Science and Engineering Laboratory (DUSEL), the South Dakota Science and Technology Authority (SDSTA) began reopening the former gold mine.

    In December 2010, the National Science Board decided not to fund further design of DUSEL. However, in 2011 the Department of Energy, through the Lawrence Berkeley National Laboratory, agreed to support ongoing science operations at Sanford Lab, while investigating how to use the underground research facility for other longer-term experiments. The SDSTA, which owns Sanford Lab, continues to operate the facility under that agreement with Berkeley Lab.

    The first two major physics experiments at the Sanford Lab are 4,850 feet underground in an area called the Davis Campus, named for the late Ray Davis. The Large Underground Xenon (LUX) experiment is housed in the same cavern excavated for Ray Davis’s experiment in the 1960s.
    LUX/Dark matter experiment at SURFLUX/Dark matter experiment at SURF

    In October 2013, after an initial run of 80 days, LUX was determined to be the most sensitive detector yet to search for dark matter—a mysterious, yet-to-be-detected substance thought to be the most prevalent matter in the universe. The Majorana Demonstrator experiment, also on the 4850 Level, is searching for a rare phenomenon called “neutrinoless double-beta decay” that could reveal whether subatomic particles called neutrinos can be their own antiparticle. Detection of neutrinoless double-beta decay could help determine why matter prevailed over antimatter. The Majorana Demonstrator experiment is adjacent to the original Davis cavern.

    Another major experiment, the Long Baseline Neutrino Experiment (LBNE)—a collaboration with Fermi National Accelerator Laboratory (Fermilab) and Sanford Lab, is in the preliminary design stages. The project got a major boost last year when Congress approved and the president signed an Omnibus Appropriations bill that will fund LBNE operations through FY 2014. Called the “next frontier of particle physics,” LBNE will follow neutrinos as they travel 800 miles through the earth, from FermiLab in Batavia, Ill., to Sanford Lab.

    Fermilab LBNE
    LBNE

     
  • richardmitnick 12:28 pm on August 30, 2016 Permalink | Reply
    Tags: A Virtual Flight Through a Catalyst Particle Finds Evidence of Poisoning, Applied Research & Technology, Fluid catalytic cracking (FCC),   

    From SLAC: “A Virtual Flight Through a Catalyst Particle Finds Evidence of Poisoning” 


    SLAC Lab

    August 30, 2016

    At SLAC Synchrotron, Two X-ray Techniques Give a 3-D View of Why Catalysts Used in Gasoline Production Go Bad
    August 30, 2016


    This visualization of the experimental data shows how scientists mapped the distribution of chemical elements in a single fluid catalytic cracking (FCC) particle and merged it with structural information about the pore networks. Because of the high resolution at which they mapped the catalyst, they were able to look deep into the pores and learn more about the metal poisoning reaction. The changing colors of the “fog” inside the pores reflect the changing chemistry. (SLAC National Accelerator Laboratory)

    Merging two powerful 3-D X-ray techniques, a team of researchers from the Department of Energy’s SLAC National Accelerator Laboratory and Utrecht University in the Netherlands revealed new details of a process known as metal poisoning that clogs the pores of catalyst particles used in gasoline production, causing them to lose effectiveness.

    The team combined their data to produce a video that shows the chemistry of this aging process and takes the viewer on a virtual flight through the pores of a catalyst particle. The results were published today in Nature Communications.

    1
    This illustration depicts concentrations of chemical elements at five different points in a catalyst pore channel. The zigzag represents the pore channel, which was reconstructed from X-ray microscopy imaging. The colors show the chemical composition, detected with X-ray fluorescence. This information was combined in a model that simulates the aging of the catalyst pore network. (SLAC National Accelerator Laboratory)

    The particles, known as fluid catalytic cracking or FCC particles, are used in oil refineries to “crack” large molecules that are left after distillation of crude oil into smaller molecules, such as gasoline. Those oil molecules flow through the catalyst particles in tiny pores and passageways, which ensure accessibility to the active domains where chemical reactions can take place. But while the catalyst material is not consumed in the reaction and in theory could be recycled indefinitely, the pores clog up and the particles slowly lose effectiveness. Worldwide, about 400 reactor systems refine oil into gasoline, accounting for about 40 to 50 percent of today’s gasoline production, and each system requires 10 to 40 tons of fresh FCC catalysts daily.

    Finding new clues about how FCCs age out could be key to improving gasoline production. But the new technique also has potential for understanding the workings of materials for powering cars of the future, according to Yijin Liu, a lead author on the paper and staff scientist at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), a DOE Office of Science User Facility.

    SLAC SSRL Tunnel
    SLAC SSRL

    “The model we created by combining these two imaging methods can readily be applied to studies of rapid changes in the pore networks of similarly structured materials, such as batteries, fuel cells and underground geological formations,” he said.

    Two Perspectives Complete the Picture

    To design materials for tomorrow’s energy solutions, scientists must understand how they work at multiple scales invisible to the human eye.

    In a previous study at SSRL, the team took a series of two-dimensional images of catalyst particles at various angles and used software they developed to combine them into three-dimensional images of whole particles showing the distribution of elements in catalysts at various ages.

    For the new study, the researchers examined an FCC particle recovered from a refinery using two different 3-D X-ray imaging techniques at two experimental stations, or beamlines, at SSRL.

    One technique, called X-ray fluorescence, provided a detailed profile of the particle’s chemical elements. The other, X-ray transmission microscopy, captured the nanoscale structure of the particle, including fine details about the porous network where metal poisoning can best be observed.

    “The high-resolution microscopy data provided a map of the pores, and the high sensitivity of X-ray fluorescence showed us where metals in the refining fluids were poisoning the catalyst, which appeared as a colored fog in our visualization,” Liu said.

    The results of the study highlight the importance of having multiple techniques to study a single sample at a facility like SSRL. “There was a lot of development on the beamlines to make it possible to register the data in 3-D at this very fine scale,” Liu said. He heads up one of the two beamlines used in the research, which allows him to understand the strength and the limitations of both imaging methods.

    “Understanding catalyst performance requires interrogating catalyst function from multiple perspectives,” SSRL Director Kelly Gaffney said. “The results of this exciting research effort highlight the value of integrating disparate X-ray imaging methods to build a deeper understanding of materials function.”

    A Model for Understanding Material Dynamics

    Going beyond the observation of the experimental data visualized in the video, the scientists developed a model explaining how the accumulation of metals poisons the efficiency of the catalyst.

    “We used an analogy between electrical resistance and the degree of pore blockage, between two points in the particle using the new combined data. We then applied formulas well-known in electrical engineering to explain accessibility through the pore network, but also how it changes when metals are blocking pores,” said the study’s co-lead researcher Florian Meirer, assistant professor of inorganic chemistry and catalysis at Utrecht University.

    The resulting model simulates the aging of the catalyst, allows scientists to quantify this virtual aging, and helps them predict the collapse of its transportation network.

    “The model explains for the first time how this happens in a connective manner, which is a big step toward improving the design of such catalysts. Furthermore, this novel approach can be applied to a broad range of other materials that involve the transport of fluids or gases, such as battery electrodes,” said Bert Weckhuysen, professor of inorganic chemistry and catalysis at Utrecht University.

    Other researchers who contributed to this work were SSRL’s Courtney Krest and Samuel Webb. This work was supported by the NWO Gravitation program, Netherlands Center for Multiscale Catalytic Energy Conversion, and a European Research Council Advanced Grant.

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 11:33 am on August 30, 2016 Permalink | Reply
    Tags: 2016 Kavli Prize in Nanoscience: A Discussion with Gerd Binnig and Christoph Gerber, Applied Research & Technology, Atomic force microscope   

    From Kavli: “2016 Kavli Prize in Nanoscience: A Discussion with Gerd Binnig and Christoph Gerber” 

    KavliFoundation

    The Kavli Foundation

    08.20.16
    Alan Brown

    The 2016 Kavli Prize laureates discuss how the ability to see and manipulate single molecules and atoms has changed our view of the nanoscale world.

    THIRTY YEARS AGO, Gerd Binnig, Christoph Gerber and Calvin Quate began developing a device that would enable us to see features smaller than one nanometer–less than 1/50,000 the diameter of a human hair and far smaller than any traditional microscope could manage. Since then, their atomic force microscope, or AFM, has become one of the most important tools for understanding the nanoscale world. Researchers have used it for such wildly different tasks as unfolding proteins, watching chemical reactions as they occur, and arranging atoms to probe their quantum properties.

    4
    Atomic force microscope. yashvant

    This breakthrough device hinged on the ability to measure the forces exerted by individual atoms. The AFM did this with a design that very much resembled a record player. Both consist of a long arm, or cantilever, with a fine tip at the end. On a record player, the tip vibrates as it traces the grooves in a record, and electronics translate those vibrations into sound. On the AFM, the arm and tip are so fine, that the tip moves when attracted or repelled by individual atoms.

    For the invention and realization of atomic force microscopy, Binnig, Gerber and Quate received the 2016 Kavli Prize in Nanoscience. During a teleconference roundtable, the laureates discussed the joys of hard problems in science, and how AFM continues to change the way we see the world.

    Our roundtable panelists were:

    GERD BINNIG –is a physicist and Nobel Laureate for his invention (with Heinrich Rohrer and Christoph Gerber) of the scanning tunneling microscope while at IBM Zurich. He began development of the atomic force microscope in 1986 to overcome the limitations of his previous invention.
    CHRISTOPH GERBER –is a physicist and director for scientific communication at the Swiss Nanoscience Institute at the University of Basel. While at IBM, Gerber worked closely with Binnig on bringing both the scanning tunneling microscope and atomic force microscope to fruition.

    Calvin Quate was unable to participate in the roundtable. The transcript has been amended and edited by the laureates

    THE KAVLI FOUNDATION: You filed your first patent for the atomic force microscope (AFM) nearly 30 years ago. How has it changed the way we look at the world since then?

    GERD BINNIG: It was like the first time people looked through an optical microscope and saw bacteria. That completely changed how we look at the world. Suddenly, we understood what was really going on in nature, and we used that knowledge to learn how diseases spread. The AFM is the next step. It lets us look at the molecules that make life possible in those bacteria – and everywhere else – and see things we could not see before. It teaches us how to make changes to surfaces or molecules that we attempted blindly in the past. And it has been used in so many different scientific studies, from looking at polymers and chemical reactions to modifying surfaces at the atomic level.

    CHRISTOPH GERBER: As Gerd explained, seeing is believing, and now we can do that onthe atomic scale. AFM has turned into the most powerful and most versatile toolkit that we have for doing nanoscience. And it keeps evolving. In just the past few years, researchers have learned to pick up a molecule on the tip of an AFM, which we can think of as the needle on a record player, and reveal chemical bonds while imaging molecules on surfaces. Nobody thought that ever would be possible.

    TKF: Has this changed how researchers think about the ways nanoscale interactions affect the things they study?

    BINNIG: Very much so. Before AFM, people who wanted to model very small structures –molecules, cell walls, semiconductors – had to make indirect measurements of them. But those structures can be complex and disordered, and indirect measurements do not always capture that, so the models they came up with were often wrong. But now, we can look at those structures and adapt our models to match what we observe. We as scientists always have to connect our theories to reality. Atomic force microscopy lets us do this.

    TKF: When you started thinking about the AFM, biology was one of the fields you had inmind. Yet even you must have been surprised at how it has revolutionized biology.

    GERBER: Yes. AFM’s capabilities keep evolving, and researchers are always finding new ways to use it. For example, in recent years, researchers have made tremendous progress in taking AFM measurements in real time. It’s like watching a movie. They can now see biological interactions, such as how molecules degrade or how antimicrobials attack bacterial membranes as they occur – something nobody could have foreseen 20 years ago. It took 15 years to get there, but we can now see biology in action and compare that to our theories.

    BINNIG: Exactly. In biology, the biggest and most important question is always whether a molecule will bind to another molecule, change it, and by changing it cause something important to happen. This is all about forces, and researchers can use AFM to bring two molecules or even two cells close together, or pull them apart, and measure those forces directly. We can learn how big those forces are and under what conditions they occur. We’re actually looking into the heart of biology when we do that.

    GERBER: And atomic force microscopy can tell us about many different types of forces that determine the outcome of chemical reactions at the nanoscale. These range from chemical, mechanical and electrostatic through, most recently, to the very weak interactions between molecules.

    BINNIG: A great example of this is how Hermann Gaub, a professor of biophysics at Ludwig Maximilians University of Munich, used AFM to unfold proteins. He actually attached one end of a protein to a surface and the other end to an AFM tip. When he pulled the tip up, the protein straightened out and he could create a fingerprint of the unfolding forces that he could compare with his model.

    TKF: And does a more accurate model of how proteins are structured help design better medicines?

    BINNIG: Exactly. In the new field of immunotherapy, for example, we want to use molecules to bind to the surface of an immune cell and activate that cell so it attacks cancer. To do this, we need to know which molecules bind to the right molecule on the immune cell. So we’re back to the essential question, bind or not bind, and accurate models can help us answer that.

    GERBER: And that’s what I mean when I say that AFM has developed into this very versatile toolkit.

    TKF: Has that surprised you? You developed the microscope to measure surfaces at the atomic scale. Today we use it to push around atoms, quantify molecular forces and image high-speed chemical interactions. This has made it possible to measure the attraction between a protein and a cell wall, or construct devices for quantum computing. Did you see any of this coming?

    GERBER: Our sole idea in developing AFM was to image nonconductive surfaces, such as ceramics or biological materials, at atomic resolution by scratching a very fine needle on a long arm, or cantilever, over that surface. It was hard to foresee how people would pick up on this very simple idea to invent all these wonderful ways to answer difficult questions. And it happened so quickly. We came up with a very precise way to measure forces with that cantilever, and within just two or three years, someone figured out how to use a laser to get even better resolution. It took only five years until the first commercial instrument, and from there, there was no holding it back.

    TKF: What about you, Dr. Binnig? Were you surprised that scientists could manipulate something as small as an atom?

    BINNIG: Not really. In principle, once you can observe something with a tool, you’re usually in a position to change or modify it. A laser, for example, can measure a surface, but turn up the power and you destroy it. The same is true of AFM. In principle, this is something we thought about from the very beginning.

    TKF: What about applications you could not have foreseen?

    BINNIG: I could not have foreseen that we can image molecules with such a high resolution. It’s unbelievable. We can see the bonds between molecules. We can watch them change during a chemical reaction, and sometimes there are surprises. Some researchers have observed an intermediate state in a chemical reaction that should not have lasted long enough to see. So they have had to rethink their theories to take into account why this intermediate state lasted so long. That’s what happens when we can observe such high-resolution details.

    GERBER: Another example is high-speed AFM, which biologists use to see the cellular machinery in action. No other technique can do that. It works by tapping a very, very thin cantilever up and down, taking one quick measurement after another.

    BINNIG: It is amazing how many people use the AFM in so many different fields. We first thought, well, maybe biology or semiconductor research. But it was picked up everywhere, from studying friction to cosmetics.

    GERBER: I recently looked it up, and AFM was mentioned in 353,000 peer-reviewed papers. Our original article was published in Physical Review Letters, the top journal in the field in which all the important theoretical work is published. Ours is the only experimental paper on its list of most-cited papers.

    TKF: Amazing. And yet AFM was actually a follow-up to another technology you worked on, the scanning tunneling microscope, or STM. It was probably the first instrument to achieve nanoscale resolution without using electrons or other high-energy beams that can damage what you are observing, right?

    BINNIG: Yes.

    TKF: And where did that idea come from?

    1
    Using a form of atomic force microscopy, scientists can differentiate the chemical bonds in a single molecule of nanographene. (Credit: IBM)

    BINNIG: We were trying to solve a problem. IBM was working on a new type of semiconductor chip, and the insulator, which keeps the electric current from escaping the semiconductor, was leaking. But no one knew why. So Heinrich Rohrer, who was working at IBM Zurich, hired me. I looked to all the available instruments, and none of them could study materials on such a fine scale to find out.

    So the two of us thought, well, okay, we’ll invent something. We thought we could take advantage of something called quantum tunneling. Quantum tunneling is when an electron tunnels through a conducting material and come out the other side. We developed STM to map the surface of the material by measuring where electrons emerged on the other side. Only later did we realize that we could move our probe from one spot to cover the entire surface.

    TKF: Dr. Gerber, you quickly became part of the STM team. What convinced you to join?

    GERBER: I felt this was such a crazy idea, and I’m always very fond of this sort of thing. I thought this was fantastic.

    BINNIG: I can confirm this. Christoph always likes crazy things. That runs through his life.

    GERBER: Actually, the development of STM was kind of an undercover project at the beginning, because Gerd and Heinrich were involved in other projects. I worked for a year or so on my own. When we started overcoming problems and we could see features on the surface of a material that were one-tenth of a nanometer, then it really took off.

    BINNIG: Once you have the idea, it’s mainly technical problems that remain. We needed a team, and Christoph joined, fortunately. His very optimistic view of the world and his way of dealing with problems made him a very important member of this group.

    GERBER: Thank you, Gerd. I’ll take the flowers. I mean, it was fantastic. Those were high times when we succeeded, and that was really an unbelievable time in my life.

    TKF: Dr. Binnig, you and Heinrich Rohrer won a Nobel Prize for the scanning tunneling microscope in 1986. How did that change your research?

    BINNIG: For some time, I actually stopped working. I helped people apply the technology, gave presentations and traveled around the world many times. But after a while, I wanted to go back to the lab. I learned to be really cruel and say, “No.” So it was painful because people didn’t like that, and would come back to me again and again. But then the Nobel Prize got helpful, because I could get more support for a project, or ask other scientists for help from any place in the world.

    TKF: How about you, Dr. Gerber? You were also part of the STM team.

    GERBER: Heinrich and Gerd deserved it. Gerd, for me, is a genius, and I’ve never worked with anybody in my life that has such high standards.

    BINNIG: Now I’m taking the flowers.

    GERBER: I mean it, you know. He has a crazy mind, you see, and that’s why I like it so much. Gerd can anticipate things, even if they are not in his field, and he is so quick in understanding what’s happening. In America, you would say, “He’s awesome!” We worked together for 10 years, and I have to admit that it was the most fruitful and fantastic time in my life.

    BINNIG: Those 10 years were fantastic, and they included our work on the AFM.

    TKF: So let’s get back to the atomic force microscope. Its predecessor only worked with conductive materials, such as metals and semiconductors. That was a problem, so how did you come up with a way to see living organisms, biomolecules, plastics, ceramics and a lot of other materials?

    2
    This year, using atomic force microscopy, researchers measured van der Waals forces – very weak attractive or repulsive forces – between individual atoms for the first time. (Credit: University of Basel, Department of Physics

    BINNIG: I thought, in principle, why do we need to have an electrical current and measure electrons? Why can’t we just measure the forces between an atom sitting on a surface and an atom sitting on the tip of a probe? Physically, it would look a lot like what we were already doing with scanning tunneling microscopy. The question was whether it was possible to measure something as small as the forces between two atoms.

    TKF: This was in 1986 and, both of you had moved to California. Dr. Gerber, you were at IBM’s Almaden Lab in San Jose. Dr. Binnig, you were working at nearby Stanford University with Calvin Quate, the third recipient of this year’s Kavli Prize in Nanoscience. How did that come about?

    BINNIG: I was actually working quite intensively with Calvin Quate’s group. He invited me to California and gave me a visiting professorship for one-and-a-half years.

    GERBER: Cal Quate had an interesting background. He was also working on microscopes, and had developed a way to use sound to achieve much better resolution than any optical microscope. But when he heard about the scanning tunneling microscope, he flew to Switzerland to visit us, and then redirected his group to begin looking at scanning tunneling microscopy. So we were very well acquainted with him and his work.

    BINNIG: I have to say that he put together a wonderful group. He was a perfect scientific manager. The atmosphere he created in his group was something I’ve never seen before at a university. If one of the team members discovered something or got some nice results, all the others gathered around and wanted to know everything about it. They were all really happy for this one person. There was no jealousy. Zero, zero jealousy. Just a real team. I’ve never seen something like that again.

    GERBER: It was just a fantastic group. And they worked in what is presumably the more American way of doing things, taking on high-risk stuff. They liked that. The European way of looking at things is usually more cautious.

    TKF: So Professor Quate was also doing advanced work in atomic-scale microscopy. Did you initially discuss your ideas about the AFM with Professor Quate?

    BINNIG: Yes, and with Christoph, too. We concluded that maybe it was actually doable, so Christoph and the rest of us started to build a system.

    TKF: So you had this great idea. How did you turn your concept into reality?

    BINNIG: We needed to build a cantilever, so Christoph and I went to a music store and bought a diamond-tipped record player needle. We took it back to the lab and smashed the tip with a hammer to get these tiny specks of diamond. We glued one of them on top of a very thin gold foil to create a little cantilever. That was the first atomic force microscope. Soon after that, Cal Quate and his team used advanced fabrication techniques to make a very sharp tip that came to a very, very small point.

    3
    The design of an atomic force microscope resembles that of a record player. Both consist of a long arm, or cantilever, with a sharp tip at the end, which gathers information about the surface of a material. (Credit: GFDL, CC-BY-SA-3.0)

    GERBER: Yes, using Quate’s tip gave us the first hint that we could get atomic resolution, though it was not yet true atomic resolution. That came later.

    TKF: Not many universities had the ability to machine such fine parts in the 1980s, did they?

    BINNIG: Cal had good foresight and understood that things had to get smaller, and he was actually building scanning tunneling microscopes on semiconductor chips when we began working with him.

    GERBER: Exactly. Cal had built up his capabilities to make very small devices. This enabled him to build AFM arms, which must be thin enough to bend and have a sharp tip to measure atomic forces.

    TKF: There were so many technical challenges. Did you ever get frustrated?

    GERBER: When it didn’t work, we went out and played a round of golf.

    BINNIG: That’s true. Actually, we never got too frustrated with each other or the rate of progress because so many exciting things were happening. There were moments when everything went wrong, but that’s part of the game. It’s like soccer. When somebody scores against you, it’s frustrating for the moment. But then you try hard to turn the game around. It’s also like that in science.

    GERBER: Gerd knows this because we had a soccer team at IBM, and he was the most gifted forward on this planet. He could use both his legs equally well, and this was mindboggling because his opponents never knew which way he would pass. He was fantastic. We did all kinds of things beside trying to do very good science, you know. It was a fantastic time.

    TKF: Did you find those breaks helped when you were struggling with a problem?

    BINNIG: When I’m running or playing football, I’m focused on something. But sometimes, when I’m just doing nothing, lying on the couch, for instance, that’s a creative situation because I’m not focused on anything. The ideas flow by themselves because I don’t have control. That is a good time to come up with something new, at least for me.

    TKF: How about you, Dr. Gerber?

    GERBER: Sometimes that’s true, but other times I get ideas when I really work at it. Working on both instruments, the STM and the AFM, was really a day and night job. We spent so many nights in the lab it was unbelievable, but we had to do it to find a way forward. You know, there are some people, in my opinion, who are afraid of their own courage. They have this great idea, but they are maybe afraid to do the step-by-step work to prove their principles. Yet they still try to turn their idea into a Ferrari, and are surprised that it doesn’t work. By proving those principles systematically, I was better prepared to struggle with the inevitable technical problems.

    TKF: Clearly, your work on the atomic force microscope changed how other scientists explore and understand everything that happens at the nanoscale. How about yourselves? Are you still working with AFM or are you doing different things now?

    BINNIG: I like to do different things from time to time. So 16 years ago, I founded a company that develops software that makes computers a little bit more intelligent. We call it e-cognition, and it is similar to what IBM calls cognitive computing. Our software automatically analyzes medical images. Specifically, we have the computer look at tissue samples from cancer patients and try to predict the best kind of treatment. So in this respect, I’m doing something similar to Christoph, who also moved into medicine. Though I am planning to retire soon, and so maybe I will move back to AFM.

    GERBER: Hopefully.

    BINNIG: I’m thinking about it, yes, I’m really thinking about it.

    GERBER: It’s about time, Gerd, it’s about time.

    BINNIG: Yeah, we’ll be doing something. I missed you.

    TKF: And how about you, Dr. Gerber?

    GERBER: My group at the Swiss Nanoscience Institute is using AFM to study mutations of cancer patients in order to improve diagnosis and treatment. Our system uses arrays of AFM to scan RNA, the chain-like molecule that translates DNA into proteins, and look for mutations, or even fractional mutations where only an atom or two are in the wrong positions. Doctors can use this information to plan treatments for their specific type of cancer. It took us 16 years to get this technology into clinical trials, but we can make our diagnosis in less than one day compared with existing methods that take more than one week.

    BINNIG: So, in principle, Christoph and myself, we ended up in the same spot. We started with atomic-scale imaging and now we are both trying to diagnose cancer patients. It’s quite a coincidence.

    TKF: So, final question. It’s been 30 years since you started working on AFM. In all that time, what is the most surprising thing you’ve learned?

    GERBER: It goes back to what I said before, the AFM keeps evolving. The atomic resolution, the ability to see atoms and the bonds between them, the ability to see chemical reactions happen in real time – this is all just simply fantastic. It just keeps getting better and better.

    BINNIG: For me, there are two aspects. One is that AFM is used so widely in so many different fields. I never imagined that would happen. And two, as Christoph says, it keeps getting better and better, and shows us more and more. That, I think, is a surprise to me.

    See the full article here .

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    The Kavli Foundation, based in Oxnard, California, is dedicated to the goals of advancing science for the benefit of humanity and promoting increased public understanding and support for scientists and their work.

    The Foundation’s mission is implemented through an international program of research institutes, professorships, and symposia in the fields of astrophysics, nanoscience, neuroscience, and theoretical physics as well as prizes in the fields of astrophysics, nanoscience, and neuroscience.

     
  • richardmitnick 6:49 am on August 30, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , Parkinson’s disease,   

    From U Cambridge: “Tiny changes in Parkinson’s protein can have “dramatic” impact on processes that lead to the disease” 

    U Cambridge bloc

    Cambridge University

    30 Aug 2016
    Tom Kirk
    tdk25@cam.ac.uk

    1
    Image of “amyloid fibrils”; thread-like structures which form after the protein alpha-synuclein aggregates. Plaques (protein deposits) consisting of this protein have been found in the brains of Parkinson ’s Disease patients and linked to disease. Credit: Patrick Flagmeier

    In a new study, a team of academics at the Centre for Misfolding Diseases, in the Department of Chemistry at the University of Cambridge, show that tiny changes in the amino acid sequence of the protein alpha-synuclein can have a dramatic effect on microscopic processes leading to its aggregation that may occur in the brain, eventually resulting in someone being diagnosed with Parkinson’s Disease.

    Alpha-synuclein is a protein made up of 140 amino acids, and under normal circumstances plays an important part in helping with the smooth flow of chemical signals in the brain.

    Parkinson’s Disease is thought to arise because, for reasons researchers still do not fully understand, the same protein sometimes malfunctions. Instead of adopting the specific structural form needed to do its job, it misfolds and begins to cluster, creating toxic, thread-like structures known as amyloid fibrils. In the case of Parkinson’s Disease, these protein deposits are referred to as Lewy-bodies.

    The new study examined mutated forms of alpha-synuclein which have been found in people from families with a history of Parkinson’s Disease. In all cases, these mutations involved just one change to the protein’s amino acid sequence.

    Although the differences in the sequence are small, the researchers found that they can have a profound effect on how quickly or slowly fibrils start to form. They also found that the mutations strongly influence a process called “secondary nucleation”, in which new fibrils are formed, in an auto-catalytic manner, at the surface of existing ones and thus enable the disease to spread.

    The study stresses that these findings do not explain why humans get the disease. Parkinson’s Disease does not always emerge as a result of the mutations and has multiple, complex causes, which are not fully understood.

    Patrick Flagmeier, a PhD student at St John’s College, University of Cambridge, and the study’s lead author, said: “As a finding, it helps us to understand fundamental things about the system by which this disease emerges. In the end, if we can understand all of this better, that can help us to develop therapeutic strategies to confront it. Our hope is that this study will contribute to the global effort towards comprehending why people with these mutations get the disease more frequently, or at a younger age.”

    Although people who do not have mutated forms of alpha-synuclein can still develop Parkinson’s Disease, the five mutations studied by the research team were already known as “familial” variants – meaning that they recur in families where the disease has emerged, and seem to increase the likelihood of its onset.

    What was not clear, until now, is why they have this effect. “We wanted to know how these specific changes in the protein’s sequence influence its behaviour as it aggregates into fibrils,” Flagmeier said.

    To understand this, the researchers conducted lab tests in which they added each of the five mutated forms of alpha-synuclein, as well as a standard version of the protein, to samples simulating the initiation of fibril formation, their growth and their proliferation.

    The first round of tests examined the initiation of aggregation, using artificial samples recreating conditions in which misfolded alpha-synuclein attaches itself to small structures that are present inside brain cells called lipid vesicles, and then begins to cluster.

    The researchers then tested how the different versions of the protein influence the ability of pre-formed fibrils to extend and grow. Finally, they tested the impact of mutated proteins on secondary nucleation, in which, under specific conditions, the fibrils can multiply and start to spread.

    Overall, the tests revealed that while the mutated forms of alpha-synuclein do not notably influence the fibril growth, they do have a dramatic effect on both the initial formation of the fibrils, and their secondary nucleation. Some of the mutated forms of the protein made these processes considerably faster, while others made it almost “undetectably slow”, according to the researchers’ report.

    “We have only recently discovered the autocatalytic amplification process of alpha-synuclein fibrils, and the results of the present study will help us to understand in much more detail the mechanism behind this process, and in what ways it differs from the initial formation of aggregates.” said Dr. Alexander Buell, one of the senior authors on the study.

    Why the mutations have this impact remains unclear, but the study opens the door to understanding this in detail by identifying, for the first time, that they have such a dramatic impact on very particular stages of the process.

    Dr. Céline Galvagnion, another of the senior authors on the study, said: “This study quantitatively correlates individual changes in the amino acid sequence of alpha-synuclein with its tendency to aggregate. However, the effect of these mutations on other parameters such as the loss of the protein’s function and the efficiency of clearance of alpha-synuclein needs to be taken into account to fully understand the link between the familial mutations of alpha-synuclein and the onset of Parkinson’s Disease.”

    “The effects we observed were changes of several orders of magnitude and it was unexpected to observe such dramatic effects from single-point mutations,” Flagmeier said. “It seems that these single-point mutations in the sequence of alpha-synuclein play an important role in influencing particular microscopic steps in the aggregation process that may lead to Parkinson’s Disease.”

    The full study, which also involves Professors Chris Dobson and Tuomas Knowles, is published in the journal, Proceedings of the National Academy of Sciences.

    Reference:

    Flagmeier, P. et. al: Mutations associated with familial Parkinson’s disease alter the initiation and amplification steps of α-synuclein aggregation. PNAS (2016): DOI: 10.1073/pnas.1604645113

    See the full article here .

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    The University of Cambridge (abbreviated as Cantab in post-nominal letters) is a collegiate public research university in Cambridge, England. Founded in 1209, Cambridge is the second-oldest university in the English-speaking world and the world’s fourth-oldest surviving university. It grew out of an association of scholars who left the University of Oxford after a dispute with townsfolk. The two ancient universities share many common features and are often jointly referred to as “Oxbridge”.

    Cambridge is formed from a variety of institutions which include 31 constituent colleges and over 100 academic departments organised into six schools. The university occupies buildings throughout the town, many of which are of historical importance. The colleges are self-governing institutions founded as integral parts of the university. In the year ended 31 July 2014, the university had a total income of £1.51 billion, of which £371 million was from research grants and contracts. The central university and colleges have a combined endowment of around £4.9 billion, the largest of any university outside the United States. Cambridge is a member of many associations and forms part of the “golden triangle” of leading English universities and Cambridge University Health Partners, an academic health science centre. The university is closely linked with the development of the high-tech business cluster known as “Silicon Fen”.

     
  • richardmitnick 5:55 am on August 30, 2016 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From UCLA: “UCLA researchers develop method to speed up detection of infectious diseases, cancer” 

    UCLA bloc

    UCLA

    August 26, 2016
    Matthew Chin

    1
    UCLA researchers were able to use a molecular chain reaction to detect the presence of proteins in blood and plasma in a way that is faster and simpler.

    A team of UCLA researchers has found a way to speed and simplify the detection of proteins in blood and plasma opening up the potential for diagnosing the early presence of infectious diseases or cancer during a doctor’s office visit. The new test takes about 10 minutes as opposed to two to four hours for current state-of-the-art tests.

    The new approach overcame several key challenges in detecting proteins that are biomarkers of disease. First, these proteins are often at low abundance in body fluids and accurately identifying them requires amplification processes. The current approach uses enzymes to amplify the signal from proteins. However, enzymes can break down if they are not stored at proper temperatures. Also, to avoid a false positive, excess enzymes need to be washed away. This increases the complexity and cost of the test.

    The study, which included researchers from the Henry Samueli School of Engineering and Applied Science, the California NanoSystems Institute, and the David Geffen School of Medicine, was published online in the journal ACS Nano.

    The researchers included lead author Donghyuk Kim, a UCLA post-doctoral researcher in bioengineering and Dino Di Carlo, professor of bioengineering. They collaborated with Aydogan Ozcan, Chancellor’s Professor of Electrical Engineering and Bioengineering and Omai Garner, assistant professor of pathology and medicine at the David Geffen School of Medicine at UCLA.

    The UCLA team devised an approach to amplify a protein signal without any enzymes, thus eliminating the need for a complex system to wash away excess enzymes, and that would work only in the presence of the target protein. This new approach made use of a molecular chain reaction that was strongly triggered only in the presence of a target protein.

    The molecular chain reaction is driven by a cycle of DNA binding events. The process begins with a DNA key divided into two parts. If the target protein is present, the two parts bind together to form a DNA complex. The formation of the DNA complex generates DNA signaling molecules, which in turn generates the same DNA complex, leading to more signaling molecules, thus propagating repeated cycles.

    “By cutting the DNA ‘key’ into two parts, we found that each part could not catalyze or ‘open’ the reaction separately, but only when a protein acted as glue — essentially bridging the parts together, does the DNA key became functional again,” said Kim, a member of Di Carlo’s laboratory.

    The UCLA team’s findings build on previous work that employed this enzyme-free mechanism of nucleic acid amplification to detect DNA.

    “Unlike previous approaches to achieve an amplified readout of proteins, such as the proximity ligation assay, this approach does not require multiple enzymes, longer polymerization-based enzymatic reactions, or temperature control to amplify signal,” Di Carlo said. “In fact the new assay operates at room temperature and achieves results in about 10 minutes.”

    The team demonstrated the approach with two target proteins — streptavidin, widely used as a test protein for new diagnostic assays, and influenza nucleoprotein, which is a protein associated with the influenza virus.

    In the long term the team aims to combine the technique with portable readers that could be particularly beneficial in clinics in resource-poor areas.

    “Because the technique requires fewer steps than other assays, it can have a significant impact on distributed diagnostics and public health reporting, especially in combination with cost-effective portable and networked reader technology that our lab is developing,” Ozcan said.

    The team demonstrated a synergistic handheld microplate reader suitable for protein diagnostic assays based on a cellphone’s optical and computational systems earlier this year.

    Garner, who is also the associate director of the clinical microbiology lab at UCLA Health, emphasized the broad application of the technique. “Although demonstrated initially in detecting protein associated with flu, we envision the approach can be generalized to a range of protein biomarkers associated with infectious diseases and cancer,” said Garner. He noted it could be configured to detect diseases such as Zika or Ebola.

    The researchers emphasized that additional work is required to adapt the assay to complex clinical samples that may have other interfering compounds, and further optimization of the reagents for the assay can enhance performance.

    This interdisciplinary work was supported through a team science grant from the National Science Foundation Emerging Frontiers in Research and Innovation program.

    See the full article here .

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    UC LA Campus

    For nearly 100 years, UCLA has been a pioneer, persevering through impossibility, turning the futile into the attainable.

    We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

    This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

     
  • richardmitnick 7:39 pm on August 29, 2016 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From SLAC: “Poof! The Weird Case of the X-ray that Came Out Blank” 


    SLAC Lab

    August 29, 2016

    A ‘Nonlinear’ Effect that Seemingly Turns Materials Transparent is Seen for the First Time in X-rays at SLAC’s LCLS

    1
    An illustration shows what happens in a typical experiment with SLAC’s LCLS X-ray laser, top, versus what happened in this study with an especially intense X-ray pulse. Normally the X-ray pulses — which are shown coming in from the right — scatter off electrons in a sample and produce a pattern in a detector. But when researchers cranked up the intensity of the X-ray pulses, the pulses seemed to go straight through the sample, as if it were not there, and the pattern in the detector vanished. Two recent papers describe and explain this surprising result, which is due to a ‘nonlinear’ effect where particles of X-ray light team up to cause unexpected things to happen. (SLAC National Accelerator Laboratory)

    Imagine getting a medical X-ray that comes out blank – as if your bones had vanished. That’s what happened when scientists cranked up the intensity of the world’s first X-ray laser, at the Department of Energy’s SLAC National Accelerator Laboratory, to get a better look at a sample they were studying: The X-rays seemed to go right through it as if it were not there.

    This result was so weird that the leader of the experiment, SLAC Professor Joachim Stöhr, devoted the next three years to developing a theory that explains why it happened. Now his team has published a paper in Physical Review Letters describing the 2012 experiment for the first time.

    What they saw was a so-called nonlinear effect where more than one photon, or particle of X-ray light, enters a sample at the same time, and they team up to cause unexpected things to happen.

    “In this case, the X-rays wiggled electrons in the sample and made them emit a new beam of X-rays that was identical to the one that went in,” said Stöhr, who is an investigator with the Stanford Institute for Materials and Energy Sciences at SLAC. “It continued along the same path and hit a detector. So from the outside, it looked like a single beam went straight through and the sample was completely transparent.”

    This effect, called “stimulated scattering,” had never been seen in X-rays before. In fact, it took an extremely intense beam from SLAC’s Linac Coherent Light Source (LCLS), which is a billion times brighter than any X-ray source before it, to make this happen.

    SLAC/LCLS
    SLAC/LCLS

    A Milestone in Understanding How Light Interacts with Matter

    The observation is a milestone in the quest to understand how light interacts with matter, Stöhr said.

    “What will we do with it? I think we’re just starting to learn. This is a new phenomenon and I don’t want to speculate,” he said. “But it opens the door to controlling the electrons that are closest to the core of atoms ­– boosting them into higher orbitals, and driving them back down in a very controlled manner, and doing this over and over again.”

    Nonlinear optical effects are nothing new. They were discovered in the1960s with the invention of the laser – the first source of light so bright that it could send more than one photon into a sample at a time, triggering responses that seemed all out of proportion to the amount of light energy going in. Scientists use these effects to shift laser light to much higher energies and focus optical microscopes on much smaller objects than anyone had thought possible.

    The 2009 opening of LCLS as a DOE Office of Science User Facility introduced another fundamentally new tool, the X-ray free-electron laser, and scientists have spent a lot of time since then figuring out exactly what it can do. For instance, a SLAC-led team recently published [Nature Physics] the first report of nonlinear effects produced by its brilliant pulses.

    “The X-ray laser is really a quantum leap, the equivalent of going from a light bulb to an optical laser,” Stöhr said. “So it’s not just that you have more X-rays. The interaction of the X-rays with the sample is very different, and there are effects you could never see at other types of X-ray light sources.”

    “The X-ray laser is really a quantum leap, the equivalent of going from a light bulb to an optical laser,” Stöhr said. “So it’s not just that you have more X-rays. The interaction of the X-rays with the sample is very different, and there are effects you could never see at other types of X-ray light sources.”

    A Most Puzzling Result

    Stöhr stumbled on this latest discovery by accident. Then director of LCLS, he was working with Andreas Scherz, a SLAC staff scientist, who is now with the soon-to-open European XFEL in Hamburg, Germany, and Stanford graduate student Benny Wu to look at the fine structure of a common magnetic material used in data storage.

    To enhance the contrast of their image, they tuned the LCLS beam to a wavelength that would resonate with cobalt atoms in the sample and amplify the signal in their detector. The initial results looked great. So they turned up the intensity of the laser beam in the hope of making the images even sharper.

    That’s when the speckled pattern they’d been seeing in their detector went blank, as if the sample had disappeared.

    “We thought maybe we had missed the sample, so we checked the alignment and tried again,” Stöhr said. “But it kept happening. We knew this was strange – that there was something here that needed to be understood.”

    Stöhr is an experimentalist, not a theorist, but he was determined to find answers. He and Scherz dove deeply into the scientific literature. Meanwhile Wu finished his PhD thesis, which described the experiment and its unexpected result, and went on to a job in industry. But the team held off on publishing their experimental results in a scientific journal until they could explain what happened.

    Stöhr and Scherz published their explanation last fall in Physical Review Letters.

    “We are developing a whole new field of nonlinear X-ray science, and our study is just one building block in this field,” Stöhr said. “We are basically opening Pandora’s box, learning about all the different nonlinear effects, and eventually some of those will turn out to be more important than others.”

    The study included other collaborators from SLAC and Stanford, and was funded by the DOE Office of Science.

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.
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  • richardmitnick 3:40 pm on August 29, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , Jammed Cells Expose the Physics of Cancer,   

    From Quanta: “Jammed Cells Expose the Physics of Cancer” 

    Quanta Magazine
    Quanta Magazine

    August 16, 2016
    Gabriel Popkin

    The subtle mechanics of densely packed cells may help explain why some cancerous tumors stay put while others break off and spread through the body.

    1
    Ashley Mackenzie for Quanta Magazine

    In 1995, while he was a graduate student at McGill University in Montreal, the biomedical scientist Peter Friedl saw something so startling it kept him awake for several nights. Coordinated groups of cancer cells he was growing in his adviser’s lab started moving through a network of fibers meant to mimic the spaces between cells in the human body.

    For more than a century, scientists had known that individual cancer cells can metastasize, leaving a tumor and migrating through the bloodstream and lymph system to distant parts of the body. But no one had seen what Friedl had caught in his microscope: a phalanx of cancer cells moving as one. It was so new and strange that at first he had trouble getting it published. “It was rejected because the relevance [to metastasis] wasn’t clear,” he said. Friedl and his co-authors eventually published a short paper in the journal Cancer Research.

    Two decades later, biologists have become increasingly convinced that mobile clusters of tumor cells, though rarer than individual circulating cells, are seeding many — perhaps most — of the deadly metastatic invasions that cause 90 percent of all cancer deaths. But it wasn’t until 2013 that Friedl, now at Radboud University in the Netherlands, really felt that he understood what he and his colleagues were seeing. Things finally fell into place for him when he read a paper [Science Direct] by Jeffrey Fredberg, a professor of bioengineering and physiology at Harvard University, which proposed that cells could be “jammed” — packed together so tightly that they become a unit, like coffee beans stuck in a hopper.

    Fredberg’s research focused on lung cells, but Friedl thought his own migrating cancer cells might also be jammed. “I realized we had exactly the same thing, in 3-D and in motion,” he said. “That got me very excited, because it was an available concept that we could directly put onto our finding.” He soon published one of the first papers applying the concept of jamming to experimental measurements of cancer cells.

    Physicists have long provided doctors with tumor-fighting tools such as radiation and proton beams. But only recently has anyone seriously considered the notion that purely physical concepts might help us understand the basic biology of one of the world’s deadliest phenomena. In the past few years, physicists studying metastasis have generated surprisingly precise predictions of cell behavior. Though it’s early days, proponents are optimistic that phase transitions such as jamming will play an increasingly important role in the fight against cancer. “Certainly in the physics community there’s momentum,” Fredberg said. “If the physicists are on board with it, the biologists are going to have to. Cells obey the rules of physics — there’s no choice.”

    The Jam Index

    In the broadest sense, physical principles have been applied to cancer since long before physics existed as a discipline. The ancient Greek physician Hippocrates gave cancer its name when he referred to it as a “crab,” comparing the shape of a tumor and its surrounding veins to a carapace and legs.

    But those solid tumors do not kill more than 8 million people annually. Once tumor cells strike out on their own and metastasize to new sites in the body, drugs and other therapies rarely do more than prolong a patient’s life for a few years.

    Biologists often view cancer primarily as a genetic program gone wrong, with mutations and epigenetic changes producing cells that don’t behave the way they should: Genes associated with cell division and growth may be turned up, and genes for programmed cell death may be turned down. To a small but growing number of physicists, however, the shape-shifting and behavior changes in cancer cells evoke not an errant genetic program but a phase transition.

    The phase transition — a change in a material’s internal organization between ordered and disordered states — is a bedrock concept in physics. Anyone who has watched ice melt or water boil has witnessed a phase transition. Physicists have also identified such transitions in magnets, crystals, flocking birds and even cells (and cellular components) placed in artificial environments.

    But compared to a homogeneous material like water or a magnet — or even a collection of identical cells in a dish — cancer is a hot mess. Cancers vary widely depending on the individual and the organ they develop in. Even a single tumor comprises a mind-boggling jumble of cells with different shapes, sizes and protein compositions. Such complexities can make biologists wary of a general theoretical framework. But they don’t daunt physicists. “Biologists are more trained to look at complexity and differences,” said the physicist Krastan Blagoev, who directs a National Science Foundation program that funds work on theoretical physics in living systems. “Physicists try to look at what’s common and extract behaviors from the commonness.”

    In a demonstration of this approach, the physicists Andrea Liu, now of the University of Pennsylvania, and Sidney Nagel of the University of Chicago published a brief commentary in Nature in 1998 about the process of jamming. They described familiar examples: traffic jams, piles of sand, and coffee beans stuck together in a grocery-store hopper. These are all individual items held together by an external force so that they resemble a solid. Liu and Nagel put forward the provocative suggestion that jamming could be a previously unrecognized phase transition, a notion that physicists, after more than a decade of debate, have now accepted.

    Though not the first mention of jamming in the scientific literature, Liu and Nagel’s paper set off what Fredberg calls “a deluge” among physicists. (The paper has been cited more than 1,400 times.) Fredberg realized that cells in lung tissue, which he had spent much of his career studying, are closely packed in a similar way to coffee beans and sand. In 2009 he and colleagues published [Nature Physics] the first paper suggesting that jamming could hold cells in tissues in place, and that an unjamming transition could mobilize some of those cells, a possibility that could have implications for asthma and other diseases.

    2
    Lucy Reading-Ikkanda for Quanta Magazine

    The paper appeared amid a growing recognition of the importance of mechanics, and not just genetics, in directing cell behavior, Fredberg said. “People had always thought that the mechanical implications were at the most downstream end of the causal cascade, and at the most upstream end are genetic and epigenetic factors,” he said. “Then people discovered that physical forces and mechanical events actually can be upstream of genetic events — that cells are very aware of their mechanical microenvironments.”

    Lisa Manning, a physicist at Syracuse University, read Fredberg’s paper and decided to put his idea into action. She and colleagues used a two-dimensional model of cells that are connected along edges and at vertices, filling all space. The model yielded an order parameter — a measurable number that quantifies a material’s internal order — that they called the “shape index.” The shape index relates the perimeter of a two-dimensional slice of the cell and its total surface area. “We made what I would consider a ridiculously strict prediction: When that number is equal to 3.81 or below, the tissue is a solid, and when that number is above 3.81, that tissue is a fluid,” Manning said. “I asked Jeff Fredberg to go look at this, and he did [Nature Materials], and it worked perfectly.”

    Fredberg saw that lung cells with a shape index above 3.81 started to mobilize and squeeze past each other. Manning’s prediction “came out of pure theory, pure thought,” he said. “It’s really an astounding validation of a physical theory.” A program officer with the Physical Sciences in Oncology program at the National Cancer Institute learned about the results and encouraged Fredberg to do a similar analysis using cancer cells. The program has given him funding to look for signatures of jamming in breast-cancer cells.

    Meanwhile, Josef Käs, a physicist at Leipzig University in Germany, wondered if jamming could help explain puzzling behavior in cancer cells. He knew from his own studies and those of others that breast and cervical tumors, while mostly stiff, also contain soft, mobile cells that stream into the surrounding environment. If an unjamming transition was fluidizing these cancer cells, Käs immediately envisioned a potential response: Perhaps an analysis of biopsies based on measurements of tumor cells’ state of jamming, rather than a nearly century-old visual inspection procedure, could determine whether a tumor is about to metastasize.

    Käs is now using a laser-based tool to look for signatures of jamming in tumors, and he hopes to have results later this year. In a separate study that is just beginning, he is working with Manning and her colleagues at Syracuse to look for phase transitions not just in cancer cells themselves, but also in the matrix of fibers that surrounds tumors.

    More speculatively, Käs thinks the idea could also yield new avenues for therapies that are gentler than the shock-and-awe approach clinicians typically use to subdue a tumor. “If you can jam a whole tumor, then you have a benign tumor — that I believe,” he said. “If you find something which basically jams cancer cells efficiently and buys you another 20 years, that might be better than very disruptive chemotherapies.” Yet Käs is quick to clarify that he is not sure how a clinician would induce jamming.

    Castaway Cooperators

    Beyond the clinic, jamming could help resolve a growing conceptual debate in cancer biology, proponents say. Oncologists have suspected for several decades that metastasis usually requires a transition between sticky epithelial cells, which make up the bulk of solid tumors, and thinner, more mobile mesenchymal cells that are often found circulating solo in cancer patients’ bloodstreams. As more and more studies deliver results showing activity similar to that of Friedl’s migrating cell clusters, however, researchers have begun to question [Science] whether go-it-alone mesenchymal cells, which Friedl calls “lonely riders,” could really be the main culprits behind the metastatic disease that kills millions.

    Some believe jamming could help get oncology out of this conceptual jam. A phase transition between jammed and unjammed states could fluidize and mobilize tumor cells as a group, without requiring them to transform from one cell type to a drastically different one, Friedl said. This could allow metastasizing cells to cooperate with one another, potentially giving them an advantage in colonizing a new site.

    The key to developing this idea is to allow for a range of intermediate cell states between two extremes. “In the past, theories for how cancer might behave mechanically have either been theories for solids or theories for fluids,” Manning said. “Now we need to take into account the fact that they’re right on the edge.”

    Hints of intermediate states between epithelial and mesenchymal are also emerging from physics research not motivated by phase-transition concepts. Herbert Levine, a biophysicist at Rice University, and his late colleague Eshel Ben-Jacob of Tel Aviv University recently created a model of metastasis based on concepts borrowed from nonlinear dynamics. It predicts the existence of clusters of circulating cells that have traits of both epithelial and mesenchymal cells. Cancer biologists have never seen such transitional cell states, but some are now seeking them in lab studies. “We wouldn’t have thought about it” on our own, said Kenneth Pienta, a prostate cancer specialist at Johns Hopkins University. “We have been directly affected by theoretical physics.”

    Biology’s Phase Transition

    Models of cell jamming, while useful, remain imperfect. For example, Manning’s models have been confined to two dimensions until now, even though tumors are three-dimensional. Manning is currently working on a 3-D version of her model of cellular motility. So far it seems to predict a fluid-to-solid transition similar to that of the 2-D model, she said.

    In addition, cells are not as simple as coffee beans. Cells in a tumor or tissue can change their own mechanical properties in often complex ways, using genetic programs and other feedback loops, and if jamming is to provide a solid conceptual foundation for aspects of cancer, it will need to account for this ability. “Cells are not passive,” said Valerie Weaver, the director of the Center for Bioengineering and Tissue Regeneration at the University of California, San Francisco. “Cells are responding.”

    Weaver also said that the predictions made by jamming models resemble what biologists call extrusion, a process by which dead epithelial cells are squeezed out of crowded tissue — the disfunction of which has recently been implicated in certain types of cancer. Manning believes that cell jamming likely provides an overarching mechanical explanation for many of the cell behaviors involved in cancer, including extrusion.

    Space-filling tissue models like the one Manning uses, which produce the jamming behavior, also have trouble accounting for all the details of how cells interact with their neighbors and with their environment, Levine said. He has taken a different approach, modeling some of the differences in the ways cells can react when they’re being crowded by other cells. “Jamming will take you some distance,” he said, adding, “I think we will get stuck if we just limit ourselves to thinking of these physics transitions.”

    Manning acknowledges that jamming alone cannot describe everything going on in cancer, but at least in certain types of cancer, it may play an important role, she said. “The message we’re not trying to put out there is that mechanics is the only game in town,” she said. “In some instances we might do a better job than traditional biochemical markers [in determining whether a particular cancer is dangerous]; in some cases we might not. But for something like cancer we want to have all hands on deck.”

    With this in mind, physicists have suggested other novel approaches to understanding cancer. A number of physicists, including Ricard Solé of Pompeu Fabra University in Barcelona, Jack Tuszynski of the University of Alberta, and Salvatore Torquato of Princeton University, have published theory papers suggesting ways that phase transitions could help explain aspects of cancer, and how experimentalists could test such predictions.

    Others, however, feel that phase transitions may not be the right tool. Robert Austin, a biological physicist at Princeton University, cautions that phase transitions can be surprisingly complex. Even for a seemingly elementary case such as freezing water, physicists have yet to compute exactly when a transition will occur, he notes — and cancer is far more complicated than water.

    And from a practical point of view, all the theory papers in the world won’t make a difference if physicists cannot get biologists and clinicians interested in their ideas. Jamming is a hot topic in physics, but most biologists have not yet heard of it, Fredberg said. The two communities can talk to each other at physics-and-cancer workshops during meetings hosted by the American Physical Society, the American Association for Cancer Research or the National Cancer Institute. But language and culture gaps remain. “I can come up with some phase diagrams, but in the end you have to translate it into a language which is relevant to oncologists,” Käs said.

    Those gaps will narrow if jamming and phase transition theory continue to successfully explain what researchers see in cells and tissues, Fredberg said. “If there’s really increasing evidence that the way cells move collectively revolves around jamming, it’s just a matter of time until that works its way into the biological literature.”

    And that, Friedl said, will give biologists a powerful new conceptual tool. “The challenge, but also the fascination, comes from identifying how living biology hijacks the physical principle and brings it to life and reinvents it using molecular strategies of cells.”

    See the full article here .

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    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

     
  • richardmitnick 2:55 pm on August 29, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , ,   

    From JHU: “Scientists screen existing drugs in hopes of fast-tracking Zika treatment” 

    Johns Hopkins
    Johns Hopkins University

    8.29.16
    Rachel Butch

    A specialized drug screen test using lab-grown human cells has revealed two classes of compounds already in the pharmaceutical arsenal that may work against mosquito-borne Zika virus infections, scientists say.

    1
    Zika virus infection in cell death in human forebrain organoids. Image credit: Xuyu Qian, Johns Hopkins University

    In a summary of their work, published today in Nature Medicine, the investigators say they screened 6,000 existing compounds currently in late-stage clinical trials or already approved for human use for other conditions. The screening process identified several compounds that showed the ability to hinder or halt the progress of the Zika virus in lab-grown human neural cells.

    The research collaboration includes teams from the Johns Hopkins University School of Medicine, the National Institutes of Health, and Florida State University.

    “It takes years, if not decades, to develop a new drug,” says Hongjun Song, director of the Stem Cell Biology Program in the Institute of Cell Engineering at Johns Hopkins. “In this sort of global health emergency, we don’t have that kind of time.”

    Adds Guo-li Ming, professor of neurology at JHU’s School of Medicine: “Instead of using new drugs, we chose to screen existing drugs. In this way, we hope to create a therapy much more quickly.”

    The current outbreak of Zika, which began in South America last year, is known to be responsible for an increase in cases of microcephaly—a severe birth defect in which afflicted infants are born with underdeveloped brains. In the continental United States, there have been a total of 2,260 reported cases of Zika. Though most cases are associated with travel, 43 cases of local transmission have been reported in Florida, in the Miami area. In addition, Puerto Rico has reported 7,855 locally transmitted cases, spurring the Obama administration to declare a public health emergency in the territory on Aug. 12.

    The Zika virus is commonly transmitted from mosquito bites or from an infected person to an uninfected person through sexual contact. Despite the potential effects of infection, only one in four infected people will present symptoms if Zika infection, allowing the virus to spread rapidly in areas with local transmission. Because of this, the CDC recommends all pregnant women with ongoing risk of Zika infection, including residence or frequent travel to areas with active Zika virus transmission, receive screening throughout their pregnancy.

    Many research groups are fast tracking the development of vaccines, treatments, and mosquito-control measures to combat further spread of the virus.

    The new findings are an extension of previous work by the same research team, which found that Zika mainly targets specialized stem cells that give rise to neurons in the brain’s outer layer, the cortex. The researchers observed Zika’s effects in two- and three-dimensional cell cultures called “mini-brains,” which share structures with the human brain and allow researchers to study the effects of Zika in a more accurate model for human infection.

    In the current study, the research team exposed similar cell cultures to the Zika virus and the drugs one at a time, measuring for indicators of cell death, including caspase-3 activity, a chemical marker of cell death, and ATP, a molecule whose presence is indicative of cell vitality.

    Typically, after Zika infection, the damage done to neural cells is “dramatic and irreversible,” says Hengli Tang, professor of biological sciences at Florida State University. However, some of the compounds tested allowed the cells to survive longer and, in some cases, fully recover from infections.

    Further analysis of the surviving cells, Ming says, showed that the promising drugs could be divided into two classes: neuroprotective drugs, which prevent the activation of mechanisms that cause cell death; and antiviral drugs, which slow or stop viral infection or replication.

    Overall, Song says, three drugs showed robust enough results to warrant further study:

    PHA-690509, an investigational compound with antiviral properties
    emricasan, now in clinical trials to reduce liver damage from hepatitis C virus and shown to have neuroprotective effects
    niclosamide, a drug already used in humans and livestock to combat parasitic infections, which worked as an antiviral agent in these experiments

    Song cautioned that the three drugs “are very effective against Zika in the dish, but we don’t know if they can work in humans in the same way.” For example, he says, although niclosamide can safely treat parasites in the human gastrointestinal tract, scientists have not yet determined if the drug can even penetrate the central nervous system of adults or a fetus inside a carrier’s womb to treat the brain cells targeted by Zika.

    Nor, he says, do they know if the drugs would address the wide range of effects of Zika infection, which include microcephaly in fetuses and temporary paralysis from Guillain-Barre syndrome in adults.

    “To address these questions, additional studies need to be done in animal models as well as humans to demonstrate their ability to treat Zika infection,” Ming says. “So we could still be years away from finding a treatment that works.”

    The researchers say their next steps include testing the efficacy of these drugs in animal models to see if they have the ability to combat Zika in vivo.

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Zika depiction. Image copyright John Liebler, http://www.ArtoftheCell.com
    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

     
  • richardmitnick 2:41 pm on August 29, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , Research outlines cellular communication processes that make life possible   

    From phys.org: “Research outlines cellular communication processes that make life possible” 

    physdotorg
    phys.org

    August 29, 2016
    No writer credit found

    1
    Scanning electron micrograph of human T lymphocyte or T cell. Credit: NIAID/NIH

    Researchers have discovered a mechanism of intercellular communication that helps explain how biological systems and actions – ranging from a beating heart to the ability to hit a home run – function properly most of the time, and in some scenarios quite remarkably.

    The findings are an important basic advance in how cell sensory systems function, they shed light on the poorly-understood interaction between cells – and they also suggest that some of the damage done by cancer cells can be seen as a “failure to communicate.”

    The work was reported today in Proceedings of the National Academy of Sciences by physicists from Oregon State University and Purdue University, done with support from the National Science Foundation and the Simons Foundation.

    Scientists have long known that cells have various types of sensory abilities that are key to their function, such as sensing light, heat, nerve signals, damage, chemicals or other inputs.

    In this process, a chemical stimulus called ATP functions as a signaling molecule, which in turn causes calcium levels in a cell to rise and decline, and tells a cell it’s time to do its job – whether that be sending a nerve impulse, seeing a bird in flight or repairing a wound. These sensing processes are fundamental to the function of life.

    “We’ve understood for some time the basics of cellular sensory function and how it helps a cell respond to its environment,” said Bo Sun, an assistant professor of physics in the College of Science at Oregon State University, and a corresponding author on this study.

    “The thing is, individual cells don’t always get the message right, their sensory process can be noisy, confusing, and they make mistakes,” Sun said. “But there’s strength in numbers, and the collective sensory ability of many cells working together usually comes up with the right answer. This collective communication is essential to life.”

    In this study, researchers helped explain just how that works for animal cells.

    When cells meet, a small channel usually forms between them that’s called a gap junction. On an individual level, a cell in response to ATP begins to oscillate, part of its call to action. But with gap junction-mediated communications, despite significant variability in sensing from one cell to another, the sensitivity to ATP is increased. Oscillation is picked up and becomes more uniform.

    This interactive chatter continues, and a preponderance of cells receiving one sensation persuade a lesser number of cells reporting a different sensation that they must be wrong. By working in communication and collaboration, most of the cells eventually decide what the correct sensory input is, and the signal that gets passed along is pretty accurate.

    With this accuracy of communication, cells in a heart chamber collectively decide it’s time to contract at the appropriate time, and blood gets pumped, dozens of times a minute, for a lifetime. Neuron cells send accurate signals. Photoreceptor cells see clearly.

    This research was done with fibroblast cells, which are used in wound healing, but the results should apply to many cellular sensing mechanisms, researchers said.

    Cancer cells, by contrast, are poor communicators. This study showed that they resist this process of collective communication, and when enough of them are present, the communicative process begins to lessen and break down. This may be at least one of the ways in which cancer does its biologic damage.

    “These processes of collective sensory communication are usually accurate, but sometimes work better than others. Mistakes are made,” Sun said. “Even so, this process makes life possible. And when everything goes just right, the results can be remarkable.”

    Consider a baseball player trying to get a hit, which Ted Williams once called “the hardest single thing to do in sport.” A major league pitcher hurls a 93 mile-per-hour fastball, low but possibly a strike.

    The photoreceptor cells in the batter’s eyes see the pitch coming. Some cells see it as a curve in the dirt, and some mistake it for a changeup, a slower pitch. But the majority of the cells come to the correct conclusion, it’s a fastball at the knees, and they spread the word. After extensive communication between all these cells, a conclusion is reached and the correct message is sent to neurons in the brain.

    The brain cells, in turn, send a strong signal through nerves to muscles all over the batter’s body, the shoulders, legs, and especially arms. The signals arrive and once again a collaborative process takes place, deciding what the message is and how to react. Calcium ions in muscle cells are triggered and a brutally fast-but-accurate response is triggered, swinging the bat. This entire process, from the ball leaving the pitcher’s hand to contact with the bat, takes less than half a second.

    On a perfect day – the cellular debate over what pitch was coming was sufficiently short-lived, the timing exact, the muscle contractions just right – the ball explodes off the bat and sails over the center field fence.

    On a more realistic day – since the best hitters in the world only succeed 3 times out of 10 – the ball bounces weakly to the second baseman for an easy out. This in turn triggers the collective groans of 30,000 disappointed fans. But the heart has cellular communication that continues to guarantee its normal beating, and the player lives to bat another day.

    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 10:09 am on August 29, 2016 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From physicsworld.com: “Nonlinear optical quantum-computing scheme makes a comeback” 

    physicsworld
    physicsworld.com

    Aug 29, 2016
    Hamish Johnston

    A debate that has been raging for 20 years about whether a certain interaction between photons can be used in quantum computing has taken a new twist, thanks to two physicists in Canada. The researchers have shown that it should be possible to use “cross-Kerr nonlinearities” to create a cross-phase (CPHASE) quantum gate. Such a gate has two photons as its input and outputs them in an entangled state. CPHASE gates could play an important role in optical quantum computers of the future.

    Photons are very good carriers of quantum bits (qubits) of information because the particles can travel long distances without the information being disrupted by interactions with the environment. But photons are far from ideal qubits when it comes to creating quantum-logic gates because photons so rarely interact with each other.

    One way around this problem is to design quantum computers in which the photons do not interact with each other. Known as “linear optical quantum computing” (LOQC), it usually involves preparing photons in a specific quantum state and then sending them through a series of optical components, such as beam splitters. The result of the quantum computation is derived by measuring certain properties of the photons.

    Simpler quantum computers

    One big downside of LOQC is that you need lots of optical components to perform basic quantum-logic operations – and the number quickly becomes very large to make an integrated quantum computer that can perform useful calculations. In contrast, quantum computers made from logic gates in which photons interact with each other would be much simpler – at least in principle – which is why some physicists are keen on developing them.

    This recent work on cross-Kerr nonlinearities has been carried out by Daniel Brod and Joshua Combes at the Perimeter Institute for Theoretical Physics and Institute for Quantum Computing in Waterloo, Ontario. Brod explains that a cross-Kerr nonlinearity is a “superidealized” interaction between two photons that can be used to create a CPHASE quantum-logic gate.

    This gate takes zero, one or two photons as input. When the input is zero or one photon, the gate does nothing. But when two photons are present, the gate outputs both with a phase shift between them. One important use of such a gate is to entangle photons, which is vital for quantum computing.

    The problem is that there is no known physical system – trapped atoms, for example – that behaves exactly like a cross-Kerr nonlinearity. Physicists have therefore instead looked for systems that are close enough to create a practical CPHASE. Until recently, it looked like no appropriate system would be found. But now Brod and Combes argue that physicists have been too pessimistic about cross-Kerr nonlinearities and have shown that it could be possible to create a CPHASE gate – at least in principle.

    From A to B via an atom

    Their model is a chain of interaction sites through which the two photons propagate in opposite directions. These sites could be pairs of atoms, in which the atoms themselves interact with each other. The idea is that one photon “A” will interact with one of the atoms in a pair, while the other photon “B” interacts with the other atom. Because the two atoms interact with each other, they will mediate an interaction between photons A and B.

    Unlike some previous designs that implemented quantum error correction to protect the integrity of the quantum information, this latest design is “passive” and therefore simpler.

    Brod and Combes reckon that a high-quality CPHASE gate could be made using five such atomic pairs. Brod told physicsworld.com that creating such a gate in the lab would be difficult, but if successful it could replace hundreds of components in a LOQC system.

    As well as pairs of atoms, Brod says that the gate could be built from other interaction sites such as individual three-level atoms or optical cavities. He and Combes are now hoping that experimentalists will be inspired to test their ideas in the lab. Brod points out that measurements on a system with two interaction sites would be enough to show that their design is valid.

    The work is described in Physical Review Letters. Brod and Combes have also teamed-up with Julio Gea-Banacloche of the University of Arkansas to write a related paper that appears in Physical Review A. This second work looks at their design in more detail.

    See the full article here .

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    PhysicsWorld is a publication of the Institute of Physics. The Institute of Physics is a leading scientific society. We are a charitable organisation with a worldwide membership of more than 50,000, working together to advance physics education, research and application.

    We engage with policymakers and the general public to develop awareness and understanding of the value of physics and, through IOP Publishing, we are world leaders in professional scientific communications.
    IOP Institute of Physics

     
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