Abstract: Hydrogen adsorption on boron and nitrogen doped graphene is investigated in detail by means of first-principles calculations. A comprehensive study is performed of the structural, electronic, and magnetic properties of chemisorbed hydrogen atoms and atom pairs near the dopant sites. The main effect of the substitutional atoms is charge doping which is found to greatly affect the adsorption process by increasing the binding energy at the sites closest to the substitutional species. It is also found that doping does not induce magnetism despite the odd number of electrons per atom introduced by the foreign species, and that it quenches the paramagnetic response of chemisorbed H atoms on graphene. Overall, the effects are similar for B and N doping, with only minor differences in the adsorption energetics due to different sizes of the dopant atoms and the accompanying lattice distortions.

Abstract: We investigate the magnetic field dependence of the Hall and the bend resistances for a ballistic Hall bar structure containing a pn-junction sculptured from a bilayer of graphene. The electric response is obtained using the billiard model, and we investigate the cases of bilayer graphene with and without a band gap. Two different conduction regimes are possible: (i) both sides of the junction have the same carrier type and (ii) one side of the junction is n-type while the other one is p-type. The first case shows Hall plateau-like features in the Hall resistance that fade away as the band gap opens. The second case exhibits a bend resistance that is asymmetric in magnetic field as a consequence of snake states along the pn-interface, where the maximum is shifted away from zero magnetic field.

Abstract: Transverse magnetic focusing properties of graphene using a ballistic four terminal structure are investigated. The electric response is obtained using the semiclassical billiard model. The transmission exhibits pronounced peaks as a consequence of skipping orbits at the edge of the structure. When we add a pn-junction between the two probes, snake states along the pn-interface appear. Injected electrons are guided by the pn-interface to one of the leads depending on the value of the applied magnetic field. Oscillations in the resistance are found depending on the amount of particles that end up in each lead.

Abstract: An approach to observe snake states in a graphene Hall bar containing a pn-junction is proposed. The magnetic field dependence of the bend resistance in a ballistic graphene Hall bar structure containing a tilted pn-junction oscillates as a function of applied magnetic field. We show that each oscillation is due to a specific snake state that moves along the pn-interface. Furthermore, depending on the value of the magnetic field and applied potential, we can control the lead in which the electrons will end up and hence control the response of the system.

Abstract: Using a numerical tight-binding approach based on the Chebyshev–Bogoliubov–de Gennes method we describe Josephson junctions made of multilayer graphene contacted by top superconducting gates. Both Bernal (ABA) and rhombohedral (ABC) stacking are considered and we find that the type of stacking has a strong effect on the proximity effect and the supercurrent flow. For both cases the pair amplitude shows a polarization between dimer and nondimer atoms, being more pronounced for rhombohedral stacking. Even though the proximity effect in nondimer sites is enhanced when compared to single-layer graphene, we find that the supercurrent is suppressed. The spatial distribution of the supercurrent shows that for Bernal stacking the current flows only in the topmost layers while for rhombohedral stacking the current flows throughout the whole structure.

Abstract: We have performed a first-principles density functional theory investigation of the penetration of helium atoms through a graphene monolayer with defects. The relaxation of the graphene layer caused by the incoming helium atoms does not have a strong influence on the height of the energy barriers for penetration. For defective graphene layers, the penetration barriers decrease exponentially with the size of the defects but they are still sufficiently high that very large defects are needed to make the graphene sheet permeable for small atoms and molecules. This makes graphene a very promising material for the construction of nanocages and nanomembranes.

Abstract: We introduce a modified version of the Hirshfeld charge analysis method and demonstrate its accurateness by calculating the charge transfer between the paramagnetic molecule NO2 and graphene. The charge transfer between paramagnetic molecules and a graphene layer as calculated with ab initio methods can crucially depend on the size of the supercell used in the calculation. This has important consequences for adsorption studies involving paramagnetic molecules such as NO2 physisorbed on graphene or on carbon nanotubes. © 2008 American Institute of Physics.

Abstract: A robust and easy to handle 3D porous platinum structure was created via replicating the 3D channel system
of an ordered mesoporous silica material using atomic layer deposition (ALD) over micrometer distances.
After ALD of Pt in the silica material, the host template was digested using hydrogen fluoride (HF). A fully
connected ordered Pt nanostructure was obtained with morphology and sizes corresponding to that of
the pores of the host matrix, as revealed with high-resolution scanning transmission electron
microscopy and electron tomography. The Pt nanostructure consisted of hexagonal Pt rods originating
from the straight mesopores (11 nm) of the host structure and linking features resulting from Pt
replication of the interconnecting mesopore segments (2–4 nm) present in the silica host structure.
Electron tomography of partial replicas, made by incomplete infilling of Zeotile-4 material with Pt,
provided insight in the connectivity and formation mechanism of the Pt nanostructure by ALD. The Pt
replica was evaluated for its potential use as electrocatalyst for the hydrogen evolution reaction, one of
the half-reactions of water electrolysis, and as microelectrode for biomedical sensing. The Pt replica
showed high activity for the hydrogen evolution reaction and electrochemical characterization revealed
a large impedance improvement in comparison with reference Pt electrodes.

Abstract: We study the effect of mechanical deformations on the elec- tronic properties of hexagonal flakes of bilayer graphene. The behavior of electrons induced by triaxial strain can be de- scribed by an effective pseudo-magnetic field which is homo- geneous in the center of the flake. We find that in-plane strain, applied to both layers equally, can break the layer symmetry leading to different behavior in the top and bottom layers of graphene. At low energy, just one of the layers feels
the pseudo-magnetic field: the zero-energy pseudo-Landau level is missing in the second layer, thus creating a gap be- tween the lowest non-zero levels. While the layer asymmetry is most significant at zero energy, interaction with the edges of the flake extends the effect to higher pseudo-Landau lev- els. The behavior of the top and bottom layers may be re- versed by rotating the triaxial strain by 60°.

Abstract: Self-assembly of inorganic nanoparticles has been used to prepare hundreds of different colloidal crystals, but almost invariably with the restriction that the particles must be densely packed. Here,we show that non–close-packed nanoparticle arrays can be fabricated through the selective removal of one of two components comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle superlattices were prepared at the liquid-air interface, including several arrangements that were previously unknown. Molecular dynamics simulations revealed the particular role of the liquid in templating the formation of superlattices not achievable through self-assembly in bulk solution. Second, upon stabilization, all of these binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous materials having the same chemical composition but differing in their nanoscale architectures.

Abstract: Determining the three-dimensional (3D) atomic structure of nanoparticles (NPs) is critical to understand their structure-dependent properties. It is hereby important to perform such analyses under conditions relevant for the envisioned application. Here, we investigate the 3D structure of supported Au NPs at high temperature, which is of importance to understand their behavior during catalytic reactions. To overcome limitations related to conventional high-resolution electron tomography at high temperature, 3D characterization of NPs with atomic resolution has been performed by applying atom-counting using atomic resolution annular darkfield scanning transmission electron microscopy (ADF STEM) images followed by structural relaxation. However, at high temperatures, thermal displacements, which affect the ADF STEM intensities, should be taken into account. Moreover, it is very likely that the structure of a NP investigated at elevated temperature deviates from a ground state configuration, which is difficult to determine using purely computational energy minimization approaches. In this paper, we therefore propose an optimized approach using an iterative local minima search algorithm followed by molecular dynamics (MD) structural relaxation of candidate structures associated with each local minimum. In this manner, it becomes possible to investigate the 3D atomic structure of supported NPs, which may deviate from their ground state configuration.

Abstract: Electron tomography is essential for investigating the three-dimensional (3D) structure of nanomaterials. However, many of these materials, such as metal-organic frameworks (MOFs), are extremely sensitive to electron radiation, making it difficult to acquire a series of projection images for electron tomography without inducing electron-beam damage. Another significant challenge is the high contrast in high-angle annular dark field scanning transmission electron microscopy that can be expected for nanocomposites composed of a metal nanoparticle and an MOF. This strong contrast leads to so-called metal artifacts in the 3D reconstruction. To overcome these limitations, we here present low-dose electron tomography based on four-dimensional scanning transmission electron microscopy (4D-STEM) data sets, collected using an ultrafast and highly sensitive direct electron detector. As a proof of concept, we demonstrate the applicability of the method for an Au nanostar embedded in a ZIF-8 MOF, which is of great interest for applications in various fields, including drug delivery.

Abstract: Advanced electron microscopy techniques, including scanning electron microscopes (SEM), scanning transmission electron microscopes (STEM), and transmission electron microscopes (TEM), have revolutionized imaging capabilities. However, achieving high-quality experimental images remains a challenge due to various distortions stemming from the instrumentation and external factors. These distortions, introduced at different stages of imaging, hinder the extraction of reliable quantitative insights. In this paper, we will discuss the main sources of distortion in TEM and S(T)EM images, develop models to describe them, and propose a method to correct these distortions using a convolutional neural network. We validate the effectiveness of our method on a range of simulated and experimental images, demonstrating its ability to significantly enhance the signal-to-noise ratio. This improvement leads to a more reliable extraction of quantitative structural information from the images. In summary, our findings offer a robust framework to enhance the quality of electron microscopy images, which in turn supports progress in structural analysis and quantification in materials science and biology.

Abstract: Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted.

Abstract: Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms
of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In
order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for
a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such
simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently
parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most
research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will
only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and
present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as
a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag,
Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope
parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS
values for a wide range of input parameters that are commonly used for aberration-corrected transmission
electron microscopes.