bluuebunny/crossref_metadata_2025 huggingface dataset:
A small scanning tunnelling microscope with large scan range for biological studies
Authors: Emch R. , Descouts P. , Niedermann Ph.
Published: August 2011

We have developed a scanning tunnelling microscope specially designed for biological applications presenting some new features: the scanner tube is mounted parallel to the surface of the sample which enables a high resolution optical microscope to be brought close to the sample when working in air or liquids. The maximum scan range is 5×20 μm with a vertical range of 20 μm and the total size of the system does not exceed 10×40 mm. The piezo‐sensitivity of the scanner tube versus applied voltage was analysed by interferometry measurements and by using scanning tunnelling microscopes. We found a value for the piezoelectric constant d13 of −1·71 Å/V at low voltages (under a few volts) going up to −2 Å/V for higher voltages. Large‐scale images of a carbon grid showed a surprisingly good linearity of the scanner tube.
Topography of YBa2Cu3O7‐δ single crystals, spectroscopy of thin films and sintered YBa2Cu3O7‐δ: theory and STM observations
Authors: van de Leemput L. E. C. , van Bentum P. J. M. , Driessen F. A. J. M. , Gerritsen J. W. , van Kempen H. , Schreurs L. W. M. , Bennema P.
Published: August 2011

We report topographic scanning tunnelling microscopy measurements on the (001) and (100) surfaces of YBa2Cu3O7‐δ single crystals, together with a theoretical basis by which the surface structures can be understood. We show that it is possible to obtain reproducible topographic data on a clean (001) and (100) surface in air. The results show various structures at scales from 0·1 to 100 nm. Among the observed features on the (001) surface were growth steps which had heights that were multiples of the lattice constant in the [001] direction. This indicates that the bulk crystal structure extends to the surface, and that the surface is relatively stable, even in humid air. We also found small (013) facets on the (001) surface, in accordance with theoretical pradictions. Occasionally, we found evidence for a one‐dimensional corrugation on the surface. This is possibly a direct consequence of the orthorhombic distortion in the a‐b plane with ordered oxygen vacancies, which gives rise to chain‐like Cu‐O structures along the b‐axis.

In addition, we measured the energy gap of sintered pellets and thin films of this superconductor, using a low‐temperature STM. We discuss some effects which may influence the measurements and present criteria to check for these effects. We found an energy gap of δ=14±2 eV, in good agreement with the BCS pradiction 2δ/kTc=3·5. This is not contradicted by the results we obtained by far infrared spectroscopy and Andreev reflection measurements.
A spectroscopic study of some high‐temperature superconductors using a low‐temperature STM
Authors: Gallagher M. C. , Adler J. G.
Published: August 2011

We used a scanning tunnelling microscope (STM) to measure both the tunnel current, I, and the dynamic conductance, dI/dV, at 4·2 K for a number of high‐transition temperature oxide superconductors. Large spatial variations in the tunnelling characteristics are observed. At low tunnel resistances, all samples show evidence of single electron tunnelling and incremental charging. Results on BiSrCaCu2Ox show the coexistence of charging with Josephson coupling between grains within the sample. Results on both the Bi sample and a single crystal of YBa2Cu3O6·5+x reveal possible energy gap (2A) values of 17 and 20 meV, respectively. A very sharp 5 meV gap, observed in ceramic samples of YBa2Cu3O6·5+x and Y0·5Al0·05Ba2Cu3O6·5+x, may indicate the presence of a lower temperature phase in these samples.
Characterization and local modification of atomically flat gold surfaces by STM
Authors: Emch R. , Nogami J. , Dovek M. M. , Lang C. A. , Quate C. F.
Published: August 2011

In order to characterize the surface of epitaxial gold on mica in air we have used a scanning tunnelling microscope (STM) to image and to modify this surface. It was possible to create controlled features by applying voltage pulses on the tip while scanning. The voltage threshold for writing (about 3 V, 100 ns pulses) was dependent of the tip condition. The lowest pulses were associated with sub‐50 Å feature size. We observed that at ambient temperature the written features disappeared in a time scale of half an hour for the smallest (<30 Å) to a few hours for the bigger features (∼500 Å). We have used the same surface as a substrate for organic imaging. We also present images of a polymer deposited on gold.
Scanning tunnelling microscopy on reconstructed Si(110)
Authors: Neddermeyer H. , Tosch St.
Published: August 2011

We have prepared clean surfaces of reconstructed Si(110), which showed a distinct 4×5 LEED pattern with particularly high intensity of the diffraction beams corresponding to a 2×1 periodicity of the surface. Images obtained by scanning tunnelling microscopy on the same surfaces are characterized by rows of reconstructed Si atoms along the direction. On high‐resolution images, atomic subunits in a 2×5 periodicity of ideal Si(110) have been identified. By using these subunits as building blocks for both the 4×5 and the 2×1 reconstruction, a previously reported phase transition between both reconstructions may be explained by a loss of order along the direction.
Supported metal model catalyst surfaces examined by scanning tunnelling microscopy
Authors: Komiyama Masaharu , Morita Seizo , Mikoshiba Nobuo
Published: August 2011

Topographic and/or barrier‐height images of ultrafine Pt and Au metal particles supported on a vacuum‐deposited carbon film or titanium oxide thin films grown on titanium metal sheets were obtained. The topographic images of colloidal Au particles (5‐nm diameter) adsorbed on a titanium oxide thin film showed a structure elongated in the direction normal to the x scan, indicating their weak interaction with the support surface. The topographic images of Pt vacuum‐deposited on a carbon film showed c. 4‐nm diameter particles, larger than those observed in electron microscopy. The problems inherent to the STM observation of such dispersed metal systems are identified. In the case of Pt particles vacuum‐deposited on titanium oxide film, its barrier‐height image gave better indication of different phases on the surface than its topographic image. The significance of obtaining barrier‐height images along with topographic images for such sample systems is demonstrated.
Adsorbate deformation as a contrast mechanism in STM images of biopolymers in an aqueous environment: images of the unstained, hydrated DNA double helix
Authors: Lindsay S. M. , Thundat T. , Nagahara L.
Published: August 2011

A stable residual aggregate remains on a submerged gold surface after electrophoretic deposition of DNA. We present scanning tunnelling microscope (STM) images of these aggregates which show many objects with the geometry of DNA, clearly displaying the 3·4 nm helix pitch. These images are quite distinctive, and cannot be generated when the deposition technique is used without DNA in the buffer solution. A characteristic of these images is that the tip is observed to dip down over the DNA molecule at the same time as the apparent barrier height drops by a factor of about four. The tip displacement is accounted for by a model in which contrast is dominated by local fluctuations in the deformability of the adsorbate layer, a quantity deduced from measurements of the apparent barrier heights in air, water, over small molecule adsorbates, and over DNA.
STM measurements on graphite using correlation averaging of the data
Authors: Soethout L. L. , Gerritsen J. W. , Groeneveld P. P. M. C. , Nelissen B. J. , van Kempen H.
Published: August 2011

Images of the (0001) surface of highly oriented pyrolytic graphite observed using scanning tunnelling microscopy, in both constant distance and current imaging modes, show a strong asymmetry of the unit cell. This asymmetry depends on the tunnelling current and voltage. We have also found clear evidence that multiple‐tip tunnelling occurs. To improve the resolution of the imaged unit cells, a method of correlation averaging is introduced.
Comparative study of lithium fluoride and graphite by atomic force microscopy (AFM)
Authors: Meyer E. , Heinzelmann H. , Grütter P. , Jung Th. , Weisskopf Th. , Hidber H.‐R. , Lapka R. , Rudin H. , Güntherodt H.‐J.
Published: August 2011

The atomic force microscope (AFM) offers the possibility to image the topography of insulating as well as conductive surfaces. Highly oriented pyrolytic graphite (HOPG) was chosen as an example for a layered material and compared to single crystalline lithium fluoride (LiF). Both materials are easily prepared and inert at ambient pressure. Furthermore they are well characterized by Helium atom scattering experiments and other techniques.

On HOPG atomic resolution has been achieved. Distortions can be observed which we interpret as a frictional effect. In addition we performed large area scans where we seldomly observed dislocations. For the first time we present measurements on LiF, showing steps of one unit cell height. On larger areas the surface of LiF showed terraces, separated by steps of variable heights, ranging from a few ångströms to 100 Å.

We used a static method to get information about the distance dependence of the force between lever and sample. By slowly expanding and retracting the sample piezo and simultaneous measurement of the lever deflection, plots were recorded, showing the force as a function of sample position. The results were compared with theoretical calculations. We could determine the tip radius and found differences between LiF and HOPG being characteristic for the samples.
Contact resistance and saturation effects in the scanning tunnelling microscope: the resistance quantum unit
Authors: Martín‐Rodero A. , Ferrer J. , Flores F.
Published: August 2011

We present a theoretical analysis of the contact resistance in the Scanning Tunnelling Microscope. Under the assumption of a single contact atom on the tip's apex, we find that the resistance saturates at close contact, its value being h/2e2. Our analysis of the recent experimental results of Gimzewski & Möller (1987), shows that the mechanical instability pradicted by Pethica & Sutton (1988), appears for a distance 1·5 Å larger than the close contact distance between the tip and the sample.
A role of a tip geometry on STM images
Authors: Hashizume T. , Kamiya I. , Hasegawa Y. , Sano N. , Sakurai T. , Pickering H. W.
Published: August 2011

Scanning tunnelling microscopes operable in both ultrahigh vacuum (UHV) and aqueous conditions are described with emphasis on a tip geometry. An atomically resolved STM image was obtained for the Si(111)‐Mo√3 surface in UHV condition and changes of a diffraction grating surface in aqueous condition due to an electrochemical reaction were monitored.
In situ fabrication and regeneration of microtips for scanning tunnelling microscopy
Authors: Binh Vu Thien
Published: August 2011

Progress in STM, in particular for the interpretation of the tunnel signals of corrugated surfaces, is related to the possibility of sharpening and regenerating in situ reproducible tips for use as the probe. We proposed two techniques for the production of tips with controlled geometry at the atomic level. These two techniques are based on the production of tips with equilibrium profiles obtained under heat treatments in vacuum and in the presence of an electric field. Based on the pseudo‐stationary profile principle, the microtips can be sharpened in situ and in a reproducible manner, either from initial cylindrical (111)‐W wire, or from breakdown tips; in both cases without the need for heavy control devices (like FIM for example).
Design and operation of a variable temperature scanning tunnelling microscope
Authors: Lyding J.W. , Skala S. , Hubacek J.S. , Brockenbrough R. , Gammie G.
Published: August 2011

A new variable temperature STM has been developed which utilizes two concentric piezoelectric tubes; an inner scanning tube, and an outer thermal compensation tube which also provides for inertial translation of the sample into tunnelling range. With this design, continuously variable temperature operation is demonstrated for the first time in an STM. Also, by eliminating all mechanical components such as springs, levers and gears, which normally couple directly to the tunnelling gap in other designs, atomic resolution operation is demonstrated in which no vibration isolation is necessary. During operation, the inside of the scanning tube is maintained at ground potential while the feedback signal is electronically summed to the scanning voltages applied to the outer quadrants. In addition to shielding the sensitive tunnelling circuit, this mode of operation enables one to electronically balance out mechanical imperfections of the scanning tube. To date, this new STM has been operated over the 77–400 K temperature range with the observed thermal drift as low as 1 Å/h and 10 Å/K. Another useful feature of this new design is the ability to reposition a sample to within 200 Å of the same location after it has been translated macroscopic distances (several mm) out of tunnelling range.
Finite element analysis of PZT tube scanner motion for scanning tunnelling microscopy
Authors: Carr R. G.
Published: August 2011

This article is a presentation of the results of a finite element method analysis of piezoelectric tube scanners of the type presently in wide use in scanning tunnelling microscopes. The tube scanner moves a tunnelling tip by bending sideways when unsymmetrical voltages are applied to longitudinal stripes of metallization on its walls. It also can be extended and contracted in length by application of symmetrical voltages. One wishes to know the characteristics and magnitudes of the resulting three‐dimensional motion. We divided a model tube into radially polarized elements, and constructed a computer program to perform electromechanical stress calculations. The results show the dependence of motion upon applied voltage, tube material, and tube dimensions.
Increasing the scanning speed of scanning tunnelling microscopes
Authors: Robinson R. S.
Published: August 2011

The scanning speed and quality of images obtained with a scanning tunnelling microscope can be increased by replacing the tunnelling tip holder with an active, high resonance frequency piezoelectric positioner. The combination tip holder and positioner has a resonance frequency near 100 kHz, allowing fast closed‐loop feedback control of the STM. With appropriate electronic shielding, the active tip holder can also be used to modulate the tip to surface distance at high frequencies for work function mapping.

The high speed positioner is complemented by a ‘tip‐saver’ circuit which senses imminent tip‐surface contact, preventing tip crashes. The circuit, when driving the fast positioner, has a response time of under 20 μs and is not subject to the oscillation problems normally associated with closed‐loop feedback systems operated at high gains and large signal bandwidths.
Scanning tunnelling microscopy and spectroscopy on Cu(111) and Au(111)
Authors: Brodde A. , Tosch St. , Neddermeyer H.
Published: August 2011

We have studied Cu(111) and Au(111) by means of scanning tunnelling microscopy and spectroscopy. The constant current topographies showed flat parts as well as regions with a high density of monoatomic steps (in particular on Au(111)). Local I/U characteristics have been determined at a fixed sample‐tip distance in the range of −10 V≤U≤10 V. They show a linear behaviour near the Fermi level and a nearly exponential dependency for larger values of U. Neither an influence of the sp‐like surface states or an onset due to d electron contributions of the sample could be observed.
Investigation of intrinsic crystalline Si(111) and amorphous silicon surfaces in air with STM
Authors: Okoniewski A. M. , Yelon A.
Published: August 2011

Crystalline (111) and amorphous silicon surfaces have been studied by scanning tunnelling microscopy. An orientated, reproducible, corrugated structure has been observed on Si(111) surfaces. The voltage dependence of the corrugation amplitude may be attributable to surface states. The surfaces of amorphous silicon thin films show some reproducible structure in the range of a few tens of ångströms, observable only when the applied voltage between the tip and sample is between −1·3 and +0·4V.
Clean and metal‐contaminated Si(110) surfaces studied by RHEED, XPS and STM
Authors: van Loenen E. J. , Dijkkamp D. , Hoeven A. J.
Published: August 2011

We have studied the atomic structure of clean and metal‐contaminated Si(110) surfaces in real space with Scanning Tunnelling Microscopy (STM) and compared the results with Reflection High Energy Electron Diffraction (RHEED) data taken on samples from the same wafer.

On clean Si(110) surfaces flat

reconstructed regions coexist with (15 17 1), (15 173) and related facets. The

surface consists of periodically‐alternating high and low terraces, with a height difference corresponding to the interlayer spacing (0·19 nm). This structure is found in two domains, with terrace edges aligned along the and directions respectively. Atomic scale zig‐zag chains can be recognized on the terraces.

Contamination of the surface with Ni or Cu results in the formation of reconstructions with drastically different unit cells, all orientated along [001] and . The transition proceeds via a disordered 5×1‐like intermediate phase for Ni coverages around 0·007 ML.
Scanning tunnelling microscopy of oxidized graphite
Authors: Porte L. , Richard D. , Gallezot P.
Published: August 2011

Scanning tunnelling microscopy (STM) and transmission electron microscopy (TEM) have been used to investigate the surface of a pyrolitic graphite oxidized in liquid phase by NaClO. Two main features of the oxidized HOPG are revealed by STM. First, a large number of steps of different heights have developed on the graphite surface. These steps can be observed by TEM on another kind of graphite, HSAG 12, but this technique cannot give any information on their heights. Another kind of defect on the previously flat surface of HOPG consists in patches where the surface is rough and perturbed. These domains are very difficult to observe by TEM due to a poor contrast. Thus for the study of surface heterogeneities intentionally created on graphite, STM, providing information along three directions, appears to be complementary of TEM which gives only images of project area.
Investigation of Bloch wall fine structures by magnetic force microscopy
Authors: Göddenhenrich T. , Hartmann U. , Anders M. , Heiden C.
Published: August 2011

Using a magnetic force microscope (MFM), measurements have been performed on single crystal iron whiskers. These samples exhibit a comparatively simple magnetic domain structure and a high degree of crystallographic perfection. STM measurements yield an average surface corrugation of about 3 nm. These nearly ideal boundary conditions permit an investigation of the undistorted surface configuration of Bloch walls in a cubic bulk crystal. Interactions between the stray field configuration of the sample and a ferromagnetic microscope tip have been measured with a new MFM device which is based on direct compliance detection. Measurements have been performed in the constant‐current mode, as well as in the constant‐compliance, mode. Control observation by means of the Kerr magneto‐optic effect permit an interpretation of the obtained MFM data in terms of isolated 180° Bloch walls. The fine structure of these walls has been analysed and compared with results obtained from model calculations.
Real‐time scanning tunnelling microscopy of surfaces under active electrochemical control
Authors: Robinson R. S.
Published: August 2011

A scanning tunnelling microscope has been designed which allows tunnelling microscopy to be performed in the presence of an externally applied electrochemical current. Separate, isolated electrodes were used for electrochemical control, and up to 1 mA was passed during real‐time, video‐rate, in situ STM observation of the surfaces, without interfering with the operation of the STM.

The noise level of these STM images is only slightly higher than images taken with the electrochemical circuitry disconnected. Surfaces were observed during the formation of surface films in aqueous electrolytes.
Real space imaging of co‐adsorbed CO and benzene molecules on Rh(111)
Authors: Chiangs S. , Wilson R. J. , Mate C. M. , Ohtani H.
Published: August 2011

Scanning tunnelling microscope (STM) images of the c(2√3×4)rect layer of benzene and carbon monoxide co‐adsorbed on the Rh(111) surface are shown. For the first time, individual CO molecules have been resolved, as well as ring‐like benzene structures.
Polymers on graphite and gold: molecular images and substrate defects
Authors: Rabe J. P. , Sano M. , Batchelder D. , Kalatchev A. A.
Published: August 2011

Sub‐monomolecular layers of a derivatized Phthalocyaninato‐poly‐siloxane (PCPS) and a Polydiacetylene (PDA) have been prepared on highly orientated pyrolytic graphite and gold by Langmuir‐Blodgett and Langmuir‐Schäfer techniques. Raman scattering and grazing‐incidence‐reflection infrared spectroscopy were used to characterize packing and molecular orientations within these films. It was found that PCPS forms similarly well ordered monolayers on both graphite and gold while PDA does not. Scanning tunnelling microscopy (STM) was performed in air using both the constant height and constant current mode. On highly orientated pyrolytic graphite substrates various defect structures based on a √3X√3 R 30° superstructure were found near localized defects and small graphite steps. They were carefully distinguished from molecular images of densely packed hydrocarbon chains. Defect rich graphite was characterized with both STM and Raman spectroscopy. Similarly, disordered and graphite‐like regions were found on carbon fibres. The sensitivity of STM to surface defects in graphitic material turned out to be large compared to that of the Raman spectroscopic method. STM images of PCPS monolayers on graphite and gold exhibited parallel polymer rods, 2 nm apart from each other.
New developments in fast image processing and data acquisition for STM
Authors: Béjar M. A. , Gómez‐Rodríguez J. M. , Gómez‐Herrero J. , Baró A.
Published: August 2011

We have developed new easy‐to‐use but powerful software in order to obtain the best scan rates in data acquisition and image processing for a PC‐AT microcomputer.

The programs have been completely written in the C‐language, which made it possible to combine low‐level characteristics (quick access to memory, interrupt control, etc.) without losing the advantages of a high‐level language.

The data acquisition software was intended to be sufficiently flexible to acquire either topographical or spectroscopic data with no configuration changes. In topographical (z=f(x,y)) and spectroscopic (I=f(V, z)) measurements, we can obtain up to 15,000 samples/s rates, with 12‐bit resolution in a ±10V range. Spectroscopic measurements are done by acquiring I(V) with the feedback off at several z values (up to 256) until I reaches a preset value; afterwards, z is reset automatically to the initial voltage to avoid tip‐sample contact.

The image processing was designed to get the best performances in time and quality with a simple system such as a PC‐AT equipped with an IBM Professional Graphics Display (640times480 pixels and 256 simultaneous colours).

It was structured in three parts: plane subtraction, image display (3‐D shaded surfaces, 3‐D surfaces with colour scales or 2‐D contour maps), and filtering (smoothing filters or FFT convolution‐deconvolution techniques).
Preparation of STM tips for in‐situ characterization of electrode surfaces
Authors: Heben Michael J. , Dovek Moris M. , Lewis Nathan S. , Penner Reginald M. , Quate Calvin F.
Published: August 2011

The total current between the tip and the sample in a scanning tunnelling microscopy study of a solid/liquid interface can be dominated by Faradaic charge transfer currents. In such a situation, feedback control of the tunnelling gap, and imaging, is precluded. In this contribution we describe the preparation of glass and polymer coated STM tips that possess < 100 Å2 of exposed metal. These tips effectively discriminate against Faradaic current and enable STM imaging in the presence of reversible electroactive solution species at appreciable tip/sample biases.
Battery‐operated STM
Authors: Valdés J. , Kohanoff J.J. , Lobbe E.E. , Bancalari R. López , Porfiri M.E. , Cantú R. García
Published: August 2011

A scanning tunnelling microscope operating with ±12 V is described. A scanning range higher than 1 μm is achieved in the three orthogonal scanning directions for that low voltage. This translator arrangement, based on the use of piezoelectric discs mounted on metallic circular plates acting like flat springs, may provide a better performance than the tube scanners or rectangular bimorphs since it allows a greater volume to be run by the tip for a given voltage.
An STM for biological applications: Bioscope
Authors: Michel B. , Travaglini G.
Published: August 2011

We present an STM with an improved coarse positioning system and a large scan area which is especially suitable for biological applications. Three stepper motors are used to move an X‐Y‐Z table. Movements of motor axes are geared down to drive micrometer spindles so that steps of 250 nm can be performed. The stepper motors can be uncoupled from the STM for scanning operation. A piezo tube is used to scan areas of up to 10times10μm with low voltage operation. Probes can be scanned in air or in electrochemical cells. High stability against thermal drift and vibrations is achieved by a rigid and symmetrical design.
Mono‐ and multiatomic steps with constant periodicity as observed by STM in vicinal Au(111) surfaces
Authors: Ocal C. , de Parga A.L. Vazquez , Alvarez J. , Ferrer S.
Published: August 2011

Scanning tunnelling microscopy images of a vicinal Au(111) surface obtained in UHV are presented. Arrays of mono‐ and multiatomic steps along the [011] direction are seen with a peculiarly constant periodicity. The steps, exposing (100) facets, have a height ranging from one to seven atoms while the terrace width of eight atoms remains constant.
A real space investigation of the dimer defect structure of Si(001)‐(2times8)
Authors: Niehus H. , Köhler U. K. , Copel M. , Demuth J. E.
Published: August 2011

The atomic arrangement of the Si(001)‐(2 times 8) surface has been directly imaged in real space by scanning tunnelling microscopy. The superstructure is impurity induced and stablilized by as little as 1% Ni. Clean Si(001) surfaces do not form the (2times8) phase. The two‐dimensional Fourier transforms of the STM topographs correspond well to the (2times8) LEED pattern, but the real space images are in fact considerably more complex than previously concluded on the basis of recent diffraction technique measurements. The STM images clearly demonstrate that the (2times8) surface consists of a complex missing dimer structure, namely one and multiple dimer vacancies. Such a dimer defect appears related to the Ni impurity and intimately related to the ordering of the dimer defects probably by third layer dimerization to produce quasi‐ordered ‘channels’.
Imaging of hydrogen‐induced Si(111) surface with the scanning tunnelling microscope
Authors: Tokumoto Hiroshi , Miki Kazushi , Murakami Hiroshi , Morita Naotake , Bando Hiroshi , Sakai Akira , Wakiyama Shigeru , Ono Masatoshi , Kajimura Koji
Published: August 2011

We have directly observed the hydrogen‐induced changes of the Si(111)7times7 surface using a scanning tunnelling microscope (STM). The 7times7 reconstructed atomic structure was formed on a clean surface of Si(111). But when the clean surface was dosed with typically 1–2 L [1 L (Langmuir) = 1·33 times 10−4 Pa. sec] hydrogen, the 7 times 7 image was gradually smeared out and then a 1 times 1 unreconstructed pattern appeared. After dosing with 5–10 L hydrogen, the STM image exhibited a new long‐periodic structure together with the 1times1 structure underneath. These experimental results may be ascribed to the chemisorption of hydrogen atoms on clean Si surfaces.
Scanning tunnelling microscopy of B/Si(111) √3×√3 R(30°)
Authors: Dumas Ph. , Thibaudau F. , Salvan F.
Published: August 2011

The √3 superstructure induced by boron outdiffusion at the surface of highly p doped Si(111) samples is studied by means of Auger, LEED and STM. Simultaneous double imaging at different voltages allows us to probe both filled and empty electronic states. A modification of the T4 structural model of (Al, In, Ga)/Si(111) √3 is proposed for the B/Si(111) √3 superstructure.
Scanning tunnelling microscopy of charge density waves in 1T‐TaS2
Authors: Thomson R.E. , Walter U. , Ganz E. , Rauch P. , Zettl A. , Clarke J.
Published: August 2011

Using a variable temperature scanning tunnelling microscope we have observed both the lattice and the triple charge density wave (CDW) in 1T‐TaS2. We obtained images of the nearly‐commensurate (NC) phase between 350 and 200 K and the triclinic (T) phase between 220 and 280 K. We analysed the images to determine the local angle of rotation of the CDW relative to the lattice to determine if commensurate domains exist in this material. In the NC phase we do not see the hexagonal discommensurate domains proposed by Nakanishi el al. (1977), but observe a structure which is uniformly incommensurate. The orientation of the CDW relative to the lattice is observed to be locally incommensurate and to vary continuously with temperature as reported by Scruby et al. (1975). However, in the T phase we observe long narrow commensurate domains very similar to those described by Nakanishi and Shiba (1984) for this phase.
Scanning probe microscopy of biological samples and other surfaces
Authors: MARTI O. , Elings V. , Haugan M. , Bracker C. E. , Schneir J. , Drake B. , Gould S. A. C. , Gurley J. , Hellemans L. , Shaw K. , Weisenhorn A. L. , Zasadzinski J. , Hansma P. K.
Published: August 2011

Scanning probe microscopes derived from the scanning tunnelling microscope (STM) offer new ways to examine surfaces of biological samples and technologically important materials. The surfaces of conductive and semiconductive samples can readily be imaged with the STM. Unfortunately, most surfaces are not conductive. Three alternative approaches were used in our laboratory to image such surfaces.

1. Crystals of an amino acid were imaged with the atomic force microscope (AFM) to molecular resolution with a force of order 10−8 N. However, it appears that for most biological systems to be imaged, the atomic force microscope should be able to operate at forces at least one and perhaps several orders of magnitude smaller. The substitution of optical detection of the cantilever bending for the measurement by electron tunnelling improved the reliability of the instrument considerably.

2. Conductive replicas of non‐conductive surfaces enabled the imaging of biological surfaces with an STM with a lateral resolution comparable to that of the transmission electron microscope. Unlike the transmission electron microscope, the STM also measures the heights of the features.

3. The scanning ion conductance microscope scans a micropipette with an opening diameter of 0·04‐0·1 μm at constant ionic conductance over a surface covered with a conducting solution (e.g., the surface of plant leaves in saline solution).
In‐situ STM studies of electrochemical underpotential deposition of Pb on Au(111)
Authors: Green M. P. , Richter M. , Xing X. , Scherson D. , Hanson K. J. , Ross P. N. , Carr R. , Lindau I.
Published: August 2011

A modified scanning tunnelling microscope (STM) has been used to observe in‐situ deposition and stripping of an electrochemical film. With STM tip and sample immersed in an acid electrolyte, single atomic steps on Au(111) have been imaged during the deposition and stripping of a monolayer‐thick, underpotential deposit (UPD) of Pb. Integration of the electrochemical current passed during the film deposition and evidence from the STM images themselves confirm monolayer coverage. Our images show enhanced film growth at step edges and defect sites. Observations of single plating and stripping cycles indicate that the Au substrate returns unaltered. Except for atomic resolution images of Au(111), which we have not yet achieved in an electrolyte, all types of Au surface features seen in air are reproduced under the electrolytic solution. The modifications made to our STM in order to perform in‐situ electrochemical experiments are described.
Spatially resolved low‐temperature spectroscopy on niobium bulk samples
Authors: Berthe R. , Hartmann U. , Heiden C.
Published: August 2011

Using a low‐temperature STM, simultaneous measurements of the surface topography and of spatial variations in the current‐voltage characteristics have been performed on poly‐crystalline niobium bulk samples. A special electronic set‐up was developed which allows the tip bias to be swept at a constant tip position. From the resulting I(V) curves the actual magnitude of the superconducting energy gap is derived. The comparison of the surface morphology and gap distribution permits the detection of possible correlations between local variations in the superconductivity and in the topography. Upon the application of an external magnetic field, local variations of the gap are observed which have no topographic counterparts. This latter observation might indicate the existence of isolated vortices.
Fine structure in field emission resonances at surfaces
Authors: Coombs J. H. , Gimzewski J. K.
Published: August 2011

We have measured field‐emission resonances (FER) to much higher quantum states than previously observed enabling fine structure in the resonance amplitudes to be investigated. We show that this electron wave interference effect carries additional information in the resonance amplitudes and energies and is sensitive to lateral tip position in a scanning tunnelling microscope experiment. We propose a new method of data analysis that can distinguish between some of the possible origins of the fine structure.
High‐resolution force microscopy of in‐plane magnetization
Authors: Abraham David W. , Williams C. C. , Wickramasinghe H. K.
Published: August 2011

We have shown for the first time, in previous studies, that the force microscope fitted with a magnetic tip could be used to image magnetic domains in TbFe thin films. In this report we show that the information provided by the magnetic force microscope can also include a measurement of the component of magnetization in the sample which is parallel to the surface. Measurements were taken with a magnetized tip tilted at 45° with respect to the surface normal. In a first experiment, we imaged 1 μm diameter domains thermomagnetically written in a TbFe thin film. In a second measurement, we imaged a series of alternating domains in a thin film Co‐alloy disc which was decorated with small magnetized particles, allowing unambiguous identification of the domain boundaries. In both cases we interpret the asymmetric portion of the images to the in‐plane component of the sample magnetization.
Quasi‐crystals and their crystalline homologues in the Al60Mn11Ni4 ternary alloy
Authors: Van Tendeloo G. , Van Landuyt J. , Amelinckx S. , Ranganathan S.
Published: August 2011

The transition quasi‐crystalline→crystalline is found to be very sluggish in the ternary alloy Al60Mn11Ni4. This makes it possible to study in detail the relationship between the decagonal phase, obtained after furnace cooling, and two different crystalline phases, which result after long annealing at 400°C.

Use is made of electron diffraction, high resolution electron microscopy and optical diffraction.

The crystalline phases still exhibit features which are closely related to those of the decagonal phase. This can be concluded from a comparison of the electron diffraction patterns of the quasi‐crystalline phase along a number of zones, with those of the crystalline phases along corresponding zones.

The crystalline phases contain different types of defects which are analysed in detail using high resolution images and diffuse scattering in the electron diffraction patterns.

The close relationship between the electron diffraction patterns of the crystalline and quasi‐crystalline phases is explained in terms of general optical principles.

Some characteristic features of a model of the quasi‐crystalline phase are tentatively proposed.
A model for logarithmic image processing
Authors: Jourlin Michel , Pinoli Jean‐Charles
Published: August 2011

Up to now, image processing and image analysis techniques have borrowed their basic tools from functional analysis: Fourier filtering, differential and integral calculus, and so on. These tools, however, only realize their efficiency when they are put into a well‐defined algebraic frame, most of the time of a vectorial nature. Unfortunately, the class of functions modelling ‘images’, commonly referred to as ‘grey tone functions’ does not necessarily present this very type of structure. We present here an operation for the ‘addition’ of two images, with a physical justification in the context of transmitted light. Such an addition permits the construction of the family of ‘positive homothetics' of the grey tone function at hand. The vectorial context sought is well defined: The class of images associated with the class of their grey tone functions naturally becomes the positive cone of an ordered real vector space.

Furthermore, the proposed model holds for logarithmic imaging and is compatible with what is known about the human visual process. This model has been called ‘LIP’ (logarithmic image processing model).
Three‐dimensional imaging in confocal imaging systems with finite sized detectors
Authors: Wilson T. , Carlini A. R.
Published: August 2011

We consider the effect of the finite size of the detector on both the lateral and axial resolution of the confocal system. The use of a finite sized detector means that the imaging is no longer truly coherent. We find that the lateral resolution is considerably more sensitive to the detector size than is the axial response. The question of the rejection of flare light is also considered. Experimental results are shown and we find that acceptable extended‐focus, auto‐focus and height images may be obtained from non truly‐confocal systems. We also find that lens apodization has a far greater effect on the axial resolution than the lateral resolution.
Soft X‐ray contact imaging of nucleolar chromatin using synchrotron radiation: a comparative scanning and transmission electron microscope study
Authors: Hill K. S. , Myring W. J. , Clarke D. T. , Veltkamp C. J.
Published: August 2011

Contact images (CI) of dehydrated, nucleolar chromatin from amphibian oocytes have been produced by soft X‐rays from a synchrotron radiation source. These CI have been compared with the morphology of the original chromatin as seen in scanning and transmission electron microscopes. The quality and informational content of the CI depend very much on certain preparative procedures. The following factors have a marked effect on image quality and need to be carefully controlled: the total X‐ray dose, the time and nature of development and the distance of the specimen from the photoresist. The preparation of the chromatin itself, providing that it is critically point dried, is less important. By following a regime of high X‐ray dose, sufficient for penetration of the rather thick chromatin rings, and gentle development so that fine detail is not dissolved from the resist surface, it has been possible to obtain images which closely resemble the original chromatin, although the detailed resolution of the CI is not as clear. The smallest biological structures clearly resolved in the CI are ribonucleoprotein granules, which vary in size from 200 to 800 nm. However, by further refinement of preparative conditions it should be possible to improve on the informational content of these images.
Stereological analysis of three‐dimensional structure organization of surfaces in multiphase specimens: statistical methods and model‐inferences
Authors: Kroustrup J. P. , Gundersen H. J. G. , Væth M.
Published: August 2011

In a multiphase material the structural components or phases are everywhere in contact with each other. The relative area of surface contact between various phases is an important aspect of the short‐range ordering or organization of the structure. The stereological quantitation of such specific interfaces is a simple and well‐known technique. The proper statistical definition of realistic models for the frequency of contact and the quantitative estimation of phase‐specific affinities is studied. The meaningful interpretation of sets of estimated affinities poses a major problem of statistical inference which is dealt with in detail and illustrated by a worked‐out biological example.
A comparison of soft X‐ray contact microscopy with light and electron microscopy for the study of algal cell ultrastructure
Authors: Stead A. D. , Ford T. W. , Myring W. J. , Clarke D. T.
Published: August 2011

Images of filamentous and unicellular algae have been obtained by soft X‐ray (wavelength 2.05‐4.4 nm) contact microscopy (SXCM), using synchrotron radiation, and the images obtained compared to those obtained by scanning and transmission electron microscopy. After chemical development to leave areas corresponding to high X‐ray absorbance by the specimen the photoresists were examined by SEM. In two algae (Anabaena and Trebouxia) cytoplasmic detail, including photosynthetic lamellae, chloroplasts, nuclei and mitochondria, were identified. In a third alga (Cyanidium) the SXCM image revealed little internal detail due to the uniformly high X‐ray absorption by the cells. The successful imaging of whole cells by SXCM is discussed in relation to conventional TEM and the future possibilities for SXCM are outlined.
Energy‐dispersive X‐ray microanalysis of air‐dried microdroplets containing a macromolecular solute
Authors: Bostrom T. E. , Gyory A. Z. , Benson D. C. , Horgan E. , Nockolds C. E. , Beck F. X. , Cockayne D. J. H.
Published: August 2011

In the preparation of microdroplets of biological fluids for X‐ray microanalysis, we have found that incorporation of a macromolecular solute, dextran, to a final concentration of 1.5‐2.5% retards crystal formation and produces sufficiently uniform deposits on thin films to allow droplets to be analysed without prior freeze‐drying. Analyses have been carried out at 20 kV in a scanning electron microscope, using energy‐dispersive spectrometry. Absorption of Na X‐rays by the added solute can be significant but its effect is minimized by preparing droplets as thin as possible, and by using standards of similar composition. The minimum detectable concentrations are increased because of the extra background contribution, and for a single determination are about 6 mM for Na and 2 mM for Cl and K. These concentrations can be further reduced by measuring replicates.

The reproducibility of analysis is significantly improved (to less than 5% for Na and K) over the use of calibration curves by calculating the element concentrations from a known element in the sample, chlorine. Under our analytical conditions loss of Cl did not occur. This method requires that the Cl is measured separately by microcoulometry, but eliminates the need for a range of standard droplets on the grid, and determination of the unknowns is then independent of droplet volume, beam current, counting time and magnification.

We have compared, with biological samples, the results from using Cl as an internal standard with those obtained using an added standard element, cobalt. The reproducibility using Cl was approximately two‐times better than that obtained with Co, probably because of unavoidable volumetric errors when the Co is pipetted separately.
Geometric correction of digital images using orthonormal decomposition
Authors: Jeričevic ŽEljko , Benson Douglas M. , Bryan Joseph , Smith Louis C.
Published: August 2011

We have developed an algorithm which can be used to correct the geometric distortion of digital images. The method uses an orthonormal decomposition and a two‐dimensional Horner's scheme to construct and evaluate a polynomial equation of arbitrary degree in two independent variables. This numerical scheme for geometric correction combines several methods selected on the basis of their computation efficiency and numerical stability. The differences and advantages of this numerical scheme are compared with methods found in the image processing literature. The algorithm presented here has a reduced number of mathematical operations, is flexible and numerically stable. Based on the least‐squares criteria, the algorithm provides corrected pixel positions with an accuracy equal to or better than the pixel size.
Streak time‐lapse video microscopy: analysis of protoplasmic motility and cell division in Tradescantia stamen hair cells
Authors: Mineyuki Yoshinobu , Gunning Brian E. S.
Published: August 2011

We have developed a video time‐lapse analogue of a streak camera using a digital image processing technique, and have used it to analyse dynamic processes in plant cells. The same image area is selected from a succession of frames in a video tape recording. The successive images are stored in an image memory, rearranged, and displayed in a single frame according to the time course. Each image area is rectangular, with selectable length and width: the closest analogy to a streak camera is obtained when one of its sides is a single pixel. The composite image displays sequential changes in the distribution of subcellular components in the selected area. The method was shown to be useful for monitoring details of cytoplasmic streaming and organelle movement, observing the time course of chemical fixation, and also for studying kinetochore movement, shortening of chromatids and cell plate formation during mitosis and cytokinesis. Cessation and resumption of cytoplasmic movement during the cell division cycle were also clearly localized outside the nuclear region in apical cells of Tradescantia stamen hairs.
Direct measurement of the osmotic effects of buffers and fixatives in Nitella flexilis
Authors: Taylor Douglas P.
Published: August 2011

The pressure probe has been used to investigate the amount and time course of changes in turgor induced by agents used in fixation of biological material for electron microscopy. All buffers tested decreased the turgor pressure of internodal cells of the green alga Nitella flexilis in proportion to their osmotic concentration. With the exception of s‐collidine, the buffers were impermeant, as shown by the stability of the reduced turgor. The fixatives formaldehyde and glutaraldehyde caused a rapid reduction in turgor followed by recovery of turgor as the aldehyde penetrated the cell. Plasmolysis of cells can be avoided by a procedure involving stepwise increase of fixative concentration.
Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli
Authors: Frank Joachim , Bretaudiere Jean‐Pierre , Carazo Jose‐Maria , Verschoor Adriana , Wagenknecht Terence
Published: August 2011

Images of macromolecules obtained in the electron microscope are subjected to correspondence analysis. The structure inherent in the data in the resulting low‐dimensional factor space is characterized by a mixed classification method which combines the dynamic clouds clustering technique with hierarchical ascendant classification (HAC). For our data, the rejection of marginal clusters obtained by dynamic clouds clustering appears as a crucial prerequisite for a stable performance of HAC.

The method is applied to two sets of 204 and 177 images that show the 70S ribosome of Escherichia coli, in the range of overlap views as defined by A. Verschoor and co‐workers, and to two sets of 480 and 496 images of the 50S subunit of E. coli depleted of L7/L12 proteins in the well‐defined crown view. Reproducible classes are obtained, which are characterized by images reconstituted from factorial coordinates. These classes appear to be related to different orientations on the specimen grid (in the case of the 70S particle) and to different conformational states (50S subunit).