3D test sample for the calibration and quality control of stimulated emission depletion (STED) and confocal microscopes.

Multiple samples are required to monitor and optimize the quality and reliability of quantitative measurements of stimulated emission depletion (STED) and confocal microscopes. Here, we present a single sample to calibrate these microscopes, align their laser beams and measure their point spread function (PSF) in 3D. The sample is composed of a refractive index matched colloidal crystal of silica beads with fluorescent and gold cores. The microscopes can be calibrated in three dimensions using the periodicity of the crystal; the alignment of the laser beams can be checked using the reflection of the gold cores; and the PSF can be measured at multiple positions and depths using the fluorescent cores. It is demonstrated how this sample can be used to visualize and improve the quality of STED and confocal microscopy images. The sample is adjustable to meet the requirements of different NA objectives and microscopy techniques and additionally can be used to evaluate refractive index mismatches as a function of depth quantitatively.

Topographic features of nano-pores within the osteochondral interface and their effects on transport properties -a 3D imaging and modeling study.

Recent insights suggest that the osteochondral interface plays a central role in maintaining healthy articulating joints. Uncovering the underlying transport mechanisms is key to the understanding of the cross-talk between articular cartilage and subchondral bone. Here, we describe the mechanisms that facilitate transport at the osteochondral interface. Using scanning electron microscopy (SEM), we found a continuous transition of mineralization architecture from the non-calcified cartilage towards the calcified cartilage. This refurbishes the classical picture of the so-called tidemark; a well-defined discontinuity at the osteochondral interface. Using focused-ion-beam SEM (FIB-SEM) on one osteochondral plug derived from a human cadaveric knee, we elucidated that the pore structure gradually varies from the calcified cartilage towards the subchondral bone plate. We identified nano-pores with radius of 10.71 ± 6.45 nm in calcified cartilage to 39.1 ± 26.17 nm in the subchondral bone plate. The extracted pore sizes were used to construct 3D pore-scale numerical models to explore the effect of pore sizes and connectivity among different pores. Results indicated that connectivity of nano-pores in calcified cartilage is highly compromised compared to the subchondral bone plate. Flow simulations showed a permeability decrease by about 2000-fold and solute transport simulations using a tracer (iodixanol, 1.5 kDa with a free diffusivity of 2.5 × 10-10 m2/s) showed diffusivity decrease by a factor of 1.5. Taken together, architecture of the nano-pores and the complex mineralization pattern in the osteochondral interface considerably impacts the cross-talk between cartilage and bone.

An introduction to cryo-FIB-SEM cross-sectioning of frozen, hydrated Life Science samples.

The introduction of cryo-techniques to the focused ion-beam scanning electron microscope (FIB-SEM) has brought new opportunities to study frozen, hydrated samples from the field of Life Sciences. Cryo-techniques have long been employed in electron microscopy. Thin electron transparent sections are produced by cryo-ultramicrotomy for observation in a cryo-transmission electron microscope (TEM). Cryo-TEM is presently reaching the imaging of macromolecular structures. In parallel, cryo-fractured surfaces from bulk materials have been investigated by cryo-SEM. Both cryo-TEM and cryo-SEM have provided a wealth of information, despite being 2D techniques. Cryo-TEM tomography does provide 3D information, but the thickness of the volume has a maximum of 200-300 nm, which limits the 3D information within the context of specific structures. FIB-milling enables imaging additional planes by creating cross-sections (e.g. cross-sectioning or site-specific X-sectioning) perpendicular to the cryo-fracture surface, thus adding a third imaging dimension to the cryo-SEM. This paper discusses how to produce suitable cryo-FIB-SEM cross-section results from frozen, hydrated Life Science samples with emphasis on 'common knowledge' and reoccurring observations. LAY DESCRIPTION: Life Sciences studies life down to the smallest details. Visualising the smallest details requires electron microscopy, which utilises high-vacuum chambers. One method to maintain the integrity of Life Sciences samples under vacuum conditions is freezing. Frozen samples can remain in a suspended state. As a result, research can be carried out without having to change the chemistry or internal physical structure of the samples. Two types of electron microscopes equipped with cryo-sample handling facilities are used to investigate samples: The scanning electron microscope (SEM) which investigates surfaces and the transmission electron microscope (TEM) which investigates thin electron transparent sections (called lamellae). A third method of investigation combines a SEM with a focused ion beam (FIB) to form a cryo-FIB-SEM, which is the basis of this paper. The electron beam images the cryo-sample surface while the ion beam mills into the surface to expose the interior of the sample. The latter is called cross-sectioning and the result provides a way of investigating the 3rd dimension of the sample. This paper looks at the making of cross-sections in this manner originating from knowledge and experience gained with this technique over many years. This information is meant for newcomers, and experienced researchers in cryo-microscopy alike.

Cryo-FIB preparation of whole cells and tissue for cryo-TEM: use of high-pressure frozen specimens in tubes and planchets.

The desire to study macromolecular complexes within their cellular context requires the ability to produce thin samples suitable for cryo-TEM (cryo-transmission electron microscope) investigations. In this paper, we discuss two similar approaches, which were developed independently in Utrecht (the Netherlands) and Albany (USA). The methods are particularly suitable for both tissue samples and cell suspensions prepared by a high-pressure freezer (HPF). The workflows are explained with particular attention to potential pitfalls, while underlying principles are highlighted ('why to do so'). Although both workflows function with a high success rate, full execution requires considerable experience and remains demanding. In addition, throughput is low. We hope to encourage other research groups worldwide to take on the challenge of improving the HPF- cryo-FIB-SEM - cryo-TEM workflow. We discuss a number of suggestions to this end. LAY DESCRIPTION: Life is ultimately dictated by the interaction of molecules in our bodies. Highly complex equipment is being used and further developed to study these interactions. The present paper describes methods to prepare small, very thin lamellae (area of 5×5 µm2 , thickness 50-300 nm) of a cell to be studied in a cryo-transmission electron microscope (cryo-TEM). Special care must be taken to preserve the natural state of molecules in their natural environment. In the case of cryo-TEM, the samples must be frozen and kept frozen to be compatible with the vacuum conditions in the microscope. The frozen condition imposes technical challenges which are addressed. Two approaches to obtain the thin lamellae are described. Both make use of a focused ion beam (FIB) microscope. The FIB allows removal of material with nanometre precision by focusing a beam of ionised atoms (gallium ions) onto the sample. Careful control of the FIB allows cutting out of the required thin lamellae. In both strategies, the thin lamellae remain attached to the original sample, and the ensemble of sample with section and sample holder is transported from the FIB microscope to the TEM while being kept frozen.

Predicting intraparticle diffusivity as function of stationary phase characteristics in preparative chromatography.

Diffusion inside pores is the rate limiting step in many preparative chromatographic separations and a key parameter for process design in weak interaction aqueous chromatographic separations employed in food and bio processing. This work aims at relating diffusion inside porous networks to properties of stationary phase and of diffusing molecules. Intraparticle diffusivities were determined for eight small molecules in nine different stationary phases made from three different backbone materials. Measured intraparticle diffusivities were compared to the predictive capability of the correlation by Mackie and Meares and the parallel pore model. All stationary phases were analyzed for their porosity, apparent pore size distribution and tortuosity, which are input parameters for the models. The parallel pore model provides understanding of the occurring phenomena, but the input parameters were difficult to determine experimentally. The model predictions of intraparticle diffusion were of limited accuracy. We show that prediction can be improved when combining the model of Mackie and Meares with the fraction of accessible pore volume. The accessible pore volume fraction can be determined from inverse size exclusion chromatographic measurements. Future work should further challenge the improved model, specifically widening the applicability to greater accessible pore fractions (> 0.7) with corresponding higher intraparticle diffusivities (Dp/Dm  > 0.2). A database of intraparticle diffusion and stationary phase pore property measurements is supplied, to contribute to general understanding of the relationship between intraparticle diffusion and pore properties.

Bridging the gap: 3D real-space characterization of colloidal assemblies via FIB-SEM tomography.

Insight in the structure of nanoparticle assemblies up to a single particle level is key to understand the collective properties of these assemblies, which critically depend on the individual particle positions and orientations. However, the characterization of large, micron sized assemblies containing small, 10-500 nanometer, sized colloids is highly challenging and cannot easily be done with the conventional light, electron or X-ray microscopy techniques. Here, we demonstrate that focused ion beam-scanning electron microscopy (FIB-SEM) tomography in combination with image processing enables quantitative real-space studies of ordered and disordered particle assemblies too large for conventional transmission electron tomography, containing particles too small for confocal microscopy. First, we demonstrate the high resolution structural analysis of spherical nanoparticle assemblies, containing small anisotropic gold nanoparticles. Herein, FIB-SEM tomography allows the characterization of assembly dimensions which are inaccessible to conventional transmission electron microscopy. Next, we show that FIB-SEM tomography is capable of characterizing much larger ordered and disordered assemblies containing silica colloids with a diameter close to the resolution limit of confocal microscopes. We determined both the position and the orientation of each individual (nano)particle in the assemblies by using recently developed particle tracking routines. Such high precision structural information is essential in the understanding and design of the collective properties of new nanoparticle based materials and processes.

Shaping Silica Rods by Tuning Hydrolysis and Condensation of Silica Precursors.

We present the synthesis of colloidal silica particles with new shapes by manipulating the growth conditions of rods that are growing from polyvinylpyrrolidone-loaded water-rich droplets containing ammonia and ethanol. The silica rods grow by ammonia-catalyzed hydrolysis and condensation of tetraethoxysilane (TEOS). The lengthwise growth of these silica rods gives us the opportunity to change the conditions at any time during the reaction. In this work, we vary the availability of hydrolyzed monomers as a function of time and study how the change in balance between the hydrolysis and condensation reactions affects a typical synthesis (as described in more detail by our group earlier1). First, we show that in a "standard" synthesis, there are two silica growth processes occurring; one in the oil phase and one in the droplet. The growth process in the water droplet causes the lengthwise growth of the rods. The growth process in the oil phase produces a thin silica layer around the rods, but also causes the nucleation of 70 nm silica spheres. During a typical rod growth, silica formation mainly takes place in the droplet. The addition of partially hydrolyzed TEOS or tetramethoxysilane (TMOS) to the growth mixture results in a change in balance between the hydrolysis and condensation reaction. As a result, the growth also starts to take place on the surface of the water droplet and thus from the oil phase, not only from inside the droplet onto a silica rod sticking out of the droplet. Carefully tuning the growth from the droplet and the growth from the oil phase allowed us to create nanospheres, hollow silica rods, hollow sphere rod systems (colloidal matchsticks), and bent silica rods.

Isolating Clusters of Light Elements in Molecular Sieves with Atom Probe Tomography.

Understanding the 3-D distribution and nature of active sites in heterogeneous catalysts is critical to developing structure-function relationships. However, this is difficult to achieve in microporous materials as there is little relative z-contrast between active and inactive framework elements (e.g., Al, O, P, and Si), making them difficult to differentiate with electron microscopies. We have applied atom probe tomography (APT), currently the only nanometer-scale 3-D microscopy to offer routine light element contrast, to the methanol-to-hydrocarbons (MTH) catalyst SAPO-34, with Si as the active site, which may be present in the framework as either isolated Si species or clusters (islands) of Si atoms. 29Si solid-state NMR data on isotopically enriched and natural abundance materials are consistent with the presence of Si islands, and the APT results have been complemented with simulations to show the smallest detectable cluster size as a function of instrument spatial resolution and detector efficiency. We have identified significant Si-Si affinity in the materials, as well as clustering of coke deposited by the MTH reaction (13CH3OH used) and an affinity between Brønsted acid sites and coke. A comparison with simulations shows that the ultimate spatial resolution that can be attained by APT applied to molecular sieves is 0.5-1 nm. Finally, the observed 13C clusters are consistent with hydrocarbon pool mechanism intermediates that are preferentially located in regions of increased Brønsted acidity.

Electron crystallography with the EIGER detector.

Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2, frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data.

Coke Formation in a Zeolite Crystal During the Methanol-to-Hydrocarbons Reaction as Studied with Atom Probe Tomography.

Understanding the formation of carbon deposits in zeolites is vital to developing new, superior materials for various applications, including oil and gas conversion processes. Herein, atom probe tomography (APT) has been used to spatially resolve the 3D compositional changes at the sub-nm length scale in a single zeolite ZSM-5 crystal, which has been partially deactivated by the methanol-to-hydrocarbons reaction using (13) C-labeled methanol. The results reveal the formation of coke in agglomerates that span length scales from tens of nanometers to atomic clusters with a median size of 30-60 (13) C atoms. These clusters correlate with local increases in Brønsted acid site density, demonstrating that the formation of the first deactivating coke precursor molecules occurs in nanoscopic regions enriched in aluminum. This nanoscale correlation underscores the importance of carefully engineering materials to suppress detrimental coke formation.

FIB-SEM Tomography Probes the Mesoscale Pore Space of an Individual Catalytic Cracking Particle.

The overall performance of a catalyst particle strongly depends on the ability of mass transport through its pore space. Characterizing the three-dimensional structure of the macro- and mesopore space of a catalyst particle and establishing a correlation with transport efficiency is an essential step toward designing highly effective catalyst particles. In this work, a generally applicable workflow is presented to characterize the transport efficiency of individual catalyst particles. The developed workflow involves a multiscale characterization approach making use of a focused ion beam-scanning electron microscope (FIB-SEM). SEM imaging is performed on cross sections of 10.000 µm2, visualizing a set of catalyst particles, while FIB-SEM tomography visualized the pore space of a large number of 8 µm3 cubes (subvolumes) of individual catalyst particles. Geometrical parameters (porosity, pore connectivity, and heterogeneity) of the material were used to generate large numbers of virtual 3D volumes resembling the sample's pore space characteristics, while being suitable for computationally demanding transport simulations. The transport ability, defined as the ratio of unhindered flow over hindered flow, is then determined via transport simulations through the virtual volumes. The simulation results are used as input for an upscaling routine based on an analogy with electrical networks, taking into account the spatial heterogeneity of the pore space over greater length scales. This novel approach is demonstrated for two distinct types of industrially manufactured fluid catalytic cracking (FCC) particles with zeolite Y as the active cracking component. Differences in physicochemical and catalytic properties were found to relate to differences in heterogeneities in the spatial porosity distribution. In addition to the characterization of existing FCC particles, our method of correlating pore space with transport efficiency does also allow for an up-front evaluation of the transport efficiency of new designs of FCC catalyst particles.

Repulsive van der Waals forces enable Pickering emulsions with non-touching colloids.

Emulsions stabilized by solid particles, called Pickering emulsions, offer promising applications in drug delivery, cosmetics, food science and the manufacturing of porous materials. This potential stems from their high stability against coalescence and 'surfactant-free' nature. Generally, Pickering emulsions require that the solid particles are wetted by both phases and as a result, the adsorption free energy is often large with respect to the thermal energy (kBT). Here we provide the first experimental proof for an alternative scenario: non-touching (effectively non-wetting), charged, particles that are completely immersed in the oil phase through a balance of charge induced attractions and repulsions caused by van der Waals forces. These particles nonetheless stabilize the emulsion. The main advantage of this novel adsorption mechanism is that these particles can easily be detached from the interface simply by adding salt. This not only makes the finding fundamentally of interest, but also enables a triggered de-emulsification and particle recovery, which is useful in fields like enhanced oil recovery, heterogeneous catalysis, and emulsion polymerization.

Directed Self-Assembly of Micron-Sized Gold Nanoplatelets into Oriented Flexible Stacks with Tunable Interplate Distance.

A growing demand for control over the interparticle spacing and the orientation of anisotropic metallic particles into self-assembled structures is fuelled by their use in potential applications such as in plasmonics, catalysis, sensing, and optoelectronics. Here, we present an improved high yield synthesis method to fabricate micron- and submicron-sized gold nanoplatelets with a thickness less than 20 nm using silver nanoplatelets as seeds. By tuning the depth of the secondary minimum in the DLVO interaction potential between these particles, we are able to assemble the platelets into dynamic and flexible stacks containing thousands of platelets arranged face-to-face with well-defined spacing. Moreover, we demonstrate that the length of the stacks, and the interplate distance can be controlled between tens and hundreds of nm with the ionic strength. We use a high frequency external electric field to control the orientation of the stacks and direct the stacks into highly organized 2D and 3D assemblies that strongly polarize light.

Rock mechanics. Superplastic nanofibrous slip zones control seismogenic fault friction.

Understanding the internal mechanisms controlling fault friction is crucial for understanding seismogenic slip on active faults. Displacement in such fault zones is frequently localized on highly reflective (mirrorlike) slip surfaces, coated with thin films of nanogranular fault rock. We show that mirror-slip surfaces developed in experimentally simulated calcite faults consist of aligned nanogranular chains or fibers that are ductile at room conditions. These microstructures and associated frictional data suggest a fault-slip mechanism resembling classical Ashby-Verrall superplasticity, capable of producing unstable fault slip. Diffusive mass transfer in nanocrystalline calcite gouge is shown to be fast enough for this mechanism to control seismogenesis in limestone terrains. With nanogranular fault surfaces becoming increasingly recognized in crustal faults, the proposed mechanism may be generally relevant to crustal seismogenesis.

In-situ integrity control of frozen-hydrated, vitreous lamellas prepared by the cryo-focused ion beam-scanning electron microscope.

Recently a number of new approaches have been presented with the intention to produce electron beam transparent cryo-sections (lamellas in FIB-SEM terminology) from hydrated vitreously frozen cryo samples with a Focused Ion Beam (FIB) system, suitable for cryo-Transmission Electron Microscopy (cryo-TEM). As the workflow is still challenging and time consuming, it is important to be able to determine the integrity and suitability (cells vs. no cells; vitreous vs. crystalline) of the lamellas. Here we present an in situ method that tests both conditions by using the cryo-Scanning Electron Microscope (cryo-SEM) in transmission mode (TSEM; Transmission Scanning Electron Microscope) once the FIB-made lamella is ready. Cryo-TSEM imaging of unstained cells yields strong contrast, enabling direct imaging of material present in the lamellas. In addition, orientation contrast is shown to be suitable for distinguishing crystalline lamellas from vitreous lamellas. Tilting the stage a few degrees results in changes of contrast between ice grains as a function of the tilt angle, whereas the contrast of areas with vitreous ice remains unchanged as a function of the tilt angle. This orientation contrast has subsequently been validated by cryo-Electron BackScattered Diffraction (EBSD) in transmission mode. Integration of the presented method is discussed and the role it can play in future developments for a new and innovative all-in-one cryo-FIB-SEM life sciences instrument.

Defect engineering in sedimentary colloidal photonic crystals.

In this paper, lithographic methods are successfully employed to create growth templates for colloidal self-assembly, enabling the inclusion of crystallographic defects at predetermined positions. It is shown that through smart template design stacking faults can be grown predictably into face centered cubic structures. More interestingly, by precise guiding of the stacking faults hollow intergrowth channels can be grown at predetermined lateral and vertical positions. The mechanisms involved in defect growth are promising for extension of this technique to more complex crystal structures, such as the diamond structure, as well as to more complex faults, including corners and t-junctions.

The porosity, acidity, and reactivity of dealuminated zeolite ZSM-5 at the single particle level: the influence of the zeolite architecture.

A combination of atomic force microscopy (AFM), high-resolution scanning electron microscopy (HR-SEM), focused-ion-beam scanning electron microscopy (FIB-SEM), X-ray photoelectron spectroscopy (XPS), confocal fluorescence microscopy (CFM), and UV/Vis and synchrotron-based IR microspectroscopy was used to investigate the dealumination processes of zeolite ZSM-5 at the individual crystal level. It was shown that steaming has a significant impact on the porosity, acidity, and reactivity of the zeolite materials. The catalytic performance, tested by the styrene oligomerization and methanol-to-olefin reactions, led to the conclusion that mild steaming conditions resulted in greatly enhanced acidity and reactivity of dealuminated zeolite ZSM-5. Interestingly, only residual surface mesoporosity was generated in the mildly steamed ZSM-5 zeolite, leading to rapid crystal coloration and coking upon catalytic testing and indicating an enhanced deactivation of the zeolites. In contrast, harsh steaming conditions generated 5-50 nm mesopores, extensively improving the accessibility of the zeolites. However, severe dealumination decreased the strength of the Brønsted acid sites, causing a depletion of the overall acidity, which resulted in a major drop in catalytic activity.

FIB-SEM cathodoluminescence tomography: practical and theoretical considerations.

Focused ion beam-scanning electron microscope (FIB-SEM) tomography is a powerful application in obtaining three-dimensional (3D) information. The FIB creates a cross section and subsequently removes thin slices. The SEM takes images using secondary or backscattered electrons, or maps every slice using X-rays and/or electron backscatter diffraction patterns. The objective of this study is to assess the possibilities of combining FIB-SEM tomography with cathodoluminescence (CL) imaging. The intensity of CL emission is related to variations in defect or impurity concentrations. A potential problem with FIB-SEM CL tomography is that ion milling may change the defect state of the material and the CL emission. In addition the conventional tilted sample geometry used in FIB-SEM tomography is not compatible with conventional CL detectors. Here we examine the influence of the FIB on CL emission in natural diamond and the feasibility of FIB-SEM CL tomography. A systematic investigation establishes that the ion beam influences CL emission of diamond, with a dependency on both the ion beam and electron beam acceleration voltage. CL emission in natural diamond is enhanced particularly at low ion beam and electron beam voltages. This enhancement of the CL emission can be partly explained by an increase in surface defects induced by ion milling. CL emission enhancement could be used to improve the CL image quality. To conduct FIB-SEM CL tomography, a recently developed novel specimen geometry is adopted to enable sequential ion milling and CL imaging on an untilted sample. We show that CL imaging can be manually combined with FIB-SEM tomography with a modified protocol for 3D microstructure reconstruction. In principle, automated FIB-SEM CL tomography should be feasible, provided that dedicated CL detectors are developed that allow subsequent milling and CL imaging without manual intervention, as the current CL detector needs to be manually retracted before a slice can be milled. Due to the required high electron beam acceleration voltage for CL emission, the resolution for FIB-SEM CL tomography is currently limited to several hundreds of nm in XY and up to 650 nm in Z for diamonds. Opaque materials are likely to have an improved Z resolution, as CL emission generated deeper in the material is not able to escape from it.