Abstract: Experimental realizations of two-dimensional materials are hardly free of structural defects such as e.g. vacancies, which, in turn, modify drastically its pristine physical defect-free properties. In this work, we explore effects due to point defect clustering on the electronic and transport properties of bilayer graphene nanoribbons, for AA and AB stacking and zigzag and armchair boundaries, by means of the tight-binding approach and scattering matrix formalism. Evident vacancy concentration signatures exhibiting a maximum amplitude and an universality regardless of the system size, stacking and boundary types, in the density of states around the zero-energy level are observed. Our results are explained via the coalescence analysis of the strong sizeable vacancy clustering effect in the system and the breaking of the inversion symmetry at high vacancy densities, demonstrating a similar density of states for two equivalent degrees of concentration disorder, below and above the maximum value.

Abstract: Cold atmospheric plasma (CAP) is a promising technology for several medical applications, including the removal of biofilms from surfaces. However, the molecular mechanisms of CAP treatment are still poorly understood. Here we unravel the possible mechanisms of CAP‐induced oxidation of oligosaccharides, employing reactive molecular dynamics simulations based on the density functional‐tight binding potential. Specifically, we find that the interaction of oxygen atoms (used as CAP‐generated reactive species) with cellotriose (a model system for the oligosaccharides) can break structurally important glycosidic bonds, which subsequently leads to the disruption of the oligosaccharide molecule. The overall results help to shed light on our experimental evidence for cellotriose CAP. This oxidation by study provides atomic‐level insight into the onset of plasma‐induced removal of biofilms, as oligosaccharides are one of the main components of biofilm.

Abstract: Following an extensive investigation of various monolayer transition metal dichalcogenides (MX2), research interest has expanded to include multilayer systems. In bilayer MX2, the stacking order strongly impacts the local band structure as it dictates the local confinement and symmetry. Determination of stacking order in multilayer MX(2)domains usually relies on prior knowledge of in-plane orientations of constituent layers. This is only feasible in case of growth resulting in well-defined triangular domains and not useful in-case of closed layers with hexagonal or irregularly shaped islands. Stacking order can be discerned in the reciprocal space by measuring changes in diffraction peak intensities. Advances in detector technology allow fast acquisition of high-quality four-dimensional datasets which can later be processed to extract useful information such as thickness, orientation, twist and strain. Here, we use 4D scanning transmission electron microscopy combined with multislice diffraction simulations to unravel stacking order in epitaxially grown bilayer MoS2. Machine learning based data segmentation is employed to obtain useful statistics on grain orientation of monolayer and stacking in bilayer MoS2.

Abstract: We present KITE, a general purpose open-source tight-binding software for accurate real-space simulations of electronic structure and quantum transport properties of large-scale molecular and condensed systems with tens of billions of atomic orbitals (N similar to 10(10)). KITE's core is written in C++, with a versatile Python-based interface, and is fully optimized for shared memory multi-node CPU architectures, thus scalable, efficient and fast. At the core of KITE is a seamless spectral expansion of lattice Green's functions, which enables large-scale calculations of generic target functions with uniform convergence and fine control over energy resolution. Several functionalities are demonstrated, ranging from simulations of local density of states and photo-emission spectroscopy of disordered materials to large-scale computations of optical conductivity tensors and real-space wave-packet propagation in the presence of magneto-static fields and spin-orbit coupling. On-the-fly calculations of real-space Green's functions are carried out with an efficient domain decomposition technique, allowing KITE to achieve nearly ideal linear scaling in its multi-threading performance. Crystalline defects and disorder, including vacancies, adsorbates and charged impurity centres, can be easily set up with KITE's intuitive interface, paving the way to user-friendly large-scale quantum simulations of equilibrium and non-equilibrium properties of molecules, disordered crystals and heterostructures subject to a variety of perturbations and external conditions.