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At least 811 records · Page 45

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DOE OSTI2022

Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Bioeconomic benefits of managing fishing effort in a coexisting small- and large-scale fishery game

Abstract Fishing systems provide employment, income generation, poverty alleviation, and food security. The coexistence of small-scale fisheries (SSFs) and large-scale fisheries (LSFs) increases management complexity. Management actions have ecological and social implications that must be addressed carefully. We applied a bioeconomic game-theoretical model to the four-gear mullet fishery in southern Brazil—one industrial LSF (purse seine) and three artisanal SSFs (gillnet, beach seine, and drift net). All fishing gears target adult individuals during mullet's reproductive migration. First, we explored whether the current fishing efforts of all fishing gears could persist over time. Second, we investigated their interactions through a non-cooperative game. Finally, we studied the response of these interactions when fishing effort was restricted. We found that when the current fishing effort was maintained, the stock reduced to 26.4% of its capacity in 25 years. In addition, under non-cooperation, the traditional beach seine fleet exited the fishery. Interestingly, the constrained scenario had a coexistence output with increasing values for the final stock size and the per capita labour income, suggesting that limiting fishing effort can maintain all fishing gears in the fishery with social and ecological benefits.

de Azevedo, Eric Zettermann Dias (ORCID:0000000323↗

DOE OSTI2022

Constraining the baryonic feedback with cosmic shear using the DES Year-3 small-scale measurements

ABSTRACT We use the small scales of the Dark Energy Survey (DES) Year-3 cosmic shear measurements, which are excluded from the DES Year-3 cosmological analysis, to constrain the baryonic feedback. To model the baryonic feedback, we adopt a baryonic correction model and use the numerical package baccoemu to accelerate the evaluation of the baryonic non-linear matter power spectrum. We design our analysis pipeline to focus on the constraints of the baryonic suppression effects, utilizing the implication given by a principal component analysis on the Fisher forecasts. Our constraint on the baryonic effects can then be used to better model and ameliorate the effects of baryons in producing cosmological constraints from the next-generation large-scale structure surveys. We detect the baryonic suppression on the cosmic shear measurements with a ∼2σ significance. The characteristic halo mass for which half of the gas is ejected by baryonic feedback is constrained to be $M_c \gt 10^{13.2} \, h^{-1} \, \mathrm{M}_{\odot }$ (95 per cent C.L.). The best-fitting baryonic suppression is $\sim 5{{\ \rm per\ cent}}$ at $k=1.0 \, {\rm Mpc}\ h^{-1}$ and $\sim 15{{\ \rm per\ cent}}$ at $k=5.0 \, {\rm Mpc} \ h^{-1}$. Our findings are robust with respect to the assumptions about the cosmological parameters, specifics of the baryonic model, and intrinsic alignments.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Non-local contribution from small scales in galaxy–galaxy lensing: comparison of mitigation schemes

ABSTRACT Recent cosmological analyses with large-scale structure and weak lensing measurements, usually referred to as 3 × 2pt, had to discard a lot of signal to noise from small scales due to our inability to accurately model non-linearities and baryonic effects. Galaxy–galaxy lensing, or the position–shear correlation between lens and source galaxies, is one of the three two-point correlation functions that are included in such analyses, usually estimated with the mean tangential shear. However, tangential shear measurements at a given angular scale θ or physical scale R carry information from all scales below that, forcing the scale cuts applied in real data to be significantly larger than the scale at which theoretical uncertainties become problematic. Recently, there have been a few independent efforts that aim to mitigate the non-locality of the galaxy–galaxy lensing signal. Here, we perform a comparison of the different methods, including the Y-transformation, the point-mass marginalization methodology, and the annular differential surface density statistic. We do the comparison at the cosmological constraints level in a combined galaxy clustering and galaxy–galaxy lensing analysis. We find that all the estimators yield equivalent cosmological results assuming a simulated Rubin Observatory Legacy Survey of Space and Time (LSST) Year 1 like set-up and also when applied to DES Y3 data. With the LSST Y1 set-up, we find that the mitigation schemes yield ∼1.3 times more constraining S8 results than applying larger scale cuts without using any mitigation scheme.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Exploring the origin of the distance bimodality of stars in the periphery of the Small Magellanic Cloud with APOGEE and Gaia

ABSTRACT The Magellanic Cloud system represents a unique laboratory for study of both interacting dwarf galaxies and the ongoing process of the formation of the Milky Way and its halo. We focus on one aspect of this complex, three-body interaction – the dynamical perturbation of the Small Magellanic Cloud (SMC) by the Large Magellanic Cloud (LMC), and specifically potential tidal effects on the SMC’s eastern side. Using Gaia astrometry and the precise radial velocities (RVs) and multielement chemical abundances from Apache Point Observatory Galactic Evolution Experiment (APOGEE-2) Data Release 17, we explore the well-known distance bimodality on the eastern side of the SMC. Through estimated stellar distances, proper motions, and RVs, we characterize the kinematics of the two populations in the bimodality and compare their properties with those of SMC populations elsewhere. Moreover, while all regions explored by APOGEE seem to show a single chemical enrichment history, the metallicity distribution function (MDF), of the ‘far’ stars on the eastern periphery of the SMC is found to resemble that for the more metal-poor fields of the western periphery, whereas the MDF for the ‘near’ stars on the eastern periphery resembles that for stars in the SMC Centre. The closer eastern periphery stars also show RVs (corrected for SMC rotation and bulk motion) that are, on average, approaching us relative to all other SMC populations sampled. We interpret these trends as evidence that the near stars on the eastern side of the SMC represent material pulled out of the central SMC as part of its tidal interaction with the LMC.

Almeida, Andres (ORCID:0009000007332479)↗

DOE OSTI2023

Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410–DNA interaction using small angle X-ray scattering

ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to lie against the DNA binding interface of the ZF array. In solution, ZNF410 is a monomer and binds to DNA with 1:1 stoichiometry. Surprisingly, the single best-fit model for the experimental small angle X-ray scattering profile, in the absence of DNA, is the original AlphaFold model with the N-terminal long-helix and the hairpin loop occupying the ZF DNA binding surface. For DNA binding, the hairpin loop presumably must be displaced. After combining biophysical, biochemical, bioinformatic and artificial intelligence-based AlphaFold analyses, we suggest that the hairpin loop mimics the structure and electrostatics of DNA, and provides an additional mechanism, supplementary to sequence specificity, of regulating ZNF410 DNA binding.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗

DOE OSTI2025

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗

DOE OSTI2026

The small protein SbtC is a functional component of the CO 2 concentrating mechanism in Synechocystis sp. PCC 6803

Oxygenic phototrophs fix CO 2 via the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which shows relatively low CO 2 affinity and specificity. To circumvent low and fluctuating CO 2 concentrations in aquatic systems, cyanobacteria and algae have evolved sophisticated inorganic carbon (Ci) concentrating mechanisms (CCMs). Bicarbonate transporters such as SbtA play a crucial role in the cyanobacterial CCM and hence display multiple layers of tight regulation. Control of sbtA gene expression and corresponding transporter activity involves the PII-like protein SbtB, whose gene is frequently co-transcribed with sbtA. A previously non-annotated gene located upstream of the sbtAB operon in the model Synechocystis sp. PCC 6803 encodes the small protein SbtC, composed of 80 amino acids. Presence of SbtC was confirmed by immunoblotting of the sbtC-coding sequence fused to a Flag-tag. Similar to sbtAB , transcription of the sbtC locus is induced by low CO 2 availability; however, it is controlled independently. Mutation of the sbtC locus in a wild-type background produced only a mild phenotype, even under low CO 2 , but impaired diurnal growth resembled that of the mutant ΔsbtB . Biochemical analysis indicated a trimeric SbtABC complex in the membrane. Bicarbonate leakage from cells was strongly elevated when either sbtB or sbtC was deleted from recombinant Synechocystis strains harboring only SbtA as single Ci uptake system. Here, our results provide evidence that SbtC contributes to the formation of the SbtAB complex, thereby regulating bicarbonate exchange at the cytoplasmic membrane. Well-conserved SbtC-like proteins encoded in the neighborhood of sbtAB exist in many cyanobacterial genomes, pointing toward an important role in the cyanobacterial CCM.

Walke, Peter [Univ. of Rostock (Germany)] (ORCID:0↗

DOE OSTI2026

Exploring the partonic collectivity in small systems at energies available at the CERN Large Hadron Collider

Using the Hydro-Coal-Frag model that combines hydrodynamics at low p T , quark coalescence at intermediate p T , and the LBT transport model at high p T , we study the spectra and elliptic flow of identified hadrons in high multiplicity p–Pb and p–p collisions at the CERN Large Hadron Collider (LHC). In p–Pb collisions, the Hydro-Coal-Frag model gives a good description of the differential elliptic flow over the p T range from 0 to 6 GeV and the approximate number of constituent quark (NCQ) scaling at intermediate p T . Although the Hydro-Coal-Frag model can also roughly describe the elliptic flow in high multiplicity p–p collisions with the quark coalescence process, the larger contribution from the string fragmentations leads to a notable violation of the NCQ scaling of v 2 at intermediate p T as observed in the experiment. Comparison runs of the Hydro-Frag model without the coalescence process demonstrate that regardless the parameter adjustments, the Hydro-Frag model cannot simultaneously describe the p T spectra and the elliptic flow of identified hadrons in either p–Pb collisions or p–p collisions. In conclusion, the calculations in this paper thus provide support for the existence of partonic degrees of freedom and the possible formation of the QGP in the small systems created at the LHC.

Wang, Yuanyuan [Peking University, Beijing (China)↗

DOE OSTI2024

Neutrino-detector design for safeguarding small modular reactors

Nuclear reactors have long been a favored source for antineutrino measurements for estimates of power and burnup. With appropriate detector parameters and background rejection, an estimate of the reactor power can be derived from the measured antineutrino event rate. Antineutrino detectors are potentially attractive as a safeguards technology that can monitor reactor operations and thermal power from a distance. Advanced reactors have diverse features that may present challenges for current safeguards methods. By comparison, neutrino detectors offer complementary features, including a remote, continuous, unattended, and near-real-time monitoring capability, that may make them useful for safeguarding certain classes of advanced reactors. This study investigates the minimum depth and size of an antineutrino detector for a small modular reactor to meet safeguards needs for advanced reactors. Furthermore, extrapolating performance from several prior reactor antineutrino experiments, this study uses an analytical approach to develop a possible design for a remote antineutrino-based monitoring device.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Three-dimensional superconductivity induced by an extremely small amount of Li in Li x ⁢SnSe 2

Unconventional superconductivity occurs often in materials with low dimensionality. Furthermore, we report superconductivity observed in layered Li x SnSe 2 with the superconducting transition temperature T c ~ 6 K. Through L⁢i + intercalation in semiconducting SnSe 2 via electrochemical process, Li x ⁢SnSe 2 is formed with an extremely small x value as estimated from the c-axis lattice parameter, carrier concentration, and first-principles calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Exploring origins for correlations between flow harmonics and transverse momentum in small collision systems

High statistics data sets from experiments at the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC) with small and large collision species have enabled a wealth of new flow measurements, including the event-by-event correlation between observables. One exciting such observable $ρ(v^2_n, [p_T])$ gauges the correlation between the mean transverse momentum of particles in an event and the various flow coefficients (v n ) in the same event [P. Bozek, Phys. Rev. C 93, 044908 (2016)]. Recently it has been proposed that very low multiplicity events may be sensitive to initial-state glasma correlations [G. Giacalone, B. Schenke, and C. Shen, Phys. Rev. Lett. 125, 192301 (2020)] rather than flow-related dynamics. We find utilizing the ip-jazma framework that the color domain explanation for the glasma results are incomplete. We then explore predictions from pythia8, and the version for including nuclear collisions called pythia-angantyr, which have only nonflow correlations, and from the ampt model which has both nonflow and flow-type correlations. We find that pythia-angantyr has nonflow contributions to $ρ(v^2_n, [p_T])$ in p + O, p + Pb, and O + O collisions that are positive at low multiplicity and comparable to the glasma correlations. It is striking that in pythia8 in p + p collisions there is actually a sign change from positive to negative $ρ(v^2_n, [p_T])$ as a function of multiplicity. The ampt results match the experimental data general trends in Pb+Pb collisions at the LHC, except at low multiplicity where ampt has the opposite sign. In p + Pb collisions, ampt has the opposite sign from experimental data and we explore this within the context of parton geometry. Predictions for p + O, O + O, and Xe + Xe are also presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

3D structure of anisotropic flow in small collision systems at energies available at the BNL Relativistic Heavy Ion Collider

Here, we present (3 + 1)-dimensional [(3 + 1)D] dynamical simulations of asymmetric nuclear collisions at the BNL Relativistic Heavy Ion Collider (RHIC). Employing a dynamical initial state model coupled to (3 + 1)D viscous relativistic hydrodynamics, we explore the rapidity dependence of anisotropic flow in the RHIC small system scan at 200 GeV center-of-mass energy. We calibrate parameters to describe central 3 He + Au collisions and make extrapolations to d + Au and p + Au collisions. Our calculations demonstrate that approximately 50% of the v 3 (p T ) difference between the measurements by the STAR and PHENIX Collaborations can be explained by the use of reference flow vectors from different rapidity regions. This emphasizes the importance of longitudinal flow decorrelation for anisotropic flow measurements in asymmetric nuclear collisions, and the need for (3 + 1)D simulations. We also present results for the beam energy dependence of particle spectra and anisotropic flow in d + Au collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Medium-assisted enhancement of χ c 1 ( 3872 ) production from small to large colliding systems

Studies of exotic hadrons such as the χ c 1 ( 3872 ) state provide crucial insights into the fundamental force governing the strong interaction dynamics, with an emerging frontier to investigate their production in high energy collisions where a partonic medium is present. The latest experimental measurements from the Large Hadron Collider show an intriguing evolution pattern of the χ c 1 ( 3872 ) -to- ψ ( 2 S ) yield ratio from proton-proton collisions with increasing multiplicities toward proton-lead and lead-lead collisions. Here we propose a mechanism of medium-assisted enhancement for the χ c 1 ( 3872 ) production, which competes with the more conventional absorption-induced suppression and results in a nonmonotonic trend from small to large colliding systems. Realistic simulations from this model offer a quantitative description of all available data. Predictions are made for the centrality dependence of this observable in PbPb collisions as well as for its system-size dependence from OO and ArAr to XeXe and PbPb collisions. In both cases, a nonmonotonic behavior emerges as the imprint of the competition between enhancement and suppression and can be readily tested by future data. Published by the American Physical Society 2024

Physics↗

DOE OSTI2024

Unified description of DGLAP, CSS, and BFKL evolution: TMD factorization bridging large and small x

This paper introduces a transverse-momentum dependent (TMD) factorization scheme designed to unify both large and small Bjorken-x regimes. We compute the next-to-leading order quantum chromodynamics (QCD) corrections to the gluon TMD operator for an unpolarized hadron within this proposed scheme. This leads to the emergence of a new TMD evolution, incorporating those in transverse momentum, rapidity, and Bjorken-x. When matched to the collinear factorization scheme, our factorization scheme faithfully reproduces the well-established Dokshitzer-Gribov-Lipatov-Altarelli-Parisi and Collins-Soper-Sterman (CSS) evolutions. Conversely, matching with high-energy factorization not only yields the Balitsky-Fadin-Kuraev-Lipatov evolution but also reveals distinctive signatures of CSS logarithms. The development of this novel TMD factorization scheme, capable of seamlessly reconciling disparate Bjorken-x regimes and faithfully reproducing established QCD evolution equations, has the potential to significantly advance our comprehension of high-energy processes and three-dimensional parton structures of hadrons. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Infrared-safe energy weighting does not guarantee small nonperturbative effects

Infrared and collinear (IRC) safety has long been used a proxy for robustness when developing new jet substructure observables. This guiding philosophy has been carried into the deep learning era, where IRC-safe neural networks have been used for many jet studies. For graph-based neural networks, the most straightforward way to achieve IRC safety is to weight particle inputs by their energies. However, energy-weighting by itself does not guarantee that perturbative calculations of machine-learned observables will enjoy small nonperturbative corrections. Here, in this paper, we demonstrate the sensitivity of IRC-safe networks to nonperturbative effects, by training an energy flow network (EFN) to maximize its sensitivity to hadronization. We then show how to construct Lipschitz energy flow networks (L-EFNs), which are both IRC safe and relatively insensitive to nonperturbative corrections. We demonstrate the performance of L-EFNs on generated samples of quark and gluon jets, and showcase fascinating differences between the learned latent representations of EFNs and L-EFNs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Detecting dark matter substructures on small scales with fast radio bursts

The matter power spectrum is only weakly constrained on subgalactic scales, while physics beyond the Standard Model can leave unique imprints, especially on sub-parsec scales. We propose measuring the arrival-time difference of fast radio bursts (FRBs) along two adjacent sightlines as a new probe to dark matter substructures on scales down to ∼ 1 AU . We discuss two observational scenarios in which it may be possible to place interesting constraints on such models through the monitoring of repeating FRB sources: (i) By sending radio receivers to space to form a baseline of tens of AU or more and measuring the temporal variation of the arrival-time difference between receivers. (ii) By measuring the temporal variation of the arrival-time difference between two lensed images of one strongly lensed repeater. In both scenarios, obtaining interesting constraints requires correlating the voltage time series to measure the radio signal arrival time to sub-nanosecond precision. We find that two radio dishes separated by 20 AU may be sensitive to the enhancement of small-scale structures at ∼ 10 - 8 M ⊙ masses in the QCD axion dark matter scenario, or from an early epoch of matter domination with a reheating temperature up to 60 MeV. Other dark matter models, such as those composed of ∼ 10 - 13 M ⊙ primordial black holes produced during inflation, would also be probed by this method. We further show that a strong lensing situation of multiple images provides an equivalent ∼ 2000 AU ( σ v / 10 3 km s - 1 ) ( δ t / 10 yr ) baseline, for a typical velocity of dark matter substructures σ v and an observational time span δ . This is much more sensitive, but with the uncertainty that intervening decoherence from the interstellar medium may degrade the timing precision, and that spatial variation in the FRB emission spot may result in confounding signals. We show that the lensing magnifications of Type Ia supernovae constrain a similar quantity to such FRB timing, with present limits being equivalent to ruling out the same parameter space that would be probed by a 0.14 AU baseline.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗