Investigation of surface changes on mica induced by atomic force microscopy imaging under liquids

Surface changes on muscovite mica induced by tip-surface interactions in atomic force microscopy (AFM) experiments under liquids are described. Investigations have been performed with AFM operated both in contact mode (CM-AFM) and in tapping mode (TM-AFM). Additionally, force-distance measurements have been carried out. In contrast to CM-AFM pronounced surface changes can be observed in TM-AFM experiments. However, TM-AFM images of areas previously scanned in contact mode show that imaging in contact mode changes the surface, too. An evaluation of force-distance measurements reveals that these changes depend on the adhesive interaction between tip and sample, which in turn strongly depends on the surrounding medium. The artefact can be avoided by changing the pH-value of the medium or by working with mixtures of ethanol and water. This greatly enhances the applicability of TM-AFM for in-situ investigation of surface processes on mica, which is a frequently used substrate for many technological and biological applications.     

Heat-fixation method used in an atomic force microscopy study of cell morphology

In order to overcome the difficulties with existing methods for sample immobilization in imaging Halobacterium salinarum (H. salinarum) living in a highly salty medium by atomic force microscopy (AFM), a heat-fixation method was, for the first time, used to overcome existing problems in preparing samples for AFM. The effect on the cell morphology of the heat-fixation method was studied by MAC mode AFM, and was compared with the drop-and-dry and the polylysine-adhesion methods. It was found that the heat-fixation method can be successfully used for preparing Gram-negative and Gram-positive bacteria samples for AFM studies. Using this method, high-resolution AFM images of H. salinarum were obtained. Round protrusions on the cell surface and horn-like protrusions only at one pole of H. salinarum were observed.     

碳纳米管原子力显微镜针尖对脱氧核糖核酸高分辨率成像研究

运用自制的碳纳米管原子力显微镜针尖,在液体中观察了脱氧核糖核酸（DNA）分子的精细结构。结果表明,运用碳纳米管针尖获得的DNA分子的高度与电子显微镜的结果非常接近,且没有造成样品的变形损伤;碳纳米管针尖得到的DNA分子的宽度与真实值相近,减小了原子力显微镜成像的增宽效应,这是用传统的硅针尖无法获得的。DNA分子精细结构的高分辨率图像的获得为研究其功能提供了有价值的信息。     

Identification and localization of organic coating degradation onset by impedance imaging

The aim of this work was to demonstrate the potential of a localized impedance measurement technique to identify and spatially localize the onset spots of polymeric coating degradation. The technique, which has not yet been applied in the field of organic coatings, utilizes atomic force microscopy (AFM) in contact mode. During the scan a single-frequency voltage perturbation signal is applied between the AFM tip and the coated metal substrate. A current response signal is registered. As a result an impedance map of the scanned region is created. The method was applied to investigation of acrylic coating degradation during exposure to UV radiation. Localized topography and impedance images revealed formation of micro-cracks in the coating layer, which gradually converted into through-the-coating defects with an increase in the irradiation time. Thus the method allowed early identification and localization of the sites of degradation onset, which was not possible using classical impedance measurement.     

In situ AFM study of sorbed humic acid colloids at different pH

Humic acid colloids adsorbed on the basal plane of cleaved muscovite are investigated under in situ conditions by non-contact mode atomic force microscopy (AFM) in liquid (also called fluid tapping-mode AFM). Structures are found to be of nanometer scale, consisting of flat particles (8–13 nm in diameter), aggregates of particles (20–100 nm), chain-like assemblies, networks and torus-like structures. In contrast to former investigations colloids are investigated in aquatic solution and structures are not influenced by sample preparation. Nanostructure, surface coverage and particle sizes are found to depend on solution pH. Humic colloids can be distinguished from surface roughness and background noise by image processing. Furthermore, an approach to quantify the surface coverage is discussed. Therefore, non-contact mode AFM in liquid is shown to be a powerful method to study the interaction of colloids at solid–liquid interfaces.     

Origins of Baseline Drift and Distortion in Fourier Transform Spectra

The spectrum scanned by a Fourier transform spectrometer (FTIR) often has a baseline drift. However, baseline distortion rarely occurs in a laboratory owing to the insignificant effects of environmental vibrations and electromagnetic factors. Even if it occurs, the distorted spectrum can be manually eliminated. However, in a complex environment, especially after the long-term operation of a spectrometer, the scanned spectrum may be distorted to different degrees. Herein, the origins of spectral baseline drifts and distortions are analyzed and simulated using MATLAB; furthermore, a baseline correction method based on the baseline-type model is proposed. The results of experiments performed on the methane spectrum confirm that the proposed method outperformed the improved modified multi-polynomial fitting and iterative averaging methods.     

An improvement of window factor analysis for resolution of noisy HPLC-DAD data

Window factor analysis (WFA) is a powerful tool in analyzing evolutionary process. However, it was found that window factor analysis is much sensitive to the noise involved in original data matrix. An error analysis was done with the fact that the concentration profiles resolved by the conventional window factor analysis are easily distorted by the noise reserved by the abstract factor analysis (AFA), and a modified algorithm for window factor analysis was proposed. Both simulated and experimental HPLC-DAD data were investigated by the conventional and the improved methods. Results show that the improved method can yield less noise-distorted concentration profiles than the conventional method, and the ability for resolution of noisy data sets can be greatly enhanced.     

Effect of example weights on prediction of protein-protein interactions

Protein-protein interactions (PPIs) prediction is an important issue in biology. Recently many computational methods have been proposed to determine PPIs. However, there is no golden standard dataset for these methods now. Furthermore, there exists different quality among training examples and the quality is always ignored by the current methods. In the condition of low-quality examples, the system should tolerate the data noise. Example weighting strategy is used in this paper to build a robust system and solve the problem of data noise. Training examples are investigated and a new example selecting/using strategy is proposed. Training example weighting method based on confidence is proposed. Different weight setting strategies are discussed and the corresponding results are given in the experiment. A new model integrating example weighting strategy, attraction-repulsion (AR) weight model, is proposed. Experimental results on Saccharomyces cerevisiae demonstrate that the new model outperforms the original AR model in the ROC score measure by over 8%. Furthermore, the example weighting strategy is applied to another domain-based PPIs prediction method, maximum likelihood estimation (MLE) method, and the modified MLE method obtains better performance than the original MLE method. At same time, our examples weighting strategy can be applied to any other training example based PPIs prediction methods.     

Nanografting of alkanethiols by tapping mode atomic force microscopy

Nanografting, an atomic force microscopy (AFM) based nanolithography technique, is becoming a popular method for patterning self-assembled monolayers (SAMs). In this technique, a nanoscale patch of a thiol-on-gold SAM is exchanged with a different thiol by the action of an AFM tip operated in contact mode at high load. The results are then imaged in topographic or lateral force microscopy again at low values of the load. One of the problems of contact mode nanografting is that monolayers of large molecules such as proteins are likely to be deformed, damaged, or even removed from the surface by contact mode imaging even when small loads are used. Furthermore, we need to note that the stiffness of the cantilevers used in contact mode is different than that of the cantilevers used in tapping mode and that tip changing in the course of an experiment can be quite inconvenient. Here, we show that a monolayer on a gold substrate can be nanografted using tapping mode AFM (also referred to as amplitude modulation AFM) rather than the commonly used contact mode. While the grafting parameters are somewhat trickier to choose, the results demonstrate that nanografting in tapping mode can make patches of the same quality as those made by contact mode, therefore allowing for gentle imaging of the grafted molecules and the whole SAM without changing the microscope tip.     

AFM imaging and characterization of latex particles formed by copolymerization of styrene and poly(ethylene oxide) macromonomer

A new type of latex particle was prepared by copolymerization of styrene and poly(ethylene oxide) macromonomer. By controlling the concentration of styrene in reaction mixtures, several latexes with different grain sizes were obtained. The packing patterns of the latex films as well as shapes and sizes of the latex particles were measured with atomic force microscopy (AFM). AFM images revealed that the grain sizes of the latexes increase with increasing concentration of styrene. At a higher styrene concentration (10 wt%), the latex showed a rather homogenous distribution of grain sizes. Lateral force microscopy (LFM) was used to reveal frictional features of latex particles. Contact and non-contact mode AFM were employed to image the same sample of the latex films. The results show that AFM working in non-contact mode can be used to effectively eliminate the horizontal-line-like artifacts, which may obscure AFM images.     

Comparison of antibody--antigen interactions on collagen measured by conventional immunological techniques and atomic force microscopy

We have developed a means of using atomic force microscopy (AFM) to repeatedly localize a small area of interest (4 x 4 microm(2)) within a 0.5-cm(2) area on a heterogeneous sample, to obtain and localize high-resolution images and force measurements on nonideal samples (i.e., samples that better reflect actual biological systems, not prepared on atomically flat surfaces). We demonstrate the repeated localization and measurement of unbinding forces associated with antibody--antigen (ab--ag) interactions, by applying AFM in air and in liquid to visualize and measure polyclonal ab--ag interactions, using chicken collagen as a model system. We demonstrate that molecular interactions, in the form of ab--ag complexes, can be visualized by AFM when secondary antibodies are conjugated to 20-nm colloidal gold particles. We then compare those results with established immunological techniques, to demonstrate broader application of AFM technology to other systems. Data from AFM studies are compared with results obtained using immunological methods traditionally employed to investigate ab--ag interactions, including enzyme-linked immunosorbent assay, immunoblotting, and in situ immunofluorescence. Finally, using functionalized AFM tips with a flexible tether [poly(ethylene glycol) 800] to which a derivatized antibody was attached, we analyzed force curve data to measure the unbinding force of collagen antibody from its antigen, obtaining a value of approximately 90 +/- 40 pN with a MatLab code written to automate the analyses of force curves obtained in force--volume mode. The methodology we developed for embedded collagen sections can be readily applied to the investigation of other receptor--ligand interactions.     

Nano-mechanical properties of starch and gluten biopolymers from atomic force microscopy

An original method based on atomic force microscopy (AFM) in contact mode was developed to abrade progressively the surface of tablets made of starch or gluten polymers isolated from wheat. The volume of the material removed by the tip was estimated from the analysis of successive topographic images of the surface, and the shear force was measured by keeping a constant normal force. Our data together with a simple tribological model provide clear evidence for a higher hardness and shear strength of starch compared to gluten. Gluten appears to have mechanical properties close to soft materials, such as talc, whereas starch displays higher hardness close to calcite. Our results are in a better agreement with structural properties of gluten (complex protein network) and starch (granular and semi-cristalline structure) than earlier studies by micro-indentation. This work shows that the AFM scratching method is relevant for the characterization of any polymer surface, in particular in application to materials made of different polymers at the nano-scale.     

Study of hydration layers near a hydrophilic surface in water through AFM imaging

In this work, a hydrophilic silica plate exposed in air, and immersed in an aqueous solution was studied through atomic force microscopy (AFM) imaging in contact‐ and tapping‐mode operations. It was experimentally found that the tapping‐mode AFM images of the silica surface were different when it was immersed in an aqueous solution from those when it was exposed in air. The former showed fewer topographic features. However, the contact‐mode AFM images of the silica surface were almost uninfluenced by the medium in which the surface was placed. This phenomenon might be attributed to the existence of hydration layers near the silica surface in the aqueous solution. The layers are like a large sheet on the surface that hides the details, so that an AFM tip in the tapping mode can read only the hydration layer and therefore image only the rough outline of the surface. This result might suggest the existence of hydration layers near a hydrophilic surface immersed in water. Copyright © 2006 John Wiley & Sons, Ltd.     

Application of empirical mode decomposition in the field of polymer physics

Noisy data has always been a problem to the experimental community. Effective removal of noise from data is important for better understanding and interpretation of experimental results. Over the years, several methods have evolved for filtering the noise present in the data. Fast Fourier transform (FFT) based filters are widely used because they provide precise information about the frequency content of the experimental data, which is used for filtering of noise. However, FFT assumes that the experimental data is stationary. This means that: (i) the deterministic part of the experimental data obtained from a system is at steady state without any transients and has frequency components which do not vary with respect to time and (ii) noise corrupting the experimental data is wide sense stationary, that is, mean and variance of the noise does not statistically vary with respect to time. Several approaches, for example, short time Fourier transform (STFT) and wavelet transform‐based filters, have been developed to handle transient data corrupted with nonstationary noise (mean and variance of noise varies with respect to time) data. Both these approaches provide time and frequency information about the data (time at which a particular frequency is present in the signal). However, these filtering approaches have the following drawbacks: (i) STFT requires identification of an optimal window length within which the data is stationary, which is difficult and (ii) there are theoretical limits on simultaneous time and frequency resolution. Hence, filtering of noise is compromised. Recently, empirical mode decomposition (EMD) has been used in several applications to decompose a given nonstationary data segment into several characteristic oscillatory components called intrinsic mode functions (IMFs). Fourier transform of these IMFs identifies the frequency content in the signal, which can be used for removal of noisy IMFs and reconstruction of the filtered signal. In this work, we propose an algorithm for effective filtering of noise using an EMD‐based FFT approach for applications in polymer physics. The advantages of the proposed approach are: (i) it uses the precise frequency information provided by the FFT and, therefore, efficiently filters a wide variety of noise and (ii) the EMD approach can effectively obtain IMFs from both nonstationary as well as nonlinear experimental data. The utility of the proposed approach is illustrated using an analytical model and also through two typical laboratory experiments in polymer physics wherein the material response is nonstationary; standard filtering approaches are often inappropriate in such cases. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Single biomolecule imaging with frequency and force modulation in tapping-mode atomic force microscopy

A new intermittent-contact atomic force microscopy (AFM) mode (frequency and force modulation AFM, FFM-AFM) has been recently proposed to characterize soft samples. This method uses excitation force frequency and amplitude modulation to eliminate bistability and reduce the tip-sample forces. This letter describes theoretical modeling of FFM-AFM applied to a single bacteriorhodopsin molecule on a substrate, showing that its cross section can be measured without damage, in contrast to conventional tapping-mode AFM. Speculations are made regarding nonideal conditions and the ability of FFM-AFM to perform quantitative nanoelasticity measurements.     

Probing small unilamellar EggPC vesicles on mica surface by atomic force microscopy

Sonicated small unilamellar egg yolk phosphatidylcholine (EggPC) vesicles were investigated using atomic force microscopy (AFM) imaging and force measurements. Three different topographies (convex, planar, and concave shape) of the EggPC vesicles on the mica surface were observed by tapping mode in fluid, respectively. It was found that the topography change of the vesicles could be attributed to the interaction force between the AFM tip and vesicles. Force curves between an AFM tip and an unruptured vesicle were obtained in contact mode. During approach, two breaks corresponding to the abrupt penetration of upper and lower bilayer of vesicle were exhibited in the force curve. Both breaks spanned a distance of around 4 nm close to the EggPC bilayer thickness. Based on Hertz analysis of AFM approach force curves, the Young's modulus (E) and the bending modulus (kc) for pure EggPC vesicles were measured to be (1.97 +/- 0.75) x 10(6)Pa and (0.21 +/- 0.08) x 10(-19)J, respectively. The results show that the AFM can be used to obtain good images of intact and deformed vesicles by tapping mode, as well as to probe the integrity and bilayer structure of the vesicles. AFM force curve compare favorably with other methods to measure mechanical properties of soft samples with higher spatial resolution.     

A MAP-based algorithm for spectroscopic semi-blind deconvolution

Spectroscopic data often suffer from common problems of bands overlapping and random noise. In this paper, we show that the issue of overlapping peaks can be considered as a maximum a posterior (MAP) problem and be solved by minimizing an object functional that includes a likelihood term and two prior terms. In the MAP framework, the likelihood probability density function (PDF) is constructed based on a spectral observation model, a robust Huber-Markov model is used as spectra prior PDF, and the kernel prior is described based on a parametric Gaussian function. Moreover, we describe an efficient optimization scheme that alternates between latent spectrum recovery and blur kernel estimation until convergence. The major novelty of the proposed algorithm is that it can estimate the kernel slit width and latent spectrum simultaneously. Comparative results with other deconvolution methods suggest that the proposed method can recover spectral structural details as well as suppress noise effectively.     

Spatially resolved force spectroscopy of bacterial surfaces using force-volume imaging

Force spectroscopy using the atomic force microscope (AFM) is a powerful technique for measuring physical properties and interaction forces at microbial cell surfaces. Typically for such a study, the point at which a force measurement will be made is located by first imaging the cell using AFM in contact mode. In this study, we image the bacterial cell Shewanella putrefaciens for subsequent force measurements using AFM in force-volume mode and compare this to contact-mode images. It is known that contact-mode imaging does not accurately locate the apical surface and periphery of the cell since, in contact mode, a component of the applied load laterally deforms the cell during the raster scan. Here, we illustrate that contact-mode imaging does not accurately locate the apical surface and periphery of the cell since, in contact mode, a component of the applied load laterally deforms the cell during the raster scan. This is an artifact due to the deformability and high degree of curvature of bacterial cells. We further show that force-volume mode imaging avoids the artifacts associated with contact-mode imaging due to surface deformation since it involves the measurement of a grid of individual force profiles. The topographic image is subsequently reconstructed from the zero-force height (the contact distance between the AFM tip and the surface) at each point on the cell surface. We also show how force-volume measurements yield applied load versus indentation data from which mechanical properties of the cell such as Young's modulus, cell turgor pressure and elastic and plastic energies can be extracted.     

Analytical method for parameterizing the random profile components of nanosurfaces imaged by atomic force microscopy

The functional properties of many technological surfaces in biotechnology, electronics, and mechanical engineering depend to a large degree on the individual features of their nanoscale surface texture, which in turn is a function of the surface manufacturing process. Among these features, the surface irregularities and self-similarity structures at different spatial scales, especially in the range of 1 to 100 nm, are of high importance because they greatly affect the surface interaction forces acting at a nanoscale distance. An analytical method for parameterizing the surface irregularities and their correlations in nanosurfaces imaged by atomic force microscopy (AFM) is proposed. In this method, flicker noise spectroscopy--a statistical physics approach--is used to develop six nanometrological parameters characterizing the high-frequency contributions of jump- and spike-like irregularities into the surface texture. These contributions reflect the stochastic processes of anomalous diffusion and inertial effects, respectively, in the process of surface manufacturing. The AFM images of the texture of corrosion-resistant magnetite coatings formed on low-carbon steel in hot nitrate solutions with coating growth promoters at different temperatures are analyzed. It is shown that the parameters characterizing surface spikiness are able to quantify the effect of process temperature on the corrosion resistance of the coatings. It is suggested that these parameters can be used for predicting and characterizing the corrosion-resistant properties of magnetite coatings.     

A Background and noise elimination method for quantitative calibration of near infrared spectra

A new hybrid algorithm is proposed to eliminate the varying background and noise simultaneously for multivariate calibration of near infrared (NIR) spectral signals. The method is based on the use of multi-resolution, which is one of the main advantages provided by wavelet transform. The signals are firstly split into different frequency components, which keep the same data points of the original signals. In conjunction with a modified uninformative variable elimination (mUVE) criterion, the new method can be used to remove the low-frequency varying background and the high-frequency noise simultaneously. The method is successfully applied to simulated spectral data set and experimental NIR spectral data, resulting in more parsimonious multivariate models with higher precision. In addition, the proposed strategy can be applied to other spectral signals as well.