Force probing of protein crystals: An atomic force microscopy study

The atomic force microscope (AFM) was used for measuring force-distance curves on horse spleen ferritin crystals in liquid environment. In the region of the approach curve which corresponds to tip-surface contact, discrete jumps were recorded, as predicted by molecular dynamics simulations in the case of low tip-sample interaction. The observed jumps can be related to the removal of individual molecules from the surface by the AFM tip. A simple steric model, which takes into account tip and ferritin molecule size, can explain the displacements observed with excellent agreement. The elemental force jump resulting from the approach curves is a direct measure of the force required to remove a single molecule from the crystal face. We discuss the conditions under which the cantilever potential energy difference along the elemental force step provides the energy of extraction of a single molecule. The estimate of the intermolecular binding energy turns out to be in good agreement with the value calculated independently from the surface free energy of ferritin crystals. Received 10 February 2000 and Received in final form 4 May 2000     

An atomic force microscopy investigation of cyanophage structure

Marine viruses have only relatively recently come to the attention of molecular biologists, and the extraordinary diversity of potential host organisms suggests a new wealth of genetic and structural forms. A promising technology for characterizing and describing the viruses structurally is atomic force microscopy (AFM). We provide examples here of some of the different architectures and novel structural features that emerge from even a very limited investigation, one focused on cyanophages, viruses that infect cyanobacteria (blue-green algae). These were isolated by phage selection of viruses collected from California coastal waters. We present AFM images of tailed, spherical, filamentous, rod shaped viruses, and others of eccentric form. Among the tailed phages numerous myoviruses were observed, some having long tail fibers, some other none, and some having no visible baseplate. Syphoviruses and a podovirus were also seen. We also describe a unique structural features found on some tailed marine phages that appear to have no terrestrial homolog. These are long, 450 nm, complex helical tail fibers terminating in a unique pattern of 3+1 globular units made up of about 20 small proteins.     

An atomic view of crystal growth

The ability to routinely observe individual metal atoms adsorbed on metal surfaces using field ion microscopy has made it possible to directly examine atomic events important in the growth of crystals from the vapor. On the atomically smooth (111) plane of iridium, there are now available observations of the binding sites for atoms and of condensation from the vapor, together with measurements of the diffusion of atoms over the surface, as well as studies of their subsequent incorporation at both ascending and descending steps. These results are briefly reviewed, revealing a picture generally more varied and interesting than envisioned in classical theories of crystal growth.     

Laser crystallization of amorphous silicon films investigated by Raman spectroscopy and atomic force microscopy

The intrinsic and phosphorous (P)-doped hydrogenated amorphous silicon thin films were crystallized by laser annealing. The structural properties during crystallization process can be investigated. Observed redshifts of the Si Raman transverse optical phonon peak indicate tensile stress present in the films and become intense with the effect of doping, which can be relieved in P-doped films by introducing buffer layer structures. Based on experimental results, the established correlation between the stress and crystalline fraction (X_C) suggests that the relatively high stress can limit the increase in X_C and the highest crystalline fraction is obtained by a considerable stress release. At high laser energy density of 1250 mJ/cm², the poorer crystalline quality and disordered structure of the film originating from the irradiation damage and defects lead to the low electron mobility.     

Chaos in atomic force microscopy

Chaotic oscillations of microcantilever tips in dynamic atomic force microscopy (AFM) are reported and characterized. Systematic experiments performed using a variety of microcantilevers under a wide range of operating conditions indicate that softer AFM microcantilevers bifurcate from periodic to chaotic oscillations near the transition from the noncontact to the tapping regimes. Careful Lyapunov exponent and noise titration calculations of the tip oscillation data confirm their chaotic nature. AFM images taken by scanning the chaotically oscillating tips over the sample show small, but significant metrology errors at the nanoscale due to this "deterministic" uncertainty.     

Time-frequency modeling of atomic force microscopy

Atomic force microscopy is modeled in the time-frequency phase space. In this phase space it is equivalent to a succession of temporal lenses and free spaces which includes a temporal fractional Fourier device. Then, the Wigner transform and its second order moments are introduced to model the atomic force microscopy as a detector of ultrafast electrical signals.     

Theory of multifrequency atomic force microscopy

We develop a theory that explains the origin of the high force sensitivity observed in multifrequency force microscopy experiments. The ability of the microscope to extract complementary information on the surface properties is increased by the simultaneous excitation of several flexural cantilever modes. The force sensitivity in multifrequency operation is about 0.2 pN. The analytical model identifies the virial and the energy dissipated by the tip-surface forces as the parameters responsible for the material contrast. The agreement obtained among the theory, experiments and numerical simulations validates the model.     

原子力显微术研究进展

原子力显微术是微纳米尺度实空间形貌成像与结构表征的关键技术之一。近些年,原子力显微术衍生发展出了一系列令人瞩目的功能化探测模式和新技术。文章从以下两个方面论述了原子力显微术的前沿进展：(1)原子力显微术的功能化探测模式及其在微纳米尺度物性研究与测量以及微纳加工等领域的应用;(2)原子力显微术自身在更高精度、更高分辨率、更快速度、更多功能等方面的进展及在基础和应用研究领域中的应用。文章还展望了原子力显微术的下一步发展方向和正在不断扩展的研究领域。     

Eutectic alloy microstructure: atomic force microscopy analysis

The exciting microstructures found in several eutectic alloys are a result of a cooperative growth, which is connected to the atomic transfer in the melt ahead the solid/liquid interface. In a eutectic system, the growth of solid phases depends on the simultaneous rejection of constituents to the liquid phase, which causes adjustments of the melt composition and hence, mass transport by diffusion normal to the growth direction. Generally, eutectic microstructures are examined by using optical (OM) and scanning electron microscopy (SEM). While OM may not provide the necessary resolution, the eutectic microstructure may present three-dimensional features, as a result of etching, which is not always possible to be observed by SEM. As an alternative, this paper describes the use of atomic force microscopy (AFM) in understanding micro-scale feature of a eutectic microstructure. For such a purpose, directionally solidified samples of a Ni–Al–V lamellar eutectic, a Ni–Al–Mo fibrous eutectic and a Ni–Al–Nb three-phase eutectic were examined. The results obtained provided a new picture of multi-phase microstructures and allows one to understand their new characteristics.     

Thin film semiconductor nanomaterials and nanostructures prepared by physical vapour deposition: An atomic force microscopy study

Amorphous/nanocrystalline ${\mathrm{SiO}}_x/\mathrm{CdSe}$, ${\mathrm{GeS}}_2/\mathrm{CdSe}$, ${\mathrm{SiO}}_x/\mathrm{ZnSe}$ and $\mathrm{Se}/\mathrm{CdSe}$ amorphous multilayers (MLs) were grown by consecutive physical vapour deposition of the constituent materials at room substrate temperature. A step-by-step manner of deposition was applied for the preparation of each layer ($2–10\mathrm{nm}$ thick) of MLs. Surface morphology has been investigated by atomic force microscopy (AFM) in order to get information about ML interfaces. For a scanned area of $3.4\times 4\mathrm{\mu }{\mathrm{m}}^2$ ${\mathrm{SiO}}_x/\mathrm{CdSe}$ and ${\mathrm{GeS}}_2/\mathrm{CdSe}$ MLs showed surface roughness which is around three times greater than the roughness of ${\mathrm{SiO}}_x/\mathrm{ZnSe}$ MLs. This observation has been connected with effects of both film composition and deposition rate. For a scanned area of $250\times 250{\mathrm{nm}}^2$ the roughness determined in all MLs displayed close values and a similar increase with the ML period. The latter has been related to the flexible structure of amorphous materials. The AFM results, in good agreement with previous X-ray diffraction and high resolution electron microscopy data, indicate that the application of step-by-step physical vapour deposition makes possible fabrication of various amorphous/nanocrystalline MLs with smooth interfaces and good artificial periodicity at low substrate temperatures.     

High-speed atomic force microscopy with phase-detection

In order to improve the scanning speed of tapping mode AFM, we have studied the phase-detection mode AFM with a high frequency (1.5 MHz) cantilever. The phase shifts versus tip-sample distance with different types of samples including polymer, semiconductor, and graphite were measured and the interaction forces were analyzed. It was found that the phase shift in repulsive region is nearly linear as a function of distance, which can be used for feedback control in general, except that some blunt tips cause reversed polarity of phase shift due to excessive energy dissipation. High-speed image with scan rate of 100 Hz was obtained which were controlled with phase shift as a feedback signal.     

Bias-induced spatially resolved growth and removal of Si-oxide by atomic force microscopy

Three mechanisms for spatially resolved growth and removal of oxide on silicon substrates have been investigated. Thermally grown oxide layers with thicknesses in the range 2–6 nm were the distinctive feature of the system. The layers were characterized and manipulated by methodologies based on atomic force microscopy (AFM) with conducting probes in a vacuum environment of 10^-2–10^-3 Pa. The probe is then effectively a travelling electrode that generates an electrostatic field between the tip and the substrate. Oxide growth was induced for a positive sample bias greater than 5 V, but below the level corresponding to dielectric breakdown. Application of a short pulse of amplitude marginally above that corresponding to dielectric breakdown, on the other hand, had the effect of producing pits of inner diameter of about 10 nm in the pre-existing oxide layer at the point of tip-to-oxide contact. Application of a low positive sample bias (less than that required for measurable oxide growth) in combination with high linear scan speed had the effect of removing a pre-existing oxide layer from the scanned field of view. The most plausible mechanisms are based on transverse ionic diffusion (for oxide growth), controlled dielectric breakdown (for formation of pits) and lateral transport of silicaceous species (for oxide removal). Received: 24 October 2001 / Accepted: 6 January 2002 / Published online: 3 June 2002 RID="*" ID="*"Corresponding author. Fax: +617-3875-7656, E-mail: s.myhra@sct.gu.edu.au     

Kinetic contrast in atomic force microscopy

The mechanism of the formation of phase contrast in atomic force microscopy (AFM) is studied for various conditions of an oscillating tip interacting with the surface. A phase shift is detected in oscillations of the resonating AFM tip during its interaction with the substrate surface when the AFM tip moves over the surface. We substantiate kinetic mechanism of the formation of phase contrast in AFM, which is initiated when the velocity of the AFM tip moving over the substrate surface increases as a result of increasing friction force. A dependence of the kinetic contrast in AFM on the effective roughness of the surface is discovered. Images of the distribution of copper impurity over the silicon surface under atmospheric conditions are obtained using the method of kinetic phase contrast in AFM.     

Electrostatic assembly of protein lysozyme on DNA visualized by atomic force microscopy

In the present work, atomic force microscopy (AFM) has been used to study the assembly of protein lysozyme on DNA molecule. Based on the electrostatic interaction, the positively charged lysozyme can easily bind onto the negatively charged DNA molecule surface. The protein molecules appear as globular objects on the DNA scaffold, which are distinguishable in the AFM images. At the same time, lysozyme molecules can be assembled onto DNA as dense or sporadic pattern by varying the protein concentration. This work may provide fundamental aspects for building protein nanostructures and studying of DNA-protein interaction.     

Chemical resolution at ionic crystal surfaces using dynamic atomic force microscopy with metallic tips

We demonstrate that well prepared and characterized Cr tips can provide atomic resolution on the bulk NaCl(001) surface with dynamic atomic force microscopy in the noncontact regime at relatively large tip-sample separations. At these conditions, the surface chemical structure can be resolved yet tip-surface instabilities are absent. Our calculations demonstrate that chemical identification is unambiguous, because the interaction is always largest above the anions. This conclusion is generally valid for other polar surfaces, and can thus provide a new practical route for straightforward interpretation of atomically resolved images.     

General theory of amplitude-modulation atomic force microscopy

We present a general analytical theory that enables one to determine accurately the unknown tip-sample interactions from the experimental measurement of the amplitude and phase of the oscillating tip in amplitude-modulation atomic force microscopy (AM-AFM). We apply the method to the known Lennard-Jones-type forces and find excellent agreement with the reconstructed results. AM-AFM, widely used in air and liquid, is now not only an imaging tool but also a quantitative force measurement tool.     

Noncontact atomic force microscopy: Bond imaging and beyond

It was a long-cherished dream for chemists to take a direct look at chemical bonding, a fundamental component of chemistry. This dream was finally accomplished by the state-of-the-art noncontact atomic force microscopy (NC-AFM) equipped with qPlus force sensors and carbon monoxide (CO) functionalized tips. The resolved interconnectivity between atoms and molecules in NC-AFM frequency shift images is interpreted as chemical bonding, providing essential knowledge of the bond length, bond angle and even bond order. The featured contrast of different chemical bonds can serve as fingerprints for further interpretation of chemical structures toward unknown species synthesized on surfaces. This breakthrough enriches characterization tools for surface science and brings our understanding of on-surface reactions to a new level. Beyond bond imaging, the application of NC-AFM has been extended to quantifying interatomic interactions, identifying three-dimensional nanostructures, manipulating molecules and reactions, as well as determining molecular electronic characteristics. Moreover, some recent efforts address the improvement of the usability and versatility of the bond-resolved NC-AFM technique, including high-resolution molecular investigation on bulk insulators, application-specific tip modification, stable bond imaging above liquid helium temperature and autonomous experimentation implemented by artificial intelligence.     

Numerical study of the hydrodynamic drag force in atomic force microscopy measurements undertaken in fluids

When atomic force microscopy (AFM) is employed for in vivo study of immersed biological samples, the fluid medium presents additional complexities, not least of which is the hydrodynamic drag force due to viscous friction of the cantilever with the liquid. This force should be considered when interpreting experimental results and any calculated material properties. In this paper, a numerical model is presented to study the influence of the drag force on experimental data obtained from AFM measurements using computational fluid dynamics (CFD) simulation. The model provides quantification of the drag force in AFM measurements of soft specimens in fluids.The numerical predictions were compared with experimental data obtained using AFM with a V-shaped cantilever fitted with a pyramidal tip. Tip velocities ranging from 1.05 to 105 μm/s were employed in water, polyethylene glycol and glycerol with the platform approaching from a distance of 6000 nm. The model was also compared with an existing analytical model. Good agreement was observed between numerical results, experiments and analytical predictions. Accurate predictions were obtained without the need for extrapolation of experimental data. In addition, the model can be employed over the range of tip geometries and velocities typically utilized in AFM measurements.