Optical STEM detection for scanning electron microscopy

Recent advances in electron microscopy techniques have led to a significant scale up in volumetric imaging of biological tissue. The throughput of electron microscopes, however, remains a limiting factor for the volume that can be imaged in high resolution within reasonable time. Faster detection methods will improve throughput. Here, we have characterized and benchmarked a novel detection technique for scanning electron microscopy: optical scanning transmission electron microscopy (OSTEM). A qualitative and quantitative comparison was performed between OSTEM, secondary and backscattered electron detection and annular dark field detection in scanning transmission electron microscopy. Our analysis shows that OSTEM produces images similar to backscattered electron detection in terms of contrast, resolution and signal-to-noise ratio. OSTEM can complement large scale imaging with (scanning) transmission electron microscopy and has the potential to speed up imaging in single-beam scanning electron microscope.

Robust Local Thickness Estimation of Sub-Micrometer Specimen by 4D-STEM

A quantitative four-dimensional scanning transmission electron microscopy (4D-STEM) imaging technique (q4STEM) for local thickness estimation across amorphous specimen such as obtained by focused ion beam (FIB)-milling of lamellae for (cryo-)TEM analysis is presented. This study is based on measuring spatially resolved diffraction patterns to obtain the angular distribution of electron scattering, or the ratio of integrated virtual dark and bright field STEM signals, and their quantitative evaluation using Monte Carlo simulations. The method is independent of signal intensity calibrations and only requires knowledge of the detector geometry, which is invariant for a given instrument. This study demonstrates that the method yields robust thickness estimates for sub-micrometer amorphous specimen using both direct detection and light conversion 2D-STEM detectors in a coincident FIB-SEM and a conventional SEM. Due to its facile implementation and minimal dose reauirements, it is anticipated that this method will find applications for in situ thickness monitoring during lamella fabrication of beam-sensitive materials.

Correlative light and electron microscopy reveals fork-shaped structures at actin entry sites of focal adhesions

Focal adhesions (FAs) are the main cellular structures to link the intracellular cytoskeleton to the extracellular matrix. FAs mediate cell adhesion, are important for cell migration and are involved in many (patho)-physiological processes. Here we examined FAs and their associated actin fibres using correlative fluorescence and scanning electron microscopy (SEM). We used fluorescence images of cells expressing paxillin-GFP to define the boundaries of FA complexes in SEM images, without using SEM contrast enhancing stains. We observed that SEM contrast was increased around the actin fibre entry site in 98% of FAs, indicating increases in protein density and possibly also phosphorylation levels in this area. In nearly three quarters of the FAs, these nanostructures had a fork shape, with the actin forming the stem and the high-contrast FA areas the fork. In conclusion, the combination of fluorescent and electron microscopy allowed accurate localisation of a highly abundant, novel fork structure at the FA-actin interface.

Imaging resonant micro-cantilever movement with ultrafast scanning electron microscopy

Here, we demonstrate ultrafast scanning electron microscopy (SEM) for making ultrafast movies of mechanical oscillators at resonance with nanoscale spatiotemporal resolution. Locking the laser excitation pulse sequence to the electron probe pulses allows for video framerates over 50 MHz, well above the detector bandwidth, while maintaining the electron beam resolution and depth of focus. The pulsed laser excitation is tuned to the oscillator resonance with a pulse frequency modulation scheme. We use an atomic force microscope cantilever as a model resonator, for which we show ultrafast real-space imaging of the first and even the 2 MHz second harmonic oscillation as well as verification of power and frequency response via the ultrafast movies series. We detect oscillation amplitudes as small as 20 nm and as large as 9 μm. Our implementation of ultrafast SEM for visualizing nanoscale oscillatory dynamics adds temporal resolution to the domain of SEM, providing new avenues for the characterization and development of devices based on micro- and nanoscale resonant motion.

How innovations in methodology offer new prospects for volume electron microscopy

Detailed knowledge of biological structure has been key in understanding biology at several levels of organisation, from organs to cells and proteins. Volume electron microscopy (volume EM) provides high resolution 3D structural information about tissues on the nanometre scale. However, the throughput rate of conventional electron microscopes has limited the volume size and number of samples that can be imaged. Recent improvements in methodology are currently driving a revolution in volume EM, making possible the structural imaging of whole organs and small organisms. In turn, these recent developments in image acquisition have created or stressed bottlenecks in other parts of the pipeline, like sample preparation, image analysis and data management. While the progress in image analysis is stunning due to the advent of automatic segmentation and server‐based annotation tools, several challenges remain. Here we discuss recent trends in volume EM, emerging methods for increasing throughput and implications for sample preparation, image analysis and data management.

Integrated Array Tomography for 3D Correlative Light and Electron Microscopy

Volume electron microscopy (EM) of biological systems has grown exponentially in recent years due to innovative large-scale imaging approaches. As a standalone imaging method, however, large-scale EM typically has two major limitations: slow rates of acquisition and the difficulty to provide targeted biological information. We developed a 3D image acquisition and reconstruction pipeline that overcomes both of these limitations by using a widefield fluorescence microscope integrated inside of a scanning electron microscope. The workflow consists of acquiring large field of view fluorescence microscopy (FM) images, which guide to regions of interest for successive EM (integrated correlative light and electron microscopy). High precision EM-FM overlay is achieved using cathodoluminescent markers. We conduct a proof-of-concept of our integrated workflow on immunolabelled serial sections of tissues. Acquisitions are limited to regions containing biological targets, expediting total acquisition times and reducing the burden of excess data by tens or hundreds of GBs.

A cryogenic, coincident fluorescence, electron, and ion beam microscope

Cryogenic electron tomography (cryo-ET) combined with subtomogram averaging, allows in situ visualization and structure determination of macromolecular complexes at subnanometre resolution. Cryogenic focused ion beam (cryo-FIB) micromachining is used to prepare a thin lamella-shaped sample out of a frozen-hydrated cell for cryo-ET imaging, but standard cryo-FIB fabrication is blind to the precise location of the structure or proteins of interest. Fluorescence-guided focused ion beam (FIB) milling at target locations requires multiple sample transfers prone to contamination, and relocation and registration accuracy is often insufficient for 3D targeting. Here, we present in situ fluorescence microscopy-guided FIB fabrication of a frozen-hydrated lamella to address this problem: we built a coincident three-beam cryogenic correlative microscope by retrofitting a compact cryogenic microcooler, custom positioning stage, and an inverted widefield fluorescence microscope (FM) on an existing FIB scanning electron microscope. We show FM controlled targeting at every milling step in the lamella fabrication process, validated with transmission electron microscope tomogram reconstructions of the target regions. The ability to check the lamella during and after the milling process results in a higher success rate in the fabrication process and will increase the throughput of fabrication for lamellae suitable for high-resolution imaging.

Electron-Beam Induced Luminescence and Bleaching in Polymer Resins and Embedded Biomaterial

Electron microscopy is crucial for imaging biological ultrastructure at nanometer resolution. However, electron irradiation also causes specimen damage, reflected in structural and chemical changes that can give rise to alternative signals. Here, luminescence induced by electron-beam irradiation is reported across a range of materials widely used in biological electron microscopy. Electron-induced luminescence is spectrally characterized in two epoxy (Epon, Durcupan) and one methacrylate resin (HM20) over a broad electron fluence range, from 10^-4 to 10³ mC cm^-2 , both with and without embedded biological samples. Electron-induced luminescence is pervasive in polymer resins, embedded biomaterial, and occurs even in fixed, whole cells in the absence of resin. Across media, similar patterns of intensity rise, spectral red-shifting, and bleaching upon increasing electron fluence are observed. Increased landing energies cause reduced scattering in the specimen shifting the luminescence profiles to higher fluences. Predictable and tunable electron-induced luminescence in natural and synthetic polymer media is advantageous for turning many polymers into luminescent nanostructures or to fluorescently visualize (micro)plastics. Furthermore, these findings provide perspective to direct electron-beam excitation approaches like cathodoluminescence that may be obscured by these nonspecific electron-induced signals.

Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy

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The use of a negative bias potential was empirically optimized for tissue imaging with SEM.

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Optimized bias potential leads to a factor 20 increase in imaging speeds as well as an order of magnitude improvement to SNR.

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SNR increase results from a combination of BSE acceleration and detector response.

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Similar increases to SNR can be obtained when a magnetic immersion field is combined with a negative bias potential.

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Stage bias can be applied within an integrated fluorescence and electron microscope allowing for fast correlative imaging of tissue sections.

Large-scale electron microscopy (EM) allows analysis of both tissues and macromolecules in a semi-automated manner, but acquisition rate forms a bottleneck. We reasoned that a negative bias potential may be used to enhance signal collection, allowing shorter dwell times and thus increasing imaging speed. Negative bias potential has previously been used to tune penetration depth in block-face imaging. However, optimization of negative bias potential for application in thin section imaging will be needed prior to routine use and application in large-scale EM. Here, we present negative bias potential optimized through a combination of simulations and empirical measurements. We find that the use of a negative bias potential generally results in improvement of image quality and signal-to-noise ratio (SNR). The extent of these improvements depends on the presence and strength of a magnetic immersion field. Maintaining other imaging conditions and aiming for the same image quality and SNR, the use of a negative stage bias can allow for a 20-fold decrease in dwell time, thus reducing the time for a week long acquisition to less than 8 h. We further show that negative bias potential can be applied in an integrated correlative light electron microscopy (CLEM) application, allowing fast acquisition of a high precision overlaid LM-EM dataset. Application of negative stage bias potential will thus help to solve the current bottleneck of image acquisition of large fields of view at high resolution in large-scale microscopy.

Retarding Field Integrated Fluorescence and Electron Microscope

The authors present the application of a retarding field between the electron objective lens and sample in an integrated fluorescence and electron microscope. The retarding field enhances signal collection and signal strength in the electron microscope. This is beneficial for samples prepared for integrated fluorescence and electron microscopy as the amount of staining material added to enhance electron microscopy signal is typically lower compared to conventional samples in order to preserve fluorescence. We demonstrate signal enhancement through the applied retarding field for both 80-nm post-embedding immunolabeled sections and 100-nm in-resin preserved fluorescence sections. Moreover, we show that tuning the electron landing energy particularly improves imaging conditions for ultra-thin (50 nm) sections, where optimization of both retarding field and interaction volume contribute to the signal improvement. Finally, we show that our integrated retarding field setup allows landing energies down to a few electron volts with 0.3 eV dispersion, which opens new prospects for assessing electron beam induced damage by in situ quantification of the observed bleaching of the fluorescence following irradiation.

Lock-in Ultrafast Electron Microscopy Simultaneously Visualizes Carrier Recombination and Interface-Mediated Trapping

Visualizing charge carrier flow over interfaces or near surfaces meets great challenges concerning resolution and vastly different time scales of bulk and surface dynamics. Ultrafast or four-dimensional scanning electron microscopy (USEM) using a laser pump electron probe scheme circumvents the optical diffraction limit, but disentangling surface-mediated trapping and ultrafast carrier dynamics in a single measurement scheme has not yet been demonstrated. Here, we present lock-in USEM, which simultaneously visualizes fast bulk recombination and slow trapping. As a proof of concept, we show that the surface termination on GaAs, i.e., Ga or As, profoundly influences ultrafast movies. We demonstrate the differences can be attributed to trapping-induced surface voltages of approximately 100-200 mV, which is further supported by secondary electron particle tracing calculations. The simultaneous visualization of both competing processes opens new perspectives for studying carrier transport in layered, nanostructured, and two-dimensional semiconductors, where carrier trapping constitutes a major bottleneck for device efficiency.

Photoemission sources and beam blankers for ultrafast electron microscopy

Observing atomic motions as they occur is the dream goal of ultrafast electron microscopy (UEM). Great progress has been made so far thanks to the efforts of many scientists in developing the photoemission sources and beam blankers needed to create short pulses of electrons for the UEM experiments. While details on these setups have typically been reported, a systematic overview of methods used to obtain a pulsed beam and a comparison of relevant source parameters have not yet been conducted. In this report, we outline the basic requirements and parameters that are important for UEM. Different types of imaging modes in UEM are analyzed and summarized. After reviewing and analyzing the different kinds of photoemission sources and beam blankers that have been reported in the literature, we estimate the reduced brightness for all the photoemission sources reviewed and compare this to the brightness in the continuous and blanked beams. As for the problem of pulse broadening caused by the repulsive forces between electrons, four main methods available to mitigate the dispersion are summarized. We anticipate that the analysis and conclusions provided in this manuscript will be instructive for designing an UEM setup and could thus push the further development of UEM.

The 2018 correlative microscopy techniques roadmap

Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.

Nanoscale Imaging of Light-Matter Coupling Inside Metal-Coated Cavities with a Pulsed Electron Beam

Many applications in (quantum) nanophotonics rely on controlling light-matter interaction through strong, nanoscale modification of the local density of states (LDOS). All-optical techniques probing emission dynamics in active media are commonly used to measure the LDOS and benchmark experimental performance against theoretical predictions. However, metal coatings needed to obtain strong LDOS modifications in, for instance, nanocavities, are incompatible with all-optical characterization. So far, no reliable method exists to validate theoretical predictions. Here, we use subnanosecond pulses of focused electrons to penetrate the metal and excite a buried active medium at precisely defined locations inside subwavelength resonant nanocavities. We reveal the spatial layout of the spontaneous-emission decay dynamics inside the cavities with deep-subwavelength detail, directly mapping the LDOS. We show that emission enhancement converts to inhibition despite an increased number of modes, emphasizing the critical role of optimal emitter location. Our approach yields fundamental insight in dynamics at deep-subwavelength scales for a wide range of nano-optical systems.

Nanoparticle discrimination based on wavelength and lifetime-multiplexed cathodoluminescence microscopy

Nanomaterials can be identified in high-resolution electron microscopy images using spectrally-selective cathodoluminescence. Capabilities for multiplex detection can however be limited, e.g., due to spectral overlap or availability of filters. Also, the available photon flux may be limited due to degradation under electron irradiation. Here, we demonstrate single-pass cathodoluminescence-lifetime based discrimination of different nanoparticles, using a pulsed electron beam. We also show that cathodoluminescence lifetime is a robust parameter even when the nanoparticle cathodoluminescence intensity decays over an order of magnitude. We create lifetime maps, where the lifetime of the cathodoluminescence emission is correlated with the emission intensity and secondary-electron images. The consistency of lifetime-based discrimination is verified by also correlating the emission wavelength and the lifetime of nanoparticles. Our results show how cathodoluminescence lifetime provides an additional channel of information in electron microscopy.

Nanodiamonds as multi-purpose labels for microscopy

Nanodiamonds containing fluorescent nitrogen-vacancy centers are increasingly attracting interest for use as a probe in biological microscopy. This interest stems from (i) strong resistance to photobleaching allowing prolonged fluorescence observation times; (ii) the possibility to excite fluorescence using a focused electron beam (cathodoluminescence; CL) for high-resolution localization; and (iii) the potential use for nanoscale sensing. For all these schemes, the development of versatile molecular labeling using relatively small diamonds is essential. Here, we show the direct targeting of a biological molecule with nanodiamonds as small as 70 nm using a streptavidin conjugation and standard antibody labelling approach. We also show internalization of 40 nm sized nanodiamonds. The fluorescence from the nanodiamonds survives osmium-fixation and plastic embedding making them suited for correlative light and electron microscopy. We show that CL can be observed from epon-embedded nanodiamonds, while surface-exposed nanoparticles also stand out in secondary electron (SE) signal due to the exceptionally high diamond SE yield. Finally, we demonstrate the magnetic read-out using fluorescence from diamonds prior to embedding. Thus, our results firmly establish nanodiamonds containing nitrogen-vacancy centers as unique, versatile probes for combining and correlating different types of microscopy, from fluorescence imaging and magnetometry to ultrastructural investigation using electron microscopy.

Automated sub-5 nm image registration in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers

In the biological sciences, data from fluorescence and electron microscopy is correlated to allow fluorescence biomolecule identification within the cellular ultrastructure and/or ultrastructural analysis following live-cell imaging. High-accuracy (sub-100 nm) image overlay requires the addition of fiducial markers, which makes overlay accuracy dependent on the number of fiducials present in the region of interest. Here, we report an automated method for light-electron image overlay at high accuracy, i.e. below 5 nm. Our method relies on direct visualization of the electron beam position in the fluorescence detection channel using cathodoluminescence pointers. We show that image overlay using cathodoluminescence pointers corrects for image distortions, is independent of user interpretation, and does not require fiducials, allowing image correlation with molecular precision anywhere on a sample.

Time-resolved cathodoluminescence microscopy with sub-nanosecond beam blanking for direct evaluation of the local density of states

We show cathodoluminescence-based time-resolved electron beam spectroscopy in order to directly probe the spontaneous emission decay rate that is modified by the local density of states in a nanoscale environment. In contrast to dedicated laser-triggered electron-microscopy setups, we use commercial hardware in a standard SEM, which allows us to easily switch from pulsed to continuous operation of the SEM. Electron pulses of 80-90 ps duration are generated by conjugate blanking of a high-brightness electron beam, which allows probing emitters within a large range of decay rates. Moreover, we simultaneously attain a resolution better than λ/10, which ensures details at deep-subwavelength scales can be retrieved. As a proof-of-principle, we employ the pulsed electron beam to spatially measure excited-state lifetime modifications in a phosphor material across the edge of an aluminum half-plane, coated on top of the phosphor. The measured emission dynamics can be directly related to the structure of the sample by recording photon arrival histograms together with the secondary-electron signal. Our results show that time-resolved electron cathodoluminescence spectroscopy is a powerful tool of choice for nanophotonics, within reach of a large audience.

Electron Microscopy of Living Cells During in Situ Fluorescence Microscopy

We present an approach toward dynamic nanoimaging: live fluorescence of cells encapsulated in a bionanoreactor is complemented with in situ scanning electron microscopy (SEM) on an integrated microscope. This allows us to take SEM snapshots on-demand, that is, at a specific location in time, at a desired region of interest, guided by the dynamic fluorescence imaging. We show that this approach enables direct visualization, with EM resolution, of the distribution of bioconjugated quantum dots on cellular extensions during uptake and internalization.

Correlated light and electron microscopy: ultrastructure lights up!

Microscopy has gone hand in hand with the study of living systems since van Leeuwenhoek observed living microorganisms and cells in 1674 using his light microscope. A spectrum of dyes and probes now enable the localization of molecules of interest within living cells by fluorescence microscopy. With electron microscopy (EM), cellular ultrastructure has been revealed. Bridging these two modalities, correlated light microscopy and EM (CLEM) opens new avenues. Studies of protein dynamics with fluorescent proteins (FPs), which leave the investigator 'in the dark' concerning cellular context, can be followed by EM examination. Rare events can be preselected at the light microscopy level before EM analysis. Ongoing development-including of dedicated probes, integrated microscopes, large-scale and three-dimensional EM and super-resolution fluorescence microscopy-now paves the way for broad CLEM implementation in biology.

Loss of SMAD4 alters BMP signaling to promote colorectal cancer cell metastasis via activation of Rho and ROCK

BACKGROUND & AIMS

SMAD4 frequently is lost from colorectal cancers (CRCs), which is associated with the development of metastases and a poor prognosis. SMAD4 loss is believed to alter transforming growth factor β signaling to promote tumor progression. However, SMAD4 is also a central component of the bone morphogenetic protein (BMP) signaling pathway, implicated in CRC pathogenesis by human genetic studies. We investigated the effects of alterations in BMP signaling on the invasive and metastatic abilities of CRC cells and changes in members in this pathway in human tumor samples.

METHODS

We activated BMP signaling in SMAD4-positive and SMAD4-negative CRC cells (HCT116, HT-29, SW480, and LS174T); SMAD4 was stably expressed or knocked down using lentiviral vectors. We investigated the effects on markers of epithelial-mesenchymal transition and on cell migration, invasion, and formation of invadopodia. We performed kinase activity assays to characterize SMAD4-independent BMP signaling and used an inhibitor screen to identify pathways that regulate CRC cell migration. We investigated the effects of the ROCK inhibitor Y-27632 in immunocompromised (CD-1 Nu) mice with orthotopic metastatic tumors. Immunohistochemistry was used to detect BMPR1a, BMPR1b, BMPR2, and SMAD4 in human colorectal tumors; these were related to patient survival times.

RESULTS

Activation of BMP signaling in SMAD4-negative cells altered protein and messenger RNA levels of markers of epithelial-mesenchymal transition and increased cell migration, invasion, and formation of invadopodia. Knockdown of the BMP receptor in SMAD4-negative cells reduced their invasive activity in vitro. SMAD4-independent BMP signaling activated Rho signaling via ROCK and LIM domain kinase (LIMK). Pharmacologic inhibition of ROCK reduced metastasis of colorectal xenograft tumors in mice. Loss of SMAD4 from colorectal tumors has been associated with reduced survival time; we found that this association is dependent on the expression of BMP receptors but not transforming growth factor β receptors.

CONCLUSIONS

Loss of SMAD4 from colorectal cancer cells causes BMP signaling to switch from tumor suppressive to metastasis promoting. Concurrent loss of SMAD4 and normal expression of BMP receptors in colorectal tumors was associated with reduced survival times of patients. Reagents that interfere with SMAD4-independent BMP signaling, such as ROCK inhibitors, might be developed as therapeutics for CRC.

Cathodoluminescence Microscopy of nanostructures on glass substrates

Cathodoluminescence (CL) microscopy is an emerging analysis technique in the fields of biology and photonics, where it is used for the characterization of nanometer sized structures. For these applications, the use of transparent substrates might be highly preferred, but the detection of CL from nanostructures on glass is challenging because of the strong background generated in these substrates and the relatively weak CL signal from the nanostructures. We present an imaging system for highly efficient CL detection through the substrate using a high numerical aperture objective lens. This system allows for detection of individual nano-phosphors down to thirty nanometer in size as well as the up to ninth order plasmon resonance modes of a gold nanowire on ITO coated glass. We analyze the CL signal-to-background dependence on the primary electron beam energy and discuss different approaches to minimize its influence on the measurement.

Simultaneous correlative scanning electron and high-NA fluorescence microscopy

Correlative light and electron microscopy (CLEM) is a unique method for investigating biological structure-function relations. With CLEM protein distributions visualized in fluorescence can be mapped onto the cellular ultrastructure measured with electron microscopy. Widespread application of correlative microscopy is hampered by elaborate experimental procedures related foremost to retrieving regions of interest in both modalities and/or compromises in integrated approaches. We present a novel approach to correlative microscopy, in which a high numerical aperture epi-fluorescence microscope and a scanning electron microscope illuminate the same area of a sample at the same time. This removes the need for retrieval of regions of interest leading to a drastic reduction of inspection times and the possibility for quantitative investigations of large areas and datasets with correlative microscopy. We demonstrate Simultaneous CLEM (SCLEM) analyzing cell-cell connections and membrane protrusions in whole uncoated colon adenocarcinoma cell line cells stained for actin and cortactin with AlexaFluor488. SCLEM imaging of coverglass-mounted tissue sections with both electron-dense and fluorescence staining is also shown.

Selective functionalization of tailored nanostructures

The controlled positioning of nanostructures with active molecular components is of importance throughout nanoscience and nanotechnology. We present a novel three-step method to produce nanostructures that are selectively decorated with functional molecules. We use fluorophores and nanoparticles to functionalize SiO features with defined shapes and with sizes ranging from micrometers to 25 nm. The method is called MACE-ID: molecular assembly controlled by electron-beam-induced deposition. In the first step, SiO nanostructures are written with focused electron-beam-induced deposition, a direct-writing technique. In the second step, the deposits are selectively silanized. In the final step, the silanes are functionalized with fluorescent dyes, polystyrene spheres, or gold nanoparticles. This recipe gives exciting new possibilities for combining the highly accurate control of top-down patterning (e-beam direct writing) with the rich variety of the bottom-up approach (self-assembly), leading to active or responsive surfaces. An important advantage of MACE-ID is that it can be used on substrates that already contain complex features, such as plasmonic structures, nanoantennas, and cavities.

The single molecule probe: nanoscale vectorial mapping of photonic mode density in a metal nanocavity

We use superresolution single-molecule polarization and lifetime imaging to probe the local density of states (LDOS) in a metal nanocavity. Determination of the orientation of the molecular transition dipole allows us to retrieve the different LDOS behavior for parallel and perpendicular orientations with respect to the metal interfaces. For the perpendicular orientation, a strong lifetime reduction is observed for distances up to 150 nm from the cavity edge due to coupling to surface plasmon polariton modes in the metal. Contrarily, for the parallel orientation we observe lifetime variations resulting from coupling to characteristic lambda/2 cavity modes. Our results are in good agreement with calculations of the nanoscale variations of the projected LDOS, which demonstrates the potential of single molecules as nonperturbative, nanoscale vectorial point probes in photonic and biological nanostructures.

Power-Law Blinking in the Fluorescence of Single Organic Molecules

The blinking behavior of perylene diïmide molecules is investigated at the single-molecule level. We observe long-time scale blinking of individual multi-chromophoric complexes embedded in a poly(methylmethacrylate) matrix, as well as for the monomeric dye absorbed on a glass substrate at ambient conditions. In both these different systems, the blinking of single molecules is found to obey analogous power-law statistics for both the on and off periods. The observed range for single-molecular power-law blinking extends over the full experimental time window, covering four orders of magnitude in time and six orders of magnitude in probability density. From molecule to molecule, we observe a large spread in off-time power-law exponents. The distributions of off-exponents in both systems are markedly different whereas both on-exponent distributions appear similar. Our results are consistent with models that ascribe the power-law behavior to charge separation and (environment-dependent) recombination by electron tunneling to a dynamic distribution of charge acceptors. As a consequence of power-law statistics, single molecule properties like the total number of emitted photons display non-ergodicity.

Accurate and unbiased estimation of power-law exponents from single-emitter blinking data

Single emitter blinking with a power-law distribution for the on and off times has been observed on a variety of systems including semiconductor nanocrystals, conjugated polymers, fluorescent proteins, and organic fluorophores. The origin of this behavior is still under debate. Reliable estimation of power exponents from experimental data is crucial in validating the various models under consideration. We derive a maximum likelihood estimator for power-law distributed data and analyze its accuracy as a function of data set size and power exponent both analytically and numerically. Results are compared to least-squares fitting of the double logarithmically transformed probability density. We demonstrate that least-squares fitting introduces a severe bias in the estimation result and that the maximum likelihood procedure is superior in retrieving the correct exponent and reducing the statistical error. For a data set as small as 50 data points, the error margins of the maximum likelihood estimator are already below 7%, giving the possibility to quantify blinking behavior when data set size is limited, e.g., due to photobleaching.

Effect of disorder on ultrafast exciton dynamics probed by single molecule spectroscopy

We present a single-molecule study unraveling the effect of static disorder on the vibrational-assisted ultrafast exciton dynamics in multichromophoric systems. For every single complex, we probe the initial exciton relaxation process by an ultrafast pump-probe approach and the coupling to vibrational modes by emission spectra, while fluorescence lifetime analysis measures the amount of static disorder. Exploiting the wide range of disorder found from complex to complex, we demonstrate that static disorder accelerates the dephasing and energy relaxation rate of the exciton.

Energy transfer in single-molecule photonic wires

Molecular photonics is a new emerging field of research around the premise that it is possible to develop optical devices using single molecules as building blocks. Truly technological impact in the field requires focussed efforts on designing functional molecular devices as well as having access to their photonic properties on an individual basis. In this Minireview we discuss our approach towards the design and single-molecule investigation of one-dimensional multimolecular arrays intended to work as molecular photonic wires. Three different schemes have been explored: a) perylene-based dimer and trimer arrays displaying coherent exciton delocalisation at room temperature; b) DNA-based unidirectional molecular wires containing up to five different chromophores and exhibiting weak excitonic interactions between neighbouring dyes; and c) one-dimensional multichromophoric polymers based on perylene polyisocyanides showing excimerlike emission. As a whole, our single-molecule data show the importance of well-defined close packing of chromophores for obtaining optimal excitonic behaviour at room temperature. Further improvement on (bio)chemical synthesis, together with the use of single-molecule techniques, should lead in the near future to efficient and reliable photonic wires with true device functionality.

Shape-induced frustration of hexagonal order in polyhedral colloids

The effect of a nonspherical particle shape and shape polydispersity on the structure of densely packed hard colloidal particles was studied in real space by confocal microscopy. We show that the first layer at the wall of concentrated size-monodisperse but shape-polydisperse polyhedral colloids exhibits significant deviations from a hexagonal lattice. These deviations are identified as bond-orientational fluctuations which lead to percolating "mismatch lines." While the shape-induced geometrical frustration of the hexagonal symmetry suppresses translational order, bond-orientational order is clearly retained, indicating a hexaticlike structure of the polyhedral colloids.

Power-law-distributed dark states are the main pathway for photobleaching of single organic molecules

We exploit the strong excitonic coupling in a superradiant trimer molecule to distinguish between long-lived collective dark states and photobleaching events. The population and depopulation kinetics of the dark states in a single molecule follow power-law statistics over 5 orders of magnitude in time. This result is consistent with the formation of a radical unit via electron tunneling to a time-varying distribution of trapping sites in the surrounding polymer matrix. We furthermore demonstrate that this radicalization process forms the dominant pathway for molecular photobleaching.

Molecular printboards on silicon oxide: lithographic patterning of cyclodextrin monolayers with multivalent, fluorescent guest molecules

Three compounds bearing multiple adamantyl guest moieties and a fluorescent dye have been synthesized for the supramolecular patterning of beta-cyclodextrin (CD) host monolayers on silicon oxide using microcontact printing and dip-pen nanolithography. Patterns created on monolayers on glass were viewed by laser scanning confocal microscopy. Semi-quantitative analysis of the patterns showed that with microcontact printing approximately a single monolayer of guest molecules is transferred. Exposure to different rinsing procedures showed the stability of the patterns to be governed by specific supramolecular multivalent interactions. Patterns of the guest molecules created at CD monolayers were stable towards thorough rinsing with water, whereas similar patterns created on poly(ethylene glycol) (PEG) reference monolayers were instantly removed. The patterns on CD monolayers displayed long-term stability when stored under N(2), whereas patterns at PEG monolayers faded within a few weeks due to the diffusion of fluorescent molecules across the surface. Assemblies at CD monolayers could be mostly removed by rinsing with a concentrated CD solution, demonstrating the reversibility of the methodology. Patterns consisting of different guest molecules were produced by microcontact printing of one guest molecule and specific adsorption of a second guest molecule from solution to non-contacted areas, giving well-defined alternating assemblies. Fluorescent features of sub-micrometer dimensions were written using supramolecular dip-pen nanolithography.

Single molecule photobleaching probes the exciton wave function in a multichromophoric system

The exciton wave function of a trichromophoric system is investigated by means of single molecule spectroscopy at room temperature. Individual trimers exhibit superradiance and loss of vibronic structure in emission spectrum, features proving exciton delocalization. We identify two distinct photodegradation pathways for single trimers upon sequential photobleaching of the chromophores. The rate of each pathway is a measure for the contribution of the separate dyes to the collective excited state of the system, in this way probing the wave function of the delocalized exciton.

Epitaxial growth of a colloidal hard-sphere hcp crystal and the effects of epitaxial mismatch on crystal structure

We demonstrate the epitaxial growth of hard-sphere hcp and double hcp crystals using a surface pattern that directly dictates the stacking sequence. A detailed three-dimensional analysis based on real-space measurements is performed on crystal structure as a function of template-crystal mismatch, which demonstrates the possibilities of colloidal epitaxy as a model system for studying the effects of a patterned substrate on crystal structure. Perfect template-induced hcp-crystal growth occurs at an isotropically deformed template. At deformed lattices we observe growth of a non-close-packed superstructure and of a perfect (100)-aligned fcc crystal. Small mismatches lead to increased out-of-plane displacements followed by a structural breakup in "crystal" grains where particle positions in successive layers are strictly periodic and "defect" grains where these positions are displaced with respect to each other. Large mismatches prevent crystallization in the surface layers. The volume fraction was found to vary drastically (up to about 20% ) as a function of template deformation.

Hard-sphere crystals with hcp and non-close-packed structure grown by colloidal epitaxy

We demonstrate the epitaxial growth of a metastable (with respect to the bulk) hcp crystal as well as any other close-packed stacking sequence of colloidal hard spheres. At certain stretched and compressed lattices we furthermore observed growth of a non-close-packed superstructure and of a perfect (100)-aligned fcc crystal. Perfect template-induced hcp-crystal growth occurs at lattice spacings that are larger than for bulk crystallization, indicative of prefreezing. Small mismatches lead to increased out-of-plane displacements. Large mismatches prevent crystallization in the surface layers.

Colloidal epitaxy: playing with the boundary conditions of colloidal crystallization

We have studied, with quantitative confocal microscopy, epitaxial colloidal crystal growth of particles interacting with an almost hard-sphere (HS) potential in a gravitational field and density matched colloids interacting with a long-range (LR) repulsive potential with a body-centred cubic (BCC) equilibrium crystal phase. We show that in both cases it is possible to grow thick, stacking fault-free metastable crystals: close-packed crystals with any stacking sequence, including hexagonal close packed (HCP), for the HS particles and face-centred cubic (FCC) in the case of the LR colloids. In accordance with recent computer simulations done for HS particles it was found that the optimal lattice constant to grow HS HCP crystals was larger than that of equilibrium FCC crystals. In addition, because of the absence of gravity, pre-freezing could be observed for the particles with the LR potential on a template of charged lines. We also argue that the ability to manipulate colloids with highly focused light, optical traps or tweezers, will become an important tool in both the study of colloidal crystallization and in making new structures. We show how cheap 2D and 3D templates can be made with optical tweezers and demonstrate, in proof of principle experiments with core-shell colloids, how light fields can generate crystal nuclei and other structures in the bulk of concentrated dispersions and how the effect of these structures on the rest of a dispersion can be studied quantitatively in 3D.

Epitaxial crystal growth of charged colloids

A pattern of repulsive, charged lines is shown to direct three-dimensional (3D) crystallization in a system of long-range repulsive, density-matched colloids. At volume fractions where the bulk phase behavior leads to bcc crystallization, the 1D template was found to induce formation of a metastable fcc crystal. The bcc crystals were oriented with the (100) or the (110) plane, with twofold twinning, parallel to the template. The template further induced prefreezing of the (100) plane. At a large mismatch between template and interparticle spacing, 1D strings form in the surface layer of a 3D crystal.