BLOGS

The proportion of disruptive scientific papers, such as the 1953 description of DNA’s double-helix structure, has fallen since the mid-1940s.Credit: Lawrence Lawry/SPL

Topics: DNA, Education, Philosophy, Research, Science, STEM

The number of science and technology research papers published has skyrocketed over the past few decades — but the ‘disruptiveness’ of those papers has dropped, according to an analysis of how radically papers depart from the previous literature¹.

Data from millions of manuscripts show that, compared with the mid-twentieth century, research done in the 2000s was much more likely to incrementally push science forward than to veer off in a new direction and render previous work obsolete. Analysis of patents from 1976 to 2010 showed the same trend.

“The data suggest something is changing,” says Russell Funk, a sociologist at the University of Minnesota in Minneapolis and a co-author of the analysis published on 4 January in Nature. “You don’t have quite the same intensity of breakthrough discoveries you once had.”

Telltale citations

The authors reasoned that if a study were highly disruptive, subsequent research would be less likely to cite its references and instead cite the study itself. Using the citation data from 45 million manuscripts and 3.9 million patents, the researchers calculated a measure of disruptiveness called the ‘CD index,’ in which values ranged from –1 for the least disruptive work to 1 for the most disruptive.

The average CD index declined by more than 90% between 1945 and 2010 for research manuscripts (see ‘Disruptive science dwindles’) and more than 78% from 1980 to 2010 for patents. Disruptiveness declined in all analyzed research fields and patent types, even when factoring in potential differences in factors such as citation practices.

‘Disruptive’ science has declined — and no one knows why, Max Kozlov, Nature.

Fig. 1. SARS-CoV-2 N is expressed on the surface of live cells early during infection.
(A) Maximum intensity projections of laser confocal microscopy z-stack images of infected Vero cells with wt SARS-CoV-2 (top) or SARS-CoV-2_eGFP, stained live at 24 hpi (MOI = 1). Scale bars, 20 μm. Images are representative of at least three independent experiments with similar results. DAPI, 4′,6-diamidino-2-phenylindole. (B) Flow cytometry analyses of Vero cells inoculated with wt (top) or eGFP-expressing (bottom) SARS-CoV-2 (MOI = 1), stained live at 24 hpi against SARS-CoV-2 S and N proteins. Representative dot plots of flow cytometry analyses showing double staining of surface S, N, and eGFP proteins, indicating the percentage of the gated cell population for each quadrant of the double staining. Data are representative of at least three independent experiments, each performed with triplicate samples. (C and D) Time course of surface S, N, and eGFP protein expression in live infected Vero cells with wt (C) and eGFP reporter (D) SARS-CoV-2 at 8 and 12 hpi (MOI = 1). Representative histogram overlays of surface S, N, and intracellular eGFP proteins of flow cytometry analyses. Data are representative of one experiment of at least two independent experiments performed in triplicate.

Topics: Biology, COVID-19, Research

Abstract

SARS-CoV-2 nucleocapsid protein (N) induces strong antibody (Ab) and T cell responses. Although considered to be localized in the cytosol, we readily detect N on the surface of live cells. N released by SARS-CoV-2–infected cells or N-expressing transfected cells binds to neighboring cells by electrostatic high-affinity binding to heparan sulfate and heparin, but not other sulfated glycosaminoglycans. N binds with high affinity to 11 human chemokines, including CXCL12β, whose chemotaxis of leukocytes is inhibited by N from SARS-CoV-2, SARS-CoV-1, and MERS-CoV. Anti-N Abs bound to the surface of N-expressing cells activate Fc receptor-expressing cells. Our findings indicate that cell surface N manipulates innate immunity by sequestering chemokines and can be targeted by Fc-expressing innate immune cells. This, in combination with its conserved antigenicity among human CoVs, advances its candidacy for vaccines that induce cross-reactive B and T cell immunity to SARS-CoV-2 variants and other human CoVs, including novel zoonotic strains.

Cell surface SARS-CoV-2 nucleocapsid protein modulates innate and adaptive immunity, Alberto Domingo Lopez-Munoz, Ivan Kosik, Jaroslav Holly, Jonathan W. Yewdell, Science Advances

Transport dewars like this carry crucial cryogens for scientific instruments.

Topics: Chemistry, Instrumentation, Nuclear Magnetic Resonance, Physics, Research

Scientists who need the gas face tough choices in the face of reduced supply and spiking prices.

Helium supplies, already dicey, got worse this past week when production shut down in Arzew, Algeria. The curtailment joins ongoing disruptions in supplies from Russia and the US Federal Helium Reserve as well as planned maintenance at facilities in Qatar. Helium users in several locations say they are struggling to get the gas they need to keep their scientific instruments running.

“The shortage is scaring most NMR spectroscopists,” says Martha Morton, the director of research instrumentation at the University of Nebraska–Lincoln. Nuclear magnetic resonance instruments and related tools use liquid helium to cool superconducting magnets.

War in Ukraine makes helium shortage more dire, Craig Bettenhausen, Chemical & Engineering News

At CERN in 1973, John Bell (left), who was working there at the time, interacts with Martinus Veltman (right), who was then a professor at Utrecht University in the Netherlands. Since early 2020, COVID-19 has hindered physicists’ ability to travel and discuss physics in person. (Courtesy of CERN.)

Topics: COVID-19, Existentialism, Physics, Research

An excerpt. The longer article piece is at the link following.

The COVID-19 pandemic has not only killed a large number of people—approximately 5.5 million worldwide at the time Physics Today went to press in mid-January—it has also disrupted life in a fundamental, nonperturbative manner, forcing large-scale changes in human behavior from without.

It was difficult at the beginning of 2020 to anticipate the great COVID-19 calamity awaiting the world. In February of that year, I was apparently among the first people to have urged the leadership of the American Physical Society to cancel its upcoming March Meeting in Denver, which APS finally did at the last moment after considerable hesitancy.

The logistics of canceling a meeting of 10 000 people right before the event are not trivial. But given the crowd density in APS March Meetings, it is reasonable to assume that the 2020 event would have led to a few thousand COVID-19 cases just among the physicist attendees. Overall, it may have led to many tens of thousands, perhaps even hundreds of thousands, of cases, if not more. That estimate is based on research related to the now-infamous Boston Biogen superspreader conference in late February 2020. Within a month, roughly 100 people in Massachusetts who either went to the conference or were a household contact of someone who went tested positive. The genetic-code-based investigation estimated that the event led to 300 000 COVID-19 cases worldwide by the beginning of the following November. APS made the right call in canceling the meeting.

Commentary: A physicist’s perspective on COVID-19, Sankar Das Sarma, Physics Today

NIST researcher Megan Cleveland uses a PCR machine to amplify DNA sequences by copying them numerous times through a series of chemical reactions.
Credit: M. Cleveland/NIST

Topics: Biology, Biotechnology, COVID-19, Diversity in Science, NIST, Research, Women in Science

Scientists track and monitor the circulation of SARS-CoV-2, the virus that causes COVID-19, using methods based on a laboratory technique called polymerase chain reaction (PCR). Also used as the “gold standard” test to diagnose COVID-19 in individuals, PCR amplifies pieces of DNA by copying them numerous times through a series of chemical reactions. The number of cycles it takes to amplify DNA sequences of interest so that they are detectable by the PCR machine, known as the cycle threshold (Ct), is what researchers and medical professionals look at to detect the virus.

However, not all labs get the same Ct values (sometimes also called “Cq” values). In efforts to make the results more comparable between labs, the National Institute of Standards and Technology (NIST) contributed to a multiorganizational study that looked at anchoring these Ct values to a reference sample with known amounts of the virus.

Researchers published their findings in the journal PLOS One.

SARS-CoV-2 is an RNA virus: Its genetic material is single-stranded instead of double-stranded like DNA and contains some different molecular building blocks, namely uracil in place of thymine. But the PCR test only works with DNA, and labs first must convert the RNA to DNA to screen for COVID-19. For the test, RNA is isolated from a patient’s sample and combined with other ingredients, including short DNA sequences are known as primers, to transform the RNA into DNA.

RNA Reference Materials Are Useful for Standardizing COVID-19 Tests, Study Shows, NIST

Topics: Battery, Energy, Green Tech, Research, Solid-State Physics

Janus, in Roman religion, the animistic spirit of doorways (januae) and archways (Jani). Janus and the nymph Camasene were the parents of Tiberinus, whose death in or by the river Albula caused it to be renamed Tiber. Source: Encylopedia Britannica

Over the past decade, lithium-ion batteries have seen stunning improvements in their size, weight, cost, and overall performance. (See Physics Today, December 2019, page 20.) But they haven’t yet reached their full potential. One of the biggest remaining hurdles has to do with the electrolyte, the material that conducts Li⁺ ions from anode to cathode inside the battery to drive the equal and opposite flow of charge in the external circuit.

Most commercial lithium-ion batteries use organic liquid electrolytes. The liquids are excellent conductors of Li⁺ ions, but they’re volatile and flammable, and they offer no defense against the whisker-like Li-metal dendrites that can build up between the electrodes and eventually short-circuit the battery. Because safety comes first, battery designers must sacrifice some performance in favor of not having their batteries catch fire.

A solid-state electrolyte could solve those problems. But what kind of solid conducts ions? An ordered crystal won’t do—when every site is filled in a crystalline lattice, Li⁺ ions have nowhere to move to. A solid electrolyte, therefore, needs to have a disordered, defect-riddled structure. It must also provide a polar environment to welcome the Li⁺ ions, but with no negative charges so strong that the Li⁺ ions stick to them and don’t let go.

For several years, Jenny Pringle, Maria Forsyth, and colleagues at Deakin University in Australia have been exploring a class of materials, called organic ionic plastic crystals (OIPCs), that could fit the bill. As a mix of positive and negative ions, an OIPC offers the necessary polar environment for conducting Li⁺. And because the constituent ions are organic, the researchers have lots of chemical leeways to design their shapes so they can’t easily fit together into a regular lattice but are forced to adopt a disordered, Li⁺-permeable structure.

Two-faced ions form a promising battery material, Johanna L. Miller, Physics Today

Visual Abstract

Topics: Biology, Biotechnology, COVID-19, Research

To advance a novel concept of debulking virus in the oral cavity, the primary site of viral replication, virus-trapping proteins CTB-ACE2 were expressed in chloroplasts and clinical-grade plant material was developed to meet FDA requirements. Chewing gum (2 g) containing plant cells expressed CTB-ACE2 up to 17.2 mg ACE2/g dry weight (11.7% leaf protein), have physical characteristics and taste/flavor like conventional gums, and no protein was lost during gum compression. CTB-ACE2 gum efficiently (>95%) inhibited entry of lentivirus spike or VSV-spike pseudovirus into Vero/CHO cells when quantified by luciferase or red fluorescence. Incubation of CTB-ACE2 microparticles reduced SARS-CoV-2 virus count in COVID-19 swab/saliva samples by >95% when evaluated by microbubbles (femtomolar concentration) or qPCR, demonstrating both virus trapping and blocking of cellular entry. COVID-19 saliva samples showed low or undetectable ACE2 activity when compared with healthy individuals (2,582 versus 50,126 ΔRFU; 27 versus 225 enzyme units), confirming greater susceptibility of infected patients for viral entry. CTB-ACE2 activity was completely inhibited by pre-incubation with SARS-CoV-2 receptor-binding domain, offering an explanation for reduced saliva ACE2 activity among COVID-19 patients. Chewing gum with virus-trapping proteins offers a generally affordable strategy to protect patients from most oral virus re-infections through debulking or minimizing transmission to others.

Debulking SARS-CoV-2 in saliva using angiotensin-converting enzyme 2 in chewing gum to decrease oral virus transmission and infection, Molecular Therapy: Cell.com

Henry Daniell, Smruti K. Nair, Nardana Esmaeili, Geetanjali Wakade, Naila Shahid, Prem Kumar Ganesan, Md Reyazul Islam, Ariel Shepley-McTaggart, Sheng Feng, Ebony N. Gary, Ali R. Ali, Manunya Nuth, Selene Nunez Cruz, Jevon Graham-Wooten, Stephen J. Streatfield, Ruben Montoya-Lopez, Paul Kaznica, Margaret Mawson, Brian J. Green, Robert Ricciardi, Michael Milone, Ronald N. Harty, Ping Wang, David B. Weiner, Kenneth B. Margulies, Ronald G. Collman

GIF source: article link below

Topics: Applied Physics, Education, Research, Thermodynamics

Also note the Hyper Physics link on the Second Law of Thermodynamics, particularly "Time's Arrow."

"The two most powerful warriors are patience and time," Leo Tolstoy, War, and Peace

The short answer

We can measure time intervals — the duration between two events — most accurately with atomic clocks. These clocks produce electromagnetic radiation, such as microwaves, with a precise frequency that causes atoms in the clock to jump from one energy level to another. Cesium atoms make such quantum jumps by absorbing microwaves with a frequency of 9,192,631,770 cycles per second, which then defines the international scientific unit for time, the second.

The answer to how we measure time may seem obvious. We do so with clocks. However, when we say we’re measuring time, we are speaking loosely. Time has no physical properties to measure. What we are really measuring is time intervals, the duration separating two events.

Throughout history, people have recorded the passage of time in many ways, such as using sunrise and sunset and the phases of the moon. Clocks evolved from sundials and water wheels to more accurate pendulums and quartz crystals. Nowadays when we need to know the current time, we look at our wristwatch or the digital clock on our computer or phone. 

The digital clocks on our computers and phones get their time from atomic clocks, including the ones developed and operated by the National Institute of Standards and Technology (NIST).

How Do We Measure Time? NIST

Credit: Getty Images

Topics: Biology, COVID-19, DNA, Research

Note: I have friends who thankfully survived infection now affected by this phenomenon. The article thus grabbed my attention.

SARS-CoV-2 appears to travel widely across the cerebral cortex

“Brain fog” is not a formal medical descriptor. But it aptly describes an inability to think clearly that can turn up in multiple sclerosis, cancer, or chronic fatigue. Recently, the condition has grabbed headlines because of reports that it afflicts those recovering from COVID-19.

COVID’s brain-related symptoms go beyond mere mental fuzziness. They range across a spectrum that encompasses headaches, anxiety, depression, hallucinations, and vivid dreams, not to mention well-known smell and taste anomalies. Strokes and seizures are also on the list. One study showed that more than 80 percent of COVID patients encountered neurological complications.

The mystery of how the virus enters and then inhabits the brain’s protected no-fly zone is under intensive investigation. At the 50th annual meeting of the Society for Neuroscience, or SFN (held in virtual form this month after a pandemic hiatus in 2020), a set of yet-to-be-published research reports chronicle aspects of the COVID-causing SARS-COV-2 virus’s full trek in the brain—from cell penetration to dispersion among brain regions, to disruption of neural functioning.

How COVID Might Sow Chaos in the Brain, Gary Stix, Scientific American

Credit: Mark Ross

Topics: Climate Change, Existentialism, Global Warming, Research

More moisture in a warmer atmosphere is fueling intense hurricanes and flooding rains.

The summer of 2021 was a glaring example of what disruptive weather will look like in a warming world. In mid-July, storms in western Germany and Belgium dropped up to eight inches of rain in two days. Floodwaters ripped buildings apart and propelled them through village streets. A week later a year’s worth of rain—more than two feet—fell in China’s Henan province in just three days. Hundreds of thousands of people fled rivers that had burst their banks. In the capital city of Zhengzhou, commuters posted videos showing passengers trapped inside flooding subway cars, straining their heads toward the ceiling to reach the last pocket of air above the quickly rising water. In mid-August a sharp kink in the jet stream brought torrential storms to Tennessee that dropped an incredible 17 inches of rain in just 24 hours; catastrophic flooding killed at least 20 people. None of these storm systems were hurricanes or tropical depressions.

Soon enough, though, Hurricane Ida swirled into the Gulf of Mexico, the ninth named tropical storm in the year’s busy North Atlantic season. On August 28 it was a Category 1 storm with sustained winds of 85 miles per hour. Less than 24 hours later Ida exploded to Category 4, whipped up at nearly twice the rate that the National Hurricane Center uses to define a rapidly intensifying storm. It hit the Louisiana coast with winds of 150 miles an hour, leaving more than a million people without power and more than 600,000 without water for days. Ida’s wrath continued into the Northeast, where it delivered a record-breaking 3.15 inches of rain in one hour in New York City. The storm killed at least 80 people and devastated a swath of communities in the eastern U.S.

What all these destructive events have in common is water vapor—lots of it. Water vapor—the gaseous form of H₂O—is playing an outsized role in fueling destructive storms and accelerating climate change. As the oceans and atmosphere warm, additional water evaporates into the air. Warmer air, in turn, can hold more of that vapor before it condenses into cloud droplets that can create flooding rains. The amount of vapor in the atmosphere has increased about 4 percent globally just since the mid-1990s. That may not sound like much, but it is a big deal to the climate system. A juicier atmosphere provides extra energy and moisture for storms of all kinds, including summertime thunderstorms, nor’easters along the U.S. Eastern Seaboard, hurricanes, and even snowstorms. Additional vapor helps tropical storms like Ida intensify faster, too, leaving precious little time for safety officials to warn people in the crosshairs.

Vapor Storms Are Threatening People and Property, Jennifer A. Francis, Scientific American

Luis Walter Alvarez co-developed the theory that the extinction of the dinosaurs was caused by an asteroid impact (Courtesy: iStock/estt)

Topics: Dinosaurs, Nobel Prize, Research

In the run-up to the announcement of the 2021 Nobel Prize for Physics on 5 October, we’re running a series of blog posts looking at previous recipients and what they did after their Nobel-prize-winning work. In this first installment, Laura Hiscott explores the wide-ranging research of Luis Walter Alvarez, who won the prize for developing the hydrogen bubble chamber, but also investigated the Egyptian pyramids and dinosaur extinction.

I don’t remember the first time I heard the theory that the dinosaurs were wiped out by an asteroid crashing into the Earth. It’s a dramatic story that gets told to wide-eyed children in classrooms and natural history museums at an earlier age than many can remember, so it feels more like absorbed knowledge. What is less commonly known, however, is that one of the originators of this proposal was Luis Walter Alvarez, who won the 1968 Nobel Prize for Physics for his work on the hydrogen bubble chamber.

But it wasn’t just dinosaurs and asteroids that Alvarez got excited about. Throughout his long and varied career, Alvarez was also involved in sending particle detectors into the sky in high-altitude balloons and searching for hidden chambers inside ancient Egyptian pyramids. It appears that his innate curiosity and experimental creativity, which were so vital for winning the Nobel prize, also led him to investigate many more questions both within physics and beyond.

Life beyond the Nobel: how Luis Alvarez deduced the disappearance of the dinosaurs, Laura Hiscott, Physics World

Topics: Biology, COVID-19, Education, Research

During the first year of the COVID-19 pandemic, the “[lab] leak” theory gained little traction. Sure, U.S. President Donald Trump suggested SARS-CoV-2 originated in a laboratory in Wuhan, China—and called it “the China virus”—but he never presented evidence, and few in the scientific community took him seriously. In fact, early in the pandemic, a group of prominent researchers dismissed lab-origin notions as “conspiracy theories” in a letter in The Lancet. A report from a World Health Organization (WHO) “joint mission,” which sent a scientific team to China in January to explore possible origins with Chinese colleagues, described a lab accident as “extremely unlikely.”

But this spring, views began to shift. Suddenly it seemed that the lab-leak hypothesis had been too blithely dismissed. In a widely read piece, fueled by a “smoking gun” quote from a Nobel laureate, a veteran science journalist accused scientists and the mainstream media of ignoring “substantial evidence” for the scenario. The head of WHO openly pushed back against the joint mission’s conclusion, and U.S. President Joe Biden ordered the intelligence community to reassess the lab-leak possibility. Eighteen scientists, including leaders in virology and evolutionary biology, signed a letter published in Science in May that called for a more balanced appraisal of the “laboratory incident” hypothesis.

Yet behind the clamor, little had changed. No breakthrough studies have been published. The highly anticipated U.S. intelligence review, delivered to Biden on 24 August, reached no firm conclusions but leaned toward the theory that the virus has a natural origin.

Fresh evidence that would resolve the question may not emerge anytime soon. China remains the best place to hunt for clues, but its relative openness to collaboration during the joint mission seems to have evaporated. Chinese officials have scoffed at calls from Biden and WHO Director-General Tedros Adhanom Ghebreyesus for an independent audit of key Wuhan labs, which some say should include an investigation of notebooks, computers, and freezers. Chinese vice health minister Zeng Yixin said such demands show “disrespect toward common sense and arrogance toward science.” In response to the increasing pressure, China has also blocked the “phase 2” studies outlined in the joint mission’s March report, which could reveal a natural jump between species.

Despite the impasse, many scientists say the existing evidence—including early epidemiological patterns, SARS-CoV-2’s genomic makeup, and a recent paper about animal markets in Wuhan—makes it far more probable that the virus, like many emerging pathogens, made a natural “zoonotic” jump from animals to humans.

Virologist Robert Garry of Tulane University finds it improbable that a Wuhan lab worker picked up SARS-CoV-2 from a bat and then brought it back to the city, sparking the pandemic. As the WIV study of people living near bat caves shows, the transmission of related bat coronaviruses occurs routinely. “Why would the virus first have infected a few dozen lab researchers?” he asks. The virus may also have moved from bats into other species before jumping to humans, as happened with SARS. But again, why would it have infected a lab worker first? “There are hundreds of millions of people who come in contact with wildlife.”

The earliest official announcement about the pandemic came on 31 December 2019, when Wuhan’s Municipal Health Commission reported a cluster of unexplained pneumonia cases linked to the city’s Huanan seafood market. The WHO report devotes much attention to details about Huanan and other Wuhan markets but also cautions that their role remains “unclear” because several early cases had no link to any market. But after reading the report, Andersen became more convinced that the Huanan market played a critical role.

One specific finding bolsters that case, Wang says. The report describes how scientists took many samples from floors, walls, and other surfaces at Wuhan markets and were able to culture two viruses isolated from Huanan. That shows the market was bursting with a virus, Wang says: “In my career, I have never been able to isolate a coronavirus from an environmental sample.”

The report also contained a major error: It claimed there were “no verified reports of live mammals being sold around 2019” at Huanan and other markets linked to early cases. A surprising study published in June by Zhou Zhao-Min of China West Normal University and colleagues challenged that view. It found nearly 50,000 animals from 38 species, most alive, for sale at 17 shops at Huanan and three other Wuhan markets between May 2017 and November 2019. (The researchers had surveyed the markets as part of a study of a tick-borne disease afflicting animals.)

Live animals can more easily transmit a respiratory virus than meat from a butchered one, and the animals included masked palm civets, the main species that transmitted SARS-CoV to humans, and raccoon dogs, which also naturally harbored that virus and have been infected with SARS-CoV-2 in lab experiments. Minks—a species farmed for fur that has acquired SARS-CoV-2 infections from humans in many countries— were also abundant. “None of the 17 shops posted an origin certificate or quarantine certificate, so all wildlife trade was fundamentally illegal,” Zhou and his colleagues wrote in their paper. (Zhou did not respond to emails from Science.)

Call of the Wild: Why many scientists say it’s unlikely that SARS-CoV-2 originated from a “lab leak,” Jon Cohen, Science Magazine

FIG. 1. Schematic of the motivation and the method for this paper.

Topics: Applied Physics, Chemistry, Physics, Plasma, Research

ABSTRACT

Cold atmospheric plasmas have great application potential due to their production of diverse types of reactive species, so understanding the production mechanism and then improving the production efficiency of the key reactive species are very important. However, plasma chemistry typically comprises a complex network of chemical species and reactions, which greatly hinders the identification of the main production/reduction reactions of the reactive species. Previous studies have identified the main reactions of some plasmas via human experience, but since plasma chemistry is sensitive to discharge conditions, which are much different for different plasmas, widespread application of the experience-dependent method is difficult. In this paper, a method based on graph theory, namely, vital nodes identification, is used for the simplification of plasma chemistry in two ways: (1) holistically identifying the main reactions for all the key reactive species and (2) extracting the main reactions relevant to one key reactive species of interest. This simplification is applied to He + air plasma as a representative, chemically complex plasma, which contains 59 species and 866 chemical reactions, as reported previously. Simplified global models are then developed with the key reactive species and main reactions, and the simulation results are compared with those of the full global model, in which all species and reactions are incorporated. It was found that this simplification reduces the number of reactions by a factor of 8–20 while providing simulation results of the simplified global models, i.e., densities of the key reactive species, which are within a factor of two of the full global model. This finding suggests that the vital nodes identification method can capture the main chemical profile from a chemically complex plasma while greatly reducing the computational load for simulation.

Simplification of plasma chemistry by means of vital nodes identification

Bowen Sun, Dingxin Liu, Yifan Liu, Santu Luo, Mingyan Zhang, Jishen Zhang, Aijun Yang, Xiaohua Wang, and Mingzhe Rong, Journal of Applied Physics

Australian metals mining wastes (top) and the metal hyperaccumulator plants Alyssum murale and Berkheya coddii (bottom). The former plant can take up 1–3% of its weight in nickel. It has demonstrated yields of up to 400 kg of nickel per hectare annually, worth around $7000 at current prices, excluding processing and production costs. (Images adapted from A. van der Ent, A. Parbhakar-Fox, P. D. Erskine, Sci. Total Environ. 758, 143673, 2021, doi:10.1016/j.scitotenv.2020.143673.)

Topics: Climate Change, Green Tech, Materials Science, Research

When it comes to making steel greener, “only the laws of physics limit our imagination,” says Christina Chang of the Advanced Research Projects Agency-Energy (ARPA–E). Chang, an ARPA–E fellow, is seeking public input on a potential new agency program titled Steel Made via Emissions-Less Technologies. During her two-year tenure, she will guide program creation, agency strategy, and outreach. Steelmaking currently accounts for about 7% of the world’s carbon dioxide emissions, and demand for steel is expected to double by 2050 as low-income countries’ economies grow, according to the International Energy Agency.

Founded in 2009, ARPA–E is a tiny, imaginative office within the Department of Energy. SMELT is one part of a three-pronged thrust by ARPA–E to green up processes involved in producing steel and nonferrous metals, from the mine through to the finished products. Another program seeks ways to make use of the vast volumes of wastes that accumulate from mining operations around the globe—and reduce the amounts generated in the future. The agency is also exploring the feasibility of deploying plants that suck up from soils elements such as cobalt, nickel, and rare earths. Despite being essential ingredients in electric vehicles, batteries, and wind turbines, the US has little or no domestic production of them. (See Physics Today, February 2021, page 20.)

Steelmaking

The first step in steelmaking is separating iron ore into oxygen and iron metal, which produces CO₂ through both the reduction process and the fossil-fuel burning necessary to create high heat. An ARPA–E solicitation for ideas to clean up that process closed on 14 June. The agency is looking to replace the centuries-old blast furnace with greener technology that can work at the scale of 2 gigatons of steel production annually. It may or may not follow up with a request for research proposals to fund.

ARPA–E explores paths to emissions-free metal making, Physics Today

A computer simulation of the structure of the coronavirus SARS-CoV-2.Credit: Janet Iwasa, University of Utah

Topics: Biology, Biotechnology, COVID-19, DNA, Existentialism, Research

The coronavirus sports a luxurious sugar coat. “It’s striking,” thought Rommie Amaro, staring at her computer simulation of one of the trademark spike proteins of SARS-CoV-2, which stick out from the virus’s surface. It was swathed in sugar molecules, known as glycans.

“When you see it with all the glycans, it’s almost unrecognizable,” says Amaro, a computational biophysical chemist at the University of California, San Diego.

Many viruses have glycans covering their outer proteins, camouflaging them from the human immune system like a wolf in sheep’s clothing. But last year, Amaro’s laboratory group and collaborators created the most detailed visualization yet of this coat, based on structural and genetic data and rendered atom-by-atom by a supercomputer. On 22 March 2020, she posted the simulation to Twitter. Within an hour, one researcher asked in a comment: what was the naked, uncoated loop sticking out of the top of the protein?

Amaro had no idea. But ten minutes later, structural biologist Jason McLellan at the University of Texas at Austin chimed in: the uncoated loop was a receptor-binding domain (RBD), one of three sections of the spike that bind to receptors on human cells (see ‘A hidden spike’).

Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature

How the coronavirus infects cells — and why Delta is so dangerous, Megan Scudellari, Nature

Image Source: Link Below

Topics: Climate Change, COVID-19, Research, STEM

Just before dawn in the Jama-Coaque Ecological Reserve, a patch of Ecuador’s lush coastal forest, Abhimanyu Lele unfurls a tall net between two poles, then retreats out of sight. A half-hour later, he and a local assistant reappear and smile: Their catch—10 birds that collided with the net and tumbled into a pocket along its length—was a good one. The pair records species, measures and photographs the captives, and pricks wings for blood that can yield DNA before releasing the birds back into the forest. The data, Lele hopes, will shed light on how Ecuadorean songbirds adapt to different altitudes and other conditions.

The third-year graduate student at the University of Chicago (UC), who returns next week from a 10-week field season, was delighted to have made it to his destination. In a typical year, thousands of graduate students and faculty fan out across the world to tackle important research in climate change, fragile ecosystems, animal populations, and more. But the pandemic shut down travel, and fieldwork can’t be done via Zoom, depriving young scientists like Lele of the data and publications they need to climb the academic ladder and help advance science. Now, he and a few others are venturing out—into a very different world.

They are the exceptions. “Most folks have never been able to get back out there,” because COVID-19 continues to spread in much of the world, says Benjamin Halpern, an ecologist with the National Center for Ecological Analysis and Synthesis at the University of California, Santa Barbara. “They are just waiting.”

At the American Museum of Natural History, which mounts about 100 international expeditions a year, “Travel to countries still having trouble [is] just not going to happen,” says Frank Burbrink, a herpetologist there. “This is the longest I’ve ever gone without catching snakes since I was 12 years old.” The Smithsonian Institution’s National Museum of Natural History likewise “is not putting people overseas,” says Director Kirk Johnson.

How COVID-19 has transformed scientific fieldwork, Elisabeth Pennisi, Science Magazine

New territory Two candidate collider-neutrino events from the FASERν pilot detector in the plane longitudinal to (top) and transverse to (bottom) the beam direction. The different lines in each event show charged-particle tracks originating from the neutrino interaction point. Credit: FASER Collaboration.

Topics: CERN, High Energy Physics, Particle Physics, Research

Think “neutrino detector” and images of giant installations come to mind, necessary to compensate for the vanishingly small interaction probability of neutrinos with matter. The extreme luminosity of proton-proton collisions at the LHC, however, produces a large neutrino flux in the forward direction, with energies leading to cross-sections high enough for neutrinos to be detected using a much more compact apparatus.

In March, the CERN research board approved the Scattering and Neutrino Detector (SND@LHC) for installation in an unused tunnel that links the LHC to the SPS, 480 m downstream from the ATLAS experiment. Designed to detect neutrinos produced in a hitherto unexplored pseudo-rapidity range (7.2 < 𝜂 < 8.6), the experiment will complement and extend the physics reach of the other LHC experiments — in particular FASERν, which was approved last year. Construction of FASERν, which is located in an unused service tunnel on the opposite side of ATLAS along the LHC beamline (covering |𝜂|>9.1), was completed in March, while installation of SND@LHC is about to begin.

Both experiments will be able to detect neutrinos of all types, with SND@LHC positioned off the beamline to detect neutrinos produced at slightly larger angles. Expected to commence data-taking during LHC Run 3 in spring 2022, these latest additions to the LHC experiment family are poised to make the first observations of collider neutrinos while opening new searches for feebly interacting particles and other new physics.

Collider neutrinos on the horizon, Matthew Chalmers, CERN Courier

Topics: Biology, Planetary Science, Research, Tardigrades

They can survive temperatures close to absolute zero. They can withstand heat beyond the boiling point of water. They can shrug off the vacuum of space and doses of radiation that would be lethal to humans. Now, researchers have subjected tardigrades, microscopic creatures affectionately known as water bears, to impacts as fast as a flying bullet. And the animals survive them, too—but only up to a point. The test places new limits on their ability to survive impacts in space—and potentially seed life on other planets.

The research was inspired by a 2019 Israeli mission called Beresheet, which attempted to land on the Moon. The probe infamously included tardigrades on board that mission managers had not disclosed to the public, and the lander crashed with its passengers in tow, raising concerns about contamination. “I was very curious,” says Alejandra Traspas, a Ph.D. student at Queen Mary University of London who led the study. “I wanted to know if they were alive.”

Traspas and her supervisor, Mark Burchell, a planetary scientist at the University of Kent, wanted to find out whether tardigrades could survive such an impact—and they wanted to conduct their experiment ethically. So after feeding about 20 tardigrades moss and mineral water, they put them into hibernation, a so-called “tun” state in which their metabolism decreases to 0.1% of their normal activity, by freezing them for 48 hours.</em>

They then placed two to four at a time in a hollow nylon bullet and fired them at increasing speeds using a two-stage light gas gun, a tool in physics experiments that can achieve muzzle velocities far higher than any conventional gun. When shooting the bullets into a sand target several meters away, the researchers found the creatures could survive impacts up to about 900 meters per second (or about 3000 kilometers per hour), and momentary shock pressures up to a limit of 1.14 gigapascals (GPa), they report this month in Astrobiology. “Above [those speeds], they just mush,” Traspas says.</em>

Hardy water bears survive bullet impacts—up to a point, Jonathan O'Callaghan, Science Magazine

Topics: Biology, DNA, Evolution, Research

In her laboratory in Barcelona, Spain, Miki Ebisuya has built a clock without cogs, springs, or numbers. This clock doesn’t tick. It is made of genes and proteins, and it keeps time in a layer of cells that Ebisuya’s team has grown in its lab. This biological clock is tiny, but it could help to explain some of the most conspicuous differences between animal species.

Animal cells bustle with activity, and the pace varies between species. In all observed instances, mouse cells run faster than human cells, which tick faster than whale cells. These differences affect how big an animal gets, how its parts are arranged, and perhaps even how long it will live. But biologists have long wondered what cellular timekeepers control these speeds, and why they vary.

A wave of research is starting to yield answers for one of the many clocks that control the workings of cells. There is a clock in early embryos that beats out a regular rhythm by activating and deactivating genes. This ‘segmentation clock’ creates repeating body segments such as the vertebrae in our spines. This is the timepiece that Ebisuya has made in her lab.

“I’m interested in biological time,” says Ebisuya, a developmental biologist at the European Molecular Biology Laboratory Barcelona. “But lifespan or gestation period, they are too long for me to study.” The swift speed of the segmentation clock makes it an ideal model system, she says.

These cellular clocks help explain why elephants are bigger than mice, Michael Marshall, Nature

Inside the B.1.1.7 Coronavirus Variant, By Jonathan Corum and Carl ZimmerJan, The New York Times, January 18, 2021

Topics: Biology, COVID-19, DNA, Research

Download Accessible Data [XLS – 738 B]

CDC is closely monitoring these variants of concern (VOC). These variants have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines).

CDC: US COVID-19 Cases Caused by Variants