Catalyzing Bond-Dissociation in Graphene via Alkali-Iodide Molecules

Atomic design of a 2D-material such as graphene can be substantially influenced by etching, deliberately induced in a transmission electron microscope. It is achieved primarily by overcoming the threshold energy for defect formation by controlling the kinetic energy and current density of the fast electrons. Recent studies have demonstrated that the presence of certain species of atoms can catalyze atomic bond dissociation processes under the electron beam by reducing their threshold energy. Most of the reported catalytic atom species are single atoms, which have strong interaction with single-layer graphene (SLG). Yet, no such behavior has been reported for molecular species. This work shows by experimentally comparing the interaction of alkali and halide species separately and conjointly with SLG, that in the presence of electron irradiation, etching of SLG is drastically enhanced by the simultaneous presence of alkali and iodine atoms. Density functional theory and first principles molecular dynamics calculations reveal that due to charge-transfer phenomena the C-C bonds weaken close to the alkali-iodide species, which increases the carbon displacement cross-section. This study ascribes pronounced etching activity observed in SLG to the catalytic behavior of the alkali-iodide species in the presence of electron irradiation.

Self-consistent simulation of multi-component plasma turbulence and neutral dynamics in the tokamak boundary

André Calado Coroado

The interaction between neutral particles and the plasma plays a key role in determining the dynamics of the tokamak boundary that, in turn, significantly impact the overall performance of the device. Leveraging the work in Wersal and Ricci [Nucl. Fusion 55, 123014 (2015)], the present thesis describes the development and implementation in the GBS code of a mass-conserving multi-component self-consistent model to simulate the interplay between neutrals and plasma in the tokamak boundary. The simulation results are shown to be a useful tool to disentangle the physics at play in the tokamak boundary, and in particular for the interpretation of gas puff imaging (GPI).Developed in the last decade, the GBS code [Ricci et al, Plasma Phys. Control. Fusion 54, 124047 (2012)] allows for self-consistent three-dimensional numerical simulations of the turbulent plasma and neutral dynamics in the tokamak boundary. In GBS, a set of Braginskii equations in the drift limit describes the plasma time evolution, and the neutrals are modelled by solving a kinetic equation using the method of characteristics. While GBS enables simulations in arbitrary magnetic configurations, here we focus on limited plasmas. We first describe the geometrical operators and proper boundary conditions to ensure that mass conservation is satisfied. In comparison to the previous non-mass-conserving model of GBS, the mass-conserving simulations capture more accurately the sharp transition of the plasma and neutral quantities between the edge and scrape-off layer regions. In addition, we show that mass conserving simulations allow for reliable quantitative studies of particle fluxes in the tokamak boundary.A multi-component model of the neutral-plasma interaction is then developed by extending the single-component model to the description of a deuterium plasma that includes electrons, D+ ions, D atoms, D2 molecules and D2+ ions. The molecular dynamics is introduced through a set of drift-reduced Braginskii equations for the D2+ species and considering a kinetic equation for D2 molecules, in addition to the kinetic equation for D atoms, thus resulting in a coupled system of kinetic equations for the atomic and molecular neutral distribution functions. The first multi-component GBS simulations show that, in the sheath-limited regime under consideration, most of the D2 molecules cross the last closed flux surface (LCFS) and are dissociated or ionized in the edge region, thus giving rise to sources of D atoms inside the LCFS. This leads to an inward radial shift of the peak of the plasma source due to ionization of D atoms with respect to the single-component simulations.The multi-component model is applied to the simulation of GPI diagnostics, where the presence of a molecular gas puff is simulated self-consistently with the plasma and neutral dynamics of the tokamak boundary. The injected molecules interact with the boundary plasma, resulting in the emission of light in the D alpha wavelength that can be measured to infer the turbulent properties of the plasma. The simulated mechanisms underlying the light emission, which include the excitation of D atoms and dissociation of both D2 and D2+, provide a reliable tool for the interpretation of GPI experimental measurements. The impact of neutral fluctuations on the D alpha emission rate is investigated, as well as the correlation between the D alpha emission and the plasma and neutral quantities.

EPFL2021

Low-energy Electron Holography Microscope for Imaging of Single Molecules

Sven Alexander Szilagyi

Structure determination techniques are an essential tool to investigate and understand molecules, especially in biology, where functionality crucially depends on structure. The dominant high-resolution methods, such as transmission electron microscopy and X-ray diffraction, rely on ensemble averaging, making them unsuitable for evidencing structural variations of flexible molecules. Common single-molecule imaging techniques like scanning probe microscopy achieve high resolution but lack access to 3D objects. A possible way to overcome these limitations is offered by low-energy electron holography (LEEH). So far, LEEH achieved molecular imaging at resolutions in the range of 7-8 Å on the single-molecule level. A resolution in the range of a few Å, which would give access to atomic details of molecular structures, is in theory attainable. Obtaining a resolution near the theoretical limit requires a fully optimized LEEH setup and workflow, for which in particular sample and emitter preparation are crucial. Here, I present a novel LEEH microscope with a unique experimental workflow, which is capable of resolving molecular substructures with an unprecedented resolution for LEEH experiments. The newly constructed LEEH microscope takes advantage of an efficient vibration isolation system and is remote-controlled to minimize external perturbations. The setup is capable of low-temperature (50 K) measurements, which enhances the stability of the system. A reliable way for preparing highly coherent electron emitters constituted by sharp tungsten tips is presented along with different methods for improving their performance via functionalization and UHV treatments. I show an optimized and reliable substrate preparation protocol resulting in ultra-clean free-standing single-layer graphene (SLG) samples. Native electrospray ion beam deposition (ES-IBD) allows for the transfer of non-volatile molecules from solution into gas phase and onto the substrate. By employing a quadrupole mass selection, highly pure molecular ion beams are obtained, which are soft-landed onto the SLG substrate in a controlled and reproducible manner while retaining an intact structure. This versatile preparation method allows us to study a great variety of molecules by LEEH. Data on proteins with masses ranging from 12-820 kDa reveal molecular shapes consistent with model structures. Locally, structural details as small as 5 Å were identified, thus we are approaching our goal of a resolution in the range of a few Å. The application of our methodology to flexible proteins, exemplified by antibodies, allowed for the imaging of their conformational variability and for determining the influence of the sample preparation on their structure. This gave us the possibility to directly image gas-phase related conformations. Data of compact molecular systems with masses below 3 kDa reveal that our LEEH microscope is able to investigate small molecules, such as porphyrines, at high imaging contrast. The presented results indicate that an optimized LEEH setup and workflow in combination with ES-IBD is a versatile microscopy method, which is filling the gap between high-resolution and single-molecule techniques by elucidating structural details of various molecular species.

EPFL2022

Analysis of nano-sized irradiation-induced defects in Fe-base materials by means of small angle neutron scattering and molecular dynamics simulations

Gang Yu

Thermonuclear fusion of light atoms is considered since decades as an unlimited, safe and reliable source of energy that could eventually replace classical sources based on fossile fuel or nuclear fuel. Fusion reactor technology and materials studies are important parts of the fusion energy development program. For the time being, the most promising materials for structural applications in the future fusion power reactors are the Reduced Activation Ferritic/Martensitic (RAFM) steels for which the greatest technology maturity has been achieved, i.e., qualified fabrication routes, welding technology and a general industrial experience are almost available. The most important issues concerning the future use of RAFM steels in fusion power reactors are derived from their irradiation by 14 MeV neutrons that are the product, together with 3.5 MeV helium ions, of the envisaged fusion reactions between deuterium and tritium nuclei. Indeed, exposure of metallic materials to intense fluxes of 14 MeV neutrons will result in the formation of severe displacement damage (about 20-30 dpa per year) and high amounts of helium, which are at the origin of significant changes in the physical and mechanical of materials, such as hardening and embrittlement effects, for instance. This PhD Thesis work was aimed at investigating how far the Small Angle Neutron Scattering (SANS) technique could be used for detecting and characterizing nano-sized irradiation-induced defects in RAFM steels. Indeed, the resolution limit of Transmission Electron Microscopy (TEM) is about 1 nm in weak beam TEM imaging, and it is usually thought that a large number of irradiation-induced effects have a size below 1 nm in RAFM steels and that these very small defects actually contribute to the irradiation-induced hardening and embrittlement of RAFM steels occurring at irradiation temperatures below about 400°C. The aim of this work was achieved by combing SANS experiments on unirradiated and irradiated specimens of RAFM steels with Molecular Dynamics (MD) simulations of main expected nano-sized defects in irradiated pure Fe and Fe-He alloys, as model materials for RAFM steels, and simulations of their corresponding TEM images and SANS signals. In particular, the SANS signal of various types of defects was simulated for the first time. The methodology used in this work was the following: SANS experiments were performed by applying a strong saturating magnetic field to unirradiated and irradiated specimens of three types of RAFM steels, namely the European EUROFER 97, the Japanese F82H and the Swiss OPTIMAX A steels. The available irradiated specimens included specimens which had been irradiated with 590 MeV protons in the Proton IRradiation EXperiment (PIREX) facility at the Paul Scherrer Institute (PSI) at temperatures in the range of 50-350°C to doses in the range of 0.3-2.0 dpa. SANS spectra as well as values of the so-called A ratio, which represents the ratio of the total scattered intensity to the nuclear scattered intensity, were obtained for the various irradiation doses and temperatures investigated. MD simulations of atomic displacement cascades in pure Fe and in Fe-He alloys were performed using Embedded Atom Method (EAM) many-body interatomic potentials. The main nano-sized defects that should be produced in RAFM steels under irradiation were created by means of MD in pure Fe. These included dislocation loops of various types, voids, helium bubbles with various He concentration and Cr precipitates. TEM images of cascade damage and all the defects created by MD were simulated in the dark field/weak beam imaging modes by using the Electron Microscopy Software (EMS) developed by P.A. Stadelmann (EPFL) and analyzed in terms of variations of contrast intensities versus depth inside the specimen. The SANS signal provided by cascade damage and all the defects created by MD was simulated by using a slightly modified version of EMS, accounting for neutrons instead of electrons. The SANS technique has been proven in this work to be a very powerful tool for detecting nano-sized irradiation-induced defects and a tool well complementary to TEM for characterizing such very small irradiation-induced defects. Indeed, TEM appears most adapted to investigate structural defects, such as dislocation loops and helium bubbles with high helium concentration, which yield significant lattice deformation of the surrounding matrix, while SANS is most adapted to investigate phase defects, such as voids, helium bubbles with low helium concentration and Cr precipitates. By combining the results of SANS experiments with those of MD simulations, TEM image simulations and SANS signal simulations, the nano-sized irradiation-induced defects were tentatively identified as small helium bubbles. While the radiation hardening measured for RAFM steels cannot be explained by accounting only for the defects observed in TEM, it could be successfully modeled by accounting also for a reasonable number density of the nano-sized defects evidenced using the SANS technique.

EPFL2008