One puzzle known as the “radius valley” refers to the rarity of exoplanets with a radius about 1.8 times that of Earth. NASA’s Kepler spacecraft observed planets of this size about 2-3 times less frequently than it observed super-Earths with radii about 1.4 times that of Earth and mini-Neptunes with radii about 2.5 times Earth’s. The second mystery, known as “peas in a pod,” refers to neighboring planets of similar size that have been found in hundreds of planetary systems. Those include TRAPPIST-1 and Kepler-223, which also feature planetary orbits of near-musical harmony.

“I believe we are the first to explain the radius valley using a model of planet formation and dynamical evolution that self-consistently accounts for multiple constraints of observations,” said Rice University’s André Izidoro, corresponding author of a study published this week in Astrophysical Journal Letters. “We’re also able to show that a planet-formation model incorporating giant impacts is consistent with the peas-in-a-pod feature of exoplanets.”

Izidoro, a Welch Postdoctoral Fellow at Rice’s NASA-fundedCLEVER Planets project, and co-authors used a supercomputer to simulate the first 50 million years of the development of planetary systems using a planetary migration model. In the model, protoplanetary disks of gas and dust that give rise to young planets also interact with them, pulling them closer to their parent stars and locking them in resonant orbital chains. The chains are broken within a few million years, when the disappearance of the protoplanetary disk causes orbital instabilities that lead two or more planets to slam into one another.

Planetary migration models have been used to study planetary systems that have retained their resonant orbital chains. For example, Izidoro and CLEVER Planets colleagues used a migration model in 2021 to calculate the maximum amount of disruption TRAPPIST-1’s seven-planet system could have withstood during bombardment and still retained its harmonious orbital structure.

In the new study, Izidoro partnered with CLEVER Planets’ investigators Rajdeep Dasgupta and Andrea Isella, both of Rice, Hilke Schlichting of the University of California, Los Angeles, and Christian Zimmermann and Bertram Bitsch of the Max Planck Institute for Astronomy in Heidelberg, Germany.

“The migration of young planets towards their host stars creates overcrowding and frequently results in cataclysmic collisions that strip planets of their hydrogen-rich atmospheres,” Izidoro said. “That means giant impacts, like the one that formed our moon, are probably a generic outcome of planet formation.”

The research suggests planets come in two “flavors,” super-Earths that are dry, rocky and 50% larger than Earth, and mini-Neptunes that are rich in water ice and about 2.5 times larger than Earth. Izidoro said new observations seem to support the results, which conflict with the traditional view that both super-Earths and mini-Neptunes are exclusively dry and rocky worlds.

Based on their findings, the researchers made predictions that can be tested by NASA’s James Webb Space Telescope. They suggest, for instance, that a fraction of planets about twice Earth’s size will both retain their primordial hydrogen-rich atmosphere and be rich in water.

The research was funded by NASA (80NSSC18K0828), the Welch Foundation (C-2035-20200401) and the European Research Council (757448-PAMDORA).

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Materials provided by Rice University. Original written by Jade Boyd. Note: Content may be edited for style and length.

The existence of such a brain-preserving state could explain why some patients wake up days or even weeks after they stop receiving ventilation, and it suggests that physicians should take these lengthy recovery times into account when determining a patient’s prognosis.

In a study published Nov. 7 in the Proceedings of the National Academy of Sciences, the investigators connect the pattern seen among those who have survived severe COVID-19 with similar delays known to occur in a small fraction of cardiac arrest patients.

“The delayed recoveries in COVID-19 patients are very much like the rare cases we’ve documented in previous research. In this new paper, we describe a mechanism to explain what we’re seeing in both types of patients,” said study co-senior author Dr. Nicholas D. Schiff, the Jerold B. Katz Professor of Neurology and Neuroscience in the Feil Family Brain and Mind Research Institute and co-director of the Consortium for the Advanced Study of Brain Injury (CASBI) at Weill Cornell Medicine.

He found evidence for this explanation — that patients’ brains are protecting themselves — in animals, most notably painted turtles, that can tolerate extended periods without oxygen.

More than a decade ago, Dr. Schiff and his colleagues first observed these delays among comatose cardiac arrest patients who received cooling therapy to reduce brain damage caused by a loss of blood flow. In one such case, a 71-year-old patient took 37 days to awaken, before ultimately making a near-complete recovery.

During the pandemic, Dr. Schiff, who is also a neurologist at NewYork-Presbyterian/Weill Cornell Medical Center, performed neurology consultations for COVID-19 patients, and he soon began seeing similar, delayed awakenings occurring when patients were taken off ventilators and stopped receiving the sedatives given to them to reduce their movement.

In a separate analysis of a large cohort of Covid-19 patients from Weill Cornell Medicine and two other major U.S. medical centers, Dr. Schiff and his colleagues, including co-author of the current paper, Dr. Emery N. Brown, professor of anesthesia at Harvard Medical School, Edward Hood Taplin Professor of Medical Engineering and Computational Neuroscience in The Picower Institute for Learning and Memory at MIT and an anesthesiologist at Massachusetts General Hospital, found that a quarter of patients who survived ventilation took 10 days or longer to recover consciousness. The more oxygen deprivation they suffered while on the ventilator, the longer that delay.

In the prior study of cardiac patients, the researchers recorded a distinctive pattern in brain activity, one also seen in patients under deep anesthesia. (Recordings from COVID-19 patients are extremely limited.) Dr. Schiff read that a similar pattern had been seen in the brains of painted turtles, which can withstand up to five months without oxygen under ice in the winter. To do so, they activate the same inhibitory system within the brain targeted by anesthetics given to human cardiac and COVID-19 patients but in novel ways developed by evolutionary specializations.

Dr. Schiff and Dr. Brown propose that, by chance, the same protective response emerges in the patients.

“It is our theory that oxygen deprivation as well as practices in the ICU, including commonly used anesthetics, expose elements of strategies that animals use to survive in extreme conditions,” Dr. Schiff said.

“These observations may offer new insights into the mechanisms of how certain anesthetics produce unconsciousness and new approaches for ICU sedation and for fostering recovery from disorders of consciousness,” Dr. Brown added.

When patients fail to regain consciousness for an extended time, physicians may recommend withdrawing life-supporting care. This threshold is typically set at 14 days or less for cardiac patients, while no such guidelines exist for COVID-19.

In light of this new research, however, so long as they lack brain injuries, physicians should avoid making negative projections about these patients’ potential to recover, note the researchers.

Supercomputer simulations have helped scientists reveal in a bilayer moiré system a new species of an electronic phenomenon called an exciton, which is an electrically neutral quasiparticle, yet one that can carry energy and consists of an electron and electron ‘hole’ that can be created for example by light impinging certain semiconductors and other materials.

The newly discovered excitons were produced by moiré patterns from two-dimensional sheets of exotic semiconductors called transition metal dichalcogenides, with the electron bound to the hole but separated from each other by a characteristic distance in the sheet. This was named an intralayer charge-transfer exciton and was a surprise to the scientists because such excitons do not exist in the individual sheets. The research can be used in the development of new optical sensors and communication technology such as optical fibers and lasers.

Novel Exciton Discovered

“In this work we discovered a novel exciton of unforeseen intralayer charge-transfer characteristics in a moiré superlattice formed by two atomically thin layers of transition metal dichalcogenide materials,” said Steven G. Louie, a distinguished professor of physics at the University of California, Berkeley (UC Berkeley), and a senior faculty scientist at the Lawrence Berkeley National Laboratory (LBNL).

Louie is the corresponding author of research published August 2022 in the journal Nature. In it, the scientists developed computer models that go beyond the conventional parameterized models that have been used to describe moiré systems and moiré excitons. Instead, they performed ab initio calculations that only start with the identity and initial position of the 3,903 atoms of the moiré superlattice unit cell.

First Principles

“It is a powerful method to accurately predict material properties,” Louie added, “because there’s no empirical fitting involved.”

In particular, to calculate the exciton states and the optical property of the moiré systems, they used the state-of-the-art GW plus Bethe-Salpeter equation (GW-BSE) approach, considered one of the most accurate approaches to predicting the optical properties of materials.

What’s more, Louie and colleagues used their calculations to predict the different electronic and optical responses of the excitons in the system. They worked with experimental colleagues Emma C. Regan, Zuocheng Zhang and Professor Feng Wang at UC Berkeley. In a nutshell, Wang and colleagues shone light on the material and then analyzed the reflected light to see how the system responded to the impinging photons under different conditions.

Sure enough, they verified the theoretical predictions by finding distinct signatures of the intralayer charge-transfer exciton in their measurements.

Computational Challenges Overcome With TACC Support

“The GW-BSE method is very accurate, but it is also very computationally challenging,” said study co-author Mit Naik, a postdoctoral researcher working with Professor Louie at UC Berkeley and LBNL.

The challenge in simulating an exciton is that it requires solving difficult six-dimensional integrals, numerous times, and the integrals are massive in the moiré superlattice because of the large size of the moiré unit cell — composed of many unit cells of the individual layers, 25×25 for one layer and 26×26 for the other.

Typical GW-BSE calculations are performed on systems of just up to a hundred atoms in the unit cell. Here, the authors needed calculations for a whooping 3,903 atoms. “Initially, it seemed almost impossible,” Naik said.

Undaunted, the scientists hit on a new method that reduced the computational cost by a million times without loss of accuracy.

“We found a way to approximate each layer’s two thousand atom integral as a sum over many three atom integrals, which were computationally much simpler to compute,” Naik said.

The theoretical technique they developed, called the pristine unit-cell matrix projection (PUMP) method, can be generalized to study other material systems such as interlayer or hybrid moiré excitons in multi-layer moiré superlattices, shallow defects in materials, and more.

The Texas Advanced Computing Center (TACC) supported Steven Louie’s first principles study of cutting-edge materials through a large resource allocation on TACC’s Frontera supercomputer, the most powerful academic system in the U.S and funded by the National Science Foundation.

He also was awarded allocations on TACC’s Stampede2 supercomputer made through the NSF-funded Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS), formerly the Extreme Science and Engineering Discovery Environment (XSEDE).

In their bid to push the limit of the number of atoms in their calculations, the researchers initially faced some problems with running some of the large-scale moiré calculations on Frontera.

“We received support from the research associates at TACC, who helped us resolve these problems,” Naik recalled.

For instance, they were unable to run the large-scale simulations of ground-state properties on Frontera using a standard density functional theory (DFT) package called Quantum Espresso, because of the instability created by a new version of the Intel compiler used to for the DFT package.

The TACC consulting team found a way around the problem by installing an older, more stable version of the compiler. “This allowed us to compute the electronic structure of the WSe2 moiré superlattice that went into this work,” Naik said.

“Frontera and Stampede2 hardware efficiently catered to our requirements by providing state-of-the-art internode connectivity and sufficient memory on each node,” Naik added.

SCIENCE IMPACT

“The intralayer charge-transfer exciton we discovered through this artificial stacking of two monolayers has revealed an extraordinarily strong interplay of the atomic structure and the type of exciton possible in the moiré systems,” Louie said. “This is an important step in advancing the engineering of materials for desired properties.”

That’s because, once light creates charge-transfer excitons, they can be distorted or dissociated more easily with an external field or other perturbations than the standard Wannier-type excitons.

These considerations are important in many basic phenomena and potential applications, such as novel optical sensors and electro-optic modulation nanodevices. “That’s what we’re working on with our experimental colleagues right now,” Louie said.

“Excitonic properties of materials form the basic principles behind many of the optical and optoelectronic devices and sensors that we encounter in our daily lives,” said study co-author Felipe Jornada, an Assistant Professor in the Department of Materials Science and Engineering at Stanford University and a Principal Investigator at the SLAC National Accelerator Laboratory.

He gave the example of OLED TVs and displays, which use light emission from the recombination of excitons in organic semiconductors. Also, new smartwatches use advanced optical sensors to monitor the wearer’s blood oxygen levels.

“Beyond existing devices, the transition metal dichalcogenides and heterostructures of these materials that we’re working on are considered a promising material platform for post-silicon nanoscale optoelectronic devices. Moving forward, we believe that these are going to be a promising route towards novel sensors, displays, and technologies,” Jornada said.

The majority of the funding for the study was provided by the U.S. Department of Energy’s van der Waals heterostructure program (KCWF16). The theory and algorithm development for this work was carried out at the Center for Computational Study of Excited State Phenomena in Energy Materials (C2SEPEM) at the Lawrence Berkeley National Lab. They also used the National Energy Research Science Computing Center (NERSC) at the Lawrence Berkeley National Laboratory to perform part of the calculations.

Confined to a single deep limestone cave in Nevada’s Mojave Desert, 263 of them live in water that hovers around 93 degrees Fahrenheit year-round, with food resources so scarce that they are always on the edge of starvation, and with oxygen levels so low that most other fish would die immediately. The pupfish, Cyprinodon diabolis, live in the smallest habitat of any known vertebrate.

New research now documents the extreme effect that these harsh and isolated conditions have had on this fish’s genetic diversity.

In a paper published this week in the journal Proceedings of the Royal Society B, University of California, Berkeley, biologists report the first complete genome sequences of eight pupfish species from the American Southwest — 30 individuals in all, including eight Devils Hole pupfish. Astoundingly, the Devils Hole pupfish is so inbred that 58% of the genomes of these eight individuals are identical, on average.

“High levels of inbreeding are associated with a higher risk of extinction, and the inbreeding in the Devils Hole pupfish is equal to or more severe than levels reported so far in other isolated natural populations, such as the Isle Royale wolves in Michigan, mountain gorillas in Africa and Indian tigers,” said lead researcher Christopher Martin, UC Berkeley associate professor of integrative biology and curator of ichthyology in the campus’s Museum of Vertebrate Zoology. “Although we were not able to directly measure fitness, the increased inbreeding in these pupfish likely results in a substantial reduction in fitness.”

Other pupfish species are also inbred, the researchers found, but only between 10% and 30% of their genomes are identical.

Graduate student David Tian, lead author of the study, said that the level of inbreeding in the Devils Hole pupfish is equivalent to what would happen if four to five generations of siblings mated with one another. This tends to burn in or fix, rather than weed out, harmful mutations, potentially dooming a population to extinction by mutational meltdown. The Devils Hole pupfish species is currently doing well in the wild and in captive or “refuge” populations, but such low genetic diversity could spell trouble as the climate changes and human impacts become greater.

In the face of these potential threats, the new genome sequences will help scientists and conservationists assess the health of native pupfish populations and potentially intervene in refuge populations to increase the genetic diversity of these species — the Devils Hole pupfish, in particular.

“With this new genomic data, there’s a lot of potential to look not just at genetic diversity and how these species are related to each other phylogenetically, but also look at inbreeding and mutation load to get an idea of what their current status is, how evolutionary history may have influenced their current genetic variation, and think about where the population is going and what we should do, if anything, to preserve these species,” Tian said.

Population decline and rescue

Pupfish species are scattered around the globe and tend to like isolated lakes and springs, often with extreme conditions that most fish would find unsurvivable. About 30 species inhabit warm, salty desert springs and streams in California and Nevada. Martin has studied various pupfish populations, including several on San Salvador Island in the Bahamas, to understand the genetics behind their adaptation to extreme conditions and unusual ecological niches.

The Devils Hole pupfish, however, is unique in its small range and perilous existence, Martin said, making its fluctuating population in the wild worrisome to conservationists.

“Part of the question about these declines is whether they may be due to the genetic health of the population,” Martin said. “Maybe the declines are because there are harmful mutations that have become fixed because the population is so small.”

The small population is partly a result of human incursions into their habitat, Martin noted. Local ranchers and developers pumped groundwater in the region in the 1960s and ’70s that drastically reduced the water level in Devils Hole, leading to a drop in population levels. A 1976 Supreme Court ruling that allowed the federal government to limit groundwater pumping saved Devils Hole and the resident population, while captive breeding at a nearby 100,000-gallon pool in the Ash Meadows National Wildlife Refuge rescued the species. Nevertheless, a decline in the 1990s led the wild population to its nadir in 2013: 35 individuals. The wild population has since recovered, while the refuge population has ballooned to about 400, twice the wild population.

Humans are not totally to blame for the lack of genetic diversity in the Devils Hole pupfish, however. The UC Berkeley researchers also sequenced the genome of a pupfish collected in 1980 and held at the University of Michigan. It showed inbreeding and a lack of genetic diversity similar to that found in individuals collected recently, most of which died a natural death. This implies that the pupfish has likely seen population bottlenecks frequently over hundreds, if not thousands, of years.

One result of this, Martin and Tian found, is that 15 genes have disappeared entirely from the Devils Hole pupfish genome. Five of them seem to be involved in adaptation to living in low-oxygen or hypoxic environments.

“These deletions are a paradox, because this is a habitat where you’re most exposed to hypoxia,” Martin said. “It could have something to do with the stability of the habitat over time. But it looks to us like the hypoxia pathway is broken. Once you break one gene, it doesn’t really matter if you break additional genes in that regulatory pathway. Our future work is to actually look at what these deletions do. Do they increase tolerance of hypoxia? Do they decrease tolerance of hypoxia? I think those two scenarios are equally plausible at this time.”

Selective breeding within a captive population of Devils Hole pupfish could help increase the diversity and perhaps save the species from eventual extinction, he said. And to restore genes already lost, CRISPR genome editing could add them back.

The fact that the genome of the fish collected in 1980 was about as inbred as today’s fish is “maybe good news,” Martin said, “in that the population has historically been highly inbred with very low genetic diversity, suggesting that the recent decline in the ’90s, with population bottlenecks to only 35 fish in 2013 and 38 fish in 2007, doesn’t seem to have had much of an effect.”

Tian is currently analyzing about 150 complete genome sequences of nine species of American pupfish to get a more complete picture of the deleterious mutations and gene deletions in the various Southwestern populations. He sees the study as an example of what conservation genomics can do for endangered and possibly inbred populations around the world.

“We’re on a really cool cusp when it comes to using genomic data and applying it to conservation, especially at a time where it’s a problem that is likely only going to get worse with climate change and increased habitat fragmentation and just anthropogenic changes,” he said.

Tian is leery of genetic interventions, however, since little is known about how genes influence the physical and behavioral characteristics of a species and how this relates to fitness and adaptation to a specific environment. Conservation should still be a priority.

“The answer is still increased funding for these populations, protecting habitats, legal avenues for protecting these species and figuring out ways for humans and these endangered species to coexist on this planet,” he said.

Co-authors with Martin and Tian are Austin Patton of UC Berkeley and Bruce Turner of Virginia Tech in Blacksburg. The work is funded by the U.S. Fish and Wildlife Service, National Park Service, National Science Foundation (1749764) and National Institutes of Health (5R01DE027052-02).

New findings from a meta-analysis published in Nature Immunology examine the biological mechanisms responsible for why some people’s immune systems respond differently to vaccinations, which could have global implications for the development and administration of vaccines.

As part of a series of studies for The Human Immunology Project Consortium (HIPC), a network of national research institutions studying the range of responses to different infections and vaccinations, Emory researchers analyzed the molecular characteristics of 820 healthy young adults who were immunized with 13 different vaccines to identify specific biomarkers that generate antibody response to vaccines.

The participants were separated into three endotypes, or groups with a common gene expression, based on the level of inflammatory response prior to vaccination — a high inflammatory group, a low inflammatory group, and a mid-inflammatory group. After studying the immunological changes that occurred in participants following vaccination, researchers found the group that had the highest levels of inflammation prior to vaccine had the strongest antibody response.

“We were surprised because inflammation is usually depicted as something that is bad,” says Slim Fourati, PhD, bioinformatic research associate at Emory University and first author on the paper. “These data indicate that some types of inflammation can actually foster a stronger response from a vaccine.”

Fourati, Dr. Rafick-Pierre Sekaly, professor and senior author of the paper, and the HIPC team identified specific biomarkers among this group and cellular features that characterized the pre-vaccination inflammatory signature, information that can be used to predict how well an individual will respond to a vaccine.

“With the knowledge we now have about what characteristics of the immune system enable a more robust response, vaccines can be tailored to induce this response and maximize their effectiveness,” says Fourati. “But we still have more questions to answer.”

More research is needed to determine the cause of this inflammation in otherwise healthy adults. Additionally, Fourati suggests future studies should look at how these biomarkers facilitate vaccine protection in older age groups and among populations who are immunocompromised.

Published simultaneously with three other HIPC studies by researchers at Yale’s School of Medicine, Stanford University, University of Cincinnati, Harvard Medical School, and Columbia University Medical Center, these findings can serve to improve vaccine response across all individuals. Better understanding of how various pre-vaccine immune states impact antibody responses opens the possibility of altering these states in more vulnerable individuals. For example, scientists may give patients predicted to have a weaker immune response an adjuvant with the vaccine to trigger the inflammatory genes associated with greater protection.

This work will help enable improved, more efficient clinical trials for the development of new vaccines.

The HIPC program was established in 2010, renewed in 2015 and 2021, by the NIAID Division of Allergy, Immunology, and Transplantation.

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