Constituent Atoms Research Articles

A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress.

Simple Summaryγ-H2AX, a phosphorylated variant of histone H2A, is a widely used biomarker of DNA replication stress. To develop an immunological probe able to detect and track γ-H2AX in live cancer cells, we have isolated single domain antibodies (called nanobodies) that are easily expressed as functional recombinant proteins and here we report the extensive characterization of a novel nanobody that specifically recognizes γ-H2AX. The interaction of this nanobody with the C-terminal end of γ-H2AX was determined by X-ray crystallography. Moreover, the generation of a bivalent nanobody allowed us to precisely detect γ-H2AX foci in drug-treated cells as efficiently as with commercially available conventional antibodies. Furthermore, we tracked γ-H2AX foci in live cells upon intracellular delivery of the bivalent nanobody fused to the red fluorescent protein dTomato, making, consequently, this new cost-effective reagent useful for studying drug-induced replication stress in both fixed and living cancer cells.Histone H2AX phosphorylated at serine 139 (γ-H2AX) is a hallmark of DNA damage, signaling the presence of DNA double-strand breaks and global replication stress in mammalian cells. While γ-H2AX can be visualized with antibodies in fixed cells, its detection in living cells was so far not possible. Here, we used immune libraries and phage display to isolate nanobodies that specifically bind to γ-H2AX. We solved the crystal structure of the most soluble nanobody in complex with the phosphopeptide corresponding to the C-terminus of γ-H2AX and show the atomic constituents behind its specificity. We engineered a bivalent version of this nanobody and show that bivalency is essential to quantitatively visualize γ-H2AX in fixed drug-treated cells. After labelling with a chemical fluorophore, we were able to detect γ-H2AX in a single-step assay with the same sensitivity as with validated antibodies. Moreover, we produced fluorescent nanobody-dTomato fusion proteins and applied a transduction strategy to visualize with precision γ-H2AX foci present in intact living cells following drug treatment. Together, this novel tool allows performing fast screenings of genotoxic drugs and enables to study the dynamics of this particular chromatin modification in individual cancer cells under a variety of conditions.

Pengaruh model pembelajaran kooperatif tipe stad terhadap hasil belajar siswa pada materi atom dan partikel penyusunnya

This study aimed to determine: 1) the differences in student learning outcomes taught used the STAD cooperative learning model used conventional learning models on atomic material and the constituent particles, 2) the magnitude of the influence of the STAD cooperative learning model on student learning outcomes on atomic and particle material constituent. The form of this research was true experimental design with posttest only control design. The sample selection technique was carried out by simple random sampling. The data collection tool was used a learning outcome test. The results of data analysis through the U-Mann Whitney test on the posttest value obtained a Sig value of 0.000 which indicates that there were differences in learning outcomes between students who were taught used the STAD type cooperative learning model and students taught used conventional methods on atomic material and the constituent particles. Learning used the STAD cooperative learning model on atomic material and its constituent particles at SMP Negeri 9 Pontianak class IX has an effect of 37.06% on student learning outcomes.

On the Linearized Dynamics of the Neutral Cells at High Latitudes in the Earth’s Thermosphere and Exosphere

The linearized dynamics of the idealized narrow neutral cells at high latitudes in the absence or presence of auroral energy impulse of the type q0 e-at is discussed in the upper atmosphere. The general expression for the oscillation amplitude ∆z of the cells is given by ∆ z=q0 [e-at – cos (ω t) + a sin (ω t)/ω)]/(a2 + ω2) + ν0 sin (ω t)/ω Here ν0 is the cell’s initial velocity, ω is its Brunt - Vaisala frequency which varies from about 1.7x10-2 at 200 km to 1.3x10-2 radians/s at 300 km for an exospheric temperature of 1000 K. The maximum ∆z varies from a few km at 200 km for 1000 K to about 25 km at 300 km for 2000 K. For the observed high- and low-density cells, ω is less and high respectively by around 15% than those in the ambient atmosphere at 200 km in the temperature range of 1000-2000K. In absence of ν0 and q0, the cells are stable in the thermosphere. The oscillations during disturbed conditions, should eventually cease in the presence of existing nonlinear forces like collision frequencies, emission from atomic constituents, heat conduction and losses, which should be further incorporated to provide a framework for their theoretical interpretation and implications for the high latitudinal thermospheric as well for the ionospheric morphology.

Screening potential topological insulators in half-Heusler compounds via compressed-sensing

Ternary half-Heusler compounds with widely tunable electronic structures, present a new platform to discover topological insulators (TIs). Due to time-consuming computations and synthesis procedures, the identification of new TIs is however a rough task. Here, we adopt a compressed-sensing approach to rapidly screen potential TIs in half-Heusler family, which is realized via a two-dimensional descriptor that only depends on the fundamental properties of the constituent atoms. Beyond the finite training data, the proposed descriptor is employed to screen many new half-Heusler compounds, including those with integer and fractional stoichiometry, and a larger number of possible TIs are predicted.

Density functional theory investigation on lattice dynamics, elastic properties and origin of vanished magnetism in Heusler compounds CoMnVZ (Z = Al, Ga)* *Project supported by Special Fund for Introduced Talent to Initiate Scientific Research in Nanjing Tech University and the National Natural Science Foundation of China (Grant Nos. 51831003 and 51771225).

The lattice dynamics, elastic properties and the origin of vanished magnetism in equiatomic quaternary Heusler compounds CoMnVZ (Z = Al, Ga) are investigated by first principle calculations in this work. Due to the similar constituent atoms in CoMnVAl and CoMnVGa compounds, they are both stable in LiMgPdSn-type structure with comparable lattice size, phonon dispersions and electronic structures. Comparatively, we find that CoMnVAl is more structurally stable than CoMnVGa. Meanwhile, the increased covalent bonding component in CoMnVAl enhances its mechanical strength and Vickers hardness, which leads to better comprehensive mechanical properties than those of CoMnVGa. Practically and importantly, structural and chemical compatibilities at the interface make non-magnetic semiconductor CoMnVAl and magnetic topological semimetals Co2MnAl/Ga more suitable to be grown in heterostructures. Owing to atomic preferential occupation in CoMnVAl/Ga, the localized atoms Mn occupy C (0.5, 0.5, 0.5) Wyckoff site rather than B (0.25, 0.25, 0.25) and D (0.75, 0.75, 0.75) Wyckoff sites in LiMgPdSn-type structure, which results in symmetric band filling and consequently drives them to be non-magnetic. Correspondingly, by tuning localized atoms Mn to occupy B (0.25, 0.25, 0.25) or/and D (0.75, 0.75, 0.75) Wyckoff sites in off-stoichiometric Co–Mn–V–Al/Ga compounds and keeping the total valence electrons as 24, newly compensated ferrimagnetic compounds are theoretically achieved. We hope that our work will provide more choices for spintronic applications.

Spin polarized density functional theory\xa0calculations of the electronic structure and magnetism of the 112 type iron pnictide compound hbox {EuFeAs}_2

Using density-functional theory, we investigate the electronic, magnetic, and hyperfine-interaction properties of the 112-type iron-pnictide compound {hbox {EuFeAs}}_2, which is isostructural to the high-temperature iron-based superconductor {hbox {Ca}}_{1-x}{hbox {La}}_x{hbox {FeAs}}_2. We show that the band structure of {hbox {EuFeAs}}_2 is similar to that of the 112-type compounds’ family, with hole-like and electron-like bands at the Brillouin-zone center and corners, respectively. We demonstrate that the bands near the Fermi level originate mainly from the Fe atoms. The presence of a mixture of ionic and covalent bonding is predicted from the charge-density and atom-resolved density-of-states calculations. There is good agreement between the calculated hyperfine-interaction parameters with those obtained from the ^{57}Fe and ^{151}Eu Mössbauer measurements. The spatial distribution of atoms in {hbox {EuFeAs}}_2 leads to an in-plane 2D magnetism. Moreover, ab-initio calculations predict the compound’s magnetic moment and the magnetic moments of each constituent atom. Also, the density of states profile provides insight into the relative magnitude of these moments. Electronic structure calculations and Fermi surface topology reveal various physical and chemical properties of {hbox {EuFeAs}}_2. Valence electron density maps indicate the co-existence of a wide range of chemical bonds in this system, and based on structural properties, the transport characteristics are deduced and discussed. A thorough analysis of the atomic structure of {hbox {EuFeAs}}_2 and its role in the bond formation is presented.

The role of dysprosium ions as a dopant on linear and nonlinear optical dispersion parameters in a-Se thin film

Thin films of un-doped and doped a-Se with Dysprosium rare-earth ions have been prepared by the thermal evaporation technique. The optical transmission spectra of the investigated films have been measured in a wide spectral range and used to calculate the linear optical constants together with the optical energy gap of studied films. The observed decrease in the values of the energy gap against the increase of the Dysprosium (Dy) content in a-Se films has been explained using Mott and Davis Model and in terms of electronegativity difference of the constituent atoms. Furthermore, the dispersion of nonlinear parameters such as second-order refractive index and nonlinear absorption coefficient (two-photon absorption coefficient) of investigated films are presented and discussed.

Revisiting the thermal conductivity of Si, Ge and diamond from first principles: roles of atomic mass and interatomic potential

The thermal conductivity (κ) of nonmetals is determined by the constituent atoms, the crystal structure and interatomic potentials. Although the group-IV elemental solids Si, Ge and diamond have been studied extensively, a detailed understanding of the connection between the fundamental features of their energy landscapes and their thermal transport properties is still lacking. Here, starting from first principles, we analyze those factors, including the atomic mass (m) and the second- (harmonic) and third-order (anharmonic) interatomic force constants (IFCs). Both the second- and third-order IFCs of Si and Ge are very similar, and thus Si and Ge represent ideal systems to understand how the atomic mass alone affects κ. Although the group velocity (v) decreases with increasing atomic mass (), the phonon lifetime (τ) follows the opposite trend (). Since the contribution to κ from each phonon mode is approximately proportional v 2 τ, κ is lower for the heavier element, namely Ge. Although the extremely high thermal conductivity of diamond is often attributed to weak anharmonic scattering, the anharmonic component of the interatomic potential is not much weaker than those of Si and Ge, which seems to be overlooked in the literature. In fact, the absolute magnitude of the third-order IFCs is much larger in diamond, and the ratios of the third-order IFCs with respect to the second-order ones are comparable to those of Si and Ge. We also explain the experimentally measured κ of high-quality diamonds (Inyushikin et al 2018 Phys. Rev. B 97 144305) by introducing boundary scattering into the picture, and obtain good agreement between calculations and measurements.

Isotopic effects in chair graphane

Graphane is a layered material consisting of a sheet of hydrogenated graphene, with a C:H ratio of 1:1. We study isotopic effects in the properties of chair graphane, where H atoms alternate in a chairlike arrangement on both sides of the carbon layer. We use path-integral molecular dynamics simulations, which allows one to analyze the influence of nuclear quantum effects on equilibrium variables of materials. Finite-temperature properties of graphane are studied in the range 50–1500 K as functions of the isotopic mass of the constituent atoms, using an efficient tight-bonding potential. Results are presented for kinetic and internal energy, atomic mean-square displacements, fluctuations in the C–H bond direction, plus interatomic distances and layer area. At low temperature, substituting 13C for 12C gives a fractional change of −2.6 × 10−4 in C–C distance and −3.9 × 10−4 in the graphane layer area. Replacing 2H for 1H causes a larger fractional change in the C–H bond of −5.7 × 10−3. The isotopic effect in C–C bond distance increases (decreases) by applying a tensile (compressive) in-plane stress. These results are interpreted in terms of a quasiharmonic approximation for the vibrational modes. Similarities and differences with isotopic effects in graphene are discussed.

Hierarchical molecular design of high-performance infrared nonlinear Ag2HgI4 material by defect engineering strategy

Mid-far infrared nonlinear optical (NLO) materials are gaining both scientific and technological interest in wide applications. The practical properties of one crystal are determined by its constituent atoms, electrons, lattices and their coupled interaction. Herein, by applying a hierarchical molecular design strategy, we synthesized a promising NLO material Ag2HgI4 by a simple solution method, which shows the strongest second harmonic generation (SHG) response in inorganic halides (4 × AgGaS2 (AGS)) and wide transparency range. The deep insights on nonlinearity enhancement and broadening transmittance were elaborated by theoretical calculations, which are attributed to reduced phonon frequency and increased nonbonding electronic states on top valence band. This physical mechanism is applicable in all NLO optical materials generally, opening a novel and exciting avenue for explorations of new NLO candidates with high performance.

Radiation Effects in Amorphous Metallic Alloys as Revealed by Mössbauer Spectrometry: Part I. Neutron Irradiation

Iron-based amorphous metallic alloys (AMAs) of several compositions were exposed to neutron irradiation with fluences of up to 1019 n/cm2. These materials exhibit excellent magnetic properties which predetermine them for use in electronic devices operated also in radiation-exposed environments. Response of the studied AMAs to neutron irradiation is followed by Mössbauer spectrometry which probes the local microstructure. Neutron irradiation leads to rearrangement of constituent atoms, their clustering, and formation of stress centers. The observed modifications of topological short-range order result in changes of spectral parameters including average hyperfine magnetic field, ⟨B⟩, standard deviation of the distribution of hyperfine fields, and position of the net magnetic moment. After irradiation, especially differences in ⟨B⟩-values develop in two opposite directions. This apparent controversy can be explained by formation of specific atomic pairs with different exchange interactions, which depend on the composition of the samples. Part II of this paper will be devoted to radiation effects caused in Fe-based AMAs by ion irradiation.

Trusted QoS Assurance Approach for Composite Service

The characteristics of service computing environment, such as service loose coupling, resource heterogeneity, and protocol independence, propose higher demand for the trustworthiness of service computing systems. Trust provisioning for composite services has become a hot research spot worldwide. In this paper, quality of service (QoS) planning techniques are introduced into service composition-oriented QoS provisioning architecture. By QoS planning, the overall QoS requirement of the composite service is decomposed into separate QoS requirement for every constituent atom service, the QoS level of which can subsequently be satisfied through well-designed service entity selection policies. For any single service entity, its QoS level is variable when the deployment environment or the load of service node changes. To mitigate the uncertainty, we put forward QoS preprocessing algorithms to estimate the future QoS levels of service entities with their history execution data. Then, based on the modeling of composite service and QoS planning, we design three algorithms, which include the time preference algorithm, cost/availability (C/A) preference algorithm, and Euclidean distance preference algorithm, to select suitable atomic services meeting the user’s requirements. Finally, by combining genetic algorithm and local-search algorithm, we propose memetic algorithm to meet the QoS requirements of composite service. The effectiveness of the proposed methods by which the QoS requirements can be satisfied up to 90% is verified through experiments.

Pauli paramagnetism of cubic V3Al , CrVTiAl, and related 18-electron Heusler compounds with a group-13 element

Calculations suggest that ordered Heusler alloys with 18 valance electrons could exhibit a variety of unusual electronic and magnetic states that are absent in the constituent elements. They include magnetic semiconductors, spin gapless semiconductors, compensated ferrimagnetic half-metals, and metallic antiferromagnets. Magnetic order has been predicted at exceptionally high temperature. Any of this would be of interest for spin electronics. Here, we investigate the magnetic properties of bulk, single-phase ${\mathrm{V}}_{3}\mathrm{Al}$, CrVTiAl and the corresponding Ga compounds, with and without $^{57}\mathrm{Fe}$ doping. Results are compared with data on the constituent elements. We conclude that all the as-cast alloys show some degree of B2-type ordering, but all of them are Pauli paramagnets with dimensionless susceptibilities close to the average of the atomic constituents. Prolonged annealing of the single-phase as-cast alloys leads to phase segregation. Density functional theory calculations on ${\mathrm{V}}_{3}X$ and $\text{CrVTi}X$ with $X=B$, Al, Ga, and In confirm that different atomic arrangements on the four interpenetrating face-centered cubic sublattices of the Heusler structure could indeed lead to unusual magnetic properties, but both magnetism and semiconductivity are destroyed by disorder. The energy and entropy differences between different ordered magnetic phases preclude the stabilization of any single one of them. All are metastable and inaccessible in alloys prepared from the melt.

Characterizing the spectral, microstructural, and chemical effects of solar wind irradiation on the Murchison carbonaceous chondrite through coordinated analyses

We performed H+ and He+ irradiation experiments on slabs of the Murchison CM2 meteorite to simulate solar wind irradiation of carbonaceous asteroids. Two separate 6 mm × 6 mm regions were irradiated with 1 keV H+ and 4 keV He+, respectively, to fluences of 8.1 × 1017 ions/cm2 for H+ and 1 × 1018 ions/cm2 for He+. Unirradiated and irradiated surfaces were analyzed using X-ray photoelectron spectroscopy (XPS), visible to near-infrared spectroscopy (VNIR; 0.35–2.5 μm), and microprobe two-step laser-desorption mass spectrometry (μL2MS). We also performed analytical field-emission scanning transmission electron microscopy (FE-STEM) on focused ion beam (FIB) cross-sections extracted from olivine grains and matrix material within the H+- and He+-irradiated regions. In situ XPS analyses suggest that ion irradiation results in the removal of most surface carbon and the partial reduction of surface iron to lower oxidation states. In response to He+-irradiation, we observe brightening (longward of ~0.75 μm) and reddening of reflectance spectra, which is a departure from typical lunar-style space weathering. Additionally, H+- and He+-irradiation have opposing effects on organic carbon content: H+-irradiation increases the abundance of some low-molecular-weight free organic species by breaking down macromolecular material while He+-irradiation causes a decrease in overall organic content by cleaving bonds and sputtering constituent atoms. This suggests that solar wind H+-irradiation and solar wind He+-irradiation change the organic functional group chemistry of asteroidal regolith in different ways. In contrast to some previous experimental space weathering studies, we observe an increase in H2O and OH− abundances in our sample in response to both types of ion irradiation. FE-STEM and energy dispersive X-ray spectroscopy (EDX) analyses show complete amorphization of matrix phyllosilicates in ion-affected rims, partial amorphization of olivine, and changes in Si and Mg concentrations at and/or near the surface. We discuss the implications of these results for understanding the complex nature of space weathering on primitive, carbon-rich asteroids and for analyzing future returned samples from carbonaceous asteroids Bennu and Ryugu.

New Magic Au24 Cluster Stabilized by PVP: Selective Formation, Atomic Structure, and Oxidation Catalysis.

An unprecedented magic number cluster, Au24Clx (x = 0–3), was selectively synthesized by the kinetically controlled reduction of the Au precursor ions in a microfluidic mixer in the presence of a large excess of poly(N-vinyl-2-pyrrolidone) (PVP). The atomic structure of the PVP-stabilized Au24Clx was investigated by means of aberration-corrected transmission electron microscopy (ACTEM) and density functional theory (DFT) calculations. ACTEM video imaging revealed that the Au24Clx clusters were stable against dissociation but fluctuated during the observation period. Some of the high-resolution ACTEM snapshots were explained by DFT-optimized isomeric structures in which all the constituent atoms were located on the surface. This observation suggests that the featureless optical spectrum of Au24Clx is associated with the coexistence of distinctive isomers. X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy of CO adsorbates revealed the electron-rich nature of Au24Clx clusters due to the interaction with PVP. The Au24Clx:PVP clusters catalyzed the aerobic oxidation of benzyl alcohol derivatives without degradation. Hammett analysis and the kinetic isotope effect indicated that the hydride elimination by Au24Clx was the rate-limiting step with an apparent activation energy of 56 ± 3 kJ/mol, whereas the oxygen pressure dependence of the reaction kinetics suggested the involvement of hydrogen abstraction by coadsorbed O2 as a faster process.

The Stoichiometry, Structure and Possible Formation of Crystalline Diastereomeric Salts

Knowing the eutectic composition of the binary melting point phase diagrams of the diastereomeric salts formed during the given resolution, the achievable F (F = eeDia*Y) value can be calculated. The same value can also be calculated and predicted by knowing the eutectic compositions of the binary melting point phase diagrams of enantiomeric mixtures of the racemic compound or the resolving agent. An explanation was sought as to why and how the crystalline precipitated diastereomeric salt—formed in the solution between a racemic compound and the corresponding resolving agent—may be formed. According to our idea, the self-disproportionation of enantiomers (SDE) has a decisive role when the enantiomers form two nonequal ratios of conformers in solution. The self-organized enantiomers form supramolecular associations having M and P helicity, and double helices are formed. Between these double spirals, with the formation of new double spirals, a dynamic equilibrium is achieved and the salt crystallizes. During this process between acids and bases, chelate structures may also be formed. Acids appear to have a crucial impact on these structures. It is assumed that the behavior of each chiral molecule is determined by its own code. This code validates the combined effect of constituent atoms, bonds, spatial structure, charge distribution, flexibility and complementarity.

Natural Antidiabetic Agents: Molecular Docking Study using the Extra Precision Method

Background:Diabetes mellitus (DM) is the most severe, chronic metabolic disorder with abnormally elevated concentration of plasma glucose levels, leading to significant complications, such as diabetic neuropathy, retinopathy, and cardiovascular illnesses.Objective:Synthetic drugs have some disadvantages and limitations. Therefore, there is a continuous global and insisting need for new and better treatment options for Diabetes Mellitus.Methods:In this study, 42 natural anti-diabetic constituents like alkaloids, glycosides, and flavonoids were selected on the basis of mechanism of action on various molecular targets such as Glucokinase activator, Dipeptidyl peptidase 4 (DPP-4), peroxisome proliferator-activated receptors (PPARγ), and α-glucosidase inhibitor. To investigate the potential molecular targets for natural antidiabetcs agents, molecular docking study was carried out using the Glide module of Schrodinger Suit.Results:Interactions of specific amino acid of the targets with the atoms of the chemical constituents and their Gscore indicate the proper binding of chemical constituents with target. The results revealed that Myricetin, Quercetin ae interacts with active sites of the target chosen and can be used for the designing of novel compounds as anti-dibetics.Conclusion:Calculated GScore could be used as a preliminary tool for screening of anti-diabetic drugs before performing experimental activity.

First principles study of Bi12GeO20: Electronic, optical and thermodynamic characterizations

Bismuth germanium oxide (Bi12GeO20) is one of the attractive members of sillenite compounds having fascinating photorefractive characteristics. The electronic, optical and thermodynamic properties of Bi12GeO20 were investigated using density functional theory (DFT) calculations. The experimental and calculated X-ray diffraction patterns were obtained as well-consistent with each other. The lattice constant of the cubic crystalline structure of Bi12GeO20 compound was calculated as 10.304 Å. The electronic band structure and partial density of states plots were reported and contribution of constituent atoms (Bi, Ge, O) to the valence and conduction bands was presented. The band gap energy of the Bi12GeO20 was calculated as 3.20 eV. This wide direct band gap energy provides Bi12GeO20 significant potential in ultraviolet applications. The spectra of real and imaginary components of dielectric function, refractive index, extinction coefficient and absorption coefficient were drawn in the 0−10 eV energy range. Temperature-dependent heat capacity plot indicated the Dulong-Petit limit as 825 J/mol.K. The results of the present study would present worthwhile information to device application areas of Bi12GeO20 compound.

Realization of interstitial boron ordering and optimal near-surface electronic structure in Pd-B alloy electrocatalysts

The fundamental understanding and precise tuning of interatomic s,p-d orbital hybridization are critical to the design of interstitial alloy catalysts containing light constituent atoms. Here, we present a joint theoretical and experimental study that reveals the importance of distribution, concentration and ordering of interstitial boron atoms in Pd-B alloy’s near-surface electronic structure and catalytic performance. Our theoretical results demonstrate that the sub-surface location of interstitial boron atoms with a Pd:B atomic ratio of 2:1 is necessary to ensure an appropriate degree of interatomic s,p-d orbital hybridization, and thereby an optimal surface electronic structure for the hydrogen evolution reaction (HER). We experimentally achieve this with highly-crystalline intermetallic Pd2B. Due to its optimal electronic structure and ordered arrangement of interstitial boron atoms, the intermetallic Pd2B exhibits Pt-like catalytic activity for HER and has excellent catalytic stability for over seven days.

Development of an Electron-Atom Compton Scattering Apparatus Using a Picosecond Pulsed Electron Gun

An apparatus has been developed for electron-atom Compton scattering experiments that can employ a pulsed laser and a picosecond pulsed electron beam in a pump-and-probe scheme. The design and technical details of the apparatus are described. Furthermore, experimental results on the Xe atom in its ground state are presented to illustrate the performance of the pulsed electron gun and the detection and spectrometric capabilities for scattered electrons. The scope of future application is also discussed, involving real-time measurement of intramolecular force acting on each constituent atom with different mass numbers, in a transient, evolving system during a molecular reaction.