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Results for “ARM organization and structure”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Atmospheric Radiation Measurement (ARM) Management Plan

Mission and Vision Statements for the U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) Climate Research Facility Mission The ARM Climate Research Facility, a DOE scientific user facility, provides the climate research community with strategically located in situ and remote-sensing observatories designed to improve the understanding and representation, in climate and earth system models, of clouds and aerosols as well as their interactions and coupling with the Earth’s surface. Vision To provide a detailed and accurate description of the Earth atmosphere in diverse climate regimes to resolve the uncertainties in climate and Earth system models toward the development of sustainable solutions for the nation's energy and environmental challenges.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

The Correlation of Mesoscale Humidity Anomalies With Mesoscale Organization of Marine Stratocumulus From Observations Over the ARM Eastern North Atlantic Site

The structure of mesoscale cellular organization in marine cloud-topped boundary layers is found to be well characterized by using a novel compositing approach based on mesoscale variations in the column water vapor path (WVP). The approach is applied to ground-based observations from the Atmospheric Radiation Measurement (ARM) Eastern North Atlantic site. Based on a set of satellite and ground-based observational criteria, 381 hr of closed-cell and 227 hr of open-cell cases were selected from late 2015 to early 2018. Strong correlations are found between mesoscale-filtered cloud properties and WVP for both closed-cell and open-cell regimes. In the moist atmospheric columns, the clouds are thicker with higher tops and lower bases, and stronger precipitation compared to that in the dry columns. Overall, cloud properties of open and closed cells covary similarly with mesoscale moisture perturbations, except that the correlation of liquid water path with WVP is much weaker for open cells. The relations of subcloud properties with WVP are also examined. In the moist columns, surface equivalent potential temperature and relative humidity are higher than in the dry columns. A marginally negative correlation between mesoscale-filtered subcloud turbulence eddy dissipation rate and WVP is found for closed cells. These results are consistent with the conceptual model of closed cellular mesoscale circulations of Zhou and Bretherton (2019).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure and intermolecular organization. Synthetic rings are hybrid objects with conformations that display both ideal random walk and compact globular features, which can serve as models of genomic DNA. To date, emphasis has been placed on the effect of ring molecular weight on their unusual behaviors. Here, we combine simulations and a microscopic force-level theory to build a unified understanding for how key aspects of ring dynamics depend on different tunable molecular properties including backbone rigidity, monomer concentration, degree of traditional entanglement, and molecular weight. Our large-scale molecular dynamics simulations of ring melts with very different backbone stiffnesses reveal unanticipated behaviors which agree well with our generalized theory. This includes a universal master curve for center-of-mass diffusion constants as a function of molecular weight scaled by a chemistry and thermodynamic state-dependent critical molecular weight that generalizes the concept of an entanglement cross-over for linear chains. The key physics is how backbone rigidity and monomer concentration induced changes of the entanglement length, interring packing, degree of interpenetration, and liquid compressibility slow down space-time dynamic-force correlations on macromolecular scales. A power law decay of the center-of-mass diffusion constant with inverse molecular weight squared is the first consequence, followed by an ultraslow activated hopping transport regime. Our results set the stage to address slow dynamics and kinetic arrest in different families of compact synthetic and biological polymeric systems.

Science & Technology - Other Topics↗
DOE OSTI2021

Contrasting characteristics of open- and closed-cellular stratocumulus cloud in the eastern North Atlantic

Abstract. Extensive regions of marine boundary layer cloud impact the radiative balance through their significant shortwave albedo while having little impact on outgoing longwave radiation. Despite this importance, these cloud systems remain poorly represented in large-scale models due to difficulty in representing the processes that drive their life cycle and coverage. In particular, the mesoscale organization and cellular structure of marine boundary clouds have important implications for the subsequent cloud feedbacks. In this study, we use long-term (2013–2018) observations from the Atmospheric Radiation Measurement (ARM) Facility's Eastern North Atlantic (ENA) site on Graciosa Island, Azores, Portugal, to identify cloud cases with open- or closed-cellular organization. More than 500 h of each organization type are identified. The ARM observations are combined with reanalysis and satellite products to quantify the cloud, precipitation, aerosol, thermodynamic, and large-scale synoptic characteristics associated with these cloud types. Our analysis shows that both cloud organization populations occur during similar sea surface temperature conditions, but the open-cell cases are distinguished by stronger cold-air advection and large-scale subsidence compared to the closed-cell cases, consistent with their formation during cold-air outbreaks. We also find that the open-cell cases were associated with deeper boundary layers, stronger low-level winds, and higher rain rates compared to their closed-cell counterparts. Finally, raindrops with diameters larger than 1 mm were routinely recorded at the surface during both populations, with a higher number of large drops during the open-cellular cases. The similarities and differences noted herein provide important insights into the environmental and cloud characteristics during varying marine boundary layer cloud mesoscale organization and will be useful for the evaluation of model simulations for ENA marine clouds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Unnatural biosynthesis by an engineered microorganism with heterologously expressed natural enzymes and an artificial metalloenzyme

Synthetic biology enables microbial hosts to produce complex molecules from organisms that are rare or difficult to cultivate, but the structures of these molecules are limited to those formed by reactions of natural enzymes. The integration of artificial metalloenzymes (ArMs) that catalyse unnatural reactions into metabolic networks could broaden the cache of molecules produced biosynthetically. Here, in this work, we report an engineered microbial cell expressing a heterologous biosynthetic pathway, containing both natural enzymes and ArMs, that produces an unnatural product with high diastereoselectivity. We engineered Escherichia coli with a heterologous terpene biosynthetic pathway and an ArM containing an iridium–porphyrin complex that was transported into the cell with a heterologous transport system. We improved the diastereoselectivity and product titre of the unnatural product by evolving the ArM and selecting the appropriate gene induction and cultivation conditions. This work shows that synthetic biology and synthetic chemistry can produce, by combining natural and artificial enzymes in whole cells, molecules that were previously inaccessible to nature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Design, Synthesis, and Utility of Defined Molecular Scaffolds

A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.

Sato, Daisuke (ORCID:0000000305472659)↗
DOE OSTI2022

Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata

Abstract The last steps of cellular respiration—an essential metabolic process in plants—are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I–V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III 2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III 2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III 2 ’s mitochondrial processing peptidase domain and no participation of complex I’s bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme’s two arms, limiting large-scale conformational changes. Moreover, complex I’s catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata , the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III 2 . Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Reticular exploration of uranium-based metal—organic frameworks with hexacarboxylate building units

We report that the rational reticular design of metal–organic frameworks (MOFs) from building units of known geometries is essential for enriching the diversity of MOF structures. Unexpected and intriguing structures, however, can also arise from subtle changes in the rigidity/length of organic linkers and/or synthetic conditions. Herein, we report three uranium-based MOF structures—i.e., NU-135X (X = 0, 1, 2)—synthesized from trigonal planar uranyl nodes and triptycene-based hexacarboxylate ligands with variable arm lengths. A new chiral 3,6-connected nuc net was observed in NU-1350, while the extended versions of the ligand led to 3-fold catenated MOFs (NU-1351 and NU-1352) with rare 3,6-connected cml-c3 nets. Lastly, the differences in the topology of NU-1350 and NU-1351/NU-1352 could be attributed to the slight distortions of the shorter linker in the former from the ideal trigonal prism geometry to an octahedral geometry when coordinated to the trigonal planar uranyl nodes.

3,6-connected net↗
DOE OSTI2021

Complexes of Platinum Group Metals with a Conformationally Locked Scorpionate in a Metal–Organic Framework: An Unusually Close Apical Interaction of Palladium(II)

Here, we report synthetic strategies for installing platinum group metals (PGMs: Pd, Rh, Ir, and Pt) on a scorpionate-derived linker (TpmC*) within a metal–organic framework (MOF), both by room-temperature postsynthetic metalation and by direct solvothermal synthesis, with a wide range of metal loadings relevant for fundamental studies and catalysis. In-depth studies for the palladium adduct Pd(II)@Zr-TpmC* by density-functional-theory-assisted extended X-ray absorption fine structure spectroscopy reveals that the rigid MOF lattice enforces a close Pd(II)–N apical interaction between the bidentate palladium complex and the third uncoordinated pyrazole arm of the TpmC* ligand (Pd–N apical = 2.501 ± 0.067 Å), an interaction that is wholly avoided in molecular palladium scorpionates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Nanoscale morphological evolution of monocrystalline Pt surfaces during cathodic corrosion

This paper studies the cathodic corrosion of a spherical single crystal of platinum in an aqueous alkaline electrolyte, to map out the detailed facet dependence of the corrosion structures forming during this still largely unexplored electrochemical phenomenon. We find that anisotropic corrosion of the platinum electrode takes place in different stages. Initially, corrosion etch pits are formed, which reflect the local symmetry of the surface: square pits on (100) facets, triangular pits on (111) facets, and rectangular pits on (110) facets. We hypothesize that these etch pits are formed through a ternary metal hydride corrosion intermediate. In contrast to anodic corrosion, the (111) facet corrodes the fastest, and the (110) facet corrodes the slowest. For cathodic corrosion on the (100) facet and on higher-index surfaces close to the (100) plane, the etch pit destabilizes in a second growth stage, by etching faster in the (111) direction, leading to arms in the etch pit, yielding a concave octagon-shaped pit. In a third growth stage, these arms develop side arms, leading to a structure that strongly resembles a self-similar diffusion-limited growth pattern, with strongly preferred growth directions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans

Abstract O-Phosphoseryl-tRNASec selenium transferase (SepSecS) catalyzes the terminal step of selenocysteine (Sec) synthesis in archaea and eukaryotes. How the Sec synthetic machinery recognizes and discriminates tRNASec from the tRNA pool is essential to the integrity of the selenoproteome. Previously, we suggested that SepSecS adopts a competent conformation that is pre-ordered for catalysis. Herein, using high-resolution X-ray crystallography, we visualized tRNA-dependent conformational changes in human SepSecS that may be a prerequisite for achieving catalytic competency. We show that tRNASec binding organizes the active sites of the catalytic protomer, while stabilizing the N- and C-termini of the non-catalytic protomer. Binding of large anions to the catalytic groove may further optimize the catalytic site for substrate binding and catalysis. Our biochemical and mutational analyses demonstrate that productive SepSecS•tRNASec complex formation is enthalpically driven and primarily governed by electrostatic interactions between the acceptor-, TΨC-, and variable arms of tRNASec and helices α1 and α14 of SepSecS. The detailed visualization of the tRNA-dependent activation of SepSecS provides a structural basis for a revised model of the terminal reaction of Sec formation in archaea and eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Amphiphilic Baskets for Supramolecular Nanoarchitectures at Interfaces: Inverted Monolayer Formation on Water

Interfacial chemistry of molecular baskets remains poorly understood despite their promise for supramolecular applications of detection and sequestration of toxic molecules including those of illicit drugs, organophosphorus compounds, and anticancer agents. We present a fundamental investigation of the interfacial behavior of three amphiphilic supramolecular baskets (ASB 4, 8, and 12), having increasingly longer yet linear alkyl chains at the top of their bowl-shaped cavity. The studies were completed at the air−water interface to elucidate surface activity, interfacial stability, self-assembly, and monolayer organization that drive inverted monolayer formation, in which the molecular arms orient toward the aqueous phase in a configuration opposite to that typically observed for lipids. Herein, surface pressure−area isotherms of ASB 4, 8, 12, deposited on a water surface, were performed in tandem with nonequilibrium relaxation experiments to quantify surface activity, thermodynamic stability, and monolayer compressibility of the baskets’ monolayer assembly. Brewster angle microscopy enabled direct visualization of morphological evolution, aggregation, and packing at the interface. We show that systematic extension of the hydrocarbon arms, from four to 12 methylene groups, progressively modifies intermolecular packing, drives distinct two-dimensional aggregation pathways, and increases number densities at the air−water interface. Atomistic molecular dynamics simulations corroborate many of these experimentally observed trends and provide mechanistic detail on the cooperative roles of basket topology and interfacial concentration in regulating the hydration structure and dynamics within the cavities generated by surface-adsorbing baskets, consistent with observed variations in surface activity and packing. Our results establish how the topology of these unique supramolecules and their concentration govern interfacial organization and offer a rational framework for designing amphiphiles with predictable behavior at soft interfaces.

Hydrocarbons↗
DOE OSTI2021

Self-Assembly of Metallo-Supramolecules with Dissymmetrical Ligands and Characterization by Scanning Tunneling Microscopy

Asymmetrical and dissymmetrical structures are widespread and play a critical role in nature and life systems. In the field of metallo-supramolecular assemblies, it is still in its infancy for constructing artificial architectures using dissymmetrical building blocks. Herein, we report the self-assembly of supramolecular systems based on two dissymmetrical double-layered ligands. With the aid of ultra-high-vacuum, low-temperature scanning tunneling microscopy (UHV-LT-STM), we were able to investigate four isomeric structures corresponding to four types of binding modes of ligand LA with two major conformations complexes A. The distribution of isomers measured by STM and total binding energy of each isomer obtained by density functional theory (DFT) calculations suggested that the most abundant isomer could be the most stable one with highest total binding energy. Lastly, through shortening the linker between inner and outer layers and the length of arms, the arrangement of dissymmetrical ligand LB could be controlled within one binding mode corresponding to the single conformation for complexes B.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases

An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. Here, we have utilized biotin–streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S 112 E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic Fe II complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S 112 E. Two aqua ligands complete the primary coordination sphere of the Fe II center with both involved in hydrogen bond networks within Sav. The corresponding Fe III protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The Fe III protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Intramolecular structure and dynamics in computationally designed peptide-based polymers displaying tunable chain stiffness

Here, polymers assembled using computationally designed coiled coil bundlemers display tunable stiffness via control of interbundlemer covalent connectivity as confirmed using small-angle neutron scattering. Neutron spin echo spectroscopy reveals that rigid rod polymers show a decay rate Γ~Q 2 (Q is the scattering vector) expected of straight cylinders. Semirigid polymers assembled using bundlemers linked via 4-armed organic linker show flexible segmental dynamics at mid-Q and Γ~Q 2 behavior at high Q. The results give insight into linker flexibility-dependent interbundlemer dynamics in the hybrid polymers.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Mixed-phase Convective Clouds in the Polar Marine Boundary Layer

This proposal, a collaboration between two universities, firstly aims to describe the high-latitude CAO cloud regime using the array of instruments at the NSA (Barrow, Alaska) and at two mobile ARM sites (MARCUS 2017-18, and COMBLE 2020). These ARM data, and the multi-sensor variables we propose to derive, allow detailed descriptions of mesoscale organization of precipitation, thermodynamic profiles, vertical velocity, cloud depth, and cloud and precipitation properties. These observations are key for our second goal, which is to use output from validated cloud- and eddy-resolving simulations to gain insights into the linkages between microphysical processes, the MBL vertical structure, and the MBL dynamics that control cloud macrostructure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Introduction to special issue: Colloidal quantum dots

The quantum confinement effect has driven the development and exploration of colloidal semiconductor nanocrystals over approximately the past three decades. These semiconductor nanostructures are typically synthesized as stable colloidal dispersions in solution-phase chemical batch reactions at relatively low temperatures. Researchers have developed a wide range of reaction conditions to produce a variety of shapes, compositions, and structures with well-controlled sizes and low polydispersities. The shape can be controlled to produce confinement in one, two, or all three spatial dimensions, the latter defining a “quantum dot.” Combining two or more semiconductors within the various nanostructures produces additional optical and electronic degrees of freedom. These mixed compositional nanostructures have properties not accessible in bulk semiconductor systems. Further, researchers have fabricated novel nanoheterostructures, such as “dot-in-rods,” quantum wells, core/shell structures, giant-core/shell tetrapods where the core is one material and the arm is another, Janus structures that consist of spherical structures with well-defined internal heterostructures, nano-dumbbells, hollow-core structures, and many other novel and interesting structures. The structural variations are seemingly only limited by the creativity of the various researchers engaged in these endeavors.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Shaping the Water-Harvesting Behavior of Metal–Organic Frameworks Aided by Fine-Tuned GPT Models

Here, we construct a data set of metal–organic framework (MOF) linkers and employ a fine-tuned GPT assistant to propose MOF linker designs by mutating and modifying the existing linker structures. This strategy allows the GPT model to learn the intricate language of chemistry in molecular representations, thereby achieving an enhanced accuracy in generating linker structures compared with its base models. Aiming to highlight the significance of linker design strategies in advancing the discovery of water-harvesting MOFs, we conducted a systematic MOF variant expansion upon state-of-the-art MOF-303 utilizing a multidimensional approach that integrates linker extension with multivariate tuning strategies. We synthesized a series of isoreticular aluminum MOFs, termed Long-Arm MOFs (LAMOF-1 to LAMOF-10), featuring linkers that bear various combinations of heteroatoms in their five-membered ring moiety, replacing pyrazole with either thiophene, furan, or thiazole rings or a combination of two. Beyond their consistent and robust architecture, as demonstrated by permanent porosity and thermal stability, the LAMOF series offers a generalizable synthesis strategy. Importantly, these 10 LAMOFs establish new benchmarks for water uptake (up to 0.64 g g –1 ) and operational humidity ranges (between 13 and 53%), thereby expanding the diversity of water-harvesting MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗