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At least 415 records · Page 23

Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization

Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. In this report an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modular repeat protein sculpting using rigid helical junctions

The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ~10-nm-diameter “L” and “V” shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.

59 BASIC BIOLOGICAL SCIENCES↗

Bistatic image processing for a 32 x 19 inch model aircraft using scattered fields obtained in the OSU-ESL compact range

Inverse Synthetic Aperture Radar (ISAR) images for a 32 in long and 19 in wide model aircraft are documented. Both backscattered and bistatic scattered fields of this model aircraft were measured in the OSU-ESL compact range to obtain these images. The scattered fields of the target were measured for frequencies from 2 to 18 GHz with a 10 MHz increment and for full 360 deg azimuth rotation angles with a 0.2 deg step. For the bistatic scattering measurement, the compact range was used as the transmitting antenna; while, a broad band AEL double ridge horn was used as the receiving antenna. Bistatic angles of 90 deg and 135 deg were measured. Due to the size of the chamber and target, the receiving antenna was in the near field of the target; nevertheless, the image processing algorithm was valid for this case.

Lee, T-H.↗

Critical point of the solar wind by radio sounding data

Results of the close-to-Sun plasmas sounding at the transonic region of the solar wind, where the sub-to supersonic flow transition proceeds (at 10 to 40 solar radii from the Sun), are presented. Natural sources of two types were used, water vapour maser sources at 1.35 cm and guasars at 2.9 m wavelength. scattering observations cover the period of 1986 to 1993, Russian Academy of Sciences telescopes RT-22 and DCR-1000 were used, IPS index and scattering angle being the immediate results of observations. Extensive studies of the scintillation index and scattering angle radial profiles reveal a remarkable structural detail, 'transonic region forrunner'-narrow region of diminished scattering close to the internal border of the extended transonic region with its characteristic enhanced scattering. Comparisons of the scattering and plasma velocity profiles let it possible to determine the critical point positions by the comparatively simple scattering observations. This new possibility widely improves the process of the basic data accumulation in the fundamental problem of the solar wind acceleration mechanism.

Lotova, N. A.↗

Going Beyond Standard Ocean Color Observations: Lidar and Polarimetry

Passive ocean color images have provided a sustained synoptic view of the distribution of ocean optical properties and color and biogeochemical parameters for the past 20-plus years. These images have revolutionized our view of the ocean. Remote sensing of ocean color has relied on measurements of the radiance emerging at the top of the atmosphere, thus neglecting the polarization and the vertical components. Ocean color remote sensing utilizes the intensity and spectral variation of visible light scattered upward from beneath the ocean surface to derive concentrations of biogeochemical constituents and inherent optical properties within the ocean surface layer. However, these measurements have some limitations. Specifically, the measured property is a weighted-integrated value over a relatively shallow depth, it provides no information during the night and retrievals are compromised by clouds, absorbing aerosols, and low Sun zenithal angles. In addition, ocean color data provide limited information on the morphology and size distribution of marine particles. Major advances in our understanding of global ocean ecosystems will require measurements from new technologies, specifically lidar and polarimetry. These new techniques have been widely used for atmospheric applications but have not had as much as interest from the ocean color community. This is due to many factors including limited access to in-situ instruments and/or space-borne sensors and lack of attention in university courses and ocean science summer schools curricula. However, lidar and polarimetry technology will complement standard ocean color products by providing depth-resolved values of attenuation and scattering parameters and additional information about particle morphology and chemical composition. This review aims at presenting the basics of these techniques, examples of applications and at advocating for the development of in-situ and space-borne sensors. Recommendations are provided on actions that would foster the embrace of lidar and polarimetry as powerful remote sensing tools by the ocean science community.

Jamet, Cedric↗

Structure of Complex Liquid–Liquid Extraction Organic Phases for Rare Earth Separations

Complex, multicomponent liquids with hierarchical structure and phase transitions are encountered in many natural and industrial processes, including in chemical separations. One notable example is aggregation and organic phase splitting in liquid–liquid extraction (LLE) of metal ions. While these two phenomena that have long been closely associated, a mechanistic link between mesoscale structure and the capacity-limiting organic phase splitting remains elusive due to complexity of these systems. Here, in this study, we combine small-angle X-ray scattering (SAXS), X-ray photon correlation spectroscopy (XPCS), and molecular dynamics simulation to reveal a comprehensive picture of structure at the nano- and mesoscale in these complex solutions. For the representative case of rare earth extraction from an acidic aqueous phase by a malonamide extractant in dodecane, we investigate a wide range of process-relevant extractant and acid concentrations to provide a complete picture of how aggregation depends on composition. We decompose organic phase structure from SAXS into two contributions, which together can capture the scattering at all compositions: composition fluctuations described by the Ornstein–Zernike equation at low wavenumber Q, and nanostructure modeled by a “pre-peak” at intermediate Q. The former contains information about the thermodynamics of demixing, while the latter reflects nanoscopic self-assembly of the extractant and extracted solutes. While fluctuations have typically not been considered in the literature, we find they in fact dominate the total structure for nearly all practical conditions. As only the fluctuations have a strong temperature response, we confirm this attribution with temperature-dependent SAXS measurements, including for extracted europium nitrate complexes. SAXS and XPCS measurements near the critical point find static and dynamic scaling consistent with theory. Overall, this new paradigm for understanding LLE organic phases connects composition, nanoscale, and mesoscale structuring to phase behavior, providing both a comprehensive picture of solution structure and a quantitative link between aggregation and third phase formation.

Peroutka, Allison A. [Argonne National Laboratory ↗

Hunting for light dark matter with DUNE PRISM

We present the prospects for exploring low-scale dark sectors with the future DUNE experiment and the impact of the movable off-axis near detector concept, DUNE-PRISM, and a higher energy beam configuration. We focus on a simple scenario which extends the Standard Model by a “dark” U(1), comprising scalar or fermion dark matter and a dark photon kinetically mixed with the photon. We consider nucleus and electron scattering signatures of dark matter produced in the beam via neutral pseudoscalar meson decays. Our results show that, by analysing the energy spectra of single electron events in multiple off-axis angle, DUNE-PRISM can substantially increase the experimental sensitivity to these models, reaching theoretical targets for thermal relic dark matter for a wide range of dark photon and dark matter masses.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Illumination Conditions of the Lunar Polar Regions Using LOLA Topography

We use high-resolution altimetry data obtained by the Lunar Orbiter Laser Altimeter instrument onboard the Lunar Reconnaissance Orbiter to characterize present illumination conditions in the polar regions of the Moon. Compared to previous studies, both the spatial and temporal extent of the simulations are increased significantly, as well as the coverage (fill ratio) of the topographic maps used, thanks to the 28 Hz firing rate of the five-beam instrument. We determine the horizon elevation in a number of directions based on 240 m-resolution polar digital elevation models reaching down to 75 latitude. The illumination of both polar regions extending to 80 can be calculated for any geometry from those horizon longitudinal profiles. We validated our modeling with recent Lunar Reconnaissance Orbiter Wide-Angle Camera images. We assessed the extent of permanently shadowed regions (PSRs, defined as areas that never receive direct solar illumination), and obtained total areas generally larger than previous studies (12,866 and 16,055 sq. km, in the north and south respectively). We extended our direct illumination model to account for singly-scattered light, and found that every PSR does receive some amount of scattered light during the year. We conducted simulations over long periods (several 18.6-years lunar precession cycles) with a high temporal resolution (6 h), and identified the most illuminated locations in the vicinity of both poles. Because of the importance of those sites for exploration and engineering considerations, we characterized their illumination more precisely over the near future. Every year, a location near the Shackleton crater rim in the south polar region is sunlit continuously for 240 days, and its longest continuous period in total darkness is about 1.5 days. For some locations small height gains ( 10 m) can dramatically improve their average illumination and reduce the night duration, rendering some of those particularly attractive energy-wise as possible sites for near-continuous sources of solar power.

E. Mazarico↗

Measurements of Ocean Surface Scattering Using an Airborne 94-GHz Cloud Radar: Implication for Calibration of Airborne and Spaceborne W-band Radars

Scattering properties of the Ocean surface have been widely used as a calibration reference for airborne and spaceborne microwave sensors. However, at millimeter-wave frequencies, the ocean surface backscattering mechanism is still not well understood, in part, due to the lack of experimental measurements. During the Cirrus Regional Study of Tropical Anvils and Cirrus Layers-Florida Area Cirrus Experiment (CRYSTAL-FACE), measurements of ocean surface backscattering were made using a 94-GHz (W-band) cloud radar onboard a NASA ER-2 high-altitude aircraft. The measurement set includes the normalized Ocean surface cross section over a range of the incidence angles under a variety of wind conditions. Analysis of the radar measurements shows good agreement with a quasi-specular scattering model. This unprecedented dataset enhances our knowledge about the Ocean surface scattering mechanism at 94 GHz. The results of this work support the proposition of using the Ocean surface as a calibration reference for airborne millimeter-wave cloud radars and for the ongoing NASA CloudSat mission, which will use a 94-GHz spaceborne cloud radar for global cloud measurements.

Li, Li-Hua↗

Adsorption of Non-Ionic Surfactant and Monoclonal Antibody on Siliconized Surface Studied by Neutron Reflectometry

The adsorption of monoclonal antibodies (mAbs) on hydrophobic surfaces is known to cause protein aggregation and degradation. Therefore, surfactants, such as Poloxamer 188, are widely used in therapeutic formulations to stabilize mAbs and protect mAbs from interacting with liquid-solid interfaces. Here, the adsorption of Poloxamer 188, one mAb and their competitive adsorption on a model hydrophobic siliconized surface is investigated with neutron scattering coupled with contrast variation to determine the molecular structure of adsorbed layers for each case. Small angle neutron scattering measurements of the affinity of Poloxamer 188 to this mAb indicate that there is negligible binding at these solution conditions. Neutron reflectometry measurements of the mAb show irreversible adsorption on the siliconized surface, which cannot be washed off with neat buffer. Poloxamer 188 can be adsorbed on the surface already occupied by mAb, which enables partial removal of some adsorbed mAb by washing with buffer. The adsorption of the surfactant introduces significant conformational changes for mAb molecules that remain on the surface. In contrast, if the siliconized surface is first saturated with the surfactant, no adsorption of mAb is observed. Competitive adsorption of mAb and Poloxamer 188 from solution leads to a surface dominantly occupied with surfactant molecules, whereas only a minor amount of mAb absorbs. These findings clearly indicate that Poloxamer 188 can protect against mAb adsorption as well as modify the adsorbed conformation of previously adsorbed mAb.

36 MATERIALS SCIENCE↗

Cometary grain scattering versus wavelength, or 'What color is comet dust'?

Optical and near-infrared observations of comets are combined in a systematic study of the wavelength dependence of the scattering from cometary grains. The normalized rate of change of the reflectivity of cometary grains with respect to the wavelength of observations decreases as the wavelength increases. The observed wavelength dependence of the reflectivity gradient is consistent with an origin by scattering from micron-sized or larger, slightly absorbing spheres. The optically important comet grains are about an order of magnitude larger than the optically important interstellar grains. This size difference is a probable result of grain growth in the cloud from which the comets condensed. Grain properties differ so widely among the comets that any phase angle or heliocentric distance dependences of the continuum color are hidden.

Jewitt, David↗

Direct Observations of PMC Local Time Variations by Aura OMI

The Ozone Monitoring Instrument (OMI) on the Aura satellite obtains unique measurements for polar mesospheric cloud (PMC) analysis. Its wide cross-track viewing swath and high along-track spatial resolution makes it possible to directly evaluate PMC occurrence frequency and brightness variations between 6S" and 8S' latitude as a function of local time over a 12-14 h continuous period. OMI PMC local time variations are closely coupled to concurrent variations in measurement scattering angle, so that ice phase function effects must be considered when interpreting the observations. Two different phase functions corresponding to bright and faint clouds are examined in this analysis. OMI observations show maximum frequency and albedo values at 8-10 h local time in the Northern Hemisphere, with decreasing amplitude at higher latitudes. Southern Hemisphere values reach a minimum at 18-20 h LT. Larger variations are seen in Northern Hemisphere data. No statistically significant longitudinal dependence was seen.

DeLand, Matthew T.↗

Extended ecosystem signatures with application to Eos synergism requirements

The primary objective is to define the advantages of synergistically combining optical and microwave remote sensing measurements for the determination of biophysical properties important in ecosystem modeling. This objective was approached in a stepwise fashion starting with ground-based observations of controlled agricultural and orchard canopies and progressing to airborne observations of more natural forest ecosystems. This observational program is complemented by a parallel effort to model the visible reflectance and microwave scattering properties of composite vegetation canopies. The goals of the modeling studies are to verify our basic understanding of the sensor-scene interaction physics and to provide the basis for development of inverse models optimized for retrieval of key biophysical properties. These retrieval algorithms can then be used to simulate the expected performance of various aspects of Eos including the need for simultaneous SAR and HIRIS observations or justification for other (non-synchronous) relative timing constraints and the frequency, polarization, and angle of incidence requirements for accurate biophysical parameter extractions. This program completed a very successful series of truck-mounted experiments, made remarkable progress in development and validation of optical reflectance and microwave scattering models for vegetation, extended the scattering models to accommodate discontinuous and periodic canopies, developed inversion approaches for surface and canopy properties, and disseminated these results widely through symposia and journal publications. In addition, the third generation of the computer code for the microwave scattering models was provided to a number of other US, Canadian, Australian, and European investigators who are currently presenting and publishing results using the MIMICS research code.

Ulaby, Fawwaz T.↗

THOR: Cloud Thickness from Off beam Lidar Returns

Conventional wisdom is that lidar pulses do not significantly penetrate clouds having optical thickness exceeding about tau = 2, and that no returns are detectable from more than a shallow skin depth. Yet optically thicker clouds of tau much greater than 2 reflect a larger fraction of visible photons, and account for much of Earth s global average albedo. As cloud layer thickness grows, an increasing fraction of reflected photons are scattered multiple times within the cloud, and return from a diffuse concentric halo that grows around the incident pulse, increasing in horizontal area with layer physical thickness. The reflected halo is largely undetected by narrow field-of-view (FoV) receivers commonly used in lidar applications. THOR - Thickness from Off-beam Returns - is an airborne wide-angle detection system with multiple FoVs, capable of observing the diffuse halo, detecting wide-angle signal from which physical thickness of optically thick clouds can be retrieved. In this paper we describe the THOR system, demonstrate that the halo signal is stronger for thicker clouds, and validate physical thickness retrievals for clouds having z > 20, from NASA P-3B flights over the Department of Energy/Atmospheric Radiation Measurement/Southern Great Plains site, using the lidar, radar and other ancillary ground-based data.

Cahalan, Robert F.↗

A fully polarimetric scattering model for a coniferous forest

For an elliptically polarized plane wave exciting a coniferous forested canopy a fully polarimetric scattering model has been developed to account for the size and orientation distributions of each forest constituent. A canopy is divided into three layers over a rough interface. The upper two layers represent the crown with its constituents (leaves, stems, and branches). The lower layer stands for the trunks and the rough interface is the canopy-ground interface. For a plane wave exciting the canopy, the explicit expressions for the bistatic scattering coefficient associated with each scattering mechanism are given. For an elliptically polarized incidence wave, the present model can be recast in a form suitable for polarimetric wave synthesis. The model validation is justified by comparing the measured and the calculated values of the backscattering coefficients for a linearly polarized incident wave. The comparison is made over a wide range of frequencies and incident angles. Numerical simulations are conducted to calculate the radar polarization signature of the canopy for different incident frequencies and angles.

Karam, M. A.↗

Moment-preserving Monte-Carlo Coulomb collision method for particle codes

Binary-pairing Monte-Carlo methods are widely used in particle-in-cell codes to capture effects of small angle Coulomb collisions. These methods preserve momentum and energy exactly when the simulation particles have equal weights. However, when the interacting particles are of varying weight, these physical conservation laws are only preserved on average. Here, we 1) extend these methods to weighted particles such that the scattering physics is correct on average, and 2) describe a new method for adjusting the particle velocities post scatter to restore exact conservation of momentum and energy. In conclusion, the efficacy of the model is illustrated with various test problems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

Analysis of Physical Properties of Dust Suspended in the Mars Atmosphere

Methods for iteratively determining the infrared optical constants for dust suspended in the Mars atmosphere are described. High quality spectra for wavenumbers from 200 to 2000 1/cm were obtained over a wide range of view angles by the Mariner 9 spacecraft, when it observed a global Martian dust storm in 1971-2. In this research, theoretical spectra of the emergent intensity from Martian dust clouds are generated using a 2-stream source-function radiative transfer code. The code computes the radiation field in a plane-parallel, vertically homogeneous, multiply scattering atmosphere. Calculated intensity spectra are compared with the actual spacecraft data to iteratively retrieve the optical properties and opacity of the dust, as well as the surface temperature of Mars at the time and location of each measurement. Many different particle size distributions a-re investigated to determine the best fit to the data. The particles are assumed spherical and the temperature profile was obtained from the CO2 band shape. Given a reasonable initial guess for the indices of refraction, the searches converge in a well-behaved fashion, producing a fit with error of less than 1.2 K (rms) to the observed brightness spectra. The particle size distribution corresponding to the best fit was a lognormal distribution with a mean particle radius, r(sub m) 0.66 pm, and variance, omega(sup 2) = 0.412 (r(sub eff) = 1.85 microns, v(sub eff) =.51), in close agreement with the size distribution found to be the best fit in the visible wavelengths in recent studies. The optical properties and the associated single scattering properties are shown to be a significant improvement over those used in existing models by demonstrating the effects of the new properties both on heating rates of the Mars atmosphere and in example spectral retrieval of surface characteristics from emission spectra.

Snook, Kelly↗