Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structures”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe 4S] Fd activity

Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1 T11I ). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1 T11I . Electrochemical characterization revealed both Fer1 and Fer1 T11I have similar redox transitions (–480 mV and – 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron-sulfur (Fe—S) cluster of Fer1. Additionally, disruption of hydrogen bonding around an Fe—S cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1 T11I . Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1 T11I , which indicate changes to the high spin states and/or spin-spin coupling between the Fe—S clusters of Fer1. Finally, our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structures of Vanadium-Containing Silicate and Borosilicate Glasses: Vanadium Potential Development and MD Simulations

Vanadium-containing multi-component glasses have been found with widely interests in various applications. However, the complex compositions, thus structures, lead to the challenges in experiments to understand the structural origin of the property change of these glasses. In this work, we developed compatible vanadium-related parameters for a widely used pair wise potential set to enable the simulations of the vanadium-containing multi-component glasses. Various crystal structures and glass compositions (with vanadium in different oxidation states) have been tested using the newly developed parameters, and structural information of cell parameters, pair distribution function, estimated bond distance, and coordination number have been obtained. The results are in good agreement with available experimental data, which indicates the new vanadium parameters can be used to simulate the vanadium-containing multi-component glasses and thus help study those applications with wide interests.

Deng, Lu↗
DOE OSTI2021

Parton distributions and lattice-QCD calculations: Toward 3D structure

The strong force which binds hadrons is described by the theory of quantum chromodynamics (QCD). Determining the character and manifestations of QCD is one of the most important and challenging outstanding issues necessary for a comprehensive understanding of the structure of hadrons. Within the context of the QCD parton picture, the parton distribution functions (PDFs) have been remarkably successful in describing a wide variety of processes. However, these PDFs have generally been confined to the description of collinear partons within the hadron. New experiments and facilities provide the opportunity to additionally explore the transverse structure of hadrons which is described by generalized parton distributions (GPDs) and transverse-momentum-dependent parton distribution functions (TMD PDFs). In our previous report Lin et al. (2018), we compared and contrasted the two main approaches used to determine the collinear PDFs: the first based on perturbative QCD factorization theorems, and the second based on lattice-QCD calculations. In the present report, we provide an update of recent progress on the collinear PDFs, and also expand the scope to encompass the generalized PDFs (GPDs and TMD PDFs). We review the current state of the various calculations, and consider what new data might be available in the near future. We also examine how a shared effort can foster dialog between the PDF and lattice-QCD communities, and yield improvements for these generalized PDFs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Organic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scales

Organic C has many benefits for soil, but it is depleted by tillage and crop harvest, and especially so for biofuel crops. Accordingly, strategies such as partially retaining stover or planting a cover crop can help ameliorate the negative effect of C removal. We used a long-term field experiment to study the impacts of stover retention and planting cover crop on soil organic matter (SOM), its extractable components and the soil microbial community. SOM chemical composition characterization was determined by electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in sequential water, methanol (MeOH), and chloroform (CHCl3) extracts. The characteristics of the soil bacterial community were measured by phospholipid fatty acid (PLFA), real-time quantitative PCR, and 16S rRNA gene sequence. The variations in total SOM content, total microbial biomass, and bacterial population were slight among treatments, but SOM chemical compounds, arbuscular mycorrhizal fungi (AMF) biomass, and bacterial structure changed significantly, and especially so in the coupled application of stover retention and cover crop. Specifically, stover retention enriched more lignin-like compounds in soil, whereas cover crop enriched more condensed hydrocarbons, and had more compounds with an aromaticity index (AI) >0.5. The bacterial community was not altered by the cover crop, but the corn stover retention increased the relative abundances of Myxococcales (Deltaproteobacteria) and decreased that of Actinobacteria. Redundancy analysis (RDA) further unveiled that the bacterial community in the stover treatments had significantly positive association with CHCl3-extracted chemical classes, i.e. unsaturated hydrocarbon and lipid with the coupled application (stover and cover crop), and lignin and protein with the single corn stover treatment. Taken together, our study shows how different C addition practices influence the molecular composition of SOM and the structure of soil microbial communities.

Xu, Jiangbin↗
DOE OSTI2019

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Structural Tunability of Multicompartment Micelles as a Function of Lipophilic–Fluorophilic Block Length Ratio

Structural variation in multicompartment micelles consisting of lipophilic–hydrophilic–fluorophilic (hereafter referred to as BAC) triblock copolymers is investigated using the dissipative particle dynamics simulation method. It is demonstrated from our results that the structure of BAC multicompartment micelles is effectively tuned as a function of the lipophilic–fluorophilic ratio parameter, here termed $R_1$, of the constituent linear triblock copolymers. In particular, a morphological deviation from onion-like ABC micelles arises in BAC micelle systems as $R_1$ increases. The morphologies of BAC micelles with $R_1\ll$1 or $R_1\gg$1 display striking similarities, with the only notable difference being an inversion of the lipophilic and fluorophilic regions. When $R\approx$ 1, segmented worm-like structures with multiple cores are favored in BAC micelle systems. Through this study, it is confirmed that the block length ratio is an effective control parameter to tune the structure of multicompartment micelles.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Beyond Badger’s Rule: The Origins and Generality of the Structure–Spectra Relationship of Aqueous Hydrogen Bonds

The structure of hydrogen bonded networks is intimately intertwined with their dynamics. Despite the incredibly wide range of hydrogen bond strengths encountered in water clusters, ion-water clusters and liquid water, we demonstrate that the previously reported correlation between the change in the equilibrium bond length of the hydrogen bonded OH covalent bond and the corresponding shift in its harmonic frequency in water clusters is much more broadly applicable. Surprisingly, this correlation describes the ratios for both the equilibrium OH bond length/harmonic frequency, and the vibrationally averaged bond length/anharmonic frequency in water, hydronium water and halide water clusters. Consideration of harmonic and anaharmonic data leads to a correlation of -19 ± 1 cm -1 /0.001 Å. The basic nature of this correlation is further confirmed through the analysis of ab initio Molecular Dynamics (AIMD) trajectories for liquid water. We show that this simple correlation for both harmonic and anharmonic systems can be modeled by the response of an OH bond to an external field. Treating the OH bond as a Morse oscillator, we develop analytic expressions, which relate the ratio of the shift in the vibrational frequency of the hydrogen-bonded OH bond to the shift in OH bond length, to parameters in the Morse potential and the ratio of the first and second derivatives of the field-dependent projection of the dipole moment of water onto the hydrogen-bonded OH bond. Based on our analysis, we develop a protocol for reconstructing the AIMD spectra of liquid water from the sampled distribution of the OH bond lengths. Our conclusions elucidate the origins of the relationship between the molecular structure of the fleeting hydrogen-bonded network and the ensuing dynamics, which can be probed by vibrational spectroscopy.

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

Structure of Diisobutylene Maleic Acid Copolymer (DIBMA) and Its Lipid Particle as a “Stealth” Membrane-Mimetic for Membrane Protein Research

The study of membrane proteins remains challenging, especially in a native membrane environment. Recently, major progress has been made using maleic acid copolymers, such as styrene maleic acid, to purify membrane proteins and study them directly with native lipids associated with the membrane. Additional maleic acid copolymers, such as diisobutylene maleic acid (DIBMA) membrane-mimetic systems, are being developed and found to have improved spectroscopic properties and pH stability. We studied DIBMA and its lipid particles in solution to better understand its assembly, without and with the lipids, to provide an insight regarding how to use it in solution for better membrane extraction. Using small-angle neutron and X-ray scattering (SANS/SAXS), we show that DIBMA organizes into structures of different size scales at various concentrations and ionic strengths. The polymer performed reasonably well under most solvent conditions except in very low concentrations and high-salt conditions that could result in limited interaction with lipids. To explore DIBMA lipid particles as a suitable membrane-mimetic system for neutron scattering studies of membrane proteins, we measured and determined the contrast-matching point of DIBMA to be ~12% (v/v) D 2 O — similar to that of most protiated lipid molecules but distinct from that of regular protiated proteins — providing a natural contrast for separating their neutron scattering signals. Using SANS contrast variation, we demonstrated that the scattering from the whole lipid particle can be annihilated. Further, we determined that a well-defined lipid nanodisc structure with DIBMA was contrast-matched. These results demonstrate that the DIBMA lipid particle is an outstanding “stealth” membrane-mimetic for membrane proteins. The results provide a structural framework for understanding the organization and assembly process of the polymer itself and the lipid molecules. Such an understanding is imperative for structural techniques such as cryo-electron microscopy, nuclear magnetic resonance, small-angle scattering, and other biophysical techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Crystal Structure of the Ergothioneine Sulfoxide Synthase from Candidatus Chloracidobacterium thermophilum and Structure-Guided Engineering To Modulate Its Substrate Selectivity

Ergothioneine is a thiohistidine derivative with potential benefits on many aging-related diseases. The central step of aerobic ergothioneine biosynthesis is the oxidative C–S bond formation reaction catalyzed by mononuclear nonheme iron sulfoxide synthases (EgtB and Egt1). Thus far, only the Mycobacterium thermoresistibile EgtB (EgtB Mth ) crystal structure is available, while the structural information for the more industrially attractive Egt1 enzyme is not. In this paper, we reported the crystal structure of the ergothioneine sulfoxide synthase (EgtB Cth ) from Candidatus Chloracidobacterium thermophilum . EgtB Cth has both EgtB- and Egt1-type of activities. Guided by the structural information, we conducted Rosetta Enzyme Design calculations, and we biochemically demonstrated that EgtB Cth can be engineered more toward Egt1-type of activity. This study provides information regarding the factors governing the substrate selectivity in Egt1- and EgtB-catalysis and lays the groundwork for future sulfoxide synthase engineering toward the development of an effective ergothioneine process through a synthetic biology approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

The molecular structure of plant sporopollenin

Sporopollenin is a ubiquitous and extremely chemically inert biopolymer that constitutes the outer wall of all land-plant spores and pollen grains. Sporopollenin protects the vulnerable plant gametes against a wide range of environmental assaults, and is considered as a prerequisite for the migration of early plants onto land2. Despite its importance, the chemical structure of plant sporopollenin has remained elusive1. Using a newly developed thioacidolysis degradative method together with state-of-the-art solid-state NMR techniques, we determined the detailed molecular structure of pine sporopollenin. We show here that pine sporopollenin is primarily composed of aliphatic-polyketide-derived polyvinyl alcohol units and 7-O-p-coumaroylated C16 aliphatic units, crosslinked through a distinctive dioxane moiety featuring an acetal. Naringenin was also identified as a minor component of pine sporopollenin. This discovery answers the long-standing question about the chemical makeup of plant sporopollenin, laying the foundation for future explorations of sporopollenin biosynthesis and for design of new biomimetic polymers with desirable inert properties.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Measurement of the proton spin structure at long distances

Measuring the spin structure of protons and neutrons tests our understanding of how they arise from quarks and gluons, the fundamental building blocks of nuclear matter. At long distances, the coupling constant of the strong interaction becomes large, requiring non-perturbative methods to calculate quantum chromodynamics processes, such as lattice gauge theory or effective field theories. In this work, we report proton spin structure measurements from scattering a polarized electron beam off polarized protons. The spin-dependent cross-sections were measured at large distances, corresponding to the region of low momentum transfer squared between 0.012 and 1.0GeV 2 . This kinematic range provides unique tests of chiral effective field theory predictions. Our results show that a complete description of the nucleon spin remains elusive, and call for further theoretical works, for example, in lattice quantum chromodynamics. Finally, our data extrapolated to the photon point agree with the Gerasimov–Drell–Hearn sum rule, a fundamental prediction of quantum field theory that relates the anomalous magnetic moment of the proton to its integrated spin-dependent cross-sections.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Proton spin structure and generalized polarizabilities in the strong quantum chromodynamics regime

The strong interaction is not well understood at low energies or for interactions with low momentum transfer. Chiral perturbation theory gives testable predictions for the nucleonic generalized polarizabilities, which are fundamental quantities describing the nucleon’s response to an external field. We report a measurement of the proton’s generalized spin polarizabilities extracted with a polarized electron beam and a polarized solid ammonia target in the region where chiral perturbation theory is expected to be valid. The investigated structure function g2 characterizes the internal spin structure of the proton. From its moments, we extract the longitudinal–transverse spin polarizability δLT and twist-3 matrix element and polarizability d2¯. Our results provide discriminating power between existing chiral perturbation theory calculations and will help provide a better understanding of this strong quantum chromodynamics regime.

Ruth, D↗
DOE OSTI2019

Modified structure of protons and neutrons in correlated pairs

The atomic nucleus is made of protons and neutrons (nucleons), which are themselves composed of quarks and gluons. Understanding how the quark-gluon structure of a nucleon bound in an atomic nucleus is modified by the surrounding nucleons is an outstanding challenge. Although evidence for such modification-known as the EMC effect-was first observed over 35 years ago, there is still no generally accepted explanation for its cause. Recent observations suggest that the EMC effect is related to close-proximity short-range correlated (SRC) nucleon pairs in nuclei. Here we report simultaneous, high-precision measurements of the EMC effect and SRC abundances. We show that EMC data can be explained by a universal modification of the structure of nucleons in neutron-proton SRC pairs and present a data-driven extraction of the corresponding universal modification function. This implies that in heavier nuclei with many more neutrons than protons, each proton is more likely than each neutron to belong to an SRC pair and hence to have distorted quark structure. This universal modification function will be useful for determining the structure of the free neutron and thereby testing quantum chromodynamics symmetry-breaking mechanisms and may help to discriminate between nuclear physics effects and beyond-the-standard-model effects in neutrino experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Curie-Weiss behavior of liquid structure and ideal glass state

We present the results of a structural study of metallic alloy liquids from high temperature through the glass transition. We use high energy X-ray scattering and electro-static levitation in combination with molecular dynamics simulation and show that the height of the first peak of the structure function, S(Q) -1, follows the Curie-Weiss law. The structural coherence length is proportional to the height of the first peak, and we suggest that its increase with cooling may be related to the rapid increase in viscosity. The Curie temperature is negative, implying an analogy with spin-glass. The Curie-Weiss behavior provides a pathway to an ideal glass state, a state with long-range correlation without lattice periodicity, which is characterized by highly diverse local structures, reminiscent of spin-glass.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Structural origins of the electronic properties of materials via time-resolved infrared spectroscopy

Time-resolved mid-infrared (TRIR) spectroscopy offers new opportunities to investigate how the molecular and structural properties of optoelectronic materials influence their electronic and transport states. This capability emerges from the ability to measure low energy electronic transitions in the mid-infrared that are related to delocalized states in materials and to simultaneously detect the vibrational properties of the materials that influence those states. Furthermore, the ability to simultaneously measure electronic and vibrational transitions in materials offers unprecedented opportunities to correlate structural dynamics of materials with their electronic and transport properties. Here, these capabilities are introduced by first describing the basic principles of TRIR spectroscopy used to examine electronic processes in materials. Then, several applications of TRIR spectroscopy are described in which measurements of the vibrational spectra of electronic excited states are probed as a means to correlate the structural properties of materials with the delocalization of their electronic states. In one example, exciton localization mechanisms in organic semiconductors are probed through vibrational spectra of the molecules in their excited states and correlated with their crystalline packing arrangements. Another example highlights the use of TRIR spectroscopy to examine singlet fission reaction dynamics through a combination of low energy electronic transitions and the vibrational spectra that are unique to the electronic states involved in the reaction. Finally, the use of TRIR spectroscopy to investigate charge carrier localization mechanisms in lead-halide perovskites is described, followed by an outlook of future applications of the technique in optoelectronic materials research.

36 MATERIALS SCIENCE↗