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At least 703 records · Page 39

Emergence of SARS-CoV-2 through recombination and strong purifying selection

COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin, and human coronaviruses, suggesting similar evolutionary constraints in different host species. We also demonstrate that SARS-CoV-2’s entire RBM was introduced through recombination with coronaviruses from pangolins, possibly a critical step in the evolution of SARS-CoV-2’s ability to infect humans. Similar purifying selection in different host species, together with frequent recombination among coronaviruses, suggests a common evolutionary mechanism that could lead to new emerging human coronaviruses.

60 APPLIED LIFE SCIENCES↗

Emergence of the Central Atlantic Niño

The Atlantic Niño is characterized by sea surface warming in the equatorial Atlantic, which can trigger La Niña, the cold phase of El Niño–Southern Oscillation (ENSO). Although observations show that the Atlantic Niño has weakened by approximately 30% since the 1970s, its remote influence on ENSO remains strong. Here, we show that this apparent discrepancy is due to the existence of two types of Atlantic Niño with distinct patterns and climatic impacts, which we refer to as the central and eastern Atlantic Niño. Our results show that with equal strength, the central Atlantic Niño has a stronger influence on tropical climate than its eastern counterpart. Meanwhile, the eastern Atlantic Niño has weakened by approximately 50% in recent decades, allowing the central Atlantic Niño to emerge and dominate the remote impact on ENSO. Given the distinct climatic impacts of the two types, it is necessary to distinguish between them and investigate their behaviors and influences on climate in future studies.

Science & Technology - Other Topics↗

Topological magnon band structure of emergent Landau levels in a skyrmion lattice

We report the motion of a spin excitation across topologically nontrivial magnetic order exhibits a deflection that is analogous to the effect of the Lorentz force on an electrically charged particle in an orbital magnetic field. We used polarized inelastic neutron scattering to investigate the propagation of magnons (i.e., bosonic collective spin excitations) in a lattice of skyrmion tubes in manganese silicide. For wave vectors perpendicular to the skyrmion tubes, the magnon spectra are consistent with the formation of finely spaced emergent Landau levels that are characteristic of the fictitious magnetic field used to account for the nontrivial topological winding of the skyrmion lattice. This provides evidence of a topological magnon band structure in reciprocal space, which is borne out of the nontrivial real-space topology of a magnetic order.

36 MATERIALS SCIENCE↗

Emergent ferroelectricity in subnanometer binary oxide films on silicon

The critical size limit of voltage-switchable electric dipoles has extensive implications for energy-efficient electronics, underlying the importance of ferroelectric order stabilized at reduced dimensionality. Here, we report on the thickness-dependent antiferroelectric-to-ferroelectric phase transition in zirconium dioxide (ZrO 2 ) thin films on silicon. The emergent ferroelectricity and hysteretic polarization switching in ultrathin ZrO 2 , conventionally a paraelectric material, notably persists down to a film thickness of 5 angstroms, the fluorite-structure unit-cell size. This approach to exploit three-dimensional centrosymmetric materials deposited down to the two-dimensional thickness limit, particularly within this model fluorite-structure system that possesses unconventional ferroelectric size effects, offers substantial promise for electronics, demonstrated by proof-of-principle atomic-scale nonvolatile ferroelectric memory on silicon. Additionally, it is also indicative of hidden electronic phenomena that are achievable across a wide class of simple binary materials.

42 ENGINEERING↗

The Thermococcales as a model system: historical perspectives and emerging tools

Thermococcales are among the most widely studied hyperthermophilic Archaea and have become key models for understanding life at extreme temperatures. Early work in the 1980s culminated in the isolation of novel Thermococcales species from hydrothermal vents that grew rapidly, tolerated extreme heat, and metabolized diverse substrates, making them uniquely amenable for laboratory studies. Their thermostable enzymes and emerging genetic tools facilitated detailed investigations of core processes such as DNA replication, repair, and transcription under conditions that challenge most life forms. These practical advantages, together with the accumulation of tools and protocols, cemented the role of Thermococcales as a model system. Here, we recount how chance discoveries, environmental adaptations, and experimental practicality intersected to establish Thermococcales as a central model for studying archaeal biology and extremophile physiology.

59 BASIC BIOLOGICAL SCIENCES↗

REC protein family expansion by the emergence of a new signaling pathway

This report presents multi-genome evidence that REC protein family expansion occurs when the emergence of new pathways gives rise to functional discordance. Specificity between residues in REC domain containing response regulators with paired histidine kinases is under negative purifying selection, constrained by the presence of other bacterial two-component systems signaling cascades that share sequence and structural identity. Presuming that the two-component systems can evolve by neutral amino acid changes (neutral drift) when purifying evolutionary constraints are relaxed, how might the REC protein family expand by amino acid changes when these constraints remain intact? Using an unsupervised machine learning approach to observe the sequence landscape of REC domains across long phylogenetic distances, we find that within-gene recombination, a subcategory of gene conversion, switched the effector domain and, consequently, the regulatory context of a duplicated response regulator from transcriptional regulation by σ54 to that by σ70. We determined that the recombined response regulator diverged from its parent by episodic diversifying selection and neutral drift. Functional experiments of the parent of recombined response regulators in a model Pseudomonas putida KT2440 model system revealed that the parent and recombined response regulators sense and respond to different carboxylic acids. Finally, a residue-switching experiment using structural predictions and functional characterization suggests that the new residues in the recombined regulator could form a new interaction interface and mediate condition-specific phosphotransfer. Overall, our study finds that genetic perturbations can create conditions of functional discordance, whereby the REC protein family can evolve by episodic diversifying selection.

59 BASIC BIOLOGICAL SCIENCES↗

Quantum Dynamics at Scale: Ultrafast Control of Emergent Functional Materials

Confluence of extreme-scale quantum dynamics simulations (i.e. quantum@scale) and cutting-edge x-ray free-electron laser experiments are revolutionizing materials science. An archetypal example is the exciting concept of using picosecond light pulses to control emergent material properties on demand in atomically-thin layered materials. This paper describes efforts to scale our quantum molecular dynamics engine toward the United States' first exaflop/s computer, under an Aurora Early Science Program project named "Metascalable layered material genome". Key algorithmic and computing techniques incorporated are: (1) globally-scalable and locally-fast solvers within a linear-scaling divide-conquer-recombine algorithmic framework; (2) algebraic `BLASification' of computational kernels; and (3) data alignment and loop restructuring, along with register and cache blocking, for enhanced vectorization and efficient memory access. The resulting weak-scaling parallel efficiency was 0.93 on 131,072 Intel Xeon Phi cores for a 56.6 million atom (or 169 million valence-electron) system, whereas the various code transformations achieved 5-fold speedup. The optimized simulation engine allowed us for the first time to establish a significant effect of substrate on the dynamics of layered material upon electronic excitation.

Algebraic BLASification↗

Emerging Technologies for Privacy Preservation in Energy Systems

This study explores the intersection of digitalization and privacy within the energy sector, focusing on the emerging challenges and opportunities presented by integrating Distributed Energy Resources (DERs) and advanced metering infrastructure. The need for robust digital privacy measures has become crucial as the energy industry evolves towards a more decentralized, digitalized, and decarbonized future. This study delves into four cutting-edge privacy-preserving technologies—Homomorphic Encryption (HE), Secure Multiparty Computation (SMPC), Differential Privacy (DP), and Federated Learning (FL)—each offering unique solutions to safeguard consumer data by increasing digital connectivity and data exchange. Through a detailed examination of these methods, the study explains how each technology operates, its applications within the energy sector, and the specific privacy challenges it addresses. Homomorphic Encryption allows for secure computations on encrypted data, enabling data analysis without compromising privacy. Secure Multiparty Computation enables collaborative data analysis across different entities while protecting the confidentiality of the inputs. Differential Privacy introduces randomness into the assembled data set, preventing the identification of individual records in statistical databases. Lastly, Federated Learning offers a paradigm shift in data analysis, where machine learning models are trained at the edge, minimizing the centralization of sensitive data. The research underscores the significance of implementing these privacy-enhancing technologies to comply with strict data protection regulations, foster consumer trust, and enhance the security of the energy infrastructure. By providing a comprehensive overview of these methodologies and their practical implications for the energy sector, this study aims to contribute to the ongoing discourse on digital privacy, offering insights into how the energy industry can navigate the complexities of data privacy in the digital age.

Cali, Umit↗

Insights into Plastic Localization by Crystallographic Slip from Emerging Experimental and Numerical Approaches

Advanced experimental and numerical approaches are being developed to capture the localization of plasticity at the nanometer scale as a function of the multiscale and heterogeneous microstructure present in metallic materials. These innovative approaches promise new avenues to understand microstructural effects on mechanical properties, accelerate alloy design, and enable more accurate mechanical property prediction. This article provides an overview of emerging approaches with a focus on the localization of plasticity by crystallographic slip. New insights into the mechanisms and mechanics of strain localization are addressed. The consequences of the localization of plasticity by deformation slip for mechanical properties of metallic materials are also detailed.

36 MATERIALS SCIENCE↗

An emerging multi-omic understanding of the genetics of opioid addiction

Opioid misuse, addiction, and associated overdose deaths remain global public health crises. Despite the tremendous need for pharmacological treatments, current options are limited in number, use, and effectiveness. Fundamental leaps forward in our understanding of the biology driving opioid addiction are needed to guide development of more effective medication-assisted therapies. This Review focuses on the omics-identified biological features associated with opioid addiction. Recent GWAS have begun to identify robust genetic associations, including variants in OPRM1, FURIN, and the gene cluster SCAI/PPP6C/RABEPK. An increasing number of omics studies of postmortem human brain tissue examining biological features (e.g., histone modification and gene expression) across different brain regions have identified broad gene dysregulation associated with overdose death among opioid misusers. Drawn together by meta-analysis and multi-omic systems biology, and informed by model organism studies, key biological pathways enriched for opioid addiction–associated genes are emerging, which include specific receptors (e.g., GABAB receptors, GPCR, and Trk) linked to signaling pathways (e.g., Trk, ERK/MAPK, orexin) that are associated with synaptic plasticity and neuronal signaling. Studies leveraging the agnostic discovery power of omics and placing it within the context of functional neurobiology will propel us toward much-needed, field-changing breakthroughs, including identification of actionable targets for drug development to treat this devastating brain disease.

60 APPLIED LIFE SCIENCES↗

A Review of Recent and Emerging Machine Learning Applications for Climate Variability and Weather Phenomena

Abstract Climate variability and weather phenomena can cause extremes and pose significant risk to society and ecosystems, making continued advances in our physical understanding of such events of utmost importance for regional and global security. Advances in machine learning (ML) have been leveraged for applications in climate variability and weather, empowering scientists to approach questions using big data in new ways. Growing interest across the scientific community in these areas has motivated coordination between the physical and computer science disciplines to further advance the state of the science and tackle pressing challenges. During a recently held workshop that had participants across academia, private industry, and research laboratories, it became clear that a comprehensive review of recent and emerging ML applications for climate variability and weather phenomena that can cause extremes was needed. This article aims to fulfill this need by discussing recent advances, challenges, and research priorities in the following topics: sources of predictability for modes of climate variability, feature detection, extreme weather and climate prediction and precursors, observation–model integration, downscaling, and bias correction. This article provides a review for domain scientists seeking to incorporate ML into their research. It also provides a review for those with some ML experience seeking to broaden their knowledge of ML applications for climate variability and weather.

54 ENVIRONMENTAL SCIENCES↗

Scientific Directions for Cloud Chamber Research: Instrumentation, Modeling, New Chambers, and Emerging Chamber Concepts

The Workshop on Scientific Directions for Cloud Chamber Research was held 13-14 July 2024 at the National Institute for Meteorological Sciences, Jeju, South Korea. Here, over 75 scientists from 13 countries gathered to learn about and discuss the latest scientific research results from large laboratory cloud chamber facilities, as well as new developments in cloud chamber instrumentation and modeling efforts, and emerging cloud chamber designs that will open new scientific research directions.

54 ENVIRONMENTAL SCIENCES↗

The Application of a Genetic Algorithm to the Optimization of a Mesoscale Model for Emergency Response

Besides solving the equations of momentum, heat, and moisture transport on the model grid, mesoscale weather models must account for subgrid-scale processes that affect the resolved model variables. These are simulated with model parameterizations, which often rely on values preset by the user. Such “free” model parameters, along with others set to initialize the model, are often poorly constrained, requiring that a user select each from a range of plausible values. Finding the values to optimize any forecasting tool can be accomplished with a search algorithm, and one such process—the genetic algorithm (GA)—has become especially popular. As applied to modeling, GAs represent a Darwinian process: an ensemble of simulations is run with a different set of parameter values for each member, and the members subsequently judged to be most accurate are selected as “parents” who pass their parameters onto a new generation. At the U.S. Department of Energy’s Savannah River Site in South Carolina, we are applying a GA to the Regional Atmospheric Modeling System (RAMS) mesoscale weather model, which supplies input to a model to simulate the dispersion of an airborne contaminant as part of the site’s emergency response preparations. An ensemble of forecasts is run each day, weather data are used to “score” the individual members of the ensemble, and the parameters from the best members are used for the next day’s forecasts. As meteorological conditions change, the parameters change as well, maintaining a model configuration that is best adapted to atmospheric conditions. Significance Statement We wanted to develop a forecasting system by which a weather model is run over the Savannah River Site each day and repeatedly adjusted according to how well it performed the previous day. To run the model, a series of values (parameters) must be set to control how the model will calculate winds, temperatures, and other desired variables. Each day the model was run several times using different combinations of these parameters and later compared with observed meteorological conditions. Parameters that produced the most accurate forecasts were preferentially reused to create the forecasts for the next day. The process was tested for the summer of 2020 and exhibited lower errors than forecasts produced by the model using default values of the parameters.

54 ENVIRONMENTAL SCIENCES↗

Assessing Prior Emergent Constraints on Surface Albedo Feedback in CMIP6

An emergent constraint (EC) is a popular model evaluation technique, which offers the potential to reduce intermodel variability in projections of climate change. Two examples have previously been laid out for future surface albedo feedbacks (SAF) stemming from loss of Northern Hemisphere (NH) snow cover (SAF snow ) and sea ice (SAF ice ). These processes also have a modern-day analog that occurs each year as snow and sea ice retreat from their seasonal maxima, which is strongly correlated with future SAF across an ensemble of climate models. The newly released CMIP6 ensemble offers the chance to test prior constraints through out-of-sample verification, an important examination of EC robustness. Here, we show that the SAF snow EC is equally strong in CMIP6 as it was in past generations, while the SAF ice EC is also shown to exist in CMIP6, but with different, slightly weaker characteristics. We find that the CMIP6 mean NH SAF exhibits a global feedback of 0.25 ± 0.05 W m -2 K -1 , or ~61% of the total global albedo feedback, largely in line with prior generations despite its increased climate sensitivity. Additionally, the NH SAF can be broken down into similar contributions from snow and sea ice over the twenty-first century in CMIP6. Crucially, intermodel variability in seasonal SAF snow and SAF ice is largely unchanged from CMIP5 because of poor outlier simulations of snow cover, surface albedo, and sea ice thickness. These outliers act to mask the noted improvement from many models when it comes to SAF ice , and to a lesser extent SAF snow .

58 GEOSCIENCES↗

Emergence of two distinct phase transitions in monolayer CoSe2 on graphene

Abstract Dimensional modifications play a crucial role in various applications, especially in the context of device miniaturization, giving rise to novel quantum phenomena. The many-body dynamics induced by dimensional modifications, including electron-electron, electron-phonon, electron-magnon and electron-plasmon coupling, are known to significantly affect the atomic and electronic properties of the materials. By reducing the dimensionality of orthorhombic CoSe 2 and forming heterostructure with bilayer graphene using molecular beam epitaxy, we unveil the emergence of two types of phase transitions through angle-resolved photoemission spectroscopy and scanning tunneling microscopy measurements. We disclose that the 2 × 1 superstructure is associated with charge density wave induced by Fermi surface nesting, characterized by a transition temperature of 340 K. Additionally, another phase transition at temperature of 160 K based on temperature dependent gap evolution are observed with renormalized electronic structure induced by electron-boson coupling. These discoveries of the electronic and atomic modifications, influenced by electron-electron and electron-boson interactions, underscore that many-body physics play significant roles in understanding low-dimensional properties of non-van der Waals Co-chalcogenides and related heterostructures. Graphical Abstract

36 MATERIALS SCIENCE↗

Design tradeoffs between traditional hexagonal and emerging cubic In X Ga (1–X) N/GaN-based green light-emitting diodes

Here, we report on the design tradeoffs between traditional hexagonal and emerging cubic In X Ga (1–X) N/GaN -based green (520 nm≤ λ ≤550 nm) light-emitting diodes with special emphasis on the electron blocking layer, number of quantum wells, and thicknesses of quantum wells and barriers. We identified three crucial design rules for cubic green light-emitting diodes: (1) no need for an electron blocking layer; (2) use of a wide quantum well; and (3) choice of thin quantum barriers in multi-quantum well light-emitting diode designs. These design rules increase the internal quantum efficiency of cubic green light-emitting diodes by ~30.5% under 100A/cm 2 injection with respect to traditional designs. Overall, the design rules of cubic light-emitting diodes and their differentiating nature from the traditional, hexagonal ones are crucial for the advent of next-generation cubic light-emitting diodes.

42 ENGINEERING↗

Connecting Geomechanical Properties with Potential for Proppant Embedment and Production Decline for the Emerging Caney Shale, Oklahoma

The Caney Shale is emerging as a target for hydrocarbon production, creating opportunities to study rock mechanical origins of observed/anticipated challenges to effective and sustained stimulation. Here we examine five subunits within the Caney, two of which are dubbed “ductile” and three of which are dubbed “reservoir” rock types. The “ductile” versus “reservoir” identification is initially based on elastic properties ascertained from well logs. By comparing core-based mechanical tests, it is found nominally ductile and reservoir layers do not differ in terms of brittleness, but instead the nominally ductile layers tend to be weaker and more prone to creep deformation compared to the nominally more brittle reservoir layers. This difference in mechanical properties is shown to generate higher susceptibility to proppant embedment in the weaker and more creep-prone layers. Specifically, over a 5-year period, the creep is expected to have little impact on reservoir layers but is predicted to reduce propped fracture aperture by a factor of 2 in the ductile layers.

Benge, Margaret↗

Emerging Soluble Organic Redox Materials for Next-Generation Grid Energy-Storage Applications

Soluble organic redox molecules have emerged as promising candidate active materials for multiple energy storage systems due to their structural versatility, fast redox process, high capacity storage, sustainability, and environmental friendliness. This review examines recent progress in developing such materials in green and sustainable batteries for grid applications and points out directions for future research.

Zhan, Xiaowen↗