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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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response

The jumonji (JMJ) family of histone demethylases are Fe{sup 2+}- and {alpha}-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance, as well as in development, physiology and disease. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX). The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Atomic charges for modeling metal–organic frameworks: Why and how

Atomic partial charges are parameters of key importance in the simulation of Metal–Organic Frameworks (MOFs), since Coulombic interactions decrease with the distance more slowly than van der Waals interactions. But despite its relevance, there is no method to unambiguously assign charges to each atom, since atomic charges are not quantum observables. There are several methods that allow the calculation of atomic charges, most of them starting from the electronic wavefunction or the electronic density or the system, as obtained with quantum mechanics calculations. In this work, we describe the most common methods employed to calculate atomic charges in MOFs. In order to show the influence that even small variations of structure have on atomic charges, we present the results that we obtained for DMOF-1. We also discuss the effect that small variations of atomic charges have on the predicted structural properties of IRMOF-1. - Graphical abstract: We review the different method with which to calculate atomic partial charges that can be used in force field-based calculations. We also present two examples that illustrate the influence of the geometry on the calculated charges and the influence of the charges on structural properties. - Highlights: • The choice of atomic charges is crucial in modeling adsorption and diffusion in MOFs. • Methods for calculating atomic charges in MOFs are reviewed. • We discuss the influence of the framework geometry on the calculated charges. • We discuss the influence of the framework charges on structural the properties.

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

Characterization of Submicron Bubbles Formed by the Hydrophobin Cerato-ulmin

Cerato-ulmin is a fungal hydrophobin protein with a high surface activity because of its amphipathic nature. When aqueous dispersions are gently agitated by hand, cerato-ulmin (CU) assembles into cylindrical bubbles visible in an optical microscope. After approximately 1 h the larger micron-sized bubbles rise out of the solution, leaving only submicron particulates, which persist indefinitely. Dynamic light scattering experiments show that these persistent particles shrink when positive air pressure is applied to the suspension and expand when vacuum is applied. Small-angle X-ray scattering at ambient pressure suggests an extended core–shell structure, consistent with small air-filled bubbles stabilized by a protein film. A comparison between the SAXS of the persistent submicron bubbles and AFM of the buoyant larger bubbles found immediately after agitation show that both have similar film thickness of 13–15 nm or five protein molecules. The extended shapes confirm the solid-like properties of these CU membranes, even in submicron particulate structures, consistent with microtensiometry results on interfacial CU membranes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Intersubband energies in strain-compensated InGaN/AlInN quantum well structures

Intersubband transition energies in the conduction band for strain-compensated InGaN/AlInN quantum well (QW) structures were investigated as a function of strain based on an effective mass theory with the nonparabolicity taken into account. In the case of an InGaN/AlInN QW structure lattice-matched to GaN, the wavelength is shown to be longer than 1.55 μm. On the other hand, strain-compensated QW structures show that the wavelength of 1.55 μm can be reached even for the QW structure with a relatively small strain of 0.3 %. Hence, the strain-compensated QW structures can be used for telecommunication applications at 1.55 μm with a small strain, compared to conventional GaN/AlN QW structure.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Small-angle X-Ray analysis of macromolecular structure: the structure of protein NS2 (NEP) in solution

A complex structural analysis of nuclear export protein NS2 (NEP) of influenza virus A has been performed using bioinformatics predictive methods and small-angle X-ray scattering data. The behavior of NEP molecules in a solution (their aggregation, oligomerization, and dissociation, depending on the buffer composition) has been investigated. It was shown that stable associates are formed even in a conventional aqueous salt solution at physiological рН value. For the first time we have managed to get NEP dimers in solution, to analyze their structure, and to compare the models obtained using the method of the molecular tectonics with the spatial protein structure predicted by us using the bioinformatics methods. The results of the study provide a new insight into the structural features of nuclear export protein NS2 (NEP) of the influenza virus A, which is very important for viral infection development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Investigation on pseudosymmetry, twinning and disorder in crystal structure determinations: Ba(H{sub 2}O)M{sub 2}{sup III}[PO{sub 3}(OH)]{sub 4} (M=Fe, V) as examples

Twinning commonly occurs in monoclinic crystals with dimensionally similar a and c axes and results in pseudo-orthorhombic symmetries with overlapping diffractions. For example, twinning in the new synthetic compound Ba(H{sub 2}O)Fe{sub 2}[PO{sub 3}(OH)]{sub 4}, which varies in space group from P2{sub 1} to P2{sub 1}/c with approximately equal a and c axial lengths, gives rise to a pseudosymmetry of C222{sub 1}. Similarly, the related compound Ba(H{sub 2}O)V{sub 2}[PO{sub 3}(OH)]{sub 4} is commonly twinned and varies in space groups as well, arising from ordered to disordered distributions of the barium cations and water molecules in the cavities. Moreover, analyses of these and other twinned structures show that the small average standard uncertainty of bond distances is a sensitive criterion for structure determinations, especially for those involving crystal twinning as well as order-disorder. A proper structure determination leads to small standard uncertainties of the atomic displacement parameters, which further result in the small standard uncertainties of bond distances. - Graphical abstract: Ba(H{sub 2}O)M{sub 2}{sup III}[PO{sub 3}(OH)]{sub 4} (M=Fe, V) varies in space group from P2{sub 1} to P2{sub 1}/c, arising from ordered to disordered distributions of Ba{sup 2+} and H{sub 2}O in the cavities. Highlights: Black-Right-Pointing-Pointer Twinning commonly occurs in monoclinic crystals with a Almost-Equal-To c. Black-Right-Pointing-Pointer Overlapping diffractions from twin domains hamper with the determination of real space groups. Black-Right-Pointing-Pointer Conventional criteria for evaluating the real space groups are not effective in this case. Black-Right-Pointing-Pointer Small standard uncertainty of bond distances is proposed as a sensitive criterion. Black-Right-Pointing-Pointer Using this criterion we determined the order-disorder structures of Ba(H{sub 2}O)M{sub 2}{sup III}[PO{sub 3}(OH)]{sub 4} (M=Fe, V) from twinned crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Toward Fully in Silico Melting Point Prediction Using Molecular Simulations

Melting point is one of the most fundamental and practically important properties of a compound. Molecular computation of melting points. However, all of these methods simulation methods have been developed for the accurate need an experimental crystal structure as input, which means that such calculations are not really predictive since the melting point can be measured easily in experiments once a crystal structure is known. On the other hand, crystal structure prediction (CSP) has become an active field and significant progress has been made, although challenges still exist. One of the main challenges is the existence of many crystal structures (polymorphs) that are very close in energy. Thermal effects and kinetic factors make the situation even more complicated, such that it is still not trivial to predict experimental crystal structures. In this work, we exploit the fact that free energy differences are often small between crystal structures. We show that accurate melting point predictions can be made by using a reasonable crystal structure from CSP as a starting point for a free energy-based melting point calculation. The key is that most crystal structures predicted by CSP have free energies that are close to that of the experimental structure. The proposed method was tested on two rigid molecules and the results suggest that a fully in silico melting point prediction method is possible.

Zhang, Y↗
DOE OSTI2012

FILAMENTARY STAR FORMATION: OBSERVING THE EVOLUTION TOWARD FLATTENED ENVELOPES

Filamentary structures are ubiquitous from large-scale molecular clouds (a few parsecs) to small-scale circumstellar envelopes around Class 0 sources ({approx}1000 AU to {approx}0.1 pc). In particular, recent observations with the Herschel Space Observatory emphasize the importance of large-scale filaments (a few parsecs) and star formation. The small-scale flattened envelopes around Class 0 sources are reminiscent of the large-scale filaments. We propose an observationally derived scenario for filamentary star formation that describes the evolution of filaments as part of the process for formation of cores and circumstellar envelopes. If such a scenario is correct, small-scale filamentary structures (0.1 pc in length) with higher densities embedded in starless cores should exist, although to date almost all the interferometers have failed to observe such structures. We perform synthetic observations of filaments at the prestellar stage by modeling the known Class 0 flattened envelope in L1157 using both the Combined Array for Research in Millimeter-wave Astronomy (CARMA) and the Atacama Large Millimeter/Submillimeter Array (ALMA). We show that with reasonable estimates for the column density through the flattened envelope, the CARMA D array at 3 mm wavelengths is not able to detect such filamentary structure, so previous studies would not have detected them. However, the substructures may be detected with the CARMA D+E array at 3 mm and the CARMA E array at 1 mm as a result of more appropriate resolution and sensitivity. ALMA is also capable of detecting the substructures and showing the structures in detail compared to the CARMA results with its unprecedented sensitivity. Such detection will confirm the new proposed paradigm of non-spherical star formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a stable binding pocket. Consistent with a well structured binding pocket, docking analysis results correlated with experimental measures of the binding energy for most ligands. Steady state fluorescence studies of 2AP-substituted aptamers confirmed that A16 moves to a more solvent accessible position upon ligand binding while A14 moves to a less solvent accessible position, which is most likely a base stack. Analysis of binding affinities of NEO1A sequence variants showed that the base in position 16 interacts differently with each ligand and the interaction is a function of the buffer constituents. Our results show that the pentaloop provides NEO1A with the ability to adapt to external influences on its structure, with the critical base at position 16 adjusting to incorporate each ligand into a stable pocket by hydrophobic interactions and/or hydrogen bonds depending on the ligand and the ionic environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The Presence of Turbulent and Ordered Local Structure within the ICME Shock-sheath and Its Contribution to Forbush Decrease

The transient interplanetary disturbances evoke short-time cosmic-ray flux decrease, which is known as Forbush decrease. The traditional model and understanding of Forbush decrease suggest that the sub-structure of an interplanetary counterpart of coronal mass ejection (ICME) independently contributes to cosmic-ray flux decrease. These sub-structures, shock-sheath, and magnetic cloud (MC) manifest as classical two-step Forbush decrease. The recent work by Raghav et al. has shown multi-step decreases and recoveries within the shock-sheath. However, this cannot be explained by the ideal shock-sheath barrier model. Furthermore, they suggested that local structures within the ICME’s sub-structure (MC and shock-sheath) could explain this deviation of the FD profile from the classical FD. Therefore, the present study attempts to investigate the cause of multi-step cosmic-ray flux decrease and respective recovery within the shock-sheath in detail. A 3D-hodogram method is utilized to obtain more details regarding the local structures within the shock-sheath. This method unambiguously suggests the formation of small-scale local structures within the ICME (shock-sheath and even in MC). Moreover, the method could differentiate the turbulent and ordered interplanetary magnetic field (IMF) regions within the sub-structures of ICME. The study explicitly suggests that the turbulent and ordered IMF regions within the shock-sheath do influence cosmic-ray variations differently.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1985

Temperature structure in the lower atmosphere of Venus - New results derived from Pioneer Venus entry probe measurements

The Pioneer Venus Small-Probe Net Flux Radiometer temperature sensor and its calibration, the thermal model of the sensor head, the procedure for deriving atmospheric temperature from the sensor temperatures, and the new temperature results for each entry probe are reported. The new results are compared with those of the Small-Probe Atmospheric Structure experiment and with simple models of diurnal and latitudinal temperature contrasts. A dynamical inconsistency between these results and low-latitude measurements by the Sounder probe is described, and possible ways to resolve it are considered.

Sromovsky, L. A.↗
DOE OSTI2016

Use of small-angle X-ray scattering to resolve intracellular structure changes of Escherichia coli cells induced by antibiotic treatment

The application of small-angle X-ray scattering (SAXS) to whole Escherichia coli cells is challenging owing to the variety of internal constituents. To resolve their contributions, the outer shape was captured by ultra-small-angle X-ray scattering and combined with the internal structure resolved by SAXS. Building on these data, a model for the major structural components of E. coli was developed. It was thus possible to deduce information on the occupied volume, occurrence and average size of the most important intracellular constituents: ribosomes, DNA and proteins. E. coli was studied after treatment with three different antibiotic agents (chloramphenicol, tetracycline and rifampicin) and the impact on the intracellular constituents was monitored.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Differentiating Structural Changes of Glycoproteins in Solution using Small Angle Scattering Analysis

Alpha 1-Antitrypsin (A1AT) and Fibrinogen are plasma glycoproteins with different, but specific biological functions. A1AT (which forms part of the serpin family) has been shown to have protective roles of lung cells against emphysema, a disease characterized by lung tissue destruction, while fibrinogen is a major factor in the blood clotting process. While biologically distinct, the two proteins present similarities in biophysical studies due to their size and polymerization tendency. Previous approximations, using radius of gyration analysis (shape independent), have shown that there is a phase transition for A1AT under osmotic stress. The goals of this study are to better understand: the stability of A1AT's native conformation when its environment deviates from physiological conditions; and the effects on fibrin's final structure as fibrinogen undergoes polymerization under different conditions. Environmental variables include osmotic stress, crowding, and presence of other molecules (e.g. lipids, catalytic enzyme thrombin, or cholesterol) found in plasma. The method used to assess the stability of the native conformation was to observe changes in the structural envelope of the protein. Static and dynamic small angle x-ray scattering (SAXS) and small angle neutron scattering (SANS) experiments of the proteins in solution were conducted for this purpose. Scattering data was fitted using various shape dependent models in SASView. Pair distance functions (PDF) were used to validate any changes identified by the model fits. Multi-variable phase diagrams were constructed from the fitting results in order to quantify structural and conformational changes of the proteins.

Segally, Taylor N.↗
DOE OSTI2019

Electron-Quantum Transport in Pseudomorphic and Metamorphic In{sub 0.2}Ga{sub 0.8}As-Based Quantum Wells

Metamorphic high-electron-mobility transistor (HEMT) structures based on deep In{sub 0.2}Ga{sub 0.8}As/In{sub 0.2}Al{sub 0.8}As quantum wells (0.7 eV for Γ electrons) with different metamorphic buffer designs are implemented and investigated for the first time. The electronic properties of metamorphic and pseudomorphic HEMT structures with the same doping are compared. It is found that, over a temperature range of 4–300 K, both the electron mobility and concentration in the HEMT structure with a linear metamorphic buffer are higher than those in the pseudomorphic HEMT structure due to an increase in the depth of the quantum well. Low-temperature magnetotransport measurements demonstrate that the quantum momentum-relaxation time decreases considerably in metamorphic HEMT structures because of enhanced small-angle scattering resulting from structural defects and inhomogeneities, while the dominant scattering mechanism in structures of both types is still due to remote ionized impurities.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

UNVEILING THE STRUCTURE OF PRE-TRANSITIONAL DISKS

In the past few years, several disks with inner holes that are relatively empty of small dust grains have been detected and are known as transitional disks. Recently, Spitzer has identified a new class of 'pre-transitional disks' with gaps based on near-infrared photometry and mid-infrared spectra; these objects have an optically thick inner disk separated from an optically thick outer disk by an optically thin disk gap. A near-infrared spectrum provided the first confirmation of a gap in the pre-transitional disk of LkCa 15 by verifying that the near-infrared excess emission in this object was due to an optically thick inner disk. Here, we investigate the difference between the nature of the inner regions of transitional and pre-transitional disks using the same veiling-based technique to extract the near-infrared excess emission above the stellar photosphere. However, in this work we use detailed disk models to fit the excess continua as opposed to the simple blackbody fits previously used. We show that the near-infrared excess emission of the previously identified pre-transitional disks of LkCa 15 and UX Tau A in the Taurus cloud as well as the newly identified pre-transitional disk of ROX 44 in Ophiuchus can be fit with an inner disk wall located at the dust destruction radius. We also present detailed modeling of the broadband spectral energy distributions of these objects, taking into account the effect of shadowing by the inner disk on the outer disk, but considering the finite size of the star, unlike other recent treatments. The near-infrared excess continua of these three pre-transitional disks, which can be explained by optically thick inner disks, are significantly different from that of the transitional disks of GM Aur, whose near-infrared excess continuum can be reproduced by emission from sub-micron-sized optically thin dust, and DM Tau, whose near-infrared spectrum is consistent with a disk hole that is relatively free of small dust. The structure of pre-transitional disks may be a sign of young planets forming in these disks and future studies of pre-transitional disks will provide constraints to aid in theoretical modeling of planet formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2010

Introduction to phasing

This introductory paper to the CCP4 weekend on experimental phasing introduces the concept of the ‘phase problem’ for non-experts. Modern methods of phasing are explored, including some recent examples that can be downloaded as tutorials. When collecting X-ray diffraction data from a crystal, we measure the intensities of the diffracted waves scattered from a series of planes that we can imagine slicing through the crystal in all directions. From these intensities we derive the amplitudes of the scattered waves, but in the experiment we lose the phase information; that is, how we offset these waves when we add them together to reconstruct an image of our molecule. This is generally known as the ‘phase problem’. We can only derive the phases from some knowledge of the molecular structure. In small-molecule crystallography, some basic assumptions about atomicity give rise to relationships between the amplitudes from which phase information can be extracted. In protein crystallography, these ab initio methods can only be used in the rare cases in which there are data to at least 1.2 Å resolution. For the majority of cases in protein crystallography phases are derived either by using the atomic coordinates of a structurally similar protein (molecular replacement) or by finding the positions of heavy atoms that are intrinsic to the protein or that have been added (methods such as MIR, MIRAS, SIR, SIRAS, MAD, SAD or combinations of these). The pioneering work of Perutz, Kendrew, Blow, Crick and others developed the methods of isomorphous replacement: adding electron-dense atoms to the protein without disturbing the protein structure. Nowadays, methods from small-molecule crystallography can be used to find the heavy-atom substructure and the phases for the whole protein can be bootstrapped from this prior knowledge. More recently, improved X-ray sources, detectors and software have led to the routine use of anomalous scattering to obtain phase information from either incorporated selenium or intrinsic sulfurs. In the best cases, only a single set of X-ray data (SAD) is required to provide the positions of the anomalous scatters, which together with density-modification procedures can reveal the structure of the complete protein.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗