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At least 379 records · Page 21

Spectral Irradiance Measurements of Simulated Lightning in Planetary Atmospheres

Optical emissions from lightning provide information to estimate the altitude, latitude and longitude of lightning storms, the energy of the discharges, and the production of important trace species such as HCN and C2H2. Knowledge of the spectra of planetary lightning is needed to deduce the total energy dissipated by lightning (and thereby, the production of trace gases) and to help design experiments to detect and track lightning storms. Measurements of the spectral irradiance from approximately 380 to 820 nm are reported for laboratory simulations of lightning in the atmospheres of Venus, Jupiter, and Titan. In our laboratory, laser-induced plasmas (LIP) are used to simulate lightning discharges. This technique avoids contamination of the spectra by elect-ode material and maintains a safe environment while allowing the use of flammable gases, such as hydrogen and methane, found in outer planet atmospheres. The observations were made at I and 5 bars pressure for Venus and Jupiter and at 1 bar for the Titan mixture. At a pressure of one bar, our results show prominent lines from H(sub alpha), H(sub beta), H(sub gamma), and H(sub delta) lines of the Balmer Series of atomic hydrogen, a single line from Helium at 588 nm and strong continuum radiation. At pressures of 5 bars, the H(sub alpha) and H(sub beta) lines are wider, the H(sub gamma), and H(sub delta) lines merge into the continuum because of pressure broadening, and the helium line at 588 nm is no longer visible. The observed spectra of simulated lightning in the venusian atmosphere at 1 and 5 bars shows that the OI multiplet at 777.7 nm dominates the spectra, but weak features due to atomic carbon and singly excited and singly ionized oxygen atoms are also visible. Although lightning has not yet been observed on Titan, it conceivable that some form of lightning discharge could be occurring. Therefore experiments on a Titan atmosphere mixture were conducted. The most prominent features seen in the simulated spectra are the H(sub alpha) at 656 nm. from the dissociation of the methane and two strong features at 740 and 820 nm from singly excited nitrogen atoms. Most of the features between 400 and 656 nm are due to ionized nitrogen atoms. A broad, highly structured feature centered near 389 nm is molecular band radiation from CN molecules formed in the cooling plasma of atomic nitrogen, carbon, and hydrogen. It is observed in the lightning simulations of both the venusian and Titan atmospheres, For Venus, Jupiter, and Titan, narrow spectral features that are ideal for detecting lightning in the presence of sunlight are present in the spectra. These features could allow lightning to be detected and tracked by Earth-based instruments.

Borucki, W. J.↗

Using Gaussian windows to explore a multivariate data set

In an earlier paper, I recounted an exploratory analysis, using Gaussian windows, of a data set derived from the Infrared Astronomical Satellite. Here, my goals are to develop strategies for finding structural features in a data set in a many-dimensional space, and to find ways to describe the shape of such a data set. After a brief review of Gaussian windows, I describe the current implementation of the method. I give some ways of describing features that we might find in the data, such as clusters and saddle points, and also extended structures such as a 'bar', which is an essentially one-dimensional concentration of data points. I then define a distance function, which I use to determine which data points are 'associated' with a feature. Data points not associated with any feature are called 'outliers'. I then explore the data set, giving the strategies that I used and quantitative descriptions of the features that I found, including clusters, bars, and a saddle point. I tried to use strategies and procedures that could, in principle, be used in any number of dimensions.

Jaeckel, Louis A.↗

Allosteric prediction via convolutional neural networks and protein structural and dynamical features

Allostery is the phenomenon whereby a binding event or covalent modification at one site in a protein modulates function at a distal site, thus changing a protein’s functional state. As such, it is a ubiquitous aspect of protein functional regulation. Computationally predicting allosteric states is important as part of the broader challenge of functional annotation, but it also has practical implications for drug development, as targeting an allosteric site often affords greater specificity compared with targeting an orthosteric site. This study introduces a machine learning approach to predict the allosteric functional state using the small G-protein KRas as the model system, due to its implication in many types of cancer and being well studied as a result with many x-ray crystallographic structures of KRas available with different mutations and ligands bound. Using structural and dynamical features that can be cast as images, namely interatomic distances, contact maps, covariance, and mutual information, supervised learning was performed using convolutional neural networks. Two pretrained convolutional neural network architectures, GoogLeNet and ResNet18, were fine-tuned to classify KRas into active or inactive states based on these features. Across training regimes, atomic contact maps emerged as the most effective structural feature, whereas linearized mutual information outperformed covariance in capturing dynamical correlations relevant to allostery. Models achieved significant validation accuracy, with atomic contact maps yielding up to 90% accuracy. In conclusion, the findings suggest that integrating global structural rearrangements and correlated motion patterns with deep learning can reliably predict protein allosteric states, offering a promising framework for understanding allosteric regulation and developing targeted therapeutics.

Rajeshwar T., Rajitha [Oak Ridge National Laborato↗

Metal–Organic Frameworks at the Edge of Stability: Mediating Node Distortion to Access Metastable Nanoparticle Polymorphs

Metal-organic frameworks (MOFs) are emerging as unconventional precursors for nanoparticle synthesis, with potential to leverage their tunable structures and chemistry to achieve nanomaterials with structures and compositions inaccessible via traditional synthetic routes. Here we use in situ synchrotron X-ray diffraction and pair distribution function (PDF) measurements to investigate how the dynamic structure of MOFs at the edge of stability influences their transformation into different metastable polymorphs. Our study reveals that the local structural features of metal-oxo MOF nodes at elevated temperatures are linked to the resulting nanoparticle structures formed under mild conditions. Focusing on the titanium-based MOF MIL-125, we demonstrate that manipulating the chemical environment to facilitate transformation of the Ti8 node geometry promotes formation of metastable, nanometer-scale TiO2 brookite rather than the more common anatase and rutile TiO2 polymorphs typically produced through MOF pyrolysis at high temperature. These findings highlight the potential to harness the MOF topology and chemical environment to design and control node distortions and enable access to exotic metastable nanoparticle states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydrothermal synthesis of lanthanide rhenium oxides: Structures and magnetism of Ln 2 Re 2 O 7 (OH) (Ln = Pr, Nd) and Ln 4 Re 2 O 11 (Ln = Eu, Tb)

The reactions of Ln 2 O 3 (Ln =LaLu) with ReO 2 were examined in high temperature hydrothermal water (650 °C). In all cases the rhenium oxide was added in a three-fold excess. No external mineralizer was needed and the rhenate itself acted as a sufficient mineralizer to form high quality single crystals of several crystalline products. These form in good yield with compositions varying as a function of the size of the rare earth ion. The largest sesquioxide, La 2 O 3 , forms the well-known La 4 Re 6 O 19 phase, but when Ln = Nd or Pr, a new product, Ln 2 Re 2 O 7 (OH), is isolated. Reactions with Ln = SmTb form Ln 4 Re 2 O 11 , and those with DyLu form Ln 2 ReO 5 . The new Ln 2 Re 2 O 7 (OH) series was characterized as a new structure type by single crystal X-ray diffraction. This structure features a tetrameric Re 4 O 16 cluster embedded in a lanthanide oxide framework. Additional detailed structural data is also provided for Tb 4 Re 2 O 11 and Eu 4 Re 2 O 11 , which were not previously reported for the Ln 4 Re 2 O 11 family. In Ln 2 Re 2 O 7 (OH), no direct ReRe bond (ReRe = 2.60 Å) is observed while Ln 4 Re 2 O 11 appears to possess a rhenium-rhenium double bond with a ReRe distance of 2.42 Å. Single crystal Raman data supports both of these characterizations. Magnetic data is reported for Ln 2 Re 2 O 7 (OH) and Tb 4 Re 2 O 11 , and their behavior appears to be dominated by the f-element magnetic moments. At low temperatures Tb 4 Re 2 O 11 displays possible canted antiferromagnetic coupling.

36 MATERIALS SCIENCE↗

Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK)

Increased fructose consumption and its subsequent metabolism have been implicated in hepatic steatosis, dyslipidemia, obesity, and insulin resistance in humans. Since ketohexokinase (KHK) is the principal enzyme responsible for fructose metabolism, identification of a selective KHK inhibitor may help to further elucidate the effect of KHK inhibition on these metabolic disorders. Until now, studies on KHK inhibition with small molecules have been limited due to the lack of viable in vivo pharmacological tools. Herein we report the discovery of 12, a selective KHK inhibitor with potency and properties suitable for evaluating KHK inhibition in rat models. Key structural features interacting with KHK were discovered through fragment-based screening and subsequent optimization using structure-based drug design, and parallel medicinal chemistry led to the identification of pyridine 12.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure-Properties Correlation in Si Nanoparticles by Total Scattering and Computer Simulations

High-energy synchrotron X-ray diffraction coupled to atomic pair distribution function analysis and computer simulations is used to determine the atomic-scale structure of silicon (Si) nanoparticles obtained by two different synthetic routes. Results show that Si nanoparticles may have significant structural differences depending on the synthesis route and surface chemistry. In this case, one method produced Si nanoparticles that are highly crystalline but surface oxidized, whereas a different method yields organic ligand-passivated nanoparticles without surface oxide but that are structurally distorted at the atomic scale. Particular structural features of the oxide-free Si nanoparticles such as average first coordination numbers, length of structural coherence, and degree of local distortions are compared to their optical properties such as photoluminescence emission energy, quantum yield, and Raman spectra. A clear structure–properties correlation is observed indicating that the former may need to be taken into account when considering the latter.

Petkov, Valeri↗

Effect of iron redox ratio on the structures of boroaluminosilicate glasses

Iron oxide is commonly found in natural or industrial glass compositions and can exist as ferrous (Fe 2+ ) or ferric (Fe 3+ ) species, with their ratios depending on glass composition, temperature, pressure and the redox reactions during the glass forming process. The iron redox ratio plays an important role on silicate glass structures and consequently various properties. This work aims to study the effect of iron oxide, and particularly the iron redox ratio, on the structures of borosilicate and boroaluminosilicate glasses using molecular dynamics simulations with newly developed iron potential parameters that are compatible with the borosilicate potentials. The results provide detailed cation coordination states of both iron species and the effect of redox ratio on boron coordination and other structural features. Particularly, competition for charge compensating modifier cations (such as Na + ) among the fourfold-coordinated cations such as B 3+ , Al 3+ , and Fe 3+ is investigated by calculating the cation–cation pair distribution functions and coordination preferential ratios. The results show that the trivalent ferric ions, with a shorter Fe–O bond distance and better defined first coordiation shell with mainly four-fold coordination, act as a glass former whereas the divalent ferrous ions mainly play the role of glass modifier. The ferrous/ferric ratio (Fe 2+ /Fe 3+ ) was found to affect the glass chemistry and hence glass properties by regulating the amount of four-coordinated boron, the fraction of non-briding oxygen and other features. Finally, the results are compared with available experimental data to gain insights of the complex structures and charge compensation schemes of the glass system.

36 MATERIALS SCIENCE↗

Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression

Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

09 BIOMASS FUELS↗

Topological vulnerability of power grids to disasters: Bounds, adversarial attacks and reinforcement

Natural disasters like hurricanes, floods or earthquakes can damage power grid devices and create cascading blackouts and islands. The nature of failure propagation and extent of damage, among other factors, is dependent on the structural features of the grid, that are distinct from that of random networks. This paper analyzes the structural vulnerability of real power grids to impending disasters and presents intuitive graphical metrics to quantify the extent of topological damage. We develop two improved graph eigen-value based bounds on the grid vulnerability. Further we study adversarial attacks aimed at weakening the grid’s structural robustness and present three combinatorial algorithms to determine the optimal topological attack. Simulations on power grid networks and comparison with existing work show the improvements of the proposed measures and attack schemes.

24 POWER TRANSMISSION AND DISTRIBUTION↗

High energy gamma ray astronomy

High energy gamma ray astronomy has evolved with the space age. Nonexistent twenty-five years ago, there is now a general sketch of the gamma ray sky which should develop into a detailed picture with the results expected to be forthcoming over the next decade. The galactic plane is the dominant feature of the gamma ray sky, the longitude and latitude distribution being generally correlated with galactic structural features including the spiral arms. Two molecular clouds were already seen. Two of the three strongest gamma ray sources are pulsars. The highly variable X-ray source Cygnus X-3 was seen at one time, but not another in the 100 MeV region, and it was also observed at very high energies. Beyond the Milky Way Galaxy, there is seen a diffuse radiation, whose origin remains uncertain, as well as at least one quasar, 3C 273. Looking to the future, the satellite opportunities for high energy gamma ray astronomy in the near term are the GAMMA-I planned to be launched in late 1987 and the Gamma Ray Observatory, scheduled for launch in 1990. The Gamma Ray Observatory will carry a total of four instruments covering the entire energy range from 30,000 eV to 3 x 10 to the 10th eV with over an order of magnitude increase in sensitivity relative to previous satellite instruments.

Fichtel, Carl E.↗

Pressure-Induced Multiferroics via Pseudo Jahn-Teller Effects and Novel Couplings

Multiferroic materials are currently attracting a lot of interest because of the cross-coupling between their electrical and magnetic properties, which has the potential to lead to novel devices. There is a relatively small number of multiferroics and, hence, various strategies have been proposed to design materials possessing both ordered electric and magnetic dipoles. However, one strategy that has been scarcely investigated so far is the application of hydrostatic pressure because such external factor has the tendency to suppress, rather than enhance or create, electrical polarization. Here, first-principles calculations are used to demonstrate that hydrostatic pressure can, in fact, stabilize a novel polar and magnetic - and thus multiferroic - phase; the occurrence of such a phase seems very general, as it is found in many presently investigated RMnO 3 compounds, where R is a rare-earth ion. The predicted structure features original pseudo Jahn-Teller effects that induce a spontaneous electrical polarization via a previously unknown structural coupling of a rather convenient form. This discovery opens a new route to create multiferroics and tunable electronic devices.

36 MATERIALS SCIENCE↗

Polyhedral Distortions and Unusual Magnetic Order in Spinel FeMn 2 O 4

Spinel compounds AB 2 X 4 consist of both tetrahedral (AX 4 ) and octahedral (BX 6) environments with the former forming a diamond lattice and the latter a geometrically frustrated pyrochlore lattice. Exploring the fascinating physical properties and their correlations with structural features is critical in understanding these materials. FeMn 2 O 4 has been reported to exhibit one structural transition and two successive magnetic transitions. In this work, we report the polyhedral distortions and their correlations to the structural and two magnetic transitions in FeMn 2 O 4 by employing the high-resolution neutron powder diffraction. The cation distribution is found to be ($Mn_{0.9}^{2+}Fe_{0.1}^{3+}$)$_{A}$($Mn^{3+}Fe_{0.9}^{3+}Mn_{0.1}^{2+}$)$_{B}$O 4 . While large trigonal distortion is found even in the high-temperature cubic phase, the first-order cubic-tetragonal structural transition associated with the elongation of both tetrahedra and octahedra with shared oxygen atoms along the c axis occurs at T S ≈ 750 K, driven by the Jahn–Teller effect of the orbital active B-site Mn 3+ cation. Strong magnetoelastic coupling is unveiled at T N1 ≈ 400 K as manifested by the appearance of Néel-type collinear ferrimagnetic order, an anomaly in both tetrahedral and octahedral distortions, as well as an anomalous decrease of the lattice constants c and a weak anomaly of a. Upon cooling to T N2 ≈ 65 K, it evolves to a noncollinear ferrimagnetic order accompanied by the different moments at the split magnetic sites B1 and B2. Only one-half of the B-site Mn 3+ /Fe 3+ spins, i.e., the B2-site spins in the pyrochlore lattice, are canted, which is a unique magnetic order among spinels. The canting angle between A-site and B2-site moments is ~25°, but the B1-site moment stays antiparallel to the A-site moment even at 10 K. This noncollinear order is accompanied by a modification of the O–B–O bond angles in the octahedra without significant change in lattice constants or tetrahedral/octahedral distortion parameters, indicating a distinct magnetoelastic coupling. We demonstrate distinct roles of the A-site and B-site magnetic cations in the structural and magnetic properties of FeMn 2 O 4 . Our study indicates that FeMn 2 O 4 is a wonderful platform to unveil interesting magnetic order and to investigate their correlations with polyhedral distortions and lattice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strain-Induced Ferroelectric Topological Insulator

Ferroelectricity and band topology are two extensively studied yet distinct properties of insulators. Nonetheless, their coexistence has never been observed in a single material. Using first-principles calculations, we demonstrate that a noncentrosymmetric perovskite structure of CsPbI 3 allows for the simultaneous presence of ferroelectric and topological orders with appropriate strain engineering. Metallic topological surface states create an intrinsic short-circuit condition, helping stabilize bulk polarization. Exploring diverse structural phases of CsPbI 3 under pressure, we identify that the key structural feature for achieving a ferroelectric topological insulator is to suppress PbI 6 cage rotation in the perovskite structure, which could be obtained via strain engineering. Ferroelectric control over the density of topological surface states provides a new paradigm for device engineering, such as perfect-focusing Veselago lens and spin-selective electron collimator. Here, our results suggest that CsPbI 3 is a simple model system for ferroelectric topological insulators, enabling future studies exploring the interplay between conventional symmetry-breaking and topological orders and their novel applications in electronics and spintronics.

36 MATERIALS SCIENCE↗

In-situ electron microscopy mapping of an order-disorder transition in a superionic conductor

Solid-solid phase transitions are processes ripe for the discovery of correlated atomic motion in crystals. Here, we monitor an order-disorder transition in real-time in nanoparticles of the super-ionic solid, Cu 2-x Se. The use of in-situ high-resolution transmission electron microscopy allows the spatiotemporal evolution of the phase transition within a single nanoparticle to be monitored at the atomic level. The high spatial resolution reveals that cation disorder is nucleated at low co-ordination, high energy sites of the nanoparticle where cationic vacancy layers intersect with surface facets. Time-dependent evolution of the reciprocal lattice of individual nanoparticles shows that the initiation of cation disorder is accompanied by a ~3% compression of the anionic lattice, establishing a correlation between these two structural features of the lattice. The spatiotemporal insights gained here advance understanding of order-disorder transitions, ionic structure and transport, and the role of nanoparticle surfaces in phase transitions.

36 MATERIALS SCIENCE↗

Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein

Ligand-binding promiscuity in detoxification systems protects the body from toxicological harm but is a roadblock to drug development due to the difficulty in optimizing small molecules to both retain target potency and avoid metabolic events. Immense effort is invested in evaluating metabolism of molecules to develop safer, more effective treatments, but engineering specificity into or out of promiscuous proteins and their ligands is a challenging task. To better understand the promiscuous nature of detoxification networks, we have used X-ray crystallography to characterize a structural feature of pregnane X receptor (PXR), a nuclear receptor that is activated by diverse molecules (with different structures and sizes) to up-regulate transcription of drug metabolism genes. We found that large ligands expand PXR’s ligand-binding pocket, and the ligand-induced expansion occurs through a specific unfavorable compound-protein clash that likely contributes to reduced binding affinity. Removing the clash by compound modification resulted in more favorable binding modes with significantly enhanced binding affinity. We then engineered the unfavorable ligand-protein clash into a potent, small PXR ligand, resulting in marked reduction in PXR binding and activation. Structural analysis showed that PXR is remodeled, and the modified ligands reposition in the binding pocket to avoid clashes, but the conformational changes result in less favorable binding modes. Thus, ligand-induced binding pocket expansion increases ligand-binding potential of PXR but is an unfavorable event; therefore, drug candidates can be engineered to expand PXR’s ligand-binding pocket and reduce their safety liability due to PXR binding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The roles of RIIbeta linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of Type IIbeta Protein Kinase A. A small angle X-ray and neutron scattering study

Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. Moreover, the PKA holoenzyme is a tetramer (R 2 :C 2 ), with a regulatory subunit homodimer (R 2 ) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1–280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. These results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA.

59 BASIC BIOLOGICAL SCIENCES↗