Abstract: Purple non-sulphur bacteria (PNSB) are an emerging group of microbes attractive for applied microbiology applications such as wastewater treatment, plant biostimulants, microbial protein, polyhydroxyalkanoates and H-2 production. These photoorganoheterotrophic microbes have the unique ability to grow selectively on organic carbon in anaerobic photobioreactors. This so-called selectivity implies that the microbial community will have a low diversity and a high abundance of a particular PNSB species. Recently, it has been shown that certain PNSB strains can produce antimicrobials, yet it remains unclear whether these contribute to competitive inhibition. This research aimed to understand which type of antimicrobial PNSB produce and identify whether these compounds contribute to their selective growth. Mining 166 publicly-available PNSB genomes using the computational tool BAGEL showed that 59% contained antimicrobial encoding regions, more specifically biosynthetic clusters of bacteriocins and non-ribosomal peptide synthetases. Inter- and intra-species inhibition was observed in agar spot assays for Rhodobacter blasticus EBR2 and Rhodopseudomonas palustris EBE1 with inhibition zones of, respectively, 5.1 and 1.5-5.7 mm. Peptidomic analysis detected a peptide fragment in the supernatant (SVLQLLR) that had a 100% percentage identity match with a known non-ribosomal peptide synthetase with antimicrobial activity.

Abstract: The number of agricultural cooperatives increased quickly in Ethiopia since the 1990s. While many papers studied the impact of membership of Ethiopian cooperatives, not much is known on their performance. This study takes a cooperative-level perspective which is unique in an African context. It compares the economic performance proxied by sales revenue and profit of a wide range of agricultural cooperatives in northern Ethiopia. Data were collected from 511 agricultural cooperatives in 12 districts of Tigray. The contributing factors of the performance are analyzed with Ordinary Least Squares regression (OLS) and Heckman selection models. Our results underscore the importance of membership size, total assets, presence of conflict among members, and union membership. Chairperson characteristics and the internal organization of a cooperative seem to be less correlated to performance.

Abstract: In situ irradiation experiments in a high resolution electron microscope JEOL-4000EX at room temperature resulted in discovery of the isolated and combined clustering of vacancies and self-interstitial atoms on {111}- and {113}-habit planes both leading to an extended defect formation in Si crystals. The type of the defect is strongly affected by the type of supersaturation of point defects depending on the crystal thickness during electron irradiation. Because of the existence of energy barriers against recombination of interstitials with the extended aggregates of vacancies, a large family of intermediate defect configurations (IDCs) is formed on {113}- and {111}-habit planes at a low temperature under interstitial supersaturation in addition to the well-known {133}-defects of interstitial type. The formation of metastable IDCs inside vacancy aggregates prevents a way of recombination of defects in extended shape.

Abstract: Based on the Gor'kov formalism for a clean s-wave superconductor, we develop an extended version of the single-band Ginzburg-Landau (GL) theory by means of a systematic expansion in the deviation from the critical temperature T(c), i.e., tau = 1 – T/T(c). We calculate different contributions to the order parameter and the magnetic field: the leading contributions (proportional to tau(1/2) in the order parameter and. t in the magnetic field) are controlled by the standard GL theory, while the next-to-leading terms (proportional to tau(3/2) in the gap and proportional to tau(2) in the magnetic field) constitute the extended GL (EGL) approach. We derive the free-energy functional for the extended formalism and the corresponding expression for the current density. To illustrate the usefulness of our formalism, we calculate, in a semianalytical form, the temperature-dependent correction to the GL parameter at which the surface energy becomes zero, and analytically, the temperature dependence of the thermodynamic critical field. We demonstrate that the EGL formalism is not just a mathematical extension to the theory: variations of both the gap and the thermodynamic critical field with temperature calculated within the EGL theory are found in very good agreement with the full BCS results down to low temperatures, which dramatically improves the applicability of the formalism compared to its standard predecessor.

Abstract: Apart from the most studied tin-oxide compounds, SnO and SnO2, intermediate states have been claimed to exist for more than a hundred years. In addition to the known homologous series (Seko et al., Phys. Rev. Lett. 100, 045702 (2008)), we here predict the existence of several new compounds with an O concentration between 50 % (SnO) and 67 % (SnO2). All these intermediate compounds are constructed from removing one or more (101) oxygen layers of SnO2. Since the van der Waals (vdW) interaction is known to be important for the Sn-Sn interlayer distances, we use a vdW-corrected functional, and compare these results with results obtained with PBE and hybrid functionals. We present the electronic properties of the intermediate structures and we observe a decrease of the band gap when (i) the O concentration increases and (ii) more SnO-like units are present for a given concentration. The contribution of the different atoms to the valence and conduction band is also investigated.

Abstract: We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.

Abstract: In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the ul-component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets.

Abstract: The existing River Water Quality Model No. 1 (RWQM1) was extended with processes determining the fate of non-volatile pesticides in the water phase and sediments. The exchange of pesticides between the water column and the sediment is described by three transport processes: diffusion, sedimentation and resuspension. Burial of sediments is also included. The modified model was used to simulate the concentrations of diuron and chloridazon in the river Nil. A good agreement was found between the simulated pesticide concentrations and measured values resulting from a four-month intensive monitoring campaign. The simulation results indicate that pesticide concentrations in the bulk water are not sensitive to the selected biochemical model parameters. it seems that these concentrations are mainly determined by the imposed upstream concentrations, run-off and direct losses. The high concentrations in the bulk water were not observed in the sediment pore water due to a limited exchange between the water column and the sediment. According to a sensitivity analysis, the observed pesticide concentrations are highly sensitive to the diffusion and sorption coefficients. Therefore, model users should determine these parameters with accuracy in order to reduce the degree of uncertainty in their results.

Abstract: We investigate the emergence of extra Dirac points in the electronic structure of a periodically spaced barrier system, i.e., a superlattice, on single-layer graphene, using a Dirac-type Hamiltonian. Using square barriers allows us to find analytic expressions for the occurrence and location of these new Dirac points in k space and for the renormalization of the electron velocity near them in the low-energy range. In the general case of unequal barrier and well widths the new Dirac points move away from the Fermi level and for given heights of the potential barriers there is a minimum and maximum barrier width outside of which the new Dirac points disappear. The effect of these extra Dirac points on the density of states and on the conductivity is investigated.

Abstract: Chiroptically active, hierarchically structured materials are difficult to accurately characterize due to linear anisotropic contributions (i.e., linear dichroism (LD) and linear birefringence (LB)) and parasitic ellipticities that produce artifactual circular dichroism (CD) signals, in addition to chiral analyte contributions ranging from molecular-scale clusters to micron-sized assemblies. Recently, we have shown that CdS magic-sized clusters (MSC) can self-assemble into ordered films that have a hierarchical structure spanning seven orders of length-scale. These films have a strong CD response, but the chiral origins are obfuscated by the hierarchical architecture and LDLB contributions. Here, we derive and demonstrate a method for extracting the “pure” CD signal (CD generated by structural dissymmetry) from hierarchical MSC films and identified the chiral origin. The theory behind the method is derived using Mueller matrix and Stokes vector conventions and verified experimentally before being applied to hierarchical MSC and nanoparticle films with varying macroscopic orderings. Each film's extracted “true CD” shares a bisignate profile aligned with the exciton peak, indicating the assemblies adopt a chiral arrangement and form an exciton coupled system. Interestingly, the linearly aligned MSC film possesses one of the highest g-factors (0.05) among semiconducting nanostructures reported. Additionally, we find that films with similar electronic transition dipole alignment can possess greatly different g-factors, indicating chirality change rather than anisotropy is the cause of the difference in the CD signal. The difference in g-factor is controllable via film evaporation geometry. This study provides a simple means to measure “true” CD and presents an example of experimentally understanding chiroptic interactions in hierarchical nanostructures.

Abstract: Thermal expansion behavior of two-dimensional (2D) nitrides and graphene were studied by ab initio molecular dynamics (MD) simulations as well as quasiharmonic approximation (QHA). Anharmonicity of the acoustic phonon modes are related to the unusual negative thermal expansion (NTE) behavior of the nitrides. Our results also hint that direct ab initio MD simulations are a more elaborate method to investigate thermal expansion behavior of 2D materials than the QHA. Nevertheless, giant NTE coefficients are found for h-GaN and h-AlN within the covered temperature range 100-600 K regardless of the chosen computational method. This unusual NTE of 2D nitrides is reasoned with the out-of-plane oscillations related to the rippling behavior of the monolayers.

Abstract: p-Type Co3O4 nanostructured films are synthesized by a plasma-assisted process and tested in the photocatalytic production of H2 from water/ethanol solutions under both near-UV and solar irradiation. It is demonstrated that the introduction of fluorine into p-type Co3O4 results in a remarkable performance improvement with respect to the corresponding undoped oxide, highlighting F-doped Co3O4 films as highly promising systems for hydrogen generation. Notably, the obtained yields were among the best ever reported for similar semiconductor-based photocatalytic processes.

Abstract: A functionally graded multilayer NiTi thin film was deposited on a SiO2/Si substrate by d.c. sputtering using a ramped heated NiTi alloy target. The stand-alone films were crystallized at 500°C in vacuum better than 10-7 Torr. Transmission electron microscopy micrographs taken along the film cross section show two distinct regions, thin and thick, with weak R and B2 phases, respectively. The film compositions along the thickness were measured and quantified using the standard-less EELSMODEL method. The film deposited during the initial thermal ramp (thin regions) displays an average of 54 at.% Ni while the film deposited at a more elevated target temperature (thick regions) shows about 51 at.% Ni.