Direct Electron Research Articles

Methanogenic Activity and Microbial Community Structure in Response to Different Mineralization Pathways of Ferrihydrite in Paddy Soil

In soils and sediments, microbial reduction of iron (hydr)oxides and consequent formation of secondary iron minerals are important factors influencing many biogeochemical cycles and processes that including microbial methanogenesis. Here, we investigated methanogenic activity and microbial community of a paddy soil enrichment in response to different biomineralization pathways of ferrihydrite, which was reduced and transformed to magnetite and vivianite in the absence and presence of phosphate, respectively. For methanogenic degradation of both acetate and propionate, CH4 production rates in the magnetite-cultures were significantly enhanced compared with the vivianite-cultures. Characterization of 16S rRNA genes from methanogenic soils microbial community indicated that: (i) Methanocellaceae and Methanosarcinaceae were the dominant methanogens in all soil enrichments, (ii) syntrophic acetate-oxidizing bacteria of Clostridiaceae and syntrophic propionate-oxidizing bacteria of Syntrophobacteraceae were highly enriched in the magnetite-cultures, and (iii) the abundance of Anaerolineaceae was increased in the magnetite-cultures for both acetate- and propionate-fed incubations. The facilitated CH4 production in the magnetite-cultures might be related to the dynamic cycle of Fe(III)−Fe(II)−Fe(III) or magnetite-stimulated direct interspecies electron transfer between syntrophic acetate/propionate oxidizers and methanogens, which need further investigation. These results lend insight into the biogeochemical cycling of Fe, C and P in anaerobic soils and sediments, as well as the development of mitigation strategies of CH4 production.

Transmission electron microscope imaging of plasma grown electroformed silicon nitride-based light emitting diode for direct examination of nanocrystallization

We report for the first time a direct transmission electron microscope (TEM) imaging of a cross-section of a silicon nitride-based light emitting diode (LED), produced via a method patented by our research group. Grown by plasma enhanced chemical vapor deposition (PECVD) technique the LED structure (glass/Cr/p+-nc-Si:H/i-SiNx:H/n+-nc-Si:H/ITO) was then subjected to a high forward voltage stress for one time only, i.e. electroforming process. After electroforming the LED exhibited a boosted visible light emission and memory effect. To study the structural effect of the electroforming on the as-deposited LED the cross-section was extracted by focused ion beam (FIB) technique directly from the electroformed diode and thus prepared for TEM imaging. Since the electroforming process caused crystallization of ITO and its breakup in some parts of the diode surface, the FIB was conducted for the cross-section containing some regions with ITO layer and some without ITO. TEM examination revealed the nanocrystalline phase formation within the intrinsic layer (i-SiNx:H) caused by the electroforming process. The average size and distribution of Si nanocrystallites formed inside i-SiNx:H was determined. The Si nanocrystallization within i-SiNx:H was compared for the regions with and without ITO layer. The previously proposed model describing the changes taken place in the diode during electroforming process was reconsidered in the light of this TEM analysis.

Deep mineralization of bisphenol A by catalytic peroxymonosulfate activation with nano CuO/Fe3O4 with strong Cu-Fe interaction

Cu-Fe bimetal oxides yield excellent catalytic activity. However, there are some debates on Cu redox cycle and direction ofelectron transfer during PMS activation by these Cu-Fe bimetal oxides. In this paper, therefore, CuO/Fe3O4 nanoparticles with strong Cu-Fe interaction were prepared by pyrolysis of copper-hexacyanoferrate(III) at 600 °C for 1 h and used to investigate the effect of Cu-Fe interaction on catalytic performance of these Cu-Fe bimetal oxides. The as-prepared CuO/Fe3O4 as a catalyst presented much stronger reactivity than CuO and Fe3O4 for peroxymonosulfate (PMS) activation and bisphenol A (BPA) degradation. The use of 0.3 g L−1 CuO/Fe3O4 and 0.3 mmol L−1 PMS achieved deep mineralization (>99%) in 110 min for degradation of 20 mg L−1 BPA at initial pH 6.0. The k value for BPA degradation was 0.32 min−1 for CuO/Fe3O4, being about 5.3, 3.2 and 2.7 times that for the catalysts of Fe3O4, CuO and the mixture of CuO and Fe3O4, respectively. The synergistic effect between Cu and Fe sites on the surface of CuO/Fe3O4 nanoparticles was attributable to strong Cu-Fe interaction. Characterization by X-ray photoelectron spectra and temperature-programmed reduction with H2 as a reducing agent showed that the strong Cu-Fe interaction makes Cu species more easily donate electrons to PMS for radicals generation as the main reactive sites and reductive cycle of Fe species easier through accepting electrons from PMS, further promoting Cu catalytic cycle through an electron transfer between Cu and Fe. The clarification of structure activityrelationship (SAR) of interaction between bimetal species and their activity for peroxide activation facilitates deep understand of the catalytic mechanism and development of more efficient bimetal based catalysts.

Direct transmission electron microscopy observation of the oriented edge-attachment processes between single-layer graphene flakes

Oriented attachment works on super-lubric surfaces, which could be helpful for 2-dimensional material deposition.

A DFT Study on the Radical-Scavenging Properties of Ferruginol-Type Diterpenes

Ferruginol-type diterpenes have been identified in extracts from numerous plant species. These secondary metabolites are characterized by the multifaceted bioactivity and beneficial impact on the human health. Unfortunately, the antioxidant properties and function of these foods components is not well recognized so far. Therefore, in the current study the theoretical calculations based on the Density Functional Theory (DFT) method were undertaken to investigate in details the radical-scavenging mechanism of ferruginol (1) and its derivatives such as hinokiol (2) and sugiol (3) for the first time. According to these results the direct hydrogen atom transfer (HAT) and sequential proton loss electron transfer (SPLET) mechanism was exhibited by the ferruginol-type abietanes in the non-polar media and polar solvents, respectively. Ferruginol (1) and hinokiol (2) were found to be the most promising free radical scavengers with activity comparable to that of butylated hydroxytoluene (BHT), a synthetic antioxidant commonly used in the food industry.

Electron states, effective masses and transverse effective charge of InAs quantum dots

The electron energy levels, direct energy band gaps, electron and hole effective masses as well as the transverse effective charge of InAs spherically shaped quantum dots have been studied as a function of the quantum dot radius considered as varying from 1 to 10 nm. The direct energy band-gap as well as the electron and heavy hole effective masses decrease non-linearly with increasing the quantum dot radius. Nevertheless, the transverse effective charge is found to increase with increasing the quantum dot radius. It is concluded that the quantum confinement has a strong influence on all the studied physical quantities for quantum dot radius below 6 nm. The results of the present contribution show that more opportunities can be offered to tailor desired optoelectronic properties surpassing those presented by bulk InAs materials.

Cellular level in planta analysis of radial movement of artificially injected caesium in Cryptomeria japonica xylem

Ray parenchyma cells represent the main pathway for mineral radial movement from sapwood towards intermediate wood, based on direct cryo-scanning electron microscopy/energy dispersive X-ray spectroscopy analysis. Ray parenchyma cells are considered to be associated with the radial movement of some elements from sapwood to heartwood in tree trunks. However, this function has not yet been experimentally confirmed. In this study, we analysed the radial movement of caesium (Cs), as a tracer of minerals, through the xylem at the cellular level in standing trees. A solution containing a stable Cs isotope diluted in aqueous acid fuchsin was injected into the outer sapwood of Japanese cedar trees for 3 h, 1, or 4 days. After the injection, the trunk (including the injection points) was freeze-fixed with liquid nitrogen. Subsequently, the trees were felled. The red colour from acid fuchsin was detected in the outer sapwood and did not move passively in the radial direction with free water. For detailed analysis of the Cs distribution in the radial direction (from the red-coloured sapwood towards the pith), we performed cryo-scanning electron microscopy/energy-dispersive X-ray spectroscopy point analysis of the frozen-hydrated samples to analyse the Cs distribution by detecting the characteristic Cs-Lα X-ray peak. In the outer sapwood, Cs was detected in all cell structures at all injection periods. In the inner xylem tissue, Cs was detected in the cell wall and lumen of ray parenchyma cells at 4-day injection, but not at 3-h and 1-day injection. These results suggest that ray parenchyma cells represent the main pathway whereby Cs can move radially from sapwood towards intermediate wood in standing Japanese cedar trees.

Electron Transitions during the Capture of an Electron by a He2+ Ion at the Argon Atom

We have measured the absolute values of the total cross section of the one-electron capture by He2+ ions in the kinetic energy range 2–30 keV at the Ar atoms. The absolute values of the differential scattering cross sections of He+ ions formed during the one-electron capture and the electron capture with ionization at energies of 2.2, 5.4, and 30 keV have been determined. The electronic states of the formed ions have been determined using collision spectroscopy based on analysis of the change in the kinetic energy of He+ after the interaction. We have measured doubly differential (with respect to the kinetic energy and the scattering angle) cross sections of the formation of free electrons. The free electron formation channels (direct ionization and electron capture with ionization) have been analyzed by calculating the electron terms of the (HeAr)2+ system. The calculated cross section of capture with ionization is in conformity with the cross section measured using collision spectroscopy.

Crystal Defect Analysis of Latent Scratch Induced during CMP Process on 4H-SiC Wafer Using Electron Microscopy

The dislocation analysis of latent scratch induced chemical mechanical polishing process on 4H-silicon carbide (SiC) using the multi directional scanning transmission electron microscopy (STEM) method and elastic stain measurement were performed. A scanning electron microscope image shows that a latent scratch extended toward the [30] direction and the width is about 50 nm. Cross sectional STEM images shows that the depth of latent scratch due to distortion is about 20 nm. From the result of plan view STEM observation along [000] direction, it was observed that a latent scratch had two defect lines toward the [30] direction, which were a loop type on upper side and a linear type on the lower side. The Burgers vector of each defect have a component in basal plane. Elastic strain mapping was performed using transmission electron microscope equipped with a procession diffraction system. Inside the latent scratch indicates stain-free field, however around latent scratch indicates compressive strain field. About 1.5 % compressive strain field x, y direction and shear strain along latent scratch exists on typical area. As a results of STEM and elastic strain analysis, the atomic arrangement in basal plane seems to be related with the compressive strain around latent scratch.

High-order above-threshold photoemission from nanotips controlled with two-color laser fields

We investigate the process of phase-controlled high-order above-threshold photoemission from metallic nanotips under bichromatic laser fields. Experimental photoelectron spectra resulting from two-color excitation with a moderately intense near-infrared fundamental field (1560 nm) and its weak second harmonic show a strong sensitivity on the relative phase and clear indications for a plateau-like structure that is attributed to elastic backscattering. To explore the relevant control mechanisms, characteristic features, and particular signatures from the near-field inhomogeneity, we performed systematic quantum simulations employing a one-dimensional nanotip model. Besides rich phase-dependent structures in the simulated above-threshold ionization photoelectron spectra we find ponderomotive shifts as well as substantial modifications of the rescattering cutoff as function of the decay length of the near-field. To explore the quantum or classical nature of the observed features and to discriminate the two-color effects stemming from electron propagation and from the ionization rate we compare the quantum results to classical trajectory simulations. We show that signatures from direct electrons as well as the modulations in the plateau region mainly stem from control of the ionization probability, while the modulation in the cutoff region can only be explained by the impact of the two-color field on the electron trajectory. Despite the complexity of the phase-dependent features that render two-color strong-field photoemission from nanotips intriguing for sub-cycle strong-field control, our findings support that the recollision features in the cutoff region provide a robust and reliable method to calibrate the relative two-color phase.

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer.

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

Investigation into Texture and Structure of MA2-1PCh Magnesium Alloy after Equal Channel Angular Extrusion and Annealing by Quantitative X-Ray Texture Analysis and Electron Backscatter Diffraction

This article discusses application of quantitative X-ray texture analysis (QTXA) based on measurement of direct pole figures and electron backscatter diffraction (EBSD) aimed at study of peculiarities of formation of texture and structure of MA2-1pch magnesium alloy after equal channel angular extrusion (ECAE) and subsequent annealing. Shear bands with the width of 60 μm oriented at 45°–50° to the extrusion direction are revealed, where an inclined scattered basis texture is detected, and outside of these bands, a prismatic texture. As a consequence, basic sliding is activated in the shear bands, which is confirmed by the distribution of Schmid factors. The influence of texture and orientation of shear bands on anisotropy of strength mechanical properties of alloy is discussed.

Velocity map imaging of scattering dynamics in orthogonal two-color fields

In strong-field ionization processes, two-color laser fields are frequently used for controlling sub-cycle electron dynamics via the relative phase of the laser fields. Here we apply this technique to velocity map imaging spectroscopy using an unconventional orientation with the polarization of the ionizing laser field perpendicular to the detector surface and the steering field parallel to it. This geometry allows not only to image the phase-dependent photoelectron momentum distribution (PMD) of low-energy electrons that interact only weakly with the ion (direct electrons), but also to investigate the low yield of higher-energy rescattered electrons. Phase-dependent measurements of the PMD of neon and xenon demonstrate control over direct and rescattered electrons. The results are compared with semi-classical calculations in three dimensions including elastic scattering at different orders of return and with solutions of the three-dimensional time-dependent Schrödinger equation.

Polyquant CT: direct electron and mass density reconstruction from a single polyenergetic source

Quantifying material mass and electron density from computed tomography (CT) reconstructions can be highly valuable in certain medical practices, such as radiation therapy planning. However, uniquely parameterising the x-ray attenuation in terms of mass or electron density is an ill-posed problem when a single polyenergetic source is used with a spectrally indiscriminate detector. Existing approaches to single source polyenergetic modelling often impose consistency with a physical model, such as water-bone or photoelectric-Compton decompositions, which will either require detailed prior segmentation or restrictive energy dependencies, and may require further calibration to the quantity of interest. In this work, we introduce a data centric approach to fitting the attenuation with piecewise-linear functions directly to mass or electron density, and present a segmentation-free statistical reconstruction algorithm for exploiting it, with the same order of complexity as other iterative methods. We show how this allows both higher accuracy in attenuation modelling, and demonstrate its superior quantitative imaging, with numerical chest and metal implant data, and validate it with real cone-beam CT measurements.

Subcritical Water Hydrolysis of Peptides: Amino Acid Side-Chain Modifications

Previously we have shown that subcritical water may be used as an alternative to enzymatic digestion in the proteolysis of proteins for bottom-up proteomics. Subcritical water hydrolysis of proteins was shown to result in protein sequence coverages greater than or equal to that obtained following digestion with trypsin; however, the percentage of peptide spectral matches for the samples treated with trypsin were consistently greater than for those treated with subcritical water. This observation suggests that in addition to cleavage of the peptide bond, subcritical water treatment results in other hydrolysis products, possibly due to modifications of amino acid side chains. Here, a model peptide comprising all common amino acid residues (VQSIKCADFLHYMENPTWGR) and two further model peptides (VCFQYMDRGDR and VQSIKADFLHYENPTWGR) were treated with subcritical water with the aim of probing any induced amino acid side-chain modifications. The hydrolysis products were analyzed by direct infusion electrospray tandem mass spectrometry, either collision-induced dissociation or electron transfer dissociation, and liquid chromatography collision-induced dissociation tandem mass spectrometry. The results show preferential oxidation of cysteine to sulfinic and sulfonic acid, and oxidation of methionine. In the absence of cysteine and methionine, oxidation of tryptophan was observed. In addition, water loss from aspartic acid and C-terminal amidation were observed in harsher subcritical water conditions.Graphical ᅟ

Three Dimensional Dislocation Analysis of Threading Mixed Dislocation Using Multi Directional Scanning Transmission Electron Microscopy

The recently developed multi directional scanning transmission electron microscopy (MD-STEM) technique has been applied to exactly determine the Burgers vector (b) and dislocation vector (u) of a threading mixed dislocation in a silicon carbide (SiC) as-epitaxial wafer. This technique utilizes repeated focused ion beam (FIB) milling and STEM observation of the same dislocation from three orthogonal directions (cross-section, plan-view, cross-section). Cross section STEM observation in the [1-100] viewing direction showed that the burgers vector have a and c components. Subsequent plan view STEM observation in the [000-1] direction indicated that the b=[u -2uuw] (u≠0 and w≠0). Final cross section STEM observation in the [11-20] direction confirmed that the dislocation was an extended dislocation, with the Burgers vector experimentally found to be b = [1-210]a/3 + [0001]c which decomposes into two partial dislocations of bp1 = [0-110]a/3 + [0001]c/2 and bp2 = [1-100]a/3 + [0001]c/2. The dislocation vector u is [-12-10]a/3 + [0001]c. This technique is an effective method to analyze the dislocation characteristics of power electronics devices.

Biogeochemistry of methanogenesis with a specific emphasis on the mineral-facilitating effects

The Earth surface contains various oxic and anoxic environments. The later include natural wetlands, river and lake sediments, paddy field soils and landfills. In the last few decades, the biogeochemical cycle of carbon in anoxic environments, which leads to the production and emission of methane, a potent greenhouse gas in the atmosphere, has drawn great attentions from both scientific and public sectors. New organisms and mechanisms involved in methanogenesis and carbon cycling have been uncovered. Interspecies electron transfer is considered as a crucial step in methanogenesis in anoxic environments. Electron-carrying mediators, like H2 and formate, are known to play the key role in electron transfer. Recently, it has been found that in addition to the conventional electron transfer via chemical mediators, direct interspecies electron transfer (DIET) can occur. In this Review, we describe the ecology and biogeochemistry of methanogenesis and highlight the effect of microbe-mineral interaction on microbial syntrophy. Recent advances in the study of DIET may pave the way towards a mechanistic understanding of methanogenesis and the influence of microbe-mineral interaction on this process.

Analysis of proton and electron spectra observed by EPT/PROBA-V in the South Atlantic Anomaly

Proton and electron spectra observed by the Energetic Particle Telescope (EPT) on board the ESA satellite PROBA-V have been investigated at different locations in the South Atlantic Anomaly (SAA). The EPT spectrometer provides high-resolution measurements of the charged particle radiation environment in space performing with direct electron, proton and heavy ion discrimination. Dividing the SAA into 5 different bins of 5°×5° each one for protons, we obtain that the average proton spectra have often similar slopes, but greatly differ from one location to another. The highest fluxes are generally located in the North of the SAA. For some energy ranges and time periods, the South of the SAA shows different shapes, indicating different sources for the North and South populations of the SAA. Electron spectra show very low fluxes of energetic electrons, often lower than what is provided by the model AE8.

Phenothiazine dyes photosensitize protein damage through electron transfer and singlet oxygen generation

Photosensitized protein damage is an important process in medical applications of photochemical reaction, such as photodynamic therapy. A similar method has been applied to photodynamic antimicrobial chemotherapy (PACT), which can treat sinusitis and periodontal disease. For example, methylene blue is used as a photosensitizer for PACT. However, the mechanism of PACT has not been clarified completely. In this study, protein damage photosensitized by methylene blue and its analogues was examined. The scavenger effect on protein photodamage by dyes and fluorescence measurements suggests the contribution of the electron transfer mechanism to this photosensitized protein damage as the singlet oxygen generation mechanism. The quantum yields of protein damage by these photosensitizers could be determined. The electron transfer mechanism is the direct electron abstraction from the biomolecule to the photoexcited photosensitizer. Because this mechanism does not necessarily require oxygen in vivo, the mechanism of PACT, such as in sinusitis treatment by methylene blue under a hypoxic condition, might be explained by the electron transfer.

Carbon nano-onion composites: Physicochemical characteristics and biological activity

ABSTRACTCarbon nano-onion/surfactant (CNO/surfactant) composites offer the possibility to easily produce the soluble nanostructures. That approach combines the hydrophilicity of surfactants with the robustness of carbon structures to produce composites with superior and unusual physicochemical properties. We used the following surfactants: hexadecyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS), 4-(1,1,3,3-tetramethylbutyl)phenyl-polyethylene glycol (Triton X-100), and polyethylene glycol sorbitan monolaurate (Tween 20) to non-covalently modify CNO surfaces. The existence of stable CNO composites are clearly evidenced by direct transmission electron microscopy observations, which are also supported by thermogravimetric analyses. Dynamic light scattering and zeta potential confirmed their dispersion and stability. Additionally, the biological activity of well-dispersed CNO/surfactant composites against a strain of Escherichia coli was assayed. In vitro antimicrobial assays for the composites revealed that only the CNO/CTAB composite decreased cell viability. This activity could be assigned to the simple composite dissociation in water solutions, however antimicrobial properties of the composite are slightly better when compared with pure CTAB. This indicate some synergic effect with respect to the properties of the pure surfactant.