Abstract: We present a computational imaging mode for large scale electron microscopy data, which retrieves a complex wave from noisy/sparse intensity recordings using a deep learning approach and subsequently reconstructs an image of the specimen from the Convolutional Neural Network (CNN) predicted exit waves. We demonstrate that an appropriate forward model in combination with open data frameworks can be used to generate large synthetic datasets for training. In combination with augmenting the data with Poisson noise corresponding to varying dose-values, we effectively eliminate overfitting issues. The U-NET[1] based architecture of the CNN is adapted to the task at hand and performs well while maintaining a relatively small size and fast performance. The validity of the approach is confirmed by comparing the reconstruction to well-established methods using simulated, as well as real electron microscopy data. The proposed method is shown to be effective particularly in the low dose range, evident by strong suppression of noise, good spatial resolution, and sensitivity to different atom types, enabling the simultaneous visualisation of light and heavy elements and making different atomic species distinguishable. Since the method acts on a very local scale and is comparatively fast it bears the potential to be used for near-real-time reconstruction during data acquisition.

Abstract: We present a combined study of experimental and computational work for a dielectric barrier discharge (DBD) used for CH4 conversion into H2. More specifically, we investigated the influence of N2 as an impurity (150,000 ppm) and as additive gas (199%) on the CH4 conversion and H2 yield. For this purpose, a zero-dimensional chemical kinetics model is applied to study the plasma chemistry. The calculated conversions and yields for various gas mixing ratios are compared to the obtained experimental values, and good agreement is achieved. The study reveals the significance of the View the MathML source and View the MathML source metastable states for the CH4 conversion into H2, based on a kinetic analysis of the reaction chemistry.

Abstract: We present a 3D and 2D Cartesian quasi-neutral plasma model for a low current argon gliding arc discharge, including strong interactions between the gas flow and arc plasma column.
The 3D model is applied only for a short time of 0.2 ms due to its huge computational cost. It mainly serves to verify the reliability of the 2D model. As the results in 2D compare well with those in 3D, they can be used for a better understanding of the gliding arc basic characteristics. More specifically, we investigate the back-breakdown phenomenon induced by an artificially controlled plasma channel, and we discuss its effect on the gliding arc characteristics. The
back-breakdown phenomenon, or backward-jump motion of the arc, as observed in the experiments, results in a drop of the gas temperature, as well as in a delay of the arc velocity with respect to the gas flow velocity, allowing more gas to pass through the arc, and thus increasing the efficiency of the gliding arc for gas treatment applications.

Abstract: We predict enhanced electron-hole superfluidity in two coupled electron-hole armchair-edge terminated graphene nanoribbons separated by a thin insulating barrier. In contrast to graphene monolayers, the multiple subbands of the nanoribbons are parabolic at low energy with a gap between the conduction and valence bands, and with lifted valley degeneracy. These properties make screening of the electron-hole interaction much weaker than for coupled electron-hole monolayers, thus boosting the pairing strength and enhancing the superfluid properties. The pairing strength is further boosted by the quasi one-dimensional quantum confinement of the carriers, as well as by the large density of states near the bottom of each subband. The latter magnifies superfluid shape resonances caused by the quantum confinement. Several superfluid partial condensates are present for finite-width nanoribbons with multiple subbands. We find that superfluidity is predominately in the strongly-coupled BEC and BCS-BEC crossover regimes, with large superfluid gaps up to 100 meV and beyond. When the gaps exceed the subband spacing, there is significant mixing of the subbands, a rounding of the shape resonances, and a resulting reduction in the one-dimensional nature of the system.

Abstract: We placed crystals of different compounds to explore the possibility of fingerprinting them through EELS. Here are representative datasets of 7 different compounds: b-cyclodextrin hexacarboxy cyclohexane tannin TH-15 peptide TH-27 peptide two different forms of piroxicam The datasets were collected at EMAT, using a monochromated FEI Titan3 TEM, within the scope of an EUSMI request. More information as well as analysis methodologies adopted for the data are detailed in the paper: Das et al. “Reliable Characterization of Organic & Pharmaceutical Compounds with High Resolution Monochromated EEL Spectroscopy”, Polymers 2020, 12(7), 1434.

Abstract: We performed molecular dynamics simulations to investigate the effect of lipid peroxidation products on the structural and dynamic properties of the cell membrane. Our simulations predict that the lipid order in a phospholipid bilayer, as a model system for the cell membrane, decreases upon addition of lipid peroxidation products. Eventually, when all phospholipids are oxidized, pore formation can occur. This will allow reactive species, such as reactive oxygen and nitrogen species (RONS), to enter the cell and cause oxidative damage to intracellular macromolecules, such as DNA or proteins. On the other hand, upon increasing the cholesterol fraction of lipid bilayers, the cell membrane order increases, eventually reaching a certain threshold, from which cholesterol is able to protect the membrane against pore formation. This finding is crucial for cancer treatment by plasma technology, producing a large number of RONS, as well as for other cancer treatment methods that cause an increase in the concentration of extracellular RONS. Indeed, cancer cells contain less cholesterol than their healthy counterparts. Thus, they will be more vulnerable to the consequences of lipid peroxidation, eventually enabling the penetration of RONS into the interior of the cell, giving rise to oxidative stress, inducing pro-apoptotic factors. This provides, for the first time, molecular level insight why plasma can selectively treat cancer cells, while leaving their healthy counterparts undamaged, as is indeed experimentally demonstrated.

Abstract: We performed ab initio density-functional theory calculations to investigate the process of hydrogenation of a bilayer of graphene. 50% hydrogen coverage is possible in case that the hydrogen atoms are allowed to adsorb on both sides of the bilayer. In this case interlayer chemical bonding occurs which stabilizes the structure. At maximum coverage, a bilayer of graphane is formed which has properties that are similar to those of a single layer of graphane.

Abstract: We performed a molecular dynamics study of vortex-antivortex motion in a superconducting disk with a magnetic dot on top, in the Corbino disk geometry. In this system, vortices and antivortices are forced to move in opposite azimuthal directions by a radially applied current. The dot is magnetized out of plane in order to stabilize composite vortex-antivortex configurations, with vortices closer to the center of the disk and antivortices near to the disk edge. We observe that the interplay between the spatially inhomogeneous current distribution, the screening currents induced by the dipole, and the attractive vortex-antivortex (v-av) interaction result in different dynamical phases. At low current values, antivortices which are distributed at outer rings – remain bounded to vortices at inner rings and the whole configuration rotates rigidly. Above a threshold current, vortices and antivortices unbind and move at different angular velocities in a highly correlated way. Finally, at very strong drive, vortex-antivortex attraction is overhelmed by the external current Lorentz force, causing them to move in opposite directions. (C) 2011 Elsevier B.V. All rights reserved.

Abstract: We perform the wavepacket dynamics simulation of a graphene-based device where propagating electron trajectories are tamed by an applied magnetic field toward a normal/superconductor interface. The magnetic field controls the incidence angle of the incoming electronic wavepacket at the interface, which results in the tunable electron-hole ratio in the reflected wave function due to the angular dependence of the Andreev reflection. Here, mapped control of the quasiparticle trajectories by the external magnetic field not only defines an experimental probe for fundamental studies of the Andreev reflection in graphene but also lays the foundation for further development of magnetic focusing devices based on nanoengineered superconducting two-dimensional materials.

Abstract: We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.

Abstract: We perform first-principles calculations to investigate the preferred positions of B and P dopants, both neutral and in their preferred charge state, in Si and Si/SiO2 core-shell nanowires (NWs). In order to understand the observed trends in the formation energy, we isolate the different effects that determine these formation energies. By making the distinction between the unrelaxed and the relaxed formation energy, we separate the impact of the relaxation from that of the chemical environment. The unrelaxed formation energies are determined by three effects: (i) the effect of strain caused by size mismatch between the dopant and the host atoms, (ii) the local position of the band edges, and (iii) a screening effect. In the case of the SiNW (Si/SiO2 NW), these effects result in an increase of the formation energy away from the center (interface). The effect of relaxation depends on the relative size mismatch between the dopant and host atoms. A large size mismatch causes substantial relaxation that reduces the formation energy considerably, with the relaxation being more pronounced towards the edge of the wires. These effects explain the surface segregation of the B dopants in a SiNW, since the atomic relaxation induces a continuous drop of the formation energy towards the edge. However, for the P dopants, the formation energy starts to rise when moving from the center but drops to a minimum just next to the surface, indicating a different type of behavior. It also explains that the preferential location for B dopants in Si/SiO2 core-shell NWs is inside the oxide shell just next to the interface, whereas the P dopants prefer the positions next to the interface inside the Si core, which is in agreement with recent experiments. These preferred locations have an important impact on the electronic properties of these core-shell NWs. Our simulations indicate the possibility of hole gas formation when B segregates into the oxide shell.

Abstract: We outline a scheme to create a dark state by three-level mixing that is potentially a useful tool for quantum coherent transport. Magnetic-field-induced intra-dot level mixing can lead to rich quantum superposition phenomena between three approaching single-particle states in a quantum dot when probed by the ground state of an adjacent weakly coupled quantum dot in the single-electron resonant tunnelling regime. The mixing relies on non-negligible anharmonicity and anisotropy in confining potentials of realistic quantum dots. Anti-crossing and transfer of strengths between resonances can be understood with a simple coherent level mixing model. Superposition can lead to the formation of a dark state by complete cancellation of an otherwise strong resonance. This is an all-electrical analogue of coherent population trapping seen in three-level-systems from quantum and atom optics.

Abstract: We observe the evolution of single self-assembled semiconductor quantum dots into quantum rings during AsBr3 in situ etching. The direct three-dimensional imaging of In(Ga)As nanostructures embedded in GaAs matrix is demonstrated by selective wet chemical etching combined with atomic force microscopy. Single neutral excitons confined in these quantum rings are studied by magneto-photoluminescence. Oscillations in the exciton radiative recombination energy and in the emission intensity are observed under an applied magnetic field. Further, we demonstrate that the period of the oscillations can be tuned by a gate potential that modifies the exciton confinement. The experimental results, combined with calculations, indicate that the exciton Aharonov-Bohm effect may account for the observed effects.

Abstract: We numerically study the vortex-vortex interaction in multicomponent homogeneous Bose-Einstein condensates within the realm of the Gross-Pitaevskii theory. We provide strong evidence that pairwise vortex interaction captures the underlying mechanisms which determine the geometric configuration of the vortices, such as different lattices in many-vortex states, as well as the bound vortex states with two (dimer) or three (trimer) vortices. Specifically, we discuss and apply our theoretical approach to investigate intra- and intercomponent vortex-vortex interactions in two- and three-component Bose-Einstein condensates, thereby shedding light on the formation of the exotic vortex configurations. These results correlate with current experimental efforts in multicomponent Bose-Einstein condensates and the understanding of the role of vortex interactions in multiband superconductors.

Abstract: We numerically investigate the mixed pairing symmetries inmesoscopic superconducting loops in the presence of spin correlations by solving the Bogoliubov-de Gennes equations self-consistently. The spatial variations of the superconducting order parameters and the spontaneous magnetization are determined by the band structure. When the threaded magnetic flux turns on, the charge and spin currents both emerge and depict periodic evolution. In the case of a mesoscopic loop with dominant triplet p(x) +/- ip(y)-wave symmetry, a slight change of the chemical potential may lead to novel flux-dependent evolution patterns of the ground-state energy and the magnetization. The spin-polarized currents show pronounced quantum oscillations with fractional periods due to the appearance of energy jumps in flux, accompanied with a steplike feature of the enhanced spin current. Particularly, at some appropriate flux, the peaks of the zero-energy local density of states clearly indicate the occurrence of the odd-frequency pairing. In the case of a superconducting loop with dominant singlet d(x2-y2)-wave symmetry, the spatial profiles of the zero-energy local density of states and the magnetization show spin-dependent features on different sample diagonals. Moreover, the evolution of the flux-induced spin current always exhibits an hc/e periodicity.