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Home » Page 1077

Neural networks provide deep insights into the mysteries of water

Artificial neural networks have been used to simulate interactions between water molecules and provide important clues about the remarkable properties of this live-giving substance. The study has been carried out by physicists in Germany and Austria, who used the networks to perform simulations 100,000 times faster than possible with conventional computers. Their work offers explanations for two key properties of water – its maximum density at 4 °C and its melting temperature – but the technique could be expanded to include other aspects of this ubiquitous substance.

Physicists and chemists have long found water’s unusual properties difficult to explain. Its density, for example, peaks at around 4 °C, which means that frozen water floats on liquid water – a property that is vital for aquatic creatures that have to survive in cold climates. Massive computer simulations have shown that hydrogen bonds between water molecules play a key role, but these simulations do not tell the whole story.

One key challenge is understanding the role of van der Waals interactions, which arise from quantum fluctuations in the electrical polarizations of water and other molecules. Van der Waals interactions have traditionally been hard to include in computer simulations, but Tobias Morawietz and colleagues at the Ruhr-Universität Bochum and the University of Vienna have now used artificial neural networks (ANNs) to model them in water. ANNs are computer algorithms that “learn” how to perform a specific task by being fed data related to that task. An ANN could, for example, learn how to recognize an individual’s face by being fed photographs of people and being told which images are of the target person.

Computationally expensive

In this latest research, Morawietz and his team fed the ANNs data from density functional theory (DFT) calculations of the interactions between water molecules. DFT is widely used to calculate the properties of molecules, but for interactions between water molecules, it can only provide an approximate result that must then be corrected to account for van der Waals interactions. Such calculations are also computationally expensive and so are normally done at just a few temperatures and pressures.

The problem is that to understand the density maximum of water, researchers need to do lots of calculations at different temperatures, which is too computationally intensive to be practical. The team therefore taught their ANNs using data from both van der Waals-corrected and uncorrected DFT calculations, which let the ANNs learn how van der Waals interactions affect the interactions between water molecules.

The ANNs were then used to calculate the properties of water in the temperature range from –100 to 90 °C, which they could do about 100,000 times faster than possible using DFT. Morawietz and colleagues were therefore able to determine the molecular structure of water over a range of temperatures and, then, infer the density of liquid water and ice.

Competing effects

The results reproduced the density maximum at 4 °C, which Morawietz says can be understood in terms of how van der Waals interactions affect the hydrogen bonding of water molecules. As liquid-water cools, the hydrogen bonds between a water molecule and its four nearest neighbours become stronger, pulling them together and making the water denser.

However, as the bonds strengthen, Morawietz says that this group of five molecules becomes more rigid – and so it becomes less likely that a surrounding water molecule can penetrate this tightly knit group. This has the opposite effect on density: as the temperature decreases, the hydrogen bonds become more rigid, allowing fewer water molecules to penetrate the group and so decreasing the density upon cooling.

According to Morawietz and colleagues, the ANN calculations show that van der Waals interactions moderate the rigidity of the hydrogen bonds, with these two competing density effects creating a maximum density at 4 °C. “van der Waals interactions crucially modify the hydrogen-bond network in water and give hydrogen bonds the right flexibility to exhibit a density maximum,” explains Morawietz.

He adds that the ANN calculations also show that van der Waals interactions make liquid water denser than ice at 4 °C, explaining why ice floats when it is formed. The calculations were also able to predict the melting temperature of ice.

Other approaches

Alan Soper of the Rutherford Appleton Laboratory in the UK told physicsworld.com that this research demonstrates clear progress in addressing the inability of DFT to simulate van der Waals interactions. However, he points out that several alternative computational approaches have been used and have delivered results that are comparable to those of Morawietz and colleagues.

Soper also points out that the discrepancy between the measured density of water and the calculated result is either 5 or 10% – depending on which DFT scheme the team used. While the team’s predictions for pressure and structure are much closer to experimental values, he says that a density discrepancy of less than 1% is needed to validate the model.

Morawietz says that the team is now adapting its technique to study proton transfer in water – an effect that is currently difficult to simulate but plays an important role in acid-base chemistry.

The simulations are described in Proceedings of the National Academies of Science.

Electrical waves travel through bioengineered tissue

A genetically engineered tissue that can be electrically excited by light has been developed by researchers in the US. The team believes its new material could be used as a simple model of the heart, allowing information about electrical malfunctions such as arrhythmias to be gathered. It could also lead to the development of biological computers that could be interfaced with the natural world.

The human heart is an extremely complex tissue, and when things go wrong with it, doctors and scientists often struggle to determine the causes of specific symptoms and devise appropriate treatments. Researchers are therefore trying to create simplified model systems for the heart to gain a better understanding of how it functions. A simplified model of the heart can be produced using electrically coupled cells, so that a change in the electrical potential of one induces a change in the potential of its neighbours. This allows electrical waves to propagate through the tissue – just as they do in a beating heart.

In this latest research, biophysicist Adam Cohen and colleagues at Harvard University based their model on human embryonic kidney cells. Such cells are not normally electrically excitable, and Cohen says they formed a “blank slate” for the study. The researchers edited the cells’ genomes so that the cells developed four ion channels – pores that can open or close to allow specific ions in or out of the cell, altering its electrical potential. First, they added a potassium-ion channel present in the heart to allow positive potassium ions (K+) out of the cell and lower the resting electric potential. Second, they added a sodium-ion channel – also present in the real heart – that opens when the potential increases. This allows sodium ions (Na+) into the cell, creating a runaway increase in voltage.

Red and blue light

In equilibrium, the K+ channel holds the potential down, keeping the Na+ channel closed, and the cells stay negatively charged. However, an increase in applied voltage will open the Na+ channel, triggering a voltage spike that opens the Na+ channels of neighbouring cells and sends an electrical pulse like a heartbeat through the tissue. Finally, they added two light-responsive-ion channels that they had developed previously. One of these channels raises a cell’s potential in response to blue light, while the other creates a voltage-dependent fluorescence in response to red light. Together, these allowed the team to trigger and image the electrical waves in the tissue culture.

The researchers then measured various properties of their tissue culture, which revealed a few surprises. “If you drive a real heart too fast, it can go into an arrhythmia, where it starts to beat erratically,” explains Cohen. “No matter how fast we paced them, we were never able to trigger arrhythmias in these cells. There are elaborate feedback mechanisms that allow the heart to adapt to changes in demand, and it’s actually those feedbacks gone awry that lead to arrhythmias.” The researchers are now planning to add in other ion channels “one at a time”, to learn about their individual contributions.

Circulating waves

In addition to modelling the heart, the researchers showed that electrical circuits could be created and reconfigured dynamically in the tissue. After firing once, the Na+ channels are not re-armed until after the light is turned off, so permanently illuminating a region with blue light makes it unexcitable. Rings of excitable tissue could sustain continuously circulating waves in either direction for more than 1000 cycles. The waves could easily be stopped with blue light, however, before being launched in the opposite direction – thereby forming a rudimentary cellular memory.

In the future, more complex logical operations could be implemented using the tissue cultures, and these could be used to perform complex bioelectrical computations. However, the clock speed of such cellular computers would be limited to about 100 Hz by the recovery time of the cells – which is millions of times slower than standard computers. The researchers also point out that the tissues could be used in environmental sensors that detect the presence of specific chemicals. “One could put ion channels into these cells that are activated by different things one might want to sense in the environment,” says Cohen.

Gil Bub of the University of Oxford in the UK describes the work as “important”. “It’s a very nice reductionist approach with a tremendous amount of power for figuring out what specific [ion] currents are responsible for what types of behaviour,” he says. “The potential downside is that you don’t necessarily know what currents and what feedback loops are there in the intact system.” He says these kinds of experiments will be most useful if performed in tandem with experiments on the real heart.

The research is published in Physical Review X.

Physics World talks to Spanish TV about migrating Nobel laureates

 

By Hamish Johnston

A few weeks ago I was in Germany for the 66th Lindau Nobel Laureate Meeting, where I moderated a “press talk” about migration and science. This was essentially a panel discussion that involved two chemistry Nobel laureates – Martin Karplus and Daniel Shechtman – and two early-career physicists: Winifred Ayinpogbilla Atiah from Ghana and Ana Isabel Maldonado Cid from Spain.

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Relativistic electrons trapped within graphene quantum dots

Images of relativistic electrons trapped in graphene quantum dots have been taken by physicists in the US and Japan. The ability to confine and control electrons in such a way could play an important role in developing graphene-based nanoscale devices and could also provide a better understanding of these exotic “Dirac fermions”.

Graphene is a honeycomb lattice of carbon atoms just one atom thick that was first isolated in 2004. It has a number of unique electronic properties, many of which come from the fact that it is a semiconductor with a zero-energy gap between its valence and conduction bands. Near where the two bands meet, the relationship between the energy and momentum of charge carriers (electrons and holes) in the material is described by the Dirac equation and resembles that of a photon. These bands, called Dirac cones, enable these charge carriers to travel through graphene at extremely high speeds approaching that of light. This extremely high mobility means that graphene-based electronic devices such as transistors could be faster than any that exist today.

Tunnelling problems

Despite the material’s many useful properties, there are still many challenges facing researchers trying to create graphene-based devices. One problem is related to the fact that the behaviour of charge carriers in graphene is governed by Klein tunnelling – a counter-intuitive effect in which relativistic particles can pass through a potential barrier with 100% probability. Because graphene’s charge carriers behave like relativistic particles, Klein tunnelling is therefore predicted to exist in potential barriers (p–n junctions) fabricated in the material.

“This exotic behaviour, albeit very interesting, makes trapping and controlling graphene’s charge carriers very difficult,” explains team-member Jairo Velasco Jr of the University of California, Berkeley, and the University of California, Santa Cruz. “It is, however, important for us to be able to map the behaviour of these Dirac fermions at p–n junction boundaries, to explore Klein tunnelling physics in the carbon material and to better control and confine the electrons in it.”

The researchers, led by Michael Crommie, created circular p–n junctions in graphene by positioning the tip of a scanning tunnelling microscope (STM) about 2 nm above the surface of a graphene sample while applying a voltage pulse to the tip. “While doing this, we also apply a constant voltage on a silicon slab that is below the graphene, but separated from it by a silicon-oxide capping layer and a boron nitride (BN) flake,” says Velasco. “The intense electric field emanating from the STM tip ionizes defects in the BN region directly beneath the tip and the released charge migrates through the BN to the graphene. This leaves behind a space-charge build-up in the BN that screens the electric field from the silicon slab.”

Mapping wavefuctions

The next step is to take an image of the Dirac fermions in the graphene sample. “To do this, we position our STM tip about [0.1 nm] above the graphene surface,” continues Velasco. “This allows us to measure a tunnelling current between the suspended STM tip and the graphene surface.” This measurement is a direct probe of the quantum-mechanical wavefunction of electrons in the carbon material. By moving the STM tip to different lateral positions on the sample, this allows the team to build-up an image of how the wavefunction varies inside and outside the circular p–n junction (see figure).

Until now, obtaining direct images of electron wavefunctions in graphene had been notoriously difficult. This was because the systems in which researchers were trying to observe them – lithographically patterned structures, graphene edges and chemically synthesized graphene islands, for example – contained too many defects.

Mark Fromhold of Nottingham University in the UK, who was not involved in this work, says that defects are “often problematic in solid-state devices because they produce unwanted electrical or optical behaviour. But in this beautiful new experiment, the Crommie group has shown how defects can be used, together with a scanning probe, to overcome a major challenge in graphene physics, namely how to stop electrons leaking through p–n junctions by Klein tunnelling. Not only did the researchers manage to confine the electrons in a quantum dot created in the graphene layer, but they were also able to directly map both the resulting energy-level spectrum and the corresponding quantum wavefunctions.”

Quantum dots

According to Velasco and colleagues, the techniques developed in this work could now be used to study more complicated systems as well, such as multiple quantum dots with arbitrary geometries. “This is because the graphene circular p–n junctions we made (which can be considered as quantum dots too) are fully exposed, and so we can directly access them with real-space imaging probes,” Velasco says. “This is completely different to conventional semiconductor quantum dots, which are generally inaccessible.”

The team, reporting its work in Nature Physics, says that it now also plans to investigate bilayer graphene, which hosts massive Dirac charge carriers. “These charge carriers are expected to completely reflect upon impinging on a p–n junction barrier, independent of the barrier width.”

The same issue of Nature Physics also contains a paper by Christopher Gutiérrez of Columbia University and colleagues who have also obtained images from electrons trapped in a graphene quantum dot.

Dinner that’s out of this world, Higgs pizza and a cosmic symphony

 

By Michael Banks and Tushna Commissariat

Before setting off to the International Space station (ISS) for six months, UK astronaut Tim Peake revealed that one of the meals he would miss most is the classic British roast dinner. So what better way to celebrate the 44 year old’s safe return to Earth last month than to create a portrait of him made from his favourite nosh? Designed by UK “food artist” Prudence Staite for the Hungry Horse pub chain, the culinary creation took 20 hours to make – you can watch a timelapse video of it being created above. The finished portrait weighed in at 12 kg and says “Welcome Home Tim”. Hungry Horse has even offered Tim and his family free roast dinners for life.

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Thirty Meter Telescope may not be built in Hawaii, say astronomers

Officials behind the proposed Thirty Meter Telescope (TMT) are considering new locations for the $1.4bn facility, and expect to decide whether to opt for a new site early next year. The TMT is due to be built on Hawaii’s Mauna Kea mountain but, following protests from local residents, its building permit was revoked last December by the state’s Supreme Court. New locations that are being considered include Baja California in Mexico, the Canary Islands and Chile, as well as locations in India and China.

The TMT board had chosen Mauna Kea, which already hosts 13 other telescopes, as the observatory’s site in July 2009. Over the following six years, the organization received a series of necessary approvals and permits. However native Hawaiians, who regard the Mauna Kea summit as sacred – and who had previously objected to the growth in the number of telescopes there – carried out a protest at the telescope’s ground-breaking in October 2014.

Six months later, following further demonstrations, Hawaii governor David Ige announced a temporary postponement of the project. Then last December, the Hawaiian Supreme Court invalidated the TMT’s building permit, ruling that the State Board of Land and Natural Resources had not followed due process when it was approved. The court then remanded the case back to the board.

Looking for plan B

TMT managers began to consider other sites for the telescope in January. “The TMT’s board of directors decided to study other potential sites while the contested case takes its course in Hawaii,” says TMT spokesperson Scott Ishikawa. “We need a reasonable plan B, should the Hawaii option not be feasible in a timely fashion.”

Hawaii is still an option but we are very actively looking at alternatives

Fiona Harrison, Caltech

A key factor in the search for different locations is that construction of the TMT is planned to begin in April 2018 with completion in 2022. “It’s no secret that the TMT project is looking at alternatives, driven by schedule considerations; if you stretch the project out, the cost will go up,” Fiona Harrison, a physicist at the California Institute of Technology and member of the TMT International Observatory’s board of governors, told Physics World. “Hawaii is still an option but we are very actively looking at alternatives. We’ll be culling down [the list of sites] to a few options over the summer.”

Despite the uncertainty over the site, work is still continuing on the TMT. Fengchuan Liu, TMT deputy project manager, told SPIE’s Astronomical Telescopes + Instrumentation 2016 conference in Edinburgh last week that the uncertainty around the site has not delayed work on the telescope’s design and related issues. “The team is not sitting idle,” he says. “We are making progress and spending each dollar wisely.” He adds that a decision on a new site will be made “by early 2017”.

Still “first choice”

According to Ishikawa, the Hawaii site is still “first choice”, and the process to reapply for the permit is already under way. The case for Hawaii was strengthened by the addition last month of the TMT International Observatory (TIO) to the TMT organization as an applicant for the permit. Formed in May 2014, the TIO consists of the California Institute of Technology, Japan’s National Institutes of Natural Sciences, the National Astronomical Observatories of the Chinese Academy of Science, the regents of the University of California, as well as organizations from India and Canada.

Neutrinos that go bump in the night

Tripple bump: The 5 MeV bump data presented by K. Joo at Neutrino 2016 conference (Courtesy: RENO collaboration)
Triple bump: the 5 MeV bump data presented by K Joo at the Neutrino 2016 conference. (Courtesy: RENO Collaboration)

 

By Tushna Commissariat

A final mystery that was mentioned at the Neutrino 2016 I attended in London this week was yet another unexpected “bump” in data at 5 MeV, measured while monitoring the neutrino flux from nuclear power plants. Starting with the RENO experiment in 2012, it was spotted by the Double Chooz experiment in 2014 and finally by the Daya Bay neutrino experiment earlier this year. While the initial signal was not of high enough statistical significance, it has now held up over time and more measurements.

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Limiting factors for the elusive sterile neutrino

 

By Tushna Commissariat

More data are definitely needed in the quest for the sought-after sterile neutrino. That much was clear as more than 10 different global neutrino detectors announced at the Neutrino 2016 conference in London that they have found no evidence for the slippery particle’s existence. The sterile neutrino is a hypothetical and much-debated fourth type of neutrino that would contribute mass, but only interact with the other three “active neutrinos”, making it that much more difficult to detect. In the video above, Physics World features editor Louise Mayor explains why researchers are so keen to nail down this particle, should it exist, as it may single-handedly explain some of the biggest mysteries in physics today, including dark matter.

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Symmetry-violating neutrinos may hold the key to antimatter

 

Deep trap: Inside the Super-Kamiokande neutrino detector (Courtsey: T2K collaboration)
Deep trap: Inside the Super-Kamiokande neutrino detector. (Courtesy: T2K Collaboration)

By Tushna Commissariat

As you may have read, earlier this week I was at Neutrino 2016 – the 27th International Conference on Neutrino Physics and Astrophysics – in London. Although I was only at two days of the week-long conference, I still have neutrinos on my mind. A whole host of experiments presented various data and updates. Indeed, the researchers presenting the latest results from the Tokai to Kamioka (T2K) experiment in Japan and the NOvA Neutrino Experiment at Fermilab in the US had some interesting things to say.

T2K collaborator Hirohisa Tanaka, from the University of Toronto in Canada, revealed that the experiment’s most recent data seem to support earlier hints that there may be different oscillation probabilities for neutrinos and antineutrinos. If these data hold up, then it would have big consequences – the standard model of neutrino physics says that these two oscillation rates should be the same so as not to violate charge–parity (CP) symmetry. According to the collaboration, their observed “electron antineutrino appearance event rate is lower than would be expected based on the electron neutrino appearance event rate, assuming that CP symmetry is conserved”.

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Giant planet orbits three stars and enjoys multiple sunsets

Imagine a world where three “suns” set one after another on some evenings, but at other times of the year there is always daylight. That is what it would be like on HD 131399Ab, which is a newly discovered planet four times as massive as Jupiter that orbits in a system of three stars. Spotted by an international team of astronomers using the SPHERE instrument on the Very Large Telescope in Chile, its very existence challenges current theories of how planetary systems form and evolve.

Astronomers have discovered more than 3000 planets orbiting stars other than the Sun, and the nearby universe is expected to harbour vast numbers of such extrasolar planets (exoplanets). So far, the exoplanets that we know about range from rocky bodies several times more massive than Earth to gas giants that dwarf Jupiter. HD 131399Ab is the first exoplanet to be discovered by the European Southern Observatory’s SPHERE instrument, which saw first light in 2014 and is designed to detect the extremely faint infrared light coming directly from distant exoplanets. Detecting light from an exoplanet is an extraordinarily difficult task, which is why most earlier discoveries of exoplanets were made by measuring their effect on light from their companion stars.

HD 131399Ab was spotted by Kevin Wagner and Daniel Apai of the University of Arizona, along with astronomers in the US, Germany and France. The team was astounded to find the planet in a very wide orbit around one of the stars (called A), with the two bodies separated by about 50 astronomical units (AU). This is a much larger orbit than any planet in the solar system – the furthest Neptune gets from the Sun is about 30 AU. The other two stars (B and C) are bound together in a binary system that is about 300 AU from A. Star A is the largest in the system, weighing in at about 1.8 solar masses, whereas B is slightly smaller than the Sun and C is about 0.6 solar masses. The system is about 300 light-years away from Earth.

Stable or unstable?

HD 131399Ab’s very wide orbit around A – which the team has calculated takes 550 Earth years to complete – came as a big surprise because astronomers had believed that such an orbit in a three-star system would be unstable. The team created a computer model of the system to try to understand why it holds together. “Our computer simulations showed that this type of orbit can be stable; but if you change things around just a little bit, it can become unstable very quickly,” explains Apai. The team also believes that the exoplanet may not have formed in its current orbit. One possibility is that HD 131399Ab once circled two stars but its orbit was disrupted by gravitational interactions with another unseen exoplanet or with the stars in the system.

Although the simulations do not provide a complete description of the motions of the exoplanet and its three stars, it gives enough information for Wagner to paint a vivid picture of one possible scenario. “For about half of the planet’s orbit, which lasts 550 Earth years, three stars are visible in the sky; the fainter two are always much closer together, and change in apparent separation from the brightest star throughout the year,” he says. “For much of the planet’s year, the stars appear close together, giving it a familiar night-side and day-side, with a unique triple sunset and sunrise each day.”

Midnight sun

Wagner explains, however, that this day–night cycle does not last for the entire HD 131399Ab year. “As the planet orbits and the stars grow further apart each day, they reach a point where the setting of one coincides with the rising of the other – at which point the planet is in near-constant daytime for about one-quarter of its orbit, or roughly 140 Earth years,” he says.

Despite the huge distance between HD 131399Ab and star A, the temperature on the surface of the planet is expected to be about 850 K (580 °C) despite being so far from its star. This could be related to the exoplanet’s youth – it is estimated to be just 16 million years old. In comparison, the Earth has been around for about 4.5 billion years.

“It is not clear how this planet ended up on its wide orbit in this extreme system, and we can’t say yet what this means for our broader understanding of the types of planetary systems out there, but it shows there is more variety out there than many would have deemed possible,” Wagner says. “What we do know is that planets in multi-star systems are much less explored, and potentially just as numerous as planets in single-star systems.”

The research is described in Science.

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