Abstract: We have used differential magneto-optical (MO) imaging to investigate the mixed state of superconducting Bi2Sr2CaCu2O8+ (BSCCO) microdisks fabricated on a single-crystal sample. MO difference images of the stray field distribution over a range of out-of-plane fields allow us to distinguish between flux that is penetrating the disks and that entering the underlying BSCCO platelet. We find that flux preferentially flows along linear defects into the interstitial platelet regions up to a characteristic field Hp, above which flux enters the disks. We identify this as the field of first penetration of pancake vortices over the Bean-Livingston barrier around the disks, where Hp(T) at intermediate temperatures is well described by an exponentially decaying function with a characteristic temperature T0=19 K. At a given temperature, a minority of the disks exhibit a lower penetration field and we correlate the location of these disks with the linear defects in the BSCCO crystal.

Abstract: Density-functional tight-binding and classical molecular dynamics simulations are used to investigate the structural deformations and melting of planar carbon nanoclusters C-N with N = 2-55. The minimum-energy configurations for different clusters are used as starting configurations for the study of the temperature effects on the bond breaking and rotation in carbon lines (N < 6), carbon rings (5 < N < 19), and graphene nanoflakes. The larger the rings (graphene nanoflakes) the higher the transition temperature (melting point) with ring-to-line (perfect-to-defective) transition structures. The melting point was obtained by using the bond energy, the Lindemann criteria, and the specific heat. We found that hydrogen-passivated graphene nanoflakes (CNHM) have a larger melting temperature with a much smaller dependence on size. The edges in the graphene nanoflakes exhibit several different metastable configurations (isomers) during heating before melting occurs. DOI: 10.1103/PhysRevB.87.134103

Abstract: Combining the local spin density approximation (LSDA)+U and an analysis of superexchange interactions beyond density functional theory, we describe the magnetic ground state of Cr-doped TiO2, an intensively studied and debated dilute magnetic oxide. In parallel, we correct our LSDA+U (+ superexchange) ground state through GW corrections (GW@LSDA+U) that reproduce the position of the impurity states and the band gaps in satisfying agreement with experiments. Because of the different topological coordinations of Cr-Cr bonds in the ground states of rutile and anatase, superexchange interactions induce either ferromagnetic or antiferromagnetic couplings of Cr ions. In Cr-doped anatase, this interaction leads to a new mechanism which stabilizes a (nonrobust) ferromagnetic ground state, in keeping with experimental evidence, without the need to invoke F-center exchange. The interplay between structural defects and vacancies in contributing to the superexchange is also unveiled.

Abstract: Using advanced three-dimensional simulations, we show that an Abrikosov vortex, trapped inside a cavity perpendicular to an artificial Josephson junction, can serve as a very efficient source for generation of Josephson vortex-antivortex pairs in the presence of the applied electric current. In such a case, the nucleation rate of the pairs can be tuned in a broad range by an out-of-plane ac magnetic field in a broad range of frequencies. This parametrically amplified vortex-antivortex nucleation can be considered as a macroscopic analog of the dynamic Casimir effect, where fluxon pairs mimic the photons and the ac magnetic field plays the role of the oscillating mirrors. The emerging vortex pairs in our system can be detected by the pronounced features in the measured voltage characteristics, or through the emitted electromagnetic radiation, and exhibit resonant dynamics with respect to the frequency of the applied magnetic field. Reported tunability of the Josephson oscillations can be useful for developing high-frequency emission devices.

Abstract: Monte Carlo (MC) methods have a long-standing history as partners of molecular dynamics (MD) to simulate the evolution of materials at the atomic scale. Among these techniques, the uniform-acceptance force-bias Monte Carlo (UFMC) method [ G. Dereli Mol. Simul. 8 351 (1992)] has recently attracted attention [ M. Timonova et al. Phys. Rev. B 81 144107 (2010)] thanks to its apparent capacity of being able to simulate physical processes in a reduced number of iterations compared to classical MD methods. The origin of this efficiency remains, however, unclear. In this work we derive a UFMC method starting from basic thermodynamic principles, which leads to an intuitive and unambiguous formalism. The approach includes a statistically relevant time step per Monte Carlo iteration, showing a significant speed-up compared to MD simulations. This time-stamped force-bias Monte Carlo (tfMC) formalism is tested on both simple one-dimensional and three-dimensional systems. Both test-cases give excellent results in agreement with analytical solutions and literature reports. The inclusion of a time scale, the simplicity of the method, and the enhancement of the time step compared to classical MD methods make this method very appealing for studying the dynamics of many-particle systems.

Abstract: A number of recent computational material design studies based on density functional theory (DFT) calculations have put forward a new class of materials with electrically switchable chemical characteristics that can be exploited in the development of tunable gas storage and electrocatalytic applications. We find systematic flaws in almost every computational study of gas adsorption on polarized or charged surfaces, stemming from an improper and unreproducible treatment of periodicity, leading to very large errors of up to 3 eV in some cases. Two simple corrective procedures that lead to consistent results are proposed, constituting a crucial course correction to the research in the field.

Abstract: Herein we demonstrate that meticulous and in-depth analysis of the reaction mechanisms of nanoparticle formation is rewarded by full control of size, shape and crystal structure of superparamagnetic iron oxide nanocrystals during synthesis. Starting from two iron sources – iron(II)- and iron(III) carbonate -a strict separation of oleate formation from the generation of reactive pyrolysis products and concomitant nucleation of iron oxide nanoparticles was achieved. This protocol enabled us to analyze each step of nanoparticle formation independently in depth. Progress of the entire reaction was monitored via matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and gas chromatography (GC) gaining insight into the formation of various iron oleate species prior to nucleation. Interestingly, due to the intrinsic strongly reductive pyrolysis conditions of the oleate intermediates and redox process in early stages of the synthesis, pristine iron oxide nuclei were composed exclusively from wustite, irrespective of the oxidation state of the iron source. Controlling the reaction conditions provided a very broad range of size- and shape defined monodisperse iron oxide nanoparticles. Curiously, after nucleation star shaped nanocrystals were obtained, which underwent metamorphism towards cubic shaped particles. EELS tomography revealed ex post oxidation of the primary wustite nanocrystal providing a full 3D image of Fe2+ and Fe3+ distribution within. Overall, we developed a highly flexible synthesis, yielding multigram amounts of well-defined iron oxide nanocrystals of different sizes and morphologies.

Abstract: Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.

Abstract: Plasma is gaining interest for CH4 conversion into higher hydrocarbons and H2. However, the performance in terms of conversion and selectivity toward different hydrocarbons is different for different plasma types, and the underlying mechanisms are not yet fully understood. Therefore, we study here these mechanisms in different plasma sources, by means of a chemical kinetics model. The model is first validated by comparing the calculated conversions and hydrocarbon/H2 selectivities with experimental results in these different plasma types and over a wide range of specific energy input (SEI) values. Our model predicts that vibrational−translational nonequilibrium is negligible in all CH4 plasmas investigated, and instead, thermal conversion is important. Higher gas temperatures also lead to a more selective production of unsaturated hydrocarbons (mainly C2H2) due to neutral dissociation of CH4 and subsequent dehydrogenation processes, while three-body recombination reactions into saturated hydrocarbons (mainly C2H6, but also higher hydrocarbons) are dominant in low temperature plasmas.

Abstract: By using density functional theory (DFT) calculations, we predict a puckered, dynamically stable Janus single-layer black arsenic-phosphorus (b-AsP), which is composed of two different atomic sublayers, arsenic and phosphorus atoms. The calculated phonon spectrum reveals that Janus single-layer b-AsP is dynamically stable with either pure or coupled optical phonon branches arising from As and P atoms. The calculated Raman spectrum indicates that due to the relatively strong P-P bonds, As atoms have no contribution to the highfrequency optical vibrations. In addition, the orientation-dependent isovolume heat capacity reveals anisotropic contributions of LA and TA phonon branches to the low-temperature thermal properties. Unlike pristine single layers of b-As and b-P, Janus single-layer b-AsP exhibits additional out-of-plane asymmetry which leads to important consequences for its electronic, optical, and elastic properties. In contrast to single-layer b-As, Janus single-layer b-AsP is found to possess a direct band gap dominated by the P atoms. Moreover, real and imaginary parts of the dynamical dielectric function, including excitonic effects, reveal the highly anisotropic optical feature of the Janus single-layer. A tight-binding (TB) model is also presented for Janus single-layer b-AsP, and it is shown that, with up to seven nearest hoppings, the TB model reproduces well the DFT band structure in the low-energy region around the band gap. This TB model can be used in combination with the Green's function approach to study, e.g., quantum transport in finite systems based on Janus single-layer b-AsP. Furthermore, the linear-elastic properties of Janus single-layer b-AsP are investigated, and the orientation-dependent in-plane stiffness and Poisson ratio are calculated. It is found that the Janus single layer exhibits strong in-plane anisotropy in its Poisson ratio much larger than that of single-layer b-P. This Janus single layer is relevant for promising applications in optical dichroism and anisotropic nanoelasticity.