pH-Dependent structure of water-exposed surfaces of CdSe quantum dots
Weakly-bound ligands in dynamic exchange expose the surface of CdSe quantum dots to pH-dependent modification.
Westmoreland, Dana E.↗
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A structured data model frame for human factors application - 175
Building a Human Factors analysis and Verification and Validation case for new control rooms and even for control room modifications is a highly labor intensive project. Any optimization that can be made in the process translates into savings in the overall control room project schedule and budget. Several support tools from word, to excel, mind maps and databases have been traditionally used by human factors practitioners to conduct the analysis and document its results. While the use of these tools has had satisfactory results, they don't provide in our experience strong enough means for configuration control management, to avoid duplicities, streamline the analysis processes and allow collaborative team efforts. This paper documents how the established practices (methods, processes and tools) were questioned, which were the sources for comparison and how the results were translated into requirements for the new tool constituting the data frame model for Human Factors Engineering applications. The exercise has allowed us to evaluate the efficiency of our current practices in comparison to previous ones while improving our compliance with the quality assurance standards. (authors)
42 ENGINEERING↗
Polaritonic Chern Insulators in Monolayer Semiconductors
Systems with strong light-matter interaction open up new avenues for studying topological phases of matter. Examples include exciton polaritons, mixed light-matter quasiparticles, where the topology of the polaritonic band structure arises from the collective coupling between matter wave and optical fields strongly confined in periodic dielectric structures. Distinct from light-matter interaction in a uniform environment, the spatially varying nature of the optical fields leads to a fundamental modification of the well-known optical selection rules, which were derived under the plane wave approximation. Here, in this study, we identify polaritonic Chern insulators by coupling valley excitons in transition metal dichalcogenides to photonic Bloch modes in a dielectric photonic crystal slab. We show that polaritonic Dirac points, which are markers for topological phase transition points, can be constructed from the collective coupling between valley excitons and photonic Dirac cones in the presence of both time-reversal and inversion symmetries. Lifting exciton valley degeneracy by breaking time-reversal symmetry leads to gapped polaritonic bands with nonzero Chern numbers. Through numerical simulations, we predict polaritonic chiral edge states residing inside the topological gaps. Our Letter paves the way for the further study of strong exciton-photon interaction in nanophotonic structures and for exploring polaritonic topological phases and their practical applications in polaritonic devices.
74 ATOMIC AND MOLECULAR PHYSICS↗
Li x (C 5 H 5 N) y Fe 2– z Se 2 : A Defect-Resilient Expanded-Lattice High-Temperature Superconductor
Two-dimensional iron chalcogenide intercalates display a remarkable correlation of the interlayer spacing with enhancement of the superconducting critical temperature (T c ). In this work, synchrotron X-ray absorption (XAS; at the Fe and Se K-edges) and emission (XES; at the Fe Κβ) spectroscopies allow one to discuss how the important rise of T c (~44 K) in the molecule-intercalated Li x (C 5 H 5 N) y Fe 2-z Se 2 relates to the electronic and local structural changes felt by the inorganic host upon doping (x). XES shows that widely separated layers of edge-sharing FeSe 4 tetrahedra carry low-spin moieties, with a local Fe magnetic moment slightly reduced compared to the parent β-Fe 2-z Se 2 . Pre-edge XAS expresses the progressively reduced mixing of metal 3d-4p states upon lithiation. Doping-mediated local lattice modifications, probed by conventional T c optimization measures (cf. the anion height and FeSe 4 tetrahedra regularity), become less relevant when layers are spaced far away. On the basis of extended X-ray absorption fine structure, such distortions are compensated by a softer Fe network that relates to Fe-site vacancies, alleviating electron-lattice correlations and superconductivity. Density functional theory (DFT) guided modification of the isolated Fe 2-z Se 2 (z, vacant sites) planes, resembling the host layers, identify that Fe-site deficiency occurs at low energy cost, giving rise to stretched Fe sheets, in accordance with experiments. Here, the robust high-T c in Li x (C 5 H 5 N) y Fe 2-z Se 2 , arises from the interplay of electron-donating spacers and the iron selenide layer's tolerance to defect chemistry, a tool to favorably tune its Fermi surface properties.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2"-phosphotransferases
Aminoglycoside phosphotransferases (APHs) are one of three families of aminoglycoside-modifying enzymes that confer high-level resistance to the aminoglycoside antibiotics via enzymatic modification. This has now rendered many clinically important drugs almost obsolete. The APHs specifically phosphorylate hydroxyl groups on the aminoglycosides using a nucleotide triphosphate as the phosphate donor. The APH(2′′) family comprises four distinct members, isolated primarily from Enterococcus sp., which vary in their substrate specificities and also in their preference for the phosphate donor (ATP or GTP). In this work, the structure of the ternary complex of APH(2′′)-IIIa with GDP and kanamycin was solved at 1.34 Å resolution and was compared with substrate-bound structures of APH(2′′)-Ia, APH(2′′)-IIa and APH(2′′)-IVa. In contrast to the case for APH(2′′)-Ia, where it was proposed that the enzyme-mediated hydrolysis of GTP is regulated by conformational changes in its N-terminal domain upon GTP binding, APH(2′′)-IIa, APH(2′′)-IIIa and APH(2′′)-IVa show no such regulatory mechanism, primarily owing to structural differences in the N-terminal domains of these enzymes.
59 BASIC BIOLOGICAL SCIENCES↗
Multistep Solid-State Organic Synthesis of Carbamate-Linked Covalent Organic Frameworks.
Herein, we demonstrate the first example of a multistep solid-state organic synthesis, in which a new imine-linked two-dimensional covalent organic framework (COF-170, 1) was transformed through three consecutive postsynthetic modifications into porous, crystalline cyclic carbamate and thiocarbamate-linked frameworks. These linkages are previously unreported and inaccessible through de novo synthesis. While not altering the overall connectivity of the framework, these chemical transformations induce significant conformational and structural changes at each step, highlighting the key importance of noncovalent interactions and conformational flexibility to COF crystallinity and porosity. These transformations were assessed using 15 N multiCP-MAS NMR spectroscopy, providing the first quantitation of yields in COF postsynthetic modification reactions, as well as of amine defect sites in imine-linked COFs. This multistep COF linkage postsynthetic modification represents a significant step toward bringing the precision of organic solution-phase synthesis to extended solid-state compounds.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Local order origin of thermal stability enhancement in amorphous Ag doping GeTe
We demonstrate the impacts of Ag doping on the local atomic structure of amorphous GeTe phase-change material. The variations of phonon vibrational modes, boding nature, and atomic structure are shown by Raman, X-ray photoelectron spectroscopy, and ab initio calculation. Combining the experiments and simulations, we observe that the number of Ge atoms in octahedral site decreases and that in tetrahedral site increases. This modification in local order of GeTe originating from the low valence element will affect the crystallization behavior of amorphous GeTe, which is verified by differential scanning calorimetry and transmission electron microscope results. This work not only gives the analysis on the structural change of GeTe with Ag dopants but also provides a method to enhance the thermal stability of amorphous phase-change materials for memory and brain-inspired computing applications.
36 MATERIALS SCIENCE↗
S-Adenosyl-S-carboxymethyl-l-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA
The putative methyltransferase CmoA is involved in the nucleoside modification of transfer RNA. X-ray crystallography and mass spectrometry are used to show that it contains a novel SAM derivative, S-adenosyl-S-carboxymethyl-l-homocysteine, in which the donor methyl group is replaced by a carboxymethyl group. Uridine at position 34 of bacterial transfer RNAs is commonly modified to uridine-5-oxyacetic acid (cmo{sup 5}U) to increase the decoding capacity. The protein CmoA is involved in the formation of cmo{sup 5}U and was annotated as an S-adenosyl-l-methionine-dependent (SAM-dependent) methyltransferase on the basis of its sequence homology to other SAM-containing enzymes. However, both the crystal structure of Escherichia coli CmoA at 1.73 Å resolution and mass spectrometry demonstrate that it contains a novel cofactor, S-adenosyl-S-carboxymethyl-l-homocysteine (SCM-SAH), in which the donor methyl group is substituted by a carboxymethyl group. The carboxyl moiety forms a salt-bridge interaction with Arg199 that is conserved in a large group of CmoA-related proteins but is not conserved in other SAM-containing enzymes. This raises the possibility that a number of enzymes that have previously been annotated as SAM-dependent are in fact SCM-SAH-dependent. Indeed, inspection of electron density for one such enzyme with known X-ray structure, PDB entry http://scripts.iucr.org/cgi-bin/cr.cgi?rm, suggests that the active site contains SCM-SAH and not SAM.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Surface Modification of Melamine-Formaldehyde (MF-R) Macroparticles in Complex Plasma
The surface modification of melamine-formaldehyde (MF-R) macroparticles (4.12 ± 0.09 μm in diameter) in dc glow discharges in neon, argon, and an argon–oxygen mixture (90% Ar, 10% O{sub 2}) was studied experimentally. The macroparticles were treated in the discharge plasma for 10, 20, 40, and 60 min. The macroparticles were placed in ordered plasma–dust structures and then extracted from them. The results of atomic force microscopy of the surface profile are presented. Quantitative data on destruction of the surface layer and aspects of its modification are discussed. The amount of substance removed from the particle surface for the exposure time was calculated using the fractal analysis method.
36 MATERIALS SCIENCE↗
Toward the rational design of macrolide antibiotics to combat resistance
Here, macrolides, one of the most prescribed classes of antibiotics, bind in the bacterial ribosome's polypeptide exit tunnel and inhibit translation. However, mutations and other ribosomal modifications, especially to the base A2058 of the 23S rRNA, have led to a growing resistance problem. Here, we have used molecular dynamics simulations to study the macrolides erythromycin and azithromycin in wild-type, A2058G-mutated, and singly or doubly A2058-methylated Escherichia coli ribosomes. We find that the ribosomal modifications result in less favorable interactions between the base 2058 and the desosamine sugar of the macrolides, as well as greater displacement of the macrolides from their crystal structure position, illuminating the causes of resistance. We have also examined four azithromycin derivatives containing aromatic indole-analog moieties, which were previously designed based on simulations of the stalling peptide SecM in the ribosome. Surprisingly, we found that the studied moieties could adopt very different geometries when interacting with a key base in the tunnel, A751, possibly explaining their distinct activities. Based on our simulations, we propose modifications to the indole-analog moieties that should increase their interactions with A751 and, consequently, enhance the potency of future azithromycin derivatives.
59 BASIC BIOLOGICAL SCIENCES↗
Effects of deformation on the electronic properties of B-C-N nanotubes
We apply first-principles methods, using density functional theory, to investigate the effects of flattening deformation on the electronic properties of BC{sub 2}N and C-doped BNNTs. Four different types of BC{sub 2}N structures are considered. Two of them are semiconductors, and the radial compression produces a significant reduction of the energy band gap. The other two types of structures are metallic, and the effect of radial compression is quite distinct. For one of them it is found the opening of a small band gap, and for the other one no changes are observed. For C-doped tubes, it is also found that the electronic properties undergo significant modifications when subjected to radial compression. - Graphical Abstract: We apply first-principles methods, using density functional theory, to investigate the effects of flattening deformation on the electronic properties of BC{sub 2}N and C-doped BNNTs. Four different types of BC{sub 2}N structures are considered. Two of them are semiconductors, and the radial compression produces a significant reduction of the energy band gap. The other two types of structures are metallic, and the effect of radial compression is quite distinct. For one of them it is found the opening of a small band gap, and for the other one no changes are observed. For C-doped tubes, it is also found that the electronic properties undergo significant modifications when subjected to radial compression. Highlights: Black-Right-Pointing-Pointer We investigated electronic properties of flattened BC{sub 2}N nanotubes. Black-Right-Pointing-Pointer The electronic states depend strongly on compression. Black-Right-Pointing-Pointer It is studied flattened BN nanotubes doped with a carbon atom. Black-Right-Pointing-Pointer The flattened C-doped structures, presents a significant reduction of the gap.
36 MATERIALS SCIENCE↗
Suppression of alloy fluctuations in GaAs-AlGaAs core-shell nanowires
Probing localized alloy fluctuations and controlling them by growth kinetics have been relatively limited so far in nanoscale structures such as semiconductor nanowires (NWs). Here, we demonstrate the tuning of alloy fluctuations in molecular beam epitaxially grown GaAs-AlGaAs core-shell NWs by modifications of shell growth temperature, as investigated by correlated micro-photoluminescence, scanning transmission electron microscopy, and atom probe tomography. By reducing the shell growth temperature from T > 600 °C to below 400 °C, we find a strong reduction in alloy fluctuation mediated sharp-line luminescence, concurrent with a decrease in the non-randomness of the alloy distribution in the AlGaAs shell. This trend is further characterized by a change in the alloy compositional structure from unintentional quasi-superlattices of Ga- and Al-rich AlGaAs layers at high T to a nearly homogeneous random alloy distribution at low T.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities: Comparison of Native and Non-Native Ubiquitin Oligomers
Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.
59 BASIC BIOLOGICAL SCIENCES↗
Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations
Abstract Molecular analysis of interactions between IgE antibody and allergen allows the structural basis of IgE recognition to be defined. Human IgE (hIgE) epitopes of respiratory lipocalin allergens, including Can f 1, remain elusive due to a lack of IgE‐allergen complexes. This study aims to map the structure of allergenic epitopes on Can f 1. The fragment antigen‐binding (Fab) regions of Can f 1 specific human IgE monoclonal antibodies (hIgE mAb) were used to determine the structures of IgE epitopes. Epitope mutants were designed to target Can f 1 epitopes. Immunoassays and a human FcεRIαtransgenic mouse model of passive anaphylaxis in vivo were used to assess the functional activity of epitope mutants. Crystal structures of natural or recombinant Can f 1 complexed with two hIgE mAb 1J11 and 12F3 Fabs, respectively, were determined. The hIgE mAb bound to two partially overlapping epitopes and recognized two different Can f 1 conformations. The hIgE mAb 12F3 showed an unusual mode of binding by protruding its heavy chain CDR3 inside the Can f 1 calyx. Epitope mutants generated based on the structural analyses displayed a 64%–89% reduction in IgE antibody binding and failed to induce passive anaphylaxis in a human FcεRIαtransgenic mouse model. In summary, the structures of Can f 1‐hIgE Fab complexes revealed two unique and partially overlapping epitopes on Can f 1. The modification of the identified IgE epitopes provides a pathway for the design of hypoallergens to treat dog allergies.
Biochemistry & Molecular Biology↗
PolyMat: an efficient Matlab code for multi-material topology optimization
We introduce a Matlab implementation of topology optimization for compliance minimization on unstructured polygonal finite element meshes that efficiently accommodates many materials and many volume constraints. Leveraging the modular structure of the educational code, PolyTop, we extend it to the multi-material version, PolyMat, with only a few modifications. First, a design variable for each candidate material is defined in each finite element. Next, we couple a Discrete Material Optimization interpolation with the existing penalization and introduce a new parameter such that we can employ continuation and smoothly transition from a convex problem without any penalization to a non-convex problem in which material mixing and intermediate densities are penalized. Mixing that remains due to the density filter operation is eliminated via continuation on the filter radius. To accommodate flexibility in the volume constraint definition, the constraint function is modified to compute multiple volume constraints and the design variable update is modified in accordance with the Zhang-Paulino-Ramos Jr. (ZPR) update scheme, which updates the design variables associated with each constraint independently. The formulation allows for volume constraints controlling any subset of the design variables, i.e., they can be defined globally or locally for any subset of the candidate materials. Borrowing ideas for mesh generation on complex domains from PolyMesher, we conclude which design variables are associated with each local constraint of arbitrary geometry. A number of examples are presented to demonstrate the many material capability, the flexibility of the volume constraint definition, the ease with which we can accommodate passive regions, and how we may use local constraints to break symmetries or achieve graded geometries.
79 ASTRONOMY AND ASTROPHYSICS↗
Reinforcing cycling stability and rate capability of LiNi0.5Mn1.5O4 cathode by dual-modification of coating and doping of a fast-ion conductor
Highlights: • Li{sub 2}SiO{sub 3}-modified LiNi{sub 0.5}Mn{sub 1.5}O{sub 4} with well-defined octahedral morphology have been controllably obtained. • The combination of the modification of fast ions conductor and solid state method will be an optional method. • The cyclic performance and rate capability of LiNi{sub 0.5}Mn{sub 1.5}O{sub 4}-based materials have been significantly improved. - Abstract: A simple solid state method was utilized to synthesize excellent spinel Li{sub 2}SiO{sub 3}-modified LiNi{sub 0.5}Mn{sub 1.5}O{sub 4} cathodes. Dual-modification of coating and doping of fast-ion conductor Li{sub 2}SiO{sub 3} leads to stable crystal structure and additional three-dimensional (3-D) channels for Li{sup +}-ion diffusion, and protects the electrode surface from electrolyte attack. The Li{sub 2}SiO{sub 3}-modified material possesses coexistence of ordered P4{sub 3}32 and disordered Fd-3m phases. As a result of improved structure, morphology and conductivity, the Li{sub 2}SiO{sub 3}-modified LiNi{sub 0.5}Mn{sub 1.5}O{sub 4} shows more superior cyclic performance, rate capability and high temperature stability than the pristine: capacity retention of 95.17% at 0.1 C after 100 cycles vs. that of 79.23%; rate capability of 130–89.1 mAh g{sup −1} at 0.1–10 C vs. that of 120–57.6 mAh g{sup −1}; and high temperature capacity retention of 99.42% at 0.1 C vs. that of 79.59%. Our study provides a facile approach to stabilize crystal structure, optimize morphology and conductivity, and thus enhance electrochemical performance of LiNi{sub 0.5}Mn{sub 1.5}O{sub 4}-based materials.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structure-Based Design of an Iminoheterocyclic β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central Aβ in Nonhuman Primates
We describe successful efforts to optimize the in vivo profile and address off-target liabilities of a series of BACE1 inhibitors represented by 6 that embodies the recently validated fused pyrrolidine iminopyrimidinone scaffold. Employing structure-based design, truncation of the cyanophenyl group of 6 that binds in the S3 pocket of BACE1 followed by modification of the thienyl group in S1 was pursued. Optimization of the pyrimidine substituent that binds in the S2'–S2'' pocket of BACE1 remediated time-dependent CYP3A4 inhibition of earlier analogues in this series and imparted high BACE1 affinity. These efforts resulted in the discovery of difluorophenyl analogue 9 (MBi-4), which robustly lowered CSF and cortex Aβ40 in both rats and cynomolgus monkeys following a single oral dose. Compound 9 represents a unique molecular shape among BACE inhibitors reported to potently lower central Aβ in nonrodent preclinical species.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Giant Bulk Photovoltaic Effect in Vinylene-Linked Hybrid Heterocyclic Polymer
The bulk photovoltaic effect refers to the generation of a steady photocurrent from a homogeneous noncentrosymmetric material. It offers an alternative to the traditional p–n junction-based photovoltaic mechanism to directly convert sunlight to electricity. In this work, we investigate the bulk photovoltaic effect in low-dimensional polar organic materials with first-principles density functional theory calculations and shift current theory. With a strategy designed to break the inversion symmetry along the polymer chain, we demonstrate that conjugated vinylene-linked hybrid heterocyclic polymers can produce a strong bulk photovoltaic response to light, outperforming benchmark inorganic materials. The high current density results from the delocalized wave functions, composed mainly of carbon p orbitals. The great structural and electronic flexibility of polymers offers a robust paradigm to enhance the shift current response through chemical and physical modifications. The development of polymer blends with polymers of different band gaps potentially enables the utilization of the whole visible light spectrum for energy conversion.
14 SOLAR ENERGY↗