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At least 73 records · Page 4

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective

The 16S and 23S rRNA higher-order structures inferred from comparative analysis are now quite refined. The models presented here differ from their immediate predecessors only in minor detail. Thus, it is safe to assert that all of the standard secondary-structure elements in (prokaryotic) rRNAs have been identified, with approximately 90% of the individual base pairs in each molecule having independent comparative support, and that at least some of the tertiary interactions have been revealed. It is interesting to compare the rRNAs in this respect with tRNA, whose higher-order structure is known in detail from its crystal structure (36) (Table 2). It can be seen that rRNAs have as great a fraction of their sequence in established secondary-structure elements as does tRNA. However, the fact that the former show a much lower fraction of identified tertiary interactions and a greater fraction of unpaired nucleotides than the latter implies that many of the rRNA tertiary interactions remain to be located. (Alternatively, the ribosome might involve protein-rRNA rather than intramolecular rRNA interactions to stabilize three-dimensional structure.) Experimental studies on rRNA are consistent to a first approximation with the structures proposed here, confirming the basic assumption of comparative analysis, i.e., that bases whose compositions strictly covary are physically interacting. In the exhaustive study of Moazed et al. (45) on protection of the bases in the small-subunit rRNA against chemical modification, the vast majority of bases inferred to pair by covariation are found to be protected from chemical modification, both in isolated small-subunit rRNA and in the 30S subunit. The majority of the tertiary interactions are reflected in the chemical protection data as well (45). On the other hand, many of the bases not shown as paired in Fig. 1 are accessible to chemical attack (45). However, in this case a sizeable fraction of them are also protected against chemical modification (in the isolated rRNA), which suggests that considerable higher-order structure remains to be found (although all of it may not involve base-base interactions and so may not be detectable by comparative analysis). The agreement between the higher-order structure of the small-subunit rRNA and protection against chemical modification is not perfect, however; some bases shown to covary canonically are accessible to chemical modification (45).(ABSTRACT TRUNCATED AT 400 WORDS).

Review↗

Coexisting structural disorder and robust spin-polarization in half-metallic FeMnVAl

We report half-metallic ferromagnets (HMFs) are one of the most promising materials in the field of spintronics due to their unique band structure, consisting of one spin subband having metallic characteristics along with another subband with semiconductor-like behavior. In this work, we report the synthesis of a novel quaternary Heusler alloy—FeMnVAl—and we have studied the structural, magnetic, transport, and electronic properties complemented with first-principles calculations. Among different possible structurally ordered arrangements, the optimal structure is identified by theoretical energy minimization. The corresponding spin-polarized band-structure calculations indicate the presence of a half-metallic ferromagnetic ground state. A detailed and careful investigation of the x-ray diffraction data, Mössbauer spectra, and nuclear magnetic resonance spectra suggests the presence of site disorder between the Fe and Mn atoms in the stable ordered structure of the system. The magnetic susceptibility measurement clearly establishes a ferromagnetic-like transition below ~213 K. The Fe Mössbauer spectrometry measurements suggest that only the Mn spins could be responsible for the magnetic order, which is consistent with our theoretical calculation. Surprisingly, the density-functional-theory calculations reveal that the spin-polarization value is almost immunized (92.4% → 90.4%) from the Mn-Fe structural disorder, even when nonmagnetic Fe and moment-carrying Mn sites are entangled inseparably. The robustness of spin polarization and half-metallicity in the studied FeMnVAl compound comprising structural disorder is thus quite interesting and could provide a new direction to investigate and understand the exact role of disorders on spin polarization in this class of materials, beyond the available knowledge.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Highly ordered vertical structure of Synechococcus populations within the one-millimeter-thick photic zone of a hot spring cyanobacterial mat

A variety of contemporary techniques were used to investigate the vertical distribution of thermophilic unicellular cyanobacteria, Synechococcus spp., and their activity within the upper 1-mm-thick photic zone of the mat community found in an alkaline siliceous hot spring in Yellowstone National Park in Wyoming. Detailed measurements were made over a diel cycle at a 61 degrees C site. Net oxygenic photosynthesis measured with oxygen microelectrodes was highest within the uppermost 100- to 200-microm-thick layer until midmorning, but as the day progressed, the peak of net activity shifted to deeper layers, stabilizing at a depth of 300 microm from midday throughout the afternoon. Examination of vertical thin sections by bright-field and autofluorescence microscopy revealed the existence of different populations of Synechococcus which form discrete bands at different vertical positions. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments from horizontal cryosections obtained at 100-microm-thick vertical intervals also suggested vertical stratification of cyanobacterial, green sulfur bacterium-like, and green nonsulfur bacterium-like populations. There was no evidence of diel migration. However, image analysis of vertical thin sections revealed the presence of a narrow band of rod-shaped Synechococcus cells in which the cells assumed an upright position. These upright cells, located 400 to 800 microm below the surface, were observed only in mat samples obtained around noon. In mat samples obtained at other time points, the cells were randomly oriented throughout the mat. These combined observations reveal the existence of a highly ordered structure within the very thin photic zone of this hot spring microbial mat, consisting of morphologically similar Synechococcus populations that are likely to be differentially adapted, some co-occurring with green sulfur bacterium-like populations, and all overlying green nonsulfur bacterium-like populations.

Non-NASA Center↗

A General Approach for Metal Nanoparticle Encapsulation Within Porous Oxides

Abstract Encapsulation of metal nanoparticles within oxide materials has been shown as an effective strategy to improve activity, selectivity, and stability in several catalytic applications. Several approaches have been proposed to encapsulate nanoparticles, such as forming core‐shell structures, growing ordered structures (zeolites or metal‐organic frameworks) on nanoparticles, or directly depositing support materials on nanoparticles. Here, a general nanocasting method is demonstrated that can produce diverse encapsulated metal@oxide structures with different compositions (Pt, Pd, Rh) and multiple types of oxides (Al 2 O 3 , Al 2 O 3 ‐CeO 2 , ZrO 2 , ZnZrO x , In 2 O 3 , Mn 2 O 3 , TiO 2 ) while controlling the size and dispersion of nanoparticles and the porous structure of the oxide. Metal@polymer structures are first prepared, and then the oxide precursor is infiltrated into such structures and the resulting material is calcined to form the metal@oxide structures. Most Pt@oxides catalysts show similar catalytic activity, demonstrating the availability of surface Pt sites in the encapsulated structures. However, the Pt@Mn 2 O 3 sample showed much higher CO oxidation activity, while also being stable under aging conditions. This work demonstrated a robust nanocasting method to synthesize metal@oxide structures, which can be utilized in catalysis to finely tune metal‐oxide interfaces.

Zhou, Chengshuang↗

Diffusion, atomic transport, and ordering in Al-Zr alloys: FCC and liquid phases

Additive manufacturing of materials with controlled microstructure demands knowledge of atomic scale properties near the solid-liquid transition state. Many of these properties are not affordable by experimental techniques and computer modeling is the possible solution to the problem. In this paper, we present the results of an extended atomistic study of intrinsic atomic transport due to vacancy diffusion in FCC and L12 solid phases and diffusion in the liquid phase of Al-Zr alloys. A deceleration of the overall self-diffusion was observed when Zr was added to Al. The effect was stronger in the solid and weaker in the liquid. Additionally, the effect was strongly temperature dependent in the solid phases, but not in the liquid. Atomic transport was chemically biased: transport of Zr atoms was significantly slower than that of Al atoms, and this bias effect was stronger in the solid phases. The overall diffusion and chemical ordering processes in the liquid state were five to six orders in magnitude faster than in the solid. Chemical short-range order parameters in the liquid saturated at values close to those in the ordered L12 structure of Al3Zr. Chemical and structural ordering in the solid phases was negligible over the modeled microsecond time scale. Here, the results are discussed in view of optimizing additive manufacturing parameters for the controlled formation of metastable L1 2 precipitates.

36 MATERIALS SCIENCE↗

Multilayer relaxation and surface structure of ordered alloys

Using BFS, a new semiempirical method for alloys, we study the surface structure of fcc ordered binary alloys in the Ll(sub 2) structure (Ni3Al and Cu3Au). We show that the surface energy is lowest for the mixed composition truncation of the low-index faces of such systems. Also, we present results for the interlayer relaxations for planes close to the surface, revealing different relaxations for atoms of different species producing a rippled surface layer.

Kobistek, Robert J.↗

Magnetic ordering and structural distortion in PrFeAsO single crystal studied by neutron and x-ray scattering

We report the magnetic ordering and structural distortion in PrFeAsO crystals, the basis compound for one of the oxypnictide superconductors, using high-resolution x-ray diffraction, neutron diffraction, and x-ray resonant magnetic scattering (XRMS). We find the structural tetragonal-to-orthorhombic phase transition at T-S = 147K, the AFM phase transition of the Fe moments at T-Fe = 72K, and the Pr AFM phase transition at T-Pr = 21K. Combined high-resolution neutron diffraction and XRMS show unambiguously that the Pr moments point parallel to the longer orthorhombic a axis and order antiferromagnetically along the a axis but ferromagnetically along the b and c directions in the stripelike AFM order. The temperature-dependent magnetic order parameter of the Pr moments shows no evidence for a reorientation of moments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Correlations between electronic order and structural distortions and their ultrafast dynamics in the single-layer manganite P r 0.5 C a 1.5 Mn O 4

Time-resolved x-ray diffraction experiments on the half-doped single-layered manganite Pr 0.5 Ca 1.5 Mn O 4 are used to monitor the ultrafast photoinduced dynamics of the structural distortion associated with the charge and orbital ordering (CO/OO). As in the nonlayered three-dimensional counterpart, the ordered phase melts in less than 100 fs after 800-nm photoexcitation and subsequently partially recovers due to thermal equilibration of electronic and vibrational systems. Photoexciting Pr 0.5 Ca 1.5 Mn O 4 below the transition temperature of a second structural phase transition that occurs around 146 K (deep inside the CO/OO phase) releases this structural transition, but progresses on a much slower timescale. Finally, this additional reduction of crystal symmetry, which we ascribe to a further tilt of the oxygen octahedra, can thus be considered to be only weakly coupled to CO/OO. Furthermore, static hard-x-ray and resonant soft-x-ray diffraction at the Mn L 2,3 edges experiments identify correlations between structural distortions and electronic order in thermal equilibrium.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Self-Assembly of Anisotropic Particles on Curved Surfaces

The surface curvature of membranes, interfaces, and substrates plays a crucial role in shaping the self-assembly of particles adsorbed on these surfaces. However, little is known about the interplay between particle anisotropy and surface curvature and how they couple to alter the free energy landscape of particle assemblies. Using molecular dynamics simulations, we investigate the effect of prescribed curvatures on a quasi-2D assembly of anisotropic patchy particles. By varying curvature and surface coverage, we uncover a rich geometric phase diagram, with curvature inducing ordered structures entirely absent on planar surfaces. Large spatial domains of ordered structures can contain hidden microdomains of orientational textures imprinted by the surface on the assembly. The dynamical landscape is also reshaped by surface curvature, with a glass-like state emerging at modest densities and high curvature. Changes to the symmetry of the surface curvature are found to result in distinct structures, including phases with mesoscale ordering. In conclusion, our findings show that the coupling between surface curvature and particle geometry opens an unexplored space of morphologies and structures that can be exploited for material design.

Fluids↗

The structures of ordered defects in thiocyanate analogues of Prussian Blue

We report the structures of six new divalent transition metal hexathiocyanatobismuthate frameworks with the generic formula $\Big\{ M[Bi(SCN)_6]_\frac{2+x}{3} \Big\}$ $\{guest\}^{x+}$, M = Mn, Co, Ni and Zn. These frameworks are defective analogues of the perovskite-derived trivalent transition metal hexathiocyanatobismuthates M III [Bi(SCN) 6 ]. The defects in these new thiocyanate frameworks order and produce complex superstructures due to the low symmetry of the parent structure, in contrast to the related and more well-studied cyanide Prussian Blue analogues. Despite the close similarities in the chemistries of these four transition metal cations, we find that each framework contains a different mechanism for accommodating the lowered transition metal charge, making use of some combination of Bi(SCN) 6 3- vacancies, M Bi antisite defects, water substitution for thiocyanate, adventitious extra-framework cations and reduced metal coordination number. These materials provide an unusually clear view of defects in molecular framework materials and their variety suggests that similar richness may be waiting to be uncovered in other hybrid perovskite frameworks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Orientation-dependent mutual crystalline and amorphous order in a single phase solid

Amorphous materials distinguish themselves from crystalline materials by lacking long-range order while retaining structural order at the local scale (2–5 Å). However, the complexity in topological and chemical order prevents current characterization tools from fully unveiling the structure in disordered materials. Consequently, the nature of medium-range order in amorphous materials has remained elusive. The Zachariasen and crystal competing models have been proposed to describe disordered phases and have both been verified through synthesis and characterization. The main difference between them is thought to be whether the amorphous phase shows medium-range order. Here we demonstrate a form of organized inorganic matter that is amorphous in two dimensions, while exhibiting long-range order and a high degree of crystallinity in the third. The structure consists of periodically stacked 2-dimensional amorphous Nb-W-O monolayers without long-range in-plane order. The unique periodic and therefore crystalline stacking along one principal axis enables direct imaging and revealed that the amorphous Nb-W-O monolayers formed in agreement with the Zachariasen model for 2 dimensions. Our findings show that the gap between crystalline and amorphous materials does not only depend on medium-range order but can also apply to principal dimensions within the same solid.

Nanowires↗

Continuation of tailored composite structures of ordered staple thermoplastic material

The search for the cost effective composite structure has motivated the investigation of several approaches to develop composite structure from innovative material forms. Among the promising approaches is the conversion of a planar sheet to components of complex curvature through sheet forming or stretch forming. In both cases, the potential for material stretch in the fiber direction appears to offer a clear advantage in formability over continuous fiber systems. A framework was established which allows the simulation of the anisotropic mechanisms of deformation of long discontinuous fiber laminates wherein the matrix phase is a viscous fluid. Predictions for the effective viscosities of a hyper-anisotropic medium consisting of collimated, discontinuous fibers suspended in viscous matrix were extended to capture the characteristics of typical polymers including non-Newtonian behavior and temperature dependence. In addition, the influence of fiber misorientation was also modeled by compliance averaging to determine ensemble properties for a given orientation distribution. A design tool is presented for predicting the effect of material heterogeneity on the performance of curved composite beams such as those used in aircraft fuselage structures. Material heterogeneity can be induced during manufacturing processes such as sheet forming and stretch forming of thermoplastic composites. This heterogeneity can be introduced in the form of fiber realignment and spreading during the manufacturing process causing radial and tangential gradients in material properties. Two analysis procedures are used to solve the beam problems. The first method uses separate two-dimensional elasticity solutions for the stresses in the flange and web sections of the beam. The separate solutions are coupled by requiring that forces and displacements match section boundaries. The second method uses an approximate Rayleigh-Ritz technique to find the solutions for more complex beams. Analyses are performed for curved beams of various cross-sections loaded in pure bending and with a uniform distributed load. Preliminary results show that the geometry of the beam dictates the effect of heterogeneity on performance. The role of heterogeneity is larger in beams with a small average radius-to-depth ration, R/t, where R is the average radius of the beam and t is the difference between the inside and outside radii. Results of the anlysis are in the form of stresses and displacements and are compared to both mechanics of materials and numerical solutions obtained using finite element analysis.

Santare, Michael H.↗

Lewis acid–base pair doping of p-type organic semiconductors

Doping is required to increase the electrical conductivity of organic semiconductors for uses in electronic and energy conversion devices. The limited number of commonly used p-type dopants suggests that new dopants or doping mechanisms could improve the efficiency of doping and provide new means for processing doped polymers. Drawing on Lewis acid–base pair chemistry, we combined Lewis acid dopant B(C 6 F 5 ) 3 (BCF) with the weak Lewis base benzoyl peroxide (BPO). The detailed behavior of p-type doping of the model polymer poly(3-hexylthiophene) (P3HT) with this Lewis acid–base pair in solution was examined. Solution 19F-NMR spectra confirmed the formation of the expected counterion, as well as side products from reactions with solvent. BCF : BPO was also found to efficiently dope a range of semiconducting polymers with varying chemical structures demonstrating that the BCF : BPO combination has an effective electron affinity of at least 5.3 eV. In thin films of regioregular P3HT cast from the doped solutions, delocalized polarons formed due to the large counterions leading to a large polaron-counterion distance. At and above 0.2 eq. BCF : BPO doping, amorphous areas of the film became doped, disrupting the structural order of the films. Despite the change in structural order, thin films of regioregular P3HT doped with 0.2 eq. BCF : BPO had a conductivity of 25 S cm -1 . This study demonstrates the effectiveness of a two-component Lewis acid–base doping mechanism and suggests additional two-component Lewis acid–base chemistries should be explored.

36 MATERIALS SCIENCE↗

In Situ Insights into Cathode Calcination for Predictive Synthesis: Kinetic Crystallization of LiNiO 2 from Hydroxides

Abstract Calcination is a solid‐state synthesis process widely deployed in battery cathode manufacturing. However, its inherent complexity associated with elusive intermediates hinders the predictive synthesis of high‐performance cathode materials. Here, correlative in situ X‐ray absorption/scattering spectroscopy is used to investigate the calcination of nickel‐based cathodes, focusing specifically on the archetypal LiNiO 2 from Ni(OH) 2 . Combining in situ observation with data‐driven analysis reveals concurrent lithiation and dehydration of Ni(OH) 2 and consequently, the low‐temperature crystallization of layered LiNiO 2 alongside lithiated rocksalts. Following early nucleation, LiNiO 2 undergoes sluggish crystallization and structural ordering while depleting rocksalts; ultimately, it turns into a structurally‐ordered layered phase upon full lithiation but remains small in size. Subsequent high‐temperature sintering induces rapid crystal growth, accompanied by undesired delithiation and structural degradation. These observations are further corroborated by mesoscale modeling, emphasizing that, even though calcination is thermally driven and favors transformation towards thermodynamically equilibrium phases, the actual phase propagation and crystallization can be kinetically tuned via lithiation, providing freedom for structural and morphological control during cathode calcination.

36 MATERIALS SCIENCE↗

Dissecting the structural heterogeneity of proteins by native mass spectrometry

Abstract A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Digital robust active control law synthesis for large order flexible structure using parameter optimization

A generic procedure for the parameter optimization of a digital control law for a large-order flexible flight vehicle or large space structure modeled as a sampled data system is presented. A linear quadratic Guassian type cost function was minimized, while satisfying a set of constraints on the steady-state rms values of selected design responses, using a constrained optimization technique to meet multiple design requirements. Analytical expressions for the gradients of the cost function and the design constraints on mean square responses with respect to the control law design variables are presented.

Mukhopadhyay, V.↗

Eulerian and Lagrangian second-order statistics of superfluid 4 He grid turbulence

Here, we use particle-tracking velocimetry to study Eulerian and Lagrangian second-order statistics of superfluid 4 He grid turbulence. The Eulerian energy spectra at scales larger than the mean distance between quantum vortex lines behave classically with close to Kolmogorov-1941 scaling and are almost isotropic. The Lagrangian second-order structure functions and frequency power spectra, measured at scales comparable with the intervortex distance, demonstrate a sharp transition from nearly classical behavior to a regime dominated by the motion of quantum vortex lines. Employing the homogeneity of the flow, we verify a set of relations that connect various second-order statistical objects that stress different aspects of turbulent behavior, allowing a multifaceted analysis. We use the two-way bridge relations between Eulerian energy spectra and second-order structure functions to reconstruct the energy spectrum from the known second-order velocity structure function and vice versa. The Lagrangian frequency spectrum reconstructed from the measured Eulerian spectrum using the Eulerian-Lagrangian bridge differs from the measured Lagrangian spectrum in the quasiclassical range, which calls for further investigation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗