Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Structure Determination”

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 1,801 records · Page 100
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Polyelectrolyte character of rigid rod peptide bundlemer chains constructed via hierarchical self-assembly

Short α-helical peptides were computationally designed to self-assemble into robust coiled coils that are antiparallel, homotetrameric bundles. These peptide bundle units, or ‘bundlemers’, have been utilized as anisotropic building blocks to construct bundlemer-based polymers via a hierarchical, hybrid physical-covalent assembly pathway. The bundlemer chains were constructed using short linker connections via ‘click’ chemistry reactions between the N-termini of bundlemer constituent peptides. The resulting bundlemer chains appear as extremely rigid, cylindrical rods in transmission electron microscopy (TEM) images. Small angle neutron scattering (SANS) shows that these bundlemer chains exist as individual rods in solution with a cross-section that is equal to that of a single coiled coil bundlemer building block of ≈20 Å. SANS further confirms that the interparticle solution structure of the rigid rod bundlemer chains is heterogeneous and responsive to solution conditions, such as ionic-strength and pH. Due to their peptidic constitution, the bundlemer assemblies behave like polyelectrolytes that carry an average charge density of approximately 3 charges per bundlemer as determined from SANS structure factor data fitting, which describes the repulsion between charged rods in solution. This repulsion manifests as a correlation hole in the scattering profile that is suppressed by dilution or addition of salt. Presence of rod cluster aggregates with a mass fractal dimension of ≈2.5 is also confirmed across all samples. The formation of such dense, fractal-like cluster aggregates in a solution of net repulsive rods is a unique example of the subtle balance between short-range attraction and long-rage repulsion interactions in proteins and other biomaterials. With computational control of constituent peptide sequences, it is further possible to deconvolute the underlying sequence driven structure–property relationships in the modular bundlemer chains.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. During gemination, spores must degrade their cortex layer, which is a thick, protective layer of modified peptidoglycan. Cortex degradation depends on the presence of the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL), which is specifically recognized by cortex lytic enzymes. In C . difficile , MAL production depends on the CwlD amidase and its binding partner, the GerS lipoprotein. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind Zn 2+ stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to Zn 2+ , which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of Zn 2+ co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1980

Development of the Learjet 28/29 Wing Using NASTRAN Analysis

The structural development work performed on the Learjet 28/29 wing using NASTRAN analysis is discussed. The work included the basic sizing of primary structural members such as wing skins, wing skin splices, and spar caps, as well as the calculation of preliminary weight estimates utilizing the weight computation routine in NASTRAN. The eight spar redundancy of the Learjet wing made this task somewhat more complex than for more determinate type wing structures. Some of the problems that were encountered and the solutions and methods that were used are described.

Boroughs, R. R.↗
NASA NTRS1988

Deep space tracking in local reference frames

A self-calibrating deep space tracking technique is described which can potentially produce two nanoradian angular spacecraft determinations. The technique uses very long base interferometric observations of a spacecraft and several radio sources. The currently employed single source technique is described as a parameter estimation procedure. Then, the number of parameters and observations leads to the proposed local reference frame technique. Station clock, Earth rotation, and tropospheric parameters are estimated along with spacecraft position from the multisource observation sequence. The contributions to spacecraft angular uncertainty from system noise, tropospheric fluctuations, and uncalibrated radio source structure are evaluated. Of these experimental errors, radio source structure dominates the determination of the spacecraft position in the radio reference frame. It is shown, however, that the sensitivity of relative spacecraft position accuracies to time-invariant radio source structure effects may be on the order of 2 nanoradians.

Treuhaft, R. N.↗
DOE OSTI2021

Ultrafast X-ray scattering offers a structural view of excited-state charge transfer

Intramolecular charge transfer and the associated changes in molecular structure in N,N'-dimethylpiperazine are tracked using femtosecond gas-phase X-ray scattering. The molecules are optically excited to the 3p state at 200 nm. Following rapid relaxation to the 3s state, distinct charge-localized and charge-delocalized species related by charge transfer are observed. The experiment determines the molecular structure of the two species, with the redistribution of electron density accounted for by a scattering correction factor. The initially dominant charge-localized state has a weakened carbon–carbon bond and reorients one methyl group compared with the ground state. Subsequent charge transfer to the charge-delocalized state elongates the carbon–carbon bond further, creating an extended 1.634 Å bond, and also reorients the second methyl group. At the same time, the bond lengths between the nitrogen and the ring-carbon atoms contract from an average of 1.505 to 1.465 Å. The experiment determines the overall charge transfer time constant for approaching the equilibrium between charge-localized and charge-delocalized species to 3.0 ps.

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

The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein-protein interactions

In order to establish infection, pathogenic bacteria must obtain essential nutrients such as iron. Under acidic and/or anaerobic conditions, most bacteria utilize the Feo system in order to acquire ferrous iron (Fe 2+ ) from their host environment. The mechanism of this process, including its regulation, remains poorly understood. In this work, we have determined the crystal structure of FeoA from the nosocomial agent Klebsiella pneumoniae (KpFeoA). Our structure reveals an SH3-like domain that mediates interactions between neighboring polypeptides via hydrophobic intercalations into a Leu-rich surface ridge. Using docking of a small peptide corresponding to a postulated FeoB partner binding site, we demonstrate that KpFeoA can assume both “open” and “closed” conformations, controlled by binding at this Leu-rich ridge. We propose a model in which a “C-shaped” clamp along the FeoA surface mediates interactions with its partner protein, FeoB. Overall, these findings are the first to demonstrate atomic-level details of FeoA-based protein-protein interactions and provide a framework for testing FeoA-FeoB interactions, which could be exploited for future antibiotic developments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Magnetic structure and exchange interactions in the layered semiconductor CrPS 4

Compounds with two-dimensional (2D) layers of magnetic ions weakly connected by van der Waals bonding offer routes to enhance quantum behavior, stimulating both fundamental and applied interest. CrPS 4 is one such magnetic van der Waals material, however, it has undergone only limited investigation. Here we present a comprehensive series of neutron scattering measurements to determine the magnetic structure and exchange interactions. The observed magnetic excitations allow a high degree of constraint on the model parameters not normally associated with measurements on a powder sample. The results demonstrate the 2D nature of the magnetic interactions, while also revealing the importance of interactions along 1D chains within the layers. The subtle role of competing interactions is observed, which manifest in a nontrivial magnetic transition and a tunable magnetic structure in a small applied magnetic field through a spin-flop transition. Our results on the bulk compound provide insights that can be applied to an understanding of the behavior of reduced layer CrPS 4 .

36 MATERIALS SCIENCE↗
DOE OSTI2022

Giant resonances in topological spin Hall effect due to electron-skyrmion scattering in two-dimensional Rashba spin-orbit ferromagnets

Here we study a topological spin Hall effect where conduction electrons are scattered by Néel-type skyrmions in two-dimensional Rashba spin-orbit ferromagnets. We find the resonance structures in direct and Hall electric conductivities. The resonances strongly depend on the skyrmion size, the Rashba spin-orbit coupling vector value, and the relative direction between magnetization and Rashba vectors. The antiparallel arrangement of the Rashba spin-orbit coupling vector with respect to the magnetization determines the resonance structure and increases the direct conductivity by about two orders of magnitude. For the parallel arrangement the electric conductivities decrease by one to three orders of magnitude and the Hall conductivity changes the sign. The Rashba spin-orbit coupling also modifies electron bands depending on the ratio ε R /J, where ε R is Rashba energy and J is an exchange integral between conduction and localized electrons. If ε R /J ≤ 1, each energy band has the single minimum while for ε R /J > 1 the lower band has the “Mexican-hat” shape with the maximum at k = 0. We focus on the dependencies of direct and Hall electric conductivities on Fermi energy, ε F , skyrmion sizes, and Rashba spin-orbit coupling constant values and its relative direction with the magnetization. Analyzing both types of the energy bands, in general, we find two types of resonances: at the minimum of the upper band and behaviors, we employ the scattering pattern analysis. The resonance dependencies on skyrmion sizes and Rashba, a spin-orbit coupling contestant, can be qualitatively explained in terms of the Ramsauer-Townsend scattering of the upper band electrons by the skyrmion quantum well. The resonance properties can be used in spin transistors. To discover the resonances it is necessary to know the specific range of the parameters. At some values of the parameters the electric conductivity changes by about two orders of magnitude in the narrow range of ε F (< 0.01 eV). To detect the resonances it is also important to identify the relative direction of the Rashba spin-orbit coupling vector with respect to the magnetization.

36 MATERIALS SCIENCE↗
NASA NTRS1993

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Manchester, John I.↗
DOE OSTI2022

Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules

In Saccharomyces cerevisiae, the pre-mRNA leakage 39-kDa protein (ScPml39) was reported to retain unspliced pre-mRNA prior to export through nuclear pore complexes (NPCs). Pml39 homologs outside the Saccharomycetaceae family are currently unknown, and mechanistic insight into Pml39 function is lacking. Here we determined the crystal structure of ScPml39 at 2.5 Å resolution to facilitate the discovery of orthologs beyond Saccharomycetaceae, e.g. in Schizosaccharomyces pombe or human. The crystal structure revealed integrated zf-C3HC and Rsm1 modules, which are tightly associated through a hydrophobic interface to form a single domain. Both zf-C3HC and Rsm1 modules belong to the Zn-containing BIR (Baculovirus IAP repeat)-like super family, with key residues of the canonical BIR domain being conserved. Features unique to the Pml39 modules refer to the spacing between the Zn-coordinating residues, giving rise to a substantially tilted helix αC in the zf-C3HC and Rsm1 modules, and an extra helix αAB' in the Rsm1 module. Conservation of key residues responsible for its distinct features identifies S. pombe Rsm1 and Homo sapiens NIPA/ZC3HC1 as structural orthologs of ScPml39. Based on the recent functional characterization of NIPA/ZC3HC1 as a scaffold protein that stabilizes the nuclear basket of the NPC, our data suggest an analogous function of ScPml39 in S. cerevisiae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures

Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in Toxoplasma gondii, an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing cytoskeletal components are subpellicular microtubules (SPMTs) and conoid fibrils (CFs). The SPMTs help maintain shape and gliding motility, while the CFs are implicated in invasion. Here, we use cryogenic electron tomography to determine the molecular structures of the SPMTs and CFs in vitrified intact and detergent-extracted parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecture in situ. An intralumenal spiral lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite’s long axis. Each CF is composed of nine tubulin protofilaments that display a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism illustrates the versatility of tubulin to form two distinct types of assemblies, SPMTs and CFs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Overview of density pedestal structure: Role fueling versus transport

How much of the density pedestal structure profile is determined by fueling versus transport is still a valid question. In most current tokamaks, the Scrape-Off Layer is not opaque enough to screen the neutrals and limit their penetration past the separatrix. As such recycled neutrals as well as additional gas puffing can directly affect the pedestal structure through ionization. Yet, in ITER and other future burning plasma magnetic confinement devices, this ionization source will be pushed further out into the Scrape-Off Layer. This poses the question, how much of the pedestal density structure is governed by this edge ionization source versus plasma transport effects. Theoretically, several turbulent modes have been identified which could provide a 'pinch' like up-gradient transport mechanism. Up-gradient transport is necessary in a source-free region to obtain a peaked density profile, which is often observed in the core of tokamaks. In an opaque Scrape-Off Layer, without the existence of such a pinch, the pedestal density structure would eventually disappear. Not only would this limit our ability to fuel a fusion reactor, it would also affect the pedestal stability. In this paper we will give an overview of the state of the art on what sets the pedestal density structure based on experimental observations as well as theoretical models. We will complement these studies with new results from Alcator C-Mod and DIII-D where the opaqueness is increased to reach values similar to those in ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

O 2 -Dependence of reactions of 1,2-dimethoxyethanyl and 1,2-dimethoxyethanylperoxy isomers

Reaction mechanisms of Ṙ and ROȮ radicals derived from low-temperature oxidation of 1,2-dimethoxyethane (CH 3 O(CH 2 ) 2 OCH 3 ) were investigated using speciation from multiplexed photoionization mass spectrometry (MPIMS) measurements via Cl-initiated oxidation, in conjunction with electronic structure calculations. The experiments were conducted at 5 bar, from 450 K – 650 K, and O 2 concentrations from 1 · 10 14 cm –3 – 6 · 10 18 cm –3 to probe the effects on competing reaction channels of 1,2-dimethoxyethanyl (Ṙ) and 1,2-dimethoxyethanylperoxy (ROȮ) isomers. Several species were detected with photoionization spectral fitting – ethene, formaldehyde, methyl vinyl ether, and 2-methoxyacetaldehyde – and, as determined by electronic structure calculations, may form via unimolecular decomposition of 1,2-dimethoxyethanyl or 1,2-dimethoxyethanylperoxy. O 2 -dependent yield ratios show that the formation pathways for all species undergo a competition between O 2 -addition and unimolecular decomposition. Here, adiabatic ionization energies were also calculated and utilized along with exact mass determinations to infer contributions for other species derived exclusively from first- and second-O 2 -addition, including 1,2-dimethoxyethene, cyclic ethers, and dicarbonyls.

1,2-dimethoxyethane↗
DOE OSTI2024

Venturing into Unexplored Phase Space: Synthesis, Structure, and Properties of MgCo 3 B 2 Featuring a Rumpled Kagomé Network

MgCo 3 B 2 , a novel ternary boride in a previously unexplored phase space, was synthesized using the hydride route. In situ powder X-ray diffraction and DFT calculations aided in the discovery of this compound, whose structure was then determined by single-crystal X-ray diffraction. Like the closely related CeCo 3 B 2 , MgCo 3 B 2 crystallizes in centrosymmetric space group P6/mmm (a = 4.883(2) Å, c = 2.926(2) Å at 210 K, Z = 1). Unlike CeCo 3 B 2 , however, it adopts a disordered structure that features a rumpled Kagomé network of Co atoms, and Mg atoms fill the channels of a Co–B framework. Although the structural disorder leads to motifs that are similar to those observed in MgNi 3 B 2 and other related ternary borides, no evidence of an ordered superstructure was found by single-crystal X-ray diffraction or high-resolution powder X-ray diffraction. In the case of CeCo 3 B 2 , boron atoms occupy the center of regular Co 6 trigonal prisms; in MgCo 3 B 2 , boron atoms are shifted from the center of the prism to form B–B dimers with roughly the same length as those found in MgNi 3 B 2 . Magnetic susceptibility data exhibit an unusual temperature dependence that cannot be convincingly modeled by the modified Curie–Weiss equation, consistent with DFT calculations predicting a nonmagnetic ground state. Intrinsic susceptibility at 300 K is 1.42 × 10 –3 emu/mol Oe, which is comparable to that of paramagnetic YCo 3 B 2 and CeCo 3 B 2 with a similar structure and composition. Here, this study showcases the efficacy of combining several methodologies to discover new solids in unexplored phase spaces. This approach includes in situ PXRD data to monitor reactions of precursors upon heating, a diffusion-enhanced synthesis method, and DFT assessment of compound stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2017

Evidence for a Low Bulk Crustal Density for Mars from Gravity and Topography

Knowledge of the average density of the crust of a planet is important in determining its interior structure. The combination of high-resolution gravity and topography data has yielded a low density for the Moon’s crust, yet for other terrestrial planets the resolution of the gravity field models has hampered reasonable estimates. By using well-chosen constraints derived from topography during gravity field model determination using satellite tracking data, we show that we can robustly and independently determine the average bulk crustal density directly from the tracking data, using the admittance between topography and imperfect gravity. We find a low average bulk crustal density for Mars, 2582 ± 209 kgm−3. This bulk crustal density is lower than that assumed until now. Densities for volcanic complexes are higher, consistent with earlier estimates, implying large lateral variations in crustal density. In addition, we find indications that the crustal density increases with depth.

Goossens, Sander J.↗
NASA NTRS2018

VAMOS: A SmallSat Mission Concept for Remote Sensing of Venusian Seismic Activity from Orbit

The apparent youthfulness of Venus’ surface features, given a lack of plate tectonics, is very intriguing; however, longduration seismic observations are essentially impossible given the inhospitable surface of Venus. The Venus Airglow Measurements and Orbiter for Seismicity (VAMOS) mission concept uses the fact that the dense Venusian atmosphere conducts seismic vibrations from the surface to the airglow layer of the ionosphere, as observed on Earth. Similarly, atmospheric gravity waves have been observed by the European Venus Express’s Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) instrument. Such observations would enable VAMOS to determine the crustal structure and ionospheric variability of Venus without approaching the surface or atmosphere. Equipped with an instrument of modest size and mass, the baseline VAMOS spacecraft is designed to fit within an ESPA Grande form factor and travel to Venus predominantly under its own power. Trade studies have been conducted to determine mission architecture robustness to launch and rideshare opportunities. The VAMOS mission concept was studied at JPL as part of the NASA Planetary Science Deep Space SmallSat Studies (PSDS3) program, which has not only produced a viable and exciting mission concept for a Venus SmallSat, but has also examined many issues facing the development of SmallSats for planetary exploration, such as SmallSat solar electric propulsion, autonomy, telecommunications, and resource management that can be applied to various inner solar system mission architectures.

Wallace, Mark↗
DOE OSTI2026

Ab initio symmetry-adapted approaches to nuclear reactions

In this review, we discuss recent applications of the ab initio symmetry-adapted no-core shell-model (SA-NCSM) theory for study and prediction of structure and reactions of stable and unstable nuclei from light to medium mass range. We explore structure properties of neutron-rich He, Li, and Mg isotopes, with a focus on nuclear collectivity, clustering, and spectroscopic factors, as well as multi-particle excitations of utmost significance in the proximity of the drip lines. In addition, we present extensions of the SA-NCSM with continuum for determining the microscopic structure of reaction fragments, which enables calculations of reaction cross sections for targets from the lightest He to 40Ca, rooted in first principles. We illustrate this for neutron and proton elastic scattering, deuteron and alpha capture reactions, and alpha knock-out reactions. Furthermore, we discuss microscopic optical potentials with uncertainty quantification, a critical ingredient in many reaction models. As a result, we also discuss the impact of alpha clustering on reactions of significance to nuclear astrophysics, as well as on beta decays and beyond-the-standard-model physics.

Ab initio approaches to nuclear reactions↗
DOE OSTI2021

Isolating the Electrocatalytic Activity of a Confined NiFe Motif within Zirconium Phosphate

Unique classes of active-site motifs are needed for improved electrocatalysis. Herein, the activity of a new catalyst motif is engineered and isolated for the oxygen evolution reaction (OER) created by nickel–iron transition metal electrocatalysts confined within a layered zirconium phosphate matrix. It is found that with optimal intercalation, confined NiFe catalysts have an order of magnitude improved mass activity compared to more conventional surface-adsorbed systems in 0.1 m KOH. Interestingly, the confined environments within the layered structure also stabilize Fe-rich compositions (90%) with exceptional mass activity compared to known Fe-rich OER catalysts. Through controls and by grafting inert molecules to the outer surface, it is evidenced that the intercalated Ni/Fe species stay within the interlayer during catalysis and serve as the active site. After determining a possible structure (wycherproofite), density functional theory is shown to correlate with the observed experimental compositional trends. It is further demonstrated that the improved activity of this motif is correlated to the Fe and water content/composition within the confined space. This work highlights the catalytic enhancement possibilities available through zirconium phosphate and isolates the activity from the intercalated species versus surface/edge ones, thus opening new avenues to develop and understand catalysts within unique nanoscale chemical environments.

36 MATERIALS SCIENCE↗

Refine your search to explore more results.