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Wednesday, July 21, 2021

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Tuesday, July 20, 2021

Main Attraction: Scientists Create World's Thinnest Magnet

A one-atom-thin 2D magnet developed by Berkeley Lab and UC Berkeley could advance new applications in computing and electronics 
THERESA DUQUE | (510) 495-2418 | JULY 20, 2021
Credit: Marilyn Sargent/Berkeley Lab
The development of an ultrathin magnet that operates at room temperature could lead to new applications in computing and electronics – such as high-density, compact spintronic memory devices – and new tools for the study of quantum physics.  

The ultrathin magnet, which was recently reported in the journal Nature Communications, could make big advances in next-gen memory devices, computing, spintronics, and quantum physics. It was discovered by scientists at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley.

“We’re the first to make a room-temperature 2D magnet that is chemically stable under ambient conditions,” said senior author Jie Yao, a faculty scientist in Berkeley Lab’s Materials Sciences Division and associate professor of materials science and engineering at UC Berkeley.

“This discovery is exciting because it not only makes 2D magnetism
possible at room temperature, but it also uncovers a new mechanism to realize 2D magnetic materials,” added Rui Chen, a UC Berkeley graduate student in the Yao Research Group and lead author on the study.

The magnetic component of today’s memory devices is typically made of magnetic thin films. But at the atomic level, these materials are still three-dimensional – hundreds or thousands of atoms thick. For decades, researchers have searched for ways to make thinner and smaller 2D magnets and thus enable data to be stored at a much higher density. 

Previous achievements in the field of 2D magnetic materials have brought promising results. But these early 2D magnets lose their magnetism and become chemically unstable at room temperature. 

“State-of-the-art 2D magnets need very low temperatures to function. But for practical reasons, a data center needs to run at room temperature,” Yao said. “Our 2D magnet is not only the first that operates at room temperature or higher, but it is also the first magnet to reach the true 2D limit: It’s as thin as a single atom!” 

The researchers say that their discovery will also enable new opportunities to study quantum physics. “It opens up every single atom for examination, which may reveal how quantum physics governs each single magnetic atom and the interactions between them," Yao said.

The making of a 2D magnet that can take the heat

The researchers synthesized the new 2D magnet – called a cobalt-doped van der Waals zinc-oxide magnet – from a solution of graphene oxide, zinc, and cobalt. 

Just a few hours of baking in a conventional lab oven transformed the mixture into a single atomic layer of zinc-oxide with a smattering of cobalt atoms sandwiched between layers of graphene. 

In a final step, the graphene is burned away, leaving behind just a single atomic layer of cobalt-doped zinc-oxide.

“With our material, there are no major obstacles for industry to adopt our solution-based method,” said Yao. “It’s potentially scalable for mass production at lower costs.” 

To confirm that the resulting 2D film is just one atom thick, Yao and his team conducted scanning electron microscopy experiments at Berkeley Lab’s Molecular Foundry to identify the material’s morphology, and transmission electron microscopy (TEM) imaging to probe the material atom by atom.  

X-ray experiments at Berkeley Lab’s Advanced Light Source characterized the 2D material’s magnetic parameters under high temperature.

Additional X-ray experiments at SLAC National Accelerator Laboratory’s Stanford Synchrotron Radiation Lightsource verified the electronic and crystal structures of the synthesized 2D magnets. And at Argonne National Laboratory’s Center for Nanoscale Materials, the researchers employed TEM to image the 2D material’s crystal structure and chemical composition.

The researchers found that the graphene-zinc-oxide system becomes weakly magnetic with a 5-6% concentration of cobalt atoms. Increasing the concentration of cobalt atoms to about 12% results in a very strong magnet. 

To their surprise, a concentration of cobalt atoms exceeding 15% shifts the 2D magnet into an exotic quantum state of “frustration,” whereby different magnetic states within the 2D system are in competition with each other. 

And unlike previous 2D magnets, which lose their magnetism at room temperature or above, the researchers found that the new 2D magnet not only works at room temperature but also at 100 degrees Celsius (212 degrees Fahrenheit). 

“Our 2D magnetic system shows a distinct mechanism compared to previous 2D magnets,” said Chen. “And we think this unique mechanism is due to the free electrons in zinc oxide.” 

True north: Free electrons keep magnetic atoms on track

When you command your computer to save a file, that information is stored as a series of ones and zeroes in the computer’s magnetic memory, such as the magnetic hard drive or a flash memory.

And like all magnets, magnetic memory devices contain microscopic magnets with two poles – north and south, the orientations of which follow the direction of an external magnetic field. Data is written or encoded when these tiny magnets are flipped to the desired directions.  

According to Chen, zinc oxide’s free electrons could act as an intermediary that ensures the magnetic cobalt atoms in the new 2D device continue pointing in the same direction – and thus stay magnetic – even when the host, in this case the semiconductor zinc oxide, is a nonmagnetic material.

“Free electrons are constituents of electric currents. They move in the same direction to conduct electricity,” Yao added, comparing the movement of free electrons in metals and semiconductors to the flow of water molecules in a stream of water. 

The new material – which can be bent into almost any shape without breaking, and is a million times thinner than a sheet of paper – could help advance the application of spin electronics or spintronics, a new technology that uses the orientation of an electron’s spin rather than its charge to encode data. “Our 2D magnet may enable the formation of ultra-compact spintronic devices to engineer the spins of the electrons,” Chen said. 

"I believe that the discovery of this new, robust, truly two-dimensional magnet at room temperature is a genuine breakthrough,” said co-author Robert Birgeneau, a faculty senior scientist in Berkeley Lab’s Materials Sciences Division and professor of physics at UC Berkeley who co-led the study.

“Our results are even better than what we expected, which is really exciting. Most of the time in science, experiments can be very challenging,” Yao said. “But when you finally realize something new, it’s always very fulfilling.” 

Co-authors on the paper include researchers from Berkeley Lab, including Alpha N’Diaye and Padraic Shafer of the Advanced Light Source; UC Berkeley; UC Riverside; Argonne National Laboratory; and Nanjing University and the University of Electronic Science and Technology of China. 

The Advanced Light Source and Molecular Foundry are DOE national user facilities at Berkeley Lab.

The Stanford Synchrotron Radiation Lightsource is a DOE national user facility at SLAC National Accelerator Laboratory.

The Center for Nanoscale Materials is a DOE national user facility at Argonne National Laboratory.

This work was funded by the DOE Office of Science, the Intel Corporation, and the Bakar Fellows Program at UC Berkeley. 
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Founded in 1931 on the belief that the biggest scientific challenges are best addressed by teams, Lawrence Berkeley National Laboratory and its scientists have been recognized with 14 Nobel Prizes. Today, Berkeley Lab researchers develop sustainable energy and environmental solutions, create useful new materials, advance the frontiers of computing, and probe the mysteries of life, matter, and the universe. Scientists from around the world rely on the Lab’s facilities for their own discovery science. Berkeley Lab is a multiprogram national laboratory, managed by the University of California for the U.S. Department of Energy's Office of Science.
 
DOE's Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit energy.gov/science.

Monday, July 19, 2021

Deconstructing the Infectious Machinery of SARS-CoV-2

Scientists collaborate to model the complex protein responsible for SARS-CoV-2 replication, revealing its potential weak spots for drug development
ALIYAH KOVNER | (510) 486-6376 | JULY 19, 2021
This color-enhanced image, taken by scanning electron microscopy, shows huge quantities of SARS-CoV-2 particles (purple) that have burst out of kidney cells (green), which the virus hijacked for replication. The bulging, spherical cells in the upper-right and bottom-left corners are distorted and about to burst from the viral particles inside, and are beginning to self-destruct. (Credit: NIAID Integrated Research Facility)
In February 2020, a trio of bio-imaging experts were sitting amiably around a dinner table at a scientific conference in Washington, D.C., when the conversation shifted to what was then a worrying viral epidemic in China. Without foreseeing the global disaster to come, they wondered aloud how they might contribute.
 
Nearly a year and a half later, those three scientists and their many collaborators across three national laboratories have published a comprehensive study in Biophysical Journal that – alongside other recent, complementary studies of coronavirus proteins and genetics – represents the first step toward developing treatments for that viral infection, now seared into the global consciousness as COVID-19.
 
Their foundational work focused on the protein-based machine that enables the SARS-CoV-2 virus to hijack our own cells’ molecular machinery in order to replicate inside our bodies.

From structure to function to solutions

“It has been remarked that all organisms are just a means for DNA to make copies of itself, and nowhere is this truer than in the case of a virus,” said Greg Hura, a staff scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) and one of the study’s lead authors. “A virus’s singular task is to make copies of its genetic material – unfortunately, at our expense.”
 
Viruses and mammals, including humans, have been stuck in this battle for millions of years, he added, and over that time the viruses have evolved many tricks to get their genes copied inside us, while our bodies have evolved counter defenses. And although viruses often perform a long list of other activities, their ability to harm us with an infection really does come down to whether or not they can replicate their genetic material (either RNA or DNA, depending on the species) to make more viral particles, and use our cells to translate their genetic code into proteins.
 
The protein-based machine responsible for RNA replication and translation in coronaviruses – and many other viruses – is called the RNA transcription complex (RTC), and it is a truly formidable piece of biological weaponry.
 
To successfully duplicate viral RNA for new virus particles and produce the new particles’ many proteins, the RTC must: distinguish between viral and host RNA, recognize and pair RNA bases instead of highly similar DNA bases that are also abundant in human cells, convert their RNA into mRNA (to dupe human ribosomes into translating viral proteins), interface with copy error-checking molecules, and transcribe specific sections of viral RNA to amplify certain proteins over others depending on need – while at all times trying to evade the host immune system that will recognize it as a foreign protein.
As astounding as this sounds, any newly evolved virus that is successful “must have machines that are incredibly sophisticated to overcome mechanisms we have evolved,” explained Hura, who heads the Structural Biology department in Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging Division.
 
He and the other study leads – Andrzej Joachimiak of Argonne National Laboratory and Hugh M. O’Neill at Oak Ridge National Laboratory – specialize in revealing the atomic structure of proteins in order to understand how they work at the molecular level. So, the trio knew from the moment they first discussed COVID-19 at the dinner table that studying the RTC would be particularly challenging because multitasking protein machines like the RTC aren’t static or rigid, as molecular diagrams or ball-and-stick models might suggest. They're flexible and have associated molecules, called nonstructural and accessory proteins (Nsps), that exist in a multitude of rapidly rearranging forms depending on the task at hand – akin to how a gear shifter on a bike quickly adapts the vehicle to changing terrain.
 
Each of these Nsp arrangements give insights into the protein’s different activities, and they also expose different parts of the overall RTC surface, which can be examined to find places where potential drug molecules could bind and inhibit the entire machine.
 
So, following their serendipitous convergence in Washington, the trio hatched a plan to pool their knowledge and national lab resources in order to document the structure of as many RTC arrangements as possible, and identify how these forms interact with other viral and human molecules.

Science during shutdowns

The investigation hinged on combining data collected from many advanced imaging techniques, as no approach by itself can generate complete, atomic-level blueprints of infectious proteins in their natural states. They combined small-angle X-ray scattering (SAXS), X-ray crystallography, and small-angle neutron scattering (SANS) performed at Berkeley Lab’s Advanced Light Source, Argonne’s Advanced Photon Source, and Oak Ridge’s High Flux Isotope Reactor and Spallation Neutron Source, respectively, on samples of biosynthetically produced RTC.
 
Despite the extraordinary hurdles of conducting science during shelter-in-place conditions, the collaboration was able to work continuously for more than 15 months, thanks to funding for research and facility operations support from the Department of Energy’s Office of Science National Virtual Biotechnology Laboratory (NVBL). During that time, the scientists collected detailed data on the RTC’s key accessory proteins and their interactions with RNA. All of their findings were uploaded into the open-access Protein Data Bank prior to the journal article’s publication.
 
Of the many structural findings that will help with drug design, one notable discovery is that assembly of the RTC subunits is incredibly precise. Drawing on a mechanical metaphor once more, the scientists compare the assembly process to putting together a spring-based machine. You can’t put a spring in place when the rest of the machine is already in position, you must compress and place the spring at a specific step of assembly or the whole device is dysfunctional. Similarly, the RTC Nsps can’t move into place in any random or chaotic order; they must follow a specific order of operations.
 
They also identified how one of the Nsps specifically recognizes the RNA molecules it acts upon, and how it cuts long strands of copied RNA into their correct lengths.
 
“Having the vaccines is certainly huge. However, why are we satisfied with just this one avenue of defense?” said Hura. Added Joachimiak: “This was a survey study, and it has identified many directions we and others should pursue very deeply; to tackle this virus we will need multiple ways of blocking its proliferation.”

“Combining information from different structural techniques and computation will be key to achieving this goal,” said O’Neill.
 
Due to the similarity of RTC proteins across viral strains, the team believe that any drugs developed to block RTC activity could work for multiple viral infections in addition to all COVID-19 variants.
 
Reflecting back to the beginning of their research journey, the scientists marvel at the lucky timing of it all. When we started to talk, said Hura, “we had no idea that this epidemic would soon become a pandemic that would change a generation.”
 
The team’s work was supported by the DOE Office of Science through the NVBL​, a consortium of DOE national laboratories focused on the response to COVID-19, with funding provided by the Coronavirus CARES Act; and by the National Institutes of Health. The Advanced Light Source, Advanced Photon Source, High Flux Isotope Reactor, and Spallation Neutron Source are DOE Office of Science user facilities.
###

Founded in 1931 on the belief that the biggest scientific challenges are best addressed by teams, Lawrence Berkeley National Laboratory and its scientists have been recognized with 14 Nobel Prizes. Today, Berkeley Lab researchers develop sustainable energy and environmental solutions, create useful new materials, advance the frontiers of computing, and probe the mysteries of life, matter, and the universe. Scientists from around the world rely on the Lab’s facilities for their own discovery science. Berkeley Lab is a multiprogram national laboratory, managed by the University of California for the U.S. Department of Energy's Office of Science.
 
DOE's Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit energy.gov/science.
 
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