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The optical cross sections of plasmonic nanoparticles are intricately linked to the morphology of the particle. If this connection can be made accurately enough, it would become possible to determine a particles shape solely from its measured optical cross sections. For that, electromagnetic simulations can be used to bridge the morphology and optical properties assuming that they can be performed in an accurate manner. In this paper, we study key factors that influence the accuracy of electromagnetic simulations. First, we compare several standard electromagnetic simulation methods and discuss in detail the effects of the meshing accuracy, choice of dielectric function and inclusion of a substrate for the boundary element method. To help the boundary element methods complex parametrization, we develop a workflow including reconstruction, meshing and mesh simplification steps to be able to use electron tomography data as input for these simulations. In particular, we analyze how the choice of reconstruction algorithm and the intricacies of image segmentation influence the simulated optical cross sections and correlate it to induced shape errors, which can be minimized in the data processing pipeline. In our case, optimal results could be obtained by using the Total Variation Minimization (TVM) reconstruction method in combination with Otsu thresholding and slight smoothing, which was important to create a reliable and watertight surface mesh using the marching cubes algorithm, especially for more complex shapes., Comment: 32 pages, 9 figures

Electron tomography has become a commonly used tool to investigate the three-dimensional (3D) structure of nanomaterials, including colloidal nanoparticle assemblies. However, electron microscopy is typically carried out under high vacuum conditions. Therefore, pre-treatment sample preparation is needed for assemblies obtained by (wet) colloid chemistry methods, including solvent evaporation and deposition on a solid TEM support. As a result of this procedure, changes are consistently imposed on the actual nanoparticle organization. Therefore, we propose herein the application of electron tomography of nanoparticle assemblies while in their original colloidal liquid environment. To address the challenges related to electron tomography in liquid, we devised a method that combines fast data acquisition in a commercial liquid-TEM cell, with a dedicated alignment and reconstruction workflow. We present the application of this method to two different systems, which exemplify the difference between conventional and liquid tomography, depending on the nature of the protecting ligands. 3D reconstructions of assemblies comprising polystyrene-capped Au nanoparticles encapsulated in polymeric shells revealed less compact and more distorted configurations for experiments performed in a liquid medium compared to their dried counterparts. On the other hand, quantitative analysis of the surface-to-surface distance of self-assembled Au nanorods in water agrees with previously reported dimensions of the ligand layers surrounding the nanorods, which are in much closer contact when in similar but dried assemblies. This study, therefore, emphasizes the importance of developing high-resolution characterization tools that preserve the native environment of colloidal nanostructures., Comment: 32 pages, 12 figures, 2 tables, submitted

We demonstrate the first successful functionalization of epitaxial three-dimensional graphene with metal nanoparticles. The functionalization is obtained by immersing the 3D graphene in a nanoparticle colloidal solution. This method is versatile and here is demonstrated for gold and palladium, but can be extended to other types and shapes of nanoparticles. We have measured the nanoparticle density on the top-surface and in the porous layer volume by Scanning Electron Microscopy and Scanning Transmission Electron Microscopy. Samples exhibit a high coverage of nanoparticles with minimal clustering. High quality graphene has been demonstrated to promote the functionalization leading to higher nanoparticle density, both on the surface and in the pores. X-ray Photoelectron Spectroscopy allowed to verify the absence of contamination after the functionalization process. Moreover, it confirmed the thermal stability of the Au- and Pd-functionalized three-dimensional graphene up to 530{\deg}C. Our approach opens up new avenues for utilizing three-dimensional graphene as a versatile platform for catalytic applications, sensors, and energy storage and conversion.

Microplasmas can be used for a wide range of technological applications and to improve our understanding of fundamental physics. Scanning electron microscopy, on the other hand, provides insights into the sample morphology and chemistry of materials from the mm-down to the nm-scale. Combining both would provide direct insight into plasma-sample interactions in real-time and at high spatial resolution. Up till now, very few attempts in this direction have been made, and significant challenges remain. This work presents a stable direct current glow discharge microplasma setup built inside a scanning electron microscope. The experimental setup is capable of real-time in-situ imaging of the sample evolution during plasma operation and it demonstrates localized sputtering and sample oxidation. Further, the experimental parameters such as varying gas mixtures, electrode polarity, and field strength are explored and experimental $V$-$I$ curves under various conditions are provided. These results demonstrate the capabilities of this setup in potential investigations of plasma physics, plasma-surface interactions, and materials science and its practical applications. The presented setup shows the potential to have several technological applications, e.g., to locally modify the sample surface (e.g., local oxidation and ion implantation for nanotechnology applications) on the $\mu$m-scale., Comment: LG, DC, and RDM contributed equally to this work. The videos mentioned in the manuscript can be found in the Zenodo repository linked in the paper

Electron tomography is a widely used technique for 3D structural analysis of nanomaterials, but it can cause damage to samples due to high electron doses and long exposure times. To minimize such damage, researchers often reduce beam exposure by acquiring fewer projections through tilt undersampling. However, this approach can also introduce reconstruction artifacts due to insufficient sampling. Therefore, it is important to determine the optimal number of projections that minimizes both beam exposure and undersampling artifacts for accurate reconstructions of beam-sensitive samples. Current methods for determining this optimal number of projections involve acquiring and post-processing multiple reconstructions with different numbers of projections, which can be time-consuming and requires multiple samples due to sample damage. To improve this process, we propose a protocol that combines golden ratio scanning and quasi-3D reconstruction to estimate the optimal number of projections in real-time during a single acquisition. This protocol was validated using simulated and realistic nanoparticles, and was successfully applied to reconstruct two beam-sensitive metal-organic framework complexes., Comment: accepted in Nanoscale journal. 17 pages, 9 figures, 9 supplementary figures

Films of close-packed Au nanoparticles are coupled electrodynamically through their collective plasmon resonances. This collective optical response results in enhanced light-matter interactions, which can be exploited in various applications. Here, we demonstrate their application in sensing volatile organic compounds, using methanol as a test-case. Ordered films over several cm2 were obtained by interfacial self-assembly of colloidal Au nanoparticles (~10 nm diameter) through controlled evaporation of the solvent. Even though isolated nanoparticles of this size are inherently non-scattering, when arranged in a close-packed film the plasmonic coupling results in a strong reflectance and absorbance. The in-situ tracking of vapor phase methanol concentration through UV-Vis transmission measurements of the nanoparticle film is first demonstrated. Next, in-situ ellipsometry of the self-assembled films in the Kretschmann (also known as ATR) configuration is shown to yield enhanced sensitivity, especially with phase difference measurements. Our study shows the excellent agreement between theoretical models of the spectral response of self-assembled films with experimental in-situ sensing experiments. At the same time, the theoretical framework provides the basis for the interpretation of the various observed experimental trends. Combining periodic nanoparticle films with ellipsometry in the Kretschmann configuration is a promising strategy towards highly sensitive and selective plasmonic thin-film devices based on colloidal fabrication methods for volatile organic compound (VOC) sensing applications., Comment: 19 pages

The optical response of metal nanoparticles is governed by plasmonic resonances, which are dictated by the particle morphology. A thorough understanding of the link between morphology and optical response requires quantitatively measuring optical and structural properties of the same particle. Here we present such a study, correlating electron tomography and optical micro-spectroscopy. The optical measurements determine the scattering and absorption cross-section spectra in absolute units, and electron tomography determines the 3D morphology. Numerical simulations of the spectra for the individual particle geometry, and the specific optical setup used, allow for a quantitative comparison including the cross-section magnitude. Silver nanoparticles produced by photochemically driven colloidal synthesis, including decahedra, tetrahedra and bi-tetrahedra are investigated. A mismatch of measured and simulated spectra is found when assuming pure silver particles, which is resolved by the presence of a few atomic layers of tarnish on the surface, not evident in electron tomography. The presented method tightens the link between particle morphology and optical response, supporting the predictive design of plasmonic nanomaterials.

Functionalization of photocatalytic metal oxide nanoparticles of TiO2, ZnO, WO3 and CuO with amine-terminated (oleylamine) and thiol-terminated (1-dodecanethiol) alkyl chained ligands was studied under ambient conditions. A high selectivity was observed in the binding specificity of a ligand towards nanoparticles of these different oxides. It was observed that oleylamine binds stably to only TiO2 and WO3, while 1-dodecanethiol binds stably only to ZnO and CuO. Similarly, polar to non-polar solvent phase transfer of TiO2 and WO3 nanoparticles could be achieved by using oleylamine, but not by 1-dodecanethiol, while the contrary holds for ZnO and CuO. The surface chemistry of ligand functionalized nanoparticles was probed by ATR-FTIR spectroscopy, that enabled to elucidate the occupation of the ligands at the active sites. The photo-stability of the ligands on the nanoparticle surface was determined by the photocatalytic self-cleaning properties of the material. While TiO2 and WO3 degrade the ligands within 24 hours under both UV and visible light, ligands on ZnO and CuO remain unaffected. The gathered insights are also highly relevant from an application point of view. As an example, since the ligand functionalized nanoparticles are hydrophobic in nature, they can thus be self-assembled at the air-water interface, for obtaining nanoparticle films with demonstrated photocatalytic as well as anti-fogging properties.

Chirality in inorganic nanoparticles and nanostructures has gained increasing scientific interest, because of the possibility to tune their ability to interact differently with left- and right-handed circularly polarized light. In some cases, the optical activity is hypothesized to originate from a chiral morphology of the nanomaterial. However, quantifying the degree of chirality in objects with sizes of tens of nanometers is far from straightforward. Electron tomography offers the possibility to faithfully retrieve the three-dimensional morphology of nanomaterials, but only a qualitative interpretation of the morphology of chiral nanoparticles has been possible so far. We introduce herein a methodology that enables us to quantify the helicity of complex chiral nanomaterials, based on the geometrical properties of a helix. We demonstrate that an analysis at the single particle level can provide significant insights into the origin of chiroptical properties.

Nanoporous materials represent a versatile solution for a number of applications ranging from sensing, energy applications, catalysis, drug delivery, and many others. The synergy between the outstanding properties of graphene with a three-dimensional porous structure, circumventing the limits of its 2D nature, constitutes therefore a breakthrough for many fields. We report the first three-dimensional growth of epitaxial graphene on a porousified crystalline 4H-SiC(0001). The wafer porosification is performed via a sequence of metal-assisted photochemical and photoelectrochemical etching in hydrofluoric acid based electrolytes. Pore dimensions of the matrix have been evaluated by electron tomography resulting in an average diameter of 180 nm. Graphene growth is performed in an ultra high vacuum environment at a base pressure of $10^{-11}$ mbar. The graphene growth inside the pores is uniform as confirmed by Transmission Electron Microscopy (TEM) analysis. Raman spectroscopy confirms the high quality of the graphene with a 2D/G ratio $>1$ and an average graphene crystal size of $\approx$ 100 nm. Furthermore, it demonstrates a uniform coverage of graphene across the whole sample area. The surface-to-volume ratio of this novel material, its properties, the tunability of the pore size and the scalability of the surface porosification process offer a game changing perspective for a large number of applications.

Electron tomography is a widely used experimental technique for analyzing nanometer-scale structures of a large variety of materials in three dimensions. Unfortunately, the acquisition of conventional electron tomography tilt series can easily take up one hour or more, depending on the complexity of the experiment. Using electron tomography, it is therefore far from straightforward to obtain statistically meaningful 3D data, to investigate samples that do not withstand long acquisition, or to perform in situ 3D characterization using this technique. Various acquisition strategies have been proposed to accelerate the tomographic acquisition, and reduce the required electron dose. These methods include tilting the holder continuously while acquiring a projection movie and a hybrid, incremental, methodology which combines the benefits of the conventional and continuous technique. In this paper, the different acquisition strategies will be experimentally compared in terms of speed, resolution and electron dose, based on experimental tilt series acquired for various metallic nanoparticles.

In computed tomography, the reconstruction is typically obtained on a voxel grid. In this work, however, we propose a mesh-based reconstruction method. For tomographic problems, 3D meshes have mostly been studied to simulate data acquisition, but not for reconstruction, for which a 3D mesh means the inverse process of estimating shapes from projections. In this paper, we propose a differentiable forward model for 3D meshes that bridge the gap between the forward model for 3D surfaces and optimization. We view the forward projection as a rendering process, and make it differentiable by extending recent work in differentiable rendering. We use the proposed forward model to reconstruct 3D shapes directly from projections. Experimental results for single-object problems show that the proposed method outperforms traditional voxel-based methods on noisy simulated data. We also apply the proposed method on electron tomography images of nanoparticles to demonstrate the applicability of the method on real data., Comment: Accepted in Ultramicroscopy

The influence of geometry on the local and global packing of particles is important to many fundamental and applied research themes such as the structure and stability of liquids, crystals and glasses. Here, we show by experiments and simulations that a binary mixture of hard-sphere-like particles crystallizing into the MgZn2 Laves phase in bulk, spontaneously forms 3D icosahedral quasicrystals in slowly drying droplets. Moreover, the local symmetry of 70-80% of the particles changes to that of the MgCu2 Laves phase. Both of these findings are significant for photonic applications. If the stoichiometry deviates from that of the Laves phase, our experiments show that the crystallization of MgZn2 is hardly affected by the spherical confinement. Our simulations show that the quasicrystals nucleate away from the spherical boundary and grow along five-fold symmetric structures. Our findings not only open the way for particle-level studies of nucleation and growth of 3D quasicrystals, but also of binary crystallization., Comment: 35 pages, 18 figures