Exploring quantum electron highways with laser light

 The translucent crystal at the center of this illustration is a topological insulator, a quantum material where electrons (white dots) flow freely on its surface but not through its interior. By hitting a TI with powerful pulses of circularly polarized laser light (red spiral), SLAC and Stanford scientists generated harmonics that revealed what happens when the surface switches out of its quantum phase and becomes an ordinary insulator.
Credit: Greg Stewart/SLAC National Accelerator Laboratory

Topological insulators, or TIs, have two faces: Electrons flow freely along their surface edges, like cars on a superhighway, but can’t flow through the interior of the material at all. It takes a special set of conditions to create this unique quantum state – part electrical conductor, part insulator – which researchers hope to someday exploit for things like spintronics, quantum computing and quantum sensing. For now, they’re just trying to understand what makes TIs tick.

In the latest advance along those lines, researchers at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University systematically probed the “phase transition” in which a TI loses its quantum properties and becomes just another ordinary insulator.

They did this by using spiraling beams of laser light to generate harmonics – much like the vibrations of a plucked guitar string – from the material they were examining. Those harmonics make it easy to distinguish what’s happening in the superhighway layer from what’s happening in the interior and see how one state gradually gives way to the other, they reported in Nature Photonics.

“The harmonics generated by the material amplify the effects we want to measure, making this a very sensitive way to see what’s going on in a TI,” said Christian Heide, a postdoctoral researcher with the Stanford PULSE Institute at SLAC who led the experiments.

Breaking in a New Planet

Brandon Johnson, an expert in impact crater dynamics, surrounded by some of his favorite research subjects: Mercury, Mars and the moon.
Credit: Purdue University | Rebecca McElhoe

The harder you hit something – a ball, a walnut, a geode – the more likely it is to break open. Or, if not break open, at least lose a little bit of its structural integrity, the way baseball players pummel new gloves to make them softer and more flexible. Cracks, massive or tiny, form and bear a silent, permanent witness to the impact.

Studying how those impacts affect planetary bodies, asteroids, moons and other rocks in space helps planetary scientists including Brandon Johnson, associate professor, and Sean Wiggins, postdoctoral researcher, in the College of Science’s Department of Earth, Atmospheric, and Planetary Sciences at Purdue University, understand extraplanetary geology, especially where to look for precious matter including water, ice and even, potentially, microbial life. A YouTube video is available online.

Every solid body in the solar system is constantly pummeled by impacts, both large and small. Even on Earth, every single spot has been affected by at least three big impacts. Using the moon as a test subject, Johnson, Wiggins and their team set out to quantify the relationship between impacts and a planet’s porosity.

Medieval monks were ‘riddled with worms’, study finds

Augustinian friars being excavated by the Cambridge Archaeological Unit. 
Credit: Cambridge Archaeological Unit

A new analysis of remains from medieval Cambridge shows that local Augustinian friars were almost twice as likely as the city’s general population to be infected by intestinal parasites.

This is despite most Augustinian monasteries of the period having latrine blocks and hand-washing facilities, unlike the houses of ordinary working people.

Researchers from the University of Cambridge’s Department of Archaeology say the difference in parasitic infection may be down to monks manuring crops in friary gardens with their own feces, or purchasing fertilizer containing human or pig excrement.

The study, published today in the International Journal of Paleopathology, is the first to compare parasite prevalence in people from the same medieval community who were living different lifestyles, and so might have differed in their infection risk.

The population of medieval Cambridge consisted of residents of monasteries, friaries and nunneries of various major Christian orders, along with merchants, traders, craftsmen, laborers, farmers, and staff and students at the early university.

Cambridge archaeologists investigated samples of soil taken from around the pelvises of adult remains from the former cemetery of All Saints by the Castle parish church, as well as from the grounds where the city’s Augustinian Friary once stood.

University Scientists Found Out How to Efficiently Extract Silver

Yulia Petrova is engaged in the selection of sorbents in the Laboratory of Chemical Design for New Multifunctional Oxide Materials.
Photo credit: Daniil Kovalenko

Chemists at Ural Federal University have identified the best sorbent based on aminopolymers modified with sulfoethyl groups for the extraction of silver ions from multicomponent solutions. The results of the research lead to the production of sorbents for the extraction of metals which concentration in solutions is insignificant. The obtained sorbents are potentially applicable, for example, in the purification of natural drinking water, fish ponds, and in the processing of industrial waste. The research was supported financially by the Russian Science Foundation (grant № 21-73-00052) and is described in a scientific article published in the Russian Journal of Inorganic Chemistry.

"Sorption of metal ions is facilitated by the very nature of the aminopolymer matrix of the sorbents. Adding sulfoethyl groups to it, as our studies show, leads to a significant increase in the selective properties of sorbents, that is the ability to absorb only certain ions from a wide set of different ions. The higher the degree of modification of sorbents by sulfoethyl groups, i.e. the more sulfoethyl groups in their composition, the better their selective properties. This particular work is dedicated to studying the extraction rate of silver ions from multicomponent solutions in the presence of copper, nickel, cobalt, zinc, and several other metals," says Yulia Petrova, Head of the research group and Associate Professor at the Department of Analytical and Environmental Chemistry at UrFU.

First image of antigen-bound T-cell receptor at atomic resolution

The cryo-EM structure of the fully assembled T-cell receptor (TCR) complex with a tumor-associated peptide/MHC ligand provides important insights into the biology of TCR signaling. These insights into the nature of TCR assembly and the unusual cell membrane architecture reveal the basis of antigen recognition and receptor signaling. 
Credit: Robert Tampé | Goethe University Frankfurt

T cells are our immune system's customized tools for fighting infectious diseases and tumor cells. On their surface, these special white blood cells carry a receptor that recognizes antigens. With the help of cryo-electron microscopy, biochemists and structural biologists from Goethe University Frankfurt, in collaboration the University of Oxford and the Max Planck Institute of Biophysics, were able to visualize the whole T-cell receptor complex with bound antigen at atomic resolution for the first time. Thereby they helped to understand a fundamental process which may pave the way for novel therapeutic approaches targeting severe diseases.

The immune system of vertebrates is a powerful weapon against external pathogens and cancerous cells. T cells play a crucial role in this context. They carry a special receptor called the T-cell receptor on their surface that recognizes antigens – small protein fragments of bacteria, viruses and infected or cancerous body cells – which are presented by specialized immune complexes. The T-cell receptor is thus largely responsible for distinguishing between “self" and “foreign". After binding of a suitable antigen to the receptor, a signaling pathway is triggered inside the T cell that “arms" the cell for the respective task. However, how this signaling pathway is activated has remained a mystery until now – despite the fact that the T-cell receptor is one of the most extensively studied receptor protein complexes.

Increased risk of some neurological and psychiatric disorders remains two years after COVID-19 infection

New diagnoses of disorders including psychosis, dementia, seizures and ‘brain fog’ remain commoner two years after COVID-19 than after other respiratory infections, whereas the increased risks of depression and anxiety after COVID-19 are short-lived and there is no overall excess of cases.

Published in The Lancet Psychiatry, the new study from the University of Oxford and the National Institute for Health and Care Research (NIHR) Oxford Health Biomedical Research Centre investigated neurological and psychiatric diagnoses in over 1.25 million people following diagnosed COVID-19 infection, using data from the US-based TriNetX electronic health record network.

The study reports on 14 neurological and psychiatric diagnoses over a 2-year period and compares their frequency with a matched group of people recovering from other respiratory infections. It also reports data on children and older adults separately, and compares data across three waves of the pandemic. To our knowledge, these are the first robust data addressing these important questions.

Confirming previous studies, many of the disorders are more common after COVID-19. Notably, the increased risk of anxiety and depression subsides within two months of COVID-19 and, over the whole 2-year period, are no more likely to occur than after other respiratory infections. In contrast, diagnoses of many neurological disorders (such as dementia and seizures), as well as psychotic disorders and ‘brain fog’, continue to be made more often after COVID-19 throughout the 2 years.

Results in children (under 18) showed similarities and differences to adults. The likelihood of most diagnoses after COVID-19 was lower than in adults, and they were not at greater risk of anxiety or depression than children who had other respiratory infections. However, like adults, children recovering from COVID-19 were more likely to be diagnosed with some conditions, including seizures and psychotic disorders.

A new neuromorphic chip for AI on the edge, at a small fraction of the energy and size of today’s compute platforms

 The NeuRRAM chip is an innovative neuromorphic chip
Credit: David Baillot/University of California San Diego

An international team of researchers has designed and built a chip that runs computations directly in memory and can run a wide variety of AI applications–all at a fraction of the energy consumed by computing platforms for general-purpose AI computing.

The NeuRRAM neuromorphic chip brings AI a step closer to running on a broad range of edge devices, disconnected from the cloud, where they can perform sophisticated cognitive tasks anywhere and anytime without relying on a network connection to a centralized server. Applications abound in every corner of the world and every facet of our lives, and range from smart watches, to VR headsets, smart earbuds, smart sensors in factories and rovers for space exploration.

The NeuRRAM chip is not only twice as energy efficient as the state-of-the-art “compute-in-memory” chips, an innovative class of hybrid chips that runs computations in memory, it also delivers results that are just as accurate as conventional digital chips. Conventional AI platforms are a lot bulkier and typically are constrained to using large data servers operating in the cloud.

In addition, the NeuRRAM chip is highly versatile and supports many different neural network models and architectures. As a result, the chip can be used for many different applications, including image recognition and reconstruction as well as voice recognition.

Lungless Salamanders Develop Lungs as Embryos Despite Lung Loss in Adults for Millions of Years

 Hemidactylium scutatum larvae, lungless salamander native to eastern North America
Credit: Zachary R Lewis

Lungs are essential to many vertebrates including humans. However, four living amphibian clades have independently eliminated pulmonary respiration and lack lungs, breathing primarily through their wet skin. Little is known of the developmental basis of lung loss in these clades.

In a new study in Science Advances researchers in the Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology at Harvard University examined the Plethodontidae, a dominant family of salamanders, all of which are lungless as adults, and find they actually do develop lungs as embryos shedding light on the evolution of lung loss over millions of years.

The lungless salamander family Plethodontidae is the most species-rich family of salamanders accounting for more than two-thirds of existing salamander diversity. All adult plethondontids are lungless, breathing entirely through nonpulmonary tissues, mainly the skin and the mucus membranes in the mouth and throat. Lung loss has occurred independently at least four times among distantly related amphibians and there are other instances of lung reduction or loss in both amphibians and some vertebrates. The developmental reason for this loss, however, remains a mystery.

“Clearly lungless salamanders do fine without lungs given that they make up about two-thirds of all salamander species,” said lead author Zachary R. Lewis, former doctoral candidate (PhD ’16), “perhaps losing lungs enabled, rather than hindered, this remarkable evolutionary success.”

UBC researchers discover ‘weak spot’ across major COVID-19 variants

Cryo-electron microscopy reveals how the VH Ab6 antibody fragment (red) attaches to the vulnerable site on the SARS-CoV-2 spike protein (grey) to block the virus from binding with the human ACE2 cell receptor (blue).
Credit: Dr. Sriram Subramaniam, UBC

Researchers at the University of British Columbia have discovered a key vulnerability across all major variants of the SARS-CoV-2 virus, including the recently emerged BA.1 and BA.2 Omicron subvariants.

The weakness can be targeted by neutralizing antibodies, potentially paving the way for treatments that would be universally effective across variants.

The findings, published today in Nature Communications, use cryo-electron microscopy (cryo-EM) to reveal the atomic-level structure of the vulnerable spot on the virus’ spike protein, known as an epitope. The paper further describes an antibody fragment called VH Ab6 that is able to attach to this site and neutralize each major variant.

“This is a highly adaptable virus that has evolved to evade most existing antibody treatments, as well as much of the immunity conferred by vaccines and natural infection,” says Dr. Sriram Subramaniam (he/him), a professor at UBC’s faculty of medicine and the study’s senior author. “This study reveals a weak spot that is largely unchanged across variants and can be neutralized by an antibody fragment. It sets the stage for the design of pan-variant treatments that could potentially help a lot of vulnerable people.”

Scientists are relieved to discover ‘curious’ creature with no anus is not earliest human ancestor

Left to right: Saccorhytus, Saccorhytus dorsal, Saccorhytus side-on.
Credit: Philip Donoghue et al

An international team of researchers have discovered that a mysterious microscopic creature from which humans were thought to descend is part of a different family tree.

Resembling an angry Minion, the Saccorhytus is a spikey, wrinkly sack, with a large mouth surrounded by spines and holes that were interpreted as pores for gills – a primitive feature of the deuterostome group, from which our own deep ancestors emerged.

However, extensive analysis of 500-million-year-old fossils from China has shown that the holes around the mouth are bases of spines that broke away during the preservation of the fossils, finally revealing the evolutionary affinity of the microfossil Saccorhytus.

“Some of the fossils are so perfectly preserved that they look almost alive,” says Yunhuan Liu, professor in Paleobiology at Chang’an University, Xi’an, China. “Saccorhytus was a curious beast, with a mouth but no anus, and rings of complex spines around its mouth.”

The findings, published today in Nature, make important amendments to the early phylogenetic tree and the understanding of how life developed.