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.

TRANSIENT SCANNING ELECTRON BEAM ANNEALING METHODS USED TO STUDY DIFFUSION AND DEFECTS IN IMPLANTED SILICON.

Rapid thermal annealing of arsenic and boron difluoride implants, such as those used for source/drain regions in CMOS, has been carried out using a scanning electron beam annealer, as part of a study of transient diffusion effects. Three types of e-beam anneal have been performed, with peak temperatures in the range 900 -1200 degree C; the normal isothermal e-beam anneals, together with sub-second fast anneals and 'dual-pulse' anneals, in which the sample undergoes an isothermal pre-anneal followed by rapid heating to the required anneal temperature is less than 0. 5s. The diffusion occuring during these anneal cycles has been modelled using SPS-1D, an implant and diffusion modelling program developed by one of the authors. This has been modified to incorporate simulated temperature vs. time cycles for the anneals. Results are presented applying the usual equilibrium clustering model, a transient point-defect enhancement to the diffusivity proposed recently by Fair and a new dynamic clustering model for arsenic. Good agreement with SIMS measurements is obtained using the dynamic clustering model, without recourse to a transient defect model.

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.

The application of STEM and in situ controlled dehydration to bacterial systems using ESEM.

Transmission imaging with an environmental scanning electron microscope (ESEM) (Wet STEM) is a recent development in the field of electron microscopy, combining the simple preparation inherent to ESEM work with an alternate form of contrast available through a STEM detector. Because the technique is relatively new, there is little information available on how best to apply this technique and which samples it is best suited for. This work is a description of the sample preparation and microscopy employed by the authors for imaging bacteria with Wet STEM (scanning transmission electron microscopy). Three different bacterial samples will be presented in this study: first, used as a model system, is Escherichia coli for which the contrast mechanisms of STEM are demonstrated along with the visual effects of a dehydration-induced collapse. This collapse, although clearly in some sense artifactual, is thought to lead to structurally meaningful morphological information. Second, Wet STEM is applied to two distinct bacterial systems to demonstrate the novel types of information accessible by this approach: the plastic-producing Cupriavidus necator along with wild-type and ΔmreC knockout mutants of Salmonella enterica serovar Typhimurium. Cupriavidus necator is shown to exhibit clear internal differences between bacteria with and without plastic granules, while the ΔmreC mutant of S. Typhimurium has an internal morphology distinct from that of the wild type.

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.

The application of STEM and in situ controlled dehydration to bacterial systems using ESEM

Transmission imaging with an environmental scanning electron microscope (ESEM) (Wet STEM) is a recent development in the field of electron microscopy, combining the simple preparation inherent to ESEM work with an alternate form of contrast available through a STEM detector. Because the technique is relatively new, there is little information available on how best to apply this technique and which samples it is best suited for. This work is a description of the sample preparation and microscopy employed by the authors for imaging bacteria with Wet STEM (scanning transmission electron microscopy). Three different bacterial samples will be presented in this study: first, used as a model system, is Escherichia coli for which the contrast mechanisms of STEM are demonstrated along with the visual effects of a dehydration-induced collapse. This collapse, although clearly in some sense artifactual, is thought to lead to structurally meaningful morphological information. Second, Wet STEM is applied to two distinct bacterial systems to demonstrate the novel types of information accessible by this approach: the plastic-producing Cupriavidus necator along with wild-type and δmreC knockout mutants of Salmonella enterica serovar Typhimurium. Cupriavidus necator is shown to exhibit clear internal differences between bacteria with and without plastic granules, while the δmreC mutant of S. Typhimurium has an internal morphology distinct from that of the wild type. © 2012 Wiley Periodicals, Inc.

Polishing Treatment of Molasses Wastewater with Iron Salts: the Role of Counter-ions

The effect of counter-ions on the coagulation of biologically treated molasses wastewater using iron-based coagulants was investigated. Parameters such as removals of chemical oxygen demand (COD) and color, and residual turbidity, were measured to evaluate coagulation performance. Experimental results showed that ferric chloride and ferric nitrate were more effective than ferric sulfate at optimal dosages, achieving 89 to 90% and 98 to 99% of COD and color removals, respectively, with residual turbidity of less than 5 NTU. High-performance size exclusion chromatography (HPSEC) results revealed differences in the removal of the molecular weight fraction of organic compounds using iron salts. Scanning electron microscopy (SEM) showed randomly formed coagulated flocs characterized with irregular, sheet-like shapes. Nitrate and chloride counter-ions had similar effects on coagulation performance compared to sulfate. Both FeCl3 and Fe(NO3)(3) yielded better results than Fe(SO4)(2) under underdosed and optimum dosage conditions. Coagulation efficiency was less adversely affected in the overdosed regions, however, if sulfate rather than chloride or nitrate was present. Water Environ. Res., 81, 2293 (2009).

Light and scanning electron microscopic study of Balantidium ctenopharyngodoni Chen, 1955 (Class : Litostomatea) from China

Redescription of Balantidium ctenopharyngodoni "Chen (Acta Hydrobiol Sin 1:123-164, 1955)", collected from the hindgut of grass carp (Ctenopharyngodon idella), especially the segment of 6-10 cm upstream from the anus, from Honghu Lake, Hubei Province, central China in November 2005, is presented in this paper to complete Chen's description at both light and scanning electron microscopic levels. Some revisions were done: the vestibulum is fairly symmetrical, with compactly arranged cilia rather than assembled membrane bordering on the left vestibular side; four contractile vacuoles actually exist in the latter body, three of which surround the posterior portion of the macronucleus, whereas the fourth lies antero-left to it. Somatic monokinetids were compared among the species of genus Balantidium. The cysts were described, and possible infection routes of B. ctenopharyngodoni were also discussed.

Quantitative strain characterization of SiGe heterostructures by high-resolution transmission electron microscopy

We report the quantitative strain characterization in semiconductor heterostructures of silicon-germaniums (Si(0.76)Geo(0.24)) grown on Si substrate by an ultra-high vacuum chemical vapor deposition system. The relaxed SiGe virtual substrate has been achieved by thermal annealing of the SiGe film with an inserted Ge layer. Strain analysis was performed using a combination of high-resolution transmission electron microscopy and geometric phase analysis.

Nucleation of diamond by pure carbon ion bombardment - a transmission electron microscopy study

A cross-sectional high-resolution transmission electron microscopy (HRTEM) study of a film deposited by a 1 keV mass-selected carbon ion beam onto silicon held at 800 degrees C is presented. Initially, a graphitic film with its basal planes perpendicular to the substrate is evolving. The precipitation of nanodiamond crystallites in upper layers is confirmed by HRTEM, selected area electron diffraction, and electron energy loss spectroscopy. The nucleation of diamond on graphitic edges as predicted by Lambrecht [W. R. L. Lambrecht, C. H. Lee, B. Segall, J. C. Angus, Z. Li, and M. Sunkara, Nature, 364 607 (1993)] is experimentally confirmed. The results are discussed in terms of our recent subplantation-based diamond nucleation model. (c) 2005 American Institute of Physics.

Atomic configurations of dislocation core and twin boundaries in 3C-SiC studied by high-resolution electron microscopy

The defects in 3C-SiC film grown on (001) plane of Si substrate were studied using a 200 kV high-resolution electron microscope with point resolution of 0.2 nm. A posterior image processing technique, the image deconvolution, was utilized in combination with the image contrast analysis to distinguish atoms of Si from C distant from each other by 0.109 nm in the [110] projected image. The principle of the image processing technique utilized and the related image contrast theory is briefly presented. The procedures of transforming an experimental image that does not reflect the crystal structure intuitively into the structure map and of identifying Si and C atoms from the map are described. The atomic configurations for a 30 degrees partial dislocation and a microtwin have been derived at atomic level. It has been determined that the 30 degrees partial dislocation terminates in C atom and the segment of microtwin is sandwiched between two 180 degrees rotation twins. The corresponding stacking sequences are derived and atomic models are constructed according to the restored structure maps for both the 30 degrees partial dislocation and microtwin. Images were simulated based on the two models to affirm the above-mentioned results.

Near-field scanning optical microscopy with an active probe

A near-field scanning optical microscopy (NSOM) system employing a very-small-aperture laser (VSAL) as an active probe is reported in this Letter. The VSAL in our experiment has an aperture size of 300 nmx300 nm and a near-field spot size of about 600 nm. The resolution of the NSOM system with the VSAL can reach about 600 nm, and even 400 nm. Considering the high output power of the VSAL, such a NSOM system is a potentially useful tool for nanodetection, data storage, nanolithography, and nanobiology.

Scanning electron microscope studies of cubic AlxGa1-xN films grown on GaAs(100) by metal organic vapor phase epitaxy (MOVPE)

Cubic AlGaN films were grown on GaAs(100) substrates by MOVPE. Scanning electron microscope and photoluminescence were used to analyze the surface morphology and the crystalline quality of the epitaxial layers. We found that both NH, and TEGa fluxes have a strong effect on the surface morphology of AlGaN films. A model for the lateral growth mechanism is presented to qualitatively explain this effect. The content of hexagonal AlGaN in the cubic AlGaN films was also related to the NH3 flux. (C) 1999 Elsevier Science B.V. All rights reserved.