Results for “Dynamic Scattering” — Page 44

DOE OSTI2023

Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM

Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5’ G-tetrad interface with a persistently unstacked 3’ duplex. The surrogate complement poly dT loop preferably stacks onto the 3’ G-tetrad interface resulting in occlusion of both 5’ and 3’ tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Orbital-selective time-domain signature of nematicity dynamics in the charge-density-wave phase of La 1.65 Eu 0.2 Sr 0.15 CuO 4

Understanding the interplay between charge, nematic, and structural ordering tendencies in cuprate superconductors is critical to unraveling their complex phase diagram. Using pump–probe time-resolved resonant X-ray scattering on the (0 0 1) Bragg peak at the Cu L 3 and O K resonances, we investigate nonequilibrium dynamics of Q a = Q b = 0 nematic order and its association with both charge density wave (CDW) order and lattice dynamics in La 1.65 Eu 0.2 Sr 0.15 CuO 4 . The orbital selectivity of the resonant X-ray scattering cross-section allows nematicity dynamics associated with the planar O 2 p and Cu 3 d states to be distinguished from the response of anisotropic lattice distortions. A direct time-domain comparison of CDW translational-symmetry breaking and nematic rotational-symmetry breaking reveals that these broken symmetries remain closely linked in the photoexcited state, consistent with the stability of CDW topological defects in the investigated pump fluence regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Drift-cyclotron loss-cone instability in 3-D simulations of a sloshing-ion simple mirror

The kinetic stability of collisionless, sloshing beam-ion (45° pitch angle) plasma is studied in a three-dimensional (3-D) simple magnetic mirror, mimicking the Wisconsin high-temperature superconductor axisymmetric mirror experiment. The collisional Fokker–Planck code CQL3D-m provides a slowing-down beam-ion distribution to initialize the kinetic-ion/fluid-electron code Hybrid-VPIC, which then simulates free plasma decay without external heating or fuelling. Over 1 – 10 μs, drift-cyclotron loss-cone (DCLC) modes grow and saturate in amplitude. The DCLC scatters ions to a marginally stable distribution with gas-dynamic rather than classical-mirror confinement. Sloshing ions can trap cool (low-energy) ions in an electrostatic potential well to stabilize DCLC, but DCLC itself does not scatter sloshing beam-ions into the said well. Instead, cool ions must come from external sources such as charge-exchange collisions with a low-density neutral population. Manually adding cool ∼1keV ions improves beam-ion confinement several-fold in Hybrid-VPIC simulations, which qualitatively corroborates prior measurements from real mirror devices with sloshing ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Correlated atomic dynamics in liquid seen in real space and time

In liquids, the timescales for structure, diffusion, and phonon are all similar, of the order of a pico-second. This not only makes characterization of liquid dynamics difficult but also renders it highly questionable to describe liquids in these terms. In particular, the current definition of the structure of liquids by the instantaneous structure may need to be expanded because the liquid structure is inherently dynamic. Here, we advocate describing the liquid structure through the distinct-part of the Van Hove function, which can be determined by inelastic neutron and x-ray scattering measurements as well as by simulation. It depicts the dynamic correlation between atoms in space and time, starting with the instantaneous correlation function at t = 0. The observed Van Hove functions show that the atomic dynamics is strongly correlated in some liquids, such as water. The effect of atomic correlation on various transport properties of fluid, including viscosity and diffusivity, is discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗

DOE OSTI2020

Shaping the terahertz sound propagation in water under highly directional confinement

Here, we consider the possibility of shaping the high-frequency acoustic propagation in a liquid upon directional confinement. This hypothesis is investigated by inelastic x-ray scattering measurements on water confined in aligned multiwalled carbon nanotubes, in which the momentum transfer was either parallel or orthogonal to the confinement axis. The comparison between the spectra measured in these two scattering geometries highlights the anisotropic nature of the dynamic response of directionally confined water, thus potentially inspiring pathways to shape high-frequency sound propagation in isotropic systems. Finally, a Bayesian analysis of measured spectra unravels close similarities in the phonon dispersions of multiwalled nanotubes and graphite.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Spin dynamics in linear magnetoelectric material Mn 3 Ta 2 O 8

We performed inelastic neutron scattering experiments on single crystal samples of a linear magnetoelectric material Mn 3 Ta 2 O 8 , which exhibits a collinear antiferromagnetic order, to reveal the spin dynamics. Numerous modes observed in the neutron spectra were reasonably reproduced by linear spin-wave theory on the basis of the spin Hamiltonian including eight Heisenberg interactions and an easy-plane type single-ion anisotropy. In conclusion, the presence of strong frustration was found in the identified spin Hamiltonian.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Elastic nucleon-pion scattering at m π = 200 MeV from lattice QCD

Elastic nucleon-pion scattering amplitudes are computed using lattice QCD on a single ensemble of gauge field configurations with N f = 2 + 1 dynamical quark flavors and m π = 200 MeV. The s-wave scattering lengths with both total isospins I = 1/2 and I = 3/2 are inferred from the finite-volume spectrum below the inelastic threshold together with the I = 3/2 p-wave containing the Δ(1232) resonance. The amplitudes are well-described by the effective range expansion with parameters constrained by fits to the finite-volume energy levels, enabling a determination of the I = 3/2 scattering length with statistical errors below 5%, while the I = 1/2 scattering length is somewhat less precisely evaluated. Systematic errors due to excited states and the influence of higher partial waves are controlled, providing a step toward future computations down to physical light quark masses with multiple lattice spacings and volumes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Exploring fingerprints of ultrafast structural dynamics in molecular solutions with an X-ray laser

We apply ultrashort x-ray laser pulses to track optically excited structural dynamics of [Ir 2 (dimen) 4 ] 2+ molecules in solution. In our exploratory study we determine angular correlations in the scattered x-rays, which comprise a complex fingerprint of the ultrafast dynamics. Model-assisted analysis of the experimental correlation data allows us to elucidate various aspects of the photoinduced changes in the excited molecular ensembles. We unambiguously identify that in our experiment the photoinduced transition dipole moments in [Ir 2 (dimen) 4 ] 2+ molecules are oriented perpendicular to the Ir-Ir bond. The analysis also shows that the ground state conformer of [Ir 2 (dimen) 4 ] 2+ with a larger Ir–Ir distance is mostly responsible for the formation of the excited state. We also reveal that the ensemble of solute molecules can be characterized with a substantial structural heterogeneity due to solvent influence. In conclusion, the proposed x-ray correlation approach offers an alternative path for studies of ultrafast structural dynamics of molecular ensembles in the liquid and gas phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Analysis of Organic Electron Materials using Neutron Scattering (Final Report)

Neutron scattering is a powerful suite of measurement techniques that enable unique analysis of structure and dynamics of a wide variety of materials. Specifically, neutrons interact strongly with protons, which enables excellent contrast in light element organic materials that cannot be obtained with any other measurements. This series of three proposals focused on using inelastic neutron scattering (INS) to study the vibrations (dynamics) of the organic molecules involved in organic electronic devices. Our main goals were to demonstrate that INS is capable of elucidating new, useful, and unique knowledge about organic electronic samples that could be used to improve the function of devices or to solve outstanding problems that could not be solved using other measurement techniques. Since all of the goal involved using INS or other neutron techniques to do something “new” a large part of the effort was focused on complex data interpretation and development of modeling workflows that could be used by other members of the organic electronics community to study their materials. To facilitate the goal of making INS measurements more accessible to a broader community and for a wider range of materials, we optimized and engineered the computational workflows to be well documented, publicly available, and user friendly. The individual titles of the three sequential DOE-BES awards are: (1) Engineering doping profiles in organic semiconducting materials, (2) Measurement and modeling of molecular dopant structure and dynamics, and (3) Quantification of Dynamic Disorder in Electronic and Excitonic Organic Materials. For readability, this report is organized to highlight the progress of the research thematically. Many of the ideas started in one grant period and then spilled over into later awards and collaborative research.

36 MATERIALS SCIENCE↗

NASA NTRS1985

Directional reflectance factor distributions for cover types of Northern Africa

Directional reflectance factors that spanned the entire exitance hemisphere were collected on the ground throughout the morning period for common cover types in Tunisia, Africa. NOAA 7/8 AVHRR bands 1(0.58-0.68 micron) and 2 (0.7301.1 micron) were used in data collection. The cover types reported were a plowed field, annual grassland, steppe grassland, hard wheat, salt plain, and irrigated wheat. Several of these cover types had geometric structures that are extreme as compared to those reported in the literature. Comparisons were made between the dynamics of the observed reflectance distributions and those reported in the literature. It was found that the dynamics of the measured data could be explained by a combination of soil and vegetation scattering components. The data and analysis further validated physical principles that cause the reflectance distribution dynamics as proposed by field and simulation studies in the literature. Finally, the normalized difference transformation (Band 2 - Band 1)/(Band 1 + Band 2), which is useful in monitoring vegetation cover, generally decreased the variation in signal with changing view angle. However, several exceptions were noted.

Kimes, D. S.↗

DOE OSTI2019

A Robust and Efficient Deep Learning Method for Dynamical Mass Measurements of Galaxy Clusters

We demonstrate the ability of convolutional neural networks (CNNs) to mitigate systematics in the virial scaling relation and produce dynamical mass estimates of galaxy clusters with remarkably low bias and scatter. We present two models, CNN 1D and CNN 2D , which leverage this deep learning tool to infer cluster masses from distributions of member galaxy dynamics. Our first model, CNN 1D , infers cluster mass directly from the distribution of member galaxy line-of-sight velocities. Our second model, CNN 2D , extends the input space ofCNN 1D to learn on the joint distribution of galaxy line-of-sight velocities and projected radial distances. We train each model as a regression over cluster mass using a labeled catalog of realistic mock cluster observations generated from the MultiDark simulation and UniverseMachine catalog. We then evaluate the performance of each model on an independent set of mock observations selected from the same simulated catalog. The CNN models produce cluster mass predictions with lognormal residuals of scatter as low as 0.132 dex, greater than a factor of 2 improvement over the classical M–σ power-law estimator. Furthermore, the CNN model reduces prediction scatter relative to similar machinelearning approaches by up to 17% while executing in drastically shorter training and evaluation times (by a factor of 30) and producing considerably more robust mass predictions (improving prediction stability under variations in galaxy sampling rate by 30%).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

High Ammonia Adsorption in MFM-300 Materials: Dynamics and Charge Transfer in Host–Guest Binding

Ammonia (NH 3 ) is a promising energy resource owing to its high hydrogen density. However, its widespread application is restricted by the lack of efficient and corrosion-resistant storage materials. In this work, we report high NH 3 adsorption in a series of robust metal-organic framework (MOF) materials, MFM-300(M) (M = Fe, V, Cr, In). MFM-300(M) (M = Fe, V III , Cr) show fully reversible capacity for >20 cycles, reaching capacities of 16.1, 15.6, and 14.0 mmol g -1 , respectively, at 273 K and 1 bar. Under the same conditions, MFM-300(V IV ) exhibits the highest uptake among this series of MOFs of 17.3 mmol g -1 . In situ neutron powder diffraction, single-crystal X-ray diffraction, and electron paramagnetic resonance spectroscopy confirm that the redox-active V center enables host-guest charge transfer, with V IV being reduced to V III and NH 3 being oxidized to hydrazine (N 2 H 4 ). A combination of in situ inelastic neutron scattering and DFT modeling has revealed the binding dynamics of adsorbed NH 3 within these MOFs to afford a comprehensive insight into the application of MOF materials to the adsorption and conversion of NH 3 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Temporal and spatial separations between spin glass and short-range order

Broken-symmetry-induced order parameters account for many phenomena in physics. For spin glasses, this framework dictates the theoretical construction, whereas experiments have only established dynamical behaviors but not the physical entity. Experimental techniques have limitations when the spin glass is probed as an isolated state. Here, we create an evolution from a long-range order using well-controlled non-magnetic substitution on a sublattice. Neutron magnetic diffuse scattering of pico-second timescale reveals that the dynamics of short- and long-range order formation are not affected by disorder, but their spatial ranges are. Across all specimens, the inflection point of spin correlation length’s temperature dependence fully matches with the peak in heat capacity, while spin glass can freeze at millisecond timescale either above or below this characteristic temperature of spin-order formation. Our results identify the spin glass as single, uncorrelated spins at domain walls between spin clusters, and an uncorrelated coexistence of the two.

Dronova, Margarita G [Okinawa Institute of Science↗