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PyLRO: A Python calculator for analyzing long-range structural order

We present PyLRO, an open-source Python calculator designed to detect, quantify, and display long-range order in periodic structures. The program’s design methodology, workflow, and approach to order quantification are described and demonstrated using a simple toy model. Additionally, we apply PyLRO to a series of metastable AlPO 4 structural intermediates from a prior high-pressure study, demonstrating how to compute and visualize structural order in all directions on a Miller sphere. We further highlight the program’s capabilities through a high-throughput analysis of structural patterns in the pressure-induced amorphization of AlPO 4 , revealing atomistic insights into specific energy regions of massive amorphous structures. These results suggest that PyLRO can be a valuable tool for investigating crystal–amorphous transition in materials research.

36 MATERIALS SCIENCE↗

Detection of ratcheting in finite element calculations

The distinction between a ratcheting and non-ratcheting response is critical for many high temperature design methods. Non-ratcheting is generally considered safe deformation remain bounded over the lifetime of the component while ratcheting is undesirable. As a particular example, the elastic perfectly plastic (EPP) design methods described in recent ASME Section III, Division 5 code cases require a designer to distinguish ratcheting from non-ratcheting for finite element analyses using a relatively simple, elastic perfectly-plastic constitutive response. However, it can be quite difficult to distinguish these two deformation regimes using finite element (FE) analysis particularly in the case where the actual ratcheting strain is small. In practice FE analysis of structures that are analytically in either the plastic shakedown or ratcheting regimes will result in small, cycle to -cycle accumulated strains characteristic of ratcheting. Distinguishing false ratcheting the structure is actually in the plastic shakedown regime from true ratcheting can be challenging. We describe the characteristics of nonlinear FE analysis that cause these false ratcheting strains and describe practical methods for distinguishing a ratcheting from a non-ratcheting response.

Messner, M. C.↗

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity in the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.

Lu, Jun↗

Flow Patterns, Microstructure and Mechanical Properties of AZ31/Al6061 Dissimilar Friction Stir-Welded Joints

Dissimilar joints between die-cast AZ31 and extruded Al6061-T6 were joined using friction stir welding technology at a constant transverse speed (50 mm/min) and rotation rate of 800 or 1000 rpm. The flow patterns, microstructure evolution and intermetallic compounds in dissimilar joints were studied by optical and scanning electron microscopy. The relationship between microstructure and tensile properties was analyzed. The microhardness distribution along the horizontal centerline in cross section was investigated. Local flow without obvious mixing existed between Mg and Al metals in the tool shoulder-affected zone. For the tool-pin-affected zone, two typical zones, namely, the “extrusion zone” and “flow zone” existed because of the different flow modes of the plastic metals. The phase analysis showed that intermetallic compounds, including Al{sub 12}Mg{sub 17} and Al{sub 3}Mg{sub 2} formed in banded structures. Phase analysis showed that a joint with welding parameters of 800 rpm and 50 mm/min (Joint-500) had good mechanical properties because of the more uniform microstructure distribution and fewer intermetallic compounds. Fracture analysis indicated some microvoids and lamellate intermetallic compounds in the fracture surface of the joint with welding parameters of 1000 rpm and 50 mm/min (Joint-1000), which deteriorated its tensile strength significantly.

36 MATERIALS SCIENCE↗

Adsorption of rare earth elements in carboxylated mesoporous carbon

The separation of Rare Earth Elements (REEs) from various non-conventional sources is critically important to maintain the supply–demand balance of REEs in the western world. Here, in this research, we have investigated coal Fly Ash (CFA) as the non-conventional source of REEs. In order to recover REEs, we have synthesized carboxylate-functionalized mesoporous carbon (CMC) to harness the chelation-induced adsorption of REEs. These adsorbents were characterized with pore textural properties, FTIR spectroscopy, and SEM-EDX mapping. In the initial study with single-component La(III) Dy(III) and Lu(III), it was revealed that CMC can adsorb those REEs 2–4 times more than that of pristine mesoporous carbon confirming the effective role of the carboxylate group in the REE separation. Furthermore, the affiliation of the carboxylate group towards heavier REEs (Lu>Dy>La, when present is equal amounts) provides an added benefit of this adsorbent owing to the high demand for heavier REEs in the technology sectors. The leachate solution produced from CFA contained sixteen REEs in the range of 50–200 ppb for most of the REEs. It was revealed that CMC can extract 80–90% of all the REEs thereby further confirming the success of the CMC as an effective REE sorbent. Three successive cycles of adsorption and desorption of REEs with the same CMC revealed the consistent adsorption capacity of REEs. In-situ X-ray Absorption Near Edge Spectroscopy (XANES) analysis confirmed the +3 oxidation states of La, Dy, and Lu within CMC. In-situ Extended X-ray Absorption Fine Structure (EXAFS) analysis revealed the shortening of mean La-O, Dy-O, and Lu-O bond distance by 0.03–0.05 Å thereby confirming the coordination of these REEs with carboxylate groups present on CMC.

36 MATERIALS SCIENCE↗

Molecular structure of vapor-deposited amorphous selenium

The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. In this work, we developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

36 MATERIALS SCIENCE↗

Electric explosion of fine wires: Three groups of materials

Experimental data demonstrating differences in the structures of channels formed during nanosecond discharges through fine wires made of different materials are presented. In addition to the traditional two classes of metals and alloys (the copper and tungsten groups), a new class is proposed to which materials of the nickel type belong. Their properties combine the characteristic properties of the two traditional groups, due to which they occupy an intermediate position between the latter. This manifests itself in the unstable character of explosion, the type of which can change drastically when changing the ambient medium or other conditions. Most of the reported results were obtained at a small setup with maximum values of the current and voltage of 10 kA and 20 kV, respectively, the current rise time being about 300 ns. An attempt is made to construct a scenario of the development of a nanosecond explosion that would make it possible to qualitatively describe the formation of the discharge channel structure. The analysis is based on the recent experimental results indicating that the cores formed in the course of the discharge have a tubular structure.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Low-dimensional compounds containing cyanido groups. XXVIII. Crystal structure, spectroscopic and magnetic properties of two copper(II) tetracyanidoplatinate complexes with 1,2-diaminopropane

Violet crystals of ([Cu(pn){sub 2}]{sub 2}[Pt(CN){sub 4}])[Pt(CN){sub 4}]·2H{sub 2}O (1, pn=1,2-diaminopropane) and blue crystals of [Cu(pn)Pt(CN){sub 4}]{sub n}·nH{sub 2}O (2) were prepared under hydrothermal conditions and characterized using elemental analysis, IR and UV–vis spectroscopy and by X-ray crystal structure analysis. Different number of ν(C≡N) absorption bands of these two compounds reflects their different structures. An X-ray crystal structure analysis has shown that complex 1 is of ionic character and is formed from trinuclear [Cu(pn){sub 2}–Pt(CN){sub 4}–Cu(pn){sub 2}]{sup 2+} complex cation and discrete [Pt(CN){sub 4}]{sup 2–} anion together with two molecules of crystal water. On the other hand, complex 2 is of polymeric character and is formed by 2D networks of [Cu(pn)Pt(CN){sub 4}]{sub n} composition and completed by n molecules of crystal water. Magnetic measurements show the presence of a weak antiferromagnetic exchange interaction in complex 1 (Θ=–0.2 K), while the magnetic susceptibility of complex 2 is well described by the model of uniform S=1/2 spin chain with exchange interaction J/k{sub B}=–1.64 K. - Graphical abstract: Two complexes of different structural types from the system Cu(II) – 1,2–diaminopropane – [Pt(CN){sub 4}]{sup 2–} have been isolated. These were characterized by IR and UV–VIS spectroscopy, X–ray crystal structure analysis together with the magnetic measurements. On one hand ([Cu(pn){sub 2}]{sub 2}[Pt(CN){sub 4}])[Pt(CN){sub 4}]∙2H{sub 2}O is of ionic character and is formed from trinuclear complex cation and discrete anion together with two molecules of crystal water. On the other hand, [Cu(pn)Pt(CN){sub 4}]{sub n}∙nH{sub 2}O is of polymeric character and is formed by 2D networks of [Cu(pn)Pt(CN){sub 4}]{sub n} composition and completed by n molecules of crystal water. - Highlights: • Two complexes of different compositions from one system have been isolated. • First complex is of ionic character and second one is of polymeric character. • Polymeric complex described as a spin chain in contrast to its bilayer structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. Among the proteins required for alginate production, Alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding activity post-translationally regulates alginate secretion. In this study, we report the 1.8 Å crystal structure of the cytoplasmic region of Alg44 in complex with dimeric self-intercalated c-di-GMP and characterize its dinucleotide-binding site using mutational analysis. The structure shows that the c-di-GMP binding region of Alg44 adopts a PilZ domain fold with a dimerization mode not previously observed for this family of proteins. Moreover, calorimetric binding analysis of residues in the c-di-GMP binding site demonstrate that mutation of Arg-17 and Arg-95 alters the binding stoichiometry between c-di-GMP and Alg44 from 2:1 to 1:1. Introduction of these mutant alleles on the P. aeruginosa chromosome show that the residues required for binding of dimeric c-di-GMP in vitro are also required for efficient alginate production in vivo. Our results suggest that the dimeric form of c-di-GMP represents the biologically active signaling molecule needed for the secretion of an important virulence factor produced by P. aeruginosa.

36 MATERIALS SCIENCE↗

An Efficient Algorithm for Automatic Structure Optimization in X-ray Standing-Wave Experiments

We present that x-ray standing-wave photoemission experiments involving multilayered samples are emerging as unique probes of the buried interfaces that are ubiquitous in current device and materials research. Such data require for their analysis a structure optimization process comparing experiment to theory that is not straightforward. In this work, we present a new computer program for optimizing the analysis of standing-wave data, called SWOPT, that automates this trial-and-error optimization process. The program includes an algorithm that has been developed for computationally expensive problems: so-called black-box simulation optimizations. It also includes a more efficient version of the Yang X-ray Optics Program (YXRO) [Yang, S.-H., Gray, A.X., Kaiser, A.M., Mun, B.S., Sell, B.C., Kortright, J.B., Fadley, C.S., J. Appl. Phys. 113, 1 (2013)] which is about an order of magnitude faster than the original version. Human interaction is not required during optimization. We tested our optimization algorithm on real and hypothetical problems and show that it finds better solutions significantly faster than a random search approach. The total optimization time ranges, depending on the sample structure, from minutes to a few hours on a modern laptop computer, and can be up to 100x faster than a corresponding manual optimization. Finally, these speeds make the SWOPT program a valuable tool for realtime analyses of data during synchrotron experiments.

36 MATERIALS SCIENCE↗

Electric field dynamics in nitride structures containing quaternary alloy (Al, In, Ga)N

Molecular beam epitaxy growth and basic physical properties of quaternary AlInGaN layers, sufficiently thick for construction of electron blocking layers (EBL), embedded in ternary InGaN layers are presented. Transmission electron microscopy (TEM) measurement revealed good crystallographic structure and compositional uniformity of the quaternary layers contained in other nitride layers, which are typical for construction of nitride based devices. The AlInGaN layer was epitaxially compatible to InGaN matrix, strained, and no strain related dislocation creation was observed. The strain penetrated for limited depth, below 3 nm, even for relatively high content of indium (7%). For lower indium content (0.6%), the strain was below the detection limit by TEM strain analysis. The structures containing quaternary AlInGaN layers were studied by time dependent photoluminescence (PL) at different temperatures and excitation powers. It was shown that PL spectra contain three peaks: high energy donor bound exciton peak from the bulk GaN (DX GaN) and the two peaks (A and B) from InGaN layers. No emission from quaternary AlInGaN layers was observed. An accumulation of electrons on the EBL interface in high-In sample and formation of 2D electron gas (2DEG) was detected. The dynamics of 2DEG was studied by time resolved luminescence revealing strong dependence of emission energy on the 2DEG concentration. Theoretical calculations as well as power-dependence and temperature-dependence analysis showed the importance of electric field inside the structure. At the interface, the field was screened by carriers and could be changed by illumination. From these measurements, the dynamics of electric field was described as the discharge of carriers accumulated on the EBL.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cannabis monoterpene synthases: evaluating structure–function relationships

Terpene synthases catalyze the first committed step in the biosynthesis of terpenes, a structurally diverse class of natural products that also encompasses volatiles derived from precursors in the C10 to C15 range (termed monoterpenes and sesquiterpenes, respectively). In the review section of this article, we are providing information about all functionally characterized monoterpene synthases (MTSs) and sesquiterpene synthases (STSs) of Cannabis sativa L. We are also exploring the locations of MTSs and STSs in the chromosome-level assembly of the reference chemovar CBDRx. A follow-up computational structure–function analysis focuses on MTSs, as there is already a rich literature available on the topic. More specifically, by employing sequence comparisons and homology structural modeling, we infer which amino acid residues are likely to constrain the available space in the active site of cannabis MTSs. The emphasis of these studies was to investigate why some MTSs accept only a C10 diphosphate as substrate, while mixed MTS/STS enzymes also accommodate a C15 diphosphate. Here, by combining a literature review and computational analyses in a hybrid format, we are laying the foundation for future studies to better understand the determinants of substrate and product specificity in these fascinating enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Amplicon Sequencing Assessment to Measure Microbial Community Response from Heavy Metal Contaminated Soils in Savannah River site, Tims Branch watershed

Long-term presence of heavy metal contamination in soils is correlated with changes in microbial community structures and can lead to the reduction of indigenous species. Tolerance to soil heavy metal toxicity varies among different microbial communities. It remains unclear whether long term effects caused by metal perturbations are associated with soil microbial community dysregulation in Tims Branch watershed. Research Questions: Does heavy metal contamination in Tims Branch soils decrease microbial species diversity significantly compared to non-contaminated soils? Does the species richness decrease in contaminated samples? between samples? Is diversity in low, mid and high contamination soils significantly different compared to control samples? Hypothesis: The relative abundance and diversity of species are significantly altered in soils which are contaminated with heavy metals in the Tims Branch watershed. Objectives: Use amplicon sequencing technology along with bioinformatics to compare bacterial communities between four sites in Tims Branch watershed. Evaluate the percent relative abundance and diversity across the site. Conclusions: All bacterial communities exposed to different heavy metal concentrations were dominated by four major groups (Proteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia). The dominant phyla Proteobacteria, Acidobacteria and Chloroflexi accounted for 61 % of the relative abundance. Soil bacterial α-diversity, expressed as observed species richness metric and Shannon's diversity index, was the highest in sample location four (high contamination). The lowest observed was at the control location. Species richness increased when concentrations of heavy metals were localized, inferring that the metals can alter microbial community structure. PERMANOVA analysis between contaminated groups tested significant using the Adonis (F (4,29) =1.9712; p < 0.001). There is a 20 percent variation explained between groups (R2 = 0.214). This analysis proves to be beneficial in detecting microbial communities altered by contaminated soils. Moreover, certain concentrations of heavy metals can alter microbial community structures.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Spectroscopic Characterization of Highly Active Fe–N–C Oxygen Reduction Catalysts and Discovery of Strong Interaction with Nafion Ionomer

Scaling up clean-energy applications necessitates the development of platinum group metal (PGM)-free fuel cell electrocatalysts with high activity, stability, and low cost. Here, X-ray absorption (XAS) at the Fe K-edge and Fe K β X-ray emission (XES) spectroscopies were used to study the electronic structure of Fe centers in highly active Fe–N–C oxygen reduction catalysts with significant commercial potential. X-ray absorption near-edge structure (XANES) analysis has shown that the majority (>95%) of Fe centers are in the Fe 3+ oxidation state, while extended X-ray absorption fine structure (EXAFS) detected a mixture of single site Fe–N 4 centers (>95%) and centers with short (~2.5 Å) Fe–Fe interactions of Fe metal and/or Fe-carbide nanoparticles (<5%) featuring the Fe o oxidation state. Surprisingly, addition of Nafion, the most widely used ionomer, resulted in pronounced changes in the XAS spectra, consistent with a strong catalyst–ionomer interaction where long Fe–Fe interactions at ~3.1 Å were shown to be a feature of Fe 3+ ions bound with the Nafion. We conclude that exposure to Nafion during the device formulation has a different effect from the aggressive acid leaching typically used in the preparation of Fe–N–C catalysts. Furthermore, it was hypothesized that the polymer interacts with single sites’ Fe 3+ centers, as well as with graphene layers protecting the Fe o nanoparticles, and extracts some Fe ions into the Nafion matrix.

25 ENERGY STORAGE↗

Tuning Ni-catalyzed CO 2 hydrogenation selectivity via Ni-ceria support interactions and Ni-Fe bimetallic formation

CO 2 hydrogenation over Fe-modified Ni/CeO 2 catalysts was investigated in a batch reactor using time-resolved in situ FTIR spectroscopy. Low loading of Ni/CeO 2 was associated with high selectivity to CO over CH 4 , while higher Ni loading improved CO 2 hydrogenation activity with a reduced CO selectivity. X-ray absorption near-edge structure (XANES) analysis revealed Ni to be metallic for all catalysts including the CO-selective low loading 0.5% Ni catalyst, suggesting that the selectivity trend is due to structural rather than oxidation state effects. The loading amount of 1.5% Ni was selected for co-impregnation with Fe, based on the significant shift in product selectivity towards CH 4 for that loading amount, in order to shift the selectivity towards CO while maintaining high activity. Temperature programmed reduction (TPR) results indicated bimetallic interactions between Ni and Fe, and XANES analysis showed that about 70% of Fe in the bimetallic catalysts was oxidized. The Ni-Fe catalysts demonstrated improved selectivity towards CO without significantly compromising activity, coupling the high activity of Ni catalysts and the high CO selectivity of Fe. The general trends in Ni loading and bimetallic modification should guide efforts to develop non-precious metal catalysts for the selective production of CO by CO 2 hydrogenation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solving the Structure and Dynamics of Metal Nanoparticles by Combining X-Ray Absorption Fine Structure Spectroscopy and Atomistic Structure Simulations

Extended X-ray absorption fine structure (EXAFS) spectroscopy is a premiere method for analysis of the structure and structural transformation of nanoparticles. Extraction of analytical information about the three-dimensional structure and dynamics of metal–metal bonds from EXAFS spectra requires special care due to their markedly non-bulk-like character. In recent decades, significant progress has been made in the first-principles modeling of structure and properties of nanoparticles. Here, we summarize new approaches for EXAFS data analysis that incorporate particle structure modeling into the process of structural refinement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards Resolving the Spatial Metabolome with Unambiguous Molecular Annotations in Complex Biological Systems by Coupling Mass Spectrometry Imaging with Structures for Lossless Ion Manipulations

We demonstrate the coupling of liquid extraction surface analysis (LESA) to structures for lossless ion manipulations in conjunction with serpentine ultralong path with extending routing (SLIM SUPER) ion mobility-mass spectrometry (IM-MS) for the unambiguous annotation of important isomeric glycoforms in carbon-fixing communities. A major bottleneck of current mass spectrometry imaging (MSI) methods is their inability to accurately and confidently delineate amongst isomers within a single probing area. Our methodology provides gains in both sensitivity and IM resolution, while simultaneously gaining insight on the spatial distribution of these biological isomers in a mixed organism composed of moss, cyanobacteria and fungus. We envision this methodology will be broadly applicable to other mass spectrometry imaging modalities and invaluable in multiplexed, untargeted, analyses of a single probing location.

Nagy, Gabe↗

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