Application Of Atomic Force Microscopy Research Articles

Application of triangular atomic force microscopy cantilevers to friction measurement with the improved parallel scan method

The atomic force microscopy (AFM) can provide tribological information in micro/nanoscale. However, the general measurement techniques require rigorous value of stiffness and relationship between AFM cantilever deformation and corresponding photodetector response. In this study, triangular AFM cantilevers with different dimensions are applied to quantitatively measure the coefficient of friction with the improved parallel scan method [Y. L. Wang, X. Z. Zhao, and F. Q. Zhou, Rev. Sci. Instrum. 78, 036107 (2007)]. An analytical model is first presented with the plan-view geometrical dimensions of cantilevers. Finite element analysis (FEA) models are set up to validate the analytical model. The results show good agreement between analytical calculation and FEA simulation. More importantly, the coefficient of friction obtained with different cantilevers on silicon surface shows a good consistency. At last, the factors which may affect measurement are discussed. The advantage of the model presented here is that the general uncertainties of thickness and Young's modulus are not necessary to be known for the friction force calibration in AFM application.

Application of AFM in a study of the selective oxidation behavior of materials during the early oxidation stage

The roughening kinetics of the oxide scales formed on a novel electrodeposited nanocomposite Ni–12.6 wt.% Cr having a nanocrystalline Ni matrix with a dispersion of Cr nanoparticles and on a conventional coarse-grained, chromia-forming Ni–20Cr alloy have been studied with atomic force microscopy (AFM). The results show that it is possible to use AFM to check the validity of the model proposed which links the selective oxidation behavior of the two materials with different roughening process.

Selective Deposition of Titanium Dioxide Thin Film on Glass Monolayers by Impregnating Method

Titanium dioxide (TiO2) thin film was fabricated on the surface of glass monolayers at room temperature, using KH-550 as self-assembled monolayers (SAMs). The TiO2 gel precursor was characterized with differential scanning calorimetry – thermogravimetry (DSC-TG), and the TiO2 powder was analyzed with X-ray diffraction (XRD). The TiO2 thin film was tested with X-ray fluorescence spectroscopy (XRF). With the application of atomic force microscope (AFM) the surface topography of siloxane layer and TiO2 film were studied. Their hydrophilicities were measured. The transmittance of TiO2 film was detected by using dual beam ultraviolet - visible spectrophotometer. The results show that the TiO2 thin film is in monolayer with nanometer level, the deposition is the anatase structure. TiO2 is deposited on the surface instead of channel or gap of siloxane, the hydrophilicities of TiO2 monolayer film are perfect, and TiO2 monolayer film has a good transmissivity in the visible light area.

Biomedical applications of AFM

The atomic force microscopy (AFM) is a technique that is widely used to study the mechanical properties of biological samples in conditions close to natural. In particular, the technique can deliver the information about both the cell stiffness and the unbinding force of individual molecular complexes. Cell stiffness seems to be a global parameter describing the overall changes occurring in the cell structure, particularly in the cellular scaffold called cytoskeleton. The determination of the unbinding forces, acting between a single pair of molecules, brings more specific information about the interaction forces. Both types of AFM measurements can be successfully applied for the detection and quantification of the alterations of mechanical properties in cancerous cells with the special emphasis on the development of a new technique for the cancer detection on a single cell level.

TORSIONAL RESONANCE MODE ATOMIC FORCE MICROSCOPY OF A PROTEIN–DNA COMPLEX

Precise mapping of protein-binding sites on DNA is an important application of atomic force microscope (AFM) imaging. For a reliable measurement of distances on curved DNA molecules, an image-processing algorithm is required, which extracts the DNA contour from topographic AFM data. To this end we implemented an image analysis method providing an efficient way to obtain the contour together with a physical map of single and multiple protein-binding sites. This method relies on a calculation of the height profile along the DNA fragment, allowing one to determine the DNA length and the relative position of the binding site occupied by a protein. As a first test, complexes of the LexA repressor protein from the Escherichia coli SOS system and DNA fragments containing a specific LexA binding site (recA operator) were imaged by the torsional resonance mode (TR mode) and analyzed using the specialized algorithm. A topographic height of less than 0.5 nm of the DNA molecules indicates repulsive imaging conditions.

Atomic force microscopy investigation of the denudation of the envelope of influenza virus treated with Nonidet P-40

Through observing the morphology and topography of the prepared influenza viruses (H1N1) treated with the different Nonidet P-40 solutions using atomic force microscopy (AFM), to explore the application of AFM on the research of the internal character of viral morphology and structural virology. The virus samples were treated with serial diluted Nonidet P-40 solutions from 0.05% to 0.20% and then investigated by AFM with the tapping mode in air at room temperature to obtain the morphology and topography changes including height data,amplitude data and phase data for both spherical and filamentous influenza virus A. The serial AFM images show that the erosion degree of the virions is proportional with the improvement of NP-40 concentration,and partly denuded virion image appeared at 0.05% NP-40 treatment, which was revealed clearly on both amplitude images and phase images. This work demonstrated for the first time that the internal topography of influenza virion could be revealed by AFM via suitable nonionic surfactants chemical dissection.

An AFM Observation on Fossil Cytoplasm

Abstract: Fossil cytoplasm is a new research topic of interest in paleobotany. Atomic force microscope (AFM) is a new technology applied widely in physics and biology; however, it is rarely used in paleontology. Here we applied AFM for the first time to study fossil cytoplasm. The results indicate that the fossil cytoplasm is heterogeneous and full of ultrastructures, just like extant cytoplasm, and that the application of AFM, especially in combination with other techniques, can reveal the subcellular details of fossil plants with more confidence.

Atomic Force Microscopy: A Versatile Tool for Studying Cell Morphology, Adhesion and Mechanics

The atomic force microscope (AFM), a member of the scanning probe family of microscopes, generates height maps of sample surfaces with subnanometer resolution. Importantly, AFM offers the opportunity to image samples with little or no treatment and under physiologically-relevant conditions, making it well-suited for investigating the structure of biological samples, including fixed or living cells and tissues. In addition to its high-resolution imaging capability, AFM used in force spectroscopy mode is a sensitive force measuring device, able to detect or exert forces ranging from the pico- to the nanonewton scale. Here we review a broad range of cell biological applications of AFM, including high resolution imaging of adherent cells, measuring cell adhesion down to the single-receptor level and characterizing the mechanical properties of cells. Furthermore, we present recent examples of how the combined use of AFM and advanced light microscopy techniques can provide complementary structural information.

Time-dependent surface adhesive force and morphology of RBC measured by AFM

Atomic force microscopy (AFM) is a rapidly developing tool recently introduced into the evaluation of the age of bloodstains, potentially providing legal medical experts useful information for forensic investigation. In this study, the time-dependent, morphological changes of red blood cells (RBC) under three different conditions (including controlled, room-temperature condition, uncontrolled, outdoor-environmental condition, and controlled, low-temperature condition) were observed by AFM, as well as the cellular viscoelasticity via force-vs-distance curve measurements. Firstly, the data indicate that substrate types have different effects on cellular morphology of RBC. RBC presented the typical biconcave shape on mica, whereas either the biconcave shape or flattened shape was evident on glass. The mean volume of RBCs on mica was significantly larger than that of cells on glass. Surprisingly, the adhesive property of RBC membrane surfaces was substrate type-independent (the adhesive forces were statistically similar on glass and mica). With time lapse, the changes in cell volume and adhesive force of RBC under the controlled room-temperature condition were similar to those under the uncontrolled outdoor-environmental condition. Under the controlled low-temperature condition, however, the changes in cell volume occurred mainly due to the collapse of RBCs, and the curves of adhesive force showed the dramatic alternations in viscoelasticity of RBC. Taken together, the AFM detections on the time-dependent, substrate type-dependent, environment (temperature/humidity)-dependent changes in morphology and surface viscoelasticity of RBC imply a potential application of AFM in forensic medicine or investigations, e.g., estimating age of bloodstain or death time.

AFM for analysis of structure and dynamics of DNA and protein–DNA complexes

This paper describes protocols for studies of structure and dynamics of DNA and protein–DNA complexes with atomic force microscopy (AFM) utilizing the surface chemistry approach. The necessary specifics for the preparation of functionalized surfaces and AFM probes with the use of silanes and silatranes, including the protocols for synthesis of silatranes are provided. The methodology of studies of local and global conformations DNA with the major focus on the time-lapse imaging of DNA in aqueous solutions is illustrated by the study of dynamics of Holliday junctions including branch migration. The analysis of nucleosome dynamics is selected as an example to illustrate the application of the time-lapse AFM to studies of dynamics of protein–DNA complexes. The force spectroscopy is the modality of AFM with a great importance to various fields of biomedical studies. The AFM force spectroscopy approach for studies of specific protein–DNA complexes is illustrated by the data on analysis of dynamics of synaptic SfiI–DNA complexes. When necessary, additional specifics are added to the corresponding example.

Application of Atomic Force Microscopy on Studying Micro- and Nano-Structures of Starch

This paper reviews the application of atomic force microscopy (AFM) to the study of starch structures, including both macrostructure of starch granules and the nanostructure of molecular chains. It introduces the different techniques of sample preparation and discusses what AFM could observe. The paper summarises the present situation of the application of AFM in the study of starch structures and guides the direction for further research.

Characterization of defects in flexible circuits with ultrasonic atomic force microscopy

Flexible circuit technology is a key factor in the continued shrinkage of microelectronic components and devices. One of the important applications of the flexible circuits is in hard disk drive industry, where they are used as an interconnection between the preamplifier and head slider assembly of a hard disk drive. At present, defect characterization of flexible circuits is often performed after manufacture usually with optical microscopy. While this may be sufficient for certain low-tech applications, for advanced ultra high-density hard disk components may not be enough. With a continuing reduction of the dimension of the current carrying conductor wires, the size of defects that may affect long-term reliability of the system is reaching the resolution limit of traditional techniques used to characterize the defects. This paper presents combined application of atomic force microscope (AFM) and ultrasonic atomic force microscope (UAFM) to characterize defects in flexible circuits. Three identical flexible circuits from different manufactures are examined using AFM and UAFM. The AFM and UAFM images of a particular region, in the flexible circuit in all the three samples are compared. Images from pure polymer region of the flexible circuit are compared with the images of the regions containing copper and polymer. In general, the UAFM images show subsurface features while AFM images show surface topography. This capability of UAFM can be used to image the grain structure of the copper film without removing the polymer cover layer film. It also detects the sub-micron defects present at the polymer/metal interface. Analysis of the grain structure of copper, distribution of defects at the polymer/metal interface is presented. Based on these observations, the applicability of AFM/UAFM to image the microstructure of copper in flexible circuits and possible effect of defects in flexible circuits on the long-term reliability of the hard disc drive are discussed.

Climbing the steps of viral atomic force microscopy: visualization of Dengue virus particles

In recent years, the application of atomic force microscopy (AFM) to biological systems has highlighted the potential of this technology. AFM provides insights into studies of biological structures and interactions and can also identify and characterize a large panel of pathogens, including viruses. The Flaviviridae family contains a number of viruses that are important human and animal pathogens. Among them, Dengue virus causes epidemics with fatal outcomes mainly in the tropics. In this study, Dengue virus is visualized for the first time using the in air AFM technique. Images were obtained from a potassium-tartrate gradient-purified virus. This study enhances the application of AFM as a novel tool for the visualization and characterization of virus particles. Because flavivirus members are closely related, studies of the morphologic structure of the Dengue virus can reveal strategies that may be useful to identify and study other important viruses in the family, including the West Nile virus.

Structure and Mechanics of Membrane Proteins

Evolution has tuned membrane proteins to exist in a lipid bilayer, provide for cell-cell communication, transport solutes, and convert energies. These proteins exhibit a hydrophobic belt that interacts with the lipid bilayer. Detergents are therefore used to extract membrane proteins and keep them in solution for purification and subsequent analyses. However, most membrane proteins are unstable when solubilized and hence often not accessible to NMR or X-ray crystallography. The atomic force microscope (AFM) is a powerful tool for imaging and manipulating membrane proteins in their native state. Superb images of native membranes have been recorded, and a quantitative interpretation of the data acquired using the AFM tip has become possible. In addition, multifunctional probes to simultaneously acquire information on the topography and electrical properties of membrane proteins have been produced. This progress is discussed here and fosters expectations for future developments and applications of AFM and single-molecule force spectroscopy.

Atomic force microscopy dynamic modes: modeling and applications

This paper contains a review of the development in modeling and applications ofatomic force microscopy (AFM) modes. AFM is commonly used for atomic andnano-scale surface measurement. Two operational modes of AFM exist: static modeand dynamic mode. In dynamic AFM mode, a cantilever is driven to vibrate byits holder or the sample. The changes of cantilever vibration parameters due totip–sample interaction are used to reveal surface properties of samples. Analyticaland numerical models that can accurately simulate surface-coupled cantileverdynamics are essential for explaining AFM scanning images and evaluating a sample’smaterial properties. The objective of this paper is to categorize the existing AFMdynamic modes and measurement techniques in terms of cantilever deflection andexcitation mechanism, summarize AFM cantilever models presented in the literature,and demonstrate the applications of these models in AFM mode simulations.Based on the relations between cantilever responses and tip–sample interaction,methods for quantitative evaluation of a sample’s mechanical parameters aredescribed.

Atomic Force Microscopy (AFM)

The atomic force microscope (AFM) is an important tool for studying biological samples due to its ability to image surfaces under liquids. The AFM operates by physical interaction of a cantilever tip with the molecules on the cell surface. Adhesion forces between the tip and cell surface molecules are detected as cantilever deflections. Thus, the cantilever tip can be used to image live cells with atomic resolution and to probe single molecular events in living cells under physiological conditions. Currently, this is the only technique available that directly provides structural, mechanical, and functional information at high resolution. This unit presents the basic AFM components, modes of operation, useful tips for sample preparation, and a short review of AFM applications in microbiology.

Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology

The recent technical development of atomic force microscopy (AFM) has made nano-biology of the nucleus an attractive and promising field. In this paper, we will review our current understanding of nuclear architecture and dynamics from the structural point of view. Especially, special emphases will be given to: (1) How to approach the nuclear architectures by means of new techniques using AFM, (2) the importance of the physical property of DNA in the construction of the higher-order structures, (3) the significance and implication of the linker and core histones and the nuclear matrix/scaffold proteins for the chromatin dynamics, (4) the nuclear proteins that contribute to the formation of the inner nuclear architecture. Spatio-temporal analyses using AFM, in combination with biochemical and cell biological approaches, will play important roles in the nano-biology of the nucleus, as most of nuclear structures and events occur in nanometer, piconewton and millisecond order. The new applications of AFM, such as recognition imaging, fast-scanning imaging, and a variety of modified cantilevers, are expected to be powerful techniques to reveal the nanostructure of the nucleus.

Observing fibrillar assemblies on scrapie-infected cells

The infectious agent in prion diseases is an aberrant-folded isoform of the cellular prion protein (PrPC). This scrapie-related prion protein (PrPSc) has an increased beta-sheet content, is detergent insoluble and proteinase K resistant, and accumulates in prion-infected organisms and cells. In vitro, PrPSc self-aggregates into amyloid fibrils. However, there is no direct experimental proof for the occurrence of PrPSc-containing fibrils in vivo or in cell cultures. Applying atomic force microscopy (AFM) to scrapie-infected mouse neuroblastoma (ScN2a) cells, we discovered growing patch-like assemblies of amyloid-like fibrillar structures on the cell surfaces. Immunofluorescence and AFM images showed heterogeneous accumulation and aggregation of PrPSc in ScN2a cell cultures. The percentage of cells having characteristic fibrils on their surface increased with time after scrapie infection. These endogeneous fibrils had lengths from 0.5 to 3 microm and protruded from the cell surface by 108 +/- 30 nm, and thus resembled the heterogeneous shapes and networks of in vitro prepared amyloid fibrils.

Nanoscale surface property estimation using proper orthogonal decomposition in atomic force microscopy

Atomic force microscopy (AFM) in a dynamic mode operation uses a resonating tip to measure the nanoscale surface topography and other properties. The dynamic response of the tip includes the complex tip–surface interactions due to the surface properties. We found that conventional tapping mode had a limitation in the accurate set-point control on soft and high adhesion surfaces. This study employed the proper orthogonal decomposition (POD)-based AFM microcantilever characterization method to estimate the surface property with more reliable control. The POD extracted the dominant empirical modes of the AFM microcantilever during tapping and scanning on the surface. Also the corresponding eigenvalues represented the significance of the empirical modes and the characteristic features of the nanoscale surface property. This experimental approach can offer a new insight on the novel application of nanoscale surface property estimation in dynamic AFM applications.

Application of AFM in understanding biomineral formation in diatoms

We review previous work and present new data on the application of atomic force microscopy (AFM) to study biomineral formation in diatoms, unicellular algae that make cell walls of silica. Previous studies examined a small subset of mostly larger diatom species, identifying a prevalence of large particulate silica on the nanoscale. We survey different structures including valves, girdle bands, and elongated spines called setae, in a variety of species, and show a diversity of nano- and meso-scale silica morphologies, even on different portions of the same structure. A general trend of highly organized mesoscale silica structure on the proximal face of cell wall components was observed, with less organized structure occurring on the distal face. The highly organized structures have features suggestive of an underlying linear template, which defines the area of initial silica polymerization. Such features have not been imaged with such clarity previously, demonstrating the advantages of AFM to image small differences in surface morphology and providing new insights and confirming evidence for models of diatom silica structure formation. In addition to its imaging capability, more developed application of AFM to map locations of organic template components on the nanoscale will greatly aid in elucidating mechanisms of diatom biosilica synthesis.