Excited-state spectroscopy on an individual quantum dot using atomic force microscopy

We present a new charge sensing technique for the excited-state spectroscopy of individual quantum dots, which requires no patterned electrodes. An oscillating atomic force microscope cantilever is used as a movable charge sensor as well as gate to measure the single-electron tunneling between an individual self-assembled InAs quantum dot and back electrode. A set of cantilever dissipation versus bias voltage curves measured at different cantilever oscillation amplitudes forms a diagram analogous to the Coulomb diamond usually measured with transport measurements. The excited-state levels as well as the electron addition spectrum can be obtained from the diagram. In addition, a signature which can result from inelastic tunneling by phonon emission or a peak in the density of states of the electrode is also observed, which demonstrates the versatility of the technique.     

原子力显微镜在合成膜表征中的应用

原子力显微镜(AFM)在其发明不久即应用于膜科学领域，并以其无可比拟的优势获得了广泛的应用．它不仅可以定性地表征膜的表面三维形貌，还能定量地研究膜表面的粗糙度、孔径大小和分布及球粒尺寸．综述了近年来原子力显微镜在合成膜表征中的应用，对其中几个重要方面进行了举例介绍．     

Spin-stretching of DNA and protein molecules for detection by fluorescence and atomic force microscopy

We have developed a rapid and efficient way of stretching DNA and denatured protein molecules for detection by fluorescence microscopy and atomic force microscopy (AFM). In the described method, a viscous drag created by transient rotational flow stretches randomly coiled DNA molecules or denatured proteins. Stretching is achieved by dispensing a droplet of sample solution containing DNA or denatured protein on a MgCl2-soaked mica surface. We present fluorescent images of straightened lambdaDNA molecules and AFM images of stress-shared, reduced von Willebrand factor as well as straightened lambdaDNA. The described quick and reliable spin-stretching technique will find wide applications in the analysis of single biopolymer molecules.     

Nanodissection of single- and double-stranded DNA by atomic force microscopy

Nanodissection of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) has been investigated by atomic force microscopy (AFM). It is found that both ss- and dsDNA can be repeatedly dissected by an AFM tip. However, a comparison study indicates that ssDNA is a little bit more easily broken by the AFM tip than dsDNA. This is supported by the fact that the time requested to break ssDNA is shorter than that of dsDNA in the same dissection procedure under the same load. Our experiment also shows that dissection of the DNA strand is very sensitive to the load applied, and a small change of the load lead to different results.     

MutS-mediated detection of DNA mismatches using atomic force microscopy

We have developed an atomic force microscopy-based method for detecting DNA base-pair mismatches using MutS protein isolated from E. coli. MutS is a biological sensor and a locator of DNA base-pair mismatches. It binds specifically to a mismatched DNA base pair and initiates a process of DNA repair. To test the possibility of visually detecting mismatched base pairs by atomic force microscopy, we prepared DNA templates approximately 500 bp in length consisting of a single or multiple base-pair mismatches. We demonstrate that MutS binding sites on individual DNA molecules were readily detectable by atomic force microscopy and that the observed positions were in good agreement with the predicted sites of base-pair mismatches at a few-nanometer resolution. The technique described here is rapid and sensitive and is expected to be useful in screening mutations and DNA polymorphisms.     

Nanoscale detection of ionizing radiation damage to DNA by atomic force microscopy

The detection and quantification of ionizing radiation damage to DNA at a single-molecule level by atomic force microscopy (AFM) is reported. The DNA damage-detection technique combining supercoiled plasmid relaxation assay with AFM imaging is a direct and quantitative approach to detect gamma-ray-induced single- and double-strand breaks in DNA, and its accuracy and reliability are validated through a comparison with traditional agarose gel electrophoresis. In addition, the dependence of radiation-induced single-strand breaks on plasmid size and concentration at a single-molecule level in a low-dose (1 Gy) and low-concentration range (0.01 ng microL(-1)-10 ng microL(-1)) is investigated using the AFM-based damage-detection assay. The results clearly show that the number of single-strand breaks per DNA molecule is linearly proportional to the plasmid size and inversely correlated to the DNA concentration. This assay can also efficiently detect DNA damage in highly dilute samples (0.01 ng microL(-1)), which is beyond the capability of traditional techniques. AFM imaging can uniquely supplement traditional techniques for sensitive measurements of damage to DNA by ionizing radiation.     

Scanned gate microscopy of a one-dimensional quantum dot

We analyze electrostatic interaction between a sharp conducting tip and a thin one-dimensional wire, e.g., a carbon nanotube, in a scanned gate microscopy (SGM) experiment. The problem is analytically tractable if the wire resides on a thin dielectric substrate above a metallic backgate. The characteristic spatial scale of the electrostatic coupling to the tip is equal to its height above the substrate. Numerical simulations indicate that imaging of individual electrons by SGM is possible once the mean electron separation exceeds this scale (typically, a few tens of nm). Differences between weakly and strongly invasive SGM regimes are pointed out.     

Atomic force microscopy and atomic force acoustic microscopy characterization of photo-induced changes in some Ge-As-S amorphous films

Amorphous Ge₂₇As₁₃S₆₀, Ge₁₄As₂₇S₅₉ and Ge₁₆As₂₆S₅₈ thin films were prepared by thermal evaporation. Well annealed films were photodarkened by the photons with energy little exceeding the band gap energy. Using Atomic Force Microscopy we observed significant photoexpansion of studied films. Atomic Force Acoustic Microscopy revealed domains like structure of the surface and near surface parts of the samples which one was found to be more disintegrated after illumination.     

Monitoring DNA immobilization and hybridization on surfaces by atomic force microscopy force measurements

DNA immobilization and hybridization was carried out on Au substrates that were modified with mercaptopropanoic acid and then treated with aluminum(III) solution. The positively charged AI(III) film can be used to immobilize both ds-DNA and ss-DNA. Atomic force microscopy (AFM) was used to monitor the process by force measurements between a negatively charged silica tip and the substrates while immersed in dilute electrolyte. Surface hybridization of ss-DNA produces an increase in the surface charge and surface potential of the substrates, which is reflected by the increasing repulsive force as determined from AFM force-separation curves. A single-base mismatch was detectable in surface hybridization. The AFM force measuring technique was also employed to investigate the interaction of Ru(phen)3(2+) with ss-DNA and ds-DNA. The force measurement results showed that there is a small interaction between Ru(phen)3(2+) and ss-DNA, which was ascribed to the electrostatic binding of Ru(phen)3(2+) to the ss-DNA surface. For ds-DNA, there is a strong interaction which is believed to be due to the association or intercalation of Ru(phen)3(2+) with ds-DNA.     

Electrical characterization of silicon tips using conducting atomic force microscopy

The electrical properties of n-doped Si tips have been characterized in conducting atomic force microscopy under various conditions. Si tips with SiO2 layer on them present complex electric properties: which include a larger positive threshold bias, which is different from that of its doped semiconductor material. Silicon tips after removing their SiO2 layer had smaller positive threshold bias; such bias varied with the loading force: smaller loading forces corresponding to larger positive threshold biases, and it remained constant at lower levels for larger loading forces. Humidity of experiments influenced the threshold bias: lower relative humidities (<25%) and larger loading forces were in favor of getting stable threshold bias. The conductance increased remarkably in high relative humidity although it was kept in a narrow range when relative humidity was lower than 40%. Loading force didn't affect the conductance in the examined relative humidity conditions. One advantage of bare silicon tips over commercial conducting ones is that they smaller radius than gold-coated tips; this is in more favor of reaching single molecular electronics.     

A high performance lipase preparation: characterization and atomic force microscopy

The goal of obtaining enzyme forms which show greater stability, higher catalytic efficiency, and reusability has been pursued since last several decades. Some novel biocatalyst designs have been evolved and protein coated micro-crystals (PCMCs) is one of them. Pseudomonas cepacia lipase coated micro-crystals were prepared by simultaneous precipitation of mixture of aqueous lipase solution and salts such as potassium sulphate by organic solvents. This resulted in lipase coated micro-crystals. The structures of micro-crystals were studied by atomic force microscopy (AFM). The AFM picture confirmed the enzyme coating over the potassium sulphate crystals. These PCMCs are in the size range of 500-1000 nm. These enzyme coated micro-crystals showed enhanced transesterification rates. Also, the PCMC were stable at 60 degrees C whereas the free enzyme lost all its activity. The enzyme coated micro-crystals prepared by 50 mg Pseudomonas cepacia lipase gave 96% conversion in 90 min whereas free enzyme gave 8% conversion. Even PCMCs prepared from 3.12 mg lipase gave 90% conversion in 10 h at 60 degrees C where as free lipase was inactive at 60 degrees C.     

Electrical characterization of Ge microcrystallites by atomic force microscopy using a conducting probe

We have studied the nucleation and growth of Ge microcrystallities on Si(100) or evaporated Cr substrates from an rf glow discharge decomposition of GeH₄ highly-diluted with H₂, where the crystallinity, the surface microroughness and the local electric transport of the films have been measured as a function of the film thickness. For the film growth thicker than ∼65 nm, Raman scattering spectra show that the evolution of the microcrystalline phase tends to be saturated. In the thickness range of 7-65 nm, the nucleation and/or microcrystalline grain formation with progressive film growth and corresponding significant difference in the electrical conductivity in the direction of the film thickness between the grains and their boundaries have been demonstrated from topographic and current images taken simultaneously by an atomic force microscope with a conducting probe.     

Monitoring molecular beacon/DNA interactions using atomic force microscopy

The molecular beacon (MB) is a new fluorescence probe containing a single-stranded oligonucleotide with a probe sequence embedded in complementary sequences that form a hairpin stem. Due to the inherent fluorescent signal transduction mechanism, an MB functions as a sensitive probe with a high signal-to-background ratio for real-time monitoring and provides a variety of exciting opportunities in DNA, RNA, and protein studies. To better understand the properties of MBs, the specific interactions between MB and target DNA (complementary and one-base mismatch) have been directly investigated by atomic force microscopy. The interaction force between a linear DNA probe and the target DNA was also detected and compared to that between MB and target DNA. The results demonstrate the high specificity of the MB/target DNA compared to the linear DNA/target DNA interaction.     

Investigation of radiation damage in DNA by using atomic force microscopy

The effect of radiations on supercoiled plasmid DNA has been investigated by using atomic force microscopy (AFM). The DNA molecules were deposited on a substrate and observed by AFM. Alternatively, DNA at different scavenger concentrations was initially exposed to different types of radiations (alpha and X rays) at various doses. After irradiation, fragments (open circular and linearised strands) were observed corresponding to single strand breaks and double strand breaks in DNA. This result indicates the capabilities of AFM for the qualitative detection of strand modifications due to irradiation. The amount of each class of topology enables a quantitative response to be determined for both types of radiation (alpha, X). A value of the radiosensitivity of DNA was obtained as a function of the scavenger concentration. Strong accordance was found between AFM results and those obtained by use of gel electrophoresis. The advantage of AFM in comparison with traditional techniques is the possibility of analysing the radiation effects on one molecule. Indeed, taking the example of alpha particles, it is shown that it is easy to measure the sizes of linear strands by AFM. Such additional or even precise results are difficult to obtain with gel electrophoresis since, in such a case, data are lost through smearing.     

Covalent immobilization of DNA onto functionalized mica for atomic force microscopy

The immobilization of DNA on the self-assembled monolayer of 3-aminopropyltrimethoxysilane (APTES) on mica wafer functionalized with glutaraldehyde (GA) by chemical bonding was studied by atomic force microscopy (AFM). The DNA used for our investigation was amplified by polymerase chain reaction, and primers were labeled with a -NH2 group at their 5' terminus. The surfaces were analyzed by X-ray photoelectron spectroscopy (XPS) and AFM. Results from XPS and AFM showed that the mica with the APTES and activated with GA can be formed, and the flatness of the mica can be adapted for AFM images. We found that the modified surface was capable of binding DNA molecules so that it withstood a thorough rinsing with a solution of sodium dodecylsulfate. Covalent binding between the aldehyde-terminated membrane and -NH2 groups at both ends of double-stranded DNA resulted in immobilization and straightening of the DNA.     

Space charge limited current measurements on conjugated polymer films using conductive atomic force microscopy

We describe local (~150 nm resolution), quantitative measurements of charge carrier mobility in conjugated polymer films that are commonly used in thin-film transistors and nanostructured solar cells. We measure space charge limited currents (SCLC) through these films using conductive atomic force microscopy (c-AFM) and in macroscopic diodes. The current densities we measure with c-AFM are substantially higher than those observed in planar devices at the same bias. This leads to an overestimation of carrier mobility by up to 3 orders of magnitude when using the standard Mott-Gurney law to fit the c-AFM data. We reconcile this apparent discrepancy between c-AFM and planar device measurements by accounting for the proper tip-sample geometry using finite element simulations of tip-sample currents. We show that a semiempirical scaling factor based on the ratio of the tip contact area diameter to the sample thickness can be used to correct c-AFM current-voltage curves and thus extract mobilities that are in good agreement with values measured in the conventional planar device geometry.     

Superlocalization spectral imaging microscopy of a multicolor quantum dot complex

The key factor of realizing super-resolution optical microscopy at the single-molecule level is to separately position two adjacent molecules. An opportunity to independently localize target molecules is provided by the intermittency (blinking) in fluorescence of a quantum dot (QD) under the condition that the blinking of each emitter can be recorded and identified. Herein we develop a spectral imaging based color nanoscopy which is capable of determining which QD is blinking in the multicolor QD complex through tracking the first-order spectrum, and thus, the distance at tens of nanometers between two QDs is measured. Three complementary oligonucleotides with lengths of 15, 30, and 45 bp are constructed as calibration rulers. QD585 and QD655 are each linked at one end. The measured average distances are in good agreement with the calculated lengths with a precision of 6 nm, and the intracellular dual-color QDs within a diffraction-limited spot are distinguished.     

Surface roughness characterization of Nicalon and HI-Nicalon ceramic fibers by atomic force microscopy

The behavior of ceramic composites is governed by the nature of the fiber/matrix interface. Fiber surface roughness is a key parameter in the behavior at the fiber/matrix interface (e.g., debonding, interfacial sliding) and the overall behavior of a composite. Using an atomic force microscope (AFM), quantitative surface roughness values of ceramic fibers can be obtained, with an uncertainty of 1nm. The AFM technique was used to obtain surface roughness profiles and analysis on Si-C-O and Si-C fibers (Nicalon, and a new, virtually oxygen-free Si-C fiber, HI-Nicalon). The latter fiber had a slightly higher roughness amplitude, which may be caused by differences in processing. Although the differences in roughness between the fibers were small, the calculated radial strain and radial normal stress in composites reinforced with HI-Nicalon were higher than in those reinforced with Nicalon. This result indicates that small changes in the roughness of a fiber can significantly affect the debonding and sliding properties between the fiber and matrix.