Abstract: The interest in 2-dimensional systems with a honeycomb lattice and related Dirac-­type electronic bands has exceeded the prototype graphene1. Currently, 2-­dimensional atomic2,3 and nanoscale4-­8 systems are extensively investigated in the search for materials with novel electronic properties that can be tailored by geometry. The immediate question that arises is how to fabricate 2-­D semiconductors that have a honeycomb nanogeometry, and as a consequence of that, display a Dirac-­type band structure? Here, we show that atomically coherent honeycomb superlattices of rocksalt (PbSe, PbTe) and zincblende (CdSe, CdTe) semiconductors can be obtained by nanocrystal self-­assembly and facet-­to-­facet atomic bonding, and subsequent cation exchange. We present a extended structural analysis of atomically coherent 2-­D honeycomb structures that were recently obtained with self-assembly and facet-­to-­facet bonding9. We show that this process may in principle lead to three different types of honeycomb structures, one with a graphene type-­, and two others with a silicene-­type structure. Using TEM, electron diffraction, STM and GISAXS it is convincingly shown that the structures are from the silicene-­type. In the second part of this work, we describe the electronic structure of graphene-­type and silicene type honeycomb semiconductors. We present the results of advanced electronic structure calculations using the sp3d5s* atomistic tight-­binding method10. For simplicity, we focus on semiconductors with a simple and single conduction band for the native bulk semiconductor. When the 3-­D geometry is changed into 2-­D honeycomb, a conduction band structure transformation to two types of Dirac cones, one for S-­ and one for P-­orbitals, is observed. The width of the bands depends on the honeycomb period and the coupling between the nanocrystals. Furthermore, there is a dispersionless P-­orbital band, which also forms a landmark of the honeycomb structure. The effects of considerable intrinsic spin-­orbit coupling are briefly considered. For heavy-­element compounds such as CdTe, strong intrinsic spin-­‐orbit coupling opens a non-­trivial gap at the P-­orbital Dirac point, leading to a quantum Spin Hall effect10-­12. Our work shows that well known semiconductor crystals, known for centuries, can lead to systems with entirely new electronic properties, by the simple action of nanogeometry. It can be foreseen that such structures will play a key role in future opto-­electronic applications, provided that they can be fabricated in a straightforward way.

Abstract: Structure, morphology and composition of different tin oxide and germanium oxide thin film catalysts for the methanol steam reforming (MSR) reaction have been studied by a combination of (high-resolution) transmission electron microscopy, selected area electron diffraction, dark-field imaging and electron energy-loss spectroscopy. Deposition of the thin films on NaCl(0 0 1) cleavage faces has been carried out by thermal evaporation of the respective SnO2 and GeO2 powders in varying oxygen partial pressures and at different substrate temperatures. Preparation of tin oxide films in high oxygen pressures (10−1 Pa) exclusively resulted in SnO phases, at and above 473 K substrate temperature epitaxial growth of SnO on NaCl(0 0 1) leads to well-ordered films. For lower oxygen partial pressures (10−3 to 10−2 Pa), mixtures of SnO and β-Sn are obtained. Well-ordered SnO2 films, as verified by electron diffraction patterns and energy-loss spectra, are only obtained after post-oxidation of SnO films at temperatures T ≥ 673 K in 105 Pa O2. Preparation of GeOx films inevitably results in amorphous films with a composition close to GeO2, which cannot be crystallized by annealing treatments in oxygen or hydrogen at temperatures comparable to SnO/SnO2. Similarities and differences to neighbouring oxides relevant for selective MSR in the third group of the periodic system (In2O3 and Ga2O3) are also discussed with the aim of cross-correlation in formation of nanomaterials, and ultimately, also catalytic properties.

Abstract: Purple non-sulfur bacteria (PNSB) are known for their metabolic versatility and thrive as anoxygenic photoheterotrophs. In environmental engineering and resource recovery, cells would grow on mixtures of volatile fatty acids (VFA) generated by anaerobic fermentation of waste streams. In this study, we aim to better understand the behavior of Rhodospirillum rubrum, a model PNSB species, grown using multiple VFA as carbon sources. We highlighted that assimilation of individual VFA follows a sequential pattern. Based on observations in other PNSB, this seems to be specific to isocitrate lyase-lacking organisms. We hypothesized that the inhibition phenomenon could be due to the regulation of the metabolic fluxes in the substrate cycle between acetoacetyl-CoA and crotonyl-CoA. Developed macroscopic dynamic models showed a good predictive capability for substrate competition for every VFA mixture containing acetate, propionate, and/or butyrate. These novel insights provide valuable input for better design and operation of PNSB-based waste treatment solutions.

Abstract: Topological semimetal phases in two-dimensional (2D) materials have gained widespread interest due to their potential applications in novel nanoscale devices. Despite the growing number of studies on 2D topological nodal lines (NLs), candidates with significant topological features that combine nontrivial topological semimetal phase with superconductivity are still rare. Herein, we predict Al2B2 and AlB4 monolayers as new 2D nonmagnetic Dirac nodal line semimetals with several novel features. Our extensive electronic structure calculations combined with analytical studies reveal that, in addition to multiple Dirac points, these 2D configurations host various highly dispersed NLs around the Fermi level, all of which are semimetal states protected by time-reversal and in-plane mirror symmetries. The most intriguing NL in Al2B2 encloses the K point and crosses the Fermi level, showing a considerable dispersion and thus providing a fresh playground to explore exotic properties in dispersive Dirac nodal lines. More strikingly, for the AlB4 monolayer, we provide the first evidence for a set of 2D nonmagnetic open type-II NLs coexisting with superconductivity at a rather high transition temperature. The coexistence of superconductivity and nontrivial band topology in AlB4 not only makes it a promising material to exhibit novel topological superconducting phases, but also a rather large energy dispersion of type-II nodal lines in this configuration may offer a platform for the realization of novel topological features in the 2D limit.

Abstract: By using density functional theory (DFT) based first-principles calculations, electronic, vibrational, piezo-electric, and optical properties of monoclinic Janus single-layer Ga2TeX (X = S or Se) are investigated. The dynamical, mechanical, and thermal stability of the proposed Janus single layers are verified by means of phonon bands, stiffness tensor, and quantum molecular dynamics simulations. The calculated vibrational spectrum reveals the either pure or coupled optical phonon branches arising from Ga-Te and Ga-X atoms. In addition to the in-plane anisotropy, single-layer Janus Ga2TeX exhibits additional out-of-plane asymmetry, which leads to important consequences for its electronic and optical properties. Electronic band dispersions indicate the direct band-gap semiconducting nature of the constructed Janus structures with energy band gaps falling into visible spectrum. Moreover, while orientation-dependent linear-elastic properties of Janus single layers indicate their strong anisotropy, the calculated in-plane stiffness values reveal the ultrasoft nature of the structures. In addition, predicted piezoelectric coefficients show that while there is a strong in-plane anisotropy between piezoelectric constants along armchair (AC) and zigzag (ZZ) directions, there exists a tiny polarization along the out-of-plane direction as a result of the formation of Janus structure. The optical response to electromagnetic radiation has been also analyzed through density functional theory by considering the independent-particle approximation. Finally, the optical spectra of Janus Ga2TeX structures is investigated and it showed a shift from the ultraviolet region to the visible region. The fact that the spectrum is between these regions will allow it to be used in solar energy and many nanoelectronics applications. The predicted monoclinic single-layer Janus Ga2TeX are relevant for promising applications in optoelectronics, optical dichroism, and anisotropic nanoelasticity.

Abstract: Gold-silver alloy nanoparticles display surface plasmon resonance (SPR) over a broad range of the UV-vis spectrum. We propose a model to predict the SPR wavelength of gold-silver alloy colloids based on the combined effect of alloy composition and particle size. The SPR wavelength is derived from extinction spectra simulated using available experimental dielectric constant data and accounts for particle size by applying Mie theory. Comparison of calculated values with experimental data evidences the accuracy of the model. The new SPR wavelength estimation tool will be of particular interest for developing dedicated bimetallic plasmonic nanostructures.

Abstract: In this study we investigate the model uncertainties involved in predicting long-term permeable reactive barrier (PRB) remediation efficiency based on a lab-scale column experiment under accelerated flow conditions. A PRB consisting of 20% iron and 80% sand was simulated in a laboratory-scale column and contaminated groundwater was pumped into the column for approximately 1 year at an average groundwater velocity of 3.7E – 1 m d(-1). Dissolved contaminants (PCE. TCE, cis-DCE, trans-DCE and VC) and inorganic (Ca2+, Fe2+, TIC and pH) concentrations were measured in groundwater sampled at different times and at eight different distances along the column. These measurements were used to calibrate a multi-component reactive transport model, which subsequently provided predictions of long-term PRB efficiency under reduced flow conditions (i.e., groundwater velocity of 1.4E -3 m d(-1)), representative of a field site of interest in this study. Iron reactive surface reduction due to mineral precipitation and iron dissolution was simulated using four different models. All models were able to reasonably well reproduce the column experiment measurements, whereas the extrapolated long-term efficiency under different flow rates was significantly different between the different models. These results highlight significant model uncertainties associated with extrapolating long-term PRB performance based on lab-scale column experiments. These uncertainties should be accounted for at the PRB design phase, and may be reduced by independent experiments and field observations aimed at a better understanding of reactive surface deactivation mechanisms in iron PRBs. (C) 2012 Elsevier B.V. All rights reserved.

Abstract: Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.

Abstract: We measured the electrical resistivity R(T) and specific heat C-p(T) between room temperature (RT) and 4.2 K as well as the microstructure by transmission electron microscopy (TEM) of a Ni-52 Ti-48 SMA quenched from 1000degreesC (B2-Phase range) to RT and then annealed for 1h at T=380degreesC, 550degreesC and 650degreesC. In the “as quenched” and the “650degreesC annealed” state no martensitic transformations (MT's) occur. The diffraction patterns show faint reflections originating from coherent Ni4Ti3 precipitates in an early state of formation. Additional reflections of the type 1/2 <110>, 1/2 <111> and 1/3 <110> result from various lattice displacement waves, which are precursors of the MT's to the B19' and R-phase, respectively. Indeed, high resolution TEM micrographs of the [001] zone of the “as quenched” sample reveal transverse 1/2 <110> <110> lattice displacement waves, precursors of the B19' martensite. The coherent Ni4Ti3 precipitates, homogeneously distributed on a small length scale, binder the MT's in the “as quenched” and the “650degreesC annealed” state, and thus only the precursors appear. When annealed at T=380degreesC, however, coherent Ni4Ti3 precipitates with a length of 10nm are clearly visible in TEM. These precipitates trigger the NIT from the B2 to the R-phase on cooling, as evidenced also by anomalies in R(T) and C-p(T). Annealing at T-550degreesC leads to the well known two step MT's from the B2 to the R-phase and then into the B19'-phase. These martensitic transitions are clearly seen as additional peaks in the specific heat and anomalies in the resistance, while the “as quenched” and 650degreesC annealed samples show weak features in R(T) and C-p(T).