Bound neutrons pave way to free ones

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The major hurdle for scientists who study the internal structure of the neutron is that mostneutronsare bound up inside the nucleus of atoms to protons. In nature, a free neutron lasts for only a few minutes, while in the nucleus, neutrons are always encumbered by the ubiquitous proton.

To tease out a description of a free neutron, a group of scientists compared data collected at Jefferson Lab and the SLAC National Accelerator Laboratory that detail how bound protons and neutrons in the nucleus of the atom display two very different effects. Bothprotonsand neutrons are referred to as nucleons.

"Both effects are due to the nucleons behaving like they are not free,"says Doug Higinbotham, a Jefferson Lab staff scientist.

Nucleons appear to differ when they are tightly bound in heavier nuclei versus when they are loosely bound in light nuclei. In the first effect, experiments have shown that nucleons tightly bound in a heavy nucleus pair up more often than those loosely bound in a light nucleus.

"The first thing was the probability of finding two nucleons close together in the nucleus, what we call a short-range correlation,"says Larry Weinstein, a professor at Old Dominion University."And the probability that the two nucleons are in a short-range correlation increases as the nucleus gets heavier."

Meanwhile, other experiments have shown a clear difference in how the proton's building blocks, called quarks, are distributed in heavy nuclei versus light nuclei. This difference is called the EMC Effect.

"People were measuring and discussing the EMC effect. And people were discussing things about the short-range correlations effect. Nobody bothered to look to see if there's any connection between them,"adds Eliezer Piasetzky, a professor at Tel Aviv University in Israel.

When the group combined the data from a half-dozen experiments regarding these two different effects on one graph, they found that the two effects were correlated.

"Take a quantity that tells you how strong the EMC Effect is. And then take another quantity that tells you how many short-range correlations you have,"Higinbotham explains."And you see that when one is big, the other one is big. When one is small, the other one is small."

The scientists say that it's unlikely that one effect causes the other. Rather, the data shows that there is a common cause for both.

"I think that we certainly agree that from the position picture, it's due to nucleons overlapping that is causing this. And in the momentum picture, it is the high-momentum nucleons that are causing this. And, of course, it's quantum mechanics, so choose your picture,"Higinbotham explains.

The group says the common cause may have remained a mystery for so long, because while the two effects they are studying are obviously related when laid out on a graph, the connection was previously obscured by the different, yet related ways in which the two effects are studied.

"When you do a measurement for the EMC Effect, what you do is you look inside the nucleon. You break open the nucleon and see inside. What happens inside the nucleon is very different from the short-range correlations, which is what happens between two different nucleons,"Piasetzky says.

"What's very new here is that we have linked two fields that were completely disconnected. So now you can start asking questions about what that connection can help us learn,"Higinbotham says.

They say the next step is to further compare the data from all of the source experiments that they used in their analysis to see if data for one effect may now be used to learn something new about the other. Then, of course, they'd like to use the knowledge that the two effects are connected to design new experiments for shining a light on other secrets buried in the nucleus of the atom.

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Dynamic systems in living cells break the rules

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The researchers studied fatmoleculeswhich are naturally occurring in cells. Using a special state-of-the-art instrument, an optical tweezer, they were able to hold onto the small fat molecules inside livingyeast cellsusing an extremely focusedlaser light. By measuring the movement of the fat molecules over several hours they could observe that they were not behaving as expected.

The laws of physics for motion

In the world of physics, there is something called Brownian motion. Ordinary Brownian motion describes how a substance passively spreads in a liquid. For example, when you pour a spoonful of sugar into a glass of water the sugar will distribute itself evenly after a while. Would fat molecules behave 'ordinarily' and simple distribute itself evenly in the cell fluid?

In any case, the researchers had expected that the Ergodicity theorem (tenet), which is a generally recognized law of nature, would be adhered to. The Ergodicity theorem predicts that statistically, the result of throwing 10 dice once would have the same average distribution as throwing one die 10 times.

The Ergodicity theorem is expected to apply for anomalous transport processes in unorganized materials, for example, biological systems. The researchers expected therefore, that if you observe the transport of fat molecules in many cells at once, then you would get the same result as by looking a single cell repeatedly over a long period of time. You expect a pattern.

Breaks common wisdom

"But neither the one nor the other common wisdom held true. It turned out the fat molecules broke with all the patterns. Our analysis of the spreading of liquid fat granules in living yeast cells showed that not only was the distribution abnormal, but that the movement in the relevant time period was also in conflict with the statistics for ergodicity. They almost have their own will", explains Lene Oddershede, associate professor in the biophysics group,Optical Tweezersat the Niels Bohr Institute at the University of Copenhagen. The experimental studies were performed here, while researchers from DTU as well as Germany and Israel have worked with the theoretical calculations.

The researchers studied fat molecules whichare naturally occurring in cells. Using a specialstate-of-the-art instrument, an optical tweezer,they were able to hold onto the small fatmolecules inside living yeast cells using anextremely focused laser light.

The conclusion is that controlling living systems is more complicated than previously thought and that the basic concepts in statistical physics must be replaced when analysing certain aspects of biomolecular dynamics incells.

"We have gained very important knowledge. What we thought would apply, did not hold up at all, so now we need to find a completely new law for the physics in living organisms. Our goal is to discover how the cell signals and how it communicates both internally and with its environment", explains Lene Oddershede.

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Soap films help to solve mathematical problems

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"With the aid of soap films we have solved variational mathematical problems, which appear in the formulation of many physical problems", explains Carlos Criado, professor at the University of Málaga, speaking to SINC. Together with his colleague NievesÁlamo, he has just published his work in theAmerican Journal of Physics.

Soap films always adopt the shape which minimises their elastic energy, and therefore their area, so that they turn out to be ideal in the calculus of variations,"where we look for a function that minimises a certain quantity (depending on the function)", adds the researcher.

"Of course there are other ways to solve variational problems, but it turns out to be surprising, fun and educative to obtain soap films in the shape of brachistochrones, catenaries and semicircles", Criado emphasises.

The professor offers the example of the famous problem of the brachistochrone curve. What shape must a wire be in order that a ball travels down it from one end to the other (at a different height) as rapidly as possible? The answer is the brachistochrone (from the Greek brachistos, the shortest, and cronos, time), the curve of fastest descent.

New methods for old problems

The mathematician Johann Bernoulli found the answer centuries ago when he realised that it was a cycloid (the curve described by a point on a circle rolling along a line). That was the origin of the calculus of variations, which was also used in other classic problems, like that of the catenary (the shape of a chain suspended by its endpoints) and the isoperimetric curve (a curve which maximises the area it encloses).

The study shows that these calculations may be related to Plateau's problem, that is, to find the shape adopted by a soap film under certain boundary restrictions. Besides, the researchers show how to design the experiments, constraining the soap films between two surfaces in such a way as to obtain the appropriate curves.

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Physicists study mechanics of 'crackling'

A study led by postdoctoral associate Stefanos Papanikolaou and Professor of Physics James Sethna provides new insights into the patterns created when things crackle. For the experiments, Sethna's colleagues in Italy and Brazil used magnets, which the researchers call an"excellent playground"for studying such phenomena. The work was published online Jan. 23 in the journalNature Physics.

Crumple a piece of paper and watch small areas bend and crease abruptly. In the same way, as a magnetic front moves forward, it advances in sharp jumps. As it grows, the magnetized region gets stuck on impurities and imperfections in the material, jumping from one bunch of dirt and getting stuck on another. Physicists call these"crackles"avalanches.

The scientists listened to this magnetic crackling in a one micron-thickmetal film-- so thin that they introduced new methods to extract the crackles from the noisy data. As was predicted by theory, they saw that the big avalanches were scaled-up versions of the small ones, as well as mergers of the small ones.

Physicists use this so-called scale invariance to explain the relative number of avalanches with large and small sizes, or short and long durations, and other properties. For example, there are many more small earthquakes than larger ones, which is a"power law"distribution -- that is, the number of earthquakes is given by a power of their size. The Cornell researchers were able to go beyond these power laws to predict the avalanches' average shapes, and also, the shapes of their size and duration distributions.

The researchers' success in describing avalanches in thin magnets gives hope for understanding the larger phenomena that follow these self-similar patterns -- for example, the way the Earth cracks during anearthquake. Earthquakes are avalanches, too -- the Earth's crackling response to moving tectonic plates. The scaling that explains how magnets crackle and how paper crunches may be useful in predicting how earthquakes spread.

"We don't know how to predict when earthquakes will happen -- which is what people want -- but we are gaining real control about what avalanches look like in magnets -- their shapes and sizes and speeds. Magnets are a place to do experiments to understand earthquakes,"Sethna said.

The work was done in Cornell's Laboratory for Atomic and Solid State Physics and was supported by the National Research Council of Italy and the Department of Energy.

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'Tall order' sunlight-to-hydrogen system works, neutron analysis confirms

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Photosynthesis, the natural process carried out by plants, algae and some bacterial species, converts sunlight energy into chemical energy and sustains much of the life on earth. Researchers have long sought inspiration from photosynthesis to develop new materials to harness the sun's energy for electricity and fuel production.

In a step toward synthetic solar conversion systems, the ORNL researchers have demonstrated and confirmed with small-angle neutron scattering analysis that light harvesting complex II (LHC-II) proteins can self-assemble with polymers into a syntheticmembranestructure and produce hydrogen.

The researchers envision energy-producing photoconversion systems similar to photovoltaic cells that generatehydrogen fuel, comparable to the way plants and otherphotosynthetic organismsconvert light to energy.

"Making a, self-repairing synthetic photoconversion system is a pretty tall order. The ability to control structure and order in these materials for self-repair is of interest because, as the system degrades, it loses its effectiveness,"ORNL researcher Hugh O'Neill, of the lab's Center for Structural Molecular Biology, said.

"This is the first example of a protein altering the phase behavior of asynthetic polymerthat we have found in the literature. This finding could be exploited for the introduction of self-repair mechanisms in future solar conversion systems,"he said.

Small angle neutron scattering analysis performed at ORNL's High Flux Isotope Reactor (HFIR) showed that the LHC-II, when introduced into a liquid environment that contained polymers, interacted with polymers to form lamellar sheets similar to those found in natural photosynthetic membranes.

The ability of LHC-II to force the assembly of structural polymers into an ordered, layered state -- instead of languishing in an ineffectual mush -- could make possible the development of biohybrid photoconversion systems. These systems would consist of high surface area, light-collecting panes that use the proteins combined with a catalyst such as platinum to convert the sunlight into hydrogen, which could be used for fuel.

The research builds on previous ORNL investigations into the energy-conversion capabilities of platinized photosystem I complexes -- and how synthetic systems based on plant biochemistry can become part of the solution to the global energy challenge.

"We're building on the photosynthesis research to explore the development of self-assembly in biohybrid systems. The neutron studies give us direct evidence that this is occurring,"O'Neill said.

The researchers confirmed the proteins' structural behavior through analysis with HFIR's Bio-SANS, a small-angle neutron scattering instrument specifically designed for analysis of biomolecular materials.

"Cold source"neutrons, in which energy is removed by passing them through cryogenically chilled hydrogen, are ideal for studying the molecular structures of biological tissue and polymers.

The LHC-II protein for the experiment was derived from a simple source: spinach procured from a local produce section, then processed to separate the LHC-II proteins from other cellular components. Eventually, the protein could be synthetically produced and optimized to respond to light.

O'Neill said the primary role of the LHC-II protein is as a solar collector, absorbing sunlight and transferring it to the photosynthetic reaction centers, maximizing their output."However, this study shows that LHC-II can also carry out electron transfer reactions, a role not known to occur in vivo,"he said.

The research team, which came from various laboratory organizations including its Chemical Sciences Division,Neutron ScatteringSciences Division, the Center for Structural Molecular Biology and the Center for Nanophase Materials Sciences, consisted of O'Neill, William T. Heller, and Kunlun Hong, all of ORNL; Dimitry Smolensky of the University of Tennessee; and Mateus Cardoso, a former postdoctoral researcher at ORNL now of the Laboratio Nacional de Luz Sincrotron in Brazil.

"That's one of the nice things about working at a national laboratory. Expertise is available from a variety of organizations,"O'Neill said.

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Giant virus, tiny protein crystals show X-ray laser's power and potential

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In one study, an international research team used the LCLS to demonstrate a shortcut for determining the 3-D structures of proteins. The laser's brilliant pulses of X-ray light pulled structural data from tinyproteinnanocrystals, avoiding the need to use large proteincrystalsthat can be difficult or impossible to prepare. This could lop years off the structural analysis of some proteins and allow scientists to decipher tens of thousands of others that are out of reach today, including many involved in infectious disease.

In a separate paper, the same team reported making the first single-shot images of intact viruses, paving the way for snapshots and movies of molecules, viruses and live microbes in action.

Led by Henry Chapman of the Center for Free-Electron Laser Science at the German national laboratory DESY and Janos Hajdu of Sweden's Uppsala University, the team of more than 80 researchers from 21 institutions performed these experiments in December 2009, just two months after the LCLS opened for research. Their studies are the first to demonstrate the power and potential of the LCLS for biology.

"The LCLS beam is a billion times brighter than previous X-ray sources, and so intense it can cut through steel,"Chapman said."Yet these incredible X-ray bursts are used with surgical, microscopic precision and exquisite control, and this is opening whole new realms of scientific possibilities,"including the ability to observe atoms moving andchemical bondsforming and breaking in real time.

Outrunning a laser blast

In the experiments, scientists sprayed viruses or nanocrystals into the path of the X-ray beam and zapped them with bursts of laser light. Each strobe-like laser pulse is so brief—a few millionths of a billionth of a second long—that it gathers all the information needed to make an image before the sample explodes.

Hajdu had proposed this method nearly a decade earlier. Researchers at Arizona State University, Lawrence Livermore National Laboratory, SLAC and Uppsala spent years developing specialized equipment for injecting samples into the beam, and Germany's Max Planck Advanced Study Group brought in a 10-ton, $7 million instrument called CAMP to record every single photon of data with a fast, ultra-sensitive X-ray camera for later analysis.

Tests at DESY and Lawrence Berkeley National Laboratory showed that the concept worked at lower X-ray energies."But as you go to higher energies, can you still outrun the damage?"said team member Michael Bogan, a SLAC staff scientist and principal investigator at the PULSE Institute for Ultrafast Energy Science, jointly located at SLAC and Stanford University. The answer, he said, was yes:"The physics still holds."

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The experimentally measured X-ray diffraction pattern of a single Mimivirus particle, imaged at the Linac Coherent Light Source, the world's first hard X-ray free-electron laser, located at SLAC National Accelerator Laboratory. Very short and extremely bright X-ray pulses can be used to obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma. The structure of the virus can be determined from such patterns. In this study, the X-ray pulse lasted a millionth of a billionth of a second and heated the virus to 100,000 degrees Celsius, but not before this image was obtained. Credit: Janos Hajdu (Uppsala University)

A big payoff from tiny crystals

The protein structure experiments were led by Chapman and Arizona State's John Spence and Petra Fromme. They chose as their target Photosystem I, a biological factory in plant cells that converts sunlight to energy during photosynthesis. It's one of an important class of proteins known as membrane proteins that biologists and drug developers are eager to understand better.

Embedded in cell membranes, these proteins control traffic in and out of the cell and serve as docking points for infectious agents and disease-fighting drugs; in fact, they are the targets of more than 60 percent of the drugs on the market. Yet scientists know the structures of only six of the estimated 30,000 membrane proteins in the human body, given the difficulty of turning them into big crystals for conventional X-ray analysis.

To get around this bottleneck, the researchers squirted millions of nanocrystals containing copies of Photosystem I across the X-ray beam. Laser pulses hit the crystals at various angles and scattered into the detector, forming the patterns needed to reconstitute images. Each crystal immediately vaporized, but by the time the next pulse arrived another crystal had moved into the bull's eye.

The team combined 10,000 of the three million snapshots they took to come up with a good match for the known molecular structure of Photosystem I.

"I attended several meetings this summer where this work was presented and I was extraordinarily excited by it,"Michael Wiener of the University of Virginia, who was not involved in the research, said of the results. He leads one of nine institutes set up by the National Institutes of Health to decipher the structures of membrane proteins."Preparation of these nanocrystals is likely to be very, very much easier than the larger crystals used to date,"Wiener said, leaving scientists more time and money to find out how these important biomolecules work.

The team is scheduled to return to the LCLS this month to repeat the experiments with X-raylaserpulses that are much faster and deliver four times as much energy as they did in the initial round. If the physics still hold, future images should capture the extraordinarily complex structure of Photosystem I in atom-by-atom detail.

Portraits of a virus

For the second experiment, the team went a step beyond nanocrystals to no crystals at all. Led by Hajdu, they made single-shot portraits of individual virus particles. These snapshots are a step toward eventually producing stop-action movies of chemical changes taking place in molecules and within living cells.

Biologists have long dreamed of making images of viruses, whole microbes and living cells without freezing, slicing or otherwise disturbing them. This is one of the goals of the LCLS, and the researchers tested its capabilities on Mimivirus, the world's largest known virus, which infects amoebas.

Of the hundreds of Mimiviruses hit by the LCLS beam, two produced enough data to allow scientists to reconstitute their images. The images show the 20-sided structure of the Mimi's outer coat and an area of denser material inside, which may represent its genetic material. Shorter, brighter pulses focused to a smaller area should greatly improve the resolution of these images to reveal details as small as one nanometer, the team wrote in their Feb. 3 Nature report.

Getting a detailed picture of the internal structure of an individual virus"would be a great achievement,"said team member Jean-Michel Claverie, director of the Structural&Genomic Information Lab in Marseille and one of the scientists who discovered Mimi's viral nature.

"This is a brand-new way to look at a biological object,"he said."This will allow us to address not only the questions related to the internal structure of the virus, but its intrinsic variability from one individual virus particle to the next—a microscopic variability that might play a fundamental role in evolution."

The team returned to the LCLS in January to look at the Mimivirus at X-ray wavelengths that should maximize the amount of contrast and detail in the images. They will be analyzing the results in the months to come.

SLAC Director Persis Drell, who sat in a control room packed with scientists as raw data from the two experiments came in, said the experience was thrilling—and so is the potential for biology and medicine.

"This first data and these first papers are really just the first view of a new research frontier,"she said."They represent a turning point for the LCLS, demonstrating new technologies that will be great steps forward."

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Physicists scale up invisibility cloaks using natural crystals

The scientists have shown that they are able to hide an object that is much bigger than those cloaked by other research groups. Previous studies have demonstrated cloaking by using a metamaterial - a fabricated composite withoptical propertiesnot found in nature - which limits the size of the cloaking region, while the team from UK and Denmark have used a natural crystal called calcite, which has enabled them to hide a larger object.

Calcite is a transparent mineral with birefringent or double-refraction properties, which means that light enters the calcite and splits into two rays of different polarizations travelling at different speeds and in different directions.

The team has been able to cloak larger objects because it has employed a cloaking design that did not require inhomogeneous material properties, as all the previous works did. This demonstration was performed, both in the air and in a container of liquid, by using two triangular pieces of calcite glued together, placed on a mirror. The size of the cloaking area is not limited by the technology available, only by the size of the calcite crystal.

Dr Shuang Zhang, lead investigator from the University of Birmingham’s School of Physics and Astronomy, said:‘‘This is a huge step forward as, for the first time, the cloaking area is rendered at a size that is big enough for the observer to‘see’ the invisible object with the naked eye.

‘By using natural crystals for the first time, rather than artificial meta-materials, we have been able to scale up the size of the cloak and can hide larger objects, thousands of times bigger than the wavelength of the light.’

He continues:‘Previous cloaks have succeeded at the micron level (much smaller than the thickness of a human hair) using a nano- or micro-fabricated artificial composite material. It is a very slow process to make these structures and they also restrict the size of the cloaking area. We believe that by using calcite, we can start to develop a cloak of significant size that will open avenues for future applications of cloaking devices.’

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