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At least 235 records · Page 13

All sources NASA NTRS DOE OSTI

DOE OSTI2021

Functional proteoliposome-like structure derived from simultaneous evisceration and enucleation of T-lymphoblastoid A3R5.7 cells: A top-down story

Highlights: • A3R5.7 and TF228.1.16 are capable of CD4-mediated membrane fusion. • Cytoplasmic and nuclear material can be removed simultaneously from A3R5.7 cells. • Resultant cell membrane remains intact, and retains presentation of CD4 and CXCR4. • Products are still capable of CD4-mediated membrane fusion with a target cell. • Useful for host-pathogen studies, and developing targeted delivery vehicles. Structurally-reduced cells and cell-derived structures are powerful tools for membrane studies. Using this approach, we probed whether a cell, without its nucleus and cytoplasm, is still capable of undergoing CD4-mediated membrane fusion. For this, we needed a cell-derived structure, akin to a giant liposome functionalised with CD4 and chemokine receptors. We present a method for the simultaneous removal of cytoplasmic and nuclear material from cells presenting CD4, CCR5, and CXCR4, using Colcemid treatment followed by hypotonic cytolysis, and then enriched using preparative flow cytometry. We show that the resultant cell membrane remains intact, retains presentation of CD4, CCR5, and CXCR4, and is still capable of CD4-mediated membrane fusion with a target cell. Finally, we detail how this protocol was developed, as well as how such samples should be handled for storage and assays. We envision the use of such systems for host-pathogen interaction studies, and the development of targeted delivery vehicles.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Mitochondrial genome diversity across the subphylum Saccharomycotina

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Inter-Oligomer Interaction Influence on Photoluminescence in Cis-Polyacetylene Semiconductor Materials

Semiconducting conjugated polymers (CPs) are pivotal in advancing organic electronics, offering tunable properties for solar cells and field-effect transistors. Here, we carry out first-principle calculations to study individual cis-polyacetylene (cis-PA) oligomers and their ensembles. The ground electronic structures are obtained using density functional theory (DFT), and excited state dynamics are explored by computing nonadiabatic couplings (NACs) between electronic and nuclear degrees of freedom. We compute the nonradiative relaxation of charge carriers and photoluminescence (PL) using the Redfield theory. Our findings show that electrons relax faster than holes. The ensemble of oligomers shows faster relaxation compared to the single oligomer. The calculated PL spectra show features from both interband and intraband transitions. The ensemble shows broader line widths, redshift of transition energies, and lower intensities compared to the single oligomer. This comparative study suggests that the dispersion forces and orbital hybridizations between chains are the leading contributors to the variation in PL. It provides insights into the fundamental behaviors of CPs and the molecular-level understanding for the design of more efficient optoelectronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Budding yeasts in the subphylum Saccharomycotina Genome sequencing and assembly

Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial reads from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.

diversity↗

DOE OSTI2026

Localizing tetrahedral aluminum in nitrate-bearing gibbsite to constrain defect-impurity coupling

The enhanced radiolytic stability of gibbsite (α-Al(OH) 3 ) containing trace nitrate (NO 3 − ) is a phenomenon in nuclear waste management, but its structural origins remain unresolved. Motivated by the detection of minority tetrahedral aluminum (T d ) defects in synthetic gibbsite, we hypothesized that these sites may participate in NO 3 − retention or mediate H 2 suppression. To evaluate this, we combined orthogonal techniques comprised of spatially selective solid-state 27 Al MAS NMR, comparative spectroscopy, and density functional theory (DFT) modeling. Paramagnetic editing and dynamic nuclear polarization (DNP) MAS NMR confirm that T d defects are confined to the particle interior. DFT calculations reveal no energetic stabilization of NO 3 − near T d sites. Comparative NMR analysis shows that T d is also present in chloride-bearing gibbsite, which exhibits high radiolytic hydrogen yields. These three independent disqualifications rule out T d as a structural contributor to nitrate-mediated suppression and narrow the scope of defect-driven explanations. The findings redirect mechanistic attention away from coordination defects and toward redox-active impurity pathways, providing a refined foundation for understanding radiation tolerance in Al(OH) 3 .

Graham, Trent R. [Pacific Northwest National Labor↗

DOE OSTI2026

Transition Metal Taggants in UO 2 from First Principles

The incorporation of transition metals into nuclear fuel has gained attention both to improve fuel properties and as a possible nuclear forensics tool. Recent experimental studies by Ulrich et al. and Adorno Lopes et al. have investigated Ni and Fe as candidate transition metal dopants for potential nuclear forensics purposes and found that there is minimal alteration to key UO 2 fuel properties. In the present work, we performed density functional theory (DFT) investigations into possible defect structures for Ni and Fe incorporation. The dynamic stability of these defect structures was validated by calculating the phonon density of states. We found that transition metal incorporation likely occurs via substitution at U sites in the fluorite crystal structure with a nearby O vacancy for charge-balancing, which agrees with experimentally proposed structures. Additionally, this defect structure does not cause long-range alterations to the crystal parameters—an important consideration for use as a nuclear fuel taggant. Future needed work involves computational investigation of additional defect concentrations using larger supercells, additional transition metal charge states, and thermal effects. Such investigations can be carried forward into sintering models for a more complete understanding of the suitability of Ni and Fe as fuel taggants.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Local measurement of bulk thermal diffusivity using photothermal radiometry

Here, an experimental methodology using photothermal radiometry is developed for the accurate measurement of bulk thermal diffusivity of nuclear fuels and materials irradiated to high doses. Under these conditions, nuclear fuels, such as uranium oxide, and moderator materials, such as graphite, become friable, which requires characterization techniques that can accommodate irregularly shaped fragments. Photothermal radiometry, a good candidate for this application, involves locally heating a sample by using a laser and measuring the temperature field by monitoring blackbody radiation. The interaction volume for this study, less than a millimeter, is carefully chosen to sample a statistically significant number of large-scale structural features, such as pores and gas filled bubbles, and is small enough that the sample fragments can be treated as a thermal half-space. The thermal diffusivity standards considered in this study cover a range of thermal diffusivities representative of both fresh and spent nuclear fuels. We also consider a sample having a porous microstructure representative of large-scale structures found in materials irradiated to high doses. Our measurement methodology circumvents complex thermal wave models that address optical diffraction, nonlinear transfer function associated with blackbody radiation, and finite sample size effects. Consequently, the large measurement uncertainty associated with modeling these effects can be avoided. While the emphasis here is on nuclear fuels and materials, this measurement approach is well suited to measure thermal transport in a variety of technologically important materials associated with advanced synthesis techniques. Examples range from small, exotic single crystals grown using hydrothermal growth techniques to additively manufactured components having complex geometries.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Ultra-rapid, physics-based development pathway for reactor-relevant RF antenna materials

This paper presents a rapid, atomistically-informed, experimental development pathway for fusion reactor-relevant radio frequency (RF) antenna materials in the Cu-Cr-(Nb,Al,Zr) composition system, with the goal of improving upon GRCop-84. RF antennas in a tokamak fusion reactor will face a unique set of challenges as both structural and functional materials. The desired material must simultaneously achieve and maintain high electrical conductivity, high strength, high thermal conductivity, resist high temperatures, possess low nuclear activation, and incur low damage due to neutron bombardment. The GRCop-84 alloy serves as a starting point for iterative improvement, with the desire to reduce or eliminate Nb from the material to minimize nuclear activation. The rapid development pathway makes use of a multi-target combinatorial thick film sputtering process to produce full ternary phase diagrams on a Si wafer substrate. Transient grating spectroscopy (TGS), a laser-ultrasonic method, will determine spatially-varying thermo-elastic properties, while four terminal electrical conductivity measurements will map out the best per- forming regions of the sample for in-depth study at larger length scales. High energy proton and self-ion irradiation emulates the effects of neutron damage on the thermal/electric properties. With rapid turnaround time (∼days) in terms of mapping radiation damage-induced material property changes in the full ternary system, these techniques allow rapid iteration towards an optimal material, testing hundreds of nearby compositions in the time it took to test one. Focused testing of larger, single composition samples (produced in an arc furnace or by laser sintering) provides data on structural and high power RF properties, and validates our thick-film based workflow.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Structure optimization with stochastic density functional theory

Linear-scaling techniques for Kohn–Sham density functional theory are essential to describe the ground state properties of extended systems. Still, these techniques often rely on the localization of the density matrix or accurate embedding approaches, limiting their applicability. In contrast, stochastic density functional theory (sDFT) achieves linear- and sub-linear scaling by statistically sampling the ground state density without relying on embedding or imposing localization. In return, ground state observables, such as the forces on the nuclei, fluctuate in sDFT, making optimizing the nuclear structure a highly non-trivial problem. In this work, we combine the most recent noise-reduction schemes for sDFT with stochastic optimization algorithms to perform structure optimization within sDFT. We compare the performance of the stochastic gradient descent approach and its variations (stochastic gradient descent with momentum) with stochastic optimization techniques that rely on the Hessian, such as the stochastic Broyden–Fletcher–Goldfarb–Shanno algorithm. In conclusion, we further provide a detailed assessment of the computational efficiency and its dependence on the optimization parameters of each method for determining the ground state structure of bulk silicon with varying supercell dimensions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Review of SiC material development for nuclear fusion applications: Cross-cutting research and emerging opportunities

The SiC-based materials, particularly SiC-fiber-reinforced SiC matrix (SiC/SiC) composites, show strong potential for structural and functional applications in future fusion power plants because they can operate at high temperatures with a range of coolants and breeders, thereby enabling higher energy conversion efficiency. Here, this paper presents recent advancements in the development of SiC-based materials, focusing on processing techniques and material performance and resistance under fusion-relevant environments. The processing activities have emphasized near-net-shape fabrication and the joining of SiC subcomponents, with processing methods and material compositions informed by previous irradiation experiments on various grades of SiC. Research on irradiation effects has remained focused on degradation mechanisms and the microstructural optimization of SiC/SiC composites irradiated to high neutron damage levels. Analysis of irradiation defects in SiC has advanced via the application of cutting-edge characterization methods, among which Raman spectroscopy is becoming a common tool to assess atomic-scale chemical disorder. Fusion–fission crosscutting irradiation research has explored combined effects in SiC/SiC composites with application-relevant geometries, including bowing of SiC/SiC composite channels under neutron flux gradients, stress evolution in SiC/SiC composite tubes under through-thickness temperature gradients, and irradiation-enhanced corrosion in SiC. Finally, research opportunities for component testing and assessment under fusion-relevant conditions, in support of emerging concepts from the private fusion sector, are discussed.

Advanced manufacturing↗

DOE OSTI2024

Mixed Valence {Ni 2+ Ni 1+ } Clusters as Models of Acetyl Coenzyme A Synthase Intermediates

Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4] n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni 2+ Ni 1+ } cluster, [K(12-crown-4) 2 ][1], effectively replicates the coordination number and oxidation state of the proposed “A red ” state of the A-cluster. Addition of carbon monoxide to [1] - allows for isolation of a dinuclear {Ni 2+ Ni 1+ (CO)} complex, [K(12-crown-2) n ][2] (n = 1–2), which bears similarity to the “A NiFeC ” enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1] – is more stable than the Y-conformation by 22 kcal mol –1 , and that binding of CO to Ni 1+ is barrierless and exergonic by 6 kcal mol –1 . UV/vis absorption spectroscopy on [2] - in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2] - promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

The LISE package: solvers for static and time-dependent superfluid local density approximation equations in three dimensions

Nuclear implementation of the density functional theory (DFT) is at present the only microscopic framework applicable to the whole nuclear landscape. The extension of DFT to superfluid systems in the spirit of the Kohn-Sham approach, the superfluid local density approximation (SLDA) and its extension to time-dependent situations, time-dependent superfluid local density ap- proximation (TDSLDA), have been extensively used to describe various static and dynamical problems in nuclear physics, neutron star crust, and cold atom systems. In this paper, we present the codes that solve the static and time-dependent SLDA equations in three-dimensional coordinate space without any symmetry restriction. These codes are fully parallelized with the message passing interface (MPI) library and take advantage of graphic processing units (GPU) for accelerating execution. The dynamic codes have checkpoint/restart capabilities and for initial conditions one can use any generalized Slater determinant type of wave function. The code can describe a large number of physical problems: nuclear fission, collisions of heavy ions, the interaction of quantized vor- tices with nuclei in the nuclear star crust, excitation of superfluid fermion systems by time dependent external fields, quantum shock waves, domain wall generation and propagation, the dynamics of the Anderson-Bogoliubov-Higgs mode, dynamics of fragmented condensates, vortex rings dynamics, generation and dynamics of quantized vortices, their crossing and recombinations and the incipient phases of quantum turbulence.

Jin, Shi↗

DOE OSTI2024

Nuclear level density and γ -decay strength of Sr 93

This work presents the first experimentally determined nuclear level density and γ-ray strength function of the short-lived fission product 93 Sr, accomplished using the β-Oslo method. Direct measurement of the 92 Sr(n, γ) 93 Sr cross section is not currently possible, as the half-life of 2.66 hours is too short; instead, 93 Sr was formed through β decay of 93 Rb to excitation energies around the neutron separation energy. The γ-ray spectra were measured using a total absorption spectrometer at the National Superconducting Cyclotron Laboratory (NSCL) at Michigan State University (MSU). The statistical properties of the 93 Sr nucleus were experimentally determined, including the γ-ray strength function and nuclear level density. At low energies, the γ-ray strength function exhibits a constant γ-decay strength, rather than a slightly increasing strength with decreasing γ-ray energy as had been previously observed for several nuclei in this mid-mass region. Finally, these statistical properties were then implemented in the reaction code TALYS1.95 to calculate the 92 Sr(n, γ) 93 Sr cross section.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

New Measurements of the Deuteron-to-Proton 𝐹 2 Structure-Function Ratio

Nucleon structure functions, as measured in lepton-nucleon scattering, have historically provided a critical observable in the study of partonic dynamics within the nucleon. However, at very large parton momenta, it is both experimentally and theoretically challenging to extract parton distributions due to the probable onset of nonperturbative contributions and the unavailability of high-precision data at critical kinematics. Extraction of the neutron structure and the d quark distribution have been further challenging because of the necessity of applying nuclear corrections when utilizing scattering data from a deuteron target to extract the free neutron structure. However, a program of experiments has been carried out recently at the energy-upgraded Jefferson Lab electron accelerator aimed at significantly reducing the nuclear correction uncertainties on the d quark distribution function at large partonic momentum. This allows leveraging the vast body of deuterium data covering a large kinematic range to be utilized for d quark parton distribution function extraction. In this Letter, we present new data from experiment E12-10-002, carried out in Jefferson Lab Experimental Hall C, on the deuteron to proton cross section ratio at large Bjorken 𝑥. These results significantly improve the precision of existing data and provide a first look at the expected impact on quark distributions extracted from parton distribution function fits.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

The symmetric quasi-classical model using on-the-fly time-dependent density functional theory within the Tamm–Dancoff approximation

The primary computational challenge when simulating nonadiabatic ab initio molecular dynamics is the unfavourable compute costs of electronic structure calculations with molecular size. Simple electronic structure theories, like time-dependent density functional theory within the Tamm–Dancoff approximation (TDDFT/TDA), alleviate this cost for moderately sized molecular systems simulated on realistic time scales. Although TDDFT/TDA does have some limitations in accuracy, an appealing feature is that, in addition to including electron correlation through the use of a density functional, the cost of calculating analytic nuclear gradients and nonadiabatic coupling vectors is often computationally feasible even for moderately sized basis sets. Here in this work, some of the benefits and limitations of TDDFT/TDA are discussed and analysed with regard to its applicability as a ‘back-end’ electronic structure method for the symmetric quasi-classical Meyer–Miller model (SQC/MM). In order to investigate the benefits and limitations of TDDFT/TDA, SQC/MM is employed to predict and analyse a prototypical example of excited-state hydrogen transfer in gas-phase malonaldehyde. Then, the ring-opening dynamics of selenophene are simulated, which highlight some of the deficiencies of TDDFT/TDA. Additionally, some new algorithms are proposed that speed up the calculation of analytic nuclear gradients and nonadiabatic coupling vectors for a set of excited electronic states.

molecular dynamics↗

DOE OSTI2023

Hadronic structure on the light front. IX. Orbital-spin-isospin wave functions of baryons

Not Available

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Calculating the hyperfine tensors for group-IV impurity-vacancy centers in diamond using hybrid density functional theory

The hyperfine interaction is an important probe for understanding the structure and symmetry of defects in a semiconductor. Density functional theory has shown that it can provide useful first-principles predictions for both the hyperfine tensor and the hyperfine constants that arise from it. Recently there has been great interest in using group-IV impurity-vacancy color centers XV – (where X = Si, Ge, Sn, or Pb and V is a carbon vacancy) for important applications in quantum computing and quantum information science. In this paper we have calculated the hyperfine tensors for these XV – color centers using the HSE06 screened Hartree-Fock hybrid exchange-correlation functional with the inclusion of core electron spin polarization. We have compared our results to calculations which only use the PBE exchange-correlation functional without the inclusion of core electron spin polarization and we have found that our results are in very good agreement with available experimental results. Lastly, we have theoretically shown that these XV – color centers exhibit a Jahn-Teller distortion which explains the observed anisotropic distribution of the hyperfine constants among the neighboring 13 C nuclear spins.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Model for Independent Particle Motion

Independent particle model in nuclear physics assumes that the nucleon in the nucleus moves in the average (mean field) potential generated by all other nucleons. This chapter gives a short overview of basic features of the independent particle motion in atomic nuclei and its theoretical realization in the framework of shell models for spherical, deformed, and rotating nuclei as well as in more sophisticated approaches such as microscopic+macroscopic model and density functional theories. Independent particle motion of nucleons leads to global and single-particle consequences. The global ones manifest themselves in the shell structure, and its consequences for the global structure of nuclear landscape, the existence of superheavy nuclei, and the superdeformation at high spin are briefly reviewed. Finally, the latter shows itself in the single-particle properties such as energies, alignments, and densities; their manifestations are illustrated on specific examples.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗