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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Statistics of pressure fluctuations in turbulent kinetic plasmas

ABSTRACT In this study, we explore the statistics of pressure fluctuations in kinetic collisionless turbulence. A 2.5D kinetic particle-in-cell simulation of decaying turbulence is used to investigate pressure balance via the evolution of thermal and magnetic pressure in a plasma with β of order unity. We also discuss the behaviour of thermal, magnetic, and total pressure structure functions and their corresponding wavenumber spectra. The total pressure spectrum exhibits a slope of −7/3 extending for about a decade in the ion-inertial range. In contrast, shallower −5/3 spectra are characteristic of the magnetic pressure and thermal pressure. The steeper total pressure spectrum is a consequence of cancellation caused by density-magnetic field magnitude anti-correlation. Further, we evaluate higher order total pressure structure functions in an effort to discuss intermittency and compare the power exponents with higher order structure functions of velocity and magnetic fluctuations. Finally, applications to astrophysical systems are also discussed.

Astronomy & Astrophysics↗
DOE OSTI2022

Granal thylakoid structure and function: explaining an enduring mystery of higher plants

Summary In higher plants, photosystems II and I are found in grana stacks and unstacked stroma lamellae, respectively. To connect them, electron carriers negotiate tortuous multi‐media paths and are subject to macromolecular blocking. Why does evolution select an apparently unnecessary, inefficient bipartition? Here we systematically explain this perplexing phenomenon. We propose that grana stacks, acting like bellows in accordions, increase the degree of ultrastructural control on photosynthesis through thylakoid swelling/shrinking induced by osmotic water fluxes. This control coordinates with variations in stomatal conductance and the turgor of guard cells, which act like an accordion's air button. Thylakoid ultrastructural dynamics regulate macromolecular blocking/collision probability, direct diffusional pathlengths, division of function of Cytochrome b 6 f complex between linear and cyclic electron transport, luminal pH via osmotic water fluxes, and the separation of pH dynamics between granal and lamellar lumens in response to environmental variations. With the two functionally asymmetrical photosystems located distantly from each other, the ultrastructural control, nonphotochemical quenching, and carbon‐reaction feedbacks maximally cooperate to balance electron transport with gas exchange, provide homeostasis in fluctuating light environments, and protect photosystems in drought. Grana stacks represent a dry/high irradiance adaptation of photosynthetic machinery to improve fitness in challenging land environments. Our theory unifies many well‐known but seemingly unconnected phenomena of thylakoid structure and function in higher plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Fungal community structure and function shifts with atmospheric nitrogen deposition

Fungal decomposition of soil organic matter depends on soil nitrogen (N) availability. This ecosystem process is being jeopardized by changes in N inputs that have resulted from a tripling of atmospheric N deposition in the last century. Soil fungi are impacted by atmospheric N deposition due to higher N availability, as soils are acidified, or as micronutrients become increasingly limiting. Fungal communities that persist with chronic N deposition may be enriched with traits that enable them to tolerate environmental stress, which may trade-off with traits enabling organic matter decomposition. We hypothesized that fungal communities would respond to N deposition by shifting community composition and functional gene abundances toward those that tolerate stress but are weak decomposers. We sampled soils at seven eastern US hardwood forests where ambient N deposition varied from 3.2 to 12.6 kg N ha -1 year -1 , five of which also have experimental plots where atmospheric N deposition was simulated through fertilizer application treatments (25–50 kg N ha -1 year -1 ). Fungal community and functional responses to fertilizer varied across the ambient N deposition gradient. Fungal biomass and richness increased with simulated N deposition at sites with low ambient deposition and decreased at sites with high ambient deposition. Fungal functional genes involved in hydrolysis of organic matter increased with ambient N deposition while genes involved in oxidation of organic matter decreased. One of four genes involved in generalized abiotic stress tolerance increased with ambient N deposition. In summary, we found that the divergent response to simulated N deposition depended on ambient N deposition levels. Fungal biomass, richness, and oxidative enzyme potential were reduced by N deposition where ambient N deposition was high suggesting fungal communities were pushed beyond an environmental stress threshold. Fungal community structure and function responses to N enrichment depended on ambient N deposition at a regional scale.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

More is definitely different: the zebrafish as witness: Comment on ”Structure and function in artificial, zebrafish and human neural networks” by Peng Ji et al.

We report half a century ago, in his foundation paper More is different, Anderson stated the relevance of including multiple scales of interaction, instead of trying to reduce everything to fundamental principles. By doing so, one may witness phenomena that were not expected by looking at each individual components separately. This idea finds indeed numerous realizations such as the synchronization phenomenon, where a multitude of dynamical systems suddenly start to behave coherently together, or the spreading of diseases over entire populations, to name only two examples. But if one would have to give a single example of a system where the multiplicity of interaction scales is of utmost importance, it would probably be the brain. In their review, Ji et al. give a comprehensive overview of the multiple scales of science required in the investigation of structural and functional brain networks, as well as their interplay.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Influence of cellular redox reactions on the structure and function of light harvesting and photosystems

Photosynthesis enables the conversion of one of the most abundant and free forms of energy, sunlight, into chemical bonds through the utilization of highly tailored protein complexes. These enzymes work in unison to absorb, convert, and transform light into high-energy electrons which are used for various functions important to metabolism and cellular protection. Over the last ∼50 years, photosynthetic organisms, such as cyanobacteria, have been adapted and engineered to produce valuable compounds like hydrogen and ethylene, among others. Often this is performed by removing native and/or adding in exogenous energy utilization pathways so that light energy is re-directed towards the synthesis of desired compounds. However, the interplay between primary light capture, conversion reactions, and the downstream electron utilization sinks is not fully understood. Further complicating these strategies are the plethora of compensatory mechanisms that facilitate steady electron flow and the maintenance of photosynthesis under dynamic conditions. This manifests as structural and functional plasticity of the photosynthetic machinery, often seen in modulations of oligomeric compositions or changes in protein-protein interactions and coupling with redox enzymes. Understanding these mechanisms is crucial to biotechnology applications because re-engineering electron utilization sinks has profoundly different effects on the light capture and conversion reactions of photosynthesis. Optimization requires a molecular-level understanding of the functional interrelationships between electron sinks and photosynthetic components that influence photosynthetic efficiencies to realize potential improvements in product yields. Here, we aim to highlight how perturbation of reductive reactions is revealing the functional plasticity in key components of the photosynthetic energy transduction pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Functional Janus structured liquids and aerogels

Janus structures have unique properties due to their distinct functionalities on opposing faces, but have yet to be realized with flowing liquids. We demonstrate such Janus liquids with a customizable distribution of nanoparticles (NPs) throughout their structures by joining two aqueous streams of NP dispersions in an apolar liquid. Using this anisotropic integration platform, different magnetic, conductive, or non-responsive NPs can be spatially confined to opposite sides of the original interface using magnetic graphene oxide (mGO)/GO, Ti 3 C 2 T x /GO, or GO suspensions. The resultant Janus liquids can be used as templates for versatile, responsive, and mechanically robust aerogels suitable for piezoresistive sensing, human motion monitoring, and electromagnetic interference (EMI) shielding with a tuned absorption mechanism. The EMI shields outperform their current counterparts in terms of wave absorption, i.e., SE T ≈ 51 dB, SE R ≈ 0.4 dB, and A = 0.91, due to their high porosity ranging from micro- to macro-scales along with non-interfering magnetic and conductive networks imparted by the Janus architecture.

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

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass

Abstract Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High-density Lipoprotein (HDL) Structure and Function Proteomics (JM-DP1)

The purpose of this experiment was to investigate how the interactions between APOA1 and APOA2 on the surface of high-density lipoproteins (HDL) impact particle function by studying the effect of exogenous APOA2 on HDL structure through limited proteolysis. Interactions were investigated on HDL isolated from human blood plasma using structural proteomics tools such as chemical cross-linking and limited proteolysis (LiP). The structural proteomics data was acquired using a Q-Exactive HF-X mass spectrometer and processed using MaxQuant software (v.1.6.17.0).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dual factors required for cytochrome-P450-mediated hydrocarbon ring contraction in bacterial gibberellin phytohormone biosynthesis

Cytochromes P450 (CYPs) are heme-thiolate monooxygenases that prototypically catalyze the insertion of oxygen into unactivated C–H bonds but are capable of mediating more complex reactions. One of the most remarked-upon alternative reactions occurs during biosynthesis of the gibberellin A (GA) phytohormones, involving hydrocarbon ring contraction with coupled aldehyde extrusion of ent-kaurenoic acid to form the first gibberellin intermediate. While the unusual nature of this reaction has long been noted, its mechanistic basis has remained opaque. Building on identification of the relevant CYP114 from bacterial GA biosynthesis, detailed structure–function studies are reported here, including development of in vitro assays as well as crystallographic analyses both in the absence and presence of substrate. These structures provided insight into enzymatic catalysis of this unusual reaction, as exemplified by identification of a key role for the “missing” acid from an otherwise highly conserved acid–alcohol pair of residues. Notably, the results demonstrate that ring contraction requires dual factors, both the use of a dedicated ferredoxin and absence of the otherwise conserved acidic residue, with exclusion of either limiting turnover to just the initiating and more straightforward hydroxylation. The results provide detailed insight into the enzymatic structure–function relationships underlying this fascinating reaction and support the use of a semipinacol mechanism for the unusual ring contraction reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chemistry, Structure, and Function of Lone Pairs in Extended Solids

The lone pair has been a known feature of the electronic structure of molecules for over 100 years. Beginning with the pioneering work of Lewis and others that was later developed into useful guidelines for predicting molecular structure, lone pairs and their steric consequences are now taught at the very earliest stages of a chemistry education. In the crystalline solid state, lone pairs have perhaps had a less visible yet equally consequential role, with a significant impact on a range of properties and functionalities. Important properties associated with s 2 electron-derived lone pairs include their role in creating conditions favorable for ion transport, in the formation and correlation of local dipoles and the resulting polar behavior leading to ferroics and multiferroics, in increasing the refractive index of glass, in reducing the thermal conductivity of thermoelectric materials, and in breaking local symmetry permitting second-harmonic light generation.. In recent years, the role of the lone pair in developing the electronic structure of some topological quantum materials has also been recognized. While structural distortions due to lone pairs have traditionally been characterized through their crystallography, recent advances in scattering and spectroscopy have revealed the presence of local lone pair-driven distortions that do not correlate over long length scales. The role of these crystallographically “hidden” lone pairs, their detection, and their impact on properties have become a growing body of work in the literature. Hidden lone pairs are an effective argument for considering a role for lone pairs that goes beyond their being objects that occupy space in the coordination polyhedra of cations. This Account introduces the chemistry of lone pairs in extended crystalline solids, including a discussion of when they are stereochemically active, how they manifest in the structure, and how their chemistry can be tuned by the chemical environment around them. Eventually, all of these factors work in unison to help develop and tune properties of interest. Certain specific examples of structure–property relationships in materials that are driven by lone pair behavior are described here, including the potential impact of lone pairs on the optical and electronic properties of hybrid halide perovskite compounds that are relevant to their photovoltaic applications. Here, we highlight the role of lone pairs in the dielectric behavior of geometrically frustrated pyrochlores, the temperature-dependent optoelectronic behavior of halide perovskites, the polar phase transitions in lead-free ferroelectric perovskites, and the compositional insulator-to-metal transition in ruthenium pyrochlores. The theme underpinning this Account is that the lone pair can be considered to be a powerful design element for a broad range of material function.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Revealing the structure of light pseudoscalar mesons at the electron–ion collider

The questions of how the bulk of the Universe's visible mass emerges and how it is manifest in the existence and properties of hadrons are profound, and probe the heart of strongly interacting matter. Paradoxically, the lightest pseudoscalar mesons appear to be key to a further understanding of the emergent mass and structure mechanisms. These mesons, namely, the pion and kaon, are the Nambu-Goldstone boson modes of quantum chromodynamics (QCD). Unravelling their partonic structure and the interplay between emergent and Higgs-boson mass mechanisms is a common goal of three interdependent approaches - continuum QCD phenomenology, lattice-regularised QCD, and the global analysis of parton distributions - linked to experimental measurements of hadron structure. Experimentally, the anticipated electron-ion collider will enable a revolution in our ability to study pion and kaon structures, accessed by scattering from the 'meson cloud' of the proton through the Sullivan process. With the goal of enabling a suite of measurements that can address these questions, we examine key reactions that identify the critical detector-system requirements needed to map tagged pion and kaon cross-sections over a wide range of kinematics. The excellent prospects for extracting pion structural, functional, and form-factor data are outlined, and similar prospects for kaon structures are discussed in the context of a worldwide programme. Finally, the successful completion of the programme outlined herein will deliver deep, far-reaching insights into the emergence of pions and kaons, their properties, and their role as QCD's Goldstone boson modes.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Exploration of lattice Hamiltonians for functional and structural discovery via Gaussian process-based exploration–exploitation

Statistical physics models ranging from simple lattice to complex quantum Hamiltonians are one of the mainstays of modern physics that have allowed both decades of scientific discovery and provided a universal framework to understand a broad range of phenomena from alloying to frustrated and phase separated materials to quantum systems. Traditionally, exploration of the phase diagrams corresponding to multidimensional parameter spaces of Hamiltonians was performed using a combination of basic physical principles, analytical approximations, and extensive numerical modeling. However, exploration of complex multidimensional parameter spaces is subject to the classic dimensionality problem, and the behaviors of interest concentrated on low dimensional manifolds remain undiscovered. Here, we demonstrate that a combination of exploration and exploration–exploitation with Gaussian process modeling and Bayesian optimization allows effective exploration of the parameter space for lattice Hamiltonians and effectively maps the regions at which specific macroscopic functionalities or local structures are maximized. We argue that this approach is general and can be further extended well beyond the lattice Hamiltonians to effectively explore the parameter space of more complex off-lattice and dynamic models.

42 ENGINEERING↗
DOE OSTI2024

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of the MARATHON data on F 2⁢n⁡ /F 2⁢p and off-shell effects in light nuclei

The neutron structure function, F 2⁢n⁡ , has historically been extracted from measurements of the deuteron structure function, which is limited by our understanding of the nuclear effects on the bound proton and neutron. The MARATHON Collaboration recently extracted F 2⁢n⁡ from the comparison of 3 H and 3 He targets, where the nuclear effects are larger but nearly identical, yielding a precise extraction of F 2⁢n⁡ /F 2⁢p . Here, to ensure that this comparison is not biased by the specific model of nuclear effects used by MARATHON, we examine a range of models of the nuclear effects to obtain a more conservative, but more model-independent, extraction of F 2⁢n⁡ /F 2⁢p for comparison with deuteron extractions. Even with this approach, the results are precise enough to compare to deuteron extractions, providing new constraints on the nuclear effects in the deuteron and indicating the need for larger nuclear corrections than those included in most models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

PPI DataHub Project Data Package: High-density Lipoprotein (HDL) Structure and Function Proteomics

The purpose of this experiment was to investigate how the interactions between APOA1 and APOA2 on the surface of high-density lipoproteins (HDL) impact particle function. Interactions were investigated on HDL isolated from human blood plasma using structural proteomics tools such as chemical cross-linking and limited proteolysis (LiP). The structural proteomics data was acquired using a Q-Exactive HF-X mass spectrometer and data was processed and compiled using MaxQuant sofware (v.1.6.17.0). Processed datasets are openly accessible from the download button (~2.8 GB) and contain secondary processed LiP and global proteomic results files and supporting metadata materials. Processed data downloads include a sample naming key, processed MaxQuant results/parameters, and protein annotated relative abundance files.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A Strong-QCD Regime Measurement of the Proton’s Spin Structure

The theory of the strong force, Quantum Chromodynamics (QCD) remains one of the most important ways to understand the fundamental properties of ordinary matter. However, at low momentum transfer Q 2 , in the regime where the strong force becomes extremely strong, our understanding of QCD for ordinary nucleons becomes hazy. Several cutting edge theories such as Chiral Perturbation Theory (χPT) and Lattice QCD have provided valuable predictions in this regime, but Lattice QCD has not yet extended predictions of many important quantities to this kinematic region, and Chiral Perturbation Theory has faced several important disagreements with experimental data for the neutron over the last several decades. It is therefore of extreme importance to have a benchmark of experimental data in the low energy regime for the proton’s behavior, as a test of leading theories for the behavior of QCD in this regime. The E08-027 (g2p) experiment ran at Jefferson Lab in 2012 with the goal of collecting this valuable data, and though I was still completing my undergraduate studies at the time, I became involved in the analysis in 2015 and built on the previous work to complete it and analyze the exciting results. This experiment achieved a high precision measurement of the spin structure functions g1 and g2 for the proton, quantities which describe the internal spin structure of the proton. These measurements were taken in the valuable low Q 2 region described above, and used to extract several moments of these spin structure functions which can be directly compared to the cutting-edge predictions of Chiral Perturbation Theory. Though the experiment’s timeline was such that I didn’t have a chance to work directly on the experimental setup, I had the opportunity to acquire hands-on experience working on a polarized target at UNH which is very similar to the crucial polarized target used in the g2p experiment. Full details of the g2p experiment and my experimental work at the University of New Hampshire are presented in this thesis, as well as a detailed description of the analysis process and the exciting benchmark results, which serve as a direct test of all current and future theories of QCD in the low-Q 2 regime.

Ruth, David↗