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Mapping structural heterogeneity at the nanoscale with scanning nano-structure electron microscopy (SNEM)
Here, in this work, we explore the use of scanning electron diffraction (also known as 4D-STEM) coupled with electron atomic pair distribution function analysis (ePDF) to understand the local order (structure and chemistry) as a function of position in a complex multicomponent system, a hot rolled, Ni-encapsulated, Zr 65 Cu 17.5 Ni 10 Al 7.5 bulk metallic glass (BMG), with a spatial resolution of 3 nm. We show that it is possible to gain insight into the chemistry and chemical clustering/ordering tendency in different regions of the sample, including in the vicinity of nano-scale crystallites that are identified from virtual dark field images and in heavily deformed regions at the edge of the BMG. In addition to simpler analysis, unsupervised machine learning was used to extract partial PDFs from the material, modeled as a quasi-binary alloy, and map them in space. These maps allowed key insights not only into the local average composition, as validated by EELS, but also a unique insight into chemical short-range ordering tendencies in different regions of the sample during formation. The experiments are straightforward and rapid and, unlike spectroscopic measurements, don’t require energy filters on the instrument. We spatially map different quantities of interest (QoI’s), defined as scalars that can be computed directly from positions and widths of ePDF peaks or parameters refined from fits to the patterns. We developed a flexible and rapid data reduction and analysis software framework that allows experimenters to rapidly explore images of the sample on the basis of different QoI’s. The power and flexibility of this approach are explored and described in detail. Because of the fact that we are getting spatially resolved images of the nanoscale structure obtained from ePDFs we call this approach scanning nano-structure electron microscopy (SNEM), and we believe that it will be powerful and useful extension of current 4D-STEM methods.
In situ growth, structure, and real-time chemical reactivity of well-defined CeO x -Ru(0001) model surfaces
Ceria is an important material for chemical conversion processes in catalysis. Its intrinsic properties as a reducible oxide can be exploited to achieve catalytic selectivity and activity. However, numerous phenomenological characteristics of ceria remain unknown and its active nature is ever slowly being unraveled. Well defined models of ceria (111) are an important way to systematically study these properties and take advantage of new in situ methods that require pristine materials that allow for the interrogation of the most fundamental traits of this material. The ceria-Ru(0001) model is now the most well studied model surface with numerous aspects of its preparation, atomic structure and reactivity studied by several groups. The preparation of CeO x structures oriented with a (111) surface termination can be achieved through molecular beam deposition, facilitating the growth of well-defined nanostructures, microparticles, and films on the Ru(0001) surface. The growth mechanism exploits the epitaxial relationship between CeOx and Ru to form a carpet mode of well oriented layers of Osingle bondCesingle bondO. These models can be studied to unravel the atomic structure and the oxidation state (Ce 4+ and Ce 3+ ), as prepared and under redox conditions (reduction/oxidation) or with reaction using reactants (e.g., H 2 , methanol). Here, we present a discussion of these most recent observations pertaining to the growth mode, arrangement of atoms on the surface, characteristic chemical state, and redox chemistry of the CeO x -Ru surface. As a result, with insights from these studies we propose new strategies to further unravel the chemistry of ceria.
Modeling of high-efficient direct methanol fuel cells with order-structured catalyst layer
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Structural study of the effects of mutations in proteins to identify the molecular basis of the loss of local structural fluidity leading to the onset of autoimmune diseases
Protein-Protein Interactions (PPIs) are crucial in most of the biological processes and PPI dysfunctions are known to be associated with the onsets of various diseases. One of such diseases is the auto-immune disease. Auto-immune diseases are one among the less studied group of diseases with very high mortality rates. Thus, we tried to correlate the appearances of mutations with their probable biochemical basis of the molecular mechanisms leading to the onset of the disease phenotypes. We compared the effects of the Single Amino Acid Variants (SAVs) in the wild type and mutated proteins to identify any structural deformities that might lead to altered PPIs leading ultimately to disease onset. For this we used Relative Solvent Accessibility (RSA) as a spatial parameter to compare the structural perturbation in mutated and wild type proteins. We observed that the mutations were capable to increase intra-chain PPIs whereas inter-chain PPIs would remain mostly unaltered. This might lead to more intra-molecular friction causing a deleterious alteration of protein's normal function. A Lyapunov exponent analysis, using the altered RSA values due to polymorphic and disease causing mutations, revealed polymorphic mutations have a positive mean value for the Lyapunov exponent while disease causing mutations have a negative mean value. Thus, local spatial stochasticity has been lost due to disease causing mutations, indicating a loss of structural fluidity. The amino acid conversion plot also showed a clear tendency of altered surface patch residue conversion propensity than polymorphic conversions. So far, this is the first report that compares the effects of different kinds of mutations (disease and non-disease causing polymorphic mutations) in the onset of autoimmune diseases. - Highlights: • Protein-Protein Interaction. • Changes in Relative Solvent Accessibility (RSA). • Amino acid conversion matrix. • Polymorphic mutations. • Disease causing mutations.
Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D
Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cell’s membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 Å resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the protein’s side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid
Phosphorylation regulates the secondary structure and function of dentin phosphoprotein peptides
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Investigating the Structural Impact of the Glutamine Repeat in Huntingtin Assembly
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Structural properties of ferroelectric heterostructures using coherent bragg rod analysis
Abstract not provided
Effects of temperature on the atomic structure of synthetic calcium–silicate–deuterate gels: A neutron pair distribution function investigation
Due to the nanocrystallinity of the calcium–silicate–hydrate (C–S–H) gel in ordinary Portland cement-based paste combined with the presence of nanoscale heterogeneities such as varying calcium-to-silicon ratios and incorporation of aluminum in the structure, standard characterization techniques fail to fully capture the complex atomic structure and nanoscale morphology of this important binder phase. Here, neutron pair distribution function (PDF) analysis is applied to a range of deuterated C–S–H gels with varying Ca/Si ratios (denoted C–S–D). In situ temperature measurements reveal that the local atomic bonding environments in C–S–D gel undergo large structural rearrangements due to exposure to elevated temperature (above ~ 200 °C), including the collapse of the C–S–D gel interlayer spacing to 9.6 Å and the emergence of a disordered dicalcium silicate phase (similar to larnite). At lower elevated temperatures, the atom–atom correlations are dominated by scattering from deuterium atoms and therefore can be used to quantify the dehydration kinetics.
Structure-performance relationships in lignin-based transesterification vitrimers: The role of lignin structural features
Lignin has been hailed as an ideal renewable alternative for petrochemical-based prepolymers in material synthesis for a sustainable and circular economy, due to its abundant aromatic network and high carbon content. However, the properties and performance of lignin-derived macromolecules are strongly influenced by the lignin itself. While numerous studies have explored the impact of lignin content on the thermomechanical performance of lignin-based vitrimers, literature on how the inherent structural features of lignin affect these properties is scanty. In this study, hardwood organosolv lignin was fractionated in ethyl acetate, ethanol, and acetone to obtain lignin fractions with varying structural characteristics. These fractions were then modified through carboxylation and crosslinked with epoxidized soybean oil (ESO) at a hydroxyl to epoxy group ratio of 1:1 to produce lignin-based transesterification vitrimers (LVs). The thermal properties (i.e. glass transition temperature and thermal stability), tensile strength, storage modulus, and stress relaxation behavior of the LVs were studied and carefully related to the structural features of lignin. The results revealed a positive relationship between strong hydroxyl content in modified lignin and the tensile strength (5.10–9.71 MPa), storage modulus (1099.4 – 1372.8 MPa), crosslinking density, and stress relaxation of the LVs. Additionally, both the storage modulus and tensile strength exhibited a positive relationship with the ratio of rigid linkages in modified lignin, while lignin molecular weight was found to significantly impact the thermal properties of LVs (i.e Tg and thermal stability). This study not only highlights the valorization of lignin in vitrimer synthesis but also provide insights for designing lignin-based materials with tailored properties for specific applications.
Investigation of structural and magnetic properties of rapidly-solidified iron-silicon alloys at ambient and elevated temperatures
In this work, we investigated the ambient temperature structural properties (~300 K) and the ambient and high temperature (up to 900 K) direct current (DC) magnetic properties of melt-spun Fe-x wt.% Si (x = 3, 5, & 8) alloys. The wheel surface speeds selected for the study were 30 m/s and 40 m/s. The thickness, width, lattice parameter, saturation magnetization (MS), and intrinsic coercivity (HCI) of the melt spun ribbons are presented and compared with data in the literature. The ribbons produced at the lower wheel surface speed (30 m/s) were continuous having relatively uniform edges compared to the ribbons produced at the higher wheel surface speed. The thickness and the width of the melt-spun ribbons ranged between ~15-60 μm and 500-800 μm, respectively. The x-ray diffraction spectra of the melt-spun ribbons indicated the presence of disordered α-phase, irrespective of the composition, and the wheel-surface speed. The lattice parameter decreased gradually as a function of increasing silicon content from ~0.2862 nm (Fe-3 wt.% Si) to ~0.2847 nm (Fe-8 wt.% Si). Wheel surface speed was not shown to have a significant effect on the magnetization, but primarily impacted the ribbon structure. A decreasing trend in the saturation magnetization was observed as a function of increased silicon content. The intrinsic coercivity of the melt-spun alloys ranged between ~50 to 200 A/m. Elevated temperature evaluation of the magnetization in the case of Fe-3 & 5 wt.% Si alloy ribbons was distinctly different from the Fe-8 wt.% Si alloy ribbons. The curves of the as-prepared Fe-3 wt.% Si and Fe-5 wt.% Si alloy ribbons were irreversible while that of Fe-8 wt.% Si was reversible. The MS for any of the combinations of wheel surface speed and composition decreased monotonically with the increase in temperature (from 300 – 900 K). The percentage decrease in MS from 300 K to 900 K for the Fe-3 wt.% Si and Fe-5 wt.% Si alloys was ~19-22 %, while the percentage decrease in the same temperature range for Fe-8 wt.% Si alloy was ~26-30 %. It appears that Fe-3 wt.% Si and Fe-5 wt.% Si alloys ribbons are primarily comprised of the α phase (disordered phase) with any minor constituents being beyond the detection limits of the studies performed, while the Fe-8 wt.% Si alloy ribbons are comprised of disordered and regions of short-range ordering.
Superheating suppresses structural disorder in layered BiI3 semiconductors grown by the Bridgman method
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Effects of citrate on hexavalent chromium reduction by structural Fe(II) in nontronite
Iron-bearing clay minerals and organic matter are two important components in natural environments that influence hexavalent chromium (Cr(VI)) reduction. Previous studies have shown that organic ligands could influence Cr(VI) reduction by aqueous Fe2+ and pyrite. However, the effects of organic ligands on Cr(VI) reduction by structural Fe(II) in clays are not well understood. In this study, the effects of citrate on Cr(VI) reduction by nontronite (NAu-2) were investigated under near neutral pH condition (pH=6). Our results showed that the presence of citrate decreased the rate but increased the amount of Cr(VI) reduction by structural Fe(II) in NAu-2. The decreased reaction rate was likely due to competitive sorption of citrate and polyanionic dichromate (Cr2O7- ), because sorption of dichromate appeared to be the first step for subsequent Cr(VI) reduction. The increased amount of Cr(VI) reduction in the presence of citrate was likely because citrate provided additional reducing power through ligand-metal electron transfer in the presence of soluble Fe 3+ derived from dissolution of reduced NAu-2. Soluble Cr(III)-citrate complex was the possible form of reduced chromium when citrate was present. In contrast, nanometer-sized Cr2O3 particles were the product of Cr(VI) reduction by reduced NAu-2 without citrate. Our study highlights the importance of organic ligands on Cr(VI) reduction and immobilization when iron-bearing clay minerals are applied to treat Cr(VI) contaminant in organic matter rich environments.
Structural and Biophysical Properties of a [4Fe-4S] Ferredoxin-Like Protein from Synechocystis sp. PCC 6803 with a Unique Two Domain Structure
Electron carrier proteins (ECPs), binding iron-sulfur clusters, are vital components within the intricate network of metabolic and photosynthetic reactions. They play a crucial role in the distribution of reducing equivalents. In Synechocystis sp. PCC 6803, the ECP network includes at least nine ferredoxins. Previous research, including global expression analyses and protein binding studies, has offered initial insights into the functional roles of individual ferredoxins within this network. This study primarily focuses on Ferredoxin 9 (slr2059). Through sequence analysis and computational modeling, Ferredoxin 9 emerges as a unique ECP with a distinctive two-domain architecture. It consists of a C-terminal iron-sulfur binding domain and an N-terminal domain with homology to Nil-domain proteins, connected by a structurally rigid 4-amino acid linker. Notably, in contrast to canonical [2Fe-2S] ferredoxins exemplified by PetF (ssl0020), which feature highly acidic surfaces facilitating electron transfer with photosystem I reaction centers, models of Ferredoxin 9 reveal a more neutral to basic protein surface. Using a combination of electron paramagnetic resonance spectroscopy and square-wave voltammetry on heterologously produced Ferredoxin 9, this study demonstrates that the protein coordinates 2x[4Fe-4S]2+/1+ redox-active and magnetically interacting clusters, with measured redox potentials of -420 +/- 9 mV and -516 +/- 10 mV vs SHE. A more in-depth analysis of Fdx9's unique structure and protein sequence suggests that this type of Nil-2[4Fe-4S] multi-domain ferredoxin is well conserved in cyanobacteria, bearing structural similarities to proteins involved in homocysteine synthesis in methanogens.
Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression
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Structure of the Anthrax Protective Antigen D425A Dominant Negative Mutant Reveals a Stalled Interme
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The natural armors of fish: A comparison of the lamination pattern and structure of scales
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