Observation of large-scale features on graphite by scanning tunnelling microscopy

Superlattice structures and rippling fringes were imaged on two separate pieces of graphite (HOPG) by scanning tunnelling microscopy (STM). We observed the corrugation conservation phenomenon on one of the superlattice structures where an overlayer does not attenuate the corrugation amplitude of the superlattice. Such a phenomenon may illustrate an implication that nanoscale defects a few layers underneath the surface may propagate through many layers without decay and form the superlattice structure on the topmost surface. Some rippling fringes with periodicities of 20 nm and 30 nm and corrugations of 0.1 nm and 0.15nm were observed in the superlattice area and in nearby regions. Such fringes are believed to be due to physical buckling of the surface. The stress required to generate such structures is estimated, and a possible cause is discussed. An equation relating the attenuation factor to the number of overlayers is proposed. © 2005 The Japan Society of Applied Physics.

A normal force distance regulation scheme for near-field optical microscopy

A near-field optical microscope (NFOM) has been developed that combines the features of a near-field optical microscope and an atomic force microscope. Improved control over tip-sample separation has led to improved optical imaging and independent surface topography information. The tip oscillation is normal to the sample plane thereby reducing lateral forces - important for nonperturbative imaging of soft samples. Both topographic images and reflection near-field optical images are presented which demonstrate the capability of the system. © 1996 American Institute of Physics.

On the relationship between hidden Markov Models and convex functional transforms for simulating scanning probe Microscopy

Models for simulating Scanning Probe Microscopy (SPM) may serve as a reference point for validating experimental data and practice. Generally, simulations use a microscopic model of the sample-probe interaction based on a first-principles approach, or a geometric model of macroscopic distortions due to the probe geometry. Examples of the latter include use of neural networks, the Legendre Transform, and dilation/erosion transforms from mathematical morphology. Dilation and the Legendre Transform fall within a general family of functional transforms, which distort a function by imposing a convex solution.In earlier work, the authors proposed a generalized approach to modeling SPM using a hidden Markov model, wherein both the sample-probe interaction and probe geometry may be taken into account. We present a discussion of the hidden Markov model and its relationship to these convex functional transforms for simulating and restoring SPM images.©2009 SPIE.

Shifting atomic patterns: on the origin of the different atomic-scale patterns of graphite as observed using scanning tunnelling microscopy.

We present an in-depth study of the myriad atomically resolved patterns observed on graphite using the scanning tunnelling microscope (STM) over the past three decades. Through the use of highly resolved atomic resolution images, we demonstrate how the interactions between the different graphene layers comprising graphite affect the local surface atomic charge density and its resulting symmetry orientation, with particular emphasis on interactions that are thermodynamically unstable. Moreover, the interlayer graphene coupling is controlled experimentally by varying the tip-surface interaction, leading to associated changes in the atomic patterns. The images are corroborated by first-principles calculations, further validating our claim that surface graphene displacement, coming both from lateral and vertical displacement of the top graphene layer, forms the basis of the rich variety of atomic patterns observed in STM experiments on graphite.

Hydrothermally-grown ZnO nanowire tips for scanning tunnelling microscopy.

The probe tip is pivotal in determining the resolution and nature of features observed in the Scanning Tunnelling Microscope (STM). We have augmented a conventional Pt/Ir metallic tip with a hydrothermally grown ZnO nanowire (NW). Atomic resolution imaging of graphite is attained. Current-voltage (IV) characteristics demonstrate an asymmetry stemming from the unintentional n-type doping of the ZnO NW, whereas the expected Schottky barrier at the ZnO-Pt/Ir interface is shown to have negligible effect. Moreover the photoconductivity of the system is investigated, paving the way towards a photodetector capable of atomic resolution.

Differential Dynamic Microscopy: a High-Throughput Method for Characterizing the Motility of Microorganism

We present a fast, high-throughput method for characterizing the motility of microorganisms in 3D based on standard imaging microscopy. Instead of tracking individual cells, we analyse the spatio-temporal fluctuations of the intensity in the sample from time-lapse images and obtain the intermediate scattering function (ISF) of the system. We demonstrate our method on two different types of microorganisms: bacteria, both smooth swimming (run only) and wild type (run and tumble) Escherichia coli, and the bi-flagellate alga Chlamydomonas reinhardtii. We validate the methodology using computer simulations and particle tracking. From the ISF, we are able to extract (i) for E. coli: the swimming speed distribution, the fraction of motile cells and the diffusivity, and (ii) for C. reinhardtii: the swimming speed distribution, the amplitude and frequency of the oscillatory dynamics. In both cases, the motility parameters are averaged over \approx 10^4 cells and obtained in a few minutes.

Probing the location of displayed cytochrome b562 on amyloid by scanning tunnelling microscopy.

Amyloid fibres displaying cytochrome b562 were probed using scanning tunnelling microscopy (STM) in vacuo. The cytochromes are electron transfer proteins containing a haem cofactor and could, in principle, mediate electron transfer between the tip and the gold substrate. If the core fibres were insulating and electron transfer within the 3D haem network was detected, then the electron transport properties of the fibre could be controlled by genetic engineering. Three kinds of STM images were obtained. At a low bias (<1.5 V) the fibres appeared as regions of low conductivity with no evidence of cytochrome mediated electron transfer. At a high bias, stable peaks in tunnelling current were observed for all three fibre species containing haem and one species of fibre that did not contain haem. In images of this kind, some of the current peaks were collinear and spaced around 10 nm apart over ranges longer than 100 nm, but background monomers complicate interpretation. Images of the third kind were rare (1 in 150 fibres); in these, fully conducting structures with the approximate dimensions of fibres were observed, suggesting the possibility of an intermittent conduction mechanism, for which a precedent exists in DNA. To test the conductivity, some fibres were immobilized with sputtered gold, and no evidence of conduction between the grains of gold was seen. In control experiments, a variation of monomeric cytochrome b562 was not detected by STM, which was attributed to low adhesion, whereas a monomeric multi-haem protein, GSU1996, was readily imaged. We conclude that the fibre superstructure may be intermittently conducting, that the cytochromes have been seen within the fibres and that they are too far apart for detectable current flow between sites to occur. We predict that GSU1996, being 10 nm long, is more likely to mediate successful electron transfer along the fibre as well as being more readily detectable when displayed from amyloid.

The inverse problem in magnetic force microscopy--inferring sample magnetization from MFM images.

Nanomagnetic structures have the potential to surpass silicon's scaling limitations both as elements in hybrid CMOS logic and as novel computational elements. Magnetic force microscopy (MFM) offers a convenient characterization technique for use in the design of such nanomagnetic structures. MFM measures the magnetic field and not the sample's magnetization. As such the question of the uniqueness of the relationship between an external magnetic field and a magnetization distribution is a relevant one. To study this problem we present a simple algorithm which searches for magnetization distributions consistent with an external magnetic field and solutions to the micromagnetic equations' qualitative features. The algorithm is not computationally intensive and is found to be effective for our test cases. On the basis of our results we propose a systematic approach for interpreting MFM measurements.

Electrostatic force microscopy and potentiometry of realistic nanostructured systems

We investigate the dependency of electrostatic interaction forces on applied potentials in electrostatic force microscopy (EFM) as well as in related local potentiometry techniques such as Kelvin probe microscopy (KPM). The approximated expression of electrostatic interaction between two conductors, usually employed in EFM and KPM, may loose its validity when probe-sample distance is not very small, as often realized when realistic nanostructured systems with complex topography are investigated. In such conditions, electrostatic interaction does not depend solely on the potential difference between probe and sample, but instead it may depend on the bias applied to each conductor. For instance, electrostatic force can change from repulsive to attractive for certain ranges of applied potentials and probe-sample distances, and this fact cannot be accounted for by approximated models. We propose a general capacitance model, even applicable to more than two conductors, considering values of potentials applied to each of the conductors to determine the resulting forces and force gradients, being able to account for the above phenomenon as well as to describe interactions at larger distances. Results from numerical simulations and experiments on metal stripe electrodes and semiconductor nanowires supporting such scenario in typical regimes of EFM investigations are presented, evidencing the importance of a more rigorous modeling for EFM data interpretation. Furthermore, physical meaning of Kelvin potential as used in KPM applications can also be clarified by means of the reported formalism. © 2009 American Institute of Physics.

Biofunctionalization of PET/SiO2 surfaces for single molecule experiments and medical applications

PET/SiO2 layers were chemically modified to maintain immobilization of functional single molecules. GFP molecules provide an ideal system due to their stability and intrinsic fluorescence. GFP in vivo biotinylated within its NH2-terminal region and attached on the substrate via the biotinstreptavidin bond was further investigated with confocal microscopy, atomic force microscopy (AFM) and spectroscopic ellipsometry (SE). AFM revealed monolayered donut-like structures representing assemblies of biotinstreptavidinbiotinGFP immobilized onto PET/SiO2 surfaces via mPEG. In particular, regions with an approximate height of 12 nm, which approaches the molecular dimensions of the above complex given by molecular modeling, could be detected. The dimensions of the donut-like structures suggest a close-to-each-other positioning of the GFP molecules - which, however, retain their functionality, as evidenced by confocal microscopy. © 2011 World Scientific Publishing Company.