. Scientific Frontline

Wednesday, January 26, 2022

Supercomputing exposes potential pathways for inhibiting COVID-19

SARS-CoV-2 spike protein in the trimer state, shown here, to pinpoint structural transitions that could be disrupted to destabilize the protein and negate its harmful effects.
Credit: Debsindhu Bhowmik/ORNL, U.S. Dept. of Energy

To explore the inner workings of severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2, researchers from the Department of Energy’s Oak Ridge National Laboratory developed a novel technique.

The team — including computational scientists Debsindhu Bhowmik, Serena Chen and John Gounley — ran molecular dynamics simulations of the novel virus that caused the COVID-19 disease pandemic on ORNL’s Summit supercomputer, an IBM AC922 system. The researchers then analyzed the output with a customized deep learning approach to produce a complete molecular picture of the “spike” protein on the virus’s surface.

This method enabled them to pinpoint specific flexible regions, which they studied in extreme detail to reveal promising therapeutic targets. Aiming for these targets could create more reliable treatment avenues that interrupt key structural transitions in the virus’s lifecycle while also supporting the body’s natural immune response.

“A better understanding of the spike protein could complement current COVID-19 vaccines by informing new treatments and providing insights into potential drug design,” Bhowmik said.

Nearly 1,000 mysterious strands revealed in Milky Way’s center

An image showing the spectral index for filaments.
Credit: Northwestern University/SAORO/Oxford University

An unprecedented new telescope image of the Milky Way galaxy’s turbulent center has revealed nearly 1,000 mysterious strands, inexplicably dangling in space.

Stretching up to 150 light years long, the one-dimensional strands (or filaments) are found in pairs and clusters, often stacked equally spaced, side by side like strings on a harp. Using observations at radio wavelengths, Northwestern University’s Farhad Yusef-Zadeh discovered the highly organized, magnetic filaments in the early 1980s. The mystifying filaments, he found, comprise cosmic ray electrons gyrating the magnetic field at close to the speed of light. But their origin has remained an unsolved mystery ever since.

Now, the new image has exposed 10 times more filaments than previously discovered, enabling Yusef-Zadeh and his team to conduct statistical studies across a broad population of filaments for the first time. This information potentially could help them finally unravel the long-standing mystery.

The study is now available online and has been accepted for publication by The Astrophysical Journal Letters.

“We have studied individual filaments for a long time with a myopic view,” said Yusef-Zadeh, the paper’s lead author. “Now, we finally see the big picture — a panoramic view filled with an abundance of filaments. Just examining a few filaments makes it difficult to draw any real conclusion about what they are and where they came from. This is a watershed in furthering our understanding of these structures.”

Yusef-Zadeh is a professor of physics and astronomy at Northwestern’s Weinberg College of Arts and Sciences and a member of the Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA).

Omicron genetics and early transmission patterns are characterized in new study

The Omicron variant was first detected in Botswana
in October 2021 and has quickly spread throughout the world
Credit: Justice Hubane / Unsplash
The Omicron variant of SARS-CoV-2 diverged from previous SARS-CoV-2 variants as a result of adaptive evolution, in which beneficial mutations are passed on to future generations through natural selection, rather than through recombination between previous variants, according to a large international team of researchers. The study, which published recently in Nature, is the first to describe the genomic profile of Omicron and explore the origins of the variant.

“We have seen SARS-CoV-2 generate three major variants — Alpha, Delta and Omicron — in about 16 months, which is very surprising because other viruses do not make such repeated big evolutionary leaps,” said Maciej Boni, associate professor of biology, Penn State, who led the recombination analysis for this global collaboration. “The latest variant — Omicron — is extraordinary because of the even bigger jump it made in the evolution of its spike protein.”

Boni noted that compared to previous variants, Omicron’s spike protein has more than 30 mutations, many of which are known to influence host antibody neutralization.

“Given that Omicron made such a big leap forward evolutionarily speaking, we wanted to investigate why and how this may have happened,” he said.

To do that, the team — which was led by the Centre for Epidemic Response and Innovation in South Africa — analyzed all 686 Omicron sequences that were available by Dec. 7, 2021. They found that Omicron falls within the B.1.1 lineage, which also includes the Alpha variant. Interestingly, the team found that Omicron is genetically distinct from Alpha, as well as any other known variants of interest.

Kirigami Robotic Grippers Are Delicate Enough to Lift Egg Yolks

Engineering researchers from North Carolina State University have demonstrated a new type of flexible, robotic grippers that are able to lift delicate egg yolks without breaking them, and that are precise enough to lift a human hair. The work has applications for both soft robotics and biomedical technologies.

The work draws on the art of kirigami, which involves both cutting and folding two-dimensional (2D) sheets of material to form three-dimensional (3D) shapes. Specifically, the researchers have developed a new technique that involves using kirigami to convert 2D sheets into curved 3D structures by cutting parallel slits across much of the material. The final shape of the 3D structure is determined in large part by the outer boundary of the material. For example, a 2D material that has a circular boundary would form a spherical 3D shape.

“We have defined and demonstrated a model that allows users to work backwards,” says Yaoye Hong, first author of a paper on the work and a Ph.D. student at NC State. “If users know what sort of curved, 3D structure they need, they can use our approach to determine the boundary shape and pattern of slits they need to use in the 2D material. And additional control of the final structure is made possible by controlling the direction in which the material is pushed or pulled.”

Tuesday, January 25, 2022

Using nanodiamonds as sensors just got easier

University of Rochester PhD student Dinesh Bommidi (left) and Andrea Pickel, an assistant professor of mechanical engineering, used an atomic force microscope to locate and move nanodiamond sensors. University of Rochester photo / J. Adam Fenster

For centuries people have placed the highest value on diamonds that are not only large but flawless.

Scientists, however, have discovered exciting new applications for diamonds that are not only incredibly small but have a unique defect.

In a recent paper in Applied Physics Letters, researchers at the University of Rochester describe a new way to measure temperature with these defects, called nitrogen vacancy centers, using the light they emit. The technique, adapted for single nanodiamonds by Andrea Pickel, assistant professor of mechanical engineering, and Dinesh Bommidi, a PhD student in her lab, allowed them to precisely measure, for the first time, the duration of these light emissions, or “excited state lifetimes,” at a broad range of temperatures.

The discovery earned the paper recognition as an American Institute of Physics “Scilight,” a showcase of what AIP considers the most interesting research across the physical sciences.

The Rochester method gives researchers a less complicated, more accurate tool for using nitrogen vacancy centers to measure the temperature of nanoscale-sized materials. The approach is also safe for imaging sensitive nanoscale materials or biological tissues and could have applications in quantum information processing.

Hungry yeast are tiny, living thermometers

This fluorescence microscopy image shows yeast vacuoles that have undergone phase separation.Luther Davis/Alexey Merz/University of Washington

Membranes are crucial to our cells. Every cell in your body is enclosed by one. And each of those cells contains specialized compartments, or organelles, which are also enclosed by membranes.

Membranes help cells carry out tasks like breaking down food for energy, building and dismantling proteins, keeping track of environmental conditions, sending signals and deciding when to divide.

Biologists have long struggled to understand precisely how membranes accomplish these different types of jobs. The primary components of membranes — large, fat-like molecules called lipids and compact molecules like cholesterol — make great barriers. In all but a few cases, it’s unclear how those molecules help proteins within membranes do their jobs.

In a paper published Jan. 25 in the Proceedings of the National Academy of Sciences, a team at the University of Washington looked at phase separation in budding yeast — the same single-celled fungus of baking and brewing fame — and reports that living yeast cells can actively regulate a process called phase separation in one of their membranes. During phase separation, the membrane remains intact but partitions into multiple, distinct zones or domains that segregate lipids and proteins. The new findings show for the first time that, in response to environmental conditions, yeast cells precisely regulate the temperature at which their membrane undergoes phase separation. The team behind this discovery suggests that phase separation is likely a “switch” mechanism that these cells use to govern the types of work that membranes do and the signals they send.

How a Smart Electric Grid Will Power Our Future

The Electricity Infrastructure Operations Center, located at PNNL, allows researchers to evaluate electric grid scenarios in the context of current industry conditions.
Photo by Andrea Starr | Pacific Northwest National Laboratory

A novel plan that offers partnership in keeping the United States electric grid stable and reliable could be a win-win for consumers and utility operators.

The largest ever simulation of its kind, modeled on the Texas power grid, concluded that consumers stand to save about 15 percent on their annual electric bill by partnering with utilities. In this system, consumers would coordinate with their electric utility operator to dynamically control big energy users, like heat pumps, water heaters and electric vehicle charging stations.

This kind of flexible control over energy supply and use patterns is called “transactive” because it relies on an agreement between consumers and utilities. But a transactive energy system has never been deployed on a large scale, and there are a lot of unknowns. That’s why the Department of Energy’s Office of Electricity called upon the transactive energy experts at Pacific Northwest National Laboratory to study how such a system might work in practice. The final multi-volume report was released today.

Hayden Reeve, a PNNL transactive energy expert and technical advisor, led a team of engineers, economists and programmers who designed and executed the study.

Novel research identifies fresh 'mixers' in river pollution 'cocktail'

Researchers from the Universities of Manchester, Birmingham and Mahavir Cancer Sansthan collecting field data along the River Ganga in Bihar
Photo - Aman Gaurav

Water quality in rivers is affected by underpinning ‘natural’ hydrogeological and biogeochemical processes, as well as interactions between people and their environment that are accelerating stress on water resources at unprecedented rates.

Pollutants can move at different speeds and accumulate in varying quantities along rivers where the mix of the complex ‘cocktail’ of chemicals that is making its way towards the ocean is constantly changing, a new study reveals.

Researchers have discovered characteristic breakpoints – often found when a tributary joins the main river or significant point sources exist – can change the behavior of some compounds, causing the concentration of these chemicals to change drastically, depending on where they are on their journey down the river.

Experts discovered the phenomenon after piloting a new, systematic approach to understanding hydrogeochemical dynamics in large river systems along the entire length of India’s River Ganges (Ganga) – from close to its source in the Himalayas down to the Indian Ocean.

This new research approach proven successful at the iconic Ganga can be applied to other large river systems across the world – hopefully shedding new light on how to tackle the global challenge of aquatic pollution by multiple interacting contaminants.

Calculating the best shapes for things to come

Wei Lu 
Professor  Mechanical Engineering 
University of Michigan
Maximizing the performance and efficiency of structures—everything from bridges to computer components—can be achieved by design with a new algorithm developed by researchers at the University of Michigan and Northeastern University.

It’s an advancement likely to benefit a host of industries where costly and time-consuming trial-and-error testing is necessary to determine the optimal design. As an example, look at the current U.S. infrastructure challenge—a looming $2.5 trillion backlog that will need to be addressed with taxpayer dollars.

Planners searching for the best way to design a new bridge need to answer a string of key questions. How many pillars are needed? What diameter do those pillars need to be? What should the radius of the bridge’s arch be? The new algorithm can determine the combination that gives the highest load capacity with lowest cost.

The team tested their algorithm in four optimization scenarios: designing structures to maximize their stiffness for carrying a given load, designing the shape of fluid channels to minimize pressure loss, creating shapes for heat transfer enhancement, and minimizing the material of complex trusses for load bearing. The new algorithm reduced the computational time needed to reach the best solution by roughly 100 to 100,000 times over traditional approaches. In addition, it outperformed all other state-of-the-art algorithms.

“It’s a tool with the potential to influence many industries—clean energy, aviation, electric vehicles, energy efficient buildings,” said Wei Lu, U-M professor of mechanical engineering and corresponding author of the study in Nature Communications.

The new algorithm plays in a space called topology optimization—how best to distribute materials within a given space to get the desired results.

“If you really want to design something rationally, you’re talking about a large number of calculations, and doing those can be difficult with time and cost considerations,” Lu said. “Our algorithm can reduce the calculations and facilitate the optimization process.”

Worldwide assessment of protected areas

According to a TUM-led study, mountain habitats as seen here in Pakistan’s Deosai National Park are quite well protected. Many other habitats do not yet have this level of protection.
Image: Ch. Hof / TUM

Protected areas are among the most effective tools for preserving biodiversity. However, new protected areas are often created without considering existing ones. This can lead to an overrepresentation of the biophysical characteristics, such as temperature or topography, that define a certain area. A research group at the Technical University of Munich (TUM) has now assessed a global analysis of the scope of protection of various biophysical conditions.

Protected areas are important for maintaining populations of various species. They ensure that many animals and plants do not lose their habitat and thus help to protect endangered species and safeguard biodiversity.

The worldwide protected area network is steadily growing in number and extent. “From a conservation standpoint, this is generally a welcome trend. But the uncoordinated expansion of protected areas can result in wasted resources worldwide if care is not taken to protect as many species communities and environmental conditions as possible,” says Dr. Christian Hof, the director of the junior research group “MintBio – Climate change impacts on biological diversity in Bavaria: Multidimensional Integration for better BIOdiversity projections” under the auspices of the Bavarian climate research network bayklif at TUM.

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