Nanometer-scale oxidation of Si(100) surfaces by tapping mode atomic force microscopy

The nanometer¿scale oxidation of Si(100) surfaces in air is performed with an atomic force microscope working in tapping mode. Applying a positive voltage to the sample with respect to the tip, two kinds of modifications are induced on the sample: grown silicon oxide mounds less than 5 nm high and mounds higher than 10 nm (which are assumed to be gold depositions). The threshold voltage necessary to produce the modification is studied as a function of the average tip¿to¿sample distance.

Atomic force microscopy of nucleoprotein complexes.

Recent data on the AFM studies of nucleoprotein complexes of different types are reviewed in this paper. The first section describes the progress in the sample preparation methods for AFM studies of nucleic acids and nucleoprotein complexes. The second part of this paper reviews AFM data on studies of complexes of DNA with regulatory proteins. These studies include two different types of DNA distortion induced by proteins binding: local bending of DNA at sites of protein binding and formation of large loops due to protein-protein interactions between molecules bound to distant sites along the DNA molecules (DNA looping). The prospects for use of AFM for physical mapping of genomes are discussed in this section as well. The third part of the paper reviews data on studies of complexes of DNA with non-sequence specific binding proteins. Special emphasis is given to studies of chromatin which have resulted in progress in the understanding of structure of native chromatin fiber. In this section, novel data on AFM studies of RecA-DNA filaments and complexes of dsRNA with the dsRNA-specific protein p25 are also presented. Discussion of the substrate preparation procedures in relation to the AFM studies of nucleoprotein complexes is given in the final section.

Atomic Force Microscopy Stiffness Tomography on Living Arabidopsis thaliana Cells Reveals the Mechanical Properties of Surface and Deep Cell-Wall Layers during Growth.

Cell-wall mechanical properties play a key role in the growth and the protection of plants. However, little is known about genuine wall mechanical properties and their growth-related dynamics at subcellular resolution and in living cells. Here, we used atomic force microscopy (AFM) stiffness tomography to explore stiffness distribution in the cell wall of suspension-cultured Arabidopsis thaliana as a model of primary, growing cell wall. For the first time that we know of, this new imaging technique was performed on living single cells of a higher plant, permitting monitoring of the stiffness distribution in cell-wall layers as a function of the depth and its evolution during the different growth phases. The mechanical measurements were correlated with changes in the composition of the cell wall, which were revealed by Fourier-transform infrared (FTIR) spectroscopy. In the beginning and end of cell growth, the average stiffness of the cell wall was low and the wall was mechanically homogenous, whereas in the exponential growth phase, the average wall stiffness increased, with increasing heterogeneity. In this phase, the difference between the superficial and deep wall stiffness was highest. FTIR spectra revealed a relative increase in the polysaccharide/lignin content.

Microcontroller-driven fluid-injection system for atomic force microscopy.

We present a programmable microcontroller-driven injection system for the exchange of imaging medium during atomic force microscopy. Using this low-noise system, high-resolution imaging can be performed during this process of injection without disturbance. This latter circumstance was exemplified by the online imaging of conformational changes in DNA molecules during the injection of anticancer drug into the fluid chamber.

Atomic force microscopy: probing the nanoworld

Atomic Force Microscope and related techniques have played a key role in the development of the nanotechnology revolution that is taking place in science. This paper reviews the basic principles behind the technique and its different operation modes and applications, pointing out research worksperformed in the Nanometric Techniques Unit of the CCiTUB in order to exemplify the vast array of capabilities of these instruments.

Fuzzy logic algorithm to extract specific interaction forces from atomic force microscopy data

The atomic force microscope is not only a very convenient tool for studying the topography of different samples, but it can also be used to measure specific binding forces between molecules. For this purpose, one type of molecule is attached to the tip and the other one to the substrate. Approaching the tip to the substrate allows the molecules to bind together. Retracting the tip breaks the newly formed bond. The rupture of a specific bond appears in the force-distance curves as a spike from which the binding force can be deduced. In this article we present an algorithm to automatically process force-distance curves in order to obtain bond strength histograms. The algorithm is based on a fuzzy logic approach that permits an evaluation of "quality" for every event and makes the detection procedure much faster compared to a manual selection. In this article, the software has been applied to measure the binding strength between tubuline and microtubuline associated proteins.

Stiffness tomography by atomic force microscopy.

The atomic force microscope is a convenient tool to probe living samples at the nanometric scale. Among its numerous capabilities, the instrument can be operated as a nano-indenter to gather information about the mechanical properties of the sample. In this operating mode, the deformation of the cantilever is displayed as a function of the indentation depth of the tip into the sample. Fitting this curve with different theoretical models permits us to estimate the Young's modulus of the sample at the indentation spot. We describe what to our knowledge is a new technique to process these curves to distinguish structures of different stiffness buried into the bulk of the sample. The working principle of this new imaging technique has been verified by finite element models and successfully applied to living cells.

Atomic force microscopy imaging of living cells

Over the last two decades, Atomic Force Microscopy (AFM) has emerged as the tool of choice to image living organisms in a near-physiological environment. Whereas fluorescence microscopy techniques allow labeling and tracking of components inside cells and the observation of dynamic processes, AFM is mainly a surface technique that can be operated on a wide range of substrates including biological samples. AFM enables extraction of topographical, mechanical and chemical information from these samples.

Assessing dystrophies and other muscle diseases at the nanometer scale by atomic force microscopy.

AIM: Atomic force microscopy nanoindentation of myofibers was used to assess and quantitatively diagnose muscular dystrophies from human patients. MATERIALS & METHODS: Myofibers were probed from fresh or frozen muscle biopsies from human dystrophic patients and healthy volunteers, as well as mice models, and Young's modulus stiffness values were determined. RESULTS: Fibers displaying abnormally low mechanical stability were detected in biopsies from patients affected by 11 distinct muscle diseases, and Young's modulus values were commensurate to the severity of the disease. Abnormal myofiber resistance was also observed from consulting patients whose muscle condition could not be detected or unambiguously diagnosed otherwise. DISCUSSION & CONCLUSION: This study provides a proof-of-concept that atomic force microscopy yields a quantitative read-out of human muscle function from clinical biopsies, and that it may thereby complement current muscular dystrophy diagnosis.

Atomic Force Microscopy Investigation of NI Particles Deposited on Porous Silicon

In this thesis properties and influence of modification techniques of porous silicon were studied by Atomic Force Microscope (AFM). This device permits to visualize the surface topography and to study properties of the samples on atomic scale, which was necessary for recent investigation. Samples of porous silicon were obtained by electrochemical etching. Nickel particles were deposited by two methods: electrochemical deposition and extracting from NiCl2 ethanol solution. Sample growth was conducted in Saint-Petersburg State Electrotechnical University, LETI. Kelvin probe force microscopy (KPFM) and Magnetic force microscopy (MFM) were utilized for detailed information about surface properties of the samples. Measurements showed the difference in morphology correlating with initial growth conditions. Submicron size particles were clearly visible on surfaces of the treated samples. Although their nature was not clarified due to limitations of AFM technique. It is expected that surfaces were covered by nanometer scale Ni particles, which can be verified by implication of RAMAN device.

Comparative characterisation by atomic force microscopy and ellipsometry of soft and solid thin films

Ellipsometry and atomic force microscopy (AFM) were used to study the film thickness and the surface roughness of both 'soft' and solid thin films. 'Soft' polymer thin films of polystyrene and poly(styrene-ethylene/butylene-styrene) block copolymer were prepared by spin-coating onto planar silicon wafers. Ellipsometric parameters were fitted by the Cauchy approach using a two-layer model with planar boundaries between the layers. The smooth surfaces of the prepared polymer films were confirmed by AFM. There is good agreement between AFM and ellipsometry in the 80-130 nm thickness range. Semiconductor surfaces (Si) obtained by anisotropic chemical etching were investigated as an example of a randomly rough surface. To define roughness parameters by ellipsometry, the top rough layers were treated as thin films according to the Bruggeman effective medium approximation (BEMA). Surface roughness values measured by AFM and ellipsometry show the same tendency of increasing roughness with increased etching time, although AFM results depend on the used window size. The combined use of both methods appears to offer the most comprehensive route to quantitative surface roughness characterisation of solid films. Copyright (c) 2007 John Wiley & Sons, Ltd.

Surface structure of thin asymmetric PS-b-PMMA diblock copolymers investigated by atomic force microscopy

Asymmetric poly(styrene-b-methyl methacrylate) (PS-b-PMMA) diblock copolymers of molecular weight M-n = 29,700g mol(-1) (M-PS = 9300 g mol(-1) M-PMMA = 20,100 g mol(-1), PD = 1.15, chi(PS) = 0.323, chi(PMMA) = 0.677) and M-n = 63,900 g mol(-1) (M-PS = 50,500 g mol(-1), M-PMMA = 13,400 g mol(-1), PD = 1.18, chi(PS) = 0.790, chi(PMMA) = 0.210) were prepared via reversible addition-fragmentation chain transfer (RAFT) polymerization. Atomic force microscopy (AFM) was used to investigate the surface structure of thin films, prepared by spin-coating the diblock copolymers on a silicon substrate. We show that the nanostructure of the diblock copolymer depends on the molecular weight and volume fraction of the diblock copolymers. We observed a perpendicular lamellar structure for the high molar mass sample and a hexagonal-packed cylindrical patterning for the lower molar mass one. Small-angle X-ray scattering investigation of these samples without annealing did not reveal any ordered structure. Annealing of PS-b-PMMA samples at 160 degrees C for 24 h led to a change in surface structure.

Direct visualisation of lipid bilayer cubic phases using Atomic Force Microscopy

Inverse bicontinuous cubic (Q(II)) phases are nanostructured materials formed by lipid self-assembly. We have successfully imaged thin films of hydrated Q(II) phases from two different systems using AFM. The images show periodic arrays of water channels with spacing and symmetry consistent with published SAXS data on the bulk materials.