Atomic force microscope (AFM) combined with the ultramicrotome: a novel device for the serial section tomography and AFM/TEM complementary structural analysis of biological and polymer samples

A new device (NTEGRA Tomo) that is based on the integration of the scanning probe microscope (SPM) (NT‐MDT NTEGRA SPM) and the Ultramicrotome (Leica UC6NT) is presented. This integration enables the direct monitoring of a block face surface immediately following each sectioning cycle of ultramicrotome sectioning procedure. Consequently, this device can be applied for a serial section tomography of the wide range of biological and polymer materials. The automation of the sectioning/scanning cycle allows one to acquire up to 10 consecutive sectioned layer images per hour. It also permits to build a 3‐D nanotomography image reconstructed from several tens of layer images within one measurement session. The thickness of the layers can be varied from 20 to 2000 nm, and can be controlled directly by its interference colour in water. Additionally, the NTEGRA Tomo with its nanometer resolution is a valid instrument narrowing and highlighting an area of special interest within volume of the sample. For embedded biological objects the ultimate resolution of SPM mostly depends on the quality of macromolecular preservation of the biomaterial during sample preparation procedure. For most polymer materials it is comparable to transmission electron microscopy (TEM). The NTEGRA Tomo can routinely collect complementary AFM and TEM images. The block face of biological or polymer sample is investigated by AFM, whereas the last ultrathin section is analyzed with TEM after a staining procedure. Using the combination of both of these ultrastructural methods for the analysis of the same particular organelle or polymer constituent leads to a breakthrough in AFM/TEM image interpretation. Finally, new complementary aspects of the object's ultrastructure can be revealed.     

Characterization of biological macromolecules by combined mass mapping and electron energy-loss spectroscopy

The combination of scanning transmission electron microscopy (STEM) and parallel-detection energy-loss spectroscopy (EELS) was used to detect specific bound elements within macromolecules and macromolecular assemblies prepared by direct freezing. After cryotransferring and freeze-drying in situ, samples were re-cooled to liquid nitrogen temperature and low-dose (about 10³ e/nm²) digital dark-field images were obtained with single-electron sensitivity using a beam energy of approximately 100 keV and a probe current of approximately 5 pA. These maps provided a means of characterizing the molecular weights of the structures at low dose. The probe current was subsequently increased to about 5 nA in order to perform elemental analysis. The 320 copper atoms in a keyhole limpet haemocyanin molecule (mol.wt = 8 MDa) were detected with a sensitivity of ± 30 atoms in an acquisition time of 200 s. Phosphorus was detected in an approximately 10-nm length of single-stranded RNA contained in a tobacco mosaic virus particle (mol.wt = 130 kDa/nm) with a sensitivity of ± 25 atoms. Near single-atom sensitivity was achieved for the detection of iron in one haemoglobin molecule (mol.wt = 65 kDa, containing four Fe atoms). Such detection limits are only feasible if special processing methods are employed, as is demonstrated by the use of the second-difference acquisition technique and multiple least-squares fitting of reference spectra. Moreover, an extremely high electron dose (about 10¹⁰ e/nm²) is required resulting in mass loss that may be attributable to ‘knock-on’ radiation damage.     

Micro-fabricated mechanical sensors for lateral molecular-force microscopy

Atomic force microscopy (AFM) has been very successful in measuring forces perpendicular to the sample plane. Here, we present the advantages of turning the AFM cantilever 90° in order for it to be perpendicular to the sample. This rotation leads naturally to the detection of in-plane forces with some extra advantages with respect to the AFM orientation. In particular, the use of extremely small (1 μm wide) and soft (k≅10^–5 N/m) micro-fabricated cantilevers is demonstrated by recording their thermal power spectral density in ambient conditions and in liquid. These measurements lead to the complete characterisation of the sensors in terms of their stiffness and resonant frequency. Future applications, which will benefit from the use of this force microscopy technique, are also described.     

Nano/microtribology Stick-Slip Number Under an Atomic Force Microscope and Its Characteristics

The atomic force microscope (AFM) has become a main instrument in observing nano/microtribological characteristics of sample surfaces. In this paper, we investigated the micro-scale adhesive contact between the AFM tip and the sample surface based on the Maugis–Dugdale contact model, and analyzed the energy conversion and dissipation process during the AFM scanning process. A dimensionless stick-slip number = 8U₁h²/(kR_s ²) was defined, which can serve as a characteristic index for the appearance of nano/microtribology stick-slip behavior. If the stick-slip number is less than one, i.e., <1, the AFM tip slides on the sample surface and no stick-slip behavior occurs in the AFM lateral force signal. When the stick-slip number equals one, i.e., = 1, the tip jumps on the sample surface and the AFM lateral force signal begins to exhibit a stick-slip behavior but without energy dissipation. Only in the case of >1 does the stick-slip behavior appear in the AFM lateral force signal accompanied by an obvious energy dissipation. The defined stick-slip number demonstrates that the nano/microtribological stick-slip behavior is due to the adhesive hysteresis as well as the instability motion of the AFM tip during the scanning process. Finally, the influence on nano/microtribology stick-slip behavior of sample surface energy, surface topography, scanning velocity, spring constant of AFM cantilever probe, etc. are investigated theoretically and experimentally. Various experimental results of nano/microtribology stick-slip behavior under AFM are successfully interpreted according to the stick-slip number.     

Investigations on the leaf surface ultrastructure in grapevine (Vitis vinifera L.) by scanning microscopy

Several Scanning microscopy techniques were used to investigate the leaf surface ultrastructure in the local “Razegui” grapevine cultivar (Vitis vinifera L.). Conventional scanning electron microscopy performed on glutaraldehyde‐fixed samples allowed observation of well‐preserved epidermal cells with an overlaying waxy layer. At a high magnification, the waxy layer exhibited crystalline projections in the form of horizontal and vertical platelets. Also, to avoid eventual ultrastructural alterations inherent in the use of solvents during sample preparation, fresh leaf blade samples were directly observed by environmental scanning electron microscopy. A classical image of convex living epidermal cells was observed. At 2400× magnification, epicuticular waxes exhibited a granular structure. However, high‐magnification images were not obtained with this device. The atomic force microscopy (AFM) performed on fresh leaf blade samples allowed observation of a textured surface and heterogeneous profiles attributed to epicuticular wax deposits. AFM topography images confirmed further, the presence of irregular crystalloid wax projections as multishaped platelets on the adaxial surface of grapevine leaf. SCANNING 31: 127–131, 2009. © 2009 Wiley Periodicals, Inc.     

The tribology of advanced digital recording (ADR) systems

The advanced digital recording system, a linear tape recording system is examined with respect to the tribology involved at the head/tape interface. Using atomic force microscopy (AFM), Auger elcetron spectrocopy (AES) and scanning Auger microscopy (SAM) surface characterisation techniques, several wear mechanisms are isolated: scratching, attributed to the polishing action of the tape asperities; microfracture then pullout of the Al₂O₃–TiC ceramic used as tape bearing surface; and ploughing due to three-body action of ceramic pullouts entrapped on the recessed poles. A ceramic differential wear is found to occur at the expense of the Al₂O₃ component, which therefore forms the ceramic recessed regions. The ceramic pullouts involved in the poles' three-body abrasion, however, appear to consist of TiC particles. A model for the ceramic wear mechanism is proposed. A transferred mixture of possibly magnetic pigments, binder and lubricant from the tape to the head is observed in the form of adhesive deposits. The iron component of this transfer is found in higher concentrations on the pole tips and the prominent part of the ceramic.     

Imaging flux vortices in type II superconductors with a commercial transmission electron microscope

Flux vortices in superconductors can be imaged using transmission electron microscopy because the electron beam is deflected by the magnetic flux associated with the vortices. This technique has a better spatial and temporal resolution than many other imaging techniques and is sensitive to the magnetic flux density within each vortex, not simply the fields at the sample surface. Despite these advantages, only two groups have successfully employed the technique using specially adapted instruments. Here we demonstrate that vortices can be imaged with a modern, commercial transmission electron microscope operating at 300 kV equipped with a field emission gun, Lorentz lens and a liquid helium cooled sample holder. We introduce superconductivity for non-specialists and discuss techniques for simulating and optimising images of flux vortices. Sample preparation is discussed in detail as the main difficulty with the technique is the requirement for samples with very large (>10 μm), flat areas so that the image is not dominated by diffraction contrast. We have imaged vortices in superconducting Bi₂Sr₂CaCu₂O_8−δ and use correlation functions to investigate the ordered arrangements they adopt as a function of applied magnetic field.     

Atomic force microscopy to characterize the molecular size of prion protein

The conformational transition of α‐helix‐rich cellular prion protein (PrP^C) to an isomer with high β‐sheet content is associated with transmissible spongiform encephalopathies. With the ultimate long‐term goal of using imaging techniques to study PrP aggregation, we report the results of initial experiments to determine whether PrP molecules could be visualized as single molecules, and if the observed size corresponded to the calculated size for PrP. The investigation of single molecules, and not those embedded into larger aggregates, was the key in our experimental approach. Using atomic force microscopy (AFM) as an imaging method, the immobilization of recombinant histidine (His)₁₀‐tagged PrP on mica was performed in the presence of different heavy metal ions. The addition of Cu²⁺ resulted in an enhanced PrP immobilization, whereas Ni²⁺ reduced coverage of the surface by PrP. High‐resolution data from dried PrP preparations provided a first approximation to geometrical parameters of PrP precipitates, which indicated that the volume of a single PrP molecule was 30 nm³. Molecular dynamics simulations performed to complement the structural aspects of the AFM investigation yielded a calculated molecular volume of 33 nm³ for PrP. These experimentally observed and theoretically expected values provide basic knowledge for further studies on the size and composition of larger amyloidal PrP aggregates, PrP isoforms or mutants such as PrP molecules without octarepeats.     

Atomic force microscopy of freeze-fracture replicas of rat atrial tissue

Atomic force microscopy (AFM) has provided three-dimensional (3-D) surface images of many biological specimens at molecular resolution. In the absence of spectroscopic capability for AFM, it is often difficult to distinguish individual components if the specimen contains a population of mixed structures such as in a cellular membrane. In an effort to understand the AFM images better, a correlative study between AFM and the well-established technique of transmission electron microscopy (TEM) was performed. Freeze-fractured replicas of adult rat atrial tissue were examined by both TEM and AFM. The same replicas were analysed and the same details were identified, which allowed a critical comparison of surface topography by both techniques. AFM images of large-scale subcellular structures (nuclei, mitochondria, granules) correlated well with TEM images. AFM images of smaller features and surface textures appeared somewhat different from the TEM images. This presumably reflects the difference in the surface sensitivity of AFM versus TEM, as well as the nature of images in AFM (3-D surface contour) and TEM (2-D projection). AFM images also provided new information about the replica itself. Unlike TEM, it was possible to examine both sides of the replica with AFM; the resolution on one side was significantly greater compared with the other side. It was also possible to obtain quantitative height information which is not readily available with TEM.     

Gloss phenomena and image analysis of atomic force microscopy in molecular and cell biology

Proper sample preparation, scan setup, data collection and image analysis are key factors in successful atomic force microscopy (AFM), which can avoid gloss phenomena effectively from unreasonable manipulations or instrumental defaults. Fresh cleaved mica and newly treated glass cover were checked first as the substrates for all of the sample preparation for AFM. Then, crystals contamination from buffer was studied separately or combined with several biologic samples, and the influence of scanner, scan mode and cantilever to data collection was also discussed intensively using molecular and cellular samples. At last, images treatment and analysis with off‐line software had been focused on standard and biologic samples, and artificial glosses were highly considered for their high probability. SCANNING 31: 49–58, 2009. © 2009 Wiley Periodicals, Inc.     

A novel sample holder allowing atomic force microscopy on transmission electron microscopy specimen grids: repetitive, direct correlation between AFM and TEM images

A novel sample holder that allows atomic force microscopy (AFM) to be performed on transmission electron microscope (TEM) grids is described. Consequently, AFM and TEM images were repeatedly obtained on exactly the same sample area. For both techniques, a thin carbon film was used as the imaging substrate. Although these techniques have been previously used in conjunction, AFM and TEM images on exactly the same area have not been repeatedly obtained for any system. Correlation of AFM and TEM images is useful for work where the three‐dimensional topographical information provided by the AFM could be used to better interpret the two‐dimensional images provided by the TEM and vice versa. To demonstrate the applicability of such correlation, new results pertaining to a fibrillar collagen system are summarized.     

Evaluation of surface topography changes in three NiTi file systems using rotary and reciprocal motion: An atomic force microscopy study

Aim: To evaluate the surface topography changes in three nickel‐titanium (NiTi) file systems using either rotary or reciprocal motion using atomic force microscopy (AFM), and to determine the effect of scanning area on the AFM results in this study. Methodology: Five points on a F2 Protaper file, R25 Reciproc file, and a Primary file from WaveOne systems were scanned preoperatively in 1 × 1 and 5 × 5 µm² with an AFM device that can scan an intact (not sectioned) file. One standardized resin block was used for each instrument, according to the manufacturer's recommendations. Points were re‐scanned postoperatively using the same AFM and settings. Root‐mean‐square (RMS) and roughness average (Ra) values were obtained. The preoperative and postoperative surface topographies were compared separately in terms of RMS and Ra values. The surface topography change scores were analyzed using Kruskal–Wallis and Mann–Whitney U tests using a 0.10 significance level. Results: There were no significant differences preoperatively among the NiTi file systems in 1 × 1 or 5 × 5 µm² areas. Postoperatively, the WaveOne Primary had more surface irregularities (significant for 5 × 5 µm² scan in Ra evaluation). Conclusions: Three‐dimensional AFM images of instrument surfaces showed topographic irregularities preoperatively and postoperatively. AFM results differ depending on the scanning area and file used. Microsc. Res. Tech. 77:177–182, 2014. © 2013 Wiley Periodicals, Inc.     

High resolution imaging of surface patterns of single bacterial cells

We systematically studied the origin of surface patterns observed on single Sinorhizobium meliloti bacterial cells by comparing the complementary techniques atomic force microscopy (AFM) and scanning electron microscopy (SEM). Conditions ranged from living bacteria in liquid to fixed bacteria in high vacuum. Stepwise, we applied different sample modifications (fixation, drying, metal coating, etc.) and characterized the observed surface patterns. A detailed analysis revealed that the surface structure with wrinkled protrusions in SEM images were not generated de novo but most likely evolved from similar and naturally present structures on the surface of living bacteria. The influence of osmotic stress to the surface structure of living cells was evaluated and also the contribution of exopolysaccharide and lipopolysaccharide (LPS) by imaging two mutant strains of the bacterium under native conditions. AFM images of living bacteria in culture medium exhibited surface structures of the size of single proteins emphasizing the usefulness of AFM for high resolution cell imaging.     

原子力显微镜在多糖分子结构研究中的应用

评述原子力显微镜在多糖分子结构和功能研究的进展,AFM不仅可以在空气和液体中对多糖分子单分子和聚集体成像,得到单分子的直径、长度等量化信息和分子聚集体形貌特征。近年来AFM还用于在液体池中操纵单个多糖分子,获取单分子力学谱研究分子的弹性与构型转变的关系,在单分子水平上对多糖进行鉴定,用于细胞表面大分子黏附作用和细胞识别的研究等。AFM新技术的不断出现,必将在高分子科学的研究中起到越来越重要的作用。     

Visualization and characterization of engineered nanoparticles in complex environmental and food matrices using atmospheric scanning electron microscopy

Imaging and characterization of engineered nanoparticles (ENPs) in water, soils, sediment and food matrices is very important for research into the risks of ENPs to consumers and the environment. However, these analyses pose a significant challenge as most existing techniques require some form of sample manipulation prior to imaging and characterization, which can result in changes in the ENPs in a sample and in the introduction of analytical artefacts. This study therefore explored the application of a newly designed instrument, the atmospheric scanning electron microscope (ASEM), which allows the direct characterization of ENPs in liquid matrices and which therefore overcomes some of the limitations associated with existing imaging methods. ASEM was used to characterize the size distribution of a range of ENPs in a selection of environmental and food matrices, including supernatant of natural sediment, test medium used in ecotoxicology studies, bovine serum albumin and tomato soup under atmospheric conditions. The obtained imaging results were compared to results obtained using conventional imaging by transmission electron microscope (TEM) and SEM as well as to size distribution data derived from nanoparticle tracking analysis (NTA). ASEM analysis was found to be a complementary technique to existing methods that is able to visualize ENPs in complex liquid matrices and to provide ENP size information without extensive sample preparation. ASEM images can detect ENPs in liquids down to 30 nm and to a level of 1 mg L^?1 (9×10⁸ particles mL^?1, 50 nm Au ENPs). The results indicate ASEM is a highly complementary method to existing approaches for analyzing ENPs in complex media and that its use will allow those studying to study ENP behavior in situ, something that is currently extremely challenging to do.     

Novel method for the plan-view TEM preparation of thin samples on brittle substrates by mechanical and ion beam thinning

A new preparation method has been developed in order to avoid the breaking of brittle samples for plan-view TEM investigation during and after mechanical and ion beam thinning. The thinning procedure is carried out on a reduced size piece of the sample (about 1.6 x 0.8 mm(2) or about 1-1.6 mm diameter) that is embedded into a 3-mm-diameter Ti disk, which fits the sample holder of the TEM. The small sample size and the supporting metal disk assure the mechanical stability and minimize the possibility of breaking during and after the preparation: The Ti disk is placed on adhesive kapton tape, a cut piece of the sample is put into the slot of the disk, pressed onto the tape and embedded with glue. The tape keeps the parts in place and in the same plane, keeps the sample surface safe from the embedding glue and can be removed easily after the glue solidifies. Subsequently, the embedded sample is thinned from the rear by well-known mechanical and ion beam techniques until electron transparency. This simple solution lowers the risk of failed sample preparation remarkably and makes it possible to reduce the thickness of the sample to about 50 microm by mechanical thinning. As a result, dimpling becomes unnecessary and low angle ion milling gives a large transparent area for TEM. Its efficiency has been proved by successful preparation of numerous thin film samples on Si, sapphire, and glass substrates. The method is compatible with the widespread cross-sectional thinning procedures, and can be easily adopted by TEM laboratories.     

Rippling on Wear Scar Surfaces of Nanocrystalline Diamond Films After Reciprocating Sliding Against Ceramic Balls

The formation of nanoscopic ripple patterns on top of material surfaces has been reported for different materials and processes, such as sliding against polymers, high-force scanning in atomic force microscopy (AFM), and surface treatment by ion beam sputtering. In this work, we show that such periodic ripples can also be obtained in prolonged reciprocating sliding against nanocrystalline diamond (NCD) films. NCD films with a thickness of 0.8 µm were grown on top of silicon wafer substrates by hot-filament chemical vapor deposition using a mixture of methane and hydrogen. The chemical structure, surface morphology, and surface wear were characterized by Raman spectroscopy, scanning electron microscopy (SEM), and AFM. The tribological properties of the NCD films were evaluated by reciprocating sliding tests against Al₂O₃, Si₃N₄, and ZrO₂ counter balls. Independent of the counter body material, clear ripple patterns with typical heights of about 30 nm induced during the sliding test are observed by means of AFM and SEM on the NCD wear scar surfaces. Although the underlying mechanisms of ripple formation are not yet fully understood, these surface corrugations could be attributed to the different wear phenomena, including a stress-induced micro-fracture and plastic deformation, a surface smoothening, and a surface rehybridization from diamond bonding to an sp ² configuration. The similarity between ripples observed in the present study and ripples reported after repeated AFM tip scanning indicates that ripple formation is a rather universal phenomenon occurring in moving tribological contacts of different materials.     

High accuracy FIONA-AFM hybrid imaging

Multi-protein complexes are ubiquitous and play essential roles in many biological mechanisms. Single molecule imaging techniques such as electron microscopy (EM) and atomic force microscopy (AFM) are powerful methods for characterizing the structural properties of multi-protein and multi-protein-DNA complexes. However, a significant limitation to these techniques is the ability to distinguish different proteins from one another. Here, we combine high resolution fluorescence microscopy and AFM (FIONA-AFM) to allow the identification of different proteins in such complexes. Using quantum dots as fiducial markers in addition to fluorescently labeled proteins, we are able to align fluorescence and AFM information to ≥8 nm accuracy. This accuracy is sufficient to identify individual fluorescently labeled proteins in most multi-protein complexes. We investigate the limitations of localization precision and accuracy in fluorescence and AFM images separately and their effects on the overall registration accuracy of FIONA-AFM hybrid images. This combination of the two orthogonal techniques (FIONA and AFM) opens a wide spectrum of possible applications to the study of protein interactions, because AFM can yield high resolution (5-10 nm) information about the conformational properties of multi-protein complexes and the fluorescence can indicate spatial relationships of the proteins in the complexes.     

Precise measurements of nanostructure parameters

The precision of measurements performed by atomic-force microscopy (AFM) and high-resolution electron microscopy (HREM) for solving problems of metrology and diagnostics of solid nanostructures is discussed. The HREM-measured height of a monatomic step on a Si(111) surface covered by a thin natural oxide film is demonstrated to be 0.314 ± 0.001 nm. The same accuracy is ensured by AFM measurements through controlling the Si surface relief with heating in ultra-high vacuum on specially created test objects with the distance between the steps being approximately 2 μm. It is shown that the geometric phase method can be used to quantify the strains in the crystal lattice of strained heterostructures on the basis of HREM images with accuracy to 10⁻⁴%, and in situ irradiation by electrons in HREM measurements can be used to visualize ordered clusterization of vacancies and self-interstitial atoms in {113} planes in Si samples.     

Surface micromorphology of dental composites [CE‐TZP]‐[Al2O3] with Ca+2 modifier

The objective of this study was to characterize the three‐dimensional (3D) surface micromorphology of the ceramics produced from nanoparticles of alumina and tetragonal zirconia (t‐ZrO₂) with addition of Ca⁺² for sintering improvement. The 3D surface roughness of samples was studied by atomic force microscopy (AFM), fractal analysis of the 3D AFM‐images, and statistical analysis of surface roughness parameters. Cube counting method, based on the linear interpolation type, applied for AFM data was used for fractal analysis. The morphology of non‐modified ceramic sample was characterized by the rather big (1–2 μm) grains of α‐Al₂O₃ phase with a habit close to hexagonal drowned in solid solution of t‐ZrO₂ with smooth surface. The pattern surfaces of modified composite content a little amount of elongated prismatic grains with composition close to the phase of СаСеAl₃О₇ as well as hexahedral α‐Al₂O₃‐grains. Fractal dimension, D, as well as height values distribution have been determined for the surfaces of the samples with and without modifying. It can be concluded that the smoothest surface is of the modified samples with Ca⁺² modifier but the most regular one is of the non‐modified samples. A connection was observed between the surface morphology and the physical properties as assessed in previous works. Microsc. Res. Tech. 78:840–846, 2015. © 2015 Wiley Periodicals, Inc.