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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Do not forget the electrons: Extending moderately-sized nuclear networks for multidimensional hydrodynamic codes

Context.Nuclear networks are widely used coupled with hydrodynamical simulations of explosive scenarios to account for the change of nuclear species and energy generation rate due to nuclear reactions. In this way, there is a feedback mechanism between the hydrodynamical state and the nuclear processes. Unfortunately, the timescale of nuclear reactions is orders of magnitude smaller than the dynamical timescale that drives hydrodynamical simulations. Therefore, these nuclear networks are usually very small, reduced in most cases to a dozen elements, especially when simulations are carried out in more than one dimension. Aims.We present here an extended nuclear network, with 90 species, designed for being coupled with hydrodynamic simulations, which includes neutrons, protons, electrons, positrons, and the corresponding neutrino and anti-neutrino emission. This network is also coupled with temperature, making it extremely robust and, together with its size, unique of its kind. The inclusion of electron captures on free protons makes the network very appropriate for multidimensional studies of Type Ia supernova explosions, especially when the exploding object is a massive white dwarf. Methods.We perform several tests that are relevant to simulate explosive scenarios, such as Type Ia supernovae and core-collapse supernovae. We compare the results of the 90 nuclei network with a standardα-chain network with 14 elements to evaluate the differences in the energy generation rate. We also evaluate the relevance of including the electrons in the network in terms of generated yields and how it affects the pressure of a degenerate fluid such as that of white dwarfs. The results obtained with the 90-nuclei network have been verified with a much larger 2000-nuclei network built from REACLIB (WinNet), in terms of nuclear energy generation rate, pressure, and produced yields. Results.The results obtained with the proposed medium-sized network compare fairly well, to a few percent, with those computed withWinNetin scenarios reproducing the gross physical conditions of current Type Ia supernova explosion models. In those cases where the carbon and oxygen fuel ignites at high density, the high-temperature plateau typical of the nuclear statistical equilibrium regime is well defined and stable, allowing large integration time steps. We show that the inclusion of electron captures on free protons substantially improves the estimation of the electron fraction of the mixture. Therefore, the pressure is better determined than in networks where electron captures are excluded, which will ultimately lead to more reliable hydrodynamic models. Explosive combustion of helium at low density, occurring near the surface layer of a white dwarf, is also better described with the proposed network, which gives nuclear energy generation rates much closer toWinNetthan typical reduced alpha networks. Conclusions.A nuclear network withN= 90 species, including electrons, aimed at multidimensional calculations of supernova explosions is described and verified. The proposed network is suitable for the study of Type Ia supernova explosions because it provides better values of pressure and electron abundance than other existing networks with smaller or even a similar size but without including electron capture processes.

Astronomy & Astrophysics↗
DOE OSTI2025

Infalling ultra-faint dwarfs as emissaries of the Axiverse

Recent discoveries of ultra-faint dwarf galaxies (UFDs) infalling onto the Milky Way, namely Leo K & M at r ≃ 450 kpc, considerably strengthens the case that UFDs constitute a distinct galaxy class that is inherently smaller and fainter, and metal-poorer than the classical dwarf spheroidals (dSph). This distinction is at odds with the inherent continuity of galaxy halo masses formed under scale-free gravity for any standard dark-matter (DM) model. Here, we show that distinct galaxy classes do evolve in cosmological simulations of multiple light bosons representing the “Axiverse” proposal of string theory, where a discrete mass spectrum of axions is generically predicted to span many decades in mass. In this context, the observed UFD class we show corresponds to a relatively heavy boson of 3 × 10 −21 eV, including Leo K & M, whereas a lighter axion of 10 −22 eV comprises the bulk of DM in all larger galaxies including the dSphs. Although Leo M is larger in size than Leo K, we predict its velocity dispersion to be smaller ( ≃ 1.7 km/s) than that of Leo K ( ≃ 4.5 km/s) because of the inverse de Broglie scale dependence on momentum. This scenario can be definitively tested using millisecond pulsars close to the Galactic center, where the Compton frequencies of the heavy and light bosons imprint monotone timing residuals that may be detected by the Square Kilometre Array (SKA) on timescales of approximately one week and four months, respectively.

dark matter↗
DOE OSTI2026

ZTF SN Ia DR2 follow-up: Exploring the origin of the Type Ia supernova host galaxy step through Si II velocities

The relation between Type Ia supernovae (SNe Ia) and the stellar masses of their host galaxy is well documented. In particular, Hubble residuals display a distinct luminosity shift based on host mass. This is known as the mass step. This effect is widely used as an additional correction factor in the standardisation of SN Ia luminosities. We investigate the Hubble residuals and the mass step of normal SNe Ia in the context of Si IIλ6355 velocities based on 277 normal SNe Ia that are near their peak in the second data release (DR2) of the Zwicky Transient Facility (ZTF). We divided the sample into high-velocity (HV) and normal-velocity (NV) SNe Ia, separated at 12,000 km s −1 . This produced a sample of 70 HV and 207 NV objects. We then explored potential environment- and/or progenitor-related effects by investigating the Si IIλ6355 velocities with parameters such as the light-curve stretch x 1 , the colour c, and the host galaxy properties. Although we only find a marginal difference between the Hubble residuals of HV and NV SNe Ia, the NV mass step is 0.149 ± 0.024 mag (6.3σ). The HV mass step is smaller, 0.046 ± 0.041 mag (1.1σ), and is consistent with zero. The difference between the NV and HV mass steps is modest, at ∼2.2σ. Moreover, the clearest subtype difference appears for SNe in central regions (d DLR < 1), where NV SNe Ia show a large mass step, whereas HV SNe Ia are consistent with no step, yielding a difference of 3.1–3.6σ between NV and HV SNe Ia. We observe a host-colour step for both subtypes. NV SNe Ia show a step of 0.142 ± 0.024 mag (5.9σ), while HV SNe Ia show a step of 0.158 ± 0.042 mag (3.8σ), where the HV SNe Ia step appears to be larger, but the significance is lower because the sample size is smaller. Overall, the NV and HV colour steps are statistically consistent. HV SNe Ia also show modest (∼2.5–3σ) steps in certain subsets, such as those in outer regions (d DLR > 1), whereas NV SNe display stronger environmental trends. Our results indicate that NV SNe Ia appear to be more environmentally sensitive, particularly in central likely metal-rich and older regions, while HV SNe Ia show weaker and subset-dependent trends. This suggests that applying a universal mass-step correction might introduce biases, and that incorporating refined classifications and/or environment-dependent factors, such as the location within the host, might improve future cosmological analyses beyond the standard x 1 and c cuts.

supernovae: general↗
DOE OSTI2024

Efficient backward x-ray emission in a finite-length plasma irradiated by a laser pulse of picosecond duration

Motivated by experiments employing picosecond-long, kilojoule laser pulses, we examined x-ray emission in a finite-length underdense plasma irradiated by such a pulse using two-dimensional particle-in-cell simulations. We found that, in addition to the expected forward emission, the plasma also efficiently emits in the backward direction. Our simulations reveal that the backward emission occurs when the laser exits the plasma. The longitudinal plasma electric field generated by the laser at the density down-ramp turns around some of the laser-accelerated electrons and re-accelerates them in the backward direction. As the electrons collide with the laser, they emit hard x rays. The energy conversion efficiency is comparable to that for the forward emission, but the effective source size is smaller. We show that the picosecond laser duration is required for achieving a spatial overlap between the laser and the backward energetic electrons. At peak laser intensity of 1.4×1020 W/cm2, backward-emitted photons (energies above 100 keV and 10° divergence angle) account for 2×10−5 of the incident laser energy. This conversion efficiency is three times higher than that for similarly selected forward-emitted photons. The source size of the backward photons (5 μm) is three times smaller than the source size of the forward photons.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Ferro-ionic states and domains morphology in Hf x Zr 1–x O 2 nanoparticles

Unique polar properties of nanoscale hafnia-zirconia oxides (Hf x Zr 1–x O 2 ) are of great interest for condensed matter physics, nanophysics, and advanced applications. These properties are connected (at least partially) to the ionic–electronic and electrochemical phenomena at the surface, interfaces, and/or internal grain boundaries. Here, we calculated the phase diagrams, dielectric permittivity, spontaneous polar, and antipolar ordering, as well as the domain structure morphology in Hf x Zr 1–x O 2 nanoparticles covered by ionic–electronic charge originating from surface electrochemical adsorption. We revealed that the ferro-ionic coupling supports the polar long-range order in nanoscale Hf x Zr 1–x O 2 , induces, and/or enlarges the stability region of the labyrinthine domains toward smaller sizes and smaller environmental dielectric constant at low concentrations of the surface ions. The ferro-ionic coupling causes the transition to the single-domain ferro-ionic state at high concentrations of the surface ions. We predict that the labyrinthine domain states, being multiple-degenerated, may significantly affect the emergence of the negative differential capacitance state in the nanograined/nanocrystalline Hf x Zr 1–x O 2 films.

36 MATERIALS SCIENCE↗
DOE OSTI2025

The effect of composition on helium bubble nucleation in complex concentrated alloys

Molecular dynamics simulations of helium implantation have been performed in the MoNbTaTi complex concentrated alloy (CCA) to determine the impact of composition on helium clustering and bubble nucleation. It was found that compositions with lower interstitial atomic volume resulted in smaller cluster sizes, higher helium-to-vacancy ratios, and larger migration barriers. As the atomic volume decreases, it is harder to accommodate additional helium in the lattice and for helium to diffuse between interstitial sites, resulting in smaller cluster sizes. In particular, increasing molybdenum directly correlated with a decreased interstitial atomic volume and increased migration barrier. Niobium exhibited the opposite trend, where more niobium in the material resulted in larger interstitial atomic volumes and cluster sizes but lower migration barriers. The atomic volume was determined to be an indicator of the susceptibility of the material to helium bubble growth and could potentially be used as a metric to screen compositions for resistance to helium damage. In this way, properties such as available interstitial volumes could be used to screen materials more rapidly given the vast compositional space of CCAs.

McCarthy, Megan Jeanne [Sandia National Laboratori↗
DOE OSTI2025

A charged particle transport approximation for thick and thin plasmas

In this work, we will construct a simple method to be utilized in the interpretation of the properties of a thin plasma from a study of the transport of charged particles through it. We do so by first demonstrating how charged particle fluxes encode local plasma information in their spectra for sufficiently thick plasmas and then propose how to extend that analysis to the thin plasma limit where the extensive geometry cannot be neglected through arguments from scale separation. We provide a numerical treatment of the transport problem and demonstrate that it is in good agreement with the approximation we present. Finally, we utilize both the numerical solution and our novel approximation to study the impact of the extensive scale of the plasma on the yield and flux normalized high-energy neutron spectra resulting from the upscattering of charged fuel ions. Using this analysis, we show that (after controlling for fusion yield) for the same uniform densities and temperatures, larger plasmas have higher magnitude but softer reaction-in-flight (RIF) neutron spectra relative to smaller plasmas. This is because larger plasmas retain more knocked-on suprathermal ions within their bulk and can downscatter them to lower average energies, while smaller plasmas allow a larger fraction of high energy particles to “range out” of the system prior to substantial downscattering or inducing an RIF reaction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Electronic, magnetic, and structural properties of V2CoAl: Experimental and computational study

Here, we present results of combined experimental and computations study of V2CoAl, a Heusler alloy that exhibits nearly perfect spin-polarization. Our calculations indicate that this material maintains a high degree of spin-polarization (over 90%) in the wide range of lattice parameters, except at the largest considered unit cell volume. The magnetic alignment of V2CoAl is ferrimagnetic, due to the antialignment of the magnetic moments of vanadium atoms in their two sublattices. The calculated total magnetic moment per formula unit is nearly integer at the optimal lattice parameter and at the smaller volumes of the unit cell, but it deviated from the integer values as the unit cell expands. This is consistent with the calculated variation in the degree of spin polarization with lattice constant. The expected ferrimagnetic behavior has been observed in the arc-melted V2CoAl sample, with a Curie temperature of about 80 K. However, the saturation magnetization is significantly smaller than the theoretical prediction of ∼2 μB/f.u., most likely due to the observed B2-type atomic disorder. The samples exhibit metallic electron transport across the measurement range of 2 K to 300 K.

Kharel, Parashu (ORCID:0000000171330718)↗
DOE OSTI2025

The glass-ceiling convective regime and the origin and diversity of coronae on Venus

Venus and Earth are rocky planets of roughly the same size and bulk density, yet their surface volcanic and tectonic features appear substantially different. On Venus, the coexistence of large volcanic highlands—interpreted as the surface expression of long-lived mantle plumes—alongside coronae, smaller features thought to be caused by transient thermal diapirs, remains enigmatic. Using two-dimensional numerical models of mantle convection with sharp and broad mineral phase transitions for pyrolite, we show that both scales of upwellings can be generated in a stagnant lid planet with an interior temperature 250 to 400 K warmer than Earth’s. The smaller plumes originate from a ~600 km deep internal layer that exists as a consequence of the different sequence of mineral phase transitions that occur in warmer mantles less processed and differentiated by partial melting and volcanism. Future models that include melting will provide further tests of our hypothesis.

Science & Technology - Other Topics↗
DOE OSTI2025

FAST Irradiations, Postirradiation Examinations, and Modeling of U-Mo for Light Water Reactor Applications

Many next generation light water reactor (LWR) concepts, such as mobile small modular reactors, are seeking to use smaller core dimensions than conventional reactor types. Smaller reactor cores require an increase in fissile material to maintain reactivity. For non-proliferation purposes, enrichment increases are limited to less than 20% (high assay low enriched uranium, [HALEU]) and so higher uranium density fuels than UO 2 must be considered. To this end, uranium-molybdenum alloys were tested using the Fission Accelerated Steady-state Test (FAST) approach. The experiment test matrix is focused on identifying the temperature transition between low swelling and high fission gas retention to break away swelling and low fission gas retention. This paper documents the results of irradiation tests and post-irradiation examinations (PIE) including neutron radiography, rodlet profilometry, fission gas collection analysis, and optical metallography. The results of these tests showed that unconstrained U-Mo fuels (solid, Na-bonded rodlets) have a swelling threshold between 400-450°C with minimal fission gas release below this point. Higher temperature solid fuel showed microstructural zoning with small pore networks while lower temperature solid fuels have a uniform microstructure with large pore networks. U-Annular Mo fuels where swelling had some self-constraint imposed upon it, were shown to have much reduced swelling compared to their solid counterparts as well as very low fission gas release for irradiation temperatures up to 500°C. These initial results show that the use of U-Mo in constrained fuel geometries could be used as a high uranium density HALEU fuel for LWRs.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Performance of pumped counterflow virtual impactors to study aerosol interactions with laboratory generated warm clouds

Pumped Counterflow Virtual Impactors (PCVI) are designed to separate aerosols based on aerodynamic diameter, which is particularly useful for isolating cloud droplets and ice crystals from smaller particles. However, the PCVI transmission efficiency (TE) values reported in the literature show considerable variability, and little information is available on the TEs for cloud liquid droplets. Here, we determined the optimal flow conditions for PCVI sampling for different activation ratios from the MTU Pi-cloud chamber, highlighting the conditions that maximize droplet residual sampling while minimizing interstitial transmission. Even for a lower limit cloud activation ratio = 1:10, an add flow of 1.5 LPM achieves a residual fraction greater than 0.80, with a droplet TE of ∼15% for typical Pi-Chamber droplets with diameters between 3.5 to 10 µm. This framework can be adapted for field cloud measurements based on the cloud conditions of interest. TE for cloud droplets under flow conditions at which ∼99% of the unactivated submicron particles were removed was substantially lower between 8 and 16% than for supermicron dry particles (∼30 to 40% for 3 µm polystyrene latex spheres). In addition, we conducted a comparison of the performances of three similar PCVI units to assess repeatability for dry aerosols and cloud droplets. All three PCVIs performed similarly in rejecting submicron particles smaller than the desired cutoff diameter. One of the units showed lower TEs due to a misalignment of the internal orifice. We discuss a procedure that improved alignment and performance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Search for light long-lived particles decaying to displaced jets in proton–proton collisions at $\sqrt{s} = 13.6$ TeV

A search for light long-lived particles (LLPs) decaying to displaced jets is presented, using a data sample of proton–proton collisions at a center-of-mass energy of 13.6 TeV, corresponding to an integrated luminosity of 34.7 fb −1 , collected with the CMS detector at the CERN LHC in 2022. Novel trigger, reconstruction, and machine-learning techniques were developed for and employed in this search. After all selections, the observations are consistent with the background predictions. Limits are presented on the branching fraction of the Higgs boson to LLPs that subsequently decay to quark pairs or tau lepton pairs. An improvement by up to a factor of 10 is achieved over previous limits for models with LLP masses smaller than 60 GeV and proper decay lengths smaller than 1 m. The first constraints are placed on the fraternal twin Higgs (FTH) and folded supersymmetry (FSUSY) models, where the lower bounds on the top quark partner mass reach up to 350 GeV for the FTH model and 250 GeV for the FSUSY model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Suppressing the sample variance of DESI-like galaxy clustering with fast simulations

Ongoing and upcoming galaxy redshift surveys, such as the Dark Energy Spectroscopic Instrument (DESI) survey, will observe vast regions of sky and a wide range of redshifts. In order to model the observations and address various systematic uncertainties, N-body simulations are routinely adopted, however, the number of large simulations with sufficiently high mass resolution is usually limited by available computing time. Therefore, achieving a simulation volume with the effective statistical errors significantly smaller than those of the observations becomes prohibitively expensive. In this study, we apply the Convergence Acceleration by Regression and Pooling (CARPool) method to mitigate the sample variance of the DESI-like galaxy clustering in the AbacusSummit simulations, with the assistance of the quasi-N-body simulations FastPM. Based on the halo occupation distribution (HOD) models, we construct different FastPM galaxy catalogs, including the luminous red galaxies (LRGs), emission line galaxies (ELGs), and quasars, with their number densities and two-point clustering statistics well matched to those of AbacusSummit. We also employ the same initial conditions between AbacusSummit and FastPM to achieve high cross-correlation, as it is useful in effectively suppressing the variance. Our method of reducing noise in clustering is equivalent to performing a simulation with volume larger by a factor of 5 and 4 for LRGs and ELGs, respectively. We also mitigate the standard deviation of the LRG bispectrum with the triangular configurations k 2 = 2k 1 = 0.2 h Mpc -1 by a factor of 1.6. With smaller sample variance on galaxy clustering, we are able to constrain the baryon acoustic oscillations (BAO) scale parameters to higher precision. The CARPool method will be beneficial to better constrain the theoretical systematics of BAO, redshift space distortions (RSD) and primordial non-Gaussianity (NG).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Full calibration of the tomographic redshift distribution from the HSC PDR3 Shape Catalog with DESI

The calibration of tomographic redshift distributionsis essential for cosmological analysis of weak lensing data.In this work, we calibrate all four tomographic bins of the Hyper Suprime Camera (HSC) weak lensing catalog with the Dark Energy Spectroscopic Instrument (DESI) Data Release 1 and 2 using the clustering redshifts technique. We include z > 1.2 redshift sources such as emission line galaxies (ELG) and quasars (QSO) sources in our calibration, which were not available in the previous HSC calibration (Rau et al. (2022), Mon. Not. Roy. Astron. Soc. 524 (2023) 5109), allowing a complete calibration of all the redshift bins. We find the first tomographic bin exhibits a small shift towards low redshifts. The second bin is in good agreement with the photometric calibration, while third and fourth bin exhibit a shift towards higher redshifts. However, these shifts are considerably smaller than the shifts obtained in the HSC Year 3 cosmic shear analyses. We evaluate the impact of galaxy bias and magnification effects from all the samples on the measurements, finding them to be small, and we propose corrections to reduce them further. Specifically, we relax the assumption of linear bias and only assume no redshift evolution of the cross-correlation coefficient, allowing us to leverage smaller clustering scales. We model the redshift distributions with splines and compare our results to previous analyses as well as to other parameterizations found in literature. For the two high-redshift tomographic bins, we find the shifts to higher redshifts with respect to the measurements performed in Rau+2022 to be Δz$_{3}$ =-0.039$^{+0.020}$$_{-0.021}$ and Δz$_{4}$ = -0.048$^{+0.012}$$_{-0.012}$.

Choppin de Janvry, J. [LBL, Berkeley; UC, Berkeley↗
DOE OSTI2024

Simulation of triggering and evolution of ELM by pellet injection in EAST under BOUT++ framework

A BOUT ++ three-field magnetohydrodynamic model is employed to study the triggering and evolution of edge localized mode (ELM) by Li pellets injected along the outer mid-plane in the EAST configuration. The linear simulation shows that compared with a large deposition on the pedestal top (scenario I), a smaller deposition within the steep-gradient pedestal region (scenario II) can stimulate much larger linear growth rates of all-n peeling-ballooning modes (PBMs). The nonlinear simulation shows that there exists a pellet size threshold for ELM triggering for two deposition locations; the threshold for scenario I predicted in the present study matches the EAST observation well. Comparison of the two scenarios reveals that a smaller deposition is sufficient to trigger an ELM in a much shorter time in scenario II, whose ELM size is comparable to that in scenario I. This conclusion confirms previous DIII-D and ASDEX-Upgrade observations, suggesting that the steep-gradient pedestal region is a favorable deposition location for ELM triggering with minimum pellet size. Simulation analyses also find that the positive radial gradient of the hump-like pressure profile in the outer mid-plane induced by the pellet deposition plays a different role in the two scenarios. In scenario I, the force resulting from the gradient hinders the outflow of core plasmas and in return, the perturbation is suppressed from spreading inwards after ELM crashes. In scenario II, with a sizable deposition, the gradient results in another competitive perturbation growth region during the linear phase, thus dispersing the free energy and reducing the efficiency of destabilizing PBMs by pellet injection. The suppressing effect of saturated zonal flow on other modes, the short ELM fast crash phase, and the restricting transport effect of the positive radial pressure gradient work together to constrain the pedestal energy loss, especially when the pellet deposition amount is high.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Characterization of ELM pacing via vertical jogs on DIII-D

Edge localized mode (ELM) pacing via vertical plasma oscillations or jogging has been successfully demonstrated on DIII-D. Rapid vertical movement of the plasma toward the X-point has been shown to effectively trigger ELMs. By vertically oscillating the plasma at a rate of 10 Hz, the ELM frequency increased from ~5 Hz, the natural ELM frequency in similar DIII-D discharges, to 20 Hz. Downward jogs have been observed to trigger multiple ELMs in one cycle. ELMs triggered at higher than natural frequencies lead to smaller decreases in stored energy, from 8% to as little as below 1%. As a consequence, the peak heat flux to the divertor has been observed to be reduced by a factor of ~2. In addition, a reduction in the carbon impurity concentration has been observed. During downward jogs in the lower single null (LSN) configuration, the X-point movement is slower and smaller than the top of the plasma. As a result, a reduction in the plasma cross-section and hence volume has been observed. To understand the mechanism of ELM triggering by jogging, a toy model of the edge toroidal current has been built and tested with DIII-D experiment data. The experimental data and model suggest that when the plasma moves down toward the X-point, a net positive toroidal current is locally induced in the edge region. ELITE stability analysis suggests that this current pushes the plasma state across the peeling side of the peeling–ballooning stability boundary into the unstable region triggering ELMs.

ELM pacing↗
DOE OSTI2025

A haplotype-resolved reference genome for Eucalyptus grandis

Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70-90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.

Lötter, Anneri↗
DOE OSTI2024

The Interplay of Binary and Quantitative Structure on the Stability of Mutualistic Networks

Synopsis Understanding how the structure of biological systems impacts their resilience (broadly defined) is a recurring question across multiple levels of biological organization. In ecology, considerable effort has been devoted to understanding how the structure of interactions between species in ecological networks is linked to different broad resilience outcomes, especially local stability. Still, nearly all of that work has focused on interaction structure in presence-absence terms and has not investigated quantitative structure, i.e., the arrangement of interaction strengths in ecological networks. We investigated how the interplay between binary and quantitative structure impacts stability in mutualistic interaction networks (those in which species interactions are mutually beneficial), using community matrix approaches. We additionally examined the effects of network complexity and within-guild competition for context. In terms of structure, we focused on understanding the stability impacts of nestedness, a structure in which more-specialized species interact with smaller subsets of the same species that more-generalized species interact with. Most mutualistic networks in nature display binary nestedness, which is puzzling because both binary and quantitative nestedness are known to be destabilizing on their own. We found that quantitative network structure has important consequences for local stability. In more-complex networks, binary-nested structures were the most stable configurations, depending on the quantitative structures, but which quantitative structure was stabilizing depended on network complexity and competitive context. As complexity increases and in the absence of within-guild competition, the most stable configurations have a nested binary structure with a complementary (i.e., anti-nested) quantitative structure. In the presence of within-guild competition, however, the most stable networks are those with a nested binary structure and a nested quantitative structure. In other words, the impact of interaction overlap on community persistence is dependent on the competitive context. These results help to explain the prevalence of binary-nested structures in nature and underscore the need for future empirical work on quantitative structure.

Zoology↗