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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2026

Physical instabilities and the phase of the Euclidean path integral

We compute the phase of the Euclidean gravity partition function on manifolds of the form S p × M q . We find that the total phase is equal to the phase in pure gravity on S p times an extra phase that arises from negative mass squared fields that we obtain when we perform a Kaluza-Klein reduction to S p . The latter can be matched to the phase expected for physical negative modes seen by a static path observer in dS p . In the case of S p × S q the answer can be interpreted in terms of a computation in the static patch of dS p or dS q . We also provide the phase when we have a product of many spheres. We clarify the procedure for determining the precise phase factor. We discuss some aspects of the interpretation of this phase.

Models of Quantum Gravity↗
DOE OSTI2020

De Sitter diagrammar and the resummation of time

Light scalars in inflationary spacetimes suffer from logarithmic infrared divergences at every order in perturbation theory. This corresponds to the scalar field values in different Hubble patches undergoing a random walk of quantum fluctuations, leading to a simple toy “landscape” on superhorizon scales, in which we can explore questions relevant to eternal inflation. However, for a sufficiently long period of inflation, the infrared divergences appear to spoil computability. Some form of renormalization group approach is thus motivated to resum the log divergences of conformal time. Such a resummation may provide insight into De Sitter holography. We present here a novel diagrammatic analysis of these infrared divergences and their resummation. Basic graph theory observations and momen- tum power counting for the in-in propagators allow a simple and insightful determination of the leading-log contributions. One thus sees diagrammatically how the superhorizon sector consists of a semiclassical theory with quantum noise evolved by a first-order, interacting classical equation of motion. This rigorously leads to the “Stochastic Inflation” ansatz developed by Starobinsky to cure the scalar infrared pathology nonperturbatively. Our approach is a controlled approximation of the underlying quantum field theory and is systematically improvable.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Entanglement in De Sitter space

This paper expands on two recent proposals and, for generalizing the Ryu-Takayanagi and Hubeny-Rangamani-Takayanagi formulas to de Sitter space. The proposals (called the monolayer and bilayer proposals) are similar; both replace the boundary of AdS by the boundaries of static-patches — in other words event horizons. After stating the rules for each, we apply them to a number of cases and show that they yield results expected on other grounds. The monolayer and bilayer proposals often give the same results, but in one particular situation they disagree. To definitively decide between them we need to understand more about the nature of the thermodynamic limit of holographic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗