Abstract: Van der Waals (vdW) interaction between two-dimensional crystals (2D) can trap substances in high pressurized (of order 1 GPa) on nanobubbles. Increasing the adhesion between the 2D crystals further enhances the pressure and can lead to a phase transition of the trapped material. We found that the shape of the nanobubble can depend critically on the properties of the trapped substance. In the absence of any residual strain in the top 2D crystal, flat nanobubbles can be formed by trapped long hydrocarbons (that is, hexadecane). For large nanobubbles with radius 130 nm, our atomic force microscopy measurements show nanobubbles filled with hydrocarbons (water) have a cylindrical symmetry (asymmetric) shape which is in good agreement with our molecular dynamics simulations. This study provides insights into the effects of the specific material and the vdW pressure on the microscopic details of graphene bubbles.

Abstract: Auger processes involving the filling of holes in the valence band are thought to make important contributions to the low-energy photoelectron and secondary electron spectrum from many solids. However, measurements of the energy spectrum and the efficiency with which electrons are emitted in this process remain elusive due to a large unrelated background resulting from primary beam-induced secondary electrons. Here, we report the direct measurement of the energy spectra of electrons emitted from single layer graphene as a result of the decay of deep holes in the valence band. These measurements were made possible by eliminating competing backgrounds by employing low-energy positrons (<1.25 eV) to create valence-band holes by annihilation. Our experimental results, supported by theoretical calculations, indicate that between 80 and 100% of the deep valence-band holes in graphene are filled via an Auger transition.

Abstract: Recently, black phosphorus quantum dots were fabricated experimentally. Motivated by these experiments, we theoretically investigate the electronic and optical properties of rectangular phosphorene quantum dots (RPQDs) in the presence of an in-plane electric field and a perpendicular magnetic field. The energy spectra and wave functions of RPQDs are obtained numerically using the tight-binding approach. We find edge states within the band gap of the RPQD which are well separated from the bulk states. In an undoped RPQD and for in-plane polarized light, due to the presence of well-defined edge states, we find three types of optical transitions which are between the bulk states, between the edge and bulk states, and between the edge states. The electric and magnetic fields influence the bulk-to-bulk, edge-to-bulk, and edge-to- edge transitions differently due to the different responses of bulk and edge states to these fields.

Abstract: By making use of circularly polarized light and electrostatic gating, monolayer molybdenum disulfide (ML – MoS2) can form a platform supporting multiple types of charge carriers. They can be discriminated by their spin, valley index, or whether they are electrons or holes. We investigate the collective properties of those charge carriers and are able to identify distinct plasmon modes. We analyze the corresponding dispersion relation, lifetime, and oscillator strength, and calculate the phase relation between the oscillations in the different components of the plasmon modes. All platforms in ML-MoS2 support a long-wavelength root q plasmon branch at zero kelvins. In addition to this, for an n-component system, n-1 distinct plasmon modes appear as acoustic modes with linear dispersion in the long-wavelength limit. These modes correspond to out-of-phase oscillations in the different fermion liquids and have, although being damped, a relatively long lifetime. Additionally, we also find distinct modes at large wave vectors that are more strongly damped by intraband processes.

Abstract: We propose a tight-binding (TB) model, that includes spin-orbit coupling (SOC), to describe the electronic properties of methyl-substituted germanane (GeCH3). This model gives an electronic spectrum in agreement with first principle results close to the Fermi level. Using the Z(2) formalism, we show that a topological phase transition from a normal insulator (NI) to a quantum spin Hall (QSH) phase occurs at 11.6% biaxial tensile strain. The sensitivity of the electronic properties of this system on strain, in particular its transition to the topological insulating phase, makes it very attractive for applications in strain sensors and other microelectronic applications.

Abstract: Synthetic methods that allow for the controlled design of well-defined Pt nanoparticles are highly desirable for fundamental catalysis research. In this work, we propose a strategy that allows precise and independent control of the Pt particle size and coverage. Our approach exploits the versatility of the atomic layer deposition (ALD) technique by combining two ALD processes for Pt using different reactants. The particle areal density is controlled by tailoring the number of ALD cycles using trimethyl(methylcyclopentadienyl) platinum and oxygen, while subsequent growth using the same Pt precursor in combination with nitrogen plasma allows for tuning of the particle size at the atomic level. The excellent control over the particle morphology is clearly demonstrated by means of in situ and ex situ X-ray fluorescence and grazing incidence small angle X-ray scattering experiments, providing information about the Pt loading, average particle dimensions, and mean center-to-center particle distance.

Abstract: Using the tight-binding approach, we investigate the energy spectrum of square, triangular, and hexagonal MoS2 quantum dots (QDs) in the presence of a perpendicular magnetic field. Novel edge states emerge in MoS2 QDs, which are distributed over the whole edge which we call ring states. The ring states are robust in the presence of spin-orbit coupling (SOC). The corresponding energy levels of the ring states oscillate as a function of the perpendicular magnetic field which are related to Aharonov-Bohm oscillations. Oscillations in the magnetic field dependence of the energy levels and the peaks in the magneto-optical spectrum emerge (disappear) as the ring states are formed (collapsed). The period and the amplitude of the oscillation decrease with the size of the MoS2 QDs.

Abstract: By employing density functional theory-based methods, the structural, vibrational, electronic, and magnetic properties of monolayer -RuCl3 were investigated. It was demonstrated that ferromagnetic (FM) and zigzag-antiferromagnetic (ZZ-AFM) spin orders in the material have very close total energies with the latter being the ground state. We found that each Ru atom possesses a magnetic moment of 0.9 (B) and the material exhibits strong magnetic anisotropy. While both phases exhibit indirect gaps, the FM phase is a magnetic semiconductor and the ZZ-AFM phase is a non-magnetic semiconductor. The structural stability of the material was confirmed by phonon calculations. Moreover, dynamical analysis revealed that the magnetic order in the material can be monitored via Raman measurements of the crystal structure. In addition, the magnetic ground state of the material changes from ZZ-AFM to FM upon certain applied strains. Valence and conduction band-edges of the material vary considerably under in-plane strains. Owing to the stable lattice structure and unique and controllable magnetic properties, monolayer -RuCl3 is a promising material in nanoscale device applications.

Abstract: SIRT6 and COX-2 are oncogenes target that promote the expression of proinflammatory and pro-survival proteins through a signaling pathway, which leads to increased survival and proliferation of tumor cells. However, COX-2 also suppresses skin tumorigenesis and their relationship with SIRT6, making it an interesting target for the discovery of drugs with anti-inflammatory and anti-cancer properties. Herein, we studied the interaction of thieno[3,2-c] pyran analogs and RONS species with SIRT6 and COX-2 through the use of molecular docking and molecular dynamic simulations. Molecular docking studies revealed the importance of hydrophobic and hydrophilic amino acid residues for the stability. The molecular dynamics study examined conformational changes in the enzymes caused by the binding of the substrates and how those changes affected the stability of the protein-drug complex. The average RMSD values of the backbone atoms in compounds 6 and 10 were calculated from 1000 ps to 10000 ps and were found to be 0.13 nm for both compounds. Similarly, the radius of gyration values for compounds 6 and 10 were found to be 1.87 +/- 0.03 nm and 1.86 +/- 0.02 nm, respectively. The work presented here, will be of great help in lead identification and optimization for early drug discovery.

Abstract: Measuring temperature in biological environments is an ambitious goal toward supporting medical treatment and diagnosis. Minimally invasive techniques based on optical probes require very specific properties that are difficult to combine within a single material. These include high chemical stability in aqueous environments, optical signal stability, low toxicity, high emission intensity, and, essential, working at wavelengths within the biological transparency windows so as to minimize invasiveness while maximizing penetration depth. We propose CaF2:Nd3+,Y3+ as a candidate for thermometry based on an intraband ratiometric approach, fully working within the biological windows (excitation at 808 nm; emission around 1050 nm). We optimized the thermal probes through the addition of Y3+ as a dopant to improve both emission intensity and thermal sensitivity. To define the conditions under which the proposed technique can be applied, gold nanorods were used to optically generate subtissue hot areas, while the resulting temperature variation was monitored with the new nanothermometers.

Abstract: Methane needle-plane discharge has practical application prospect and scientific research significance since methane conversion heavy oil hydrogenation is formed by coupling methane needle-plane discharge with heavy oil hydrogenation, which can achieve high-efficient heavy oil hydrogenation and increase the yields of high value-added light olefins. In this paper, a two-dimensional fluid model is built up for numerically simulating the methane needle-plane discharge plasma at atmospheric pressure. Spatial and axial distributions of electric intensity, electron temperature and particle densities are obtained. Reaction yields are summarized and crucial pathways to produce various kinds of charged and neutral particles are found out. Simulation results indicate that axial evolutions of CH3+ and CH4+ densities, electric intensity and electron temperature are similar and closely related. The CH5+ and C2H5+ densities first increase and then decrease along the axial direction. The CH3 and H densities have nearly identical spatial and axial distributions. Particle density distributions of CH2, C2H4 and C2H5 are obviously different in the area near the cathode but comparatively resemblant in the positive column region. The CH3+ and CH4+ are produced by electron impact ionizations between electrons and CH4. The CH5+ and C2H5+ are respectively generated by molecular impact dissociations between CH3+ and CH4 and between CH4+ and CH4. Electron impact decomposition between electrons and CH4 is a dominated reaction to produce CH3, CH2, CH and H. The reactions between CH2 and CH4 and between electrons and C2H4 are critical pathways to produce C2H4 and C2H2, respectively. In addition, the yields of electron impact decomposition reactions between electrons and CH4 and reactions between CH2 and CH4 account for 52.15% and 47.85% of total yields of H-2 respectively.

Abstract: Using first-principles calculations, we study the dependence of the electronic and vibrational properties of multilayered PbI2 crystals on the number of layers and focus on the electronic-band structure and the Raman spectrum. Electronic-band structure calculations reveal that the direct or indirect semiconducting behavior of PbI2 is strongly influenced by the number of layers. We find that at 3L thickness there is a direct-to-indirect band gap transition (from bulk-to-monolayer). It is shown that in the Raman spectrum two prominent peaks, A(1g) and E-g, exhibit phonon hardening with an increasing number of layers due to the interlayer van der Waals interaction. Moreover, the Raman activity of the A(1g) mode significantly increases with an increasing number of layers due to the enhanced out-of-plane dielectric constant in the few-layer case. We further characterize rigid-layer vibrations of low-frequency interlayer shear (C) and breathing (LB) modes in few-layer PbI2. A reduced monatomic (linear) chain model (LCM) provides a fairly accurate picture of the number of layers dependence of the low-frequency modes and it is shown also to be a powerful tool to study the interlayer coupling strength in layered PbI2.

Abstract: When slow ions incident on a surface are neutralized, the excess potential energy is passed on to an electron inside the surface, leading to emission of secondary electrons. The microscopic description of this process, as
well as the calculation of the secondary electron yield, is a challenging problem due to its complexity as well
as its sensitivity to surface properties. One of the first quantitative descriptions was articulated in the 1950s by
Hagstrum, who based his calculation on a parametrization of the density of states of the material. In this paper, we
present a model for calculating the secondary electron yield, derived from Hagstrum’s initial approach. We use
first-principles density functional theory calculations to acquire the necessary input and introduce the concept of
electron cascades to Hagstrum’s model in order to improve the calculated spectra, as well as remove its reliance
on fitting parameters. We apply our model to He+ and Ne+ ions incident on Ge(111) and Si(111) and obtain
yield spectra that match closely to the experimental results of Hagstrum.

Abstract: The mechanical and electronic properties of a graphene membrane placed on top of a triangular superlattice of nanopillars are investigated. We use molecular dynamics simulations to access the deformation fields and the tight-binding approaches to calculate the electronic properties. Ripples form in the graphene layer that span across the unit cell, connecting neighboring pillars, in agreement with recent experiments. We find that the resulting pseudo-magnetic field (PMF) varies strongly across the unit cell. We investigate the dependence of PMF on unit cell boundary conditions, height of the pillars, and the strength of the van der Waals interaction between graphene and the substrate. We find direct correspondence with typical experiments on pillars, showing intrinsic “slack” in the graphene membrane. PMF values are confirmed by the local density of states calculations performed at different positions of the unit cell showing pseudo-Landau levels with varying spacings. Our findings regarding the relaxed membrane configuration and the induced strains are transferable to other flexible 2D membranes.

Abstract: The structural modification of ssDNA-based aptamers upon specific binding of its target molecule leads to changes of the charge-transfer resistance (Rct) of a negatively-charged free-diffusing redox probe. The aptamer adopts a structure due to self-hybridization which is stabilized using profalvine as intercalator. The pre-organized aptamer structure is used to detect chloramphenicol (CAP) requiring a substantial change of the aptamer structure indicated by a CAP concentration dependent increase in the Rct values. Pre-incubation of the aptamer-modified electrode with an intercalator allows for the modulation of the aptamer/target interaction and hence for a modulation of the CAP-dependent variation of the Rct values.