The reactivity of basal surfaces, steps and edges of muscovite was studied by imaging surface precipitates of PbCl2 using atomic force microscopy (AFM). We reacted PbCl2 solution with freshly cleaved muscovite surfaces and found that PbCl2 precipitates were formed on the basal surfaces, steps and edges. It was observed that PbCl2 precipitated preferentially along the steps compared to the basal surfaces and that PbCl2 precipitates at multiple-layer edges were needle-shaped and oriented in different directions. One of the muscovite samples we cleaved had muscovite fragments sitting on the freshly cleaved surfaces. These fragments resulted from previously formed cracks. Thus, we were able to compare the reactivity of the weathered surfaces with that of freshly cleaved surfaces. It was found that PbCl2 was not precipitated along the edges of previously cracked muscovite fragments. These results clearly demonstrated that the edges of freshly cleaved muscovite are the most reactive surface sites, whereas the edges of weathered muscovite are not as reactive. We believe that the surface reactivity of the edges of freshly cleaved muscovite is likely due to terminal or Al-OH1/2− groups on these crystalline surfaces, which favor adsorption of Pb2+ ions and the subsequent nucleation and precipitation reactions. We also investigated the effect of drying rate on the morphology of the surface precipitates. Fast drying resulted in a nearly complete covered surface with a leaflike morphology, whereas slow drying resulted in more isolated surface clusters.

The coefficient of friction of clay minerals at the micro-scale has generally not been studied due to difficulties in obtaining measurements in a bulk-soil volume undergoing shear at such small scales. Information on friction at the micro-scale may provide insight into grain-scale processes that operate in bulk samples or in natural faults. The objective of this study was to develop a method to measure the microscale friction coefficient of smectites. The experiments described show that the axial atomic force microscopy method can be adapted to easily obtain accurate coefficient of friction (μ) measurements for smectites from force curves involving colloidal probes. The method allows for the measurements to be performed over spatial scales of a few μm, can be carried out under dry conditions or a wide range of aqueous solutions, and requires no calibration beyond making a few microscopic measurements of the probe. This method provides measurements of micro-scale normal and shear forces between minerals, which can be used for a variety of applications such as the study of shear deformation, consolidation, and fault dynamics. Control tests of silica on mica (μ = 0.29±0.02) agree with literature values where limits indicate one standard deviation. Coefficient of friction values for wet and dry Na-montmorillonite were determined to be 0.20±0.03 and 0.72±0.03, respectively.

In order to obtain nanopatterned surfaces, natural allophane particles originating from Japanese soils were immobilized as single particles on Si wafer substrates.When derived from aqueous suspensions, only a few nanoparticles were deposited and detected on the surface due to the weak adsorption of allophanes on the substrate. The amount of immobilized allophane was increased significantly, however, by using an organic solvent in combination with a micelle-based technique to suspend the allophane particles. The micelles were formed from a tailored, aliphatic diblock copolymer that was dissolved in toluene and contained several allophane particles. A cleaned silica chip was used as a substrate on which a monolayer of micelles was immobilized equidistant from each other by dip coating. To remove the polymer from the substrate and to produce free, single allophane nanoparticles, ultraviolet (UV) irradiation was used. After UV treatment, single allophane particles formed ring-shaped deposition patterns with a high surface density. Transmission electron microscopy (TEM) was used to verify the presence of single allophane nanoparticles in the Japanese samples which came from natural sources. The single allophane particles as well as the allophane-containing di-block copolymer micelles, both immobilized on Si substrates and TEM sample grids, were imaged by atomic force microscopy and TEM. In this way, the diameters of the single allophane particles, as well as the distances between the immobilized micelles and the particles and their topography on the substrates, were determined.

In Ecuador, DINAGE (known today as the Servicio Geológico Nacional) and the German Federal Institute for Geosciences and Natural Resources have discovered a huge allophane deposit covering an area of >4000 km2. This study presents the results from an investigation of a 16-m thick vertical sequence from this deposit, supposedly the weathering product of two different volcanic ash deposits. In particular, the distribution of alkali metals within the uppermost layer indicates that the weathering process is still ongoing.

According to the mineralogical composition, an allophane-rich layer (allophane facies) could be distinguished from the underlying halloysite-rich layer (halloysite facies). A 2-m thick transition zone is characterized by the presence of gibbsite and intermediate specific surface area values. Only a few imogolite fibers could be identified (by scanning electron microscopy), indicating the dominance of allophane over imogolite in the allophane facies. Single allophane particles were investigated by atomic force microscopy, though this method was less accurate than transmission electron microscopy with respect to the determination of the primary particle diameter. Carbon isotope analysis (14C) suggested an age of ∼20,000 y for the allophane layer.

Within the allophane facies, a 4-m thick layer occurs containing 70–80 wt.% allophane with an N2-BET specific surface area of >300 m2/g. Based on infrared and energy-dispersive X-ray diffraction measurements, an Al/Si ratio of 1.3–1.4 was established for this allophane, which is between Al-rich and Si-rich allophane. The allophane layer may be of economic value due to the large allophane content, the small amount of organic matter, and the significant thickness of the deposit.

Natural and synthetic micas have been used widely as substrates to study biological systems; but, as in the case of negatively charged DNA, anionic charge repulsion may render micas a less than ideal templating surface for many biological systems. The purpose of this study was to investigate the potential for the chlorite clinoclore, which contains a positively charged interlayer octahedral sheet, to serve as a substrate for DNA adsorption. The relationships between clinochlore cleavage characteristics, in terms of nano-morphology, and surface potential are investigated, as are its average crystal chemistry and topology. That the structural features of clinochlore can be used successfully to condense, order, and self assemble complex biomolecules, such as DNA is also proven.

A natural IIb-4 clinochlore [$C\overline{1}$\$\end{document} symmetry, unit-cell parameters a = 0.53301(4); b = 0.92511(6); c = 1.4348(1) (nm); α = 90.420(3); β = 97.509(3); γ = 89.996(4) (°)] with chemical composition $\left({\text{Mg}}_{1.701}{\text{Fe}}_{0.245}^{2+}{\text{Ti}}_{0.004}{\text{Al}}_{0.998}{\text{Cr}}_{0.052}^{3+}\right){\text{Mg}}_3\left({\text{Si}}_{2.939}{\text{Al}}_{1.015}{\text{Fe}}_{0.046}^{3+}\right){\text{O}}_{10}\left({\text{OH}}_{7.913}{\text{F}}_{0.087}\right)$\$\end{document} was selected. The octahedral sites of the silicate layer (<M(1)−O> = 0.2080 nm and <M(2)−O> = 0.2081 nm) are equal and occupied by Mg, whereas the octahedral sites in the interlayer M(3) and M(4) (<M(3)−O> = 0.2088 nm and <M(4) − O> = 0.1939 nm) show different sizes and are mostly completely occupied by divalent (Mg2+ and Fe2+) and trivalent (Al3+) cations, respectively.

The clinochlore cleaved surface is present in two forms: (1) the stripe type (0.40 nm in height, up to several micrometers long and ranging from some nanometers to a few microns in lateral size); and (2) the triangular type (0.40 nm in height). Both features may result either from interlayer sheets whose cleavage weak directions are related to the different M(3) and M(4) site occupancy, or from weak interlayer bonding along specific directions to the 2:1 layer underneath. The cleaved surface, particularly at the cleaved edges, presents high DNA affinity, which is directly related to an average positive surface and ledge potential.

A microtexture analysis by TEM and AFM of palygorskite deposits from the Hawthorne Formation, southern Georgia is given. Palygorskite is the dominant mineral comprising an average of 65–70% of the sample volume with smaller volumes of smectite, illite and kaolinite. Morphologic observations indicate that the palygorskite formed in an unconfined environment, such as in the water column or in open-pore space. Some palygorskite textures appear to be secondary growths filling voids. An unusual texture is observed where smectite or illite-smectite (Reichweite, R = 0) form epitaxially on detrital illite and kaolinite particles. Oxides of Fe and Ti are common, and authigenic cassiterite is present but rare. Apatite is a common trace mineral in these sediments and occurs in a variety of textures. Apatite occurs as clusters which are believed to be small fecal pellets. These clusters have been partially dissolved and recrystallized and the crystals in the clusters are 50–100 µm in diameter. Other apatite crystals occur either as single crystals or in clusters that are not associated with fecal pellets.

The textural data of this study suggest that there was an evolving and complex mineralogical and geochemical system during and after deposition of the palygorskite deposits in the Hawthorne. The epitaxial overgrowths of smectite on detrital illite and kaolinite particles indicate an intermittent stratified water column occurring in the system. Freshwater was introduced into the system from the northeast of the Apalachicola embayment and overrode more saline water in the southwest portion of the embayment. The results of this study are consistent with previous environmental interpretations and provide additional details.

The sizes and shapes of single clay mineral layers are difficult to determine though they are important parameters which determine the final properties of clay polymer nanocomposites and of ultrathin clay mineral films. To determine these sizes and shapes, hybrid monolayers of clay minerals (saponite, hectorite, Wyoming bentonite, and Laponite) and Rhodamine B octadecyl ester Perchlorate (RhB18) were prepared using the Langmuir-Blodgett (LB) technique and studied with atomic force microscopy (AFM). The AFM images reveal monolayers of elementary clay mineral layers, which are randomly oriented and have a wide range of sizes. The layers have typical shapes: lath-like for hectorite, plates for Wyoming bentonite, a mixture of laths and plates for saponite, and aggregates of very small layers of Laponite. Two types of layers were present in the LB films of saponite, Wyoming bentonite, and hectorite in a 40:60 ratio: (1) single layers 0.96 nm thick hybridized with RhB18; and (2) particles consisting of two clay layers with an intercalated monomolecular layer of water molecules and hybridized with RhB18. The Laponite particles in the hybrid LB films consist mainly of aggregates of two and three single layers.

Nine halloysite nanotubes (HNTs) have been examined using scanning electron microscopy (SEM), atomic force microscopy (AFM) and (cross-sectional) transmission electron microscopy (TEM) to evaluate details of their external and internal morphologies. The samples span morphologies within the cylindrical to prismatic-polygonal framework proposed by Hillier et al. (2016). The ‘carpet roll’ model assumed in the conceptualization of most technological applications of HNTs is shown to be far too simplistic. Both cylindrical and prismatic forms have abundant edge steps traversing their surfaces that, by analogy with plates of kaolinite, correspond to prism faces. The mean value for the diameter of the central lumen of the tubes is 12 nm. Numerous slit-like nanopores, with diameters up to 18 nm, also occur between packets of layers, particularly in prismatic forms at the junction between a central cylindrical core and outer packets of planar layers. These pores expose aluminol and siloxane surfaces, but unlike the lumen, which is assumed only to expose an aluminol surface, they do not extend along the entire length of the nanotube. Edge steps seen most clearly by AFM correspond in height to the packets of layers seen in TEM. TEM cross-sections suggest that tube growth occurs by accretion of a spiralled thickening wedge of layers evolving from cylindrical to polygonal form and reveal that planar sectors may be joined by either abrupt angular junctions or by short sections of curved layers. A more realistic model of the internal and external morphologies of HNTs is proposed to assist with understanding of the behaviour of HNTs in technological applications.

The viral replication cycle is controlled by information transduced through both molecular and mechanical interactions. Viral infection mechanics remains largely unexplored, however, due to the complexity of cellular mechanical responses over the course of infection as well as a limited ability to isolate and probe these responses. Here, we develop an experimental system consisting of herpes simplex virus type 1 (HSV-1) capsids bound to isolated and reconstituted cell nuclei, which allows direct probing of capsid–nucleus mechanics with atomic force microscopy (AFM). Major mechanical transformations occur in the host nucleus when pressurised viral DNA ejects from HSV-1 capsids docked at the nuclear pore complexes (NPCs) on the nuclear membrane. This leads to structural rearrangement of the host chromosome, affecting its compaction. This in turn regulates viral genome replication and transcription dynamics as well as the decision between a lytic or latent course of infection. AFM probing of our reconstituted capsid–nucleus system provides high-resolution topographical imaging of viral capsid docking at the NPCs as well as force volume mapping of the infected nucleus surface, reflecting mechanical transformations associated with chromatin compaction and stiffness of nuclear lamina (to which chromatin is tethered). This experimental system provides a novel platform for investigation of virus–host interaction mechanics during viral genome penetration into the nucleus.

This paper presents a proof of concept for the discrimination of several nanoparticle populations mixed in consumer products. The methodology proposes correlation of AFM, SEM, and EDS data to obtain structural and chemical information on each particle in a mixed population. To this end, emphasis is placed on sample preparation, imaging specifications for each instrument, and data correlation with adapted software.

Atomic force microscope (AFM) based nanomanipulation has been proved to be a possible way to assemble various nanoparticles into complex patterns and devices. To achieve an efficient and full-automatic nanomanipulation, the nanoparticles as well as other features on the substrate must be quickly identified by the computer. This work focuses on an autodetection method for flexible nanowires based on deep learning. The You Only Look Once (YOLO) network is applied to find all movable nanowires in the AFM images. A series of morphology transformation algorithms, including an adaptive threshold edge detection, are applied to refine the skeletons of the nanowires. The bidirectional long short-term memory model with conditional random field layer (BI-LSTM-CRF) is proposed to precisely determine the posture and position of the detected nanowires. Benefiting from these algorithms, our detecting program is able to automatically detect the nanowires of different morphology with nanometer resolution and with over 80% reliability in the testing set. The detecting results are less affected by the image quality, which demonstrates good robustness of this algorithm.

A mineral, mimetite Pb5(AsO4)3Cl, is one of the most insoluble minerals and continues to be considered a viable remedial strategy for immobilization of Pb and As from contaminated soils. It has been recognized that many well-known, naturally-occurring, and synthetic chelators strongly influence dissolution processes in near-surface geological environments. In this study, crystals of mimetite were observed in scanning electron microscopy (SEM) and atomic force microscopy (AFM) before and after dissolution in EDTA (ethylene diamine tetra-acetic acid) solution. Direct in situ observations at room temperature made in an AFM fluid cell revealed that the grain surface roughness has increased due to development of etch pits. Both hexagonal and prismatic walls developed dissolution features between 0.6 and 1.2 µm, respectively, during duration of the experiment. AFM observations suggest surface-controlled dissolution dominated step retrieval on both prismatic and hexagonal surfaces. SEM observations showed the development of rounded edges on hexagonal walls and elongated, oval etch pits on the prismatic wall. These results, representing early dissolution patterns on mimetite surfaces, might suggest that low pH conditions in soils containing organic acids similar to EDTA might contribute to remobilization of Pb and As from mimetite when applied to stabilization of these toxic metals in contaminated soils.

Possible multidrug-resistant (MDR) mechanisms of four resistant strains of Escherichia coli to a model β-lactam, ampicillin, were investigated using contact angle measurements of wettability, crystal violet assays of permeability, biofilm formation, fluorescence imaging, and nanoscale analyses of dimensions, adherence, and roughness. Upon exposure to ampicillin, one of the resistant strains, E. coli A5, changed its phenotype from elliptical to spherical, maintained its roughness and biofilm formation abilities, decreased its length and surface area, maintained its cell wall integrity, increased its hydrophobicity, and decreased its nanoscale adhesion to a model surface of silicon nitride. Such modifications are suggested to allow these cells to conserve energy during metabolic dormancy. In comparison, resistant strains E. coli D4, A9, and H5 elongated their cells, increased their roughness, increased their nanoscale adhesion forces, became more hydrophilic, and increased their biofilm formation upon exposure to ampicillin. These results suggest that these strains resisted ampicillin through biofilm formation that possibly introduces diffusion limitations to antibiotics. Investigations of how MDR bacterial cells modify their surfaces in response to antibiotics can guide research efforts aimed at designing more effective antibiotics and new treatment strategies for MDR bacterial infections.

In situ measurements were carried out to quantify montmorillonite dissolution rates at a compaction pressure ranging from 0.04 to 10.00 MPa and temperature of 70°C in 0.3 M NaOH solution (pH 12.1 at 70°C) using vertical scanning interferometry (VSI) and an auto-compaction cell. Ex situ measurements of the reacted samples using atomic force microscopy (AFM) were performed to quantify the ratio of edge surface area (ESA) to total surface area (TSA) (XESA = ESA/TSA). Accordingly, the actual ESA for the montmorillonite examined by in situ VSI could be estimated. The XESA value increases as a function of run duration or compaction pressure. At atmospheric pressure, XESA is approximately 0.0054 and converges to ∼0.0107 at 10 MPa, An expression that relates reactive surface area and montmorillonite compaction (XESA/XESA initial = kXESA, k: variable factor) is kXESA = 1.0 + 0.64628 P0.1527 where P is in MPa. Using the calculated XESA, dissolution rates from the in situ VSI measurements are obtained. The early dissolution (<1500 min) at less compaction pressure tends to show faster rates (>1.0 × 10-11 mol/m2/s) than that at higher compaction pressure. The rates after >1500 min are slower, with values of less than 3×6 10-12 mol/m2/s, but there is no significant dependency on the density in the range from 1.0 to 1.7 Mg/m3. These observed rates for compacted montmorillonite are two-orders of magnitude slower (2.63×10-13 mol/m2/s) than dissolution rates in the suspended state.

The golden iridescence observed in orthoamphiboles from the Nuuk district, southern West Greenland has been shown by analytical transmission electron microscopy to be the result of the interference of light reflected from alternate, coherent gedrite and anthophyllite exsolution lamellae parallel to (010). The lamellae are periodic with an average spacing of ∼180 nm; lamellae with this spacing would give rise to yellow iridescence. It is concluded that the exsolution lamellae are the origin of the features previously seen on cleaved surfaces of the amphiboles in the atomic force microscope (AFM). The suggestion is that the 0.75° difference in the cleavage angle for the two phases produces corrugations that are imaged by AFM. The morphology of the lamellae is consistent with an origin by spinodal decomposition.

In situ atomic force microscopy (AFM) experiments were used to study the effect of trace amounts of a commercial inhibitor on the (001) baryte surface during growth. The additive tested was a copolymer, used as a scale inhibitor in oil recovery (maleic acid/allyl sulfonic acid copolymer with phosphonate groups, partial sodium salt). The morphology of the growth was used to gain a better understanding of the inhibition mechanism. Without an inhibitor, barium sulfate growth occurred by 2D island nucleation and spreading. The addition of a small amount (0.1 ppm and 0.5 ppm) of copolymer inhibitor enhances 2D nucleation but blocks growth. Just 1 ppm of inhibitor blocks nucleation and growth by adsorption of a copolymer layer onto the baryte surface. Similarly in 3D studies, small amounts of inhibitor seem to act on growth and not on nucleation and larger amounts of copolymer act on both by adsorption of the copolymer to all baryte surfaces keeping the particles in their embryo stage.

Calcite growth rates were measured in the presence of sulphate using mixed-flow reactors and in situ Atomic Force Microscopy. Preliminary observations reveal that the kinetics and mechanism of the calcite growth was altered by the presence of sulphate. Calcite growth rates in the presence of sulphate (≥ mM) were decreased and two-dimensional nuclei tend to grow on top of existing nuclei, rather than spreading. The height of new nuclei was ~4 Å, 1 Å greater than that of pure calcite growth. This difference reflects the incorporation of tetrahedral SO2-4 anions into the calcite lattice.

In this work we analyzed the effect of the atomic force microscopy probe tip apex shape on Kelvin Probe Force Microscopy (KPFM) potential sensitivity and spatial resolution. It was found that modification of the apex shape from spherical to planar upon thinning of the conductive coating leads to enhanced apex contribution to the total electrostatic force between the probe and the sample. The effect results in extended potential sensitivity and spatial resolution of KPFM. Experimental results were supported by calculations.

The determination of reliable weathering/dissolution rates for cement phases is of fundamental importance for the modelling of the temporal evolution of both radioactive waste repositories and CO2 geological storage sites (e.g. waste matrix, plug in boreholes). Here, the dissolution kinetics of AFm-Cl (hydrated calcium aluminates containing interlayer Cl) has been studied using flow-through experiments conducted at pH values ranging from 9.2 to 13. Mineralogical (XRD) and chemical (EPMA, TEM) analyses have been performed to determine the evolution of the phases during the dissolution experiments. For pH values between 10 and 13, the dissolution of AFm-Cl is congruent (i.e. Ca/Al ratios close to 2 both for solids and outlet concentrations). In contrast, the precipitation of amorphous Al-phases and possibly amorphous mixed Al/Ca phases is observed at pH 9.2, leading to Ca/Al ratios in the outlet solutions higher than those of the initial solid. Therefore, at pH 9.2, even if Cl–/OH– exchange occurs, estimation of dissolution rate from released Cl appears to be the best proxy. Dissolution rates were normalized to the final specific surface areas (ranging from 6.1 to 35.4 m2 g−1). Dissolution rate appears to be pH-independent and therefore the far-from-equilibrium dissolution rate at room temperature is expressed as: logR(mol m–2 s–1) = –9.23 ± 0.18