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At least 811 records · Page 45

Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and Rubredoxin-ENH1 to the stromal side of Photosystem II in higher plants

TLP18.3 and Psb27 are known proteins on the luminal side of photosystem II. The structural locations of these two proteins are still absent in the currently available higher plant photosystem II cryo-EM structures. We interrogated the structural locations of these proteins using chemical cross-linking followed by liquid chromatography/tandem MS analysis. Structural mass spectrometry results then provided chemical restrains to direct structural modelling to determine the collective binding/stabilization of these two proteins to the luminal PSII CP43 protein. Using this pipeline, we also found the structural location of a Rubredoxin protein on the stromal side of PSII. Discovery of this redox active iron-sulfur protein in the vicinity of PSII subunit D1/D2 proteins, greatly showcases the importance of the redox processes that are potentially involved in PSII assembly or less known steady state functionality or photoprotection. This structural mass spectrometry platform high-lights its powerful applicability in protein complex discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Random forest models accurately classify synthetic opioids using high-dimensionality mass spectrometry datasets

Detection of novel threat agents presents several challenges, a principle one being the development of untargeted methods to screen an increasing number of threat chemicals whose exact structures are unknown. With the use of Machine Learning (ML) tools, we can guide the development of analytical methods for broad-spectrum detection of unbounded threat chemical families in complex mixtures. Toward this goal, we used nominal mass and high-resolution mass spectrometry data for hundreds of synthetic opioids and non-opioid compounds. We tested two ML techniques, logistic regression and random forest, to develop models towards a practical, implementable method for opioid detection. We found that of these tested ML methods, random forest models resulted in the highest validation accuracy (95+%) for both nominal mass and high-resolution classification of opioids versus non-opioids, with low false positive and false negative rates. The RF models were then used to successfully predict the classification of 10 compounds—five opioids and five non-opioids not part of the training and validation analysis. This application of ML is a critical step towards the development of field-deployable nominal mass spectrometers with ML-driven analyses for classification of emergent threats.

Chemistry↗

Random forest models accurately classify synthetic opioids using high-dimensionality mass spectrometry datasets

Detection of novel threat agents presents several challenges, a principle one being the development of untargeted methods to screen an increasing number of threat chemicals whose exact structures are unknown. With the use of Machine Learning (ML) tools, we can guide the development of analytical methods for broad-spectrum detection of unbounded threat chemical families in complex mixtures. Toward this goal, we used nominal mass and high-resolution mass spectrometry data for hundreds of synthetic opioids and non-opioid compounds. We tested two ML techniques, logistic regression and random forest, to develop models towards a practical, implementable method for opioid detection. We found that of these tested ML methods, random forest models resulted in the highest validation accuracy (95+%) for both nominal mass and high-resolution classification of opioids versus non-opioids, with low false positive and false negative rates. The RF models were then used to successfully predict the classification of 10 compounds—five opioids and five non-opioids not part of the training and validation analysis. This application of ML is a critical step towards the development of field-deployable nominal mass spectrometers with ML-driven analyses for classification of emergent threats.

Arasteh, Kourosh [Lawrence Livermore National Labo↗

Boundary-Layer Flow Simulations Over Ablating Woven Thermal Protection System Material

Spallation is the mechanical removal of small chunks of material gets removed typically due to high shear conditions of the flow field. This reduces the ability of the thermal protection system (TPS) material to protect the spacecraft as well as cause turbulence in the flow causing higher heating rates. In this work, we focus on the material removal through ablation and high shear flow within the boundary layer region of woven TPS material. Woven TPS (WTPS) material is the latest class of material developed by NASA, to be used within the next generation of space flights. They are complex interlocked weaves designed to create a rigid structure that is highly resistant to heat and can be easily designed and tailored for a wide variety of entry environments. Due to material removal resulting from chemical degradation, the structural integrity of TPS material is affected. Spallation occurs when this structurally compromised material is exposed to the high shear flow conditions within the boundary layer. In order to understand the spallation mechanism within WTPS material, we first perform the material removal simulations which occur primarily through oxidation to obtain the microstructure at various stages of degradation. These simulations are performed using the Porous Microstructure Analysis (PuMA) software developed at NASA Ames. The micro-structure geometry used within these simulations were generated artificially to be similar to the 3D weave architecture of MSR-EEV (Mars Sample Return - Earth Entry Vehicle). The various eroded TPS micro-structures are then subjected to the boundary layer flow conditions to obtain critical surface quantities which contribute to the structural failure mechanism such as heat flux, pressure, and shear stress. The direct simulation Monte Carlo (DSMC) methodology is used to perform these simulations in order to accurately capture the strong gradients within the high-temperature boundary layer flow over the intricate geometry of WTPS material. The boundary layer profile is directly taken from the Computational Fluid Dynamics (CFD) simulation and provided as boundary conditions to the DSMC inlet and outlet. Further, the variation of these properties as the microstructure undergoes changes due to oxidation is also investigated. Finally, these quantities are used as input in PuMA to understand the material expansion/compression and strain within the woven TPS geometry and help in developing a comprehensive spallation and structure failure model.

microstructure↗

Boundary-Layer Flow Simulations Over Ablating Woven Thermal Protection System Material

Spallation is the mechanical removal of small chunks of material gets removed typically due to high shear conditions of the flow field. This reduces the ability of the thermal protection system (TPS) material to protect the spacecraft as well as cause turbulence in the flow causing higher heating rates. In this work, we focus on the material removal through ablation and high shear flow within the boundary layer region of woven TPS material. Woven TPS (WTPS) material is the latest class of material developed by NASA, to be used within the next generation of space flights. They are complex interlocked weaves designed to create a rigid structure that is highly resistant to heat and can be easily designed and tailored for a wide variety of entry environments. Due to material removal resulting from chemical degradation, the structural integrity of TPS material is affected. Spallation occurs when this structurally compromised material is exposed to the high shear flow conditions within the boundary layer. In order to understand the spallation mechanism within WTPS material, we first perform the material removal simulations which occur primarily through oxidation to obtain the microstructure at various stages of degradation. These simulations are performed using the Porous Microstructure Analysis (PuMA) software developed at NASA Ames. The micro-structure geometry used within these simulations were generated artificially to be similar to the 3D weave architecture of MSR-EEV (Mars Sample Return - Earth Entry Vehicle). The various eroded TPS micro-structures are then subjected to the boundary layer flow conditions to obtain critical surface quantities which contribute to the structural failure mechanism such as heat flux, pressure, and shear stress. The direct simulation Monte Carlo (DSMC) methodology is used to perform these simulations in order to accurately capture the strong gradients within the high-temperature boundary layer flow over the intricate geometry of WTPS material. The boundary layer profile is directly taken from the Computational Fluid Dynamics (CFD) simulation and provided as boundary conditions to the DSMC inlet and outlet. Further, the variation of these properties as the microstructure undergoes changes due to oxidation is also investigated. Finally, these quantities are used as input in PuMA to understand the material expansion/compression and strain within the woven TPS geometry and help in developing a comprehensive spallation and structure failure model.

microstructure↗

Volume 35, AMT-1 Cruise Report and Preliminary Results

This report documents the scientific activities on board the Royal Research Ship (RRS) 'James Clark Ross' during the irst Atlantic Meridional Transect (AMT-1), 21 September to 24 October 1995. The ship sailed from Grimsby (England) for Montevideo (Uruguay) and then continued on to Stanley (Falkland Islands). The primary objective of the AMT program is to investigate basic biological processes in the open Atlantic Ocean over very broad spatial scales. For AMT-1, the meridional range covered was approximately 50 deg N to 50 deg S or nearly 8,000 nmi. The measurements to be taken during the AMT cruises are fundamental for the calibration, validation, and continuing understanding of remotely sensed observations of biological oceanography. They are also important for understanding plankton community structure over latitudinal scales and the role of the world ocean in global carbon cycles. During AMT-1 a variety of instruments were used to map the physical, chemical, and biological structure of the upper 200 m of the water column. Ocean color measurements were made using state-of-the-art sensors, whose calibration was traceable to the highest international standards. New advances in fluorometry were used to measure photosynthetic activity, which was then used to further interpret primary productivity. A unique set of samples and data were collected for the planktonic assemblages that vary throughout the range of the transect. These data will yield new interpretations on community composition and their role in carbon cycling. While the various provinces of the Atlantic Ocean were being crossed, the partial pressure of CO2 was related to biological productivity. This comparison revealed the areas of drawdown of atmospheric CO2 and how these areas relate to the surrounding biological productivity. These data, plus the measurements of light attenuation and phytoplankton optical properties, will be used as a primary input for basin-scale biological productivity models to help develop ecosystem dynamics models which will be important for improving the forecasting abilities of modelers. The AMT program is also attempting to meet the needs of international agencies in their implementation of Sensor Intercomparison and Merger for Biological and Interdisciplinary Ocean Studies (SIMBIOS), a program to develop a methodology and operational capability to combine data products from the various ocean color satellite missions.

Hooker, Stanford B.↗

The seeding of life by comets

The chemical and morphological structures of comets and interstellar dust are reviewed to demonstrate the feasibility of comets providing the necessary prebiotic molecules for the formation of life on the early earth. The chemical evolution of interstellar dust is shown to be the source of organics in comets, and the molecules observed in the grains are listed as are the products resulting from grain photolysis. It is emphasized that comets could only transfer prebiotic molecules to the earth if they are fluffy aggregates that break up into fine fragments. The contributions to the early earth are considered in terms of the competition between the evolution of the living organisms and the destructive effects of impacts. It is considered that life began as the bombardment during the first 5 x 10 exp 8 years began to tail off.

Greenberg, J. M.↗

Electron–Ion Covariance Reveals Geometry-Resolved Inner-Shell Spectra in CS 2 Photodissociation

The chemical shifts of inner-shell atomic orbitals are highly sensitive to chemical bonding and molecular structure. In evolving systems, however, the spectra of distinct molecular species and geometries overlap, obscuring the underlying chemical dynamics. Here we demonstrate the use of electron–ion covariance analysis to combine the structural sensitivity of Coulomb explosion imaging with inner-shell spectroscopy, yielding geometry-specific spectra of transient and product species. We apply this approach to the excited state dynamics of CS 2 probed by ionization above the S 2p edge. Electron–ion covariance with time- and momentum-selected S + and S 2+ ions isolates distinct S 2p photoelectron spectra for ground-state CS 2 , bent photoexcited CS 2 , the CS photoproduct, and bare atomic sulfur ─ species whose spectra overlap strongly in the channel-averaged measurement. Clear chemical shifts are observed in the covariance photoelectron spectrum for each of these species, all of which are consistent with high-level calculations. Here, by extracting the atomic S contribution to the photoelectron spectrum in a finely time-resolved manner we can disentangle this contribution to the overall time-resolved photoelectron spectrum as the photodissociation proceeds. These results demonstrate the promise of electron–ion covariance as a general approach to geometry-resolved inner-shell spectroscopy, opening a route to tracking structural evolution through chemical shifts in complex photoexcited molecules.

Ionization↗

Quantitative Interpretation of Optical Emission Sensors for Microgravity Experiments

Microgravity flight experiments uniquely test our knowledge and understanding of the coupling between chemistry and fluid mechanics. However, compared to ground based laboratory experiments the number of useful diagnostic tools suitable for microgravity environments is severely limited by the space, weight, power consumption, and operator complexity requirements. One of the available tools is the observation of optical emission, and total emission has already proven useful for observations of stable "flame balls" on the space shuttle. Wavelength resolved tomographic measurements of flame emission offer the promise of diagnostics to test our understanding of flame chemistry and structure. Individual emissions from electronically excited radicals, e.g., CH*, OH*, and C2*, can be identified in a methane/air flame. Spatially resolved measurements of the intensity of this resolved optical emission from a specific excited molecule enable chemically resolved flame structure studies. Wavelength resolved emission measurements to determine such structure in diffusion flames are being readied for flight experiments by a group at Yale headed by Profs. Smooke and Long. A quantitative relationship between emission intensity and flame properties, as expressed by a flame model, is needed for species specific optical emission measurements to fulfill its promise. The Yale group compared models and measurements of optical emission in laboratory tests at 1-g. Unfortunately, these experiments show disagreement between measurement and state-of-the-art flame models by over a factor of 50. Therefore, an improved chemical mechanism for optical emission from flames is needed to enable quantitative tests of microgravity flame models. The connection between excited state emission and flame chemistry is not yet adequate.

Jeffries, Jay B.↗

Enhanced Phase Stability of Sm 2 (Fe, Al) 17 C x

Aluminum doping can improve the phase stability of metastable compound Sm 2 Fe 17 C x with a high carbon content (x > 1.5). We investigated the preferential site substitution of Al, chemical bonding, and structural stability in Sm 2 (Fe,Al) 17 C 3 using first-principle calculations. Our results reveal a strong correlation between the preferential substitution of Fe by Al and the atomic site chemical environment, which affects the overall phase stability. Specifically, Al preferentially occupies the 9d site in Sm 2 (Fe,Al) 17 C 3 . At the same time, Al prefers the site 6c in its parent phase Sm 2 (Fe,Al) 17 . Partial replacement of Fe with Al leads to a more negative formation energy, indicating enhanced thermodynamic stability. Crystal Orbital Hamilton Population (COHP) and Crystal Orbital Bond Index (COBI) analysis suggest that insertion of carbon weakens the bonding strength of Sm-Fe (18f) and Sm-Fe (18h), resulting in metastability of Sm 2 Fe 17 C x . Doping Al strengthens Al-Fe, Al-Sm, Sm-Fe (18f, 18h) and Fe–C bonding in Sm 2 (Fe,Al) 17 C 3 , as revealed by calculated COHP and COBI. These effects contribute to improved phase stability in the Al-doped 2:17 interstitial compound.

chemical bonding↗

Oxygen chemistry of shocked interstellar clouds. III - Sulfur and oxygen species in dense clouds

The chemical evolution of oxygen and sulfur species in shocked dense clouds is studied. Reaction rate constants for several important neutral reactions are examined, and revised values are suggested. The one-fluid magnetohydrodynamic shock structure and postshock chemical evolution are calculated for shocks of velocity v(s) = 10 km/s through clouds of initial number density n(0) = 100,000/cu cm and of molecule/atom ratios H2/H = 10, 1000, and 100,000 with most sulfur contained initially in molecules SO2 and SO. Abundances of SO2, SO, CS, and OCS remain near their preshock values, except in clouds containing substantial amounts of atomic hydrogen, where significant destruction of sulfur-oxygen species occurs. Abundances of shock-enhanced molecules HS and H2O are sensitive to the molecule/atom ratio. Nonthermal oxygen-hydrogen chemistry has a minor effect on oxygen-sulfur molecules in the case H2/H = 10.

Leen, T. M.↗

Chemical nature of the barrier in Pb/YBa2Cu3O(7-x) tunneling structures

Several reports of reproducible tunneling measurements on YBa2Cu3O(7-x) thin films or single crystals with a Pb counterelectrode have recently appeared. The nature of the tunnel barrier, formed by air exposure, in these structures has been unknown. In the present work, the chemical nature of the tunnel barrier is studied with X-ray photoelectron spectroscopy (XPS). Laser-ablated films grown on LaAlO3 which have been chemically etched and heated in air are found to form nonsuperconducting surface Ba species, evident in an increase of the high binding energy Ba 3d and O 1s signals. A deposited Pb film about 10 A thick is found to be oxidized, and Cu(+2) is partially reduced to Cu(+1). The tunneling barrier thus appears to consist of species resulting from a combination of the air exposure and a reaction between the superconductor and the deposited Pb counterelectrode.

Vasquez, R. P.↗

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗

Synthesis and characterization of photo-cross-linkable quince seed-based hydrogels for soft tissue engineering applications

The convenience, versatility, and biocompatibility of photocrosslinkable hydrogel precursors make them promising candidates for developing tissue engineering scaffolds. However, the current library of photosensitive materials is limited. This study reports, for the first time, the modification of quince seed mucilage (QS) with glycidyl methacrylate (GM), resulting in the synthesis of methacrylated QS (QSGM). The chemical composition and structure of QS were analyzed. The effects of reaction time, temperature, QS concentration, and GM/QS ratio on the degree of methacrylation, as well as the physicochemical, rheological, mechanical, and biological properties of the synthesized materials were explored. Chemical characterization using 1H NMR and FTIR confirmed the successful methacrylation of QS. Hydrogels fabricated from QSGMs at a 0.5 wt% concentration exhibited high swelling ratios of 320 to 580 g/g, and compressive strengths between 0.6 ± 0.1 and 1.2 ± 0.3 kPa. No significant changes in the rheological properties of hydrogel precursors were observed. Moreover, QSGM-based hydrogels supported cell encapsulation for 14 days with minimal cytotoxicity and immune cell activation. Finally, as a proof of concept, the potential use of QSGM for 3D printing was demonstrated. Overall, the results highlight the significant potential of QSGMs as a biomaterial of choice for soft tissue engineering applications.

3D printing↗

Ellipsometric study of metal-organic chemically vapor deposited III-V semiconductor structures

An ellipsometric study of MOCVD-grown layers of AlGaAs and InGaAs in thick films and strained layer complex structures is presented. It is concluded that the ternary composition of thick nonstrained layers can be accurately determined to within experimental errors using numerical algorithms. In the case of complex structures, thickness of all layers and the alloy composition of nonstrained layers can be determined simultaneously, provided that the correlations between parameters is no higher than 0.9.

Alterovitz, Samuel A.↗

Hybrid Deployable Foam Antennas and Reflectors

Hybrid deployable radio antennas and reflectors of a proposed type would feature rigid narrower apertures plus wider adjoining apertures comprising reflective surfaces supported by open-cell polymeric foam structures (see figure). The open-cell foam structure of such an antenna would be compressed for compact stowage during transport. To initiate deployment of the antenna, the foam structure would simply be released from its stowage mechanical restraint. The elasticity of the foam would drive the expansion of the foam structure to its full size and shape. There are several alternatives for fabricating a reflective surface supported by a polymeric foam structure. One approach would be to coat the foam with a metal. Another approach would be to attach a metal film or a metal-coated polymeric membrane to the foam. Yet another approach would be to attach a metal mesh to the foam. The hybrid antenna design and deployment concept as proposed offers significant advantages over other concepts for deployable antennas: 1) In the unlikely event of failure to deploy, the rigid narrow portion of the antenna would still function, providing a minimum level of assured performance. In contrast, most other concepts for deploying a large antenna from compact stowage are of an "all or nothing" nature: the antenna is not useful at all until and unless it is fully deployed. 2) Stowage and deployment would not depend on complex mechanisms or actuators, nor would it involve the use of inflatable structures. Therefore, relative to antennas deployed by use of mechanisms, actuators, or inflation systems, this antenna could be lighter, cheaper, amenable to stowage in a smaller volume, and more reliable. An open-cell polymeric (e.g., polyurethane) foam offers several advantages for use as a compressible/expandable structural material to support a large antenna or reflector aperture. A few of these advantages are the following: 3) The open cellular structure is amenable to compression to a very small volume - typically to 1/20 of its full size in one dimension. 4) At a temperature above its glass-transition temperature (T(sub g)), the foam strongly damps vibrations. Even at a temperature below T(sub g), the damping should exceed that of other materials. 5) In its macroscopic mechanical properties, an open-cell foam is isotropic. This isotropy facilitates computational modeling of antenna structures. 6) Through chemical formulation, the T(sub g) of an open-cell polyurethane foam can be set at a desired value between about - 100 and about 0 C. Depending on the application, it may or may not be necessary to rigidify a foam structure after deployment. If rigidification is necessary, then the T(sub g) of the foam can be tailored to exceed the temperature of the deployment environment, in conjunction with providing a heater to elasticize the foam for deployment. Once deployed, the foam would become rigidified by cooling to below T(sub g). 7) Techniques for molding or machining polymeric foams (especially including open-cell polyurethane foams) to desired sizes and shapes are well developed.

Rivellini, Tommaso↗

Influence of isoelectronic mass modulation on phonon decay and transport in layered pnictogen-carbon systems

This study systematically investigates the structural, electronic, and thermal transport properties of layered pnictogen–carbon (Pn 2 C 2 ; Pn = P, As, Sb, Bi) monolayers, revealing a profound influence of isoelectronic mass modulation on phonon dynamics and thermal conductivity. Through first-principles calculations and lattice dynamics analysis, we demonstrate that increasing the atomic mass of pnictogens leads to elongated Pn-C bonds, weakened interatomic interactions, and enhanced phonon-phonon scattering, resulting in a dramatic reduction in lattice thermal conductivity (κ). Specifically, κ decreases exponentially from 65.6 W/m-K in P 2 C 2 to an ultralow 0.37 W/m-K in Bi 2 C 2 , driven by suppressed acoustic-optical phonon gaps Δ$^{Γ}_{A-0}$, increased anharmonicity, and reduced phonon lifetimes and group velocities. The transition from semiconducting to metallic behavior in heavier pnictogen-based systems further enhances phonon-electron scattering, contributing to thermal conductivity suppression. Structural analysis highlights the strengthening of out-of-plane C—C bonds and the contraction of C—Pn—C bond angles, which disrupt in-plane phonon transport. Further, these findings establish a design framework for engineering ultralow-κ materials through chemical substitution and structural tuning, offering significant potential for thermoelectric and thermal management applications. This work provides fundamental insights into phonon decay mechanisms and thermal transport in 2D materials, paving the way for advanced phononic and energy-efficient devices.

2D materials↗

Hierarchically Structured Catalysts Toward Sustainable Hydrogen Economy: Electro‐ and Thermo‐Chemical Pathways

Abstract Hydrogen, as an important clean energy source, plays a more and more crucial role in decarbonizing the planet and meeting the global climate challenge due to its high energy density and zero‐emission. The demand for sustainable hydrogen is increasing drastically worldwide as driven by the global shift towards low‐carbon energy solutions. Thermochemical catalysis process dominates hydrogen production at scale given its relatively mature technology and commercialization status, as well as the established manufacturing infrastructure. While due to its environmentally friendly nature and growing abundant sources of renewable electricity, the electrochemical path for hydrogen production is rising as a major alternative to the thermochemical means. Nevertheless, hierarchically structured catalysts and devices have gradually taken the center stage toward replacing the traditional counterparts, especially with the rapid advancement of the design and manufacture of such ordered nanostructure assemblies toward high activity, efficient mass transport, and superb stability. In this review, the latest progress of the hierarchically structured catalysts for hydrogen production have been surveyed on electro‐ and thermo‐ chemical pathways comparatively. It covers the structure designs of atomic dispersion, nanoscale surfaces and interfaces for achieving highly active and durable catalysts, components, and devices. Both electrochemical and thermochemical approaches are reviewed in terms of the vast design details, engineered benefits, and understandings of various Pt‐group metal (PGM) and non‐PGM based transition metal catalysts for hydrogen production. As the growing trend, brief discussions are also presented toward the high‐level assembly and manufacture of complexly structured components and devices at scale in the electrochemical and thermochemical energy systems.

Deng, Chenxin↗