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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Habitat fragmentation alters the distance of abiotic seed dispersal through edge effects and direction of dispersal

Habitat loss and fragmentation are leading causes of species declines, driven in part by reduced dispersal. Isolating the effects of fragmentation on dispersal, however, is daunting because the consequences of fragmentation are typically intertwined, such as reduced connectivity and increased prevalence of edge effects. We used a large-scale landscape experiment to separate consequences of fragmentation on seed dispersal, considering both distance and direction of local dispersal. We evaluated seed dispersal for five wind- or gravity-dispersed, herbaceous plant species that were planted at different distances from habitat edges, within fragments that varied in their connectivity and shape (edge-to-area ratio). Dispersal distance was affected by proximity and direction relative to the nearest edge. For four of five species, dispersal distances were greater further from habitat edges and when seeds dispersed in the direction of the nearest edge. Connectivity and patch edge-to-area ratio had minimal effects on local dispersal. Here our findings illustrate how some, but not all, landscape changes associated with fragmentation can affect the key population process of seed dispersal.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Uncertainty quantification of bank vegetation impacts on the flood flow field in the American River, California, using large‐eddy simulations

Bank vegetation plays a key role in both hydrodynamics and morphodynamics of natural rivers; however, these effects are often unaccounted for in the computational flow dynamics of natural waterways. Recent studies using the large‐eddy simulation (LES), however, have attempted to gain insights into the impacts of bank vegetation on the mean flow field of the natural rivers using a vegetation model, which applies a sink term to the momentum equations of motion. This approach accounts for the effects of the vegetation and provides a practical approach to account for the complex patches of bank vegetation in large‐scale rivers. To implement the vegetation model, a drag coefficient reflecting the overall resistance of vegetal structures to the flow is needed, but due to the lack of calibrated data and range of size, density and type of vegetation, this parameter can be a significant source of uncertainty in the model results. Here, in this study, we use uncertainty quantification (UQ) to investigate the hydrodynamics and bed shear results when a bank vegetation is incorporated in an LES model. To this end, we used the polynomial chaos expansion and Monte Carlo sampling techniques to determine the uncertainties associated with the drag coefficient in the vegetation model and from uncertainties in the bed roughness and inflow discharge. The UQ analysis provided spatially varying confidence levels for the spanwise and vertical distribution of velocity magnitude and for the bed shear stress distributions. In addition, Sobol indices were computed to indicate the relative influence that each parameter had on the overall uncertainty. In general, it was found that uncertainty in flow discharge was the dominant source of uncertainty; however, the drag coefficient in the vegetation model and the bed roughness parameter also made significant contribution to the uncertainty near the banks and bed, respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A dynamic variational multiscale method on unstructured meshes for stationary transport problems

Here, this paper presents a variational multiscale (VMS) based finite element method where the stabilization parameter is computed dynamically. The current dynamic procedure takes in a general structure/form of the stabilization parameter with unknown coefficients and computes them dynamically in a local fashion resulting in a dynamic VMS-based finite element method. Thus, a static stabilization parameter with pre-defined coefficients is not needed. A variational Germano identity (VGI) based local procedure suitable for unstructured meshes is developed to perform the dynamic computation in a local fashion. The local VGI based procedure is applied for each interior vertex in the mesh and unknown coefficients are first determined locally at each vertex, and subsequently, for each element a maximum value is taken over the vertices of the element. To make the current procedure practical, a coarser secondary solution is constructed from the primary coarse-scale solution, which is done locally over a patch of elements around each interior vertex. Further, averaging steps are employed to make the local dynamic procedure robust. Currently, the new dynamic VMS formulation is applied to steady problems governed by the advection-diffusion and incompressible Navier-Stokes equations in both 1D and 2D to demonstrate its efficacy and effectiveness.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Abundance and Migration Success of Overshoot Steelhead in the Upper Columbia River

Abstract Summer steelhead Oncorhynchus mykiss may enter freshwater almost a year before spawning and potentially make long migrations (>1,000 km) to interior headwater habitats. However, in response to suboptimal freshwater habitat conditions (e.g., warmer water temperatures), adult summer steelhead may exhibit complex behaviors during upstream migration in the Columbia River basin. Steelhead may migrate upstream of their natal tributary (hereafter, referred to as “overshoot”) and spend days to several months before subsequently migrating downstream (hereafter, referred to as “fallback”) to their natal tributary to spawn. An expansion of an existing Bayesian patch occupancy model, derived from observations of adult steelhead that were PIT-tagged to estimate population-specific abundance upstream of the tagging location, incorporated downstream detection locations to estimate the abundance of overshoot fallbacks. Overshoot steelhead abundance at the tagging location was estimated based on the relationship between the number of known overshoot fallbacks (i.e., the number of steelhead that overshot and successfully migrated downstream to their natal tributary) and their model-estimated abundance. During the study period (2010–2017), the annual mean proportion of overshoot steelhead that successfully migrated downstream of the tagging location (Priest Rapids Dam) was 0.59 (SD = 0.14). The number of dams encountered by overshoot steelhead during their downstream migration was negatively correlated with their downstream migration success probability. Improved downstream passage survival for adult steelhead will increase the abundance of affected populations while reducing potential genetic introgression of upstream populations (i.e., strays). This is the first study to estimate the abundance of overshoot and fallback steelhead, providing the data necessary for scientists to estimate potential conservation benefits of improved downstream survival. For example, surface flow passage routes (e.g., sluiceways and temporary spillway weirs) are very effective in guiding and passing adult steelhead downstream of Columbia River hydroelectric projects and data from this assessment show that changes in dam operations throughout the downstream migration period may maximize conservation benefits.

Murdoch, Andrew R. (ORCID:0000000324827689)↗
DOE OSTI2021

Extending a 10‐node composite tetrahedral finite element for solid mechanics

Abstract We propose to extend the composite tetrahedral finite element first introduced by Thoutireddy et al. (2002) and recently reformulated by Ostien et al. (2016). We generalize the gradient operator and mass matrix to curved domains through analytical expressions weighted by subtetrahedra Jacobians. Optimal integration weights are constructed to increase the accuracy of Gaussian quadrature. We preserve the variational structure of the formulation through a new five‐field functional with additional, independent fields for the Jacobian and the pressure. This approach not only obviates volumetric locking but also yields symmetry. A deleterious soft mode, common to both the quadratic and composite tetrahedral element with constant pressure formulations is effectively stabilized through a novel convex energy penalty function. Numerous numerical examples spanning a patch test to the impact of a Taylor bar demonstrate the accuracy, robustness, and convergence of the extended composite tetrahedral element for application to structural metals.

Foulk III, James W.↗
DOE OSTI2023

Comparison of open‐source three‐dimensional reconstruction pipelines for maize‐root phenotyping

Abstract Understanding three‐dimensional (3D) root traits is essential to improve water uptake, increase nitrogen capture, and raise carbon sequestration from the atmosphere. However, quantifying 3D root traits by reconstructing 3D root models for deeper field‐grown roots remains a challenge due to the unknown tradeoff between 3D root‐model quality and 3D root‐trait accuracy. Therefore, we performed two computational experiments. We first compared the 3D model quality generated by five state‐of‐the‐art open‐source 3D model reconstruction pipelines on 12 contrasting genotypes of field‐grown maize roots. These pipelines included COLMAP, COLMAP+PMVS (Patch‐based Multi‐View Stereo), VisualSFM, Meshroom, and OpenMVG+MVE (Multi‐View Environment). The COLMAP pipeline achieved the best performance regarding 3D model quality versus computational time and image number needed. In the second test, we compared the accuracy of 3D root‐trait measurement generated by the Digital Imaging of Root Traits 3D pipeline (DIRT/3D) using COLMAP‐based 3D reconstruction with our current DIRT/3D pipeline that uses a VisualSFM‐based 3D reconstruction on the same dataset of 12 genotypes, with 5–10 replicates per genotype. The results revealed that (1) the average number of images needed to build a denser 3D model was reduced from 3000 to 3600 (DIRT/3D [VisualSFM‐based 3D reconstruction]) to around 360 for computational test 1, and around 600 for computational test 2 (DIRT/3D [COLMAP‐based 3D reconstruction]); (2) denser 3D models helped improve the accuracy of the 3D root‐trait measurement; (3) reducing the number of images can help resolve data storage problems. The updated DIRT/3D (COLMAP‐based 3D reconstruction) pipeline enables quicker image collection without compromising the accuracy of 3D root‐trait measurements.

09 BIOMASS FUELS↗
DOE OSTI2014

Structure and specificity of FEN-1 from Methanopyrus kandleri

DNA repair is fundamental to genome stability and is found in all three domains of life. However, many archaeal species, such as Methanopyrus kandleri, contain only a subset of the eukaryotic nucleotide excision repair (NER) homologues, and those present often contain significant differences compared to their eukaryotic homologues. To clarify the role of the NER XPG-like protein Mk0566 from M. kandleri, its biochemical activity and three dimensional structure were investigated. Ultimately, we found both to be more similar to human FEN-1 than human XPG, suggesting a biological role in replication and long-patch base excision repair rather than in NER.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262

The crystal structure of a fully glycosylated HIV-1 gp120 core in complex with CD4 receptor and Fab 17b at 4.5-Å resolution reveals 9 of the 15 N-linked glycans of core gp120 to be partially ordered. The glycan at position Asn262 had the most extensive and well-ordered electron density, and a GlcNAc 2 Man 7 was modeled. Lastly, the GlcNAc stem of this glycan is largely buried in a cleft in gp120, suggesting a role in gp120 folding and stability. Its arms interact with the stems of neighboring glycans from the oligomannose patch, which is a major target for broadly neutralizing antibodies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Growth Dynamics and Electron Reflectivity in Ultrathin Films of Chiral Heptahelicene on Metal (100) Surfaces Studied by Spin-Polarized Low Energy Electron Microscopy

Interaction of electrons with chiral matter gives rise to interesting phenomena such as the chirality-induced spin selectivity. The interdependence of reflectivity of spin-polarized low energy electrons and the absolute handedness of chiral molecules is investigated. First, the growth of homochiral films of helical aromatic hydrocarbons, so-called helicenes, on a Cu(100) surface is studied by means of low energy electron microscopy and scanning tunneling microscopy in ultrahigh vacuum. As soon as the coverage exceeds one monolayer, double-layer nucleation and growth is favored such that depletion in the first layer occurs. Spatially resolved work function measurements show that second-layer patches have a lower work function than first-layer areas. Reflectivity spectra of spin-polarized electrons do not show any asymmetry between homochiral films of the enantiomers. Laterally resolved work function measurements do not confirm work function differences such as those reported earlier for photoelectron studies of chiral peptide films on ferromagnetic substrates.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Towards Automated Assessment of Vulnerability Exposures in Security Operations

Current approaches for risk analysis of software vulnerabilities using manual assessment and numeric scoring do not complete fast enough to keep pace with the maintenance work rate to patch and mitigate the vulnerabilities. This paper proposes a new approach to modeling software vulnerability risk in the context of the network environment and firewall configuration. In the approach, vulnerability features are automatically matched up with networking, target asset, and adversary features to determine whether adversaries can exploit a vulnerability. The ability of adversaries to reach a vulnerability is modeled by automatically identifying the network services associated with vulnerabilities through a pipeline of machine learning and natural language processing and automatically analyzing network reachability. Our results show that the pipeline can identify network services accurately. We also find that only a small number of vulnerabilities pose real risks to a system. However, if left unmitigated, adversarial reach to vulnerabilities may extend to nullify the effect of firewall countermeasures.

Huff, Philip↗
DOE OSTI2024

De Sitter space is sometimes not empty

Multiple lines of evidence suggest that the Hilbert space of an isolated de Sitter universe is one dimensional but can appear larger when probed by a gravitating observer. To test this idea, we compute the von Neumann entropy of a field theory in a two-dimensional de Sitter universe which is entangled in a thermal-like state with the same field theory on a disjoint, asymptotically anti-de Sitter (AdS) black hole. Previously, it was shown that the replica trick for computing the entropy of such entangled gravitating systems requires the inclusion of a non-perturbative effect in quantum gravity — novel wormholes connecting the two spaces. Here we show that: (a) the expected wormholes connecting de Sitter and AdS universes exist, avoiding a no-go theorem via the presence of sources on the AdS boundary; (b) the entanglement entropy vanishes if the nominal entropy of the de Sitter cosmological horizon (S ds = $A^{dS}_{horizon}$/4G N ) is less than the entropy of the AdS black hole horizon (S BH = $A^{AdS}_{horizon}$/4G N ), i.e., S dS < S BH ; (c) the entanglement entropy is finite when S dS > S BH . Thus, the de Sitter Hilbert space is effectively nontrivial only when S dS > S BH . The AdS black hole we introduce can be regarded as an “observer” for de Sitter space. In this sense, our result is a non-perturbative generalization of the recent perturbative argument that the algebra of observables on the de Sitter static patch becomes nontrivial in the presence of an observer.

2D gravity↗
DOE OSTI2016

Revealing compressed stops using high-momentum recoils

In this study, searches for supersymmetric top quarks at the LHC have been making great progress in pushing sensitivity out to higher mass, but are famously plagued by gaps in coverage around lower-mass regions where the decay phase space is closing off. Within the common stop-NLSP/neutralino-LSP simplified model, the line in the mass plane where there is just enough phase space to produce an on-shell top quark remains almost completely unconstrained. Here, we show that is possible to define searches capable of probing a large patch of this difficult region, with S/B ~ 1 and significances often well beyond 5σ. The basic strategy is to leverage the large energy gain of LHC Run 2, leading to a sizable population of stop pair events recoiling against a hard jet. The recoil not only re-establishes a E T , but also leads to a distinctive anti-correlation between the E T and the recoil jet transverse vectors when the stops decay all-hadronically. Accounting for jet combinatorics, backgrounds, and imperfections in E T measurements, we estimate that Run 2 will already start to close the gap in exclusion sensitivity with the first few 10s of fb –1 . By 300 fb –1 , exclusion sensitivity may extend from stop masses of 550 GeV on the high side down to below 200 GeV on the low side, approaching the “stealth” point at m t¯ = m t and potentially overlapping with limits from tt¯ cross section and spin correlation measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Higgs and superparticle mass predictions from the landscape

Predictions for the scale of SUSY breaking from the string landscape go back at least a decade to the work of Denef and Douglas on the statistics of flux vacua. The assumption that an assortment of SUSY breaking F and D terms are present in the hidden sector, and their values are uniformly distributed in the landscape of D = 4, N = 1 effective supergravity models, leads to the expectation that the landscape pulls towards large values of soft terms favored by a power law behavior P(m soft )~m$n\atop{soft}$. On the other hand, similar to Weinberg’s prediction of the cosmological constant, one can assume an anthropic selection of weak scales not too far from the measured value characterized by mW,Z,h ~ 100 GeV. Working within a fertile patch of gravity-mediated low energy effective theories where the superpotential μ term is << m 3/2 , as occurs in models such as radiative breaking of Peccei-Quinn symmetry, this biases statistical distributions on the landscape by a cutoff on the parameter Δ EW , which measures fine-tuning in the m Z -μ mass relation. The combined effect of statistical and anthropic pulls turns out to favor low energy phenomenology that is more or less agnostic to UV physics. While a uniform selection n = 0 of soft terms produces too low a value for m h , taking n = 1 and 2 produce most probabilistically m h ~125 GeV for negative trilinear terms. For n ≥ 1, there is a pull towards split generations with m$\sim\atop{q}$,$\sim\atop{ℓ}$(1,2)~10-30 TeV whilst m$\sim\atop{t}$ 1 ~1-2 TeV. The most probable gluino mass comes in at ~ 3 - 4 TeV — apparently beyond the reach of HL-LHC (although the required quasi-degenerate higgsinos should still be within reach). We comment on consequences for SUSY collider and dark matter searches.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Characters, quasinormal modes, and Schwinger pairs in dS 2 with flux

An integral representation of the 1-loop partition function for charged scalars and spinors, minimally coupled to a uniform U(1) field on S 2 , is given in terms of SO(1, 2) Harish-Chandra group characters and evaluated exactly in terms of Hurwitz ζ-functions. Analytically continuing the U(1) field, we interpret the path integrals as quasicanonical partition functions in dS 2 with an electric field. The character itself is obtained as a trace over states living at the future boundary of de Sitter and has a quasinormal mode expansion. The imaginary part of the partition function captures Schwinger pair creation in the static patch at finite temperature. The thermal enhancement is most noticeable for scalar masses below Hubble and leads to non-monotonicity of the current as a function of the field. This parameter range, when dimensionally reducing from a charged or rotating Nariai spacetime, is excluded by Swampland-inspired bounds. Around the AdS 2 black hole, in contrast to dS 2 , there is a threshold to pair creation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

LHC SUSY and WIMP dark matter searches confront the string theory landscape

The string theory landscape of vacua solutions provides physicists with some understanding as to the magnitude of the cosmological constant. Similar reasoning can be applied to the magnitude of the soft SUSY breaking terms in supersymmetric models of particle physics: there appears to be a statistical draw towards large soft terms which is tempered by the anthropic requirement of the weak scale lying not too far from ~100 GeV. For a mild statistical draw of m softn with n = 1 (as expected from SUSY breaking due to a single F term) then the light Higgs mass is preferred at ~125 GeV while sparticles are all pulled beyond LHC bounds. We confront a variety of LHC and WIMP dark matter search limits with the statistical expectations from a fertile patch of string theory landscape. The end result is that LHC and WIMP dark matter detectors see exactly that which is expected from the landscape: a Standard Model-like Higgs boson of mass 125 GeV but as yet no sign of sparticles or WIMP dark matter. SUSY from the n = 1 landscape is most likely to emerge at LHC in the soft opposite-sign dilepton plus jet plus MET channel. Multi-ton noble liquid WIMP detectors should be able to completely explore the n = 1 landscape parameter space.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗