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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 1,657 records · Page 92
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Tree-based solvers for adaptive mesh refinement code FLASH – III: a novel scheme for radiation pressure on dust and gas and radiative transfer from diffuse sources

Radiation is an important contributor to the energetics of the interstellar medium, yet its transport is difficult to solve numerically. We present a novel approach towards solving radiative transfer of diffuse sources via backwards ray tracing. Here, we focus on the radiative transfer of infrared radiation and the radiation pressure on dust. The new module, TREERAY/RADPRESSURE, is an extension to the novel radiative transfer method TREERAY implemented in the grid-based Magneto-Hydrodynamics code FLASH. In TREERAY/RADPRESSURE, every cell and every star particle is a source of infrared radiation. We also describe how gas, dust, and radiation are coupled via a chemical network. This allows us to compute the local dust temperature in thermal equilibrium, leading to a significantly improvement over the classical grey approximation. In several tests, we demonstrate that the scheme produces the correct radiative intensities as well as the correct momentum input by radiation pressure. Subsequently, we apply our new scheme to model massive star formation from a collapsing, turbulent core of 150 M ⊙ . We include the effects of both, ionizing and infrared radiation on the dynamics of the core. We find that the newborn massive star prevents fragmentation in its proximity due to radiative heating. Over time, dust and radiation temperature equalize, while the gas temperature can be either warmer due to shock heating or colder due to insufficient dust–gas coupling. Compared to gravity, the effects of radiation pressure are insignificant for the stellar mass on the simulated time-scale in this work.

(ISM:) HII regions↗
DOE OSTI2024

guppy i : a code for reducing the storage requirements of cosmological simulations

ABSTRACT As cosmological simulations have grown in size, the permanent storage requirements of their particle data have also grown. Even modest simulations present a major logistical challenge for the groups which run these boxes and researchers without access to high performance computing facilities often need to restrict their analysis to lower quality data. In this paper, we present guppy, a compression algorithm and code base tailored to reduce the sizes of dark matter-only cosmological simulations by approximately an order of magnitude. guppy is a ‘lossy’ algorithm, meaning that it injects a small amount of controlled and uncorrelated noise into particle properties. We perform extensive tests on the impact that this noise has on the internal structure of dark matter haloes, and identify conservative accuracy limits which ensure that compression has no practical impact on single-snapshot halo properties, profiles, and abundances. We also release functional prototype libraries in C, Python, and Go for reading and creating guppy data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution

Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Mechanism of efficient double-strand break repair by a long non-coding RNA

Mechanistic studies in DNA repair have focused on roles of multi-protein DNA complexes, so how long non-coding RNAs (lncRNAs) regulate DNA repair is less well understood. Yet, lncRNA LINP1 is over-expressed in multiple cancers and confers resistance to ionizing radiation and chemotherapeutic drugs. Here, we unveil structural and mechanistic insights into LINP1’s ability to facilitate non-homologous end joining (NHEJ). We characterized LINP1 structure and flexibility and analyzed interactions with the NHEJ factor Ku70/Ku80 (Ku) and Ku complexes that direct NHEJ. LINP1 self-assembles into phase-separated condensates via RNA–RNA interactions that reorganize to form filamentous Ku-containing aggregates. Structured motifs in LINP1 bind Ku, promoting Ku multimerization and stabilization of the initial synaptic event for NHEJ. Significantly, LINP1 acts as an effective proxy for PAXX. Collective results reveal how lncRNA effectively replaces a DNA repair protein for efficient NHEJ with implications for development of resistance to cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

RNAcentral: A comprehensive database of non-coding RNA sequences

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. Furthermore, the website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

RNAcentral: a hub of information for non-coding RNA sequences

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality.

Sweeney, Blake A.↗
DOE OSTI2025

Outflowing photoionized plasma in Circinus X-1 using the high-resolution X-ray spectrometer Resolve onboard XRISM and the radiative transfer code cloudy

High-resolution X-ray spectroscopy is a key to understanding the mass inflow and outflow of compact objects. Spectral lines carry information about the ionization, density, and velocity structures through their intensity ratios and profiles. They are formed in non-local thermodynamic equilibrium conditions under the intense radiation field from the compact objects; thus radiative transfer (RT) calculation is a requisite for proper interpretations. We present such a study for a low-mass X-ray binary, Circinus X-1, from which the P Cygni profile was discovered using the X-ray grating spectrometer onboard Chandra. We observed the source using the X-ray microcalorimeter onboard XRISM at an orbital phase of 0.93–0.97 and revealed many spectral features unidentified before: the higher series transitions ($n{\rightarrow }1$; $n>2$) of highly ionized (H- and He-like) S, Ca, Ar, and Fe in emission and absorption, the Fe K$\alpha$ and K$\beta$ inner-shell excitation absorption of mildly ionized (O- to Li-like) Fe, and resolved fine-structure level transitions in the Fe Ly$\alpha$ and He$\alpha$ complexes. They blend with each other at different velocity shifts on top of apparently variable continuum emission that changed its flux by an order of magnitude within a 70 ks telescope time. Despite such complexity in the observed spectra, most of them can be explained by a simple model consisting of the photoionized plasma outflowing at $\sim$300 km s$^{-1}$ and the variable blocking material in the line of sight of the incident continuum emission from the accretion disk. We demonstrate this with the aid of the RT code cloudy for the line ratio diagnostics and spectral fitting. We further constrain the physical parameters of the outflow and argue that the outflow is launched close to the outer edge of the accretion disk and can be driven radiatively by being assisted by the line force calculated using the RT simulation.

X-rays: binaries↗
DOE OSTI2024

tonalli : an asexual genetic code to characterize APOGEE-2 stellar spectra. I. Validation with synthetic and solar spectra

ABSTRACT We present tonalli, a spectroscopic analysis python code that efficiently predicts effective temperature, stellar surface gravity, metallicity, $\alpha$-element abundance, and rotational and radial velocities for stars with effective temperatures between 3200 and 6250 K, observed with the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2). tonalli implements an asexual genetic algorithm to optimize the finding of the best comparison between a target spectrum and the continuum-normalized synthetic spectra library from the Model Atmospheres with a Radiative and Convective Scheme (MARCS), which is interpolated in each generation. Using simulated observed spectra and the APOGEE-2 solar spectrum of Vesta, we study the performance, limitations, accuracy, and precision of our tool. Finally, a Monte Carlo realization was implemented to estimate the uncertainties of each derived stellar parameter.

Adame, Lucía (ORCID:0000000263286099)↗
DOE OSTI2015

International code of nomenclature of prokaryotes

Here, this volume contains the edition of the International Code of Nomenclature of Prokaryotes that was presented in draft form and available for comment at the Plenary Session of the Fourteenth International Congress of Bacteriology and Applied Microbiology (BAM), Montréal, 2014, together with updated lists of conserved and rejected bacterial names and of Opinions issued by the Judicial Commission. As in the past it brings together those changes accepted, published and documented by the ICSP and the Judicial Commission since the last revision was published. Several new appendices have been added to this edition. Appendix 11 addresses the appropriate application of the Candidatus concept, Appendix 12 contains the history of the van Niel Prize, and Appendix 13 contains the summaries of Congresses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evidence for deconfined U(1) gauge theory at the transition between toric code and double semion

Building on quantum Monte Carlo simulations, we study the phase diagram of a one-parameter Hamiltonian interpolating between trivial and topological Ising paramagnets in two dimensions, which are dual to the toric code and the double semion. We discover an intermediate phase with stripe order which spontaneously breaks the protecting Ising symmetry. Remarkably, we find evidence that this intervening phase is gapless due to the incommensurability of the stripe pattern and that it is dual to a $U(1)$ gauge theory exhibiting Cantor deconfinement.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Surface code architecture for donors and dots in silicon with imprecise and nonuniform qubit couplings

A scaled quantum computer with donor spins in silicon would benefit from a viable semiconductor framework and a strong inherent decoupling of the qubits from the noisy environment. Coupling neighboring spins via the natural exchange interaction according to current designs requires gate control structures with extremely small length scales. In this work, we present a silicon architecture where bismuth donors with long coherence times are coupled to electrons that can shuttle between adjacent quantum dots, thus relaxing the pitch requirements and allowing space between donors for classical control devices. An adiabatic SWAP operation within each donor/dot pair solves the scalability issues intrinsic to exchange-based two-qubit gates, as it does not rely on subnanometer precision in donor placement and is robust against noise in the control fields. In conclusion, we use this SWAP together with well established global microwave Rabi pulses and parallel electron shuttling to construct a surface code that needs minimal, feasible local control.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Entanglement spectra of stabilizer codes: A window into gapped quantum phases of matter

The entanglement spectrum (ES) provides a barometer of quantum entanglement and encodes physical information beyond that contained in the entanglement entropy. In this paper, we explore the ES of stabilizer codes, which furnish exactly solvable models for a plethora of gapped quantum phases of matter. Studying the ES for stabilizer Hamiltonians in the presence of arbitrary weak local perturbations thus allows us to develop a general framework within which the entanglement features of gapped topological phases can be computed and contrasted. In particular, we study models harboring fracton order, both type-I and type-II, and compare the resulting ES with that of both conventional topological order and of (strong) subsystem symmetry protected topological (SSPT) states. We find that nonlocal surface stabilizers (NLSS), a set of symmetries of the Hamiltonian which form on the boundary of the entanglement cut, act as purveyors of universal nonlocal features appearing in the entanglement spectrum. While in conventional topological orders and fracton orders, the NLSS retain a form of topological invariance with respect to the entanglement cut, subsystem symmetric systems—fracton and SSPT phases—additionally show a nontrivial geometric dependence on the entanglement cut, corresponding to the subsystem symmetry. This sheds further light on the interplay between geometric and topological effects in fracton phases of matter and demonstrates that strong SSPT phases harbour a measure of quasilocal entanglement beyond that encountered in conventional SPT phases. Here, we further show that a version of the edge-entanglement correspondence, established earlier for gapped two-dimensional topological phases, also holds for gapped three-dimensional fracton models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Sensitivity study with a $\textit{D}$ and $\textit{B}$ mesons modular simulation code of heavy flavor $R_{AA}$ and azimuthal anisotropies based on beam energy, initial conditions, hadronization, and suppression mechanisms

Heavy flavor probes provide important information about the in-medium properties of the quark-gluon plasma produced in heavy-ion collisions. In this work, we investigate the effects of 2D + 1 event-by-event fluctuating hydrodynamic backgrounds on the nuclear suppression factor and momentum anisotropies of heavy flavor mesons and nonphotonic electrons. Using the state-of-the-art $\textit{D}$ and $\textit{B}$ mesons modular simulation code (called “DAB-MOD”), we perform a systematic comparison of different transport equations in the same background, including a few energy-loss models—with and without energy-loss fluctuations—and a relativistic Langevin model with different drag parametrizations. We present the resulting $\textit{D}$ and $\textit{B}$ mesons $R_{A A}, v_2, v_3,$ and $v_4$ as well as multiparticle cumulants, in AuAu collisions at $\sqrt{s_{NN}}$ = 200 GeV and PbPb collisions at $\sqrt{s_{NN}}$ = 2.76 TeV and $\sqrt{s_{NN}}$ = 5.02 TeV , and compare them to the available experimental data. The $v_2${4}/$v_2${2} ratio, which is known to be a powerful probe of the initial conditions and flow fluctuations in the soft sector, is also studied in the context of heavy flavor. We also investigate the correlations between the transverse anisotropies of heavy mesons and all charged particles to better understand how heavy quarks couple to the hydrodynamically expanding quark-gluon plasma. Finally, we study the influence that different initial conditions and the implementation of heavy-light quark coalescence has on our results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2013

Experimental differential cross sections, level densities, and spin cutoffs as a testing ground for nuclear reaction codes

Proton double-differential cross sections from 59 Co(α,p) 62 Ni, 57 Fe(α,p) 60 Co, 56 Fe( 7 Li,p) 62 Ni, and 55 Mn( 6 Li,p) 60 Co reactions have been measured with 21-MeV α and 15-MeV lithium beams. Cross sections have been compared against calculations with the empire reaction code. Different input level density models have been tested. It was found that the Gilbert and Cameron [A. Gilbert and A. G. W. Cameron, Can. J. Phys. 43, 1446 (1965)] level density model is best to reproduce experimental data. Level densities and spin cutoff parameters for 62 Ni and 60 Co above the excitation energy range of discrete levels (in continuum) have been obtained with a Monte Carlo technique. Furthermore, excitation energy dependencies were found to be inconsistent with the Fermi-gas model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Superdense Coding over Optical Fiber Links with Complete Bell-State Measurements

Adopting quantum communication to modern networking requires transmitting quantum information through a fiber-based infrastructure. In this paper, we report the first demonstration of superdense coding over optical fiber links, taking advantage of a complete Bell-state measurement enabled by time-polarization hyperentanglement, linear optics, and common single-photon detectors. Finally, we demonstrate the highest single-qubit channel capacity to date utilizing linear optics, 1.665 ± 0.018, and we provide a full experimental implementation of a hybrid, quantum-classical communication protocol for image transfer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

On Using Linux Kernel Huge Pages with FLASH, an Astrophysical Simulation Code

We present efforts at improving the performance of FLASH, a multi-scale, multi-physics simulation code principally for astrophysical applications, by using huge pages on Ookami, an HPE Apollo 80 A64FX platform. FLASH is written principally in modern Fortran and makes use of the PARAMESH library to manage a block-structured adaptive mesh. We explored options for enabling the use of huge pages with several compilers, but we were only able to successfully use huge pages when compiling with the Fujitsu compiler. As a result, the use of huge pages substantially reduced the number of translation lookaside buffer misses, but overall performance gains were marginal.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Gold Code-Phase-Shift Keying: A Power and Bandwidth Efficient Communication Scheme for Smart Buildings

Advanced communications, sensors and controls play an important role in reducing the energy consumption of smart buildings. Wireless sensors have been recently deployed in buildings to provide monitoring and control of several devices such as heating, ventilation, and air-conditioning (HVAC) and lighting systems. In this paper, we present a low-power bandwidth-efficient communication scheme that can be driven by energy harvesting in self-powered wireless sensors. The proposed communication scheme is based on Gold code-phase-shift keying (CPSK) spread-spectrum signaling that improves both transmitter range and power consumption. We present our efforts toward exploring the design, implementation, and performance evaluation of a hardware prototypic Gold CPSK spread-spectrum radio transceiver. Experimental testing in addition to end-to-end system-level simulation-based studies are conducted to evaluate the performance of the Gold CPSK transceiver in terms of receiver sensitivity, coverage range, average probability of bit-error over standard Gaussian and Rayleigh fading-type channels, and multiple access capabilities. The specific engineering tradeoffs are also discussed.

Killough, Stephen M.↗
DOE OSTI2022

LaRIS: Targeting Portability and Productivity for LAPACK Codes on Extreme Heterogeneous Systems by Using IRIS

In keeping with the trend of heterogeneity in high-performance computing, hardware manufacturers and vendors are developing new architectures and associated software stacks (e.g., libraries) to harness the best possible performance from commonly used kernels (e.g., linear algebra kernels). However, kernels tuned for one architecture are not portable to others. Moreover, the coexistence of different architectures in a single node makes orchestration difficult. To address these challenges, we introduce LaRIS, a portable framework for LAPACK functionalities. LaRIS ensures a separation between linear algebra algorithms and vendor-library kernels by using the IRIS run time and IRIS-BLAS library. Such abstraction at the algorithm level makes the implementation completely agnostic to the vendor library and architecture. LaRIS uses the IRIS run time to dynamically select the vendor-library kernel and suitable processor architecture at run time. Through LU factorization, we demonstrate that LaRIS can fully utilize different heterogeneous systems by launching and orchestrating different vendor-library kernels without any change in the source code.

Monil, M. A. H.↗