Experimental Atomic Force Microscopy Images Research Articles

Automated structure discovery in atomic force microscopy.

Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules due to difficulties with interpretation of highly distorted AFM images originating from nonplanar molecules. Here, we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to applying high-resolution AFM to a large variety of systems, for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.

A Parametric Three-Dimensional Phase-Field Study of the Physical Vapor Deposition Process of Metal Thin Films Aiming at Quantitative Simulations

In this paper, a parametric three-dimensional (3D) phase-field study of the physical vapor deposition process of metal thin films was performed aiming at quantitative simulations. The effect of deposition rate and model parameters on the microstructure of deposited thin films was investigated based on more than 200 sets of 3D phase-field simulations, and a quantitative relationship between the deposition rate and model parameters was established. After that, the heat maps corresponding to the experimental atomic force microscopy images were plotted for characterization of the surface roughness. Different roughness parameters including the arithmetic average roughness (Ra), root mean square roughness (Rq), skewness (Rsk), and kurtosis (Rku), as well as the ratio of Rq to Ra were calculated and carefully analyzed. A quantitative relationship between the surface roughness and the deposition rate and model parameters was obtained. Moreover, the calculated Rq to Ra ratios for the thin films at the deposition rates of 0.22 and 1.0 nm s−1 agreed very well with the experimental data of the deposited Mo and Ti thin films. Finally, further discussion about the correlative behaviors between the surface roughness and the density was proposed for reasoning the shadowing effect as well as the formation of voids during the thin film production.

Experimental and simulation studies on temporal evolution of chemically etched Si surface: Tunable light trapping and cold cathode electron emission properties

Anisotropic alkaline etching of single crystalline p-Si(100) substrates is carried out for different times (in the range of 30–2400 s). This leads to the formation of randomly distributed pyramidal structures on Si surfaces, as observed from atomic force microscopy (AFM) and scanning electron microscopy images. During early stages of etching, rough surfaces evolve, but for longer etching times, pyramidally textured surfaces (having dimensions in the range of 0.2–2 μm) are formed. The formation of pyramidal structures is explained in light of simulation studies based on the continuum theory of stress-induced morphological instability. The power spectral density plots extracted from the experimental AFM images and the simulated images show that while the correlation length increases for lower etching times, it gets saturated for higher etching times. These facts corroborate well with our experimental results that reveal increasing pyramidal size with etching time. In addition, we study the temporal evolution of antireflection and field emission properties of such pyramidally textured-silicon substrates in line with their potential use in solar cells and moderate level cold cathode electron emission, respectively. For instance, it is interesting to note that surface reflectance of these pyramidally textured surfaces (formed at higher etching times) can be brought down to as low as 0.4% over a broad spectral range, viz., 300–3000 nm. Likewise, the field emission data show that turn-on potential decreases with increasing etching time (e.g., 2.62 V μm−1 for an etching time of 1200 s).

Tuning the copper Cluster´s size on HOPG by electrodeposition from perchlorate aqueous solutions. An AFM study

In this work, we report the electrochemical synthesis of nanometric copper clusters smaller than 3 nm of height and 14.3 nm of diameter from perchlorate solutions. From the number of copper clusters counted directly from the AFM (Atomic force microscopy) images, it was possible to derive an equation, which is able to predict the number of clusters formed in function on the applied potential. Also, qualitative AFM images were simulated employing a spreadsheet and the freeware ImageJ, the results obtained show concordance with the experimental AFM images.

The conformation and dynamics of P-glycoprotein in a lipid bilayer investigated by atomic force microscopy

The membrane-bound P-glycoprotein (Pgp) transporter plays a major role in human disease and drug disposition because of its ability to efflux a chemically diverse range of drugs through ATP hydrolysis and ligand-induced conformational changes. Deciphering these structural changes is key to understanding the molecular basis of transport and to developing molecules that can modulate efflux. Here, atomic force microscopy (AFM) is used to directly image individual Pgp transporter molecules in a lipid bilayer under physiological pH and ambient temperature. Analysis of the Pgp AFM images revealed “small” and “large” protrusions from the lipid bilayer with significant differences in protrusion height and volume. The geometry of these “small” and “large” protrusions correlated to the predicted extracellular (EC) and cytosolic (C) domains of the Pgp X-ray crystal structure, respectively. To assign these protrusions, simulated AFM images were produced from the Pgp X-ray crystal structures with membrane planes defined by three computational approaches, and a simulated 80 Å AFM cantilever tip. The theoretical AFM images of the EC and C domains had similar heights and volumes to the “small” and “large” protrusions in the experimental AFM images, respectively. The assignment of the protrusions in the AFM images to the EC and C domains was confirmed by changes in protrusion volume by Pgp-specific antibodies. The Pgp domains showed a considerable degree of conformational dynamics in time resolved AFM images. With this information, a model of Pgp conformational dynamics in a lipid bilayer is proposed within the context of the known Pgp X-ray crystal structures.

A new approach of recognition of ellipsoidal micro- and nanoparticles on AFM images and determination of their sizes

In this work we develop an approach of automatic recognition of ellipsoidal particles on the atomic force microscopy (AFM) image and determination of their size, which is based on image segmentation and the surface approximation by ellipsoids. In addition to the comparative simplicity and rapidity of processing, this method allows us to determine the size of particles, the surface of which is not completely visible on the image. The proposed method showed good results on simulated images including noisy ones. Using this algorithm the size distributions of silica particles on experimental AFM images have been determined.

Improving dimensional measurement from noisy atomic force microscopy images by non-local means filtering.

Quantitative evaluation of dimensional parameters from noisy atomic force microscopy (AFM) images was investigated. Non-local means (NLM) denoising was adopted to reduce noise and maintain fine image structures. Major tuning parameters in NLM filtering, such as the patch size and the window size, were optimized on simulated surface structures. The ability of dimensional evaluation from noisy data was demonstrated to be improved by almost 15 times. Finally, NLM filtering with optimal settings was applied on experimental AFM images, which were scanned on a patterned few-layer graphene specimen. Evaluations of the step height and the pattern size were verified to be much more accurate and robust. Such a data processing method can enhance the AFM dimensional measurements, particularly when the noise-level is reached.

FtsZ protein on bilayer membranes: effects of specific lateral bonds

We use a simple lattice model to explore the self-assembled structures of protein filaments. Monte Carlo simulations show polymorphic structures, formed by the competition between the bundling of filaments, their branching and the spontaneous curvature. In the top-down approach, typical of statistical physics, we compare the simulation results with experimental atomic force microscopy images of the bacterial protein FtsZ anchored on bilayer membranes. We identify the relevant aspects of the interactions between protein monomers, which are amplified as a collective effect of the whole system. From the perspective of soft-matter physics, the experimental system and its model representation provide an interesting example of living polymers with tunable interactions.

Atomic force microscopy analysis of morphology of thin pentacene films deposited on parylene-C and benzocyclobutene

This paper reports on an atomic force microscopy (AFM) investigation of the surface of pentacene films deposited onto parylene-C and benzocyclobutene (BCB), two polymers dedicated to organic field effect transistors (OFETs). A thorough grain analysis was carried out by power spectral density (PSD) on pentacene films of different thicknesses (ca. 15–60nm). PSD spectra of experimental AFM images were analyzed by using fractal, ABC and superstructure models. These approaches permitted to explain the difference of the pentacene morphology on the two substrates and to illustrate structural specificities related to change in the growth mode. Superstructures larger for the pentacene on BCB than for the pentacene on parylene were revealed. On both substrates, larger superstructures occurred for 30nm thick pentacene layers. This thickness also corresponded to the highest field effect mobility in top gate OFETs parylene/pentacene deposited on BCB. The superstructure model applied on the PSD curves showed that the increase of mobility for a 30nm thickness was not related to an increase of the grain size but to an increase of the island size.

Identification and surface structure of crystalline cellulose studied by atomic force microscopy

SummaryA combination of molecular modelling and atomic force microscopy (AFM) techniques was used to study the surface structure of crystalline cellulose. Two‐dimensional Fourier analysis of the AFM raw data gave crystal parameters as well as a highly filtered inverse‐transformed image. Molecular modelling was used to generate Connolly surfaces based on electron diffraction data for crystalline cellulose. The modelled surfaces were used to interpret the experimental AFM images. Monoclinic () crystal faces were identified. The method used enables the structural analysis of cellulose surfaces at the molecular level, where all biological processes involving cellulose take place.