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1.  An NC-AFM and KPFM study of the adsorption of a triphenylene derivative on KBr(001) 
Summary
The adsorption on KBr(001) of a specially designed molecule, consisting of a flat aromatic triphenylene core equipped with six flexible propyl chains ending with polar cyano groups, is investigated by using atomic force microscopy in the noncontact mode (NC-AFM) coupled to Kelvin probe force microscopy (KPFM) in ultrahigh vacuum at room temperature. Two types of monolayers are identified, one in which the molecules lie flat on the surface (MLh) and another in which they stand approximately upright (MLv). The Kelvin voltage on these two structures is negatively shifted relative to that of the clean KBr surface, revealing the presence of surface dipoles with a component pointing along the normal to the surface. These findings are interpreted with the help of numerical simulations. It is shown that the surface–molecule interaction is dominated by the electrostatic interaction of the cyano groups with the K+ ions of the substrate. The molecule is strongly adsorbed in the MLh structure with an adsorption energy of 1.8 eV. In the MLv layer, the molecules form π-stacked rows aligned along the polar directions of the KBr surface. In these rows, the molecules are less strongly bound to the substrate, but the structure is stabilized by the strong intermolecular interaction due to π-stacking.
doi:10.3762/bjnano.3.25
PMCID: PMC3323911  PMID: 22496995
atomic force microscopy; insulating surfaces; Kelvin force probe microscopy; molecular adsorption
2.  A measurement of the hysteresis loop in force-spectroscopy curves using a tuning-fork atomic force microscope 
Summary
Measurements of the frequency shift versus distance in noncontact atomic force microscopy (NC-AFM) allow measurements of the force gradient between the oscillating tip and a surface (force-spectroscopy measurements). When nonconservative forces act between the tip apex and the surface the oscillation amplitude is damped. The dissipation is caused by bistabilities in the potential energy surface of the tip–sample system, and the process can be understood as a hysteresis of forces between approach and retraction of the tip. In this paper, we present the direct measurement of the whole hysteresis loop in force-spectroscopy curves at 77 K on the PTCDA/Ag/Si(111) √3 × √3 surface by means of a tuning-fork-based NC-AFM with an oscillation amplitude smaller than the distance range of the hysteresis loop. The hysteresis effect is caused by the making and breaking of a bond between PTCDA molecules on the surface and a PTCDA molecule at the tip. The corresponding energy loss was determined to be 0.57 eV by evaluation of the force–distance curves upon approach and retraction. Furthermore, a second dissipation process was identified through the damping of the oscillation while the molecule on the tip is in contact with the surface. This dissipation process occurs mainly during the retraction of the tip. It reaches a maximum value of about 0.22 eV/cycle.
doi:10.3762/bjnano.3.23
PMCID: PMC3323909  PMID: 22496993
atomic force microscopy; energy dissipation; force spectroscopy; hysteresis loop; PTCDA/Ag/Si(111) √3 × √3
3.  Effect of the tip state during qPlus noncontact atomic force microscopy of Si(100) at 5 K: Probing the probe 
Summary
Background: Noncontact atomic force microscopy (NC-AFM) now regularly produces atomic-resolution images on a wide range of surfaces, and has demonstrated the capability for atomic manipulation solely using chemical forces. Nonetheless, the role of the tip apex in both imaging and manipulation remains poorly understood and is an active area of research both experimentally and theoretically. Recent work employing specially functionalised tips has provided additional impetus to elucidating the role of the tip apex in the observed contrast.
Results: We present an analysis of the influence of the tip apex during imaging of the Si(100) substrate in ultra-high vacuum (UHV) at 5 K using a qPlus sensor for noncontact atomic force microscopy (NC-AFM). Data demonstrating stable imaging with a range of tip apexes, each with a characteristic imaging signature, have been acquired. By imaging at close to zero applied bias we eliminate the influence of tunnel current on the force between tip and surface, and also the tunnel-current-induced excitation of silicon dimers, which is a key issue in scanning probe studies of Si(100).
Conclusion: A wide range of novel imaging mechanisms are demonstrated on the Si(100) surface, which can only be explained by variations in the precise structural configuration at the apex of the tip. Such images provide a valuable resource for theoreticians working on the development of realistic tip structures for NC-AFM simulations. Force spectroscopy measurements show that the tip termination critically affects both the short-range force and dissipated energy.
doi:10.3762/bjnano.3.3
PMCID: PMC3304327  PMID: 22428093
force spectroscopy; image contrast; noncontact AFM; qPlus; Si(001); Si(100); tip (apex) structure
4.  Electronic structure and bandgap of γ-Al2O3 compound using mBJ exchange potential 
Nanoscale Research Letters  2012;7(1):488.
γ-Al2O3 is a porous metal oxide and described as a defective spinel with some cationic vacancies. In this work, we calculate the electronic density of states and band structure for the bulk of this material. The calculations are performed within the density functional theory using the full potential augmented plan waves plus local orbital method, as embodied in the WIEN2k code. We show that the modified Becke-Johnson exchange potential, as a semi-local method, can predict the bandgap in better agreement with the experiment even compared to the accurate but much more expensive green function method. Moreover, our electronic structure analysis indicates that the character of the valence band maximum mainly originates from the p orbital of those oxygen atoms that are close to the vacancy. The charge density results show that the polarization of the oxygen electron cloud is directed toward aluminum cations, which cause Al and O atoms to be tightly connected by a strong dipole bond.
doi:10.1186/1556-276X-7-488
PMCID: PMC3503660  PMID: 22937842
Bandgap; mBJ exchange potential; Density functional theory
5.  Atomic Structures of Silicene Layers Grown on Ag(111): Scanning Tunneling Microscopy and Noncontact Atomic Force Microscopy Observations 
Scientific Reports  2013;3:2399.
Silicene, the considered equivalent of graphene for silicon, has been recently synthesized on Ag(111) surfaces. Following the tremendous success of graphene, silicene might further widen the horizon of two-dimensional materials with new allotropes artificially created. Due to stronger spin-orbit coupling, lower group symmetry and different chemistry compared to graphene, silicene presents many new interesting features. Here, we focus on very important aspects of silicene layers on Ag(111): First, we present scanning tunneling microscopy (STM) and non-contact Atomic Force Microscopy (nc-AFM) observations of the major structures of single layer and bi-layer silicene in epitaxy with Ag(111). For the (3 × 3) reconstructed first silicene layer nc-AFM represents the same lateral arrangement of silicene atoms as STM and therefore provides a timely experimental confirmation of the current picture of the atomic silicene structure. Furthermore, both nc-AFM and STM give a unifying interpretation of the second layer (√3 × √3)R ± 30° structure. Finally, we give support to the conjectured possible existence of less stable, ~2% stressed, (√7 × √7)R ± 19.1° rotated silicene domains in the first layer.
doi:10.1038/srep02399
PMCID: PMC3739010  PMID: 23928998
6.  Origin of New Broad Raman D and G Peaks in Annealed Graphene 
Scientific Reports  2013;3:2700.
Since graphene, a single sheet of graphite, has all of its carbon atoms on the surface, its property is very sensitive to materials contacting the surface. Herein, we report novel Raman peaks observed in annealed graphene and elucidate their chemical origins by Raman spectroscopy and atomic force microscopy (AFM). Graphene annealed in oxygen-free atmosphere revealed very broad additional Raman peaks overlapping the D, G and 2D peaks of graphene itself. Based on the topographic confirmation by AFM, the new Raman peaks were attributed to amorphous carbon formed on the surface of graphene by carbonization of environmental hydrocarbons. While the carbonaceous layers were formed for a wide range of annealing temperature and time, they could be effectively removed by prolonged annealing in vacuum. This study underlines that spectral features of graphene and presumably other 2-dimensional materials are highly vulnerable to interference by foreign materials of molecular thickness.
doi:10.1038/srep02700
PMCID: PMC3776959  PMID: 24048447
7.  Dipole-driven self-organization of zwitterionic molecules on alkali halide surfaces 
Summary
We investigated the adsorption of 4-methoxy-4′-(3-sulfonatopropyl)stilbazolium (MSPS) on different ionic (001) crystal surfaces by means of noncontact atomic force microscopy. MSPS is a zwitterionic molecule with a strong electric dipole moment. When deposited onto the substrates at room temperature, MSPS diffuses to step edges and defect sites and forms disordered assemblies of molecules. Subsequent annealing induces two different processes: First, at high coverage, the molecules assemble into a well-organized quadratic lattice, which is perfectly aligned with the <110> directions of the substrate surface (i.e., rows of equal charges) and which produces a Moiré pattern due to coincidences with the substrate lattice constant. Second, at low coverage, we observe step edges decorated with MSPS molecules that run along the <110> direction. These polar steps most probably minimize the surface energy as they counterbalance the molecular dipole by presenting oppositely charged ions on the rearranged step edge.
doi:10.3762/bjnano.3.32
PMCID: PMC3323918  PMID: 22497002
alkali halide surface; noncontact atomic force microscopy; organic molecule; self-organization; zwitterion
8.  Field Dependence of the Spin Relaxation Within a Film of Iron Oxide Nanocrystals Formed via Electrophoretic Deposition 
Nanoscale Research Letters  2010;5(10):1540-1545.
The thermal relaxation of macrospins in a strongly interacting thin film of spinel-phase iron oxide nanocrystals (NCs) is probed by vibrating sample magnetometry (VSM). Thin films are fabricated by depositing FeO/Fe3O4 core–shell NCs by electrophoretic deposition (EPD), followed by sintering at 400°C. Sintering transforms the core–shell structure to a uniform spinel phase, which effectively increases the magnetic moment per NC. Atomic force microscopy (AFM) confirms a large packing density and a reduced inter-particle separation in comparison with colloidal assemblies. At an applied field of 25 Oe, the superparamagnetic blocking temperature is TBSP ≈ 348 K, which is much larger than the Néel-Brown approximation of TBSP ≈ 210 K. The enhanced value of TBSP is attributed to strong dipole–dipole interactions and local exchange coupling between NCs. The field dependence of the blocking temperature, TBSP(H), is characterized by a monotonically decreasing function, which is in agreement with recent theoretical models of interacting macrospins.
doi:10.1007/s11671-010-9674-2
PMCID: PMC2956047  PMID: 21076671
Electrophoretic deposition; Core–shell; Superparamagnetic; EPD; Iron oxide; Thin film
9.  Field Dependence of the Spin Relaxation Within a Film of Iron Oxide Nanocrystals Formed via Electrophoretic Deposition 
Nanoscale Research Letters  2010;5(10):1540-1545.
The thermal relaxation of macrospins in a strongly interacting thin film of spinel-phase iron oxide nanocrystals (NCs) is probed by vibrating sample magnetometry (VSM). Thin films are fabricated by depositing FeO/Fe3O4 core–shell NCs by electrophoretic deposition (EPD), followed by sintering at 400°C. Sintering transforms the core–shell structure to a uniform spinel phase, which effectively increases the magnetic moment per NC. Atomic force microscopy (AFM) confirms a large packing density and a reduced inter-particle separation in comparison with colloidal assemblies. At an applied field of 25 Oe, the superparamagnetic blocking temperature is TBSP ≈ 348 K, which is much larger than the Néel-Brown approximation of TBSP ≈ 210 K. The enhanced value of TBSP is attributed to strong dipole–dipole interactions and local exchange coupling between NCs. The field dependence of the blocking temperature, TBSP(H), is characterized by a monotonically decreasing function, which is in agreement with recent theoretical models of interacting macrospins.
doi:10.1007/s11671-010-9674-2
PMCID: PMC2956047  PMID: 21076671
Electrophoretic deposition; Core–shell; Superparamagnetic; EPD; Iron oxide; Thin film
10.  Multimode Resistive Switching in Single ZnO Nanoisland System 
Scientific Reports  2013;3:2405.
Resistive memory has attracted a great deal of attention as an alternative to contemporary flash memory. Here we demonstrate an interesting phenomenon that multimode resistive switching, i.e. threshold-like, self-rectifying and ordinary bipolar switching, can be observed in one self-assembled single-crystalline ZnO nanoisland with base diameter and height ranging around 30 and 40 nm on Si at different levels of current compliance. Current-voltage characteristics, conductive atomic force microscopy (C-AFM), and piezoresponse force microscopy results show that the threshold-like and self-rectifying types of switching are controlled by the movement of oxygen vacancies in ZnO nanoisland between the C-AFM tip and Si substrate while ordinary bipolar switching is controlled by formation and rupture of conducting nano-filaments. Threshold-like switching leads to a very small switching power density of 1 × 103 W/cm2.
doi:10.1038/srep02405
PMCID: PMC3740279  PMID: 23934276
11.  Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction 
Summary
Noncontact atomic force microscopy (NC-AFM) is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation.
In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface.
doi:10.3762/bjnano.3.73
PMCID: PMC3458610  PMID: 23019560
atomic force microscopy; force spectroscopy; NC-AFM; three-dimensional atomic force microscopy; tip asymmetry; tip elasticity
12.  Tooth Bleaching Increases Dentinal Protease Activity 
Journal of Dental Research  2013;92(2):187-192.
Hydrogen peroxide is an oxidative agent commonly used for dental bleaching procedures. The structural and biochemical responses of enamel, dentin, and pulp tissues to the in vivo bleaching of human (n = 20) premolars were investigated in this study. Atomic force microscopy (AFM) was used to observe enamel nanostructure. The chemical composition of enamel and dentin was analyzed by infrared spectroscopy (FTIR). The enzymatic activities of dental cathepsin B and matrix metalloproteinases (MMPs) were monitored with fluorogenic substrates. The amount of collagen in dentin was measured by emission of collagen autofluorescence with confocal fluorescence microscopy. The presence of Reactive Oxygen Species (ROS) in the pulp was evaluated with a fluorogenic 2′,7′-dichlorodihydrofluorescein diacetate (DCFDA) probe. Vital bleaching of teeth significantly altered all tested parameters: AFM images revealed a corrosion of surface enamel nanostructure; FTIR analysis showed a loss of carbonate and proteins from enamel and dentin, along with an increase in the proteolytic activity of cathepsin-B and MMPs; and there was a reduction in the autofluorescence of collagen and an increase in both cathepsin-B activity and ROS in pulp tissues. Together, these results indicate that 35% hydrogen peroxide used in clinical bleaching protocols dramatically alters the structural and biochemical properties of dental hard and soft pulp tissue.
doi:10.1177/0022034512470831
PMCID: PMC3545693  PMID: 23242228
tooth bleaching; cysteine proteases; matrix metalloproteinase; collagen; FTIR; confocal microscopy
13.  Modeling noncontact atomic force microscopy resolution on corrugated surfaces 
Summary
Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid). The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.
doi:10.3762/bjnano.3.26
PMCID: PMC3323912  PMID: 22496996
graphene; model; noncontact atomic force microscopy; SiO2; van der Waals
14.  Scanned Probe Oxidation onp-GaAs(100) Surface with an Atomic Force Microscopy 
Nanoscale Research Letters  2008;3(7):249-254.
Locally anodic oxidation has been performed to fabricate the nanoscale oxide structures onp-GaAs(100) surface, by using an atomic force microscopy (AFM) with the conventional and carbon nanotube (CNT)-attached probes. The results can be utilized to fabricate the oxide nanodots under ambient conditions in noncontact mode. To investigate the conversion of GaAs to oxides, micro-Auger analysis was employed to analyze the chemical compositions. The growth kinetics and the associated mechanism of the oxide nanodots were studied under DC voltages. With the CNT-attached probe the initial growth rate of oxide nanodots is in the order of ~300 nm/s, which is ~15 times larger than that obtained by using the conventional one. The oxide nanodots cease to grow practically as the electric field strength is reduced to the threshold value of ~2 × 107 V cm−1. In addition, results indicate that the height of oxide nanodots is significantly enhanced with an AC voltage for both types of probes. The influence of the AC voltages on controlling the dynamics of the AFM-induced nanooxidation is discussed.
doi:10.1007/s11671-008-9144-2
PMCID: PMC3244860
Atomic force microscopy; p-GaAs(100); Nanooxidation; Multi-walled carbon nanotube; Auger electron spectroscopy
15.  Measuring bacterial cells size with AFM 
Brazilian Journal of Microbiology  2012;43(1):341-347.
Atomic Force Microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria revealing surface details and cell integrity. During scanning however, the interactions between the AFM probe and the membrane results in distortion of the images. Such distortions or artifacts are the result of geometrical effects related to bacterial cell height, specimen curvature and the AFM probe geometry. The most common artifact in imaging is surface broadening, what can lead to errors in bacterial sizing. Several methods of correction have been proposed to compensate for these artifacts and in this study we describe a simple geometric model for the interaction between the tip (a pyramidal shaped AFM probe) and the bacterium (Escherichia coli JM-109 strain) to minimize the enlarging effect. Approaches to bacteria immobilization and examples of AFM images analysis are also described.
doi:10.1590/S1517-838220120001000040
PMCID: PMC3768968  PMID: 24031837
Atomic force microscopy (AFM); Escherichia coli; cell dimensions; bacteria visualization
16.  Improved Adhesion, Growth and Maturation of Vascular Smooth Muscle Cells on Polyethylene Grafted with Bioactive Molecules and Carbon Particles 
High-density polyethylene (PE) foils were modified by an Ar+ plasma discharge and subsequent grafting with biomolecules, namely glycine (Gly), polyethylene glycol (PEG), bovine serum albumin (BSA), colloidal carbon particles (C) or BSA and C (BSA + C). As revealed by atomic force microscopy (AFM), goniometry and Rutherford Backscattering Spectroscopy (RBS), the surface chemical structure and surface morphology of PE changed dramatically after plasma treatment. The contact angle decreased for the samples treated by plasma, mainly in relation to the formation of oxygen structures during plasma irradiation. A further decrease in the contact angle was obvious after glycine and PEG grafting. The increase in oxygen concentration after glycine and PEG grafting proved that the two molecules were chemically linked to the plasma-activated surface. Plasma treatment led to ablation of the PE surface layer, thus the surface morphology was changed and the surface roughness was increased. The materials were then seeded with vascular smooth muscle cells (VSMC) derived from rat aorta and incubated in a DMEM medium with fetal bovine serum. Generally, the cells adhered and grew better on modified rather than on unmodified PE samples. Immunofluorescence showed that focal adhesion plaques containing talin, vinculin and paxillin were most apparent in cells on PE grafted with PEG or BSA + C, and the fibres containing α-actin, β-actin or SM1 and SM2 myosins were thicker, more numerous and more brightly stained in the cells on all modified PE samples than on pristine PE. An enzyme-linked immunosorbent assay (ELISA) revealed increased concentrations of focal adhesion proteins talin and vinculin and also a cytoskeletal protein β-actin in cells on PE modified with BSA + C. A contractile protein α-actin was increased in cells on PE grafted with PEG or Gly. These results showed that PE activated with plasma and subsequently grafted with bioactive molecules and colloidal C particles, especially with PEG and BSA + C, promotes the adhesion, proliferation and phenotypic maturation of VSMC.
doi:10.3390/ijms10104352
PMCID: PMC2790113  PMID: 20057950
plasma irradiation; bioactivity; biocompatibility; tissue engineering and reconstruction
17.  The transport properties of oxygen vacancy-related polaron-like bound state in HfOx 
Scientific Reports  2013;3:3246.
The oxygen vacancy-related polaron-like bound state migration in HfOx accounting for the observed transport properties in the high resistance state of resistive switching is investigated by the density functional theory with hybrid functional. The barrier of hopping among the threefold oxygen vacancies is strongly dependent on the direction of motion. Especially, the lowest barrier along the <001> direction is 90 meV, in agreement with the experimental value measured from 135 K to room temperature. This hopping mainly invokes the z-directional motion of hafnium and threefold oxygen atoms in the vicinity of the oxygen vacancy resulted from the synergized combination of coupled phonon modes. In the presence of surface, the lowest barrier of hopping between the surface oxygen vacancies is 360 meV along the <101> direction, where the significant surface perpendicular motion of hafnium and twofold oxygen atoms surrounding the oxygen vacancy is identified to facilitate this type of polaron-like bound state migration. Thus, the migration on the surfaces could be more important at the high temperature.
doi:10.1038/srep03246
PMCID: PMC3856482  PMID: 24317593
18.  DeStripe: frequency-based algorithm for removing stripe noises from AFM images 
Background
Atomic force microscopy (AFM) is a relatively recently developed technique that shows a promising impact in the field of structural biology and biophysics. It has been used to image the molecular surface of membrane proteins at a lateral resolution of one nanometer or less. An immediate obstacle of characterizing surface features in AFM images is stripe noise. To better interpret structures at a sub-domain level, pre-processing of AFM images for removing stripe noises is necessary. Noise removal can be performed in either spatial or frequency domain. However, denoising processing in the frequency domain is a better solution for preserving edge sharpness.
Results
We have developed a denoising protocol, called DeStripe, for AFM bio-molecular images that are contaminated with heavy and fine stripes. This program adopts a divide-and-conquer approach by dividing the Fourier spectrum of the image into central and off-center regions for noisy pixels detection and intensity restoration; it is also applicable to other images interfered with high-density stripes such as those acquired by the scanning electron microscope. The denoising effect brought by DeStripe provides better visualization for image objects without introducing additional artifacts into the restored image.
Conclusions
The DeStripe denoising effect on AFM images is illustrated in the present work. It allows extracting extended information from the topographic measurements and implicitly enhances the molecular features in the image. All the presented images were processed by DeStripe with the raw image as the only input without any requirement for other prior information. A web service, http://biodev.cea.fr/destripe, is available for running DeStripe.
doi:10.1186/1472-6807-11-7
PMCID: PMC3749244  PMID: 21281524
19.  Atomic Force Microscopy of Cell Growth and Division in Staphylococcus aureus 
Journal of Bacteriology  2004;186(11):3286-3295.
The growth and division of Staphylococcus aureus was monitored by atomic force microscopy (AFM) and thin-section transmission electron microscopy (TEM). A good correlation of the structural events of division was found using the two microscopies, and AFM was able to provide new additional information. AFM was performed under water, ensuring that all structures were in the hydrated condition. Sequential images on the same structure revealed progressive changes to surfaces, suggesting the cells were growing while images were being taken. Using AFM small depressions were seen around the septal annulus at the onset of division that could be attributed to so-called murosomes (Giesbrecht et al., Arch. Microbiol. 141:315-324, 1985). The new cell wall formed from the cross wall (i.e., completed septum) after cell separation and possessed concentric surface rings and a central depression; these structures could be correlated to a midline of reactive material in the developing septum that was seen by TEM. The older wall, that which was not derived from a newly formed cross wall, was partitioned into two different surface zones, smooth and gel-like zones, with different adhesive properties that could be attributed to cell wall turnover. The new and old wall topographies are equated to possible peptidoglycan arrangements, but no conclusion can be made regarding the planar or scaffolding models.
doi:10.1128/JB.186.11.3286-3295.2004
PMCID: PMC415778  PMID: 15150213
20.  Atomic Force Microscopy of Mammalian Urothelial Surface 
Journal of molecular biology  2007;374(2):365-373.
SUMMARY
The mammalian urothelium apical surface plays important roles in bladder physiology and diseases, and it provides a unique morphology for ultrastructural studies. Atomic force microscopy (AFM) is an emerging tool for studying the architecture and dynamic properties of biomolecular structures in near physiological conditions. But AFM imaging of soft tissues remains a challenge due to the lack of efficient methods for sample stabilization. Using a porous nitrocellulose membrane as the support, we were able to immobilize large pieces of soft mouse bladder tissue thus enabling us to carry out the first AFM investigation of the mouse urothelial surface. The sub-micron resolution AFM images revealed many details of the surface features, including the geometry of the urothelial plaques that cover the entire surface and the membrane interdigitation at the cell borders. This interdigitation creates a membrane-zipper, likely contributing to the barrier function of the urothelium. In addition, we were able to image the intracellular bacterial communities (IBCs) of type 1-fimbriated bacteria grown between the intermediate filament bundles of the umbrella cells, shedding light on the bacterial colonization of urothelium.
doi:10.1016/j.jmb.2007.09.040
PMCID: PMC2096708  PMID: 17936789
Atomic force microscopy; urothelium; tissue; surface; cell junction
21.  Mapping the local reaction kinetics by PEEM: CO oxidation on individual (100)-type grains of Pt foil 
Surface Science  2011;605(23-24):1999-2005.
The locally-resolved reaction kinetics of CO oxidation on individual (100)-type grains of a polycrystalline Pt foil was monitored in situ using photoemission electron microscopy (PEEM). Reaction-induced surface morphology changes were studied by optical differential interference contrast microscopy and atomic force microscopy (AFM). Regions of high catalytic activity, low activity and bistability in a (p,T)-parameter space were determined, allowing to establish a local kinetic phase diagram for CO oxidation on (100) facets of Pt foil. PEEM observations of the reaction front propagation on Pt(100) domains reveal a high degree of propagation anisotropy both for oxygen and CO fronts on the apparently isotropic Pt(100) surface. The anisotropy vanishes for oxygen fronts at temperatures above 465 K, but is maintained for CO fronts at all temperatures studied, i.e. in the range of 417 to 513 K. A change in the front propagation mechanism is proposed to explain the observed effects.
Highlights
► Kinetics of the CO oxidation on (100)-type grains of a polycrystalline Pt foil was studied in situ. ► Photoemission electron microscopy was used to study the local reaction kinetics on a mm-scale. ► Local kinetic phase diagrams for individual Pt(100) grains were obtained. ► Anisotropy of propagating reaction fronts on the apparently isotropic Pt(100) surface is explained.
doi:10.1016/j.susc.2011.07.018
PMCID: PMC3191274  PMID: 22140277
Surface reactions; Photoemission electron microscopy; Atomic force microscopy; Platinum; CO oxidation
22.  Atomic structure of titania nanosheet with vacancies 
Scientific Reports  2013;3:2801.
Titania nanosheets are two-dimensional single crystallites of titanium oxide with a thickness of one titanium or two oxygen atoms, and they show attractive material properties, such as photocatalytic reactions. Since a titania (Ti0.87O2) nanosheet is synthesized by the delamination of a parent layered K0.8Ti1.73Li0.27O4 crystal using a soft chemical procedure, substantial Ti vacancies are expected to be included and affect the material properties. The atomic arrangement of a titania nanosheet with vacancies has not been revealed owing to the difficulties of direct observation. Here, we have directly visualized the atomic arrangement and Ti vacancies of a titania nanosheet using advanced lower-voltage transmission electron microscopy (TEM). Analyses of the results of first-principles calculations and TEM image simulations for various Ti vacancy structure models indicate that two particular oxygen atoms around each Ti vacancy are desorbed, suggesting the sites where atomic reduction first occurs.
doi:10.1038/srep02801
PMCID: PMC3786289  PMID: 24077611
23.  Growth, structure, morphology, and magnetic properties of Ni ferrite films 
Nanoscale Research Letters  2013;8(1):196.
The morphology, structure, and magnetic properties of nickel ferrite (NiFe2O4) films fabricated by radio frequency magnetron sputtering on Si(111) substrate have been investigated as functions of film thickness. Prepared films that have not undergone post-annealing show the better spinel crystal structure with increasing growth time. Meanwhile, the size of grain also increases, which induces the change of magnetic properties: saturation magnetization increased and coercivity increased at first and then decreased. Note that the sample of 10-nm thickness is the superparamagnetic property. Transmission electron microscopy displays that the film grew with a disorder structure at initial growth, then forms spinel crystal structure as its thickness increases, which is relative to lattice matching between substrate Si and NiFe2O4.
doi:10.1186/1556-276X-8-196
PMCID: PMC3653778  PMID: 23622034
Crystal growth; Sputtering; Thin films; NiFe2O4; Spinel structure; 75.70.-i; 75.70.Ak; 75.60.Ej
24.  Unique mechanical properties of nanostructured transparent MgAl2O4 ceramics 
Nanoscale Research Letters  2013;8(1):261.
Nanoindentation tests were performed on nanostructured transparent magnesium aluminate (MgAl2O4) ceramics to determine their mechanical properties. These tests were carried out on samples at different applied loads ranging from 300 to 9,000 μN. The elastic recovery for nanostructured transparent MgAl2O4 ceramics at different applied loads was derived from the force-depth data. The results reveal a remarkable enhancement in plastic deformation as the applied load increases from 300 to 9,000 μN. After the nanoindetation tests, scanning probe microscope images show no cracking in nanostructured transparent MgAl2O4 ceramics, which confirms the absence of any cracks and fractures around the indentation. Interestingly, the flow of the material along the edges of indent impressions is clearly presented, which is attributed to the dislocation introduced. High-resolution transmission electron microscopy observation indicates the presence of dislocations along the grain boundary, suggesting that the generation and interaction of dislocations play an important role in the plastic deformation of nanostructured transparent ceramics. Finally, the experimentally measured hardness and Young’s modulus, as derived from the load–displacement data, are as high as 31.7 and 314 GPa, respectively.
doi:10.1186/1556-276X-8-261
PMCID: PMC3672023  PMID: 23724845
Nanostructured transparent ceramic; Nanoindentation; Hardness; Elastic modulus
25.  Application of atomic force microscopy in morphological observation of antisense probe labeled with magnetism 
Molecular Vision  2008;14:114-117.
Purpose
To explore the possibility of the c-erbB2 oncogene antisense probe labeled with superparamagnetic iron oxide (SPIO) nanoparticles as a target contrast agent for magnetic resonance (MR) imaging whose morphology was observed with atomic force microscopy (AFM), and its efficiency was examined by MR imaging.
Methods
The c-erbB2 oncogene antisense probe labeled with SPIO was synthesized by a chemical cross-linking approach. Its morphology was observed with AFM.
Results
The chemical constitution of c-erbB2 oncogene antisense probes can be observed with AFM. The molecular structure of probes is easily visualized under AFM. Probes with diameters of 25–40 nm are in order, follow uniformity and the arrangement rule, can be separated from each other, and appear as cubes with a rugged surface morphology. Strong, low signals of the probes in transfected cells were observed by MR cellular imaging.
Conclusions
AFM is ideal for morphological observation and for analyzing the molecular structure of synthesized c-erbB2 oncogene antisense probes.
PMCID: PMC2254963  PMID: 18253092

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