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DOE OSTI2025

Quantitative approaches for multiscale structural analysis with atomic resolution electron microscopy

Atomic-resolution imaging with scanning transmission electron microscopy is a powerful tool for characterizing the nanoscale structure of materials, in particular features such as defects, local strains, and symmetry-breaking distortions. In addition to advanced instrumentation, the effectiveness of the technique depends on computational image analysis to extract meaningful features from complex datasets recorded in experiments, which can be complicated by the presence of noise and artifacts, small or overlapping features, and the need to scale analysis over large representative areas. Here, we present image analysis approaches which synergize real and reciprocal space information to efficiently and reliably obtain meaningful structural information with picometer scale precision across hundreds of nanometers of material from atomic-resolution electron microscope images. Damping superstructure peaks in reciprocal space allows symmetry-breaking structural distortions to be disentangled from other sources of inhomogeneity and measured with high precision. Real-space fitting of the wavelike signals resulting from Fourier filtering enables absolute quantification of lattice parameter variations and strain, as well as the uncertainty associated with these measurements. Implementations of these algorithms are made available as an open source python package.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Second spectrum of Manganese (Mn II), Part II: Revised fine and hyperfine structure analysis of odd-parity levels

In the first part of this global work, we have achieved the fine and hyperfine structure (fs and hfs) parametric study of even-parity levels, which confirmed in the whole the well-founded basis of previous analyses. Unfortunately, in the present work devoted to odd-parity levels, some divergences appear. For instance, the three levels w{sup 5}P{sub 3}, w{sup 5}P{sub 2}, w{sup 5}P{sub 1} located respectively at 86898, 86937 and 86961 cm{sup −1} should not belong to the 3d{sup 4}({sup 5}D)4s4p configuration, as indicated earlier, but rather to 3d{sup 5}({sup 4}P)5p. In the other hand, the levels whose energies are: 88 840, 89 079 and 89 429 cm{sup −1} should belong this time to 3d{sup 4}({sup 5}D)4s4p instead of 3d{sup 5}5p, as mentioned previously. Our analysis is strengthened when using experimental hfs data as finger prints, even if the comparison between these experimental hfs data, given in the literature, and our calculated results also shows in numerous cases some notable discrepancies, concerning particularly the sign of the electric quadrupole factor. The main monoelectronic hfs parameter values, extracted from our least square fitting procedure, are: a{sub 3d}{sup 01}(3d{sup 5}4p)= 17.58 mK, b{sub 3d}{sup 02}(3d{sup 5}4p)= 10.27 mK, a{sub 3d}{sup 01} (3d{sup 4}4s4p)= 18.74 mK and a{sub 4s}{sup 10}(3d{sup 4}4s4p)= 274.9 mK. These parameter values, displayed for the first time, were analyzed and compared with ab-initio calculations. As in the first part, we conclude this work by giving the predicted hfs A and B constants of low-lying levels of these two configurations, whose splitting are not yet measured.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2018

An approach to structural analysis using Moore-Shannon network reliability

We develop a formalism for approaching many questions dealing with network structure. The formalism is based on Shannon-Moore network reliability and on the Birnbaum definition of importance that uses it. The methods we suggest based on this formalism apply to a wide variety of dynamics on very general inter- action networks. They are designed to answer specific questions about how network structure affects particular aspects of the dynamics. We first introduce the concepts that make up the formalism, explain basic methods of using these concepts, and demonstrate applications to problems such as edge ranking.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2013

Structure analysis of aluminium silicon manganese nitride precipitates formed in grain-oriented electrical steels

We report a detailed structural and chemical characterisation of aluminium silicon manganese nitrides that act as grain growth inhibitors in industrially processed grain-oriented (GO) electrical steels. The compounds are characterised using energy dispersive X-ray spectrometry (EDX) and energy filtered transmission electron microscopy (EFTEM), while their crystal structures are analysed using X-ray diffraction (XRD) and TEM in electron diffraction (ED), dark-field, high-resolution and automated crystallographic orientation mapping (ACOM) modes. The chemical bonding character is determined using electron energy loss spectroscopy (EELS). Despite the wide variation in composition, all the precipitates exhibit a hexagonal close-packed (h.c.p.) crystal structure and lattice parameters of aluminium nitride. The EDX measurement of ∼ 900 stoichiometrically different precipitates indicates intermediate structures between pure aluminium nitride and pure silicon manganese nitride, with a constant Si/Mn atomic ratio of ∼ 4. It is demonstrated that aluminium and silicon are interchangeably precipitated with the same local arrangement, while both Mn{sup 2+} and Mn{sup 3+} are incorporated in the h.c.p. silicon nitride interstitial sites. The oxidation of the silicon manganese nitrides most likely originates from the incorporation of oxygen during the decarburisation annealing process, thus creating extended planar defects such as stacking faults and inversion domain boundaries. The chemical composition of the inhibitors may be written as (AlN){sub x}(SiMn{sub 0.25}N{sub y}O{sub z}){sub 1−x} with x ranging from 0 to 1. - Highlights: • We study the structure of (Al,Si,Mn)N inhibitors in grain oriented electrical steels. • Inhibitors have the hexagonal close-packed symmetry with lattice parameters of AlN. • Inhibitors are intermediate structures between pure AlN and (Si,Mn)N with Si/Mn ∼ 4. • Al and Si share the same local arrangement; Mn is incorporated in both Mn{sup 2+} and Mn{sup 3+}. • Oxygen incorporation is invoked to account for the thermal stability of (Al,Si,Mn)N.

36 MATERIALS SCIENCE↗

DOE OSTI2013

Band-structure analysis from photoreflectance spectroscopy in (Ga,Mn)As

Modulation photoreflectance spectroscopy has been applied to study the band-structure evolution in (Ga,Mn)As epitaxial layers with increasing Mn content. Structural and magnetic properties of the layers were characterized with high-resolution X-ray diffractometry and SQUID magnetometery, respectively. The revealed results of decrease in the band-gap-transition energy in the (Ga,Mn)As layers with increasing Mn content are interpreted in terms of a disordered valence band, extended within the band gap, formed, in highly Mn-doped (Ga,Mn)As, as a result of merging the Mn-related impurity band with the host GaAs valence band.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Insights on the dissolution of water in an albite melt at high pressures and temperatures from a direct structural analysis

The water dissolution mechanism in silicate melts under high pressures is not well understood. Here we present the first direct structure investigation of a water-saturated albite melt to monitor the interactions between water and the network structure of silicate melt at the molecular level. In situ high-energy X-ray diffraction was carried out on the NaAlSi 3 O 8 -H 2 O system at 800 °C and 300 MPa, at the Advanced Photon Source synchrotron facility. The analysis of the X-ray diffraction data was augmented with classical Molecular Dynamics simulations of a hydrous albite melt, incorporating accurate water-based interactions. The results show that metal–oxygen bond breaking at the bridging sites occurs overwhelmingly at the Si site upon reaction with H 2 O, with subsequent Si–OH bond formation and negligible Al–OH formation. Furthermore, we see no evidence for the dissociation of the Al 3+ ion from the network structure upon breaking of the Si–O bond in the hydrous albite melt. The results also indicate that the Na + ion is an active participant in the modifications of the silicate network structure of the albite melt upon water dissolution at high P–T conditions. We do not find evidence for the Na + ion dissociating from the network structure upon depolymerization and subsequent formation of NaOH complexes. Instead, our results show that the Na + ion persists as a structure modifier with a shift away from Na–BO bonding to an increase in the extent of Na-NBO bonding, in parallel with pronounced depolymerization of the network. Our MD simulations show that the Si–O and Al–O bond lengths are expanded by about 6% in the hydrous albite melt compared to those of the dry melt at high P–T conditions. The changes in the network silicate structure of a hydrous albite melt at high pressure and temperature, as revealed in this study, must be considered in the advancement of water dissolution models of hydrous granitic (or alkali aluminosilicate) melts.

36 MATERIALS SCIENCE↗

DOE OSTI2025

LiPF 6 under pressure: a symmetry-mode-based structural analysis

The lithium salt LiPF 6 is a key component in commercial lithium-ion battery (LIB) electrolytes. However, its structural properties under pressure remain unexplored, despite increasing interest in the effect of pressure on electrolyte behaviour, and a growing interest in high pressure synthesis of new Li-hexafluoride cathode materials. Here, we present the first high pressure neutron diffraction study of solid LiPF 6 up to 7.4 GPa. Refinements reveal that the ambient rhombohedral structure (space group R$\overline{3}$) remains stable throughout, with pressure accommodated primarily by tilting of the corner-shared LiF 6 and PF 6 octahedra and contraction of the LiF 6 units. In conclusion, this study establishes a foundation for understanding the phase behaviour of Li-based hexafluorides under extreme conditions.

25 ENERGY STORAGE↗

DOE OSTI2017

Crystal structure analysis of a hypothetical protein (MJ0366) from Methanocaldococcus jannaschii revealed a novel topological arrangement of the knot fold

The crystal structure of a hypothetical protein MJ0366, derived from Methanocaldococcus jannaschii was solved at 1.9 Å resolution using synchrotron radiation. MJ0366 was crystallized as a monomer and has knot structural arrangement. Intriguingly, the solved structure consists of novel ‘KNOT’ fold conformation. The 3{sub 1} trefoil knot was observed in the structure. The N-terminal and C-terminal ends did not participate in knot formation. - Highlights: • Crystal structure of a hypothetical protein from Methanocaldococcus jannaschii was determined. • The protein adopts novel knot fold conformation. • Structure of the first smallest knot protein was solved.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Solid-state NMR of unlabeled plant cell walls: high-resolution structural analysis without isotopic enrichment

Abstract Background Multidimensional solid-state nuclear magnetic resonance (ssNMR) spectroscopy has emerged as an indispensable technique for resolving polymer structure and intermolecular packing in primary and secondary plant cell walls. Isotope ( 13 C) enrichment provides feasible sensitivity for measuring 2D/3D correlation spectra, but this time-consuming procedure and its associated expenses have restricted the application of ssNMR in lignocellulose analysis. Results Here, we present a method that relies on the sensitivity-enhancing technique Dynamic Nuclear Polarization (DNP) to eliminate the need for 13 C-labeling. With a 26-fold sensitivity enhancement, a series of 2D 13 C– 13 C correlation spectra were successfully collected using the unlabeled stems of wild-type Oryza sativa (rice). The atomic resolution allows us to observe a large number of intramolecular cross peaks for fully revealing the polymorphic structure of cellulose and xylan. NMR relaxation and dipolar order parameters further suggest a sophisticated change of molecular motions in a ctl1 ctl2 double mutant: both cellulose and xylan have become more dynamic on the nanosecond and microsecond timescale, but the motional amplitudes are uniformly small for both polysaccharides. Conclusions By skipping isotopic labeling, the DNP strategy demonstrated here is universally extendable to all lignocellulose materials. This time-efficient method has landed the technical foundation for understanding polysaccharide structure and cell wall assembly in a large variety of plant tissues and species.

09 BIOMASS FUELS↗

DOE OSTI2024

Parametrized ion-distribution model for extended x-ray absorption fine-structure analysis at high-energy-density conditions

Experiments today can compress solids near isentropically to pressures approaching 100 × 106 atmospheres; however, determining the temperature of such matter remains a major challenge. Extended x-ray absorption fine-structure (EXAFS) spectroscopy is one of the few techniques sensitive to the bulk temperature of highly compressed solid matter, and the validity of this temperature measurement relies on constraining the local ion structure from the EXAFS spectrum. At high-energy-density (HED) conditions, the local ion structure often becomes distorted, which must be accounted for during the EXAFS analysis. Described here is a technique, using a parametrized ion-distribution model to directly analyze EXAFS spectra that provides a better constraint on the local structure than traditional second- or third-order cumulant expansion techniques at HED conditions. The parametrized ion-distribution model is benchmarked by analyzing EXAFS spectra from nickel molecular-dynamics simulations at ∼100 GPa and shown to provide a 10%–20% improvement in constraining the cumulants of the true ion distribution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Foldy: An open-source web application for interactive protein structure analysis

Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. With many deployment options, it can be employed by individuals, labs, universities, and companies in the cloud without requiring hardware resources, but it can also be configured to utilize locally available computers. Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. In our manuscript, we detail Foldy’s interface design, deployment strategies, and optimization for various user scenarios. We demonstrate its application through case studies including rational enzyme design and analyzing proteins with domains of unknown function. Furthermore, we compare Foldy’s interface and management capabilities with other open and closed source tools in the field, illustrating its practicality in managing complex data and computation tasks. Our manuscript underlines the benefits of Foldy as a day-to-day tool for life science researchers, and shows how Foldy can make modern tools more accessible and efficient.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression

The structure of the new class of controller proteins (exemplified by C.Csp231I) in complex with its 21 bp DNA-recognition sequence is presented, and the molecular basis of sequence recognition in this class of proteins is discussed. An unusual extended spacer between the dimer binding sites suggests a novel interaction between the two C-protein dimers. In a wide variety of bacterial restriction–modification systems, a regulatory ‘controller’ protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

Synthesis of Zn–Fe layered double hydroxides via an oxidation process and structural analysis of products

The synthesis of Zn–Fe(III) layered double hydroxides was attempted, employing different pathways using either Fe(II) or Fe(III) species together with Zn as the initial reagents. The product derived from the synthesis employing Fe(II) was found to transition to a Zn–Fe(III) layered double hydroxides phase following oxidation process. In contrast, the product obtained with Fe(III) did not contain a layered double hydroxides phase, but rather consisted of simonkolleite and hydrous ferric oxide. It was determined that the valency of the Fe reagent used in the initial synthesis affected the generation of the layered double hydroxides phase. Fe(II) species have ionic radii and electronegativities similar to those of Zn, and therefore are more likely to form trioctahedral hydroxide layers with Zn species. - Graphical abstract: The synthesis of Zn–Fe(III) layered double hydroxides was attempted, employing different pathways using either Fe(II) or Fe(III) species together with Zn as the initial reagents. - Highlights: • Iron valency affected the generation of Zn–Fe layered double hydroxides. • Zn–Fe layered double hydroxides were successfully synthesized using Fe(II). • Fe(II) species were likely to form trioctahedral hydroxide layers with Zn species.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Structural analysis of WO 3 -TeO 2 glasses by neutron, high energy X-ray diffraction, reverse Monte Carlo simulations and XANES

The structure of WO 3 -TeO 2 glasses containing 15, 20 and 25 mol% WO 3 are studied by neutron diffraction (ND), high energy X-ray diffraction (XRD) and X-ray Absorption Near Edge spectroscopy (XANES). The short-range structural properties of glasses i.e. Te-O and W-O speciation, coordination number distributions, bond-lengths, and the O-Te-O, O-W-O and O-O-O bond angle distributions in the glass network are determined by the Reverse Monte Carlo (RMC) simulations of the ND and XRD data. RMC technique successfully determined all partial pair correlation functions and the coordination number distributions revealed that glass network consists predominantly of TeO 4 and WO 4 units with small amounts of triangular, penta and hexa co-ordinated units. The average W-O and Te-O bond lengths are in the ranges: 1.69-1.75 +/- 0.01 angstrom and 1.99-2.00 +/- 0.01 angstrom respectively. Both W-O and Te-O correlation peaks are asymmetrical, that indicate a distribution of their bond lengths in the respective structural units. The O-Te-O bond angle distribution has a peak at 107 +/- 2 degrees. Similarly the O-W-O bond angle distribution has a peak at 108 +/- 5 degrees. On increasing the WO3 concentration from 15 to 25 mol%, the average Te-O coordination number decreases from 3.80 to 3.61 +/- 0.02 due to the structural transformation: TeO 4 → TeO 3 , similarly the W-O coordination also decreases and is in the range: 3.79-3.67 +/- 0.02. XANES studies found that the oxidation state of Te and W ions in the glasses are 4 + and 6 + respectively.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Multi-scale structural analysis of proteins by deep semantic segmentation

Abstract Motivation Recent advances in computational methods have facilitated large-scale sampling of protein structures, leading to breakthroughs in protein structural prediction and enabling de novo protein design. Establishing methods to identify candidate structures that can lead to native folds or designable structures remains a challenge, since few existing metrics capture high-level structural features such as architectures, folds and conformity to conserved structural motifs. Convolutional Neural Networks (CNNs) have been successfully used in semantic segmentation—a subfield of image classification in which a class label is predicted for every pixel. Here, we apply semantic segmentation to protein structures as a novel strategy for fold identification and structure quality assessment. Results We train a CNN that assigns each residue in a multi-domain protein to one of 38 architecture classes designated by the CATH database. Our model achieves a high per-residue accuracy of 90.8% on the test set (95.0% average per-class accuracy; 87.8% average per-structure accuracy). We demonstrate that individual class probabilities can be used as a metric that indicates the degree to which a randomly generated structure assumes a specific fold, as well as a metric that highlights non-conformative regions of a protein belonging to a known class. These capabilities yield a powerful tool for guiding structural sampling for both structural prediction and design. Availability and implementation The trained classifier network, parser network, and entropy calculation scripts are available for download at https://git.io/fp6bd, with detailed usage instructions provided at the download page. A step-by-step tutorial for setup is provided at https://goo.gl/e8GB2S. All Rosetta commands, RosettaRemodel blueprints, and predictions for all datasets used in the study are available in the Supplementary Information. Supplementary information Supplementary data are available at Bioinformatics online.

Eguchi, Raphael R.↗

DOE OSTI2017

Structural Analysis of ZnO Nanoparticles Reinforced P(3HB-co-15 mol% 3HHx) Bioplastic Composite

Bioplastics are gaining interest due to their biodegradable and biocompatible nature which can be used as a replacement for petroleum based plastics. Poly (3-hydroxybutyrate-co-15 mol% 3-hydroxyhexanoate) [P(3HB-co-15 mol% 3HHx)]/ZnO nanoparticles (NPs) blended bioplastic films were fabricated by solution casting method using chloroform as solvent. The structural characteristics such as peak intensity analysis, crystallite size, dislocation density, and texture coefficient of ZnO NPs mixed P(3HB-co-15 mol% 3HHx) samples were studied using X-Ray Diffraction (XRD) and Fourier Transform Infra-Red (FTIR) analyses. It is clear from the XRD analyses that the crystallinity of P(3HB-co-15 mol% 3HHx) was decreased considerably as ZnO NPs concentration increased. The crystallite size of P(3HB-co-15 mol% 3HHx) was decreased with an increase in ZnO NPs concentration and observed within 150 nm and the dislocation density was decreased with respect to the orientation of P(3HB-co-15 mol% 3HHx) crystals. Simultaneously, the structural properties of ZnO NPs in P(3HB-co-15 mol% 3HHx) matrix were affected noticeably with respect to the ZnO NPs and copolymer concentrations. The characteristic peak positions from FTIR spectra of P(3HB-co-15 mol% 3HHx) copolymer shifted towards higher frequency and evidenced the existence of structural defects. Overall, it was found from both XRD and FTIR analyses that the presence of ZnO NPs affected the crystallinity of P(3HB-co-15 mol% 3HHx) copolymer due to the formation of intermolecular bonds, which restricted the preferential orientation of P(3HB-co-15 mol% 3HHx) molecules which was observed from the texture coefficient analyses. Based on these observations, ZnO NPs at low concentrations can be used with P(3HB-co-15 mol% 3HHx) copolymer effectively and the resulting composite may be used for packaging application.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2016

Structural analysis and ferroelectric properties of Fe doped BaTiO{sub 3}

The polycrystalline samples of Fe doped BaTiO{sub 3} (BTO) with compositional formula BaTi{sub 1-x}Fe{sub x}O{sub 3} (x = 0, 0.03, 0.04 and 0.05) were prepared by solid-state reaction route. The influence of the Fe content on the structural, vibrational and electric properties of BaTiO{sub 3} was investigated using X-ray powder diffraction (XRD), Raman spectroscopy and Polarization techniques. XRD analysis indicates the formation of single-phase tetragonal structure for all the prepared samples. Tetragonal cubic structure with space group P4mm of all samples is further approved by Rietveld refinement. Room temperature Raman spectra of pure BaTiO{sub 3} show four active modes of vibration whose intensity decreases with increasing Fe doping. Small shift in Raman modes and increment in the line width has been observed with the doping ions. The hysteresis loop is very well performed with regular sharp characteristic of ferroelectric materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗