Optimizing single DNA molecules manipulation by AFM

Recent progress in single DNA manipulation with atomic force microscope has proved its potential in analysing genetic information at the molecular level instead of macro ensemble approach. However, current manipulation of DNA is mainly carried out by manual operations, which is labour-intensive and time-consuming, thus limits the further applications in other fields. In this paper, an optimized DNA manipulation method is successfully established. An image correlation technique is introduced to realize automatic thermal drift compensation. Combined with elaborately designed tip movement control for different manipulation purposes, accurate and efficient DNA manipulations such as dissection, folding and picking are realized. The efficiency has been improved for an order of magnitude compare to manual manipulations, whereas the performance is demonstrated to be the same. This newly developed method has shed light on high-efficiency nanomanipulation of small molecules with complex structures, and thus provides the possibility of deeply understanding the intrinsic properties of single biomolecules.     

纳结构的连续激光复合微纳探针刻划加工

为了加工形貌稳定且尺寸尽可能小的纳结构,建立了一套连续激光复合微纳探针的加工系统,并研究了光纤探针导光的连续激光辐照微纳探针的近场增强效应以及该系统的加工性能。首先,根据表面等离子体激元理论仿真分析了激光辐照原子力显微镜(AFM)探针的近场增强因子,并研究了微纳探针的针尖温度场和针尖热膨胀。接着,搭建了基于光纤探针导光的连续激光复合微纳探针的纳结构加工系统。最后,对聚乙烯片状材料样品进行了纳结构加工。结果显示:加工得到的纳米点尺度为200nm左右;纳米线的尺度为30~40nm。结果表明:光纤探针导光连续激光复合微纳探针系统避免了复杂的空间光路结构,是一种成本低廉,结构简单的系统,能够实现纳结构的加工。     

Atom probe,AFM, and STM studies on vacuum-fired stainless steels

The surface morphology of grades 304L and 316LN stainless steels, after low-temperature bake-out process and vacuum annealing, has been studied by atomic force microscopy (AFM) and scanning tunnelling microscopy (STM). The local elemental composition on the surface before and after thermal treatment has been investigated by atom probe (AP) depth profiling measurements. After vacuum annealing, AFM and STM show significant changes in the surface structure and topology. Recrystallization and surface reconstruction is less pronounced on the 316LN stainless steel. AP depth profiling analyses result in noticeable nickel enrichment on the surface of grade 304L samples. Since hydrogen recombination is almost controlled by surface structure and composition, a strong influence on the outgassing behaviour by the particular surface microstructure can be deduced.     

Nano-wear of the diamond AFM probing tip under scratching of silicon, studied by AFM

In order to improve such a widely used microtribological testing procedure as surface scratching by an AFM diamond tip, an experimental study has been carried out using single-crystalline silicon as the tested material. Wear of the AFM diamond tip under scratching was observed by a decrease in the scratch depth with increasing wear cycles and by the direct imaging of the diamond tip shape using a Si₃N₄ AFM tip. It was shown that the current widely used experimental method, which assumes the diamond tip to be non-wearable, introduces uncontrollable error into the obtained values for the tested material's wear rate. The harder the tested material, the larger may be the tip wear, and, therefore, the bigger may be its effect on the obtained wear rate values. The specific wear rates for the diamond tip and a silicon wafer were estimated to be 1.4 × 10^-9 and 4.5 × 10^-4 mm³/(N m), respectively.     

Cleaning AFM colloidal probes by mechanically scrubbing with supersharp “brushes”

Contamination control of atomic force microscope (AFM) tips (including standard but supersharp imaging tips and particle/colloidal probes) is very important for reliable AFM imaging and surface/interface force measurements. Traditional cleaning methods such as plasma, UV–ozone and solvent treatments have their shortcomings. Here, we demonstrate that calibration gratings with supersharp spikes can be employed to scrub away contaminants accumulated on a colloidal sphere probe by scanning the probe against the spikes at high load at constant-force mode. The present method is superior to traditional cleaning methods in several aspects. First, accumulated lump-like organic/inorganic material can be removed; second, removal is non-destructive and highly efficient based on a “targeted removal” strategy; third, removal and probe shape/morphology study can be completed in a single step (we report, to our best knowledge, the first evidence of the wear of the colloidal sphere during force measurements); and fourth, both colloidal/particle probes and standard but supersharp AFM imaging tips can be treated.     

AFM characterization of biomolecules in physiological environment by an advanced nanofabricated probe

Many relevant questions in biology and medicine require both topography and chemical information with high spatial resolution. Several biological events that occur at the nanometer scale level need to be investigated in physiological conditions. In this regard Atomic Force Microscopy (AFM) is one of the most powerful tools for label‐free nanoscale characterization of biological samples in liquid environment. Recently, the coupling of Raman spectroscopy to scanning probe microscopies has opened new perspectives on this subject; however, the coupling of quality AFM spectroscopy with Raman spectroscopy in the same probe is not trivial. In this work we report about the AFM capabilities of an advanced high‐resolution probe that has been previously nanofabricated by our group for coupling with Raman spectroscopy applications. We investigate its use for liquid AFM measurements on biological model samples like lipid bilayers, amyloid fibrils, and titin proteins. We demonstrate topography resolution down to nanometer level, force measurement and stable imaging capability. We also discuss about its potential as nanoscale chemical probe in liquid phase. Microsc. Res. Tech., 2012. © 2012 Wiley Periodicals, Inc.     

Application of AFM from microbial cell to biofilm

Atomic Force Microscopy (AFM) has proven itself over recent years as an essential tool for the analysis of microbial systems. This article will review how AFM has been used to study microbial systems to provide unique insight into their behavior and relationship with their environment. Immobilization of live cells has enabled AFM imaging and force measurement to provide understanding of the structure and function of numerous microbial cells. At the macromolecular level AFM investigation into the properties of surface macromolecules and the energies associated with their mechanical conformation and functionality has helped unravel the complex interactions of microbial cells. At the level of the whole cell AFM has provided an integrated analysis of how the microbial cell exploits its environment through its selective, adaptable interface, the cell surface. In addition to these areas of study the AFM investigation of microbial biofilms has been vital for industrial and medical process analysis. There exists a tremendous potential for the future application of AFM to microbial systems and this has been strengthened by the trend to use AFM in combination with other characterization methods, such as confocal microscopy and Raman spectroscopy, to elucidate dynamic cellular processes. SCANNING 32: 134–149, 2010. © 2010 Wiley Periodicals, Inc.     

金属薄膜导线的亚微米局域电导率精确测量技术

作为薄膜器件最重要物理量之一的局域电导率的定量测定,能在保证性能、提高成品率、完善制作工艺等方面起关键作用.利用基于原子力显微镜(Atomic force microscope,AFM)的4电极微探针局域电导率测量技术,精确测量厚度为350nm、宽度分别为50.0 μm、25.0μm、5.0 μm、2.0μm及600 ...     

Lateral Displacement of an AFM Tip Observed by In-Situ TEM/AFM Combined Microscopy: The Effect of the Friction in AFM

When the lateral displacement of an AFM tip due to friction is comparable to or larger than the scan size, for example during atomic-scale friction measurement, the interpretation of the friction image is different from the situation where the scan size is much larger than the lateral displacement of the tip and the image is a simple direct mapping of the friction value. This is because, due to the lateral displacement of the tip, the tip is not at the position where the scan indicates, as can be clearly observed by an in-situ TEM/AFM combined microscopy and atomic-scale friction analysis. This lateral displacement of the tip at the nanometer scale affects the shape of the force-distance curve. We discuss the effect of the tip lateral displacement in AFM data and its normal load dependence.     

Rigid design of fast scanning probe microscopes using finite element analysis

To improve the performance of atomic force microscopes regarding speed and noise sensitivity, it is important to consider the mechanical rigidity of the actuator (scanner), and the overall mechanical structure. Using finite element analysis in the design process, it was possible to increase the first resonance frequency from 950 Hz for the whole system to 23.4 kHz for the whole system. This constitutes a factor of 25 in resonance frequency and a factor of 625 in stiffness and, hence, noise immunity.     

Surface modification of AFM silicon probes for adhesion and wear reduction

Tip wear of silicon probes used for an atomic force microscope (AFM) is a critical issue. Wear can result in an increase of tip radius and adhesion between tip and sample, thus reducing the image resolution and introducing artifacts. In order to reduce adhesion, friction, and wear so as to reduce tip related artifacts, liquid lubricant (Z-TETRAOL), self-assembled monolayers (pentafluorophenyltriethoxysilane (PFPTES)), and fluorocarbon polymer (Fluorinert™) were applied on the silicon probe. A comprehensive investigation of adhesion, friction, and wear of the uncoated/coated tips in both ambient air and various humidity levels as well as the influence of the coatings on the image resolution was performed. Experiments showed that the coatings reduced the adhesion, friction, and wear of the silicon tip, improved the initial image resolution, and exhibited less deterioration as compared to that of uncoated tip in the long-term test.     

Analysis of photopolymerized acrylic films by AFM in pulsed force mode

This paper highlights the potential of atomic force microscopy in the pulsed force mode to investigate the photopatterning of acrylic‐based films. The pulsed force mode is a nonresonant mode designed to allow approach curves to be recorded along the scanning path. It thereby provides the topography of the sample and a direct and simple local characterization of adhesion and stiffness. This mode can be used either for imaging or for locally probing the mechanical properties of a surface. In particular, a correlation between stiffness and conversion of the monomer was established. The close examination of the pulsed force mode signal brought accurate information on the photoinduced modification of the film. Polymer films with submicron photopatterning generated by interferometric illumination were analyzed by pulsed force mode. It was established that the gradient of mechanical properties throughout the films was strongly dependant on the irradiation conditions.     

Localized etching of silicon in water using a catalytically active platinum-coated atomic force microscopy probe

This paper presents a novel atomic force microscopy (AFM)-based nanofabrication technique for Si in water that is based on highly localized catalytic etching with a Pt-coated AFM probe. It has been shown that nanoscale grooves can be fabricated on the Si surface at room temperature via Pt-assisted catalytic chemical etching in water without the addition of any chemicals. Furthermore, dissolved oxygen (O₂) in water has been found to be a key element for driving the chemical reaction of Si with water in the Si removal process. Experimental results have also suggested that an oscillating cantilever of the Pt-coated AFM probe for the stirring of water is essential in order to overcome the oxygen mass-transfer limitations and enhance the Si removal rate. The elementary chemical reactions taking place during the etching of Si has been estimated on the basis of electrochemical theory. It is proposed that in the first step, dissolved oxygen is reduced and forms hydroxide ions (OH⁻) with water molecules (H₂O) on the surface of the Pt-coated tip. In the second step, Si atoms are oxidized on reaction with OH⁻ ions and water soluble silicates are formed. The catalytic reaction taking place on the surface of a Pt-coated tip can be enhanced by the application of an anodic potential to an additional Pt wire electrode, resulting in a dramatic fifty-fold increase in the Si removal rate.     

Evidence of commensurate contact and rolling motion: AFM manipulation studies of carbon nanotubes on HOPG

We report on experiments in which multiwall carbon nanotubes (CNTs) are manipulated with AFM on a graphite (HOPG) substrate. We find certain discrete orientations in which the lateral force of manipulation dramatically increases as we rotate the CNT in the plane of the HOPG surface with the AFM tip. The three-fold symmetry of these discrete orientations indicates commensurate contact of the hexagonal graphene surfaces of the HOPG and CNT. As the CNT moves into commensurate contact, we observe the motion change from sliding/rotating in-plane to stick–roll motion.     

Measuring the activation energy of thiol desorption using lateral force microscopy

Thermal stability of self-assembled monolayers (SAMs) is important for applications in various surface science applications. As a model material, 16-mercaptohexadecanoic acid (MHA) on template stripped gold surfaces was investigated to determine the effect of temperature on the change of lateral force signal using atomic force microscopy (AFM). Friction force signals were obtained at various temperatures in order to determine whether it was possible to correlate the friction signal with desorption of the thiol molecule from the surface. Samples were heated for up to 10 h ranging from 40 to 80 °C in air and scanned every hour. A kinetic model was introduced to correlate the lateral force signal to the activation energy of desorption of the SAM from gold surface with heating. The activation energy of the detachment using this technique is 25.4 kcal/mol, which is consistent with other more complex techniques.     

Broadening the applications of the atom probe technique by ultraviolet femtosecond laser

Laser assisted field evaporation using ultraviolet (UV) wavelength gives rise to better mass resolution and signal-to-noise ratio in atom probe mass spectra of metals, semiconductors and insulators compared to infrared and green lasers. Combined with the site specific specimen preparation techniques using the lift-out and annular Ga ion milling in a focused ion beam machine, a wide variety of materials including insulating oxides can be quantitatively analyzed by the three-dimensional atom probe using UV laser assisted field evaporation. After discussing laser irradiation conditions for optimized atom probe analyses, recent atom probe tomography results on oxides, semiconductor devices and grain boundaries of sintered magnets are presented.     

基于AFM的纳米梁杨氏模量和残余应力测量

针对同一工艺流程下相同杨氏模量和残余应力的双端固支梁阵列,建立了简化的杨氏模量和残余拉应力的弯曲测试模型,并将应力刚化理论应用到几何非线性有限元分析中用于上述模型的理论误差评价.提出将拉曼频移测试与原子力显微镜(AFM)弯曲测试相结合的实验方案,首先利用拉曼频移判断结构中的应力拉压性质,随后利用AFM测量梁阵列的弹性系数,最终利用MATLAB求解超定方程组的方法解得梁阵列的杨氏模量和残余应力,测试结果证明了该实验方案的可行性.     

Preparation of cell membranes for high resolution imaging by AFM

Studies of cell membrane structure by atomic force microscopy (AFM) have been limited because of the softness of cell membranes. Here, we utilize a new technique of sample preparation to lay red blood cell membranes on the top of a mica surface to obtain high resolution images by in-situ AFM on both sides of cell membranes. Our results indicate that the location of oligosaccharides and proteins in red blood cell membranes might be different from the current membrane model. The inner membrane leaflet is covered by dense proteins with fewer free lipids than expected. In contrast, the outer membrane leaflet is quite smooth; oligosaccharides and peptides supposed to protrude out of the outer membrane leaflet surface might be actually hidden in the middle of hydrophilic lipid heads; transmembrane proteins might form domains in the membranes revealed by PNGase F and trypsin digestion. Our result could be significant to interpret some functions about red blood cell membranes and guide to heal the blood diseases related to cell membranes.     

Comparisons of the topographic characteristics and electrical charge distributions among Babesia‐infected erythrocytes and extraerythrocytic merozoites using AFM

Tick‐borne Babesia parasites are responsible for costly diseases worldwide. Improved control and prevention tools are urgently needed, but development of such tools is limited by numerous gaps in knowledge of the parasite–host relationships. We hereby used atomic force microscopy (AFM) and frequency‐modulated Kelvin probe potential microscopy (FM‐KPFM) techniques to compare size, texture, roughness and surface potential of normal and infected Babesia bovis, B. bigemina and B. caballi erythrocytes to better understand the physical properties of these parasites. In addition, AFM and FM‐KPFM allowed a detailed view of extraerythrocytic merozoites revealing shape, topography and surface potential of paired and single parasites. B. bovis‐infected erythrocytes display distinct surface texture and overall roughness compared to noninfected erythrocytes. Interestingly, B. caballi‐infected erythrocytes do not display the surface ridges typical in B. bovis parasites. Observations of extraerythrocytic B. bovis, B. bigemina and B. caballi merozoites using AFM revealed differences in size and shape between these three parasites. Finally, similar to what was previously observed for Plasmodium‐infected erythrocytes, FM‐KPFM images reveal an unequal electric charge distribution, with higher surface potential above the erythrocyte regions that are likely associated with Babesia parasites than over its remainder regions. In addition, the surface potential of paired extraerythrocytic B. bovis Mo7 merozoites revealed an asymmetric potential distribution. These observations may be important to better understand the unique cytoadhesive properties of B. bovis‐infected erythrocytes, and to speculate on the role of differences in the distribution of surface charges in the biology of the parasites.     

检测纳米微粒粒径方法的研究

用光子相关法、原子力显微镜和扫描电镜三种测试方法测定了同一标准样品的粒径，比较了三种测试方法在纳米粒径检测方面的特点。光子相关法给出纳米微粒的平均粒径和多分散系数，而原子力显微镜和扫描电镜在测定粒径的同时直接观察到微粒的外貌。