Uncertainty in California winter precipitation linked to future projections of North Pacific large-scale atmospheric circulation
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Environmental sciences↗
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Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits
Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.
59 BASIC BIOLOGICAL SCIENCES↗
Next-generation large-scale binary protein interaction network for Drosophila melanogaster
Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the ‘FlyBi’ dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.
59 BASIC BIOLOGICAL SCIENCES↗
Temperature and composition dependent screw dislocation mobility in austenitic stainless steels from large-scale molecular dynamics
Abstract Extensive molecular dynamics simulations are performed to determine screw dislocation mobility in austenitic Fe 0.7 Ni x Cr 0.3-x stainless steels as a function of temperature ranging from 100 to 1300 K, resolved shear stress from 30 to 140 MPa, and Ni composition from 0.0 to 30.0 at%. These mobility data are fitted to a linear mobility law with a nonzero stress offset, referred to as the threshold stress. We find that both the linear drag coefficient and the threshold stress increase with Ni composition. The drag coefficient increases with temperature, whereas the threshold stress decreases with temperature. Based on these calculations, we determine fitting functions for the linear solute drag coefficient as a function of temperature and composition. The mobility laws determined in this study may serve to inform dislocation dynamics simulations pertinent to dislocation network evolution at elevated temperatures for a wide composition range of austenitic stainless steels.
Chu, Kevin (ORCID:000000031929710X)↗
JARVIS-Leaderboard: a large scale benchmark of materials design methods
Abstract Lack of rigorous reproducibility and validation are significant hurdles for scientific development across many fields. Materials science, in particular, encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC), and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard/
36 MATERIALS SCIENCE↗
Learning dislocation dynamics mobility laws from large-scale MD simulations
Not Available
97 MATHEMATICS AND COMPUTING↗
Large-scale simulations of Floquet physics on near-term quantum computers
Abstract Periodically driven quantum systems exhibit a diverse set of phenomena but are more challenging to simulate than their equilibrium counterparts. Here, we introduce the Quantum High-Frequency Floquet Simulation (QHiFFS) algorithm as a method to simulate fast-driven quantum systems on quantum hardware. Central to QHiFFS is the concept of a kick operator which transforms the system into a basis where the dynamics is governed by a time-independent effective Hamiltonian. This allows prior methods for time-independent simulation to be lifted to simulate Floquet systems. We use the periodically driven biaxial next-nearest neighbor Ising (BNNNI) model, a natural test bed for quantum frustrated magnetism and criticality, as a case study to illustrate our algorithm. We implemented a 20-qubit simulation of the driven two-dimensional BNNNI model on Quantinuum’s trapped ion quantum computer. Our error analysis shows that QHiFFS exhibits not only a cubic advantage in driving frequency ω but also a linear advantage in simulation time t compared to Trotterization.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Potential use of engineered nanoparticles in ocean fertilization for large-scale atmospheric carbon dioxide removal
Artificial ocean fertilization (AOF) aims to safely stimulate phytoplankton growth in the ocean and enhance carbon sequestration. AOF carbon sequestration efficiency appears lower than natural ocean fertilization processes due mainly to the low bioavailability of added nutrients, along with low export rates of AOF-produced biomass to the deep ocean. Here we explore the potential application of engineered nanoparticles (ENPs) to overcome these issues. Data from 123 studies show that some ENPs may enhance phytoplankton growth at concentrations below those likely to be toxic in marine ecosystems. ENPs may also increase bloom lifetime, boost phytoplankton aggregation and carbon export, and address secondary limiting factors in AOF. Life-cycle assessment and cost analyses suggest that net CO 2 capture is possible for iron, SiO 2 and Al 2 O 3 ENPs with costs of 2–5 times that of conventional AOF, whereas boosting AOF efficiency by ENPs should substantially enhance net CO 2 capture and reduce these costs. Therefore, ENP-based AOF can be an important component of the mitigation strategy to limit global warming.
54 ENVIRONMENTAL SCIENCES↗
Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation
Our understanding of Alzheimer’s disease (AD) pathophysiology remains incomplete. Here, for this work, we used quantitative mass spectrometry and coexpression network analysis to conduct the largest proteomic study thus far on AD. A protein network module linked to sugar metabolism emerged as one of the modules most significantly associated with AD pathology and cognitive impairment. This module was enriched in AD genetic risk factors and in microglia and astrocyte protein markers associated with an anti-inflammatory state, suggesting that the biological functions it represents serve a protective role in AD. Proteins from this module were elevated in cerebrospinal fluid in early stages of the disease. In this study of >2,000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brains that may serve as therapeutic targets and fluid biomarkers for the disease.
60 APPLIED LIFE SCIENCES↗
Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants
Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesion studies require removal of the skull as well as hazardous chemicals, dehydration, or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of hippocampal brain lesions.
3-D reconstruction↗
Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits
Abstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.
59 BASIC BIOLOGICAL SCIENCES↗
Summertime low clouds mediate the impact of the large-scale circulation on Arctic sea ice
The rapid Arctic sea ice retreat in the early 21 st century is believed to be driven by several dynamic and thermodynamic feedbacks, such as ice-albedo feedback and water vapor feedback. However, the role of clouds in these feedbacks remains unclear since the causality between clouds and these processes is complex. Here, we use NASA CERES satellite products and NCAR CESM model simulations to suggest that summertime low clouds have played an important role in driving sea ice melt by amplifying the adiabatic warming induced by a stronger anticyclonic circulation aloft. The upper-level high pressure regulates low clouds through stronger downward motion and increasing lower troposphere relative humidity. The increased low clouds favor more sea ice melt via emitting stronger longwave radiation. Then decreased surface albedo triggers a positive ice-albedo feedback, which further enhances sea ice melt. Considering the importance of summertime low clouds, accurate simulation of this process is a prerequisite for climate models to produce reliable future projections of Arctic sea ice.
54 ENVIRONMENTAL SCIENCES↗
Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics
Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.
Zheng, Mei↗
Additive engineered SnO 2 -based electron transport layer for the robust and high-efficiency large-scale perovskite solar cell
Potassium fluoride (KF) incorporation to an SnO 2 nanoparticles (NPs) colloidal dispersion for an electron transport layer of enhanced performance and stability for a perovskite solar cell with improved uniformity of the deposited SnO 2 layer.
Kim, Byeong Jo [Department of Chemistry – Angstrom↗
A multilayer multi-configurational approach to efficiently simulate large-scale circuit-based quantum computers on classical machines
Here, a multilayer multi-configurational theory framework is adapted to simulate circuit-based quantum computers. Quantum addition of superpositions of an exponential number of summands is performed in polynomial time with high accuracy. We demonstrate numerically accurate calculations including up to one million qubits for entangling benchmarks. Simulation cost can be assessed by entropy-based entanglement measures. For the considered systems, we show that the entanglement only grows weakly with the system size. The present simulations demonstrate how quantum algorithms in low-entropy regimes can be used efficiently on classically simulated quantum computers.
97 MATHEMATICS AND COMPUTING↗
Measurements of ion velocity distributions in a large scale laser-produced plasma
Laser-produced plasma velocity distributions are an important, but difficult quantity to measure. In this work, we present a noninvasive technique for measuring individual charge state velocity distributions of laser-produced plasmas using a high temporal and spectral resolution monochromator. The novel application of this technique is its ability to detect particles up to seven meters from their inception (significantly larger than most laboratory plasma astrophysics experiments, which take place at or below the millimeter scale). The design and assembly of this diagnostic is discussed in terms of maximizing the signal to noise ratio, maximizing the spatial and temporal resolution, and other potential use cases. The analysis and results of this diagnostic are demonstrated by directly measuring the time-of-flight velocity of all ion charge states in a laser produced carbon plasma.
47 OTHER INSTRUMENTATION↗