“We found that the interactions among the basic building blocks of the Spike protein become more symmetrical in the G form, and that gives it more opportunities to bind to the receptors in the host — in us,” said Gnana Gnanakaran, corresponding author of the paper published today in Science Advances. “But at the same time, that means antibodies can more easily neutralize it. In essence, the variant puts its head up to bind to the receptor, which gives antibodies the chance to attack it.”

Researchers knew that the variant, also known as D614G, was more infectious and could be neutralized by antibodies, but they didn’t know how. Simulating more than a million individual atoms and requiring about 24 million CPU hours of supercomputer time, the new work provides molecular-level detail about the behavior of this variant’s Spike.

Current vaccines for SARS-CoV-2, the virus that causes COVID-19, are based on the original D614 form of the virus. This new understanding of the G variant — the most extensive supercomputer simulations of the G form at the atomic level — could mean it offers a backbone for future vaccines.

The team discovered the D614G variant in early 2020, as the COVID-19 pandemic caused by the SARS-CoV-2 virus was ramping up. These findings were published in Cell. Scientists had observed a mutation in the Spike protein. (In all variants, it is the Spike protein that gives the virus its characteristic corona.) This D614G mutation, named for the amino acid at position 614 on the SARS-CoV-2 genome that underwent a substitution from aspartic acid, prevailed globally within a matter of weeks.

The Spike proteins bind to a specific receptor found in many of our cells through the Spike’s receptor binding domain, ultimately leading to infection. That binding requires the receptor binding domain to transition structurally from a closed conformation, which cannot bind, to an open conformation, which can.

The simulations in this new research demonstrate that interactions among the building blocks of the Spike are more symmetrical in the new G-form variant than those in the original D-form strain. That symmetry leads to more viral Spikes in the open conformation, so it can more readily infect a person.

A team of postdoctoral fellows from Los Alamos — Rachael A. Mansbach (now assistant professor of Physics at Concordia University), Srirupa Chakraborty, and Kien Nguyen — led the study by running multiple microsecond-scale simulations of the two variants in both conformations of the receptor binding domain to illuminate how the Spike protein interacts with both the host receptor and with the neutralizing antibodies that can help protect the host from infection. The members of the research team also included Bette Korber of Los Alamos National Laboratory, and David C. Montefiori, of Duke Human Vaccine Institute.

The team thanks Paul Weber, head of Institutional Computing at Los Alamos, for providing access to the supercomputers at the Laboratory for this research.

The Paper: “The SARS-CoV-2 Spike variant D614G favors an open conformational state,” Science Advances. Rachael A. Mansbach, Srirupa Chakraborty, Kien Nguyen, David C. Montefiori, Bette Korber, S. Gnanakaran.

The Funding: The project was supported by Los Alamos Laboratory Directed Research and Development project 20200706ER, Director’s Postdoctoral fellowship, and the Center of Nonlinear Studies Postdoctoral Program at Los Alamos.

“What really surprised me about the results is that we may realistically find signs of life on other planets in the next 5 to 10 years,” said Caprice Phillips, a graduate student at The Ohio State University, who will share preliminary findings at a press conference during the 2021 APS April Meeting.

Gas dwarf planets have the potential to foster life. But because none of these super-Earths or mini-Neptunes exist within our solar system, scientists struggle to determine whether their atmospheres contain ammonia and other potential signs of living things.

Phillips calculated that when the James Webb Space Telescope launches this October, it could feasibly detect ammonia around six gas dwarf planets after just a few orbits.

She and her team modeled how JWST instruments would respond to varying clouds and atmospheric conditions, then produced a ranked list of where the telescope should search for life.

“Humankind has contemplated the questions, ‘Are we alone? What is life? Is life elsewhere similar to us?'” said Phillips. “My research suggests that for the first time, we have the scientific knowledge and technological capabilities to realistically begin to find the answers to these questions.”

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“Our Earth is 45 million centuries old. But this century is the first when one species — ours — can determine the biosphere’s fate,” said Martin Rees, the United Kingdom’s Astronomer Royal and a founder of the Centre for the Study of Existential Risks at Cambridge University.*

“Our globally-linked society is vulnerable to the unintended consequences of powerful new technologies — not only nuclear, but (even more) biotech, cyber, advanced AI, space technology,” he added.

Royal astronomer predicts the world in 2050 and beyond

Rees thinks biohackers pose a particularly underappreciated threat to humanity. In the near future, simple equipment will enable people to reengineer the human genome irrevocably or build a superspreading influenza. Like drug laws, regulations could never prevent all such actions — and in a world more interconnected than ever before, the consequences would spread globally.

He will discuss other dangers: population rise leading to plummeting biodiversity, disastrous climate change, uncontrollable cybercriminals, plans for artificial intelligence that erodes privacy, security, and freedom.

But Rees is an optimist. He will offer a path toward avoiding these risks and achieving a sustainable future better than the world we live in today.

“If all of us passengers on ‘spaceship Earth’ want to ensure that we leave it in better shape for future generations we need to promote wise deployment of new technologies, while minimizing the risk of pandemics, cyberthreats, and other global catastrophes,” he said.

Scaling back missile defense could prevent a nuclear attack

A single nuclear weapon could kill millions and destroy a city instantaneously. Hundreds of weapons could wipe out functioning society in a large nation. Even a limited nuclear war could cause a climate catastrophe, leading to the starvation of hundreds of millions of people.

Recently, Russia, China, and North Korea have deployed new types of nearly unstoppable missiles.

“Missile defense is an idea that can sound appealing at first — doesn’t defense sound like the right thing to do?” said Frederick Lamb, astrophysicist at the University of Illinois at Urbana-Champaign, cochair of the 2003 APS Study of Boost-Phase Missile Defense, and chair of the current APS Panel on Public Affairs Study of Missile Defense and National Security.

“But when the technical challenges and arms race implications are considered, one can see that deploying a system that is intended to defend against intercontinental ballistic missiles is unlikely to improve the security of the United States,” he said.

Lamb points to the United Kingdom’s decision to increase its nuclear arsenal by 44%, possibly motivated by Russia’s new missile defense system around Moscow. He sees the move as yet another sign that existing limits on nuclear weapons are unraveling. Even missile defenses that would never work in practice can catalyze the development of new nuclear weapons and increase global risk.

Lamb will share what may happen if the United States ramps up new missile defense systems.

“What is done about nuclear weapons and missile defenses by the United States and other countries affects the safety and survival of every person on the planet,” he said.

*Scientists will forecast the fate of the planet at a press conference during the 2021 APS April Meeting.

A joint research team led by Professor Junsuk Rho of departments of mechanical and chemical engineering and Dr. Inki Kim of Department of Mechanical Engineering with Professor Young-Ki Kim and Ph.D. candidate Won-Sik Kim of Department of Chemical Engineering at POSTECH has integrated metasurface with gas-reactive liquid crystal optical modulator to develop a sensor that provides an immediate visual holographic alarm when harmful gases are detected. The findings from this study were published in Science Advances on April 7, 2021.

For those working in hazardous environments such as petrochemical plants, gas sensors are life. However, conventional gas sensing devices are not widely used due to their high cost of being made with complex machines and electronic devices. In addition, commercial gas sensors have limitations in that they are difficult to use, and have poor portability and reaction speed.

To solve these issues, the research team utilized the metasurface, well known as a future optical device known to have the invisible cloak effect through making visible objects disappear by controlling the refractive index of light. Metasurface is especially used to transmit two-way holograms or 3D video images by freely controlling light.

Using the metasurface, the research team developed a gas sensor that can float a holographic image alarm in space in just a few seconds by using the polarization control of transmitted light that transforms due to the change in orientation of liquid crystal molecules in the liquid crystal layer inside the sensor device when exposed to gas. Moreover, this gas sensor developed by the research team requires no support from external mechanical or electronic devices, unlike other conventional commercial gas sensors. The researchers used isopropyl alcohol as the target hazardous gas, known as a toxic substance that can cause stomach pain, headache, dizziness, and even leukemia.

The newly developed sensor was confirmed to detect even the minute amount of gas of about 200ppm. In an actual experiment using a board marker, a volatile gas source in our daily life, a visual holographic alarm popped up instantaneously the moment the marker was brought to the sensor.

Moreover, the research team developed a one-step nanocomposite printing method to produce this flexible and wearable gas sensor. The metasurface structure, which was previously processed on a hard substrate, was designed to enable rapid production with a single-step nanocasting process on a curved or flexible substrate.

When the flexible sensor fabricated using this method attaches like a sticker on safety glasses, it can detect gas and display a hologram alarm. It is anticipated to be integrable with glass-type AR display systems under development at Apple, Samsung, Google, and Facebook.

Going a step further, the research team is developing a high-performance environmental sensor that can display the type and concentration level of gases or biochemicals in the surroundings with a holographic alarm, and is studying optical design techniques that can encode various holographic images. If these studies are successful, they can be used to reduce accidents caused by biochemical or gas leaks.

“This newly developed ultra-compact wearable gas sensor provides a more intuitive holographic visual alarm than the conventional auditory or simple light alarms,” remarked Prof. Junsuk Rho. “It is anticipated to be especially effective in more extreme work environments where acoustic and visual noise are intense.”

“All the stars aligned,” said Elke-Caroline Aschenauer, Brookhaven National Laboratory Staff Scientist and a leader in developing the EIC plans. “We have the technology to build this unique particle accelerator and detector to do the measurements that, together with the underlying theory, can for the first time provide answers to longstanding fundamental questions in nuclear physics.”

The EIC isn’t the only Brookhaven project poised to reshape nuclear and particle physics. Forthcoming data from the Relativistic Heavy Ion Collider could finally detect the elusive chiral magnetic effect. Meanwhile, planned accelerators could run on sustainable energy, a drastic departure from today’s machines.

At a press conference during the 2021 APS April Meeting, researchers will discuss how cutting-edge accelerators could collide with both energy consumption and our assumptions about the nature of matter.

A powerful new facility for nuclear physics

“The scientific advances of the EIC will help us all to understand where we come from and how the visible matter around us is composed from its elementary building blocks,” said Aschenauer.

The accelerator and detector will serve as a kind of camera, taking 3D images and movies of electrons colliding with polarized protons and ions. Like a CT scanner for atoms, the EIC will let scientists see how force-carrying gluon particles hold together quarks, the internal components of protons and neutrons. It will also offer insights into the spin of fundamental particles.

Aschenauer will give status updates from the first year of the EIC project — a collaboration between BNL and Thomas Jefferson National Accelerator Facility — and an overview of its experimental equipment.

Hunting for the chiral magnetic effect

The EIC will build on the Relativistic Heavy Ion Collider, which will soon produce major results of its own.

In summer 2021, data analysis will likely conclude on an experiment searching for decisive proof of the chiral magnetic effect. This proposed effect helps explain many fundamental features of the Standard Model and could unlock why our universe contains overwhelmingly more matter than antimatter, crucial to human existence.

Jinfeng Liao, a theoretical nuclear physicist at Indiana University Bloomington, will share key predictions about what the experiment might uncover.

“The signatures, as predicted by our theoretical study, show clear promise of unambiguously establishing the existence of chiral magnetic effect in the isobar collision experiment,” said Liao.

Liao and colleagues created a custom fluid-dynamics-based computational tool to simulate experimental collisions and any changes the chiral magnetic effect would cause.

They show that the new experiment has a better chance of detecting the effect than previous attempts, long plagued by weak signals and strong background contamination. The predictions were published in Physical Review Letters.

Probing profound subatomic questions requires a lot of power.

“Large particle accelerators use a shockingly large amount of energy,” said Georg Hoffstaetter, a professor at Cornell University.

He will share results from the Cornell-BNL Test Accelerator, or CBETA, the world’s first to accelerate a beam multiple times while powering itself by reusing beam energy. It further reduces electricity demands with superconducting and magnetic equipment.

The Energy Recovery Linacs technology that enables the test accelerator could lead to smaller particle accelerators with higher beam currents and reduced energy consumption.

“People may benefit from the industrial applications of Energy Recovery Linacs by using better computer chips, by being cured in radiation therapy centers that guide beams with permanent magnets, or by inhaling accelerator-produced medical isotopes,” said Hoffstaetter.

Building on the success of the test accelerator, its principal investigator and Brookhaven Senior Physicist Dejan Trbojevic will present designs for a new green energy collider. Particles speed along racetrack beam lines, formed from high-quality permanent magnets which require no use of electrical power.

“The ‘green accelerator’ shows a completely new way of accelerating particles with very tight control of their motion and with an extremely high energy range. It has never been done before,” said Trbojevic.

He will demonstrate how the EIC, as well as a similar accelerator under consideration at the Large Hadron Collider, could incorporate the energy-saving features.

An international team of researchers, including Carnegie Mellon University’s Saoirse Foley, set out on an ancestry.com-like investigation to find the answer to this question. They looked to the transcriptomes, the sum of all the transcripts from the mRNA, of many tarantulas and other spiders from different time periods. Their findings were published online by PeerJ on April 6.

They used the transcriptomes to build a genetic tree of spiders and then time-calibrated their tree with fossil data. Tarantula fossils are extremely rare, but the software used in the study managed to estimate the ages of older tarantulas relative to the ages of fossils from other spiders.

They found that tarantulas are ancient, first emerging in the piece of land now considered the Americas about 120 million years ago during the Cretaceous period. At that time South America would have been attached to Africa, India and Australia as part of the Gondwana supercontinent. The spiders ultimately reached their present destinations due to continental drift, with a few interesting departures.

For example, the nature of their entry into Asia suggests tarantulas may also be surprisingly proficient dispersers. The researchers were able to establish two separate lineages of tarantulas that diverged on the Indian subcontinent before it crashed into Asia, with one lineage being predominantly ground dwelling and the other predominantly arboreal. They found that these lineages colonized Asia about 20 million years apart. Surprisingly, the first group that reached Asia also managed to cross the Wallace Line, a boundary between Australia and the Asian islands where many species are found in abundance on one side and rarely or not at all on the other.

“Previously, we did not consider tarantulas to be good dispersers. While continental drift certainly played its part in their history, the two Asian colonization events encourage us to reconsider this narrative. The microhabitat differences between those two lineages also suggest that tarantulas are experts at exploiting ecological niches, while simultaneously displaying signs of niche conservation,” said Foley.

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Materials provided by Carnegie Mellon University. Original written by Jocelyn Duffy. Note: Content may be edited for style and length.