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Home » Page 1011

New gold standard for determining protein structure

Naoki Kunishama and his team at RIKEN’s SPring-8 Center in Japan have found that a new technique to determine protein structures is better for structure-based drug design than conventional X-ray crystallography using synchrotron radiation (SR). The main advantage of this technique, called serial femtosecond crystallography (SFX), is that it can be performed at room temperature without significant noise from radiation damage, while SR relies on cryo-cooling proteins to reduce radiation damage to an acceptable level.

SFX works by exploiting ultrashort pulses of high-energy radiation delivered by an X-ray free-electron laser (XFEL), which is similar in size to a synchrotron but with a linear configuration. To date there are two XFEL facilities, one in California and the one in Japan used by Kunishama and his team, while a third one will soon be operational in Germany.

SFX has been optimized for protein crystallography over the last five years. It exploits diffraction from protein crystals, in the same way as synchrotron-based crystallography. Although the radiation used is so intense that it destroys the crystal after a few femtoseconds of exposure, the femtosecond speed of the procedure allows the diffraction data to be captured before radiation damage and the explosion of the crystal can add noise to the data. A full dataset is obtained by working through many crystals each at a fixed random angle, instead of rotating one crystal to take multiple images as in synchrotron techniques. A water- or oil-based stream moves the crystals in line for the radiation pulse.

SFX crystals are more reproducible

In this new study the researchers crystallized thermolysin, a very stable protein that has been used as a model protein for crystallography before, and soaked its ligand into the crystal (Acta Cryst. D73, 702–709). They used SFX to obtain three structures of the complex, and SR for the other two. Comparing the structures to each other, and to previously published structures, Kunishama and colleagues found that SFX yields structures that are more similar to the physiological conditions of both the protein and the water surrounding it. The SFX structures were also much more reproducible than the SR versions.

The big advantages of SFX for generating such highly reproducible structures are that it enables room-temperature operation and generates less radiation damage. In contrast, SR crystallography requires the crystals to be cooled in liquid nitrogen to keep radiation damage within acceptable limits, which in turn needs cryo-protection agents to prevent water crystals from forming inside the protein crystal and destroying it. Kunishama and his team showed that these cryo-protectants affect the conformations of amino acids in the crystal and consequently the observed structure, while cryo-cooling also shrinks the crystal cell dimensions by up to 2.8%.

The devil is in the detail

The authors believe that the more physiological structures obtained by SFX are a better basis for drug design than SR-based structures. Knowing the details of amino-acid conformations is crucial for predicting how drugs can bind to target proteins, especially those concerning the ligand and its binding site, and this study shows that these details might be altered by radiation damage or cryo-cooling in conventional SR crystallography. Kunishama and his team conclude that SFX is the better choice for structure-based drug design, as long as plenty of crystals are available to feed into an SFX crystal stream.

The American eclipse: wonder, science and festivities

 

by David Appell in Salem, Oregon, US

The Moon partially blocks the Earth’s view of the Sun at least twice, but the 21 August total solar eclipse – the “Great American Eclipse” –  is “likely to be the single most viewed natural phenomenon in history of America”, according to Randall Milstein, an astronomy instructor at Oregon State University. He says a total of 324 million people live within a 9-hour drive of the path of totality.

While the total solar eclipse will span the US – the first to do so since 1891 – the UK will only see a slight partial eclipse, where a sliver of the Moon covers the Sun. Starting over Belfast at 7:37 p.m. BST and leaving Plymouth at 8:33 p.m. BST, this partial eclipse will extend to eastern continental Europe. But it will only be a 4% blockage at best – so be sure to use eclipse safety glasses!

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Documentary explores the history of astronomy in China

By James Dacey

A new documentary explores the development of astronomy in China, taking viewers from the protoscience of ancient China through to the nation’s ambitious space exploration programmes of today. Directed by Beijing-based filmmaker René Seegers, the film has recently been broadcast on Shanghai Television along with screenings at a range of academic institutions, cultural and scholarly societies and embassies throughout China. Now, you can watch the film on the Physics World YouTube channel (with English subtitles).

“The Ancient Chinese believed that Heaven was a power, or a deity, which judged humans. Heaven was responsible for weather and for natural disasters. It was not a realm accessible to humans,” explains Ying Da, the documentary’s presenter. Ying is a media personality who shot to fame in China for directing the family sitcom I Love My Family (1993–1994).

Of course, in recent times Chinese scientists and engineers have taken a much more proactive approach to understanding the cosmos. Since the People’s Republic of China launched its first satellite in 1970 (Dong Fang Hong I), the nation has been ramping up its space programmes. The documentary takes viewers to observatories and the final construction phase of the Five-hundred-meter Aperture Spherical Telescope (FAST), the largest single-dish radio telescope on Earth. It also joins Chinese scientists in Antarctica and explores the leading role China is playing in the construction and operation of the Thirty Meter Telescope in Hawaii.

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Coherent neutrino scattering seen with compact detector

Detecting neutrinos is one of the hardest tasks in particle physics, owing to their extremely low interaction rate with particles. Huge quantities of matter are monitored just to catch a precious few events. Now, however, researchers have unveiled a new technique to catch neutrinos with much smaller detectors. It could potentially lead to extensions of the Standard Model of particle physics, and also have practical applications in nuclear non-proliferation.

Neutrinos were first detected in 1956 through inverse beta decay – an observation that would eventually win the 1995 Nobel Prize in Physics. They are detected by the weak interaction, which is mediated by the exchange of charged W and neutral Z bosons. A neutrino scattering off a proton exchanges a W boson, producing a neutron and a positron. Although this can provide valuable information, it can only detect neutrinos with fairly high energy.

Alternatively, one can detect the recoil of target particles exchanging neutral Z bosons with neutrinos. This was first achieved in 1973 at CERN’s Gargamelle detector in Geneva. The following year, theoretical physicist Daniel Freedman of the US National Accelerator Laboratory in Illinois predicted that the interaction of a low-energy neutrino could be around 100 times greater. “A particle with a long wavelength is essentially delocalized over a relatively large distance,” explains Juan Collar of the University of Chicago, “So the Z boson is effectively probing the whole nucleus and interacting with all the nucleons at the same time. To a good approximation, the probability of interaction scales with the square of the number of neutrons in the nucleus.” In principle, this so-called coherent scattering could allow a much stronger signal.

Grave difficulties

Unfortunately, a heavy, neutron-rich nucleus recoils only very slightly from the impact of a low-energy neutrino. Freedman wrote in his 1974 paper that his proposal of coherent neutrino scattering might “be an act of hubris, because the inevitable constraints of interaction rate, resolution and background pose grave experimental difficulties.” In the intervening years, however, dark matter astronomers have refined detection of low-energy nuclear recoils in detectors for hypothetical WIMPs (weakly interacting massive particles). “We have profited from all this knowledge,” says Collar.

Collar and colleagues in the COHERENT collaboration, which includes scientists in Russia, Canada, Korea and various parts of the US, performed their experiment at the most intense pulsed neutron source in the world at Tennessee’s Oak Ridge National Laboratory, where vast numbers of neutrinos are also generated. The researchers discovered a basement corridor well-screened from cosmic rays that, with the shielding (plus an extra 12 m of concrete and gravel), filtered out almost all neutrons. “Of course the neutrinos go through it like it’s not there,” says Collar. The researchers placed a target comprising just 14.6 kg of sodium-doped caesium iodide (traditional neutrino detectors require thousands of tonnes of material), and calculated the nuclear recoil from coherent neutrino scattering by measuring the increase in their signal during each pulse. Over 15 months, the researchers acquired clear evidence of coherent neutrino scattering.

Freedman, now at Stanford University, is impressed: “This process was in the background of people’s thinking,” he says. “If [the researchers] had ruled out a signal with confidence, it would have undermined not just the Standard Model but basic quantum mechanics.”

Long list of questions

The researchers have already provided new constraints to potential interactions between neutrinos and quarks that might result from some extensions to the Standard Model. Future results, says Collar, may help to answer key questions, such as whether the neutrino has an intrinsic magnetic moment and whether there are additional “sterile” neutrinos that do not interact through the Standard Model. “The list [of questions] is actually very long,” he says.

Theoretical particle physicists Joel Walker and James Dent of Sam Houston State University in Texas, who were not involved, are excited. “The neutrino sector is a very strange sector that has surprised the physics community several times already,” says Walker. Dent adds, “It would have been very surprising to people if the Standard Model signal had not been there, but that doesn’t mean it’s the only signal there. Part of our excitement is that now we can start testing this section of the Standard Model for beyond-the-standard-model physics.” Fellow theorist Patrick Huber of Virginia Tech has proposed the technique could detect “breeding blankets” placed around nuclear reactors to produce weapons-grade plutonium. “For many years, people like myself have been saying ‘Let’s assume we could detect coherent neutrino-nucleus scattering’. Now it’s happened, all these what-if scenarios become real!”

The research is published in Science.

Why being average is bad news for ants

For an ant that’s fallen into a pit dug in the sand by the larvae of “antlion” insects, the ability to climb up a granular slope is a matter of life or death. Now, a group of scientists in France has discovered why certain medium-sized ants are unlikely to make it out alive of these conical, centimetre-sized traps – no matter how hard they try. The physics of friction, the researchers found, dictates that these ants are heavy enough to deform a pit’s sandy slope but not so heavy that they create stabilising footprints. Instead, the unlucky creatures slide to the bottom of the pit and are eaten alive.

It was a 17th-century French scientist – physicist Guillaume Amontons – who formulated three laws of friction still in use today. The first states that the frictional force experienced by an object resting on a surface is proportional to that object’s gravitational force – and hence its mass. But in the latest research, Jérôme Crassous of the University of Rennes and colleagues have shown that friction’s dependence on mass is much more complicated for tiny objects on granular surfaces, and it is this complexity that determines the fate of ants in antlion pits.

Box of beads

Crassous and co-workers filled a box with glass beads of varying sizes, tipping the box each time so that the beads formed a slope with a range of angles approaching that at which avalanches most readily cascade down a mountainside – the angle that antlions also use in their pits. The researchers then rested small discs of metal covered in cardboard on the granular slope and recorded how easily the discs slid down it, repeating the exercise many times over. This they did for discs of various masses and with differing surface areas in contact with the slope.

The researchers found, as expected, that the probability for a disc to slide to the bottom of the slope increased as the slope’s angle approaches that characteristic of avalanches (the precise value depending on the size of the beads). What was far more remarkable, they report, was how that probability depended on the pressure that a disc exerts on the slope; in other words, on the disc’s mass. Rather than being independent of pressure, they found that for a given angle the chances of sliding were greatest at particular, intermediate pressures.

To understand what was going on, the researchers photographed the tracks that the discs made in the granular material (in their paper, they actually show tracks made in sand). Very small discs did not slide and so left no tracks, whereas intermediate-sized discs created tracks that became more visible as their mass increased. The most massive objects also created tracks, but because they built up ridges of granular material ahead of them they did not slide far.

Model creatures

Crassous and co-workers were able to model this behaviour mathematically. To investigate the onset of sliding at low masses, they assumed that the beads underneath a disc act like damped springs and that once the vertical force acting on them crosses a threshold the granular surface destabilises. At higher masses, instead, they devised an expression for the resistive force imparted on a disc by the accumulated beads, and then used that to work out the pressure at which sliding should cease.

The researchers also carried out a separate experiment in which they used a sensor to measure the frictional force on an object as it moved along a horizontal granular surface. They found, in agreement with their slope experiment, that the lowest coefficient of friction occurred for objects exerting a small, but not very small, pressure. As they point out, previous studies of friction on granular surfaces – which do not report such a dip in the coefficient – were carried out using larger masses.

Ant magic

Applying their work to the natural world, the researchers compared their results to those reported two years ago by a group comprising two of the current team (Antoine Humeau and Jérôme Casas of the CNRS Insect Biology Research Institute in Tours). That earlier research investigated which of various sized ant species – the biggest weighing in at 8 mg – an antlion could most readily capture in traps built from small glass beads. The easiest prey, in fact, were ants weighing about 2 mg. In other words, both studies indicate that it is ants with an intermediate mass that are most vulnerable to antlions.

Daniel Goldman, a biomechanics expert at the Georgia Institute of Technology in the US, praises the “creative” work of the French group, agreeing that it “points to novel granular slope physics which could be relevant to antlion prey capture”. He also believes the research could have practical applications, helping scientists to better tune robots’ motion so that they generate appropriate pressures when ascending sandy slopes on Earth and other planets.

The research is published in Physical Review Letters.

Cosmic-ray detector heads to the International Space Station

The Cosmic Ray Energetics And Mass for the International Space Station launches from NASA’s Kennedy Space Center in Florida (Courtesy: NASA TV)

NASA has launched a space-based probe that will study the origins of highly energetic particles, known as cosmic rays. Sent into space by a Space X rocket yesterday, the Cosmic Ray Energetics And Mass for the International Space Station (ISS-CREAM) will now be installed on the Japanese Experiment Module, where it will study cosmic rays for three years.

Cosmic rays zoom through space at nearly the speed of light and consist of a range of particles from protons to carbon atoms. When cosmic rays enter the Earth’s atmosphere they collide with another particle setting off a cascade of secondary particles. While Earth-bound detectors only see the secondary particles, a probe that is above Earth’s atmosphere will be able to spot the primary particles.

ISS-CREAM is a successor to six similar missions that have flown on long-duration balloons, which began in 2004 with the first flight of the Cosmic Ray Energetics and Mass mission. “The mysterious nature of cosmic rays serves as a reminder of just how little we know about our universe,” says Eun-Suk Seo from the University of Maryland, who is the lead investigator for ISS-CREAM. “This is a very exciting time for us as well as others in the field of high-energy particle astrophysics.”

Plasmonic nanoparticles boost light emission

Plasmonic nanoparticle arrays have the potential to improve the emission efficiency of solid-state lighting. Silver and gold nanoparticles were already known to enhance efficiency at visible wavelengths, but they require a complicated, multi-step fabrication process. Now, researchers at the University of Michigan in the US have included plasmonic gallium (Ga) nanoparticle arrays at buried interfaces within semiconducting layers. The nanoparticles can be easily incorporated into targeted areas in a wide range of semiconductor devices. The resulting structures show improved photoluminescence efficiency for emission wavelengths from near-infrared to ultraviolet.

Writing in Journal of Applied Physics, lead authors Myungkoo Kang and Sunyeol Jeon describe how an array of Ga nanoparticles was produced by rastering a Ga+ focused ion beam across a gallium arsenide (GaAs) substrate. The trick is to tilt the beam to an off-normal angle to the substrate, which prompts Ga nanoparticles to self-assemble in close-packed arrays. The diameter of the Ga nanoparticles was controlled by the angle of incidence of the beam on the GaAs surface. Kang and Jeon then grew a layer of GaAs on top of the substrate and the nanoparticles using molecular-beam epitaxy, embedding the Ga nanoparticles within the GaAs material.

Top: plasmonic Ga nanoparticles are produced on a GaAs substrate in a one-step process using a focused ion beam (FIB). Subsequent GaAs overgrowth embeds the Ga nanoparticles. Middle: atomic force microscope image of the FIB-patterned Ga nanoparticles on a GaAs substrate (left); a transmission electron microscope image of the Ga nanoparticles embedded between a GaAs substrate and an overgrown GaAs layer (right). Bottom: The steps of the growth process illustrated by chocolate chip muffins. Courtesy: M Kang et al.

To investigate the effect of nanoparticle diameter and overgrown GaAs layer thickness on photoluminescence efficiency, the researchers used a combination of photoluminescence spectroscopy and electromagnetic computational simulations. They found that the optimal combination of nanoparticle diameter and embedment depth led to improved photoluminescence efficiency compared to high-quality GaAs epilayers without embedded nanoparticle arrays.

Polycrystalline or not?

Structural characterization by transmission electron microscopy revealed that the Ga nanoparticles were amorphous, while the overgrown zincblende-structured GaAs layers were polycrystalline. Usually polycrystallinity is undesirable in such devices, so the team is now working on improving the crystallinity of the overgrown material.

As the researchers point out in their paper, however, “polycrystalline III-V compound semiconductors have been proposed for LEDs in large-area displays. Indeed, this new Ga nanoparticle plasmonics approach would enable polycrystalline gain media deposited on large-area substrates to maintain reasonable light-emitting characteristics. Thus, this approach provides an opportunity to enhance the photoluminescence efficiency from a variety of semiconductor heterostructures.”

The work is detailed in Journal of Applied Physics 10.1063/1.4990946

Structure and mechanics determine cell performance

The environment that surrounds cells in a tissue or organ, the extracellular matrix, is arguably just as critical to cell function as the cell itself. Researchers from the University of Illinois at Urbana-Champaign have now devised a lab-based method to alter the stiffness of this surrounding architecture, and have shown that softer environments increase the functional properties of vascular cells (Biomaterials 140 45). They also found that applying a mechanical force to the cells – designed to mimic the effect of blood flow over vascular cells – increased functionality in cells with stiffer surrounding environments, which are typically associated with aged or diseased vascular systems.

Deborah Leckband and her team showed that a combination of extracellular stiffness and mechanical force disrupts the vascular system, which then initiates a remodelling of the intracellular architecture. They assessed the functionality of vascular cells by measuring the distance between specialized proteins that sense changes in the physical environment surrounding cells, and then translate them into signals that alter cell function. The researchers found that disturbing the receptors of these so-called gap-junction proteins with a mechanical force had a negative biophysical effect on the cells, confirming that both mechanical and physical properties surrounding a cell affect its functionality.

Stiffness regulation

The team used special biomaterials called hydrogels to alter the stiffness of the extracellular matrix surrounding vascular cells. Hydrogels offer extremely useful properties, since they have the structural properties of a solid but can also attain a water saturation of more than 99%. By altering the concentration of the primary material within the hydrogel, the researchers were able to vary the stiffness of the surrounding environment between 1.1 kPa and 1 GPa.

In these experiments, the cells were placed on top of a hydrogel, but other researchers have encapsulated cells within a hydrogel to provide a 3D environment. In future, this approach could also be used by the Illinois group, and it can also be applied to many different types of cells, not just to vascular cells.

Vascular translation

With this new research, Leckband and her team have provided a better understanding of how the biophysical properties surrounding vascular cells affect their function. By probing the effect of increased stiffness on vascular cells, they have shown how cell function can be disturbed by the stiffening of the vascular architecture that’s observed with age. The results could also lead to improved strategies for modelling disease, since in vitro models could replicate vascular diseases more effectively by using stiff hydrogels to mimic aged and diseased vascular environments.

‘Solar glasses’ provide power as well as shade

The dark lenses of sunglasses have been replaced with organic solar cells by scientists in Germany. The cells are able to power a small mircocontroller that sends information on ambient conditions to a couple of displays in the spectacle arms, and in future might provide power for personal devices such as hearing aids.

Organic solar cells are less efficient than conventional silicon devices and not as resistant to continuous strong sunlight, making them less suited to providing power from rooftops. But, according to team member Daniel Bahro of the Karlsruhe Institute of Technology (KIT), the fact that they are light, flexible and transparent opens up a number of new, previously impractical applications.

Bahro and colleagues designed the new “lenses” to have a similar weight and transmission spectrum to those in normal sunglasses. The lenses are made from a polymer and two types of fullerene molecules sandwiched between electrodes and layers of glass. They are then inserted into a commercially available plastic frame. Once connected to a printed circuit board and liquid crystal display in each spectacle arm, they provide information on the ambient light intensity and temperature.

Can’t handle the light

The team found that in outdoor light with an intensity of 1 “sun” the device converted just 0.06% of incoming power to electricity and yielded under a milliwatt of power. Bahro says that this was in part due to the use of a single piece of solar cell for each lens. He and his colleagues could instead have joined lots of narrow cells together in order to limit the “Ohmic losses” that result when charge carriers travel through a cell’s electrodes. However, he explains, doing so would have impaired vision.

The fact that Ohmic losses are proportional to the square of the current, which rises with light intensity, meant that the glasses performed proportionally much better at lower intensities. At 0.01 suns the efficiency of each cell reached 2.4%, which yielded an output of 400 μW. As such, the researchers tailored their electronics to duller conditions such as those typical to offices and other indoor environments.

At about 0.002 suns, which is typical of indoor lighting, each lens had an efficiency of 6.7% and produced around 200 μW. That is too low for mobile phones, common light-emitting diodes or portable music players, but, says Bahro, would be enough for hearing aids, remote controls and some wrist watches. He also believes the technology could reduce the size of the battery or limit the frequency of recharging in power-hungry “smart glasses”, such as the Google Glass headset.

Showing off

Bahro acknowledges that the technology is not yet practical for many applications, given the need for cables to join the glasses to wherever the power is required (as well as the fact that the device works best in conditions that make sunglasses largely redundant). But he says that he and his colleagues were not aiming to commercialise the technology; rather they intended it as a way of showing off the benefits of organic solar cells.

Indeed, Bahro adds that many visitors to the Hannover Messe trade fair in Germany this April, where the device was on display, couldn’t tell the difference between the solar glasses and normal sunglasses. “People usually think of solar cells as bluish-coloured modules,” he says. “They don’t expect them to be transparent, or coming in different shapes and colours.”

The research is published in the journal Energy Technology.

Ancient eclipse art, asteroid finds early fame, unwitting face of graphene underwear

By Sarah Tesh, Matin Durrani and Michael Banks

The approaching total solar eclipse on 21 August is the subject of much interest and excitement — but the Earth has of course been in and out of the Moon’s shadow since it formed. While we have the technology to take spectacular photos of the corona framing the Moon, our ancestors were limited to much cruder means of recording such events. For example, the ancient petroglyph (a carving in rock) shown above may represent a total eclipse that occurred in 1097.  The carving is on a free standing rock known Piedra del Sol  in New Mexico’s Chaco Canyon.  “I think it is quite possible that the Chacoan people may have congregated around Piedra del Sol at certain times of the year and were watching the sun move away from the summer solstice when the eclipse occurred,” says solar physicist J. McKim Malville from the University of Colorado, Boulder in the US, who focuses on archaeoastronomy. Other nearby carvings may be related to the 1054 supernova and the passing of Halley’s Comet in 1066. “The appearance of the spectacular supernova and comet may have alerted the residents of the canyon to pay attention to powerful and meaningful events in the sky,” says Malville. Hopefully our records of astronomical events will be as long lasting as those of the Chacoan people.

They say asteroids crashing into the Earth is one scientific topic you can guarantee will always make it into the mainstream media. And so it proved this week, with plenty of coverage of asteroid 2012 TC4, which will pass close to Earth on 12 October this year. Quite why this story made it onto various news outlets, from the Guardian and the Daily Mail to MSN News and the Telegraph isn’t quite clear. That’s because the asteroid, which is about 15-30 metres long, will “zoom harmlessly” at a distance of about 44,000km past the Earth, according to a press release from Agence France-Presse (AFP). As Detlef Koschny from the European Space Agency’s near-Earth bojects team told AFP: “There is no possibility for this object to hit the Earth”. The asteroid’s trajectory is a close miss for sure – the farthest satellites are 36,000 km from our planet – but we’re scratching our heads why this rocky body’s trajectory is has made it into the news two months before it flies by. I guess people just love click-bait scare stories. Look at us, even we’ve been snared. And so, now, have you.

“It’s absolutely shameful for them to use my name in their marketing campaign without my permission,” proclaimed the Nobel laureate Andre Geim from the University of Manchester. For the past two years Geim, who recently said that he could leave the UK because of Brexit, has been the face of a Chinese underwear company that claims to have incorporated graphene into its products. The firm, Shenquan, says that by putting graphene into its garments it can help them retain heat, eliminate odours, kill bacteria and even improve sexual performance. “I was told that because the material is ‘very black’ it retains heat better. I pointed out that this contradicted basic science because dark surfaces emit heat better, not retain it,” Geim told the South China Morning Post. “After this remark, the company gave me boxers and a pair of socks to try for myself to see how it works … I never put them on because their textile felt low quality and uncomfortable, at least in 2015.” Ouch.

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