Abstract: Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.

Abstract: MicroRNAs (miRNAs) are small oligonucleotides (18–25 bases), biologically relevant for epigenetic regulation of key processes, particularly in association with cancer. Research effort has therefore been directed towards the monitoring and detection of miRNAs to progress (early) cancer diagnoses. Traditional detection strategies for miRNAs are expensive, with a lengthy time-to-result. In this study we develop an oligonucleotide-based assay using electrochemistry for the specific, selective and sensitive detection of a circulating miRNA (miR-141) associated with prostate cancer. In the assay, the excitation and readout of the signal are independent: an electrochemical stimulation followed by an optical readout. A ‘sandwich’ approach is incorporated, consisting of a biotinylated capture probe immobilised on streptavidin-functionalised surfaces and a detection probe labelled with digoxigenin. We show that the assay allows the detection of miR-141 in human serum, even in the presence of other miRNAs, with a LOD of 0.25 pM. The developed electrochemiluminescent assay has, therefore, the potential for efficient universal oligonucleotide target detection via the redesign of capture and detection probes.

Abstract: The local and long range structure of polycrystalline samples of Bi0.75Sr0.25FeO3-delta has been probed by neutron and synchrotron X-ray diffraction coupled with transmission electron microscopy. It is found that the long range structure on average can be described by the cubic space group Pm-3m (a(p) congruent to 3.951 angstrom). However, the refinements revealed large atomic displacements for the (Bi, Sr) cations and the oxygen atoms from their ideal positions. The electron microscopy study indicates the existence of local phenomena like local ordering of oxygen vacancies, which are segregated at the randomly spaced parallel (FeO2-delta) planes, or the existence of region of different symmetry, probably R3c. At room temperature, the compound exhibits G-type antiferromagnetism (T-N congruent to 650 K) with a magnetic moment of congruent to 3.7 mu(B). (C) 2012 Elsevier Ltd. All rights reserved.

Abstract: By means of density functional theory based first-principles calculations, the structural, vibrational, and electronic properties of 1H- and 1T-phases of single-layer CaX2 (X = F, Cl, Br, or I) structures are investigated. Our results reveal that both the 1H- and 1T-phases are dynamically stable in terms of their phonon band dispersions with the latter being the energetically favorable phase for all single-layers. In both phases of single-layer CaX2 structures, significant phonon softening occurs as the atomic radius increases. In addition, each structural phase exhibits distinctive Raman active modes that enable one to characterize either the phase or the structure via Raman spectroscopy. The electronic band dispersions of single-layer CaX2 structures reveal that all structures are indirect bandgap insulators with a decrease in bandgaps from fluorite to iodide crystals. Furthermore, the calculated linear elastic constants, in-plane stiffness, and Poisson ratio indicate the ultra-soft nature of CaX2 single-layers, which is quite important for their nanoelastic applications. Overall, our study reveals that with their dynamically stable 1T- and 1H-phases, single-layers of CaX2 crystals can be alternative ultra-thin insulators.

Abstract: Nutrient losses in our food chain severely surpass our planetary boundaries. Resource recovery can contribute to mitigation, for instance through converting wastewater resources to microbial protein for animal feed. Wastewater typically holds a complex mixture of organics, posing a challenge to selectively produce heterotrophic biomass. Ensuring the product's quality could be achieved by anaerobic generation of volatile fatty acids (VFAs) followed by photoheterotrophic production of purple non-sulfur bacteria (PNSB) with infrared light. This study aimed to determine the most suitable PNSB culture for VFA conversion and map the effect of acetate, propionate, butyrate and a VFA mixture on growth and biomass yield. Six cultures were screened in batch: (i) Rhodopseudomonas palustris, (ii) Rhodobacter sphaeroides, (iii) Rhodospirillum rubrum, (iv) a 3-species synthetic community (i+ii+iii), (v) a community enriched on VFA holding Rb. capsulatus, and (vi) Rb. capsulatus (isolate v). The VFA mixture elevated growth rates with a factor 1.32.5 compared to individual VFA. Rb. capsulatus showed the highest growth rates: 1.82.2 d−1 (enriched) and 2.33.8 d−1 (isolated). In a photobioreactor (PBR) inoculated with the Rb. capsulatus enrichment, decreasing sludge retention time (SRT) yielded lower biomass concentrations, yet increased productivities, reaching 1.7 g dry weight (DW) L−1 d−1, the highest phototrophic rate reported thus far, and a growth rate of up to 5 d−1. PNSB represented 2657% of the community and the diversity index was low (37), with a dominance of Rhodopseudomonas at long SRT and Rhodobacter at short SRT. The biomass yield for all cultures, in batch and reactor cultivation, approached 1 g CODBiomass g−1 CODRemoved. An economic estimation for a two-stage approach on brewery wastewater (load 2427 kg COD d−1) showed that 0.5 d SRT allowed for the lowest production cost ( 10 kg−1 DW; equal shares for capex and opex). The findings strengthen the potential for a novel two-stage approach for resource recovery from industrial wastewater, enabling high-rate PNSB production.

Abstract: Infrared absorption spectra of oxygen precipitates in boron-doped silicon with a boron concentration between 10(17) and 10(19) cm(-3) are analyzed, applying the spectral function representation of composite materials. The aspect ratio of the platelet precipitates is determined by transmission electron microscopy measurements. The analysis shows that in samples with moderate doping levels (<10(18) B cm(-3)) SiOγ precipitates are formed with the same composition as in the lightly doped case. In the heavily boron-doped (>10(18) cm(-3)) samples, however, the measured spectra of the precipitates are consistent with a mixture of SiO2 and B2O3, with a volume fraction of B2O3 as high as 0.41 in the most heavily doped case. (C) 2004 The Electrochemical Society.

Abstract: In this paper we explore the desirability of a transmission electron microscope in which the phase of the electron wave can be freely controlled. We discuss different existing methods to manipulate the phase of the electron wave and their limitations. We show how with the help of current techniques the electron wave can already be crafted into specific classes of waves each having their own peculiar properties. Assuming a versatile phase modulation device is feasible, we explore possible benefits and methods that could come into existence borrowing from light optics where the so-called spatial light modulators provide programmable phase plates for quite some time now. We demonstrate that a fully controllable phase plate building on Harald Rose׳s legacy in aberration correction and electron optics in general would open an exciting field of research and applications.

Abstract: Electrochemistry offers highly flexible routes to fabrication of a wide variety of mesostructures, including three-dimensional (3D) crystallites, thin films and nanowires. Using this method we have grown various 3D superconducting Pb mesostructures with vastly different morphologies. We present here results on a truncated(half)-icosahedron with a hexagonal base and a tripod structure with a triangular base. Using Hall probe magnetometry we have obtained magnetisation curves for these structures at several temperatures and see evidence of geometry-driven flux entry and exit as well as flux trapping caused by specific sample geometries. We also observe behaviour that we interpret in terms of the formation of giant vortices, bearing in mind that bulk Pb is a type-I superconducting material.

Abstract: The magnetic-field dependence of the energy spectrum of GaAs doped with nitrogen impurities is investigated. Our theoretical model is based on the phenomenological band anticrossing model (BAC) which we extended in order to include the magnetic field and electronphonon interaction. Due to the highly localized nature of the nitrogen state, we find that the energy levels are very different from those of pure GaAs. The polaron correction results in a lower cyclotron resonance energy as compared to pure GaAs. The magneto-absorption spectrum exhibits series of asymmetric peaks close to the cyclotron energy ħωc.

Abstract: Since Ehrenfests theorem, the role and importance of classical paths in quantum dynamics have been examined by several means. Along this line, we show that the classical equations of motion provide a solution to quantum dynamics, if appropriately incorporated into the Wigner distribution function, exactly reformulated in a type of Boltzmann equation. Also the quantum-mechanical features of the canonical ensemble can be studied in this framework of Newtonian dynamics, if the initial distribution function is appropriately constructed from the statistical operator.

Abstract: We have used high resolution Hall probe microscopy to image vortex-antivortex (V-AV) 'molecules' induced in superconducting Pb films by the stray fields from square arrays of ferromagnetic Co/Pt dots. We have directly observed spontaneous V-AV pairs and studied how they interact with added 'free' (anti)fluxons in an applied magnetic field. We observe a rich variety of subtle phenomena arising from competing symmetries in our system which can either drive added antivortices to join AV shells around nanomagnets or stabilise the translationally symmetric AV lattice between the dots. Added vortices annihilate AV shells, leading eventually to a stable 'nulling' state with no free fluxons, which should exhibit a strongly (field-)enhanced critical current. At higher densities we actually observe vortex shells around the magnets, stabilised by the asymmetric anti-pinning potential. Our experimental findings are in good agreement with Ginzburg-Landau calculations.