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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Template and target-site recognition by human LINE-1 in retrotransposition

The long interspersed element-1 (LINE-1, hereafter L1) retrotransposon has generated nearly one-third of the human genome and serves as an active source of genetic diversity and human disease. L1 spreads through a mechanism termed target-primed reverse transcription, in which the encoded enzyme (ORF2p) nicks the target DNA to prime reverse transcription of its own or non-self RNAs. Here we purified full-length L1 ORF2p and biochemically reconstituted robust target-primed reverse transcription with template RNA and target-site DNA. We report cryo-electron microscopy structures of the complete human L1 ORF2p bound to structured template RNAs and initiating cDNA synthesis. The template polyadenosine tract is recognized in a sequence-specific manner by five distinct domains. Among them, an RNA-binding domain bends the template backbone to allow engagement of an RNA hairpin stem with the L1 ORF2p C-terminal segment. Moreover, structure and biochemical reconstitutions demonstrate an unexpected target-site requirement: L1 ORF2p relies on upstream single-stranded DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick generating a staggered DNA break. Our research provides insights into the mechanism of ongoing transposition in the human genome and informs the engineering of retrotransposon proteins for gene therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Elucidating molecular interactions of L-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance

Emtricitabine (FTC) and lamivudine (3TC), containing an oxathiolane ring with unnatural (-)-stereochemistry, are widely used nucleoside reverse transcriptase inhibitors (NRTIs) in anti-HIV therapy. Treatment with FTC or 3TC primarily selects for the HIV-1 RT M184V/I resistance mutations. Here we provide a comprehensive kinetic and structural basis for inhibiting HIV-1 RT by (-)-FTC-TP and (-)-3TC-TP and drug resistance by M184V. (-)-FTC-TP and (-)-3TC-TP have higher binding affinities (1/K d 200-fold) K d for the L-nucleotides and moderately higher (>9-fold) K d for the D-isomers compared to dCTP. The M184V RT structure illustrates how the mutation repositions the oxathiolane of (-)-FTC-TP and shifts its triphosphate into a non-productive conformation.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2024

Candidate spin-liquid ground state in CsNdSe 2 with an effective spin-1/2 triangular lattice

Rare-earth-based triangular lattice materials are extremely attractive for studying unconventional magnetism. Here, we report the magnetic properties of layered CsNdSe 2 based on direct current (DC) and alternating current (AC) susceptibility measurements down to 0.04 K. While the AC susceptibility at the zero DC field shows a broad hump below 0.5 K, there is no sign of any long-range magnetic ordering. Quantitative analysis of the DC magnetic susceptibility gives the negative Curie-Weiss (CW) temperature θ CW < 0 in all directions, indicating antiferromagnetic interaction between Nd ions. Of particular interest is the low temperature magnetic susceptibility, which reflects the effective spin-1/2 state with $\theta^a_{\text {cw}}/\theta^c_{\text {cw}}$ > 3. The estimated exchange interactions are J a /k B = 1.42 K (in-plane) and J c /k B = 0.44 K (out-of-plane), pointing to the anisotropic magnetism. First-principles calculations that include spin-orbit coupling and Coulomb correlations reveal multiple states with zero net magnetization for CsNdSe 2 . Both experiment and simulation strongly suggest CsNdSe 2 has the spin liquid ground state with effective spin-1/2. Application of a magnetic field can induce long-range antiferromagnetic ordering with the maximum transition temperature around 0.3 K, in further support of the zero-field spin liquid state.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Electronic relaxation dynamics in [Au 25 (SR) 18 ] -1 (R = CH 3 , C 2 H 5 , C 3 H 7 , MPA, PET) thiolate-protected nanoclusters

Here we investigate the excited electron dynamics in [Au 25 (SR) 18 ] -1 (R = CH3, C 2 H 5 , C 3 H 7 , MPA, PET) [MPA = mercaptopropanoic acid, PET = phenylethylthiol] nanoparticles to understand how different ligands affect the excited state dynamics in this system. The population dynamics of the core and higher excited states lying in the energy range 0.00–2.20 eV are studied using a surface hopping method with decoherence correction in a real-time DFT approach. All of the ligated clusters follow a similar trend in decay for the core states (S 1 –S 6 ). The observed time constants are on the picosecond time scale (2–19 ps), which agrees with the experimental time scale, and this study confirms that the time constants observed experimentally could originate from core-to-core transitions and not from core-to-semiring transitions. In the presence of higher excited states, R = H, CH 3 , C 2 H 5 , C 3 H 7 , and PET demonstrate similar relaxations trends whereas R = MPA shows slightly different relaxation of the core states due to a smaller gap between the LUMO+1 and LUMO+2 gap in its electronic structure. The S 1 (HOMO → LUMO) state gives the slowest decay in all ligated clusters, while S 7 has a relatively long decay. Furthermore, separate electron and hole relaxations were performed on the [Au 25 (SCH 3 ) 18 ] -1 nanocluster to understand how independent electron and hole relaxations contribute to the overall relaxation dynamics.

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

Luminescent 1 H -1,3-benzazaphospholes

2-R-1 H -1,3-Benzazaphospholes (R-BAPs) are an interesting class of fluorescent σ 2 P heterocycles containing PC bonds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

High-resolution X-ray spectroscopy of the stellar wind in Vela X-1 during a flare

In this work, we present a ~130 ks observation of the prototypical wind-accreting, high-mass X-ray binary Vela X-1 collected with XMM-Newton at orbital phases between 0.12 and 0.28. A strong flare took place during the observation that allows us to investigate the reaction of the clumpy stellar wind to the increased X-ray irradiation. To examine the wind’s reaction to the flare, we performed both time-averaged and time-resolved analyses of the RGS spectrum and examined potential spectral changes. We focused on the high-resolution XMM-Newton RGS spectra and divided the observation into pre-flare, flare, and post-flare phases. We modeled the time-averaged and time-resolved spectra with phenomenological components and with the self-consistent photoionization models calculated via CLOUDY and XSTAR in the pre-flare phase, where strong emission lines due to resonant transitions of highly ionized ions are seen. In the spectra, we find emission lines corresponding to K-shell transitions in highly charged ions of oxygen, neon, magnesium, and silicon as well as radiative recombination continua (RRC) of oxygen. Additionally, we observe potential absorption lines of magnesium at a lower ionization stage and features identified as iron L lines. The, CLOUDY and XSTAR photoionization models provide contradictory results, either pointing towards uncertainties in theory or possibly a more complex multi-phase plasma, or both. We are able to demonstrate the existence of a plethora of variable narrow features, including the firm detection of oxygen lines and RRC that RGS enables to observe in this source for the first time. We show that Vela X-1 is an ideal source for future high-resolution missions, such as XRISM and Athena.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Magnetic phases of spatially modulated spin-1 chains in Rydberg excitons: Classical and quantum simulations

Here, in this work, we study the magnetic phases of a spatially modulated chain of spin-1 Rydberg excitons. Using the Density Matrix Renormalization Group (DMRG) technique, we study various magnetic and topologically nontrivial phases using both single-particle properties, such as local magnetization and quantum entropy, and many-body ones, such as pair-wise Néel and long-range string correlations. In particular, we investigate the emergence and robustness of the Haldane phase, a topological phase of anti-ferromagnetic spin-1 chains. Furthermore, we devise a hybrid quantum algorithm employing restricted Boltzmann machine to simulate the ground state of such a system that shows very good agreement with the results of exact diagonalization and DMRG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Foreground removal with ILC methods for AliCPT-1

One of the main goals of most future CMB experiments is the precise measurement of CMB B-mode polarization, whose major obstacle is the Galactic foregrounds. In this paper, we evaluate the foreground cleaning performance of the variants of the ILC method on partial sky B-modes and analyze the main sources of biases on the BB power spectrum. Specially, we compare the NILC, the cILC (in three domains) and the cMILC methods for AliCPT-1 simulations. We find that the cILC methods implemented in harmonic space and needlet space are both competent to clean different models of foregrounds, which bias the tensor-to-scalar ratio about 0.008 at maximum, and constrain the tensor-to-scalar ratio to r < 0.043(95%CL) for the AliCPT-1 configuration. We also note that the deviation of the estimated noise bias from the actual one for ILC, dubbed the noise bias error (NBE) in this paper, might make significant effects on the power spectrum for a small footprint and low signal-to-noise ratio CMB experiment. We finally obtain its relation with respect to the noise residual which fits well with the simulated results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Performance of the CMS Level-1 trigger in proton-proton collisions at $\sqrt{s} =$ 13 TeV

At the start of Run 2 in 2015, the LHC delivered proton-proton collisions at a center-of-mass energy of 13\TeV. During Run 2 (years 2015–2018) the LHC eventually reached a luminosity of 2.1× 1034 cm-2s-1, almost three times that reached during Run 1 (2009–2013) and a factor of two larger than the LHC design value, leading to events with up to a mean of about 50 simultaneous inelastic proton-proton collisions per bunch crossing (pileup). The CMS Level-1 trigger was upgraded prior to 2016 to improve the selection of physics events in the challenging conditions posed by the second run of the LHC. This paper describes the performance of the CMS Level-1 trigger upgrade during the data taking period of 2016–2018. The upgraded trigger implements pattern recognition and boosted decision tree regression techniques for muon reconstruction, includes pileup subtraction for jets and energy sums, and incorporates pileup-dependent isolation requirements for electrons and tau leptons. In addition, the new trigger calculates high-level quantities such as the invariant mass of pairs of reconstructed particles. The upgrade reduces the trigger rate from background processes and improves the trigger efficiency for a wide variety of physics signals.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

The CMS Phase-1 Pixel Detector Upgrade

The CMS detector at the CERN LHC features a silicon pixel detector as its innermost subdetector. The original CMS pixel detector has been replaced with an upgraded pixel system (CMS Phase-1 pixel detector) in the extended year-end technical stop of the LHC in 2016/2017. The upgraded CMS pixel detector is designed to cope with the higher instantaneous luminosities that have been achieved by the LHC after the upgrades to the accelerator during the first long shutdown in 2013–2014. Compared to the original pixel detector, the upgraded detector has a better tracking performance and lower mass with four barrel layers and three endcap disks on each side to provide hit coverage up to an absolute value of pseudorapidity of 2.5. This paper describes the design and construction of the CMS Phase-1 pixel detector as well as its performance from commissioning to early operation in collision data-taking.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Integration of a new Cryogenic Liquefier into the IB-1 Cryogenic Test Facility

The increase over the last years of the testing activities related to quantum systems, SRF cavities for the PIP-II and the LCLS-II projects, as well as superconducting magnets for the HL-LHC project and Fusion research activities, has required the addition of a new Helium cryogenic plant into the existing IB-1 Industrial Cryogenic Test Facility. The new cryogenic plant is composed of a cryogenic liquefier (Cold Box) able to provide up to 340 L/h, a 4 kL Dewar and two Mycom ® compressors providing up to 120 g/s. AL-AT (Air Liquide Advanced Technologies) has taken part of this project by designing and manufacturing the cryogenic liquefier. This new cryogenic plant is connected through a cryogenic distribution system to a 10 kL Dewar, which is part of the existing cryogenic test facility, itself composed of another Cold Box and a Sullair ® compressor. The new cryogenic plant has two main operating modes: one allows to transfer liquid helium at 1.7 bar between the two Dewars, the other allows to transfer supercritical Helium at 2 bar or more between the new Cold Box and the 10 kL Dewar. The entire industrial cryogenic facility is handled by a common Inventory Control System, composed of three control valves, and 9 tanks giving a total buffer volume of more than 1000 m3. This paper presents the technical features of the new Helium cryogenic plant, as well as the main results of the liquefier commissioning phase and details of the helium transfer between the two Dewars, making the connection between the cryogenic plants at the IB-1 Industrial Cryogenic Test Facility.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Kinematics of the H α and H β broad-line region in an SDSS sample of type-1 AGNs

Here, we investigate the kinematics of the part of the broad-line region (BLR) in active galactic nuclei (AGNs) emitting H β and H α emission lines. We explore the widths and asymmetries of the broad H β and H α emission lines in a sample of high-quality (i.e. high signal-to-noise ratio) spectra of type-1 AGN taken from the Data Release 16 of the Sloan Digital Sky Survey in order to explore possible deviation from the gravitationally bound motion. To find only the broad component of H β and H α, we use the FANTASY (Fully Automated pythoN Tool for AGN Spectra analYsis) code for the multicomponent modelling of the AGN spectra and for careful extraction of the broad emission-line parameters. Here, we show that based on the broad-line profiles widths and asymmetries, the BLR gas emitting H β and H α lines follows similar kinematics, and seems to be virialized in our sample of type-1 AGN.

79 ASTRONOMY AND ASTROPHYSICS↗
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 OSTI2026

Semi-inclusive deep-inelastic scattering on a polarized spin-1 target. I. Cross section and spin observables

We develop the theoretical framework for semi-inclusive deep-inelastic scattering on a polarized spin-1 target and apply it to scattering on the polarized deuteron with spectator nucleon tagging. In Part I (this article) we present the general form of the semi-inclusive cross section and polarization observables for the spin-1 target. A relativistically covariant formulation in terms of four-vectors and invariant polarization parameters is employed. The target polarization is described by a spin density matrix with vector and tensor polarization. The spin and azimuthal angle dependence of the semi-inclusive cross section is derived and parametrized in terms of invariant structure functions. To validate the result, the structure functions are expressed as photon-target helicity amplitudes with known symmetry properties. The expressions presented here are kinematic (no assumptions about particle production dynamics) and valid in all regions of the deep-inelastic final state (current and target fragmentation regions). In Part II (following article), we consider deep-inelastic scattering on the polarized deuteron with spectator nucleon tagging as a special case of target fragmentation. The semi-inclusive structure functions are computed by separating nuclear and hadronic structure, and the polarization observables are explored as functions of the tagged nucleon momentum.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Semi-inclusive deep-inelastic scattering on a polarized spin-1 target. II. Deuteron and spectator nucleon tagging

We develop the theoretical framework for semi-inclusive deep-inelastic scattering on a polarized spin-1 target and apply it to scattering on the polarized deuteron with spectator nucleon tagging. In Part I (previous article), we present the general form of the semi-inclusive cross section and polarization observables for the spin-1 target. In Part II (this article), we consider deep-inelastic scattering on the polarized deuteron with spectator nucleon tagging as a special case of target fragmentation. Methods of light-front quantization are employed to separate nuclear and hadronic structure in the high-energy process and achieve a composite description. The light-front wave function of the polarized deuteron is obtained from a rotationally covariant three-dimensional wave function in the center-of-mass frame of the proton-neutron system. The tagged structure functions are computed in the impulse approximation. The momentum and spin distribution of the active nucleon are controlled by the deuteron polarization and the detected spectator momentum (𝐷/𝑆 wave ratio). The cross section and spin asymmetries are evaluated for general deuteron polarization (vector and tensor, longitudinal and transverse) as functions of the spectator momentum. Tensor-polarized spin asymmetries of order unity are achieved for spectator momenta of approximately 300 MeV, which select configurations with a large 𝐷 wave. Sum rules for the tagged spin structure functions are derived. The results can be used for simulations of spectator tagging in future polarized fixed-target experiments (Jefferson Lab) or at the Electron-Ion Collider.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Emergent spin-1 Haldane gap and ferroelectricity in a frustrated spin- 1 2 ladder

We report experimental and theoretical evidence that Rb 2 Cu 2 Mo 3 O 12 has a nonmagnetic tetramer ground state of a two-leg ladder comprising antiferromagnetically coupled frustrated spin-12 chains and exhibits a Haldane spin gap of emergent spin-1 pairs. Three spin excitations split from the spin-1 triplet by a Dzyaloshinskii-Moriya interaction are identified in inelastic neutron-scattering and electron spin resonance spectra. A tiny magnetic field generates ferroelectricity without closing the spin gap, indicating a unique class of ferroelectricity induced by a vector spin chirality order.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Low-energy physics of isotropic spin-1 chains in the critical and Haldane phases

Using a matrix product state algorithm with infinite boundary conditions, we compute high-resolution dynamic spin and quadrupolar structure factors in the thermodynamic limit to explore the low-energy excitations of isotropic bilinear-biquadratic spin-1 chains. Haldane mapped the spin-1 Heisenberg antiferromagnet to a continuum field theory, the nonlinear sigma model (NLσM). In this work, we find that the NLσM fails to capture the influence of the biquadratic term and provides only an unsatisfactory description of the Haldane phase physics. But several features in the Haldane phase can be explained by noninteracting multimagnon states. The physics at the Uimin-Lai-Sutherland point is characterized by multisoliton continua. Moving into the extended critical phase, we find that these excitation continua contract, which we explain using a field-theoretic description. New excitations emerge at higher energies and, in the vicinity of the purely biquadratic point, they show simple cosine dispersions. Using block fidelities, we identify them as elementary one-particle excitations and relate them to the integrable Temperley-Lieb chain.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗