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At least 361 records · Page 20

2024 roadmap on 2D topological insulators

Abstract 2D topological insulators promise novel approaches towards electronic, spintronic, and quantum device applications. This is owing to unique features of their electronic band structure, in which bulk-boundary correspondences enforces the existence of 1D spin–momentum locked metallic edge states—both helical and chiral—surrounding an electrically insulating bulk. Forty years since the first discoveries of topological phases in condensed matter, the abstract concept of band topology has sprung into realization with several materials now available in which sizable bulk energy gaps—up to a few hundred meV—promise to enable topology for applications even at room-temperature. Further, the possibility of combining 2D TIs in heterostructures with functional materials such as multiferroics, ferromagnets, and superconductors, vastly extends the range of applicability beyond their intrinsic properties. While 2D TIs remain a unique testbed for questions of fundamental condensed matter physics, proposals seek to control the topologically protected bulk or boundary states electrically, or even induce topological phase transitions to engender switching functionality. Induction of superconducting pairing in 2D TIs strives to realize non-Abelian quasiparticles, promising avenues towards fault-tolerant topological quantum computing. This roadmap aims to present a status update of the field, reviewing recent advances and remaining challenges in theoretical understanding, materials synthesis, physical characterization and, ultimately, device perspectives.

Weber, Bent (ORCID:000000018586127X)↗

Actinomycetota isolated from the sponge Hymeniacidon perlevis as a source of novel compounds with pharmacological applications: diversity, bioactivity screening, and metabolomic analysis

Abstract Aims To combat health conditions, such as multi-resistant bacterial infections, cancer, and metabolic diseases, new drugs need to be urgently found and, in this respect, marine Actinomycetota have a high potential to produce secondary metabolites with pharmacological importance. We aimed to study the cultivable Actinomycetota community associated with a marine sponge from the Portuguese coast, Hymeniacidon perlevis, and investigate the potential of the retrieved isolates to produce compounds with antimicrobial, anticancer and anti-obesity properties. Methods and results The analysis of the 16S rRNA gene revealed 79 Actinomycetota isolates affiliated with 12 genera—Brachybacterium, Dietzia, Glutamicibacter, Gordonia, Micrococcus, Micromonospora, Nocardia, Nocardiopsis, Paenoartrhobacter, Rhodococcus, Streptomyces, and Tsukamurella, most of which affiliated with the genus Streptomyces. The screening of antimicrobial activity revealed 13 strains, all belonging to the Streptomyces genus, capable of inhibiting the growth of Candida albicans, Bacillus subtilis, or Staphylococcus aureus. Forty-three extracts exhibited cytotoxic activity against at least one tested cell line (HepG2, HCT-116, and hCMEC-D3). Three extracts that were active against the two cancer cell lines tested, did not reduce the viability of the non-cancer endothelial cell line, hCMEC-D3. One Gordonia strain exhibited anti-obesity activity, revealed by its ability to reduce the neutral lipids in zebrafish larvae. Mass spectrometry-based dereplication analysis of active extracts identified several compounds associated with known Actinomycetota natural products. Nonetheless, five clusters contained metabolites that did not match any annotated natural products, suggesting they may represent new bioactive molecules. Conclusions This work contributed to increase the knowledge on the diversity and bioactive potential of Actinomycetota associated with H. perlevis.

Fonseca, Ana C.↗

On the discovery of stars, quasars, and galaxies in the Southern Hemisphere with S-PLUS DR2

ABSTRACT This paper provides a catalogue of stars, quasars, and galaxies for the Southern Photometric Local Universe Survey Data Release 2 (S-PLUS DR2) in the Stripe 82 region. We show that a 12-band filter system (5 Sloan-like and 7 narrow bands) allows better performance for object classification than the usual analysis based solely on broad bands (regardless of infrared information). Moreover, we show that our classification is robust against missing values. Using spectroscopically confirmed sources retrieved from the Sloan Digital Sky Survey DR16 and DR14Q, we train a random forest classifier with the 12 S-PLUS magnitudes + 4 morphological features. A second random forest classifier is trained with the addition of the W1 (3.4 $\mu\mathrm{m} $) and W2 (4.6 $\mu\mathrm{m} $) magnitudes from the Wide-field Infrared Survey Explorer (WISE). Forty-four per cent of our catalogue have WISE counterparts and are provided with classification from both models. We achieve 95.76 per cent (52.47 per cent) of quasar purity, 95.88 per cent (92.24 per cent) of quasar completeness, 99.44 per cent (98.17 per cent) of star purity, 98.22 per cent (78.56 per cent) of star completeness, 98.04 per cent (81.39 per cent) of galaxy purity, and 98.8 per cent (85.37 per cent) of galaxy completeness for the first (second) classifier, for which the metrics were calculated on objects with (without) WISE counterpart. A total of 2926 787 objects that are not in our spectroscopic sample were labelled, obtaining 335 956 quasars, 1347 340 stars, and 1243 391 galaxies. From those, 7.4 per cent, 76.0 per cent, and 58.4 per cent were classified with probabilities above 80 per cent. The catalogue with classification and probabilities for Stripe 82 S-PLUS DR2 is available for download.

79 ASTRONOMY AND ASTROPHYSICS↗

Strange quark matter as dark matter: 40 yr later, a reappraisal

ABSTRACT Forty years ago Witten suggested that dark matter could be composed of macroscopic clusters of strange quark matter. This idea was very popular for several years, but it dropped out of fashion once lattice quantum chromodynamics calculations indicated that the confinement/deconfinement transition, at small baryonic chemical potential, is not first order, which seemed to be a crucial requirement in order to produce large clusters of quarks. Here, we revisit the conditions under which strangelets can be produced in the Early Universe. We discuss the impact of an instability in the hadronic phase separating a low density, positive-strange-charge phase from a high-density phase with a negative strange charge. This second phase can rapidly stabilize by forming colour-superconducting gaps. The strangelets then undergo partial evaporation. In this way, we obtain distributions of their sizes in agreement with the observational constraints and we discuss the many astrophysical and cosmological implications of these objects. Finally, we examine the most promising techniques to detect this type of strangelets. We also show that strangelets can exist with masses $\lesssim $1017 g, while primordial black holes are ruled out in that mass range, allowing us to distinguish between these two dark matter candidates.

Clemente, Francesco Di (ORCID:0000000282573819)↗

Spatial proteomics reveals signal sequence characteristics correlated with localization in cyanobacteria

Abstract Cyanobacteria have an inner and outer cell membrane enclosing the periplasm and cell wall and an additional set of internal membranes (called the thylakoid membranes) enclosing the thylakoid lumen. The periplasm and thylakoid lumen have unique proteomes, but the mechanisms regulating protein sorting to these locations have remained elusive. Here, proximity-based proteomics using the engineered peroxidase APEX2 was performed in the cyanobacteria Synechococcus sp. PCC 7002 to profile the proteomes of the cytoplasm, thylakoid lumen, and the periplasm and outer membrane (P-OM). Our analyses revealed specific roles for the thylakoid lumen in photosynthesis and energy generation, as well as roles for the periplasm in metabolite transport and binding, cell motility, and cell wall maintenance. Forty proteins localized to both the thylakoid lumen and the P-OM; however, their biological functions remain unclear. We also analyzed the correlation between signal sequence characteristics and differential protein localization to either the thylakoid lumen or the P-OM. In PCC 7002, as well as Synechocystis sp. PCC 6803 and Nostoc sp. PCC 7120, thylakoid lumen proteins translocated across membranes via the Secretory (Sec) system possessed more hydrophobic and alpha-helical signal sequence H-regions than P-OM proteins. The signal sequences of homologous proteins in Gloeobacter violaceus PCC 7421, a cyanobacterial species with a combined thylakoid lumen and periplasmic space, did not exhibit such differences. Therefore, the pattern of increased H-region hydrophobicity and alpha helix content is specific to cyanobacteria with a separate thylakoid lumen space and likely contributes to proper protein sorting between the thylakoid lumen and periplasm.

Plant Sciences↗

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of single-stranded DNA phages infecting marine and terrestrial Alphaproteobacteria

The Microviridae family represents one of the major clades of single-stranded DNA (ssDNA) phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in the genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteriaceae and cluster within the ‘Alpavirinae’, ‘Amoyvirinae’, and Gokushovirinae. We have isolated ‘Ascunsovirus oldenburgi’ ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources sixty-five new Microviridae prophages and episomes in bacterial genomes and retrieved forty-seven environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named ‘Tainavirinae’ and ‘Occultatumvirinae’. They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here sheds light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.

59 BASIC BIOLOGICAL SCIENCES↗

Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron

Abstract New variants of SARS-CoV-2 show remarkable heterogeneity in their relative fitness over both time and space. In this paper we extend the tools available for estimating the selection strength for new SARS-CoV-2 variants to a hierarchical, mixed-effects, renewal equation model. This formulation allows us to estimate selection effects at the global level while incorporating both measured and unmeasured heterogeneity among countries. Applying this model to the spread of Omicron in forty countries, we find evidence for very strong but very heterogeneous selection effects. To test whether this heterogeneity is explained by differences in the immune landscape, we considered several measures of vaccination rates and recent population-level infection as covariates, finding moderately strong, statistically significant effects. We also found a significant positive correlation between the selection advantage of Delta and Omicron at the country level, suggesting that other region-specific explanatory variables of fitness differences do exist. Our method is implemented in the Stan programming language, can be run on standard consumer-grade computing resources, and will be straightforward to apply to future variants.

59 BASIC BIOLOGICAL SCIENCES↗

Simulations and Experimental Verifications of an Algorithm for Radiation Source Mapping and Navigational Path Generation

Accurate and efficient mapping and localization of both ionizing and non-ionizing radiation sources are important across many different fields. As such, a versatile mapping and navigational path generation algorithm, which can be applied to any point source measurements that follow an inverse-square characteristic, was developed using non-linear least squares methods. Forty thousand simulations were performed on the algorithm, which located sources successfully in a 10 m × 10 m × 10 m three-dimensional space with a success rate of over 80% across different noise functions, given a proportional constant of 10 to 1,000. The algorithm was also verified experimentally with small-scale radioactive decontamination of a 70 cm × 70 cm surface and localization of a lost Wi-Fi router in a 70 m × 70 m open field. One hundred twenty-one measurements were taken from each experiment, which were then fed into the algorithm for navigation. For the radioactive 137Cs source, the estimated locations were within 7 cm × 7 cm of the answer in 79.3% of the scenarios, while the Wi-Fi router was located to within 7 m × 7 m in 57.9% of the tests. In general, the method requires much less information and data than a geographically comprehensive survey and thus shows a lot of potential for practical applications, such as lost source retrieval with unmanned aerial vehicles, small-scale decontamination, mapping undocumented Wi-Fi routers or radio towers, and radiation simulation with radio signals. Here, the different failure modes, desirable features, and potential improvements were also identified but remain as future work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Effective Gaps Are Not Effective: Quasipolynomial Classical Simulation of Obstructed Stoquastic Hamiltonians

All known examples suggesting an exponential separation between classical simulation algorithms and stoquastic adiabatic quantum computing (StoqAQC) exploit symmetries that constrain adiabatic dynamics to effective, symmetric subspaces. The symmetries produce large effective eigenvalue gaps, which in turn make adiabatic computation efficient. We present a classical algorithm to subexponentially sample from an effective subspace of any k -local stoquastic Hamiltonian H , without a priori knowledge of its symmetries (or near symmetries). Our algorithm maps any k -local Hamiltonian to a graph G = ( V , E ) with | V | = O (poly (n)) , where n is the number of qubits. Given the well-known result of Babai [Graph isomorphism in quasipolynomial time, in Proceedings of the Forty-Eighth Annual ACM Symposium on Theory of Computing (2016), pp. 684–697], we exploit graph isomorphism to study the automorphisms of G and arrive at an algorithm quasipolynomial in | V | for producing samples from effective subspace eigenstates of H . Our results rule out exponential separations between StoqAQC and classical computation that arise from hidden symmetries in k -local Hamiltonians. Our graph representation of H is not limited to stoquastic Hamiltonians and may rule out corresponding obstructions in nonstoquastic cases, or be useful in studying additional properties of k -local Hamiltonians.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

R ( 3780 ) Resonance Interpreted as the 1 D 1 3 -Wave Dominant State of Charmonium from Precise Measurements of the Cross Section of e + e − → Hadrons

We report the precise measurements of the cross section of e + e − → hadrons at center-of-mass energies from 3.645 to 3.871 GeV. We thereby perform the most precise study of the cross sections and find a complex system composed of three resonances of R ( 3760 ) , R ( 3780 ) , and R ( 3810 ) . For the first time, we measure the R ( 3810 ) electronic width to be ( 19.4 ± 7.4 ± 12.1 ) eV . For the R ( 3760 ) resonance, we measure the mass to be ( 3751.9 ± 3.8 ± 2.8 ) MeV / c 2 , the total width to be ( 32.8 ± 5.8 ± 8.7 ) MeV , and the electronic width to be ( 184 ± 75 ± 86 ) eV . For the R ( 3780 ) resonance, we measure its mass to be ( 3778.7 ± 0.5 ± 0.3 ) MeV / c 2 , total width to be ( 20.3 ± 0.8 ± 1.7 ) MeV , and electronic width to be ( 265 ± 67 ± 83 ) eV . Forty-seven years ago, the ψ ( 3770 ) resonance was discovered, and was subsequently interpreted as the 1 D 1 3 -wave dominant state of charmonium. However, our analysis of the total-hadron cross sections indicates that the ψ ( 3770 ) is not a single state, but a complex system composed of the R ( 3760 ) , R ( 3780 ) , and R ( 3810 ) resonances. Among these, we interpret the R ( 3780 ) is a resonance dominated by the 1 D 1 3 charmonium state. Published by the American Physical Society 2024

Ablikim, M.↗

Quench Protection by Putting a Current-pulse Into a Coil Center-Tap in HTS Coils

Forty years ago, Lawrence Berkeley Laboratory (LBL) tested a pulsed current quench protection system for a high current density two-meter diameter two-layer solenoid at 4.5 K with a stored energy of 8.5 MJ. The energy needed to protect this magnet was 13.4 kJ from an electrolytic capacitor system charged to voltages 800 V. This method also involved the use of a well-coupled shorted secondary circuits and quench-back. The applicability of this quench protection method to HTS magnets operating at temperatures >25 K could be of interest. There are a number of questions that should be asked, as follows: 1) Can this method work for HTS coils operating at temperatures >25 K? 2) Are there batteries or capacitors that can store 2 MJ or more that have short enough discharge times for quench protection at voltages less than 2 kV? 3) Is this quench protection system cost low enough to be reasonable?

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Gas‐Phase Ion‐Molecule Interactions in a Collision Reaction Cell with ICP‐MS / MS : Investigations with CO 2 as the Reaction Gas

Carbon dioxide (CO 2 ) was used as a reaction gas to investigate the gas‐phase ion‐molecule interactions using the Agilent 8900 ICP‐MS/MS. A solution containing forty‐five elements representative of the periodic table was used to supply the ions to react with CO 2 in the collision/reaction cell (CRC). The only significant product ions formed were monoxides. The general reactivity was shown to be consistent with density functional theory (DFT)‐predicted reaction enthalpies, such that all predicted exothermic reactions produced product ions at levels of at least 1% of the unreacted ion. Most endothermic reactions observed had sufficient kinetic energy in excess of the reaction enthalpies. Our results suggest that reaction enthalpy is a reasonable predictor of reactivity with CO 2 on the timescales of the interactions in non‐thermal ICP‐MS/MS systems. The ease and rapidity of data collection with the ICP‐MS/MS and DFT calculations using the NWChem suite has value given the scarcity of thermochemical data of CO 2 reactions in the literature. These studies are especially useful for the identification of targeted reaction chemistries to be leveraged for analytical method development, such as for the inline separation of isobaric interferences from analytes of interest.

36 MATERIALS SCIENCE↗

Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Summary Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field‐based model species for genetics and epigenetics. The availability of a high‐quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome‐level genome assembly of var. MN106‐Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32‐10) that are highly amenable to genetic transformation. We describe non‐coding RNAs, pseudogenes and transposable elements, and highlight tissue‐specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome‐wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic QTL mapping for plant height in the hybrid population of Agropyron Gaertn.

Abstract Plant height (PH) plays a very important role for plant breeding and also serves as a model trait to dynamic development study. The dynamic quantitative trait locus (QTL) analysis for PH of Agropyron Gaertn. was carried out in a cross‐pollination (CP) hybrid population of A. Gaertn. based on the phenotypic data of PH at different developmental stages in four year‐sites and the constructed single‐nucleotide polymorphism (SNP) genetic map. The results showed that 69 QTL and nine major QTL were detected by unconditional QTL mapping. A total of 107 QTL and 13 major QTL were found using conditional QTL mapping. Forty‐seven QTL were detected by two methods. Two unconditional QTL, Qph2‐5 and Qph3‐4, were expressed as major and stable QTL for PH. Four major stable conditional QTL for PH, cQph4‐1 , cQph4‐8, cQph6‐2 and cQph6‐7 , were detected. Two conditional PH QTL, cQph3‐5 and cQPh3‐7 , were identified in four environments over multiple stages. The gene/QTL controlling PH was expressed in a certain spatiotemporal manner. These results could also provide a reference for genetic and breeding research of related plant.

Che, Yonghe↗

Application of automated iterative target detection for standoff hyperspectral imaging

The utility of hyperspectral imaging (HSI) has been well established for a wide array of applications but has generated a need for automated screening of high volumes of large HSI cubes. We report two important automated algorithms for more efficient standoff processing: atmospheric correction and target detection. The atmospheric correction method is based on a fast asymmetric least squares approach that is applied on a pixel-by-pixel basis. Here, the correction can be applied to entire images without manually identifying regions of interest and utilizes only in-scene information, no ancillary modeling of the atmosphere is required. An iterative target detection approach is also introduced which demonstrates faster speeds relative to moving window approaches. The target detection algorithm classifies each pixel as true target detections, near target detections, clutter, and no-calls. The algorithms were tested on forty images of twenty-two solid mineral targets placed at a 14-meter standoff distance allowing general observations on expected detection performance for a variety of minerals. In addition to identifying anomalous pixels, the inclusion of “no-calls” reduced the number of false detections significantly.

47 OTHER INSTRUMENTATION↗

Genome Sequences of 42 Bacteria Isolated from Sorghum bicolor Roots

Forty-two bacterial strains were isolated from root samples of Sorghum bicolor. The strains spanned 17 genera, including Dechloromonas, Duganella, Dyella, Flavobacterium, Herbaspirillum, Lutibacter, Mucilaginibacter, Novosphingobium, Paraburkholderia, Pedobacter, Pleomorphomonas, Rhizobacter, Rhizobium, Rhizomicrobium, Rugamonas, Variovorax, and Xanthobacter. Their whole-genome sequences revealed diverse metabolic processes, including biological nitrogen fixation, in sorghum root microbiota.

59 BASIC BIOLOGICAL SCIENCES↗

Gen IV Education and Training Working Group Webinars’ Initiative

Collaboration and support among national laboratories, industry, universities, and research and development organizations are vital to not only maintain a skilled and competent nuclear workforce but also to avert the risk of human resource shortages. As stated in a recent IAEA paper [1], the world nuclear electrical generating capacity is projected to increase to 554 GW(e) by 2030 and up to 874 GW(e) by 2050 (Fig. 1). This represents a 42% increase over current levels by 2030 and a doubling of the current capacity by 2050. To promote Education and Training (E&T) on Gen IV reactor systems and other nuclear related topics of interest, the Gen IV Education and Training Working Group (ETWG) identifies and advertises training courses; engages collaboration with other international education and training organizations; delivers webinars dedicated to Gen IV systems; and maintains a modern social medium platform to exchange information and ideas on Gen IV R&D topics, as well as on related GIF education and training activities. At the end of June 2020, the GIF ETWG has produced, podcasted and posted forty-one webinars covering the six Gen IV systems and various subjects addressing e.g. the economics of the nuclear fuel cycle, sustainability aspects of Gen IV systems, nuclear fuels and materials challenges, the thorium fuel cycle, energy conversion systems, and lessons learned for knowledge management and preservation. This paper describes the development of these webinars from the initial concept to its full realization, with future webinars planned in 2021, addressing topics such as materials and fuels performance for advanced reactors, small modular reactor.

Paviet, Patricia D.↗

Evaluating kratom alkaloids using PHASE

Kratom is a botanical substance that is marketed and promoted in the US for pharmaceutical opioid indications despite having no US Food and Drug Administration approved uses. Kratom contains over forty alkaloids including two partial agonists at the mu opioid receptor, mitragynine and 7-hydroxymitragynine, that have been subjected to the FDA’s scientific and medical evaluation. However, pharmacological and toxicological data for the remaining alkaloids are limited. Therefore, we applied the Public Health Assessment via Structural Evaluation (PHASE) protocol to generate in silico binding profiles for 25 kratom alkaloids to facilitate the risk evaluation of kratom. PHASE demonstrates that kratom alkaloids share structural features with controlled opioids, indicates that several alkaloids bind to the opioid, adrenergic, and serotonin receptors, and suggests that mitragynine and 7-hydroxymitragynine are the strongest binders at the mu opioid receptor. Subsequently, the in silico binding profiles of a subset of the alkaloids were experimentally verified at the opioid, adrenergic, and serotonin receptors using radioligand binding assays. The verified binding profiles demonstrate the ability of PHASE to identify potential safety signals and provide a tool for prioritizing experimental evaluation of high-risk compounds.

60 APPLIED LIFE SCIENCES↗