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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 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein

Photoactive yellow protein (PYP) is a signaling protein whose internal p-coumaric acid chromophore undergoes reversible, light-induced trans-to-cis isomerization, which triggers a sequence of structural changes that ultimately lead to a signaling state. Since its discovery nearly 40 years ago, PYP has attracted much interest and has become one of the most extensively studied proteins found in nature. The method of time-resolved crystallography, pioneered by Keith Moffat, has successfully characterized intermediates in the PYP photocycle at near atomic resolution over 12 decades of time down to the sub-picosecond time scale, allowing one to stitch together a movie and literally watch a protein as it functions. But how close to reality is this movie? To address this question, results from numerous complementary time-resolved techniques including x-ray crystallography, x-ray scattering, and spectroscopy are discussed. Emerging from spectroscopic studies is a general consensus that three time constants are required to model the excited state relaxation, with a highly strained ground-state cis intermediate formed in less than 2.4 ps. Persistent strain drives the sequence of structural transitions that ultimately produce the signaling state. Crystal packing forces produce a restoring force that slows somewhat the rates of interconversion between the intermediates. Moreover, the solvent composition surrounding PYP can influence the number and structures of intermediates as well as the rates at which they interconvert. When chloride is present, the PYP photocycle in a crystal closely tracks that in solution, which suggests the epic movie of the PYP photocycle is indeed based in reality.

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

Magnetic functionalization and catalytic behavior of magnetic nanoparticles during laser photochemical graphitization of polyimide

We report laser-assisted photochemical graphitization of polyimides (PIs) into functional magnetic nanocomposites using laser irradiation of PI in the presence of magnetite nanoparticles (MNPs). PI Kapton sheets covered with MNP were photochemically treated under ambient conditions using a picosecond pulsed laser (1064 nm) to obtain an electrically conductive material. Scanning electron microscopy of the treated material revealed a layered magnetic nanoparticle/graphite (MNP/graphite) nanocomposite structure. Four probe conductivity measurements indicated that the nanocomposite has an electrical conductivity of 1550 ± 60 S/m. Superconducting quantum interference device magnetometer-based magnetic characterization of the treated material revealed an anisotropic ferromagnetic response in the MNP/graphite nanocomposite compared to the isotropic response of MNP. Raman spectroscopy of the MNP/graphite nanocomposite revealed a fourfold improvement in graphitization, suppression in disorder, and decreased nitrogenous impurities compared to the graphitic material obtained from laser treatment of just PI sheets. X-ray photoelectron spectroscopy, x-ray diffraction, and energy-dispersive x-ray spectroscopy were used to delineate the phase transformations of MNP during the formation of MNP/graphite nanocomposite. Post-mortem characterization indicates a possible photocatalytic effect of MNP during MNP/graphite nanocomposite formation. Under laser irradiation, MNP transformed from the initial Fe 3 O 4 phase to γ-Fe 2 O 3 and Fe 5 C 2 phases and acted as nucleation spots to catalyze the graphitization process of PI.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Transport coefficients of warm dense matter from Kohn-Sham density functional theory

We present a comprehensive study of transport coefficients including DC electrical conductivity and related optical properties, electrical contribution to the thermal conductivity, and the shear viscosity via ab initio molecular dynamics and density functional theory calculations on the “priority 1” cases from the “Second Charged-Particle Transport Coefficient Workshop” [Stanek et al., Phys. Plasmas (to be published 2024)]. The purpose of this work is to carefully document the entire workflow used to generate our reported transport coefficients, up to and including our definitions of finite size and statistical convergence, extrapolation techniques, and choice of thermodynamic ensembles. In pursuit of accurate optical properties, we also present a novel, simple, and highly accurate algorithm for evaluating the Kramers–Kronig relations. These heuristics are often not discussed in the literature, and it is hoped that this work will facilitate the reproducibility of our data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Noise reduction of stochastic density functional theory for metals

Density Functional Theory (DFT) has become a cornerstone in the modeling of metals. However, accurately simulating metals, particularly under extreme conditions, presents two significant challenges. First, simulating complex metallic systems at low electron temperatures is difficult due to their highly delocalized density matrix. Second, modeling metallic warm-dense materials at very high electron temperatures is challenging because it requires the computation of a large number of partially occupied orbitals. This study demonstrates that both challenges can be effectively addressed using the latest advances in linear-scaling stochastic DFT methodologies. Despite the inherent introduction of noise into all computed properties by stochastic DFT, this research evaluates the efficacy of various noise reduction techniques under different thermal conditions. Our observations indicate that the effectiveness of noise reduction strategies varies significantly with the electron temperature. Furthermore, we provide evidence that the computational cost of stochastic DFT methods scales linearly with system size for metal systems, regardless of the electron temperature regime.

Chemistry↗
DOE OSTI2024

Hyperfine interactions for small systems including transition-metal elements using self-interaction corrected density-functional theory

The interactions between the electronic magnetic moment and the nuclear spin moment, i.e., magnetic hyperfine (HF) interactions, play an important role in understanding electronic properties of magnetic systems and in realizing platforms for quantum information science applications. We investigate the HF interactions for atomic systems and small molecules, including Ti or Mn, by using Fermi–Löwdin orbital (FLO) based self-interaction corrected (SIC) density-functional theory. We calculate the Fermi contact (FC) and spin-dipole terms for the systems within the local density approximation (LDA) in the FLO-SIC method and compare them with the corresponding values without SIC within the LDA and generalized-gradient approximation (GGA), as well as experimental data. For the moderately heavy atomic systems (atomic number Z ≤ 25), we find that the mean absolute error of the FLO-SIC FC term is about 27 MHz (percentage error is 6.4%), while that of the LDA and GGA results is almost double that. Therefore, in this case, the FLO-SIC results are in better agreement with the experimental data. For the non-transition-metal molecules, the FLO-SIC FC term has the mean absolute error of 68 MHz, which is comparable to both the LDA and GGA results without SIC. For the seven transition-metal-based molecules, the FLO-SIC mean absolute error is 59 MHz, whereas the corresponding LDA and GGA errors are 101 and 82 MHz, respectively. Therefore, for the transition-metal-based molecules, the FLO-SIC FC term agrees better with experiment than the LDA and GGA results. We observe that the FC term from the FLO-SIC calculation is not necessarily larger than that from the LDA or GGA for all the considered systems due to the core spin polarization, in contrast to the expectation that SIC would increase the spin density near atomic nuclei, leading to larger FC terms.

Chemistry↗
DOE OSTI2024

Inferring fusion nuclear burnwidths with low gain photomultiplier impulse response functions

When an inertial confinement fusion implosion is compressed, it maintains thermonuclear density and temperatures for a very short time scale, about 100 ps. The Gamma Reaction History diagnostic measures the time evolution of the fusion burn, but its temporal resolution is limited by the use of a photomultiplier tube (PMT) to amplify the photon signal. Multichannel plate-based PMTs have a fast (~120 ps) full-width at half-max impulse response function (IRF), but the time scale is similar to the incoming physics signal. An analysis routine is used to remove the effect of the PMT IRF and infer the incident fusion burnwidth. With the National Ignition Facility achieving ignition and creating much brighter signals, the PMTs are run at gains three orders of magnitude lower than nominal operation. Calibration at these settings shows the PMT IRFs get ~15% wider. Taking the gain-dependent IRF can affect the inferred nuclear burnwidths by up to ~15%.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Improving the precision of forces in real-space pseudopotential density functional theory

The high-order finite difference real-space pseudopotential density functional theory (DFT) approach is a valuable method for large-scale, massively parallel DFT calculations. A significant challenge in the approach is the oscillating “egg-box” error introduced by aliasing associated with a coarse grid spacing. To address this issue while minimizing computational cost, we developed a finite difference interpolation (FDI) scheme [Roller et al., J. Chem. Theory Comput. 19, 3889 (2023)] as a means of exploiting the high resolution of the pseudopotential to reduce egg-box effects systematically. Here, we show an implementation of this method in the PARSEC code and examine the practical utility of the combination of FDI with additional methods for improving force precision and/or reducing its computational cost, including orbital-based forces, compensating charges (namely, adding and subtracting a judiciously chosen charge density such that the total density is unaltered), and a modified spatial domain in which the real-space grid is defined. Using selected small molecules, as well as metallic Li, as test cases, we show that a combination of all four aspects leads to a significant reduction in computational cost while retaining a high level of precision that supports accurate structures and vibrational spectra, as well as stable and accurate molecular dynamics runs.

Chemistry↗
DOE OSTI2024

Generalized quantum master equations can improve the accuracy of semiclassical predictions of multitime correlation functions

Multitime quantum correlation functions are central objects in physical science, offering a direct link between the experimental observables and the dynamics of an underlying model. While experiments such as 2D spectroscopy and quantum control can now measure such quantities, the accurate simulation of such responses remains computationally expensive and sometimes impossible, depending on the system’s complexity. A natural tool to employ is the generalized quantum master equation (GQME), which can offer computational savings by extending reference dynamics at a comparatively trivial cost. However, dynamical methods that can tackle chemical systems with atomistic resolution, such as those in the semiclassical hierarchy, often suffer from poor accuracy, limiting the credence one might lend to their results. By combining work on the accuracy-boosting formulation of semiclassical memory kernels with recent work on the multitime GQME, here we show for the first time that one can exploit a multitime semiclassical GQME to dramatically improve both the accuracy of coarse mean-field Ehrenfest dynamics and obtain orders of magnitude efficiency gains.

Chemistry↗
DOE OSTI2024

Effects of mosaic crystal instrument functions on x-ray Thomson scattering diagnostics

Mosaic crystals, with their high integrated reflectivities, are widely employed in spectrometers used to diagnose high energy density systems. X-ray Thomson scattering (XRTS) has emerged as a powerful diagnostic tool of these systems, providing in principle direct access to important properties such as the temperature via detailed balance. However, the measured XRTS spectrum is broadened by the spectrometer instrument function (IF), and without careful consideration of the IF one risks misdiagnosing system conditions. Here, we consider in detail the IF of 40 and 100 μm mosaic Highly Annealed Pyrolytic Graphite crystals, and how the broadening varies across the spectrometer in an energy range of 6.7–8.6 keV. Notably, we find a strong asymmetry in the shape of the IF toward higher energies. As an example, we consider the effect of the asymmetry in the IF on the temperature inferred via XRTS for simulated 80 eV CH plasmas and find that the temperature can be overestimated if an approximate symmetric IF is used. We, therefore, expect a detailed consideration of the full IF will have an important impact on system properties inferred via XRTS in both forward modeling and model-free approaches.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Local structure of zinc–indium–tin oxide films via grazing-incidence x-ray pair-distribution functions and theoretical methods

A detailed experimental and theoretical study on the local (r ≤ 4.5 Å) atomic structure of amorphous and crystalline zinc–indium–tin oxide (ZITO) thin films using grazing-incidence x-ray Pair-Distribution Functions (PDFs), ab initio Molecular Dynamics (MD), and Empirical Potential Structure Refinement (EPSR) Monte Carlo simulations is presented. High-energy synchrotron x rays, a two-dimensional detector, and different incident angles were used to probe the depth uniformity of five (ZnO) 0.15 (In 2 O 3 ) 0.70 (SnO 2 ) 0.15 films that were deposited via pulsed-laser deposition at growth temperatures (T G ) ranging from 25 to 300 °C. Films deposited at T G ≤ 150 °C were amorphous. The partially crystalline (T G = 200 °C) and fully crystalline (T G = 300 °C) films were highly textured. Both crystalline and amorphous structures were investigated using ab initio MD and EPSR Monte Carlo simulations. The density of the amorphous films determined from the experimental data agreed with MD calculations. Coordination numbers, bond lengths, and distortion for metal–oxygen and for both the edge- and corner-shared In–metal shells up to 4.5 Å obtained from PDF analysis closely agreed with MD and EPSR simulations. There is a pronounced decrease in the edge- and corner-shared In–Zn distances arising from the shorter Zn–O bond length, Zn–O tetrahedral coordination, and In–O–Zn angle in amorphous ZITO compared to its crystalline counterpart. A maximum in electrical mobility was observed for the amorphous film just before crystallization occurred. While the peak is broad, consistent with nearly unchanged overall cation–oxygen coordination in the amorphous films, ESPR results indicate that the tetrahedral coordination follows the conductivity trend.

Grazing Incidence X-ray↗
DOE OSTI2025

Semiclassical transition state theory through the lens of the restricted partition function

The wide adoption of transition state theory in resolving the rates of molecular processes relies on the simplification from reducing the formal and numerical expense of dynamics by a geometric constraint. Such a reduction is at odds with the uncertainty in localization that the uncertainty principle requires. While many forms of semiclassical transition state theory (SCTST) have been aimed at addressing this challenge, a popular approach has relied on resolving the underlying phase space structure of the exact rate formula to leverage Bohr–Sommerfeld quantization. Here, the Hernandez–Miller SCTST reframed the thermal rate formula into an integral of the so-called restricted partition function (RPF) over the action associated with the reaction. The density-of-state SCTST has reframed the rate formula in terms of the instanton’s density of states (DoS). Here, we show the relationship between the RPF-SCTST and the DoS-SCTST and derive the latter from the former. In this way, we help unify these branches of SCTST and provide a clearer formalism for future advances.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mixed quantum-classical methods for polaron spectral functions

In this work, using two distinct semiclassical approaches—namely, the mean-field Ehrenfest method and the mapping approach to surface hopping—we investigate the spectral function of a single charge interacting with phonons on a lattice. This quantity is relevant for the description of angle-resolved photoemission experiments. Focusing on the one-dimensional Holstein model, we compare the performance of these approaches across a range of coupling strengths and lattice sizes, exposing the relative strengths and weaknesses of each. We demonstrate that these approaches can be efficiently applied with reasonable accuracy to ab initio polaron models. Furthermore, our work provides a route to the calculation of spectral properties in realistic electron–phonon-coupled systems in a computationally inexpensive manner with encouraging accuracy.

Atomic and molecular spectra↗
DOE OSTI2026

Spectral deconvolution without the deconvolution: Extracting temperature from x-ray Thomson scattering spectra without the source-and-instrument function

X-ray Thomson scattering (XRTS) probes the dynamic structure factor of the system, but the measured spectrum is broadened by the combined source-and-instrument function (SIF) of the setup. In order to extract properties such as temperature from an XRTS spectrum, the broadening by the SIF needs to be removed. Recent work [Dornheim et al. Nat. Commun. 13 , 7911 (2022)] has suggested that the SIF may be deconvolved using the two-sided Laplace transform. However, the extracted information can depend strongly on the shape of the input SIF, and the SIF is in practice challenging to measure accurately. Here, we propose an alternative approach: we demonstrate that considering ratios of Laplace-transformed XRTS spectra collected at different scattering angles is equivalent to performing the deconvolution, but without the need for explicit knowledge of the SIF. From these ratios, it is possible to directly extract the temperature from the scattering spectra, when the system is in thermal equilibrium. We find the method to be generally robust to spectral noise and physical differences between the spectrometers, and we explore situations in which the method breaks down. Furthermore, the fact that consistent temperatures can be extracted for systems in thermal equilibrium indicates that non-equilibrium effects could be identified by inconsistent temperatures of a few eV between the ratios of three or more scattering angles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Structural and functional dynamics of human cone cGMP-phosphodiesterase important for photopic vision

Cone cGMP-phosphodiesterase (PDE6) is the key effector enzyme for daylight vision, and its properties are critical for shaping distinct physiology of cone photoreceptors. We determined the structures of human cone PDE6C in various liganded states by single-particle cryo-EM that reveal essential functional dynamics and adaptations of the enzyme. Our analysis exposed the dynamic nature of PDE6C association with its regulatory γ-subunit (Pγ) which allows openings of the catalytic pocket in the absence of phototransduction signaling, thereby controlling photoreceptor noise and sensitivity. We demonstrate evolutionarily recent adaptations of PDE6C stemming from residue substitutions in the Pγ subunit and the noncatalytic cGMP binding site and influencing the Pγ dynamics in holoPDE6C. Thus, our structural analysis sheds light on the previously unrecognized molecular evolution of the effector enzyme in cones that advances adaptation for photopic vision.

Science & Technology - Other Topics↗
DOE OSTI2025

The GRAS protein RAM1 interacts with WRI transcription factors to regulate plant genes required for arbuscule development and function

During arbuscular mycorrhiza (AM) symbiosis AM fungi form tree-shaped structures called arbuscules in root cortex cells of host plants. Arbuscules and their host cells are central for reciprocal nutrient exchange between the symbionts.REQUIRED FOR ARBUSCULAR MYCORRHIZATION1(RAM1) encodes a GRAS protein crucial for transcriptionally regulating plant genes needed for arbuscule development and nutrient exchange. Similar to other GRAS proteins, RAM1 likely does not bind to DNA and how RAM1 activates its target promoters remained elusive. Here, we demonstrate that RAM1 interacts with five AM-induced APETALA 2 (AP2) transcription factors of the WRINKLED1-like family called CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), WRI3, WRI5a, WRI5b, and WRI5c via a C-terminal domain containing the M2/M2a motif. This motif is conserved and enriched in WRI proteins encoded by genomes of AM-competent plants. RAM1 together with any of these WRI proteins activates the promoters of genes required for symbiotic nutrient exchange, namelyRAM2,STUNTED ARBUSCULES (STR),andPHOSPHATE TRANSPORTER 4 (PT4), inNicotiana benthamianaleaves. This activation as well as target promoter induction inLotus japonicushairy roots depends onMYCS(MYCORRHIZA SEQUENCE)-elements andAW-boxes, previously identified as WRI-binding sites. TheWRIgenes are activated in two waves: Transcription ofRAM1,CBX1,andWRI3is coregulated by calcium- and calmodulin-dependent protein kinase-activated CYCLOPS, through theAMCYC-REin their promoter, and DELLA, whileWRI5a,b,andcpromoters containMYCS-elements andAW-boxes and can be activated by RAM1 heterocomplexes with CBX1 or WRI3. We propose that RAM1 provides an activation domain to DNA-binding WRI proteins to activate genes with central roles in AM development and function.

Science & Technology - Other Topics↗
DOE OSTI2024

Using ground state and excited state density functional theory to decipher 3d dopant defects in GaN

Abstract Using ground state density functional theory (DFT) and implementing an occupation-constrained DFT (occ-DFT) for self-consistent excited state calculations, we decipher the electronic structure of the Mn dopant and other 3 d defects in GaN across the band gap. Our analysis, validated with broad agreement with defect levels (ground-state calculations) and photoluminescence data (excited-state calculations), mandates reinterpretation and reassignment of 3 d defect data in GaN. The Mn Ga defect is determined to span stable charge states from (1−) in n -type GaN through (2+) in p -type GaN. The Mn(2+) is predicted to be a d 2 ground state spin triplet defect with a singlet excited state, isoelectronic with the defect associated with the 1.19 eV photoluminescence in n -type GaN. The combined analysis of defect levels and excited states invites reassessment of all d 2 -capable dopants in GaN. We demonstrate that the 1.19 eV defect, a candidate defect for optically controlled quantum applications, cannot be the Cr(1+) assumed in literature and instead must be the V(0). The combined ground-state/excited-state DFT analysis is shown to be able to chemically fingerprint defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Revealing symmetry-broken superconducting configurations by density functional theory

A coherent theory for the superconductivity of both conventional and unconventional superconductors is currently lacking. Here we show that superconductivity arises from the formation of a symmetry-broken superconducting configuration (SCC) due to atomic perturbation of the normal conducting configuration (NCC). This electron–phonon interaction creates straight one-dimensional tunnels (SODTs) for charge density of electrons and/or holes as revealed by the calculations based on density functional theory (DFT). The SODTs act as resistance-free superhighways and are correlated to the Cooper pairs in the Bardeen–Cooper–Schrieffer (BCS) theory. The formation of SODTs implies that the electron–phonon interaction in the BCS theory can be represented by the difference in charge densities between SCC and NCC predicted by DFT. The present work highlights that in conventional superconductors, SODTs are embedded within the bulk materials and are easily destroyed by phonon vibrations, resulting in a low critical superconducting temperature (T C ). Conversely, in unconventional superconductors such as YBa 2 Cu 3 O 7 (YBCO 7 ), SODTs are protected by a layered pontoon structure with very weak bonding to the bulk materials, maintaining SODTs’ stability at higher temperatures and leading to a much higher T C . The present approach is validated for 14 conventional superconductors of 18 pure elements and MgB 2 examined in this work, including the presently predicted superconductivity in Cu, Ag, Au, Sb, Bi, and MgB 2 at 0 K and 0 GPa, and one unconventional superconductor of YBCO 7 . Our discovery indicates that DFT can be a practical tool for predicting superconductors, enabling a systematic search for new superconducting materials in the future.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Semi-analytical covariance matrices for two-point correlation function for DESI 2024 data

We present an optimized way of producing the fast semi-analytical covariance matrices for the Legendre moments of the two-point correlation function, taking into account survey geometry and mimicking the non-Gaussian effects. We validate the approach on simulated (mock) catalogs for different galaxy types, representative of the Dark Energy Spectroscopic Instrument (DESI) Data Release 1, used in 2024 analyses. We find only a few percent differences between the mock sample covariance matrix and our results, which can be expected given the approximate nature of the mocks, although we do identify discrepancies between the shot-noise properties of the DESI fiber assignment algorithm and the faster approximation (emulator) used in the mocks. Importantly, we find a close agreement (≤ 8% relative differences) in the projected errorbars for distance scale parameters for the baryon acoustic oscillation measurements. This confirms our method as an attractive alternative to simulation-based covariance matrices, especially for non-standard models or galaxy sample selections, making it particularly relevant to the broad current and future analyses of DESI data.

79 ASTRONOMY AND ASTROPHYSICS↗