Aurelia Butler

Musicians are helping scientists analyze data, teach protein folding and make new discoveries through sound.
A team of researchers at the University of Illinois Urbana-Champaign is using sonification — the use of sound to convey information — to depict biochemical processes and better understand how they happen.
Music professor and composer Stephen Andrew Taylor; chemistry professor and biophysicist Martin Gruebele; and Illinois music and computer science alumna, composer and software designer Carla Scaletti formed the Biophysics Sonification Group, which has been meeting weekly on Zoom since the beginning of the pandemic. The group has experimented with using sonification in Gruebele’s research into the physical mechanisms of protein folding, and its work recently allowed Gruebele to make a new discovery about the ways a protein can fold.
Taylor’s musical compositions have long been influenced by science, and recent works represent scientific data and biological processes. Gruebele also is a musician who built his own pipe organ that he plays and uses to compose music. The idea of working together on sonification struck a chord with them, and they’ve been collaborating for several years. Through her company, Symbolic Sound Corp., Scaletti develops a digital audio software and hardware sound design system called Kyma that is used by many musicians and researchers, including Taylor.
Scaletti created an animated visualization paired with sound that illustrated a simplified protein-folding process, and Gruebele and Taylor used it to introduce key concepts of the process to students and gauge whether it helped with their understanding. They found that sonification complemented and reinforced the visualizations and that, even for experts, it helped increase intuition for how proteins fold and misfold over time. The Biophysics Sonification Group — which also includes chemistry professor Taras Pogorelov, former chemistry graduate student (now alumna) Meredith Rickard, composer and pipe organist Franz Danksagmüller of the Lübeck Academy of Music in Germany, and Illinois electrical and computer engineering alumnus Kurt Hebel of Symbolic Sound — described using sonification in teaching in the Journal of Chemical Education.
Gruebele and his research team use supercomputers to run simulations of proteins folding into a specific structure, a process that relies on a complex pattern of many interactions. The simulation reveals the multiple pathways the proteins take as they fold, and also shows when they misfold or get stuck in the wrong shape — something thought to be related to a number of diseases such as Alzheimer’s and Parkinson’s. More

A new study describes previously unexpected properties in a complex quantum material known as Ta2NiSe5. Using a novel technique developed at Penn, these findings have implications for developing future quantum devices and applications. This research, published in Science Advances, was conducted by University of Pennsylvania graduate student Harshvardhan Jogand led by professor Ritesh Agarwal in collaboration with professor Eugene Mele and Luminita Harnagea from the Indian Institute of Science Education and Research.
While the field of quantum information science has experienced progress in recent years, the widespread use of quantum computers is still limited. One challenge is the ability to only use a small number of “qubits,” the unit that performs calculations in a quantum computer, because current platforms are not designed to allow multiple qubits to “talk” to one another. In order to address this challenge, materials need to be efficient at quantum entanglement, which occurs when the states of qubits remain linked no matter their distance from one another, as well as coherence, or when a system can maintain this entanglement.
In this study, Jog looked at Ta2NiSe5, a material system that has strong electronic correlation, making it attractive for quantum devices. Strong electronic correlation means that the material’s atomic structure is linked to its electronic properties and the strong interaction that occurs between electrons.
To study Ta2NiSe5, Jog used a modification of a technique developed in the Agarwal lab known as the circular photogalvanic effect, where light is engineered to carry an electric field and is able to probe different material properties. Developed and iterated in the past several years, this technique has revealed insights about materials such as silicon and Weyl semimetals in ways that are not possible with conventional physics and materials science experiments.
But the challenge in this study, says Agarwal, is that this method has only been applied in materials without inversion symmetry, whereas Ta2NiSe5 does haveinversion symmetry, Jog “wanted to see if this technique can be used to study materials which have inversion symmetry which, from a conventional sense, should not be producing this response,” says Agarwal.
After connecting with Harnagea to obtain high-quality samples of Ta2NiSe5, Jog and Agarwal used a modified version of the circular photogalvanic effect and were surprised to see that there was a signal being produced. After conducting additional studies to ensure that this was not an error or an experimental artifact, they worked with Mele to develop a theory that could help explain these unexpected results. More

For the first time, researchers have created a metasurface lens that uses a piezoelectric thin film to change focal length when a small voltage is applied. Because it is extremely compact and lightweight, the new lens could be useful for portable medical diagnostic instruments, drone-based 3D mapping and other applications where miniaturization can open new possibilities.
“This type of low-power, ultra-compact varifocal lens could be used in a wide range of sensor and imaging technologies where system size, weight and cost are important,” said research project leader Christopher Dirdal from SINTEF Smart Sensors and Microsystems in Norway. “In addition, introducing precision tunability to metasurfaces opens up completely new ways to manipulate light.”
Dirdal and colleagues describe the new technology in the Optica Publishing Group journal Optics Letters. To change focal length, a voltage is applied over lead zirconate titanate (PZT) membranes causing them to deform. This, in turn, shifts the distance between two metasurface lenses.
“Our novel approach offers a large displacement between the metasurface lenses at high speed and using low voltages,” said Dirdal. “Compared to state-of-the-art devices, we demonstrated twice the out-of-plane displacement at a quarter of the voltage.”
Combining technologies
The researchers made the new lens using metasurfaces — flat surfaces that are patterned with nanostructures to manipulate light. They are particularly interesting because they can integrate several functionalities into a single surface and can also be made in large batches using standard micro- and nanofabrication techniques at potentially low cost. More

From tiny fruit flies to human beings, all animals on Earth maintain their daily rhythms based on their internal circadian clock. The circadian clock enables organisms to undergo rhythmic changes in behavior and physiology based on a 24-hour circadian cycle. For example, our own biological clock tells our brain to release melatonin, a sleep-inducing hormone, at night time.
The discovery of the molecular mechanism of the circadian clock was bestowed The Nobel Prize in Physiology or Medicine 2017. From what we know, no one centralized clock is responsible for our circadian cycles. Instead, it operates in a hierarchical network where there are “master pacemaker” and “slave oscillator.”
The master pacemaker receives various input signals from the environment such as light. The master then drives the slave oscillator that regulates various outputs such as sleep, feeding, and metabolism. Despite the different roles of the pacemaker neurons, they are known to share common molecular mechanisms that are well conserved in all lifeforms. For example, interlocked systems of multiple transcriptional-translational feedback loops (TTFLs) composed of core clock proteins have been deeply studied in fruit flies.
However, there is still much that we need to learn about our own biological clock. The hierarchically-organized nature of master and slave clock neurons leads to a prevailing belief that they share an identical molecular clockwork. At the same time, the different roles they serve in regulating bodily rhythms also raise the question of whether they might function under different molecular clockworks.
Led by Prof. KIM Jae Kyoung and KIM Eun Young, researchers at the Institute for Basic Science (IBS) and Ajou University used a combination of mathematical and experimental approaches using fruit flies to answer this question. The team found that the master clock and the slave clock operate via different molecular mechanisms.
In both master and slave neurons of fruit flies, a circadian rhythm-related protein called PER is produced and degraded at different rates depending on the time of the day. Previously, the team found that the master clock neuron (sLNvs) and the slave clock neuron (DN1ps) have different profiles of PER in wild-type and Clk-Δ mutant Drosophila. This hinted that there might be a potential difference in molecular clockworks between the master and slave clock neurons.
However, due to the complexity of the molecular clockwork, it was challenging to identify the source of such differences. Thus, the team developed a mathematical model describing the molecular clockworks of the master and slave clocks. Then, all possible molecular differences between the master and slave clock neurons were systematically investigated by using computer simulations. The model predicted that PER is more efficiently produced and then rapidly degraded in the master clock compared to the slave clock neurons. This prediction was then confirmed by the follow-up experiments using animal.
Then, why do the master clock neurons have such different molecular properties from the slave clock neurons? To answer this question, the research team again used the combination of mathematical model simulation and experiments. It was found that the faster rate of synthesis of PER in the master clock neurons allows them to generate synchronized rhythms with a high level of amplitude. Generation of such a strong rhythm with high amplitude is critical to delivering clear signals to slave clock neurons.
However, such strong rhythms would typically be unfavorable when it comes to adapting to environmental changes. These include natural causes such as different daylight hours across summer and winter seasons, up to more extreme artificial cases such as jet lag that occurs after international travel. Thanks to the distinct property of the master clock neurons, it is able to undergo phase dispersion when the standard light-dark cycle is disrupted, drastically reducing the level of PER. The master clock neurons can then easily adapt to the new diurnal cycle. Our master pacemaker’s plasticity explains how we can quickly adjust to the new time zones after international flights after just a brief period of jet lag.
It is hoped that the findings of this study can have future clinical implications when it comes to treating various disorders that affect our circadian rhythm. Chief investigator Kim notes, “When the circadian clock loses its robustness and flexibility, the circadian rhythms sleep disorders can occur. As this study identifies the molecular mechanism that generates robustness and flexibility of the circadian clock, it can facilitate the identification of the cause of and treatment strategy for the circadian rhythm sleep disorders.”
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Materials provided by Institute for Basic Science. Note: Content may be edited for style and length. More

The time a person spends on different smartphone apps is enough to identify them from a larger group in more than one in three cases say researchers, who warn of the implications for security and privacy.
Psychologists Dr Heather Shaw, Professor Paul Taylor and Professor Stacey Conchie from Lancaster University, and Dr David Ellis from the University of Bath analysed smartphone data from 780 people.
Their paper is published in the journal Psychological Science.
They fed 4,680 days of app usage data into statistical models. Each of these days was paired with one of the 780 users, such that the models learnt people’s daily app use patterns.
The researchers then tested whether models could identify an individual when provided with only a single day of smartphone activity that was anonymous and not yet paired with a user.
Dr Ellis from the University of Bath said: “Our models, which were trained on only six days of app usage data per person, could identify the correct person from a day of anonymous data one third of the time.”
That might not sound like much, but when the models made a prediction regarding who data belonged to, it could also provide a list of the most to the least likely candidates. It was possible to view the top 10 most likely individuals that a specific day of data belonged to. Around 75% of the time, the correct user would be among the top 10 most likely candidates.
Professor Taylor from Lancaster University added: “In practical terms, a law enforcement investigation seeking to identify a criminal’s new phone from knowledge of their historic phone use could reduce a candidate pool of approximately 1,000 phones to 10 phones, with a 25% risk of missing them.”
Consequently, the researchers warn that software granted access to a smartphone’s standard activity logging could render a reasonable prediction about a user’s identity even when they were logged-out of their account. An identification is possible with no monitoring of conversations or behaviours within apps themselves.
Dr Shaw from Lancaster University said: “We found that people exhibited consistent patterns in their application usage behaviours on a day-to-day basis, such as using Facebook the most and the calculator app the least. In support of this, we also showed that two days of smartphone data from the same person exhibited greater similarity in app usage patterns than two days of data from different people.”
Therefore, it is important to acknowledge that app usage data alone, which is often collected by a smartphone automatically, can potentially reveal a person’s identity.
While providing new opportunities for law enforcement, it also poses risks to privacy if this type of data is misused.
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Materials provided by Lancaster University. Note: Content may be edited for style and length. More

Although solar cells are typically designed to turn light into power, researchers have shown that they can also be used to achieve underwater wireless optical communication with high data rates. The new approach — which used an array of series-connected solar cells as detectors — could offer a cost-effective, low-energy way to transmit data underwater.
“There is a critical need for efficient underwater communication to meet the increasing demands of underwater data exchange in worldwide ocean protection activities,” said research team leader Jing Xu from Zhejiang University in China. For example, in coral reef conservation efforts, data links are necessary to transmit data from divers, manned submarines, underwater sensors and unmanned autonomous underwater vehicles to surface ships supporting their work.
In the Optica Publishing Group journal Optics Letters, Xu and colleagues report on laboratory experiments in which they used an array of commercially available solar cells to create an optimized lens-free system for high-speed optical detection underwater. Solar cells offer a much larger detection area than the photodiodes traditionally used as detectors in wireless optical communication.
“To the best of our knowledge, we demonstrated the highest bandwidth ever achieved for a commercial silicon solar panel-based optical communication system with a large detection area,” said Xu. “This type of system could even allow data exchange and power generation with one device.”
Optimizing solar cells for communication
Compared to using radio or acoustic waves, light-based underwater wireless communication exhibits higher speed, lower latency and requires less power. However, most long-distance high-speed optical systems are not practical for underwater implementation because they require strict alignment between the transmitter emitting the light and the receiver that detects the incoming light signal. More

University of Wisconsin-Madison physicists have made one of the highest performance atomic clocks ever, they announced Feb. 16 in the journal Nature.
Their instrument, known as an optical lattice atomic clock, can measure differences in time to a precision equivalent to losing just one second every 300 billion years and is the first example of a “multiplexed” optical clock, where six separate clocks can exist in the same environment. Its design allows the team to test ways to search for gravitational waves, attempt to detect dark matter, and discover new physics with clocks.
“Optical lattice clocks are already the best clocks in the world, and here we get this level of performance that no one has seen before,” says Shimon Kolkowitz, a UW-Madison physics professor and senior author of the study. “We’re working to both improve their performance and to develop emerging applications that are enabled by this improved performance.”
Atomic clocks are so precise because they take advantage of a fundamental property of atoms: when an electron changes energy levels, it absorbs or emits light with a frequency that is identical for all atoms of a particular element. Optical atomic clocks keep time by using a laser that is tuned to precisely match this frequency, and they require some of the world’s most sophisticated lasers to keep accurate time.
By comparison, Kolkowitz’s group has “a relatively lousy laser,” he says, so they knew that any clock they built would not be the most accurate or precise on its own. But they also knew that many downstream applications of optical clocks will require portable, commercially available lasers like theirs. Designing a clock that could use average lasers would be a boon.
In their new study, they created a multiplexed clock, where strontium atoms can be separated into multiple clocks arranged in a line in the same vacuum chamber. Using just one atomic clock, the team found that their laser was only reliably able to excite electrons in the same number of atoms for one-tenth of a second. More