Analysis Of Atomic Force Microscopy Images Research Articles

Statistical analysis of aging micro-characteristics for asphalt binder AFM images based on neural network classification

To further evaluate the effect of aging behavior on microstructure for asphalt binder, the atomic force microscope (AFM) images of asphalt binder were studied by neural network classification technology, and its aging micro-characteristics were analyzed statistically. Firstly, AFM equipment was used to test 90# virgin asphalt binder and styrene–butadiene–styrene (SBS) modified asphalt binder commonly used in engineering, and the typical micromorphology AFM images of asphalt binders were obtained. Subsequently, the asphalt binder AFM images were preliminatively analyzed, and the micro-characteristics of AFM images before and after aging were compared, including the “bee structure” characteristics, distribution law and surface structure roughness. Finally, the asphalt binder AFM images were further analyzed by neural network classification, and the change of “bee structure” was statistically calculated and analyzed, and its aging micro-characteristics were quantitatively evaluated. The results show that it is feasible for neural network classification to be applied to the statistical analysis of asphalt binder AFM images, and it can further describe and evaluate the aging micro-characteristics of asphalt binder. Aging behavior reduces the proportion of intermediate category areas in asphalt binder AFM images and increases the “bee structure” areas. The cumulative percentage curve of asphalt binder AFM images is smoother (each category is more uniform), indicating that the asphalt binder performance tended to be stable after aging. The results further enrich the description of asphalt binder AFM images, and provide a new way to explore the micro-morphology of asphalt binder.

Epitaxial AlN film with improved quality on Si (111) substrates realized by boron pretreatment via MOCVD

This study investigated the growth of AlN epitaxial films on 2-in. Si(111) via metal-organic chemical vapor deposition. By introducing triethylboron (TEB) during trimethylaluminum pretreatment, a nearly crack free AlN epilayer with a thickness of 500 nm was acquired. The x-ray diffraction rocking curves of AlN (002) and (102) exhibited full width at half maximum values of 0.22° and 0.36°, respectively. Atomic force microscopy image analysis showed that after the introduction of TEB, larger grains appeared on the surface of Si(111) substrate, promoting the 3D growth pattern of the subsequent AlN buffer layer. Laytec reflection curves depicted the morphological transition from 3D to 2D growth mode during AlN deposition. At the same time, the curvature value was significantly reduced by 20 km−1, and the Raman spectrum peak of E2(high) shifted from 648.7 to 652.5 cm−1, indicating that the surface tensile stress was greatly reduced, effectively suppressing the crack problem of AlN on Si(111).

Quantifying ABCA1/apoA-1 Signaling Pathways with AFM Imaging and Lipidomic Analysis.

The role of lipid metabolic pathways in the pathophysiology of primary open-angle glaucoma (POAG) has been thoroughly elucidated, with pathways involved in lipid-related disorders such as hypercholesterolemia and hyperlipoprotein accumulation being of particular interest. The ABCA1/apoA-1 transduction pathway moderates reverse cholesterol transport (RCT), facilitating the transport of free cholesterol (FC) and phospholipids (PL) and preventing intracellular lipid aggregates in retinal ganglion cells (RGCs) due to excess FCs and PLs. A deficiency of ABCA1 transporters, and thus, dysregulation of the ABCA1/apoA-1 transduction pathway, may potentiate cellular lipid accumulation, which affects the structural and mechanical features of the cholesterol-rich RGC membranes. Atomic force microscopy (AFM) is a cutting-edge imaging technique suitable for imaging topographical surfaces of a biological specimen and determining its mechanical properties and structural features. The versatility and precision of this technique may prove beneficial in understanding the effects of ABCA1/apoA-1 pathway downregulation and decreased cholesterol efflux in RGCs and their membranes. In this protocol, ABCA1-/- RGC mouse models are prepared over the course of 3days and are then compared with non-knockout ABCA1 RGC mouse models through AFM imaging of topographical surfaces to examine the difference in membrane dynamics of knockout vs. non-knockout models. Intracellular and extracellular levels of lipids are quantified through high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS).

Characterization of polyethylene terephthalate (PET) and polyamide (PA) true-to-life nanoplastics and their biological interactions

Plastic and microplastics, including polyethylene (PE), polypropylene (PP), and polystyrene (PS), are major contributors to environmental pollution. However, there is a growing recognition of the need to investigate a wider range of plastic polymers to fully understand the extent and impacts of plastic pollution. This study focuses on the comprehensive characterization of true-to-life nanoplastics (T2LNPs) derived from polyethylene terephthalate (PET) and polyamide (PA) to enhance our understanding of environmental nanoplastics pollution. T2LNPs were produced through cryogenic mechanical fragmentation of everyday items made from these polymers. A solid methodological framework incorporating various characterization techniques was established. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and thermogravimetric analysis (TGA) were employed to study the chemical composition and confirm the absence of chemical modifications possibly occurring during fragmentation. Atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM) were used to analyze the morphology of the T2LNPs. Additionally, AFM image analysis compared to dynamic light scattering (DLS) measurements provided insights into the size distribution and the stability of the T2LNP suspensions. The results revealed the heterogeneity of T2LNPs derived from PET and PA, emphasizing the importance of studying different plastic compositions to comprehensively understand nanoplastics pollution. Lastly, the distinctive characteristics and morphology of T2LNPs were translated into the realm of biological interactions, offering initial insights into the influence of these disparities on the formation of the protein corona on the surface of T2LNPs. By proposing T2LNPs as test materials and establishing a comprehensive characterization approach, this study aims to bridge the knowledge gap regarding the behavior and toxicity of nanoplastics. Furthermore, it highlights the need for a reliable and transferable analytical package for nanoplastic characterization to facilitate future studies on the environmental impact of nanoplastics.

Advanced thin films of indium-tin oxide doping with photosensitive polymer via embossing process

We propose a sol-gel thin film formation process involving nanoimprint lithography. First, indium tin oxide was dissolved in 2-methoxyethanol at a ratio of 5:5 and the mixture were mixed with 10 wt% of a UV-curable. Subsequently, a polydimethylsiloxane sheet prepared by covering a silicon wafer with a polydimethylsiloxane mold was attached to a InSnO thin film to duplicate the nanostructure through UV irradiation exposure. The replicated nanostructured thin films formed about morphological and chemical composition changes on the surface, we progressed to x-ray photoelectron spectroscopy and atomic force microscopy analysis. Furthermore, atomic force microscopy image analysis showed superior patterned grooves for a UV exposure time of 3 min. A suitability test involving the measurement of the transmittance was performed for examining the suitability of the thin film for use in display devices.

Development of a facile method to compute collagen network pathological anisotropy using AFM imaging

Type I collagen, a fundamental extracellular matrix (ECM) component, is pivotal in maintaining tissue integrity and strength. It is also the most prevalent fibrous biopolymer within the ECM, ubiquitous in mammalian organisms. This structural protein provides essential mechanical stability and resilience to various tissues, including tendons, ligaments, skin, bone, and dentin. Collagen has been structurally investigated for several decades, and variation to its ultrastructure by histology has been associated with several pathological conditions. The current study addresses a critical challenge in the field of collagen research by providing a novel method for studying collagen fibril morphology at the nanoscale. It offers a computational approach to quantifying collagen properties, enabling a deeper understanding of how collagen type I can be affected by pathological conditions. The application of Fast Fourier Transform (FFT) coupled with Atomic Force Microscope (AFM) imaging distinguishes not only healthy and diseased skin but also holds potential for automated diagnosis of connective tissue disorders (CTDs), contributing to both clinical diagnostics and fundamental research in this area. Here we studied the changes in the structural parameters of collagen fibrils in Ehlers Danlos Syndrome (EDS). We have used skin extracted from genetically mutant mice that exhibit EDS phenotype as our model system (Col1a1Jrt/+ mice). The collagen fibrils were analyzed by AFM based descriptive-structural parameters, coupled with a 2D Fast Fourier Transform(2D-FFT) approach that automated the analysis of AFM images. In addition, each sample was characterized based on its FFT and power spectral density. Our qualitative data showed morphological differences in collagen fibril clarity (clearness of the collagen fibril edge with their neighbouring fibri), D-banding, orientation, and linearity. We have also demonstrated that FFT could be a new tool for distinguishing healthy from tissues with CTDs by measuring the disorganization of fibrils in the matrix. We have also employed FFT to reveal the orientations of the collagen fibrils, providing clinically relevant phenotypic information on their organization and anisotropy. The result of this study can be used to develop a new automated tool for better diagnosis of CTDs.

End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images

Observing the structural dynamics of biomolecules is vital to deepening our understanding of biomolecular functions. High-speed (HS) atomic force microscopy (AFM) is a powerful method to measure biomolecular behavior at near physiological conditions. In the AFM, measured image profiles on a molecular surface are distorted by the tip shape through the interactions between the tip and molecule. Once the tip shape is known, AFM images can be approximately deconvolved to reconstruct the surface geometry of the sample molecule. Thus, knowing the correct tip shape is an important issue in the AFM image analysis. The blind tip reconstruction (BTR) method developed by Villarrubia (J Res Natl Inst Stand Technol 102:425, 1997) is an algorithm that estimates tip shape only from AFM images using mathematical morphology operators. While the BTR works perfectly for noise-free AFM images, the algorithm is susceptible to noise. To overcome this issue, we here propose an alternative BTR method, called end-to-end differentiable BTR, based on a modern machine learning approach. In the method, we introduce a loss function including a regularization term to prevent overfitting to noise, and the tip shape is optimized with automatic differentiation and backpropagations developed in deep learning frameworks. Using noisy pseudo-AFM images of myosin V motor domain as test cases, we show that our end-to-end differentiable BTR is robust against noise in AFM images. The method can also detect a double-tip shape and deconvolve doubled molecular images. Finally, application to real HS-AFM data of myosin V walking on an actin filament shows that the method can reconstruct the accurate surface geometry of actomyosin consistent with the structural model. Our method serves as a general post-processing for reconstructing hidden molecular surfaces from any AFM images. Codes are available at https://github.com/matsunagalab/differentiable_BTR.

Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopy.

The protocol described in this chapter allows for acquiring topography images of RNA-based nanoring structures and assessing their dynamic properties using atomic force microscopy (AFM) imaging. AFM is an indispensable tool for characterization of nucleic acid-based nanostructures with the exceptional capability of observing complexes in the range of a few nanometers. This method can visualize structural characteristics and evaluate differences between individual structurally different RNA nanorings. Due to the highly resolved AFM topography images, we introduce an approach that allows to distinguish the differences in the dynamic behavior of RNA nanoparticles not amenable to other experimental techniques. This protocol describes in detail the preparation procedures of RNA nanostructures, AFM imaging, and data analysis.

AFM Image Analysis of the Adsorption of Xanthate and Dialkyl Dithiophosphate on Chalcocite

Atomic force microscopy (AFM) has been applied to study the adsorption morphology of various collectors, i.e., potassium ethyl xanthate (KEX) and potassium amyl xanthate (PAX) and Cytec Aerofloat 238 (sodium dibutyl dithiophosphate), on chalcocite in situ in aqueous solutions. The AFM images show that all these collectors adsorb strongly on chalcocite. Xanthate adsorbs mainly in the form of insoluble cuprous xanthate (CuX), which binds strongly with the mineral surface without being removed by flushing with ethanol alcohol. This xanthate/chalcocite adsorption mechanism is very similar to the one obtained with the xanthate/bornite system; while it is different from the one of the xanthate/chalcopyrite systems, for which oily dixanthogen is the main adsorption product on chalcopyrite surface. On the other hand, dibutyl dithiophosphate adsorbs on chalcocite in the form of hydrophobic patches, which can be removed by rinsing with ethanol alcohol. AFM images show that the adsorption of collectors increases with increasing adsorption time and collectors’ concentration. In addition, increasing the solution pH to 10 does not prevent the adsorption of xanthate and Aerofloat 238 on chalcocite and the result is in line with the fact that chalcocite floats well in a wide pH range up to 12 with xanthate and dialkyl dithiophosphate being used as collectors. The blending collectors study shows that xanthate and dialkyl dithiophosphate can co-adsorb with both insoluble cuprous xanthate and oily Cu(DTP)2 (Cu dibutyl dithiophosphate) on a chalcocite surface. The present study helps to clarify the flotation mechanism of chalcocite in industry practice using xanthate and dialkyl dithiophosphate as collectors.

Assessment of TiO2 Nanoparticle Impact on Surface Morphology of Chinese Hamster Ovary Cells.

The process of nanoparticles entering the cells of living organisms is an important step in understanding the influence of nanoparticles on biological processes. The interaction of nanoparticles with the cell membrane is the first step in the penetration of nanoparticles into cells; however, the penetration mechanism is not yet fully understood. This work reported the study of the interaction between TiO2 nanoparticles (TiO2-NPs) and Chinese hamster ovary (CHO) cells using an in vitro model. The characterization of crystalline phases of TiO2 NPs was evaluated by transmission electron microscopy (TEM), X-ray diffraction (XRD) spectrum, and atomic force microscopy (AFM). Interaction of these TiO2 nanoparticles (TiO2- NPs) with the CHO cell membrane was investigated using atomic force microscopy (AFM) and Raman spectroscopy. The XRD analysis result showed that the structure of the TiO2 particles was in the rutile phase with a crystallite size of 60 nm, while the AFM result showed that the particle size distribution had two peaks with 12.1 nm and 60.5 nm. The TEM analysis confirmed the rutile phase of TiO2 powder. Our study showed that exposure of CHO cells to TiO2-NPs caused morphological changes in the cell membranes and influenced the viability of cells. The TiO2-NPs impacted the cell membrane surface; images obtained by AFM revealed an ‘ultra structure‘ with increased roughness and pits on the surface of the membrane. The depth of the pits varied in the range of 40–80 nm. The maximal depth of the pits after the treatment with TiO2-NPs was 100% higher than the control values. It is assumed that these pits were caveolae participating in the endocytosis of TiO2-NPs. The research results suggest that the higher maximal depth of the pits after the exposure of TiO2-NPs was determined by the interaction of these TiO2-NPs with the cell’s plasma membrane. Moreover, some of pits may have been due to plasma membrane damage (hole) caused by the interaction of TiO2-NPs with membrane constituents. The analysis of AFM images demonstrated that the membrane roughness was increased with exposure time of the cells to TiO2-NPs dose. The average roughness after the treatment for 60 min with TiO2-NPs increased from 40 nm to 78 nm. The investigation of the membrane by Raman spectroscopy enabled us to conclude that TiO2-NPs interacted with cell proteins, modified their conformation, and potentially influenced the structural damage of the plasma membrane.

RELATIONSHIP ANALYSIS BETWEEN TWO DIFFERENT METHODS OF SURFACE FRACTAL DIMENSION IN METAL–CERAMIC COATINGS SPUTTERED BY RF-MAGNETRON

Existing topographical microstructure analyses obtain information based on surface properties of the analyzed material, such as scanning electron microscopy (SEM) and atomic force microscopy (AFM). However, these methods cannot provide quantitative topographical data, such as fractal analysis. In this paper, we present the relationship between two different methods in the obtaining the fractal dimension using electrochemical impedance spectroscopy (EIS) and AFM image analysis based on statistics and behavior of roughness and porosity properties of four other coating systems obtained by RF-magnetron sputtering. Our results demonstrated that the [Formula: see text] bilayer system is the best since it presented a lower porosity–roughness percentage and means. At least one of the fractal dimension values has a nonnormal distribution. However, the hypothesis testing showed no significant difference between the medians of both method’s fractal dimension values. The correlation coefficient showed a strong relationship between the roughness and porosity properties with a typical regular distribution pattern. According to the statistical data results, researchers can use both the methods due to their outstanding data precision.

AFM imaging analysis of nanoindentation-induced plastic strain in indium surface for calibrating nanoindenters area profiles

Atomic Force Microscopy (AFM)-nanoindentation is one of the most popular techniques for characterizing the nanomaterials' mechanical properties. A good calibration of the indenter area profile is essential to achieve quantitatively reliable calculations of these properties. Accurate profile estimation is particularly critical to minimize uncertainties in key mechanical properties like hardness and elastic modulus. In this work, we report the use of indium as a potential candidate for assessing the nanoindenters’ area profiles by imaging analysis of nanoindentation-induced plastic footprints. AFM-nanoindentation technique was particularly used for inducing plastic strain. A systematic and rigorous profiles study was carried out at the apex neighborhood, considering heights lower than 200 [nm] for an accurate estimation at the nanoscale. Results suggest that this methodology is useful to characterize the indenter real geometry shape at the nanoscale, representing a “fast” and low-cost alternative to other popular imaging methods like those based on electron microscopy techniques.

AFM Characterization of Track-Etched Membranes: Pores Parameters Distribution and Disorder Factor

The structural characteristics of polymer track-etched membranes (TM) were obtained by atomic force microscopy (AFM) for a set of samples (polypropylene, polycarbonate, polyethylene terephthalate, with average pore diameters ~183, 375, and 1430 nm, respectively). The analysis of AFM experimental data was performed by using a specially developed technique for computer analysis of AFM images. The method allows one to obtain such parameters of TM as distribution of pore diameters, distribution of the minimum distances between the nearest pores, pore surface density, as well as to identify defective pores. Spatial inhomogeneities in the distribution of pore parameters were revealed. No anisotropy (some specific selected direction) was found in the surface distribution of the pores in the samples under study.

Structural Identification of Individual Helical Amyloid Filaments by Integration of Cryo-Electron Microscopy-Derived Maps in Comparative Morphometric Atomic Force Microscopy Image Analysis

The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, and the specific pathologies with which they are associated. Although cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy methods have been successfully employed in recent years to determine the structures of amyloid fibrils with high resolution detail, they rely on ensemble averaging of fibril structures in the entire sample or significant subpopulations. Here, we report a method for structural identification of individual fibril structures imaged by atomic force microscopy (AFM) by integration of high-resolution maps of amyloid fibrils determined by cryo-EM in comparative AFM image analysis. This approach was demonstrated using the hitherto structurally unresolved amyloid fibrils formed in vitro from a fragment of tau (297–391), termed ‘dGAE’. Our approach established unequivocally that dGAE amyloid fibrils bear no structural relationship to heparin-induced tau fibrils formed in vitro. Furthermore, our comparative analysis resulted in the prediction that dGAE fibrils are structurally closely related to the paired helical filaments (PHFs) isolated from Alzheimer’s disease (AD) brain tissue characterised by cryo-EM. These results show the utility of individual particle structural analysis using AFM, provide a workflow of how cryo-EM data can be incorporated into AFM image analysis and facilitate an integrated structural analysis of amyloid polymorphism.

AI-based atomic force microscopy image analysis allows to predict electrochemical impedance spectra of defects in tethered bilayer membranes

Atomic force microscopy (AFM) image analysis of supported bilayers, such as tethered bilayer membranes (tBLMs) can reveal the nature of the membrane damage by pore-forming proteins and predict the electrochemical impedance spectroscopy (EIS) response of such objects. However, automated analysis involving pore detection in such images is often non-trivial and can require AI-based object detection techniques. The specific object-detection algorithm we used to determine the defect coordinates in real AFM images was a convolutional neural network (CNN). Defect coordinates allow to predict the EIS response of tBLMs populated by the pore-forming toxins using finite element analysis (FEA) modeling. We tested if the accuracy of the CNN algorithm affected the EIS spectral features sensitive to defect densities and other physical parameters of tBLMs. We found that the EIS spectra can be predicted sufficiently well, however, systematic errors of characteristic spectral points were observed and need to be taken into account. Importantly, the comparison of predicted EIS curves with experimental ones allowed to estimate important physical parameters of tBLMs such as the specific resistance of submembrane reservoir. This reservoir separates phospholipid bilayer from the solid support. We found that the specific resistance of the reservoir amounts to 10^{4.25 pm 0.10}Omega cdot cm which is approximately two orders of a magnitude higher compared to the specific resistance of the buffer bathing tBLMs studied in this work. We hypothesize that such effect may be related in part due to decreased concentration of ionic carriers in the submembrane due to decreased relative dielectric permittivity in this region.

Atomic Force Microscopy to Characterize Antimicrobial Peptide-Induced Defects in Model Supported Lipid Bilayers.

Antimicrobial peptides (AMPs) interact with bacterial cell membranes through a variety of mechanisms, causing changes extending from nanopore formation to microscale membrane lysis, eventually leading to cell death. Several AMPs also disrupt mammalian cell membranes, despite their significantly different lipid composition and such collateral hemolytic damage hinders the potential therapeutic applicability of the AMP as an anti-microbial. Elucidating the mechanisms underlying the AMP–membrane interactions is challenging due to the variations in the chemical and structural features of the AMPs, the complex compositional variations of cell membranes and the inadequacy of any single experimental technique to comprehensively probe them. (1) Background: Atomic Force Microscopy (AFM) imaging can be used in combination with other techniques to help understand how AMPs alter the orientation and structural organization of the molecules within cell membranes exposed to AMPs. The structure, size, net charge, hydrophobicity and amphipathicity of the AMPs affect how they interact with cell membranes of differing lipid compositions. (2) Methods: Our study examined two different types of AMPs, a 20-amino acid, neutral, α-helical (amphipathic) peptide, alamethicin, and a 13-amino acid, non-α-helical cationic peptide, indolicidin (which intramolecularly folds, creating a hydrophobic core), for their interactions with supported lipid bilayers (SLBs). Robust SLB model membranes on quartz supports, incorporating predominantly anionic lipids representative of bacterial cells, are currently not available and remain to be developed. Therefore, the SLBs of zwitterionic egg phosphatidylcholine (PC), which represents the composition of a mammalian cell membrane, was utilized as the model membrane. This also allows for a comparison with the results obtained from the Quartz Crystal Microbalance with Dissipation (QCM-D) experiments conducted for these peptides interacting with the same zwitterionic SLBs. Further, in the case of alamethicin, because of its neutrality, the lipid charge may be less relevant for understanding its membrane interactions. (3) Results: Using AFM imaging and roughness analysis, we found that alamethicin produced large, unstable defects in the membrane at 5 µM concentrations, and completely removed the bilayer at 10 µM. Indolicidin produced smaller holes in the bilayer at 5 and 10 µM, although they were able to fill in over time. The root-mean-square (RMS) roughness values for the images showed that the surface roughness caused by visible defects peaked after peptide injection and gradually decreased over time. (4) Conclusions: AFM is useful for helping to uncover the dynamic interactions between different AMPs and cell membranes, which can facilitate the selection and design of more efficient AMPs for use in therapeutics and antimicrobial applications.

Investigation of structural and optical properties of spin coated TiO2:Mn thin films

In the current work, we have deposited and studied various properties of spin coated undoped and Mn doped TiO 2 films annealed at 400 °C on glass substrate. The influence of Mn dopant concentrations on the properties of TiO 2 thin film is detailed. X-ray Diffraction (XRD), Raman spectroscopy, Field Emission Scanning Electron Microscopy (FESEM), Atomic Force Microscopy (AFM), UV–Vis spectroscopy and Photoluminescence (PL) studies were carried out to determine the structural parameters, surface morphology/topography and optical properties of TiO 2 films. The XRD pattern of both undoped and TiO 2 :Mn thin films have exhibited (101) plane as a preferential orientation confirming the presence of anatase phase and same reflected in the Raman study. AFM image analysis reveals an improvement in surface roughness with an increase in Mn concentration indicating the coalescence of smaller crystallites. FESEM image analysis also confirmed the effect of Mn on surface morphology. UV–Vis spectroscopic measurements indicated a red shift of absorption edge upon doping. Refractive index calculation confirmed the densification of the films with increase in Mn concentration. From the PL study, luminescence property of TiO 2 was found to improve upon Mn doping. • Mn doped TiO 2 thin films were successfully deposited by spin coating method. • XRD and Raman measurements demonstrate the presence of the pure anatase phase. • Mn doping induced defects such as vacancies and interstitials are reported. • TiO 2 :Mn thin films can be used for enhanced UV photodegradation of organic dyes.

A quantitative determination of lipid bilayer deposition efficiency using AFM.

The efficacy of a number of different methods for depositing a dimyristoylphosphatidylcholine (DMPC) lipid bilayer or DMPC–cholesterol (3 : 1) mixed bilayer onto a silicon substrate has been investigated in a quantitative manner using atomic force microscopy (AFM) image analysis to extract surface coverage. Complementary AFM-IR measurements were used to confirm the presence of the lipids. For the Langmuir–Blodgett/Schaefer deposition method at temperatures below the chain-melting transition temperature (Tm), a large number of bilayer defects resulted when DMPC was deposited from a water subphase. Addition of calcium ions to the trough led to smaller, more frequent defects, whereas addition of cholesterol to the lipid mixture led to a vast improvement in bilayer coverage. Poor coverage was achieved for deposition at temperatures above Tm. Formation of the deposited bilayer from vesicle fusion proved a more reliable method for all systems, with formation of near-complete bilayers within 60 seconds at temperatures above Tm, although this method led to a higher probability of multilayer formation and rougher bilayer surfaces.

Atomic Force Microscopy Reveals that the Drosophila Telomere-Capping Protein Verrocchio Is a Single-Stranded DNA-Binding Protein.

Atomic force microscopy (AFM) is a scanning probe technique that allows visualization of biological samples with a nanometric resolution. Determination of the physical properties of biological molecules at a single-molecule level is achieved through topographic analysis of the sample adsorbed on a flat and smooth surface. AFM has been widely used for the structural analysis of nucleic acid-protein interactions, providing insights on binding specificity and stoichiometry of proteins forming complexes with DNA substrates. Analysis of single-stranded DNA-binding proteins by AFM requires specific single-stranded/double-stranded hybrid DNA molecules as substrates for protein binding. In this chapter we describe the protocol for AFM characterization of binding properties of Drosophila telomeric protein Ver using DNA constructs that mimic the structure of chromosome ends. We provide details on the methodology used, including the procedures for the generation of DNA substrates, the preparation of samples for AFM visualization, and the data analysis of AFM images. The presented procedure can be adapted for the structural studies of any single-stranded DNA-binding protein.

Study of humidity sensing properties and ion beam induced modifications in SnO2-TiO2 nanocomposite thin films

Swift heavy ion beam induced dense electronic excitation in the nanocomposite thin film is a unique way to introduce various modifications such as track formation, atomic transport and phase transformation. Therefore, this work based on the modification in the properties of Titanium dioxide and Tin oxide nanocomposite thin films prepared by RF sputtering deposition technique in the mol% 50:50 on ITO coated glass and silicon substrates. The prepared nanocomposite thin films annealed at 500 °C and irradiated with SHI of 150 MeV Fe11+ ion beam with varied ion fluences ranging from 5 × 1012to 5 × 1013 ions.cm−2. The SRIM simulation was confirmed the electronic energy loss (Se) as 1.038 × 102 eV/nm, nuclear energy loss (Sn) as 1.33 × 10−1 eV/nm and the projectile depth of the iron ion inside the thin films was founded to be 17.18 um. Structural analyses of pristine and irradiated thin films were analyzed by X-ray diffraction technique. Changes observed in the peak intensity were confirmed by the significant variations in crystallite size, which was calculated by the Debye Scherrer equation. The crystallite size of all samples was found to be improved from 59 nm to 141 nm. The influence of ion irradiation on surface topography of nanocomposite thin films was analyzed by Atomic Force Microscopy (AFM). The sectional analysis of AFM images reveals that the grain size depends on the ion irradiation fluences. The grain size was increased from 52 nm to 129 nm. The optical properties were studied using UV–Visible spectroscopy and Photoluminescence (PL) spectroscopy. Tauc's method was used to calculate the optical energy band gap of the samples. The direct band gap was decreased as ion fluence increases may be due to creation of metastable energy states in between the valance and conduction band. The recombination and separation of photo generated charge carriers were studied by the photoluminescence spectroscopy. Rutherford Backscattering Spectrometry (RBS) was performed on all samples to ensure depth profiling, elemental composition and absence of impurities in titanium dioxide and tin oxide nanocomposite thin films. The response time, recovery time, repeatability and ageing effect after (one, two and three) weeks of nanocomposite thin films were obtained during humidity sensing measurements.