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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Correlation of plastic events with local structure in jammed packings across spatial dimensions

Significance Mean-field theories, exact in the limit of infinite spatial dimensions, succeed in describing many features of glasses and amorphous solids in low dimensions, leading to considerable effort to understand how behavior evolves with dimension. Until now, all evidence has supported a picture in which “localized physics,” responsible for deviations from mean-field behavior in low dimensions, fades away with rising dimension. Our work shows that rearrangements, in which particles change relative positions leading to fluid-like response, reveal a different picture of dimensional cross-over. We find that rearrangements, which are localized in two- and three-dimensional systems and correlated with local structure, remain just as correlated with local structure up to five dimensions, suggesting that local structure is important even in high dimensions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions

The CRISPR-Cas9 system has been deployed for precision mutagenesis in an ever-growing number of species, including agricultural crops and forest trees. Its application to closely linked genes with extremely high sequence similarities has been less explored. In this study, we used CRISPR-Cas9 to mutagenize a tandem array of seven Nucleoredoxin1 (NRX1) genes spanning ~100 kb in Populus tremula × Populus alba. We demonstrated efficient multiplex editing with one single guide RNA in 42 transgenic lines. The mutation profiles ranged from small insertions and deletions and local deletions in individual genes to large genomic dropouts and rearrangements spanning tandem genes. We also detected complex rearrangements including translocations and inversions resulting from multiple cleavage and repair events. Target capture sequencing was instrumental for unbiased assessments of repair outcomes to reconstruct unusual mutant alleles. The work highlights the power of CRISPR-Cas9 for multiplex editing of tandemly duplicated genes to generate diverse mutants with structural and copy number variations to aid future functional characterization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium

The “genomic shock” hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession “Bhyb26.” We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species’ similarity in transposable element load may account for the subtlety of the observed genome dominance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Control of Dipolar Dynamics by Geometrical Programming

We propose and theoretically analyze methods for quantum many-body control through geometric reshaping of molecular tweezer arrays. Dynamic rearrangement during entanglement is readily available due to the extended coherence times of molecular rotational qubits. We show how motional dephasing can be suppressed and enhanced spin squeezing can be achieved in an actively rearranged short-range XY model. We also analyze in detail a specific static geometry that significantly suppresses decoherence. These general methods as applied to programmable quantum systems offer robust control modalities that are well suited to molecules.

optical tweezers↗
DOE OSTI2022

Resonance-enhanced x-ray multiple ionization of a polyatomic molecule

Extremely high charge states of atoms and molecules can be created when they are irradiated by intense x-ray pulses. At certain x-ray photon energies, electron ejection from atoms can be drastically enhanced by transient resonances created during the sequential ionization process. In this study we report on the observation of such resonance effects in a molecule, CH 3 I, and show the photon-energy-dependent shift of resonance-induced structures in ion charge state distributions. By comparing the ion charge state distribution of CH 3 I with that from ionization of atomic xenon, molecule-specific features are observed, which can be attributed to ultrafast intramolecular charge rearrangement. In addition, we experimentally demonstrate that the charge-rearrangement-enhanced x-ray ionization of molecules, previously found with hard x rays, also plays a role in the soft x-ray regime.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Temperature-induced structural evolution in liquid Ag-Ga alloys

Temperature-dependent atomic structural evolutions of liquid Ag 60 Ga 40 and Ag 70 Ga 30 alloys have been studied by in situ high-energy x-ray-diffraction (HEXRD) experiments combined with ab initio molecular-dynamics simulations. The experimental data show a reversible structural crossover at about 1050 ~ 1100 (± 50) K in both liquid Ag 60 Ga 40 and Ag 70 Ga 30 alloys. Obvious changes of the electrical resistivity, absolute thermoelectric power, and atomic diffusivity around the similar temperature range for both Ag-Ga liquids strongly support the HEXRD results. The origin of the liquid-to-liquid crossover in both Ag-Ga liquids was suggested to link with the rearrangements of Ag and Ga atoms, i.e., Ag and Ga atoms prefer to associate with themselves in the higher temperature range above 1100 K, consistent with the accelerated increase of the strong covalently bonded Ga–Ga dimers in both Ag-Ga liquids. In addition, more studies from the energy aspect are still desirable to understand the rearrangements of Ag and Ga atoms in the higher temperature range in both Ag-Ga liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Pauli energy contribution to the nucleus-nucleus interaction

Background: The Pauli exclusion principle plays a crucial role as a building block of many-body quantal systems comprised of fermions. It also induces a “Pauli repulsion” in the interaction between di-nuclear systems. It has been shown in [Phys. Rev. C 95, 031601(R) (2017)] that the Pauli repulsion widens the nucleus-nucleus potential barrier, thus hindering sub-barrier fusion. Purpose: To investigate the proton and neutron contributions to the Pauli repulsion, both in the bare potential neglecting shape polarization and transfer between the reactants, as well as in the dynamical potential obtained by accounting for such dynamical rearrangements. Methods: As the basis of our study we utilize the Pauli kinetic energy (PKE) obtained by studying the nuclear localization function (NLF). Recently this approach has been generalized to incorporate all of the dynamical and time-odd terms present in the nuclear energy density functional. This approach is employed in the density constrained frozen Hartree-Fock (DCFHF) and in the density constrained time-dependent Hartree-Fock (DC- TDHF) microscopic methods. Results: The PKE spatial distribution shows that a repulsion occurs in the neck between the nuclei when they first touch. Inside the barrier, neutrons can contribute significantly more to the Pauli repulsion in neutron-rich systems. Dynamical effects tend to lower the Pauli repulsion near the barrier. Proton and neutron dynamical contributions to the PKE significantly differ inside the barrier for asymmetric collisions, which is interpreted as an effect of multinucleon transfer. Conclusions: The PKE is shown to make a significant contribution to nuclear interaction potentials. Protons and neutrons can play very different roles in both the bare potential and in the dynamical rearrangement. Further microscopic studies are required to better understand the role of transfer and to investigate the effect of pairing and deformation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Quantum simulations in effective model spaces: Hamiltonian-learning variational quantum eigensolver using digital quantum computers and application to the Lipkin-Meshkov-Glick model

Quantum simulations offer the potential to predict the structure and dynamics of nuclear many-body systems that are beyond the capabilities of classical computing. Generally, preparing the ground state of strongly-interacting many-body systems relevant to nuclear physics is however inefficient, even using ideal quantum computers. In addition, currently available NISQ-era quantum devices possess modest numbers of qubits, limiting the size of quantum many-body systems that can be simulated. In this context, a reformulation of the quantum many-body problems using truncated model spaces and Hamiltonians is desirable to make them more amenable to near-term quantum computers. The importance of symmetries in low-energy theories, including effective field theories (EFTs), lattice quantum chromodynamics (QCD), and effective model spaces for nuclear systems, in particular their interplay with the reduction of active Hilbert spaces, is well known. Lesser known is the fact that the non-commutivity of some symmetries and truncations of the model space can be profitably combined with variational calculations to rearrange the entanglement into localized structures and enable more efficient simulations. Here, the goal of the present study is to explore and utilize the non-commutivity of symmetries and model-space truncations of quantum many-body systems important to nuclear physics, particularly in combination with variational algorithms for quantum simulations and effective Hamiltonian learning. We introduce an iterative hybrid classical-quantum algorithm, Hamiltonian learning variational quantum eigensolver (HL-VQE), that simultaneously optimizes an effective Hamiltonian, thereby rearranging entanglement into the effective model space, and the associated ground-state wavefunction. Quantum simulations, using classical computers and IBM's superconducting-qubit quantum computers, are performed to demonstrate the HL-VQE algorithm, in the context of the Lipkin-Meshkov-Glick (LMG) model of interacting fermions, where the Hamiltonian transformation corresponds to an orbital rotation. We use a mapping where the number of qubits scales with the $\log$ of the size of the effective model space, rather than the particle number. HL-VQE is found to provide an exponential improvement in LMG-model calculations of the ground-state energy and wavefunction, compared to naive truncations without Hamiltonian learning, throughout a significant fraction of the Hilbert space. In the context of EFT, this corresponds to counterterms scaling exponentially with the cut-off as opposed to power law. Implementations on IBM's QExperience quantum computers and simulators for 1- and 2-qubit effective model spaces are shown to provide accurate and precise results, reproducing classical predictions. For a range of parameters defining the LMG model, the HL-VQE algorithm is found to have better scaling of quantum resources requirements than previously explored algorithms. In particular, the HL-VQE scales efficiently over a large fraction of the model space, in contrast to VQE alone. This work constitutes a step in the development of entanglement-driven quantum algorithms for descriptions of nuclear many-body systems. This, in part, leverages the potential of noisy intermediate-scale quantum (NISQ) devices. The exponential scaling of counterterms observed in this study suggests the possibility of more general applicability to other non-perturbative EFTs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

From canyons to valleys: Numerically continuing sticky-hard-sphere clusters to the landscapes of smoother potentials

Here, we study the energy landscapes of particles with short-range attractive interactions as the range of the interactions increases. Starting with the set of local minima for 6 ≤ $\textit{N}$ ≤ 12 hard spheres that are “sticky,” i.e., they interact only when their surfaces are exactly in contact, we use numerical continuation to evolve the local minima (clusters) as the range of the potential increases, using both the Lennard-Jones and Morse families of interaction potentials. As the range increases, clusters merge, until at long ranges only one or two clusters are left. We compare clusters obtained by continuation with different potentials and find that for short and medium ranges, up to about 30% of particle diameter, the continued clusters are nearly identical, both within and across families of potentials. For longer ranges, the clusters vary significantly, with more variation between families of potentials than within a family. We analyze the mechanisms behind the merge events and find that most rearrangements occur when a pair of nonbonded particles comes within the range of the potential. An exception occurs for nonharmonic clusters, i.e., those that have a zero eigenvalue in their Hessian, which undergo a more global rearrangement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Fracture mechanisms of sodium silicate glasses

Reactive classical molecular dynamics simulations of sodium silicate glasses, xNa 2 O–(100 – x)SiO 2 (x = 10–30), under quasi-static loading, were performed for the analysis of molecular scale fracture mechanisms. Mechanical properties of the sodium silicate glasses were consistent with experimentally reported values, and the amount of crack propagation varied with reported fracture toughness values. The most crack propagation occurred in NS20 systems (20-mol% Na 2 O) compared with the other simulated compositions. Dissipation via two mechanisms, the first through sodium migration as a lower activation energy process and the second through structural rearrangement as a higher activation energy process, was calculated and accounted for the energy that was not stored elastically or associated with the formation of new fracture surfaces. Here, a correlation between crack propagation and energy dissipation was identified, with systems with higher crack propagation exhibiting less energy dissipation. Sodium silicate glass compositions with lower energy dissipation also exhibited the most sodium movement and structural rearrangement within 10 Å of the crack tip during loading. Therefore, high sodium mobility near the crack tip may enable energy dissipation without requiring formation of structural defects. Therefore, the varying mobilities of the network modifiers near crack tips influence the brittleness and the crack growth rate of modified amorphous oxide systems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Biophysical and Structural Features of αβT ‐Cell Receptor Mechanosensing: A Paradigmatic Shift in Understanding T‐Cell Activation

ABSTRACT αβT cells protect vertebrates against many diseases, optimizing surveillance using mechanical force to distinguish between pathophysiologic cellular alterations and normal self‐constituents. The multi‐subunit αβT‐cell receptor (TCR) operates outside of thermal equilibrium, harvesting energy via physical forces generated by T‐cell motility and actin‐myosin machinery. When a peptide‐bound major histocompatibility complex molecule (pMHC) on an antigen presenting cell is ligated, the αβTCR on the T cell leverages force to form a catch bond, prolonging bond lifetime, and enhancing antigen discrimination. Under load, the αβTCR undergoes reversible structural transitions involving partial unfolding of its clonotypic immunoglobulin‐like (Ig) domains and coupled rearrangements of associated CD3 subunits and structural elements. We postulate that transitions provide critical energy to initiate the signaling cascade via induction of αβTCR quaternary structural rearrangements, associated membrane perturbations, exposure of CD3 ITAMs to phosphorylation by non‐receptor tyrosine kinases, and phase separation of signaling molecules. Understanding force‐mediated signaling by the αβTCR clarifies long‐standing questions regarding αβTCR antigen recognition, specificity and affinity, providing a basis for continued investigation. Future directions include examining atomistic mechanisms of αβTCR signal initiation, performance quality, tissue compliance adaptability, and T‐cell memory fate. The mechanotransduction paradigm will foster improved rational design of T‐cell based vaccines, CAR‐Ts, and adoptive therapies.

Immunology↗
DOE OSTI2024

Microsecond dynamics control the HIV-1 Envelope conformation

The HIV-1 Envelope (Env) glycoprotein facilitates host cell fusion through a complex series of receptor-induced structural changes. Although remarkable progress has been made in understanding the structures of various Env conformations, microsecond timescale dynamics have not been studied experimentally. Here, we used time-resolved, temperature-jump small-angle x-ray scattering to monitor structural rearrangements in an HIV-1 Env SOSIP ectodomain construct with microsecond precision. In two distinct Env variants, we detected a transition that correlated with known Env structure rearrangements with a time constant in the hundreds of microseconds range. A previously unknown structural transition was also observed, which occurred with a time constant below 10 μs, and involved an order-to-disorder transition in the trimer apex. Using this information, we engineered an Env SOSIP construct that locks the trimer in the prefusion closed state by connecting adjacent protomers via disulfides. Our findings show that the microsecond timescale structural dynamics play an essential role in controlling the Env conformation with impacts on vaccine design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Trojan horse method as an indirect approach to study resonant reactions in nuclear astrophysics

The primary goal of the Trojan horse method (THM) is to analyze resonant rearrangement reactions when the density of the resonance levels is low and statistical models cannot be applied. The main difficulty of the analysis is related with the facts that in the final state the THM reaction involves three particles and that the intermediate particle, which is transferred from the Trojan horse particle to the target nucleus to form a resonance state, is virtual. Another difficulty is associated with the Coulomb interaction between the particles, especially, taking into account that the goal of the THM is to study resonant rearrangement reactions at very low energies important for nuclear astrophysics. The exact theory of such reactions with three charged particles is very complicated and is not available. This is why different approximations are used to analyze THM reactions. In this review paper we describe a new approach based on a few-body formalism that provides a solid basis for deriving the THM reaction amplitude taking into account rescattering of the particles in the initial, intermediate and final states of the THM reaction. Since the THM uses a two-step reaction in which the first step is the transfer reaction populating a resonance state, we address the theory of the transfer reactions. The theory is based on the surface-integral approach and R-matrix formalism. We also discuss application of the THM to resonant reactions populating both resonances located on the second energy sheet and subthreshold resonances, which are subthreshold bound states located at negative energies close to thresholds. We consider the application of the THM to determine the astrophysical factors of resonant radiative-capture reactions at energies so low that direct measurements can hardly be performed due to the negligibly small penetrability factor in the entry channel of the reaction. Here, we elucidated the main ideas of the THM and outline necessary conditions to perform the THM experiments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Perspective—Potential Benefit of Li-Rich Cathode Materials: Reduction of Co and Ni Content Rather than Achievement of Ultra-High Capacities

In the conventional cycling protocol for lithium and manganese rich NMC layered oxides (LMRNMC), the upper cutoff voltage V cut is extended to ~ 4.8, to achieve capacities of similar to 250 mAh g -1 . With this mode of operation, structural rearrangements result in voltage fade upon cycling. Herein, a strategy is proposed to avoid these structural rearrangements based on (a) restricting V cut to values < ~ 4.6 to shut down the bulk instabilities, and (b) application of a (preferably) semi-coherent coating that protects the surface oxygen. The potential benefit of this strategy would be to minimize Co and Ni content, compared to Ni-rich NMC.

25 ENERGY STORAGE↗
DOE OSTI2022

DNA Sequence Analysis of an Inversion Hot Spot in Lobeliaceae Plastomes

The evolution of plastid genomes (plastomes) in land plants is typically conservative, with extensive structural rearrangements present in only a few groups. Early Southern blot analysis identified two Lobelia species that minimally required deletion of the plastid gene accD and five inversions to account for their plastome arrangement relative to the ancestral organization. Sixty alternative 5-step inversion scenarios could account for the observed arrangement, but only one scenario was consistent with the criterion of ‘common cause’ attributable to a putative rearrangement hot spot at the accD deletion-site. Plastome sequencing demonstrated that this previously hypothesized inversion order is historically accurate. Detailed reconstructions of the ancestral plastome organization before and after each inversion are presented herein. Stem-loop and disruption-rescue models were evaluated for each inversion. One inversion has an obvious stem-loop basis, but the other four inversions were primarily caused by serial insertion of foreign (extra-plastid) DNA bearing large open-reading frames that disrupted plastome organization at the accD deletion-site, and complete plastomes were rescued by seemingly arbitrary ligation or fortuitous recombination at the other inversion endpoint. Transposed copies of DNA segments from elsewhere in the plastome are frequently inserted at inversion junctions, and four junctions are consistent with the stem-loop ligation model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Beyond Conventional Charge Density Wave for Strongly Enhanced 2D Superconductivity in 1H‐TaS 2 Superlattices

Noncentrosymmetric transition metal dichalcogenide (TMD) monolayers offer a fertile platform for exploring unconventional Ising superconductivity (SC) and charge density waves (CDWs). However, the vulnerability of isolated monolayers to structural disorder and environmental oxidation often degrade their electronic coherence. Herein, an alternative approach is reported for fabricating stable and intrinsic monolayers of 1H-TaS2 sandwiched between SnS blocks in a (SnS) 1.15 TaS 2 van der Waals (vdW) superlattice. The SnS block layers not only decouple individual 1H-TaS 2 sublayers to endow them with monolayer-like electronic characteristics, but also protect the 1H-TaS 2 layers from electronic degradation. The results reveal the characteristic 3 × 3 CDW order in 1H-TaS 2 sublayers associated with electronic rearrangement in the low-lying sulfur p band, which uncovers a previously undiscovered CDW mechanism rather than the conventional Fermi surface-related framework. Additionally, the (SnS) 1.15 TaS 2 superlattice exhibits a strongly enhanced Ising-like SC with a layer-independent T c of ≈3.0 K, comparable to that of the isolated monolayer 1H-TaS 2 sample, presumably attributed to their monolayer-like characteristics and retained Fermi states. These results provide new insights into the long-debated CDW order and enhanced SC of monolayer 1H-TaS 2 , establishing bulk vdW superlattices as promising platforms for investigating exotic collective quantum phases in the 2D limit.

2D superconductivity↗
DOE OSTI2023

A Porous Crystalline Nitrone-Linked Covalent Organic Framework

Herein, we report the synthesis of a nitrone-linked covalent organic framework, COF-115, by combining N, N', N', N'''-(ethene-1, 1, 2, 2-tetrayltetrakis(benzene-4, 1-diyl))tetrakis(hydroxylamine) and terephthaladehyde via a polycondensation reaction. In this study, the formation of the nitrone functionality was confirmed by solid-state 13 C multi cross-polarization magic angle spinning NMR spectroscopy of the 13 C-isotope-labeled COF-115 and Fourier-transform infrared spectroscopy. The permanent porosity of COF-115 was evaluated through low-pressure N 2 , CO 2 , and H 2 sorption experiments. Water vapor and carbon dioxide sorption analysis of COF-115 and the isoreticular imine-linked COF indicated a superior potential of N-oxide-based porous materials for atmospheric water harvesting and CO 2 capture applications. Density functional theory calculations provided valuable insights into the difference between the adsorption properties of these COFs. Lastly, photoinduced rearrangement of COF-115 to the associated amide-linked material was successfully demonstrated.

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

Production of Biomass–Derived p –Hydroxybenzamide: Synthesis of p –Aminophenol and Paracetamol

As we work to transition the modern society that is based on non-renewable chemical feedstocks to a post-modern society built around renewable sources of energy, fuels, and chemicals, there is a need to identify the renewable resources and processes for converting them to platform chemicals. Herein, we explore a strategy for utilizing the p-hydroxybenzoate in biomass feedstocks (e.g., poplar and palm trees) and converting it into a portfolio of commodity chemicals. The targeted bio-derived product in the first processing stage is p-hydroxybenzamide produced from p-hydroxybenzoate esters found in the plant. In the second stage a continuous reaction process converts the p-hydroxybenzamide to p-aminophenol via the Hofmann rearrangement and recovers the unreacted p-hydroxybenzamide. In the third stage the p-aminophenol can be acetylated to form paracetamol, which is readily isolated by liquid/liquid extraction at >95 % purity and an overall p-hydroxybenzamide-to-paracetamol process yield of ~90 %. We explore how utilization of protecting groups alters the challenges in this process and expands the portfolio of possible products to include p-(methoxymethoxy)aniline and N-acetyl-p-(methoxymethoxy)aniline. These target compounds could become value-added renewably-sourced platform chemicals that could be used to produce biodegradable plastics, pigments, and pharmaceuticals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗