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At least 1,477 records · Page 82

Differences in substrate use linked to divergent carbon flow during litter decomposition

ABSTRACT Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.

59 BASIC BIOLOGICAL SCIENCES↗

Complementing model species with model clades

Abstract Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a “model clade.” These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a “model clade” and make suggestions for building global networks to support future studies in the model order Brassicales.

59 BASIC BIOLOGICAL SCIENCES↗

Ferrimagnetic Order in Tetragonal Antiperovskite Mn3GeN

The crystal and magnetic structures of the nitride antiperovskite M⁢n3⁢GeN reveals ferrimagnetic order stemming from a distorted kagome-derived lattice of the Mn atoms. Polycrystalline M⁢n3⁢GeN was synthesized via a solid-state reaction and characterized using neutron powder diffraction, dc magnetometry, and first-principles calculations. Rietveld refinement reveals near-stoichiometric composition (M⁢n3⁢Ge⁢N0.992⁢(7)) adopting a tetragonal 𝐼⁢4/𝑚⁢𝑐⁢𝑚 structure at 𝑇=500K and below, featuring axially distorted and tilted [NM⁢n6] octahedra that result in a buckled Mn kagome lattice. On heating, the tetragonal distortion and octahedral tilt angle decrease continuously before transitioning to the cubic 𝑃⁢𝑚⁢3⁢𝑚 antiperovskite phase at 𝑇≈527K. Neutron diffraction and magnetometry together reveal noncollinear ferrimagnetic ordering. For 30K≤𝑇≤500K, the magnetic structure is described by magnetic space group 𝐼⁢𝑏⁢𝑎′⁢𝑚′ (72.544), with inequivalent Mn1 and Mn2 sublattices that couple antiferromagnetically to yield a net moment. Density-functional theory-based calculations show that the different local moments originate from the bandwidths associated with distinct Mn–N bond lengths. Temperature-dependent refinements reveal distinct differences in the thermal disordering profiles of the Mn1 and Mn2 sublattices. These findings reveal a subtlety in the magnetic and structural behavior of M⁢n3⁢GeN, highlighting the interplay between structural distortions, magnetic ordering, and electronic structure in kagome-derived antiperovskite materials.

36 MATERIALS SCIENCE↗

Magnetic Bloch theorem and reentrant flat bands in twisted bilayer graphene at 2 π flux

Bloch's theorem is the centerpiece of topological band theory, which itself has defined an era of quantum materials research. However, Bloch's theorem is broken by a perpendicular magnetic field, making it difficult to study topological systems in strong flux. For the first time, moiré materials have made this problem experimentally relevant, and its solution is the focus of this paper. We construct gauge-invariant irreps of the magnetic translation group at 2π flux on infinite boundary conditions, allowing us to give analytical expressions in terms of the Siegel theta function for the magnetic Bloch Hamiltonian, non-Abelian Wilson loop, and many-body form factors. We illustrate our formalism using a simple square lattice model and the Bistritzer-MacDonald Hamiltonian of twisted bilayer graphene, obtaining reentrant ground states at 2π flux under the Coulomb interaction.

2-dimensional systems↗

Brain Connectivity Workshop Series Report

The National Institutes of Health (NIH) BRAIN Initiative aims to accelerate development and application of technologies that show how individual brain cells in complex neural circuits interact at the speed of thought and action. Complete wiring diagrams of the mammalian brain will revolutionize the capabilities of researchers to formulate and test models of how activity within brain circuits drives coordinated function and behavior. A top priority for the BRAIN Initiative, motivated by the strategic guidance of the BRAIN 2.0 Working Group report, is to muster the resources and foster the collaborations needed to generate these wiring diagrams at the level of long-range projections (“projectomes”) and synapses (“connectomes”) in whole mammalian brains, including those from rodents, humans, and other large-brained mammals. Achieving the scale and resolution necessary to characterize and use these projectomes and connectomes will not only push the boundaries of current imaging and computational capabilities to generate faster, cheaper, and more scalable technologies, but also drive broad innovation in data science, artificial intelligence, and machine learning.

42 ENGINEERING↗

Scalable and Energy-Efficient Methods for Interactive Exploration of Scientific Data

The main scientific contributions of this project are the following novel concepts for multidimensional arrays: shape-based similarity join (SIGMOD 2016), incremental view maintenance (SIGMOD 2017), user-defined stencil functions (HPDC 2017), and distributed caching for in-situ processing (SSDBM 2018). Building on our collaboration with the astrophysics group at LBNL, we applied these techniques to the data generated in the Palomar Transient Factory (PTF) astronomical survey. They played a pivotal role in the first-ever observation of a neutron star merger, which produces gravitational waves and turns out to be the origin of heavy elements, including gold. This has lead to a Science magazine article that has received extensive media coverage on ACM TechNews, Slashdot, FiveThirtyEight, and Quanta Magazine, among others. Additionally, two other articles detailing related aspects of the same discovery have been published in the Astrophysical Journal Letters journal. These publications have more than 3,000 citations according to Google Scholar (as of February 2022). This cross-disciplinary collaboration provided very good opportunities to apply database techniques to real-life scientific problems. The fact that they facilitated major discoveries in astrophysics proves the importance of our research. In addition to the work on multidimensional array databases, this project has also developed stochastic gradient descent (SGD) optimization algorithms for training large scale machine learning models, methods for querying in-situ data, and a database query optimizer based on sketch synopses.

79 ASTRONOMY AND ASTROPHYSICS↗

Tin–Lead Liquid Metal Alloy Source for Focused Ion Beams

Focused Ion Beam (FIB) systems are increasingly utilized in nanotechnology for nanostructuring, surface modification, doping, and rapid prototyping. Recently, their potential for quantum applications has been explored, leveraging FIB’s direct-write capabilities for in situ single ion implantation, which is crucial for fabricating single photon emitters. Color centers in diamond can function as qubits and are of particular interest due to their capacity to store and transmit quantum information. While Group-IV color centers exhibit high brightness, they require low temperatures to retain coherence. However, lead-vacancy in diamond (PbV) operates at the higher end (4 K) of this temperature spectrum due to larger ground-state splitting, making them particularly interesting. In this context, our study presents results for lead (Pb)-containing alloys with eutectic points below 600 °C and results on using tantalum (Ta) and titanium (Ti) as emitter materials for a Pb liquid metal alloy ion source. We show that a standard FIB system is able to resolve the different Pb isotopes and achieve nanoscale spot sizes, as required for quantum information science applications.

color center↗

Relativistic Shear Boundary Layer and the Gamma-Ray Emission of GW170817

We present an analysis of the radiation characteristics of kinetic shear boundary layers created by relativistic plasma jets. Using a model of electromagnetic field data based on particle-in-cell simulations of an electron–ion plasma, we solve the motion of individual test electrons and compute their instantaneous radiated power and peak frequency. By analyzing a large number of test electrons in this manner, we find two distinct electron populations present around the shear boundary layer. The most highly radiative electrons execute looping motion due to crossed electric and magnetic fields as they are accelerated along the bulk flow of the jet, and eventually cross the shear boundary interface at steep angles. Electrons that never cross the shear boundary interface radiate much less energy as a group. Summing over all of the highly radiative electrons, we compute the distribution of the total radiated energy as a function of the angle relative to the bulk flow. Furthermore, this result has important potential implications for the observed radiation output of short gamma-ray bursts viewed at large angles from the jet axis, such as the neutron star merger event GW170817/GRB 170817A.

79 ASTRONOMY AND ASTROPHYSICS↗

FLISR in the Presence of DERs ADMS Test Bed Use Case

Fault location, isolation, and restoration (FLISR) is one of the distribution automation applications that utilities are most interested in. It operates groups of switches on distribution feeders to improve the reliability of power delivery after localizing outages. FLISR is an essential function for enabling a self-healing grid, and it directly affects grid reliability and resilience. The presence of DERs brings both new opportunities and challenges for FLISR applications. For instance, some DERs can work as backup generation sources and help energize local networks so more switching options can be achieved with the coordination of FLISR operations; however, the existence of DERs also brings new challenges. The bidirectional power flow resulting from DERs might require dynamic changes to protective devices' fault current settings, and thus the FLISR application will need to dynamically adjust its operations in coordination with the dynamic protection settings. Also, some FLISR applications make their service restoration decisions and close tie-switches based on predefined rules; however, the presence of DERs and their impact on altering net loads on the local feeder network are not considered. For this use case, the project team is using the FLISR application of the Survalent ADMS operating on a real-time simulation of a feeder from Central Georgia EMC, a cooperative electric utility. The performance of the FLISR application is being evaluated for different locations and combinations of DERs, including grid-forming battery energy storage systems.

ADMS↗

Electronic structure of strongly correlated systems: recent developments in multiconfiguration pair-density functional theory and multiconfiguration nonclassical-energy functional theory

Strong electron correlation plays an important role in transition-metal and heavy-metal chemistry, magnetic molecules, bond breaking, biradicals, excited states, and many functional materials, but it provides a significant challenge for modern electronic structure theory. The treatment of strongly correlated systems usually requires a multireference method to adequately describe spin densities and near-degeneracy correlation. However, quantitative computation of dynamic correlation with multireference wave functions is often difficult or impractical. Multiconfiguration pair-density functional theory (MC-PDFT) provides a way to blend multiconfiguration wave function theory and density functional theory to quantitatively treat both near-degeneracy correlation and dynamic correlation in strongly correlated systems; it is more affordable than multireference perturbation theory, multireference configuration interaction, or multireference coupled cluster theory and more accurate for many properties than Kohn–Sham density functional theory. This perspective article provides a brief introduction to strongly correlated systems and previously reviewed progress on MC-PDFT followed by a discussion of several recent developments and applications of MC-PDFT and related methods, including localized-active-space MC-PDFT, generalized active-space MC-PDFT, density-matrix-renormalization-group MC-PDFT, hybrid MC-PDFT, multistate MC-PDFT, spin–orbit coupling, analytic gradients, and dipole moments. We also review the more recently introduced multiconfiguration nonclassical-energy functional theory (MC-NEFT), which is like MC-PDFT but allows for other ingredients in the nonclassical-energy functional. We discuss two new kinds of MC-NEFT methods, namely multiconfiguration density coherence functional theory and machine-learned functionals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CovS inactivation reduces CovR promoter binding at diverse virulence factor encoding genes in group A Streptococcus

The control of virulence gene regulator (CovR), also called caspsule synthesis regulator (CsrR), is critical to how the major human pathogen group A Streptococcus fine-tunes virulence factor production. CovR phosphorylation (CovR~P) levels are determined by its cognate sensor kinase CovS, and functional abrogating mutations in CovS can occur in invasive GAS isolates leading to hypervirulence. Presently, the mechanism of CovR-DNA binding specificity is unclear, and the impact of CovS inactivation on global CovR binding has not been assessed. Thus, we performed CovR chromatin immunoprecipitation sequencing (ChIP-seq) analysis in the emm1 strain MGAS2221 and its CovS kinase deficient derivative strain 2221-CovS-E281A. We identified that CovR bound in the promoter regions of nearly all virulence factor encoding genes in the CovR regulon. Additionally, direct CovR binding was observed for numerous genes encoding proteins involved in amino acid metabolism, but we found limited direct CovR binding to genes encoding other transcriptional regulators. The consensus sequence AATRANAAAARVABTAAA was present in the promoters of genes directly regulated by CovR, and mutations of highly conserved positions within this motif relieved CovR repression of the hasA and MGAS2221_0187 promoters. Analysis of strain 2221-CovS-E281A revealed that binding of CovR at repressed, but not activated, promoters is highly dependent on CovR~P state. CovR repressed virulence factor encoding genes could be grouped dependent on how CovR~P dependent variation in DNA binding correlated with gene transcript levels. Taken together, the data show that CovR repression of virulence factor encoding genes is primarily direct in nature, involves binding to a newly-identified DNA binding motif, and is relieved by CovS inactivation. These data provide new mechanistic insights into one of the most important bacterial virulence regulators and allow for subsequent focused investigations into how CovR-DNA interaction at directly controlled promoters impacts GAS pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Movement with meaning: integrating information into meta-ecology

Fluxes of matter, energy and information over space and time contribute to ecosystems' functioning and stability. The meta-ecosystem framework addresses the dynamics of ecosystems linked by these fluxes but, to date, has focused solely on energy and matter. Here, we synthesize existing knowledge of information's effects on local and connected ecosystems and demonstrate how new hypotheses emerge from the integration of ecological information into meta-ecosystem theory. First, we begin by defining information and reviewing how it flows among ecosystems to affect connectivity, local ecosystem function and meta-ecosystem dynamics. We focus on the role of semiotic information: that which can reduce an individual's – or a group's – uncertainty about the state of the world. Semiotic information elicits behavioral, developmental and life history responses from organisms, potentially leading to fitness consequences. Organisms' responses to information can ripple through trophic interactions to influence ecosystem processes, their local and regional dynamics, and the spatiotemporal flows of energy and matter, therefore information should affect meta-ecosystem dynamics such as stability and productivity. While specific subdisciplines of ecology currently consider different types of information (e.g. social and cultural information, natural and artificial light or sound, body condition, genotype and phenotype), many ecological models currently account for neither the spatio–temporal distribution of information nor its perception by organisms. We identify the empirical, theoretical and philosophical challenges in developing a robust information meta-ecology and offer ways to overcome them. Finally, we present new hypotheses for how accounting for realistic information perception and responses by organisms could impact processes such as home range formation and spatial insurance, and thus our understanding of ecological dynamics across spatial and temporal scales. Accounting for information will be essential to understanding how dynamics such as fitness, organismal movement and trophic interactions influence meta-ecosystem functioning, and predicting how ecosystem processes are affected by anthropogenic pressures.

54 ENVIRONMENTAL SCIENCES↗

Twisted bilayer graphene. V. Exact analytic many-body excitations in Coulomb Hamiltonians: Charge gap, Goldstone modes, and absence of Cooper pairing

We find exact analytic expressions for the energies and wave functions of the charged and neutral excitations above the exact ground states (at rational filling per unit cell) of projected Coulomb Hamiltonians in twisted bilayer graphene. Our exact expressions are valid for any form of the Coulomb interaction and any form of A A and A B / B A tunneling. The single charge excitation energy is a convolution of the Coulomb potential with a quantum geometric tensor of the TBG bands. The neutral excitations are (high-symmetry group) magnons, and their dispersion is analytically calculated in terms of the form factors of the active bands in TBG. The two-charge excitation energy and wave functions are also obtained, and a sufficient condition on the graphene eigenstates for obtaining a Cooper pair from Coulomb interactions is obtained. For the actual TBG bands at the first magic angle, we can analytically show that the Cooper pair binding energy is zero in all such projected Coulomb models, implying that either phonons and/or nonzero kinetic energy are needed for superconductivity. Since Vafek and Kang [Phys. Rev. Lett. 125, 257602 (2020)] showed that the kinetic energy bounds on the superexchange energy are less 10 -3 in Coulomb units, the phonon mechanism becomes then very likely. If nonetheless the superconductivity is due to kinetic terms which render the bands nonflat, one prediction of our theory is that the highest T c would not occur at the highest DOS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Phosphate‐functionalized Zirconium Metal–Organic Frameworks for Enhancing Lithium–Sulfur Battery Cycling

Abstract Lithium–sulfur batteries are promising candidates for next‐generation energy storage devices due to their outstanding theoretical energy density. However, they suffer from low sulfur utilization and poor cyclability, greatly limiting their practical implementation. Herein, we adopted a phosphate‐functionalized zirconium metal–organic framework (Zr‐MOF) as a sulfur host. With their porous structure, remarkable electrochemical stability, and synthetic versatility, Zr‐MOFs present great potential in preventing soluble polysulfides from leaching. Phosphate groups were introduced to the framework post‐synthetically since they have shown a strong affinity towards lithium polysulfides and an ability to facilitate Li ion transport. The successful incorporation of phosphate in MOF‐808 was demonstrated by a series of techniques including infrared spectroscopy, solid‐state nuclear magnetic resonance spectroscopy, and X‐ray pair distribution function analysis. When employed in batteries, phosphate‐functionalized Zr‐MOF (MOF‐808‐PO4) exhibits significantly enhanced sulfur utilization and ion diffusion compared to the parent framework, leading to higher capacity and rate capability. The improved capacity retention and inhibited self‐discharge rate also demonstrate effective polysulfide encapsulation utilizing MOF‐808‐PO4. Furthermore, we explored their potential towards high‐density batteries by examining the cycling performance at various sulfur loadings. Our approach to correlate structure with function using hybrid inorganic–organic materials offers new chemical design strategies for advancing battery materials.

Liu, Bingqian↗

Variations of organic functional chemistry in carbonaceous matter from the asteroid 162173 Ryugu

Abstract Primordial carbon delivered to the early earth by asteroids and meteorites provided a diverse source of extraterrestrial organics from pre-existing simple organic compounds, complex solar-irradiated macromolecules, and macromolecules from extended hydrothermal processing. Surface regolith collected by the Hayabusa2 spacecraft from the carbon-rich asteroid 162173 Ryugu present a unique opportunity to untangle the sources and processing history of carbonaceous matter. Here we show carbonaceous grains in Ryugu can be classified into three main populations defined by spectral shape: Highly aromatic (HA), Alkyl-Aromatic (AA), and IOM-like (IL). These carbon populations may be related to primordial chemistry, since C and N isotopic compositions vary between the three groups. Diffuse carbon is occasionally dominated by molecular carbonate preferentially associated with coarse-grained phyllosilicate minerals. Compared to related carbonaceous meteorites, the greater diversity of organic functional chemistry in Ryugu indicate the pristine condition of these asteroid samples.

Science & Technology - Other Topics↗

Spatial Engineering Direct Cooperativity between Binding Sites for Uranium Sequestration

Preorganization is a basic design principle used by nature that allows for synergistic pathways to be expressed. Herein, a full account of the conceptual and experimental development from randomly distributed functionalities to a convergent arrangement that facilitates cooperative binding is given, thus conferring exceptional affinity toward the analyte of interest. The resulting material with chelating groups populated adjacently in a spatially locked manner displays up to two orders of magnitude improvement compared to a random and isolated manner using uranium sequestration as a model application. This adsorbent shows exceptional extraction efficiencies, capable of reducing the uranium concentration from 5 ppm to less than 1 ppb within 10 min, even though the system is permeated with high concentrations of competing ions. The efficiency is further supported by its ability to extract uranium from seawater with an uptake capability of 5.01 mg g -1 , placing it among the highest-capacity seawater uranium extraction materials described to date. The concept presented here uncovers a new paradigm in the design of efficient sorbent materials by manipulating the spatial distribution to amplify the cooperation of functions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Background independent quantum field theory and gravitating vacuum fluctuations

The scale dependent effective average action for quantum gravity complies with the fundamental principle of Background Independence. Ultimately the background metric it formally depends on is selected self-consistently by means of a tadpole condition, a generalization of Einstein’s equation. Self-consistent background spacetimes are scale dependent, and therefore “going on-shell” at the points along a given renormalization group (RG) trajectory requires understanding two types of scale dependencies: the (familiar) direct one carried by the off-shell action functional, and an equally important indirect one related to the continual re-adjustment of the background geometry. This paper is devoted to a careful delineation and analysis of certain general questions concerning the indirect scale dependence, as well as a detailed explicit investigation of the case where the self-consistent metrics are determined predominantly by the RG running of the cosmological constant. Mathematically, the object of interest is the spectral flow induced by the background Laplacian which, on-shell, acquires an explicit scale dependence. Among other things, it encodes the complete information about the specific set of field modes which, at any given scale, are the degrees of freedom constituting the respective effective field theory. For a large class of RG trajectories (Type IIIa) we discover a seemingly paradoxical behavior that differs substantially from the off-shell based expectations: A Background Independent theory of (matter coupled) quantum gravity looses rather than gains degrees of freedom at increasing energies. As an application, we investigate to what extent it is possible to reformulate the exact theory in terms of matter and gravity fluctuations on a rigid flat space. It turns out that, in vacuo, this “rigid picture” breaks down after a very short RG time already (less than one decade of scales) because of a “scale horizon” that forms. Furthermore, we critically reanalyze and refute the frequent claim that the huge energy densities one obtains in standard quantum field theory by summing up to zero-point energies imply a naturalness problem for the observed small value of the cosmological constant.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Controlled catalyst-transfer polymerization in graphene nanoribbon synthesis

Exercising direct control over the unusual electronic structures arising from quantum confinement effects in graphene nanoribbons (GNRs) is intimately linked to geometric boundary conditions imposed by the structure of the ribbon. Besides composition and position of substitutional dopant atoms, the symmetry of the unit cell, width, length, and termination of a GNR govern its electronic structure. Here, we present a rational design that integrates each of these interdependent variables within a modular bottom-up synthesis. Our hybrid chemical approach relies on a catalyst-transfer polymerization that establishes excellent control over length, width, and end groups. Complemented by a surface-assisted cyclodehydrogenation step, uniquely enabled by matrix-assisted direct (MAD) transfer protocols, geometry and functional handles encoded in a polymer template are faithfully mapped onto the structure of the corresponding GNR. Bond-resolved scanning tunneling microscopy (BRSTM) and spectroscopy (STS) validate the robust correlation between polymer template design and GNR electronic structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗