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At least 433 records · Page 24

First search for an anomalous excess of charged-current $\nu_e$ interactions without visible pions using the full MicroBooNE dataset

This public note presents an investigation of low-energy electron-neutrino events in the Fermilab Booster Neutrino Beam by the MicroBooNE experiment. This search is motivated by the excess of low energy electromagnetic events observed by the MiniBooNE experiment and, more broadly, by the landscape of neutrino anomalies observed at short baselines. This is the first measurement to use all of the data collected by the MicroBooNE experiment, corresponding to $1.1\times 10^{21}$ protons on target. Two exclusive samples of electron neutrinos without visible pions are used, one with visible protons and one without any visible protons. MicroBooNE data is compared to two empirical models of the MiniBooNE low energy excess, one obtained by enhancing the electron-neutrino content as a function of the neutrino energy, and one representing the excess for the first time as a function of the kinematics of shower energy and angle. This measurement excludes an electron-like interpretation of the MiniBooNE excess based on these models at $\geq 99\%$ confidence level in all kinematic variables.

43 PARTICLE ACCELERATORS↗

Aspartate Residues in a Forisome-Forming SEO Protein Are Critical for Protein Body Assembly and Ca 2+ Responsiveness

Forisomes are protein bodies known exclusively from sieve elements of legumes. Forisomes contribute to the regulation of phloem transport due to their unique Ca 2+ -controlled, reversible swelling. The assembly of forisomes from sieve element occlusion (SEO) protein monomers in developing sieve elements and the mechanism(s) of Ca 2+ -dependent forisome contractility are poorly understood because the amino acid sequences of SEO proteins lack conventional protein–protein interaction and Ca 2+ -binding motifs. Here we selected amino acids potentially responsible for forisome-specific functions by analyzing SEO protein sequences in comparison to those of the widely distributed SEO-related (SEOR), or SEOR proteins. SEOR proteins resemble SEO proteins closely but lack any Ca 2+ responsiveness. We exchanged identified candidate residues by directed mutagenesis of the Medicago truncatula SEO1 gene, expressed the mutated genes in yeast ( Saccharomyces cerevisiae ) and studied the structural and functional phenotypes of the forisome-like bodies that formed in the transgenic cells. We identified three aspartate residues critical for Ca 2+ responsiveness and two more that were required for forisome-like bodies to assemble. The phenotypes observed further suggested that Ca 2+ -controlled and pH-inducible swelling effects in forisome-like bodies proceeded by different yet interacting mechanisms. Finally, we observed a previously unknown surface striation in native forisomes and in recombinant forisome-like bodies that could serve as an indicator of successful forisome assembly. To conclude, this study defines a promising path to the elucidation of the so-far elusive molecular mechanisms of forisome assembly and Ca 2+ -dependent contractility.

59 BASIC BIOLOGICAL SCIENCES↗

Neutron emission in ultraperipheral Pb-Pb collisions at s N N = 5.02 TeV

In ultraperipheral collisions (UPCs) of relativistic nuclei without overlap of nuclear densities, the two nuclei are excited by the Lorentz-contracted Coulomb fields of their collision partners. In these UPCs, the typical nuclear excitation energy is below a few tens of MeV, and a small number of nucleons are emitted in electromagnetic dissociation (EMD) of primary nuclei, in contrast to complete nuclear fragmentation in hadronic interactions. The cross sections of emission of given numbers of neutrons in UPCs of 208 Pb nuclei at $\sqrt{s_{NN}}$=5.02 TeV were measured with the neutron zero degree calorimeters (ZDCs) of the ALICE detector at the LHC, exploiting a similar technique to that used in previous studies performed at $\sqrt{s_{NN}}$=2.76 TeV. In addition, the cross sections for the exclusive emission of one, two, three, four, and five forward neutrons in the EMD, not accompanied by the emission of forward protons, and thus mostly corresponding to the production of 207,206,205,204,203 Pb, respectively, were measured for the first time. The predictions from the available models describe the measured cross sections well. These cross sections can be used for evaluating the impact of secondary nuclei on the LHC components, in particular, on superconducting magnets, and also provide useful input for the design of the Future Circular Collider (FCC-hh).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Identification and Classification of Fungal GPCR Gene Families

G protein-coupled receptors (GPCRs) are transmembrane proteins crucial for signal transduction in eukaryotes, responding to diverse extracellular signals. Researchers have found and systematically summarized 14 distinct types of GPCRs in fungi but their distribution among numerous fungal species remained largely unexamined. Additionally, three families of mammalian homologs (Rhodopsin, Glutamate, and Frizzled) have been found in previous studies, but they are not included in the systematic classification of fungal GPCRs. Our study establishes a unified classification of 17 GPCR classes in fungi, combining 14 fungal and 3 mammalian previously recognized groups, and classifies 28,294 GPCRs across 1357 fungal species, significantly expanding the scale of GPCRs in fungi and demonstrating their broader distribution. We found that mammalian homologs are notably more prevalent in Early Diverging Fungi (EDF), whereas the previous 14 classes are predominantly found in Ascomycota and Basidiomycota. The most abundant class detected in fungi was Pth11-like GPCRs, exclusively found in Pezizomycotina and involved in fungal pathogenicity. Our analysis suggested that Pezizomycotina ancestor possessed an extensive array of Pth11-like GPCRs, but over time, some species underwent considerable reductions in these GPCRs in conjunction with genome contractions. Utilizing a custom-built convolutional neural network (CNN) for the identification of fungal GPCRs, we identified several putative novel fungal GPCRs. Predicted interactions between these prospective new GPCRs and G-alpha proteins, as simulated by AlphaFold Multimer, provided additional support for their functional relevance. In conclusion, our work defines the first large-scale, unified classification of fungal GPCRs, reveals lineage-specific expansions and contractions, and uncovers previously unrecognized GPCR candidates with potential functional roles in fungal signaling.

G protein-coupled receptors↗

Physics-Driven Construction of Compact Primitive Gaussian Density Fitting Basis Sets

We present a model-assisted density fitting (MADF) basis set generator, an algorithm for generating primitive atomic Gaussian density fitting (DF) basis sets (DFBSs) from a contracted Gaussian orbital basis set (OBS). The MADF algorithm produces DFBSs suitable for accurate robust DF approximation of 2-particle interactions in mean-field and correlated electronic structures. The algorithm is designed to (a) saturate the OBS product space by a large regularized set of primitive solid-harmonic Gaussian shells with nonuniform distribution of exponents, followed by (b) pruning of the shells according to their contributions to the 2- body energy of a correlated atomic ensemble. Building the DFBS generator model almost exclusively on mathematical and physical principles allows one to limit the number of parameters that control the density fitting error to three, with a single set of parameters sufficient for computations with all basis cardinal numbers, with and without correlation of core electrons, with and without scalar and spin-dependent relativistic effects, spanning almost all of the Periodic Table. Performance assessment included basis sets up to quadruple-ζ quality from several major basis set families, using molecules composed of main-group, d-block, and f-block elements. The resulting DF errors in Hartree−Fock and second-order MP2 energies (with relativistic all-electron treatments, when appropriate) were on the order of 20 and 10 μE h per electron, respectively.

Approximation↗

Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes

Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.

transcriptome↗

Striving to translate shale physics across ten orders of magnitude: What have we learned?

Shales will play an important role in the successful transition of energy from fossil-based resources to renewables in the coming decades. Aside from being a significant source of low-carbon intensity fuels, like natural gas, they also serve as geologic seals of subsurface formations that may be used to isolate nuclear waste, sequester CO 2 , or store intermittent energy (e.g., solar hydrogen). Despite their importance, shales pose significant engineering and environmental challenges due to their nanoporous structure and extreme heterogeneity that spans at least ~10 orders of magnitude in spatial scale. Two challenges inhibit a system-level understanding: (1) the physics of fluid flow and phase behavior in shales are poorly understood due to the dominant molecular interactions between minerals and fluids under confinement, and (2) the apparent lack of scale separation that prevents a reliable (closed) description of the physics at any single scale of observation. In this review, we focus on the latter issue and discuss scale translation, which in its broadest sense is transforming data or simulations from one spatiotemporal scale to another. While effective scale translation is not exclusive to shales, but all geologic porous media, the need for it is especially acute in shales given their high degree of heterogeneity. Classical theories like homogenization, while indispensable, fail when scales are not separated. Other methods, like numerical upscaling, scale-translate in only one direction: small to large, but not the reverse, called downscaling. However, the confluence of advances in three areas are bringing challenging problems such as shales within reach: increased computational power and scalable algorithms; high-resolution imaging and multi-modal data acquisition; and machine learning to process massive amounts of data. While these advances equip geoscientists with a wide array of experimental and computational tools, no individual tool can probe the entire gamut of heterogeneity in shales. Their effective use, therefore, requires an ability to bridge between various data types obtained at different scales. The aim of this review is to present a coherent account of computational and experimental methods that may be used to achieve just that, i.e., to perform scale translation. We provide a broader definition of scale translation, one that transcends classical homogenization and upscaling methods, but is consistent with them and accommodates notions like downscaling and data translation. After a brief introduction to homogenization, we review hybrid methods, numerical upscaling and its recent extensions, multiscale computing, high-resolution imaging, and machine learning. We place particular emphasis on multiscale computing and propose an algorithmic framework to bridge between the pore (micro) and Darcy (macro) scales. Throughout the paper, we draw comparisons between the various methods and highlight their (often hidden) similarities, differences, benefits, and pitfalls. We finally conclude with two case studies on shales that exemplify some of the methods presented.

58 GEOSCIENCES↗

Mode shape combination in a two-dimensional vibration energy harvester through mass loading structural modification

Mode shapes in the design of mechanical energy harvesters, as a means of performance increase, have been largely overlooked. Currently, the vast majority of energy harvester designs employ some variation of a single-degree-of-freedom cantilever, and the mode shapes of such beams are well known. This is especially true for the first bending mode, which is almost exclusively the chosen vibration mode for energy harvesting. Two-dimensional beam shapes (those which curve, meander, spiral, etc., in a plane) have recently gained research interest, as they offer freedom to modify the vibration characteristics of the harvester beam for achieving higher power density. In this study, the second bending mode shape of the “Elephant” two-dimensional beam shape is examined, and its interaction with the first bending mode is evaluated. A combinatory mode shape created by using mass loading structural modification to lower the second bending modal frequency was found to interact with the first bending mode. This is possible since the first two bending modes do not share common areas of displacement. The combined mode shape is shown to produce the most power of any of the considered mode shapes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Search for low-mass electron-recoil dark matter using a single-charge sensitive SuperCDMS-HVeV detector

We present constraints on low-mass dark matter electron scattering and absorption interactions using a SuperCDMS high-voltage eV-resolution (HVeV) detector. Data were taken underground in the NEXUS facility located at Fermilab with an overburden of 225 meters of water equivalent. The experiment benefits from the minimizing of luminescence from the printed circuit boards in the detector holder used in all previous HVeV studies. A blind analysis of 6.1 g · days of exposure produces exclusion limits for dark matter-electron scattering cross sections for masses as low as 1 MeV/𝑐 2 , as well as on the photon-dark photon mixing parameter and the coupling constant between axionlike particles and electrons for particles with masses >1.2 eV/𝑐 2 probed via absorption processes.

dark matter direct detection↗

Lithiation bridged molecular conducting magnets

Combining ferromagnetism and metallic conductivity has been extensively studied in contemporary materials science. However, building such multifunctionalities in molecular chemistry is particularly challenging, on which two collective properties are long considered as mutually exclusive. Here, we report molecular conducting magnet consisting of two-dimensional graphene and molecular planar magnetic networks bridged by electrochemical lithiation, exhibiting the co-existence of distinct magnetism and conductivity and magneto-electric coupling effects. Here, the room temperature magnetoresistance and magnetoelectric coupling coefficient of such complex solid reach 10.7% and 1.77 V/Oe cm, respectively, which can be further tailored by modulating the interaction between graphene and molecular magnetic network. In addition, the graphene passivation simultaneously introduces environmental stability of molecular mag-nets. The electrochemical lithiation offers a pathway towards coupling magnetism and conductivity in molecular complexes.

2D organic complexes↗

Water anomalous thermodynamics, attraction, repulsion, and hydrophobic hydration

A model composed of van der Waals-like and hydrogen bonding contributions that simulates the low-temperature anomalous thermodynamics of pure water while exhibiting a second, liquid-liquid critical point [P. H. Poole et al., Phys. Rev. Lett. 73, 1632 (1994)] is extended to dilute solutions of nonionic species. Critical lines emanating from such second critical point are calculated. While one infers that the smallness of the water molecule may be a relevant factor for those critical lines to move towards experimentally accessible regions, attention is mainly focused on the picture our model draws for the hydration thermodynamics of purely hydrophobic and amphiphilic non-electrolyte solutes. We first focus on differentiating solvation at constant volume from the corresponding isobaric process. Both processes provide the same viewpoint for the low solubility of hydrophobic solutes: it originates from the combination of weak solute-solvent attractive interactions and the specific excluded-volume effects associated with the small molecular size of water. However, a sharp distinction is found when exploring the temperature dependence of hydration phenomena since, in contrast to the situation for the constant-V process, the properties of pure water play a crucial role at isobaric conditions. Specifically, the solubility minimum as well as enthalpy and entropy convergence phenomena, exclusively ascribed to isobaric solvation, are closely related to water’s density maximum. Furthermore, the behavior of the partial molecular volume and the partial molecular isobaric heat capacity highlights the interplay between water anomalies, attraction, and repulsion. The overall picture presented here is supported by experimental observations, simulations, and previous theoretical results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Search for dark matter produced in association with a Higgs boson decaying to bottom quarks in proton-proton collisions at $\sqrt{s}=13$ TeV

A search for dark matter particles produced in association with a Higgs boson decaying to a bottom quark-antiquark pair in proton-proton collisions at $\sqrt{s}=13$ TeV is presented. The data, collected with the CMS detector at the LHC, correspond to an integrated luminosity of 101 fb −1 . The analysis is performed in exclusive categories targeting both Lorentz-boosted (merged) and resolved 𝑏 jet pair topologies, covering a wide range of Higgs boson transverse momentum. A statistical combination is made with a previous search using data collected in 2016 and corresponding to an integrated luminosity of 35.9 fb −1 . The observed data agree with the standard model background predictions. Constraints are placed on models predicting new particles or interactions, such as those in the simplified frameworks of baryonic-𝑍′ and 2⁢HDM + 𝑎, where the latter is a type-II two-Higgs-doublet model featuring a heavy pseudoscalar with an additional light pseudoscalar. Upper limits at 95% confidence level are set on the production cross section for these models. For the baryonic-𝑍′ model, 𝑍′ boson masses below 2.25 TeV are excluded for a dark matter particle candidate mass of 1 GeV. In the 2⁢HDM + 𝑎 model, heavy pseudoscalar masses between 850 and 1300 GeV are excluded for a light pseudoscalar mass of 350 GeV.

Hayrapetyan, A. [Yerevan Physics Institute]↗

Towards a 𝜈 𝜇 CC 1𝜇 + 1p exc. cross section measurement at the NOvA Near Detector

In the recent past, the NOvA near detector has been used to perform several neutrino-matter cross section measurements as a function of final state muon or electron kinematics around $E_\nu = 2$ GeV. In this talk, I show how the muon neutrino charged-current measurement in particular can be extended into a more exclusive region of phase space in order to probe nuclear effects. This can be done by selecting a final state with 1$\mu$, 1 proton, and nothing else, and measuring the cross section in terms of transverse kinematic imbalance (TKI) variables. The measurement I describe here would also be sensitive to quasi-elastic (QEL), two-particle two-hole (2p2h), and resonant (RES) neutrino interactions. Currently, I am optimizing the selection cuts for this analysis and developing a proton momentum estimator, which is necessary for reconstructing the TKI variables.

Weber, Colin [Minnesota U.]↗

A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes

Abstract Complement evasion is a hallmark of extracellular microbial pathogens such as Borrelia burgdorferi, the causative agent of Lyme disease. Lyme disease spirochetes express nearly a dozen outer surface lipoproteins that bind complement components and interfere with their native activities. Among these, BBK32 is unique in its selective inhibition of the classical pathway. BBK32 blocks activation of this pathway by selectively binding and inhibiting the C1r serine protease of the first component of complement, C1. To understand the structural basis for BBK32-mediated C1r inhibition, we performed crystallography and size-exclusion chromatography–coupled small angle X-ray scattering experiments, which revealed a molecular model of BBK32-C in complex with activated human C1r. Structure-guided site-directed mutagenesis was combined with surface plasmon resonance binding experiments and assays of complement function to validate the predicted molecular interface. Analysis of the structures shows that BBK32 inhibits activated forms of C1r by occluding substrate interaction subsites (i.e., S1 and S1’) and reveals a surprising role for C1r B loop–interacting residues for full inhibitory activity of BBK32. The studies reported in this article provide for the first time (to our knowledge) a structural basis for classical pathway–specific inhibition by a human pathogen.

Garrigues, Ryan J. (ORCID:0000000259233250)↗

An Energetic Concept of Habitability for the Deep Subsurface

Universally, life must be characterized by a characteristic level of order and complexity. In the most general sense, habitability could then be defined as the set of factors required to allow the creation and maintenance of molecular complexity. These factors are: chemical raw materials; energy with which to assemble those materials into complex molecules and sustain the resultant state of complexity; a solvent that allows the interaction of complex molecules, promotes tertiary structure, and permits compartmentalization; and environmental conditions that permit the assembly and maintenance of complex molecules. On Earth, these general requirements correspond to the major biogenic elements C, H, O, N, P, S; chemical or light energy; the solvent water; and specific ranges of temperature, pH, radiation, ionic strength, and so forth, which have thus far been determined on and exclusively empirical basis. Importantly, while the complete absence of any of these factors ensures uninhabitable conditions, the mere presence of all four does not guarantee habitability. In each case - even that of water - it is a question of degree. This question can be couched in quantitative terms by considering the impact of each of these factors on cellular energy balance. More "extreme" conditions (e.g., high temperature, high or low pH, etc.), lower water activity, and low concentrations of nutrients incur or have potential to be addressed by increased investment of energy on the part of the cell. This must be balanced by energy conservation in the cell, noting that biochemical, mass transport, and abiotic chemical limitations intervene between environmental energy availability and biological energy capture. Similarly, lower boundary conditions are emplaced on useful environmental energy yields by the "quantized" nature of biological energy conservation, and upper boundary conditions are emplaced by energy levels or fluxes that are destructive with respect to complexity. This energetic framework, with boundary conditions supplied by the specifics of the biochemistry in question, offers a generalized, yet quantitative means of assessing the habitability of any system with respect to complex life.

Hoehler, Tori M.↗

Pillared Laminar Vermiculite Membranes with Tunable Monovalent and Multivalent Ion Selectivity

Effective membrane separation of Li + from Na + and Mg 2+ is crucial for lithium extraction from water yet challenging for conventional polymeric membranes. Two dimensional (2D) membranes with ordered laminar structures and tunable physicochemical properties offer distinctive ion-sieving capabilities promising for lithium extraction. Recently, phyllosilicates are introduced as abundant and cost-effective source materials for such membranes. However, their water instability and low inherent ion transport selectivity hinder practical applications. Herein, a new class of laminar membranes with excellent stability and tunable ion sieving is reported by incorporating inorganic alumina pillars into vermiculite interlayers. Crosslinking vermiculite flakes with alumina pillars significantly strengthens interlamellar interactions, resulting in robust water stability. Doping of Na + before the pillaring process reverses the membrane's surface charge, substantially boosting Li + separation from multivalent cations via electrostatic interactions. Lithium extraction is often complicated by the presence of co-existing monovalent cations (e.g., Na + ) at higher concentrations. Here, by introducing excess Na + into the membrane after the pillaring process, the separation of Li + from monovalent cations is enhanced through steric effects. This work realizes both monovalent/multivalent and monovalent/monovalent selective ion sieving with the same membrane platform. A separation mechanism is proposed based on Donnan exclusion and size exclusion, providing new insights for membrane design for resource recovery applications.

2D materials↗

Search for contact interactions and large extra dimensions in the dilepton mass spectra from proton-proton collisions at $ \sqrt{s}=13 $ TeV

A search for nonresonant excesses in the invariant mass spectra of electron and muon pairs is presented. The analysis is based on data from proton-proton collisions at a center-of-mass energy of 13 TeV recorded by the CMS experiment in 2016, corresponding to a total integrated luminosity of 36 fb$^{–1}$. No significant deviation from the standard model is observed. Limits are set at 95% confidence level on energy scales for two general classes of nonresonant models. For a class of fermion contact interaction models, lower limits ranging from 20 to 32 TeV are set on the characteristic compositeness scale Λ. For the Arkani-Hamed, Dimopoulos, and Dvali model of large extra dimensions, the first results in the dilepton final state at 13 TeV are reported, and values of the ultraviolet cutoff parameter Λ$_{T}$ below 6.9 TeV are excluded. A combination with recent CMS diphoton results improves this exclusion to Λ$_{T}$ below 7.7 TeV, providing the most sensitive limits to date in nonhadronic final states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Selective sorption of oxygen and nitrous oxide by an electron donor-incorporated flexible coordination network

Incorporating strong electron donor functionality into flexible coordination networks is intriguing for sorption applications due to a built-in mechanism for electron-withdrawing guests. Here we report a 2D flexible porous coordination network, [Ni 2 (4,4'-bipyridine)(VTTF) 2 ]n(1) (where H 2 VTTF = 2,2;-[1,2-bis(4-benzoic acid)-1,2ethanediylidene]bis-1,3-benzodithiole), which exhibits large structural deformation from the as-synthesized or open phase (1α) into the closed phase (1β) after guest removal, as demonstrated by X-ray and electron diffraction. Interestingly, upon exposure to electron-withdrawing species, 1β reversibly undergoes guest accommodation transitions; 1α$\supset$O 2 (90 K) and 1α$\supset$N 2 O (185 K). Moreover, the 1β phase showed exclusive O 2 sorption over other gases (N 2 , Ar, and CO) at 120 K. The phase transformations between the 1α and 1β phases under these gases were carefully investigated by in-situ X-ray diffraction, in-situ spectroscopic studies, and DFT calculations, validating that the unusual sorption was attributed to the combination of flexible frameworks and VTTF (electron-donor) that induces strong interactions with electron-withdrawing species.

36 MATERIALS SCIENCE↗