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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Good and proper: self-similarity of N -body simulations with proper force softening

ABSTRACT Analysis of self-similarity in scale-free N-body simulations reveals the spatial and temporal scales for which statistics measured in cosmological simulations are converged to the physical continuum limit. We examine how the range of scales in which the two-point correlation function is converged depends on the force softening length and whether it is held constant in comoving or proper coordinates. We find that a proper softening that reaches roughly 1/30th of the inter-particle spacing by the end of the simulation resolves the same spatial and temporal scales as a comoving softening of the same length while using a third fewer time-steps, for a range of scale factors typical to Lambda cold dark matter (ΛCDM) simulations. We additionally infer an inherent resolution limit, set by the particle mass and scaling as a−1/2, beyond which reducing the softening does not improve the resolution. We postulate a mapping of these results with spectral index n = −2 to ΛCDM simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding of plant NLR structure and function is limited to the evolutionarily young flowering plant clade. Here, we describe an extended spectrum of NLR diversity across divergent plant lineages and demonstrate the structural and functional similarities of N-terminal domains that trigger immune responses. We show that the broadly distributed coiled-coil (CC) and toll/interleukin-1 receptor (TIR) domain families of nonflowering plants retain immune-related functions through translineage activation of cell death in the angiosperm Nicotiana benthamiana. We further examined a CC subfamily specific to nonflowering lineages and uncovered an essential N-terminal MAEPL motif that is functionally comparable with motifs in resistosome-forming CC-NLRs. Consistent with a conserved role in immunity, the ectopic activation of CC MAEPL in the nonflowering liverwort Marchantia polymorpha led to profound growth inhibition, defense gene activation, and signatures of cell death. Moreover, comparative transcriptomic analyses of CC MAEPL activity delineated a common CC-mediated immune program shared across evolutionarily divergent nonflowering and flowering plants. Collectively, our findings highlight the ancestral nature of NLR-mediated immunity during plant evolution that dates its origin to at least ~500 million years ago.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Computational schemes for the Magnus expansion of the in-medium similarity renormalization group

The in-medium similarity renormalization group (IMSRG) is a popular many-body method used for computations of nuclei. It solves the many-body Schrödinger equation through a continuous unitary transformation of the many-body Hamiltonian. The IMSRG transformation is typically truncated at the normal-ordered two-body level, the IMSRG(2), but recently several approaches have been developed to capture the effects of normal-ordered three-body operators, the IMSRG(3). In particular, a factorized approximation to the IMSRG(3) proposes to capture the leading effects of three-body operators at the same computational cost as the IMSRG(2) approximation. This approach often employs an approximate scheme for solving the IMSRG equations, the so-called hunter-gatherer scheme. In this work, I study the uncertainty associated with this scheme. I find that the hunter-gatherer scheme differs by up to 7MeV for ground-state energies and 0.5MeV for excitation energies from standard IMSRG(2) approaches. These differences are in some cases comparable to the expected size of IMSRG(3) corrections.

39 ≤ A ≤ 58↗
DOE OSTI2020

Similarities and differences between nickelate and cuprate films grown on a SrTiO 3 substrate

The recent discovery of superconductivity in Sr-doped NdNiO 2 films grown on SrTiO 3 started a novel field within unconventional superconductivity. Therefore, to understand the similarities and differences between nickelate and cuprate layers on the same SrTiO 3 substrate, here based on the density functional theory we have systematically investigated the structural, electronic, and magnetic properties of NdNiO 2 / SrTiO 3 and CaCuO 2 / SrTiO 3 systems. Our results revealed a strong lattice reconstruction in the case of NdNiO 2 / SrTiO 3 , resulting in a polar film, with the surface and interfacial NiO 2 layers presenting opposite displacements. To avoid the “polar catastrophe,” the NiO 2 surface to the vacuum reconstructs as well. However, for CaCuO 2 / SrTiO 3 , the distortions of those same two CuO 2 layers were in the same direction. In addition, we found this distortion to be approximately independent of the studied range of film thickness for the nickelate films. Furthermore, we also observed a two-dimensional electron gas at the interface between NdNiO 2 and SrTiO 3 , caused by the polar discontinuity, in agreement with recent literature. For NdNiO 2 / SrTiO 3 the two-dimensional electron gas extends over several layers, while for CaCuO 2 / SrTiO 3 this electronic rearrangement is very localized at the interface between CaCuO 2 and SrTiO 3 . The electronic reconstruction found at the interface involves a strong occupation of the Ti 3 d x y state. In both cases, there is a significant electronic charge transfer from the surface Ni or Cu layers to the Ti interface layer. The interfacial Ni and Cu layers are hole and electron doped, respectively. By introducing magnetism and electronic correlation, we observed that the d 3 z 2 - r 2 orbital of Ni becomes itinerant while the same orbital for Cu remains doubly occupied, establishing a clear two- vs one-orbital active framework for the description of these systems. Furthermore, we also observed a strong magnetic reconstruction at the NdNiO 2 surface to vacuum layer where magnetism is basically suppressed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Operator evolution from the similarity renormalization group and the Magnus expansion

The Magnus expansion is an efficient alternative to solving similarity renormalization group (SRG) flow equations with high-order, memory-intensive ordinary differential equation solvers. The numerical simplifications it offers for operator evolution are particularly valuable for in-medium SRG calculations, though challenges remain for difficult problems involving intruder states. Here we test the Magnus approach in an analogous but more accessible situation, which is the free-space SRG treatment of the spurious bound states arising from a leading-order chiral effective field theory (EFT) potential with very high cutoffs. In this work, we show that the Magnus expansion passes these tests and then use the investigations as a springboard to address various aspects of operator evolution that have renewed relevance in the context of the scale and scheme dependence of nuclear processes. These aspects include SRG operator flow with band- versus block-diagonal generators, universality for chiral EFT Hamiltonians and associated operators with different regularization schemes, and the impact of factorization arising from scale separation. Implications for short-range correlations physics and the possibilities for reconciling high- and low-resolution treatments of nuclear structure and reactions are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Comparative study of He 6 β -decay based on different similarity-renormalization-group evolved chiral interactions

We report on a study of the Gamow-Teller matrix element contributing to ${}^6$He $\beta$-decay with similarity renormalization group (SRG) versions of momentum- and configuration-space two-nucleon interactions. These interactions are derived from two different formulations of chiral effective field theory ($\chi$EFT) -- without and with the explicit inclusion of $\Delta$-isobars. We consider evolution parameters $\Lambda_{\rm SRG}$ in the range between 1.2 and 2.0 fm$^{-1}$ and, for the $\Delta$-less case, also the unevolved (bare) interaction. The axial current contains one- and two-body terms, consistently derived at tree level (no loops) in the two distinct $\chi$EFT formulations we have adopted here. The ${}^6$He and ${}^6$Li ground-state wave functions are obtained from hyperspherical-harmonics (HH) solutions of the nuclear many-body problem. In $A\,$=$\,6$ systems, the HH method is limited at present to treat only two-body interactions and non-SRG evolved currents. Our results exhibit a significant dependence on $\Lambda_{\text{SRG}}$ of the contributions associated with two-body currents, suggesting that a consistent SRG-evolution of these is needed in order to obtain reliable estimates. We also show that the contributions from one-pion-exchange currents depend strongly on the model (chiral) interactions and on the momentum- or configuration-space cutoffs used to regularize them. These results might prove helpful in clarifying the origin of the sign difference recently found in No-Core-Shell-Model and Quantum Monte Carlo calculations of the ${}^6$He Gamow-Teller matrix element.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Singular value decomposition and similarity renormalization group evolution of nuclear interactions

One of the main challenges for ab initio nuclear many-body theory is the growth of computational and storage costs as calculations are extended to heavy, exotic, and structurally complex nuclei. Here, we investigate the factorization of nuclear interactions as a means to address this issue. We perform Singular Value Decompositions of nucleon-nucleon interactions in partial wave representation and study the dependence of the singular value spectrum on interaction characteristics like regularization scheme and resolution scales. We develop and implement the Similarity Renormalization Group (SRG) evolution of the factorized interaction, and demonstrate that this SVD-SRG approach accurately preserves two-nucleon observables. We find that low-resolution interactions allow the truncation of the SVD at low rank, and that a small number of relevant components is sufficient to capture the nuclear interaction and perform an accurate SRG evolution, while the Coulomb interaction requires special consideration. The rank is uniform across all partial waves, and almost independent of the basis choice in the tested cases. This suggests an interpretation of the relevant singular components as mere representations of a small set of abstract operators that can describe the interaction and its SRG flow. Following the traditional workflow for nuclear interactions, we discuss how the transformation between the center-of-mass and laboratory frames creates redundant copies of the partial wave components when implemented in matrix representation, and we discuss strategies for mitigation. Lastly, we test the low-rank approximation to the SRG-evolved interactions in many-body calculations using the In-Medium SRG. By including nuclear radii in our analysis, we verify that the implementation of the SRG using the singular vectors of the interaction does not spoil the evolution of other observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Systematics of E 2 strength in the s d shell with the valence-space in-medium similarity renormalization group

Recent developments in ab initio nuclear theory demonstrate promising results in medium- to heavy-mass nuclei. A particular challenge for many of the many-body methodologies, however, is an accurate treatment of the electric-quadrupole, E2, strength associated with collectivity. The valence-space in-medium similarity renormalization group (VS-IMSRG) is a particularly powerful method for accessing medium- and high-mass nuclei but has been found to underpredict E2 strengths. The purpose of this work is to evaluate the isospin dependence of this underprediction. We perform a systematic comparison of VS-IMSRG calculations with available literature. We make use of isoscalar and isovector contributions to the E2 matrix elements to assess isoscalar and isovector contributions to the missing strength. It is found that the E2 strength is consistent throughout T z =|12|, T z =|1|, T z =|32|, and T z =2 pairs within the sd shell. Furthermore, no isovector contribution to the deficiency is identified. A comparison with toy-models and coupled-cluster calculations is used to discuss potential origins of the missing strength, which arises from missing many-particle, many-hole excitations out of the model space. The absence of any significant isovector contribution to the missing E2 strength indicates that the E2 strength discrepancy, and therefore any correction, is largely independent of the isospin of the nuclei in question.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

In-medium similarity renormalization group with flowing 3-body operators, and approximations thereof

Here, we explore the impact of retaining three-body operators within the in-medium similarity renormalization group (IMSRG), as well as various approximations schemes. After studying two toy problems, identical fermions with a contact interaction and the Lipkin-Meshkov-Glick model, we employ the valence-space formulation of the IMSRG to investigate the even- A carbon isotopes with a chiral two-body potential. We find that retaining only those commutators expressions that scale as N 7 provides an excellent approximation of the full three-body treatment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Evidence for Similar Collectivity of High Transverse-Momentum Particles in 𝑝-Pb and Pb-Pb Collisions

Charged hadron elliptic anisotropies (𝑣 2 ) are presented over a wide transverse momentum (𝑝 T ) range for proton-lead (𝑝 ⁢Pb) and lead-lead (PbPb) collisions at nucleon-nucleon center-of-mass energies of 8.16 and 5.02 TeV, respectively. The data were recorded by the CMS experiment and correspond to integrated luminosities of 186 and 0.607 nb −1 for the 𝑝⁢Pb and PbPb systems, respectively. A four-particle cumulant analysis is performed using subevents separated in pseudorapidity to effectively suppress noncollective effects. At high 𝑝 T (𝑝 T > 8 GeV), significant positive 𝑣 2 values that are similar between 𝑝 ⁢Pb and PbPb collisions at comparable charged particle multiplicities are observed. This observation suggests a common origin for the multiparticle collectivity for high-𝑝 T particles in the two systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Scalar flux transport models for self-similar turbulent mixing

A common approach to closing turbulent species flux in multicomponent Reynolds-averaged Navier-Stokes models is to use the standard gradient diffusion approximation. While such an approach has been shown to work well when applied to many canonical turbulent mixing configurations, a gradient diffusion approach is fundamentally limited in its ability to capture complex phenomena such as countergradient transport. For this reason, complicated mixing applications may benefit by treating the turbulent diffusivity with a model transport equation in a manner analogous to second-moment momentum closure in Reynolds-stress transport models. Here, the present work explores the development and application of two different scalar flux transport (SFT) models. Self-similarity constraints are derived for these models, and they are evaluated against gradient-diffusion-based models in several one- and two-dimensional problems of turbulent mixing. It is found that the new SFT models out-perform gradient diffusion models in problems involving rapid acceleration reversal and in problems involving anisotropic transport of materials. In addition, it is found that even a hybrid-SFT approach, in which an SFT equation is utilized along with a gradient diffusion closure, provides some measure of improvement over models that transport the mass flux rather than the scalar flux.

Reynolds-averaged Navier Stokes↗
DOE OSTI2023

Approximating lattice similarity

A method is proposed for choosing unit cells for a group of crystals so that they all appear as nearly similar as possible to a selected cell. Related unit cells with varying cell parameters or indexed with different lattice centering can be accommodated.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Genomic region associated with run timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Abstract Conserving life‐history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early‐ and late‐migrating forms of Chinook salmon ( Oncorhynchus tshawytscha ) face unequal pressure from natural and anthropogenic forces that may alter the impacts of genetic variation underlying heritable migration timing. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among diverse lineages and populations in large basins such as the Columbia River. With high‐throughput genotyping (GT‐seq) and phenotyping methods, we examined the association of genetic variation in 28 markers (spanning GREB1L to ROCK1 of chromosome 28) with individual adult migration timing characteristics gleaned from passive integrated transponder recordings of over 5000 Chinook salmon from the three major phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them in putatively neutral genomic regions, each of the three lineages exhibited very similar genetic variants in the chromosome 28 region that were significantly associated with adult migration timing phenotypes. This is particularly notable for the interior stream‐type lineage, which exhibits an earlier and more constrained freshwater entry than the other lineages. In both interior stream‐type and interior ocean‐type lineages of Chinook salmon, heterozygotes of the most strongly associated linkage groups had largely intermediate migration timing relative to homozygotes, and results indicate codominance or possibly marginal partial dominance of the allele associated with early migration. Our results lend support to utilization of chromosome 28 variation in tracking and predicting run timing in these lineages of Chinook salmon in the Columbia River.

Willis, Stuart C.↗
DOE OSTI2025

Extending tetrahedral network similarity to carbon: A type-I carbon clathrate stabilized by boron

Clathrates are guest/host framework compounds composed of polyhedral cages, yet despite their prevalence among tetrahedral network formers, clathrates with a carbon host lattice remain unrealized synthetic targets. Here, we report a type-I carbon-based framework—a ubiquitous clathrate structure type found throughout compounds containing tetrahedral building blocks. Following a boron-stabilization scheme based on first-principles predictions in the Ca–B–C system at high pressure, type-I Ca 8 B x C 46−x (x ≈ 9) was synthesized in the archetypal $Pm\bar{3}n$ lattice with stability derived from substitutionally disordered boron atoms on hexagonal ring framework positions. The synthesized clathrate, which is recoverable to ambient conditions, expands topological network similarity across tetrahedral systems and opens possibilities for a broad family of diamond-like, carbon-based compounds with tunable properties based on the wide potential for guest/host-atom substitutions and framework versatility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Many paths, similar destinations: viruses and bacterial microcompartments form polyhedra inside cells

A large number of biological entities assemble into icosahedral structures, and these are ubiquitous throughout nature. Examples include eukaryotic and prokaryotic viral capsids and more recently discovered bacterial microcompartments. Viral capsids and bacterial microcompartments are both composed of pentameric and hexameric subunits; however, they differ in the type of cargo they encapsulate: nucleic acid or protein. Also, both depart from strict icosahedral symmetry: while this is less common in viruses, among bacterial microcompartments, diverse and heterogeneous polyhedra are common. We review shared principles and key distinctions between the self-directed assembly of various icosahedral architectures and their polyhedral variants in nature and explore the concept that there are multiple paths, influenced by their cargo, to arriving at similar protein cage morphologies.

bacterial microcompartments↗
DOE OSTI2020

Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fast Sparse-Vector Cosine Similarity in Go

This software provides a fast way to perform efficient sparse matrix multiplication followed by top-n multiplication result selection. Functionality for performing matrix multiplication / cosine similarity separately is included in this package as well. This package is a pure Go port of a Python package developed by ING Bank (https://github.com/ing-bank/sparse_dot_topn) which uses Cython to execute the matrix multiplication in C++. Instructions for compiling bindings which can be called from Python are included with this package as well.

Shivers, Ryan [Oak Ridge National Lab. (ORNL), Oak↗
DOE OSTI2024

Using Signal Clustering Similarity for Detecting CAN Masquerade Attacks

The computer code assumes that time series representing the physical signals of the vehicle have been extracted from the CAN bus. The main input of the computer code is the multivariate time series representation of the signals in the CAN bus. The computer code cluster these time series using agglomerative hierarchical clustering from benign and attack datasets. Based on this, it generates probability distributions from the similarity of the obtained clusters based in each scenario---benign and attack---using the CluSim method (https://github.com/Hoosier-Clusters/clusim). Finally, it compares how a new data collection compares with the previous distribution to provide and probability score for an intrusion.

Moriano, Pablo↗