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At least 1,783 records · Page 99

Retrieving functional pathways of biomolecules from single-particle snapshots

Abstract A primary reason for the intense interest in structural biology is the fact that knowledge of structure can elucidate macromolecular functions in living organisms. Sustained effort has resulted in an impressive arsenal of tools for determining the static structures. But under physiological conditions, macromolecules undergo continuous conformational changes, a subset of which are functionally important. Techniques for capturing the continuous conformational changes underlying function are essential for further progress. Here, we present chemically-detailed conformational movies of biological function, extracted data-analytically from experimental single-particle cryo-electron microscopy (cryo-EM) snapshots of ryanodine receptor type 1 (RyR1), a calcium-activated calcium channel engaged in the binding of ligands. The functional motions differ substantially from those inferred from static structures in the nature of conformationally active structural domains, the sequence and extent of conformational motions, and the way allosteric signals are transduced within and between domains. Our approach highlights the importance of combining experiment, advanced data analysis, and molecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of manganese substitution of ferrite nanoparticles on particle grain structure

To investigate the influence of manganese substitution on the saturation magnetization of manganese ferrite nanoparticles, samples with various compositions (Mn x Fe 3–x O 4 , x = 0, 0.25, 0.5, 0.75, and 1) were synthesized and characterized. The saturation magnetization of such materials was both calculated using density functional theory and measured via vibrating sample magnetometry. A discrepancy was found; the computational data demonstrated a positive correlation between manganese content and saturation magnetization, while the experimental data exhibited an inverse correlation. X-ray diffraction (XRD) and magnetometry results indicated that the crystallite diameter and the magnetic diameter decrease when adding more manganese, which could explain the loss of magnetization of the particles. For 20 nm nanoparticles, with increasing manganese substitution level, the crystallite size decreases from 10.9 nm to 6.3 nm and the magnetic diameter decreases from 15.1 nm to 3.5 nm. Further high resolution transmission electron microscopy (HRTEM) analysis confirmed the manganese substitution induced defects in the crystal lattice, which encourages us to find ways of eliminating crystalline defects to make more reliable ferrite nanoparticles.

36 MATERIALS SCIENCE↗

Direct Measurement of the Nickel Spectrum in Cosmic Rays in the Energy Range from 8.8 GeV/$\mathcal{n}$ to 240 GeV/$\mathcal{n}$ with CALET on the International Space Station

The relative abundance of cosmic ray nickel nuclei with respect to iron is by far larger than for all other transiron elements; therefore it provides a favorable opportunity for a low background measurement of its spectrum. Since nickel, as well as iron, is one of the most stable nuclei, the nickel energy spectrum and its relative abundance with respect to iron provide important information to estimate the abundances at the cosmic ray source and to model the Galactic propagation of heavy nuclei. However, only a few direct measurements of cosmic-ray nickel at energy larger than ~ 3 GeV/n are available at present in the literature, and they are affected by strong limitations in both energy reach and statistics. In this Letter, we present a measurement of the differential energy spectrum of nickel in the energy range from 8.8 to 240 GeV/n , carried out with unprecedented precision by the Calorimetric Electron Telescope (CALET) in operation on the International Space Station since 2015. The CALET instrument can identify individual nuclear species via a measurement of their electric charge with a dynamic range extending far beyond iron (up to atomic number Z = 40 ). The particle’s energy is measured by a homogeneous calorimeter (1.2 proton interaction lengths, 27 radiation lengths) preceded by a thin imaging section (3 radiation lengths) providing tracking and energy sampling. This Letter follows our previous measurement of the iron spectrum [O. Adriani et al. (CALET Collaboration), Phys. Rev. Lett. 126, 241101 (2021).], and it extends our investigation on the energy dependence of the spectral index of heavy elements. It reports the analysis of nickel data collected from November 2015 to May 2021 and a detailed assessment of the systematic uncertainties. In the region from 20 to 240 GeV/n our present data are compatible within the errors with a single power law with spectral index -2.51 ± 0.07 .

79 ASTRONOMY AND ASTROPHYSICS↗

Sources of stochasticity in the growth of cloud droplets: supersaturation fluctuations versus turbulent transport

The role played by fluctuations of supersaturation in the growth of cloud droplets is examined in this study. The stochastic condensation framework and the three regimes of activation of cloud droplets – namely, mean-dominant, fluctuation-influenced, and fluctuation-dominant, are used for analyzing the data from high-resolution large-eddy simulations of the Pi convection-cloud chamber. Based on a detailed budget analysis the significance of all the terms in the evolution of the droplet size distribution equation is evaluated in all three regimes. The analysis indicates that the mean-growth rate is a dominant process in shaping the droplet size distribution in all three regimes. Turbulence introduces two sources of stochasticity, turbulent transport and particle lifetime, and supersaturation fluctuations. The transport of cloud droplets plays an important role in all three regimes, whereas the direct effect of supersaturation fluctuations is primarily related to the activation and growth of the small droplets in the fluctuation-influenced and fluctuation-dominant regimes. Here, we compare our results against the previous studies (experimental and theory) of the Pi chamber, and discuss the limitations of the existing models based on the stochastic condensation framework. Furthermore, we extend the discussion of our results to atmospheric clouds, and in particular focus on recent adiabatic turbulent cloud parcel simulations based on the stochastic condensation framework, and emphasize the importance of entrainment/mixing and turbulent transport in shaping the droplet size distribution.

54 ENVIRONMENTAL SCIENCES↗

Understanding neutrinos with accelerator beams and liquid argon time-projection chambers: ICARUS and DUNE

A global program of experiments has worked towards characterizing neutrino oscillation over the past few decades. However, important parameters remain to be measured, and mysteries remain to be elucidated. Current and upcoming experiments are targeting the open questions and probing the consistency of the neutrino oscillation paradigm. Likewise, the liquid argon (LAr) time-projection chamber (TPC) has emerged as a sensitive particle detection technology for neutrino experiments. A current generation of LAr TPC detectors are being used to study neutrinos while also gaining important experience in operating and analyzing with this technology. SBND, MicroBooNE, and ICARUS have collected or are collecting data from beams at Fermilab (near Chicago) to explore the possibility of a sterile neutrino and/or other beyond Standard Model (BSM) physics. SBND and ICARUS will be used to conduct a two-detector analysis as part of the Short Baseline Neutrino (SBN) Program. Additionally, these detectors are enabling important neutrino interaction studies necessary to prepare for the next generation of oscillation experiments. One such oscillation experiment that will come online over the next years is the Deep Underground Neutrino Experiment (DUNE), which will install multiple 10 kiloton LAr TPCs underground in South Dakota (south of Saskatchewan) to conduct oscillation measurements with neutrinos originating in a beamline at Fermilab. A detector complex will be installed at Fermilab as well, to study the beam before the expected flavour oscillations. This “near detector” will also employ a LAr TPC, with a segmented and pixel-based design, as well as other technologies to constrain uncertainties in the oscillation measurement by characterizing the beam and neutrino interactions. This talk will discuss the ICARUS and DUNE experiments, the LAr TPC detector technology, and the efforts to realize and leverage these experiments to better understand the properties of neutrinos.

Howard, Bruce L. [Fermilab]↗

Harnessing stratospheric diffusion barriers for enhanced climate geoengineering

Stratospheric sulfate aerosol geoengineering is a proposed method to temporarily intervene in the climate system to increase the reflectance of shortwave radiation and reduce mean global temperature. In previous climate modeling studies, choosing injection locations for geoengineering aerosols has, thus far, only utilized the average dynamics of stratospheric wind fields instead of accounting for the essential role of time-varying material transport barriers in turbulent atmospheric flows. Here we conduct the first analysis of sulfate aerosol dispersion in the stratosphere, comparing what is now a standard fixed-injection scheme with time-varying injection locations that harness short-term stratospheric diffusion barriers. We show how diffusive transport barriers can quickly be identified, and we provide an automated injection location selection algorithm using short forecast and reanalysis data. Within the first 7 d days of transport, the dynamics-based approach is able to produce particle distributions with greater global coverage than fixed-site methods with fewer injections. Additionally, this enhanced dispersion slows aerosol microphysical growth and can reduce the effective radii of aerosols up to 200–300 d after injection. While the long-term dynamics of aerosol dispersion are accurately predicted with transport barriers calculated from short forecasts, the long-term influence on radiative forcing is more difficult to predict and warrants deeper investigation. Statistically significant changes in radiative forcing at timescales beyond the forecasting window showed mixed results, potentially increasing or decreasing forcing after 1 year when compared to fixed injections. We conclude that future feasibility studies of geoengineering should consider the cooling benefits possible by strategically injecting sulfate aerosols at optimized time-varying locations. Our method of utilizing time-varying attracting and repelling structures shows great promise for identifying optimal dispersion locations, and radiative forcing impacts can be improved by considering additional meteorological variables.

54 ENVIRONMENTAL SCIENCES↗

Isotopic composition of low energy beryllium in the galactic cosmic rays

The multielement charged-particle telescope on the IMP-5 satellite obtained data essentially continuously for more than three years in the interplanetary medium under stable instrument conditions which have made it possible to separate the H, He, and Be isotopes in the galactic cosmic radiation using the technique of double dE/dx vs residual E and particle range measurements. Special emphasis is placed on demonstrating that in the energy range from 50 to 150 MeV/nucleon the instrument clearly resolved Be-7 vs Be-9. A detailed analysis of approximately 100 Be events collected over the mission lifetime yields the ratios (Be-7/Be) = 0.50 plus or minus 0.07, (Be-9/Be) = 0.41 plus or minus 0.10, and (Be-10/Be) = 0.09 plus or minus 0.10. These results are consistent with current models of galactic cosmic ray propagation after taking account of the effects of solar modulation.

Garcia-Munoz, M.↗

Computational methods for analyzing the transmission characteristics of a beta particle magnetic analysis system

Computational methods were developed to study the trajectories of beta particles (positrons) through a magnetic analysis system as a function of the spatial distribution of the radionuclides in the beta source, size and shape of the source collimator, and the strength of the analyzer magnetic field. On the basis of these methods, the particle flux, their energy spectrum, and source-to-target transit times have been calculated for Na-22 positrons as a function of the analyzer magnetic field and the size and location of the target. These data are in studies requiring parallel beams of positrons of uniform energy such as measurement of the moisture distribution in composite materials. Computer programs for obtaining various trajectories are included.

Singh, J. J.↗

A Concept for the Inclusion of Analytical and Computational Capability in Existing Systems for Measurement of Neutron Flux

For approximately two decades, efforts have been sponsored by NASA's Marshall Space Flight Center to make possible high-speed, automated classification and quantification of constituent materials in various harsh environments. MSFC, along with the Air Force/Arnold Engineering Development Center, has led the work, developing and implementing systems that employ principles of emission and absorption spectroscopy to monitor molecular and atomic particulates in gas plasma of rocket engine flow fields. One such system identifies species and quantifies mass loss rates in H2/O2 rocket plumes. Other gases have been examined and the physics of their detection under numerous conditions were made a part of the knowledge base for the MSFC/USAF team. Additionally, efforts are being advanced to hardware encode components of the data analysis tools in order to address real-time operational requirements for health monitoring and management. NASA has a significant investment in these systems, warranting a spiral approach that meshes current tools and experience with technological advancements. This paper addresses current systems - the Optical Plume Anomaly Detector (OPAD) and the Engine Diagnostic Filtering System (EDIFIS) - and discusses what is considered a natural progression: a concept for migrating them towards detection of high energy particles, including neutrons and gamma rays. The proposal outlines system development to date, basic concepts for future advancements, and recommendations for accomplishing them.

Patrick, Clinton↗

Saturn's Magnetosphere Interaction with Titan for T9 Encounter: 3D Hybrid Modeling and Comparison with CAPS Observations

Global dynamics of ionized and neutral gases in the environment of Titan plays an important role in the interaction of Saturn s magnetosphere with Titan. Several hybrid simulations of this problem have already been done (Brecht et al., 2000; Kallio et al., 2004; Modolo et al., 2007a; Simon et al., 2007a, 2007b; Modolo and Chanteur, 2008). Observational data from CAPS for the T9 encounter (Sittler et al., 2009) indicates an absence of O(+) heavy ions in the upstream that change the models of interaction which were discussed in current publications (Kallio et al., 2004; Modolo et al., 2007a; Simon et al., 2007a, 2007b; Ma et al., 2007; Szego et al., 2007). Further analysis of the CAPS data shows very low density or even an absence of H(+) ions in upstream. In this paper we discuss two models of the interaction of Saturn s magnetosphere with Titan: (A) high density of H(+) ions in the upstream flow (0.1/cu cm), and (B) low density of H(+) ions in the upstream flow (0.02/cu cm). The hybrid model employs a fluid description for electrons and neutrals, whereas a particle approach is used for ions. We also take into account charge-exchange and photoionization processes and solve self-consistently for electric and magnetic fields. The model atmosphere includes exospheric H(+), H(2+), N(2+)and CH(4+) pickup ion production as well as an immobile background ionosphere and a shell distribution for active ionospheric ions (M(sub i)=28 amu). The hybrid model allows us to account for the realistic anisotropic ion velocity distribution that cannot be done in fluid simulations with isotropic temperatures. Our simulation shows an asymmetry of the ion density distribution and the magnetic field, including the formation of Alfven wing-like structures. The results of the ion dynamics in Titan s environment are compared with Cassini T9 encounter data (CAPS).

Lipatov, A. S.↗

Investigating the Differential Emission Measure and Energetics of Microflares with Combined SDO/AIA and RHESSI Observations

An important question in solar physics is whether solar microflares, the smallest currently observable flare events in X-rays, possess the same energetic properties as large flares. Recent surveys have suggested that microflares may be less efficient particle accelerators than large flares, and hence contribute less non-thermal energy, which may have implications for coronal heating mechanisms. We therefore explore the energetic properties of microflares by combining EUV and X-ray measurements. We present forward-fitting differential emission measure (DEM) analysis of 10 microflares. The fitting is constrained by combining, for the first time, high-temperature Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) observations and flux data from the Solar Dynamics Observatory (SDO) Atmospheric Imaging Assembly (AIA). Two fitting models are tested for the DEM; a Gaussian distribution and a uniform DEM profile. A Gaussian fit proved unable to explain the observations for any of the studied microflares. However, 8 of 10 events studied were reasonably fit by a uniform DEM profile. Hence microflare plasma can be considered to be significantly multi-thermal, and may not be significantly peaked or contain resolvable fine structure, within the uncertainties of the observational instruments. The thermal and non-thermal energy is estimated for each microflare, comparing the energy budget with an isothermal plasma assumption. From the multi-thermal fits the minimum non-thermal energy content was found to average approximately 30% of the estimated thermal energy. By comparison, under an isothermal model the non-thermal and thermal energy estimates were generally comparable. Hence, multi-thermal plasma is an important consideration for solar microflares that substantially alters their thermal and non-thermal energy content.

Sun: flares↗

Charged Particle Environment Definition for NGST: L2 Plasma Environment Statistics

The plasma environment encountered by the Next Generation Space Telescope satellite in a halo orbit about L2 can include the Earth's magnetotail and magnetosheath in addition to the solar wind depending on the orbital radius chosen for the mission. Analysis of plasma environment impacts on the satellite requires knowledge of the average and extreme plasma characteristics to assess the magnitude of spacecraft charging and materials degradation expected for the mission lifetime. This report describes the analysis of plasma data from instruments onboard the IMP 8 and Geotail spacecraft used to produce the plasma database for the LRAD engineering-level phenomenology code developed to provide the NGST L2 environment definition.

Minow, Joseph I.↗

CGRO/BATSE Data Support the New Paradigm For GRB Prompt Emission and the New L-i(nTh)-E-peak,i(nTh,rest) Relation

The paradigm for gamma-ray burst (GRB) prompt emission is changing. Since early in the Compton Gamma RayObservatory (CGRO) era, the empirical Band function has been considered a good description of the keV-MeV-gamma-ray prompt emission spectra despite the fact that its shape was very often inconsistent with the theoretical predictions, especially those expected in pure synchrotron emission scenarios. We have recently established a new observational model analyzing data of the NASA Fermi Gamma-ray Space Telescope. In this model, GRB prompt emission would be a combination of three main emission components: (i) a thermal-like component that we have interpreted so far as emission from the jet photosphere, (ii) a non-thermal component that we have interpreted so far as either synchrotron radiation from the propagating and accelerated charged particles within the jet or reprocessed jet photospheric emission, and (iii) an additional non-thermal (cutoff) power law (PL) extending from low to high energies in gamma-rays and most likely of inverse Compton origin. In this article we reanalyze some of the bright GRBs, namely GRBs 941017, 970111, and 990123, observed with the Burst And Transient Source Experiment (BATSE) on board CGRO with the new model. We conclude that BATSE data for these three GRBs are fully consistent with the recent results obtained with Fermi: some bright BATSE GRBs exhibit three separate components during the prompt phase with similar spectral parameters as those reported from Fermi data. In addition, the analysis of the BATSE GRBs with the new prompt emission model results in a relation between the time-resolved energy flux of the non-thermal component, F(in)(Th), and its corresponding nuFnu spectral peak energy,Epeak,inTh (i.e., FinThEpeak,inTh ), which has a similar index when fitted to a PL as the one initially derived from Fermi data. For GRBs with known redshifts (z) this results in a possible universal relation between the luminosity of the non-thermal component, LinTh, and its corresponding nuFnu spectral peak energy in the rest frame, Epeak,iNT,rest (i.e.,LinThEpeak,iNT,rest). We estimated the redshifts of GRBs 941017 and 970111 using GRB 990123 with z = 1.61as a reference. The estimated redshift for GRB 941017 is typical for long GRBs and the estimated redshift for GRB970111 is right in the range of the expected values for this burst.

acceleration of particles – black hole physics â↗

Development and Demonstration of a Computational Tool for the Analysis of Particle Vitiation Effects in Hypersonic Propulsion Test Facilities

In order to improve the understanding of particle vitiation effects in hypersonic propulsion test facilities, a quasi-one dimensional numerical tool was developed to efficiently model reacting particle-gas flows over a wide range of conditions. Features of this code include gas-phase finite-rate kinetics, a global porous-particle combustion model, mass, momentum and energy interactions between phases, and subsonic and supersonic particle drag and heat transfer models. The basic capabilities of this tool were validated against available data or other validated codes. To demonstrate the capabilities of the code a series of computations were performed for a model hypersonic propulsion test facility and scramjet. Parameters studied were simulated flight Mach number, particle size, particle mass fraction and particle material.

Perkins, Hugh Douglas↗

Cosmological preference for a negative neutrino mass

The most precise determination of the sum of neutrino masses from cosmological data, derived from analysis of the cosmic microwave background (CMB) and baryon acoustic acoustic oscillations (BAO) from the Dark Energy Spectroscopic Instrument (DESI), favors a value below the minimum inferred from neutrino flavor oscillation experiments. We explore which data is most responsible of this puzzling aspect of the current constraints on neutrino mass and whether it is related to other anomalies in cosmology. We demonstrate conclusively that the preference for negative neutrino masses is a consequence of larger than expected lensing of the CMB in both the two- and four-point lensing statistics. Furthermore, we show that this preference is robust to changes in likelihoods of the BAO and CMB optical depth analyses given the available data. We then show that this excess clustering is not easily explained by changes to the expansion history and is likely distinct from the preference for for dynamical dark energy in DESI BAO data. Finally, we discuss how future data may impact these results, including an analysis of Planck CMB with mock DESI 5-year data. Here, we conclude that the negative neutrino mass preference is likely to persist even as more cosmological data is collected in the near future.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Bulk vs Intrinsic Activity of NiFeO x Electrocatalysts in the Oxygen Evolution Reaction: The Influence of Catalyst Loading, Morphology, and Support Material

We used a combination of ultrahigh vacuum surface science techniques, X-ray spectroscopy, electrochemistry, and density functional theory (DFT), to characterize the influence of catalyst morphology, loading/coverage, and substrate material on the bulk (all atoms) and intrinsic (electrochemically accessible atoms) activity of NiFeO x electrocatalysts in the oxygen evolution reaction (OER). NiFeO x catalysts were grown on both Au(111) and highly oriented pyrolytic graphite (HOPG) electrodes. DFT predicted Fe edge-site atoms at the NiFeO x /Au(111) interface to be the most thermodynamically favorable reaction center, and X-ray absorption spectroscopy data indicated small NiFeO x catalyst particles on Au(111) contained a high population of OER active Fe edge-site atoms. However, restructuring of the Au(111) surface due to repeated oxidation and reduction cycles of the OER CV measurements encapsulated small NiFeO x nanoparticles at catalyst loadings below ~1.5 nmol metal /cm 2 , passivated catalyst edges and reduced bulk OER activity of Au-supported NiFeO x compared with HOPG-supported ones. Analysis of intrinsic activity revealed that the Au(111) support strongly benefited electrochemically accessible NiFeO x atoms, and we observed a 2–3 fold activity enhancement compared with HOPG-supported catalysts for loadings above ~1 nmol metal /cm 2 . Overall, evaluating bulk vs intrinsic activity and identifying loading/coverage-dependent support effects is important for accurately probing fundamental interfacial chemistry, choosing suitable catalyst loadings and supports, and optimizing system parameters to maximize the performance of electrocatalyst systems.

36 MATERIALS SCIENCE↗

Internal rotation of ELM filaments on NSTX

Edge localized modes (ELMs) are a threat to tokamaks due to their high heat and particle loads on plasma facing components. A significant portion of this energy is carried and deposited by the emerging ELM filaments, whose dynamics are directly connected to their impact. Therefore, understanding their underlying physics is important for the operation of future fusion reactors. Our paper extends our knowledge of ELM filaments by reporting on their internal rotation (spinning) around the magnetic field lines along which they are extended. Our analysis of gas-puff imaging data on National Spherical Torus Experiment shows that ELM filaments are characterized by internal rotation in the direction of the ion-gyromotion with ω = 15:2 krad/s median angular velocity, which is approximately three times faster than the blob rotation in the background turbulence. The characteristic size of the ELM filament was also assessed and found to be similar to the blobs. A nearly linear trend was found between the angular velocity and the radial velocity of the ELM filament. The angular velocity was found to be linearly dependent on the distance of the filament from the separatrix, as well. An analytical model called the shear-induced rotation model was identified as a candidate for explaining the physics of the observations. Our results show that the modeled mechanism could significantly influence the rotation of the ELM filament; however, it cannot be a sole contributor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Quantifying dispersity in size and shape of nanoparticles from small-angle scattering data using machine learning based CREASE

Here, we use machine learning (ML) enhanced computational reverse engineering analysis of scattering experiments (CREASE) to interpret small-angle X-ray scattering (SAXS) data obtained from a system of nanoparticles without a priori knowledge of their exact shapes (e.g. spheres or ellipsoids), sizes (0.5–50 nm) and distributions. The SAXS measurements yielded three categories of scattering profiles exhibiting 'strong', 'weak' and 'no' features. Diminishing features (e.g. broadening or disappearing peaks) in scattering profiles have always been attributed to the presence of significant dispersity in the system. Such featureless SAXS data are not suitable for traditional analysis using analytical models. If one were to fit a relevant analytical model (e.g. the lmfit analytical model for polydisperse spheres) to these 'weak' and 'no' SAXS profiles from our nanoparticle systems, one would obtain non-unique interpretations of the data. Relying on electron microscopy to identify the distributions of nanoparticle shapes and sizes is also unfeasible, especially in high-throughput synthesis and characterization loops. In such situations, to identify the distributions of particle sizes and shapes that could be present in the sample, one must rely on methods like ML-CREASE to interpret the data quickly and output all relevant interpretations about the structure present in the system. The ML-CREASE optimization loop takes the experimental scattering profile as input and outputs multiple candidate solutions whose computed scattering profiles match the SAXS profile input. The ML-CREASE method outputs distributions of relevant structural features, such as the volume fraction of the nanoparticles in the system and the mean and standard deviation of the particle size and aspect ratio, assuming a type of distribution (e.g. normal, log-normal) for size and aspect ratio. We find that, for the SAXS profiles analyzed here, accounting for the shape dispersity along with size dispersity of the nanoparticles using ML-CREASE improved the match between the computed scattering profiles and input experimental profiles.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗