Nanometer-scale oxidation of Si(100) surfaces by tapping mode atomic force microscopy

The nanometer¿scale oxidation of Si(100) surfaces in air is performed with an atomic force microscope working in tapping mode. Applying a positive voltage to the sample with respect to the tip, two kinds of modifications are induced on the sample: grown silicon oxide mounds less than 5 nm high and mounds higher than 10 nm (which are assumed to be gold depositions). The threshold voltage necessary to produce the modification is studied as a function of the average tip¿to¿sample distance.

Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations.

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure-function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure-function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications.

Nonempirical cluster-model study of the chemisorption of atomic hydrogen on the (111) surface of diamondlike crystals

The interaction of atomic hydrogen with C4H9, Si4H9, and Ge4H9 model clusters has been studied using all-electron and pseudopotential ab initio Hartree-Fock computations with basis sets of increasing flexibility. The results show that the effect of polarization functions is important in order to reproduce the experimental findings, but their inclusion only for the atoms directly involved in the chemisorption bond is usually sufficient. For the systems H-C4H9 and H-Si4H9 all-electron and pseudopotential results are in excellent agreement when basis sets of comparable quality are used. Besides, semiempirical modified-neglect-of-differential-overlap computations provide quite reliable results both for diamond and silicon and have been used to investigate larger model clusters. The results confirm the local nature of chemisorption and further justify the use of minimal X4H9 model clusters.

Chemisorption of atomic aluminum on Si(111): Evidence for an adsorbate-induced relaxation based on ab initio cluster-model calculations

Interaction models of atomic Al with Si4H9, Si4H7, and Si6H9 clusters have been studied to simulate Al chemisorption on the Si(111) surface in the atop, fourfold atop, and open sites. Calculations were carried out using nonempirical pseudopotentials in the framework of the ab initio Hartree-Fock procedure. Equilibrium bond distances, binding energies for adsorption, and vibrational frequencies of the adatoms are calculated. Several basis sets were used in order to show the importance of polarization effects, especially in the binding energies. Final results show the importance of considering adatom-induced relaxation effects to specify the order of energy stabilities for the three different sites, the fourfold atop site being the preferred one, in agreement with experimental findings.

Statistical Modeling of the Eye for Multimodal Treatment Planning for External Beam Radiation Therapy of Intraocular Tumors.

PURPOSE: Ocular anatomy and radiation-associated toxicities provide unique challenges for external beam radiation therapy. For treatment planning, precise modeling of organs at risk and tumor volume are crucial. Development of a precise eye model and automatic adaptation of this model to patients' anatomy remain problematic because of organ shape variability. This work introduces the application of a 3-dimensional (3D) statistical shape model as a novel method for precise eye modeling for external beam radiation therapy of intraocular tumors. METHODS AND MATERIALS: Manual and automatic segmentations were compared for 17 patients, based on head computed tomography (CT) volume scans. A 3D statistical shape model of the cornea, lens, and sclera as well as of the optic disc position was developed. Furthermore, an active shape model was built to enable automatic fitting of the eye model to CT slice stacks. Cross-validation was performed based on leave-one-out tests for all training shapes by measuring dice coefficients and mean segmentation errors between automatic segmentation and manual segmentation by an expert. RESULTS: Cross-validation revealed a dice similarity of 95% ± 2% for the sclera and cornea and 91% ± 2% for the lens. Overall, mean segmentation error was found to be 0.3 ± 0.1 mm. Average segmentation time was 14 ± 2 s on a standard personal computer. CONCLUSIONS: Our results show that the solution presented outperforms state-of-the-art methods in terms of accuracy, reliability, and robustness. Moreover, the eye model shape as well as its variability is learned from a training set rather than by making shape assumptions (eg, as with the spherical or elliptical model). Therefore, the model appears to be capable of modeling nonspherically and nonelliptically shaped eyes.

Ion-beam induced oxidation of GaAs and AlGaAs

The oxidation of GaAs and AlxGa1−xAs targets by oxygen irradiation has been studied in detail. It was found that the oxidation process is characterized by the strong preferential oxidation of Al as compared to Ga, and of Ga as compared to As. This experimental observation, which has been accurately quantified by using x‐ray photoelectron spectroscopy, is connected to the different heats of formation of the corresponding oxides. The oxide grown by ion beam oxidation shows a strong depletion in As and relatively low oxidation of As as well. The depletion can be associated with the preferential sputtering of the As oxide in respect to other compounds whereas the low oxidation is due to the low heat of formation. In contrast Al is rapidly and fully oxidized, turning the outermost layer of the altered layer to a single Al2O3 overlayer, as observed by transmission electron microscopy. The radiation enhanced diffusion of oxygen and aluminum in the altered layer explains the large thickness of these altered layers and the formation of Al oxides on top of the layers. For the case of ion‐beam oxidation of GaAs a simulation program has been developed which describes adequately the various growth mechanisms experimentally observed

Atomic force microscopy of nucleoprotein complexes.

Recent data on the AFM studies of nucleoprotein complexes of different types are reviewed in this paper. The first section describes the progress in the sample preparation methods for AFM studies of nucleic acids and nucleoprotein complexes. The second part of this paper reviews AFM data on studies of complexes of DNA with regulatory proteins. These studies include two different types of DNA distortion induced by proteins binding: local bending of DNA at sites of protein binding and formation of large loops due to protein-protein interactions between molecules bound to distant sites along the DNA molecules (DNA looping). The prospects for use of AFM for physical mapping of genomes are discussed in this section as well. The third part of the paper reviews data on studies of complexes of DNA with non-sequence specific binding proteins. Special emphasis is given to studies of chromatin which have resulted in progress in the understanding of structure of native chromatin fiber. In this section, novel data on AFM studies of RecA-DNA filaments and complexes of dsRNA with the dsRNA-specific protein p25 are also presented. Discussion of the substrate preparation procedures in relation to the AFM studies of nucleoprotein complexes is given in the final section.

Whole anterior segment proton beam radiotherapy for diffuse iris melanoma.

AIM: To report the results of whole anterior segment proton beam radiotherapy (PBR) for diffuse iris melanoma. METHODS: Between 2000 and 2011, 12 patients with iris melanoma received PBR to the entire iris and ciliary body. RESULTS: Patients had a mean age of 57 years and a median follow-up of 3.5 years (range 1-11.6 years). Tumour iris involvement was 1-4 h in five patients, 5-8 h in four and 9-12 h in three. Angle involvement was 6-8 h in five patients and 9-12 h in seven. The visual acuity (VA) before treatment was 6/5-6/6 in six patients, 6/8-6/9 in three and 6/18-6/38 in three. No tumour recurrence occurred during the follow-up period. Glaucoma treatment was required in 11 of 12 patients. The visual acuity at the last follow-up was 6/5-6/9 in five patients, 6/18-6/24 in three, 6/60-1/60 in two and no light perception in two. Four patients developed varying non-severe degrees of limbal stem cell deficiency, which was treatable with conservative measures. CONCLUSIONS: Whole anterior segment PBR is a useful alternative to enucleation for diffuse iris melanoma. Most patients will need treatment for glaucoma and some may require treatment for tear-film instability and/or stem cell failure.

Investigation of Two Bridge Alternatives for Low Volume Roads, Volume 1 of 2 Concept 1: Precast Steel Beam Units, HR-382, 1997

Recent reports have indicated that 23.5% of the nation's highway bridges are structurally deficient and 17.7% are functionally obsolete. A significant number of these bridges are on the Iowa secondary road system where over 86% of the rural bridge management responsibilities are assigned to the counties. Some of the bridges can be strengthened or otherwise rehabilitated, but many more are in need of immediate replacement. In a recent investigation (HR-365 "Evaluation of Bridge Replacement Alternatives for the County Bridge System") several types of replacement bridges that are currently being used on low volume roads were identified. It was also determined that a large number of counties (69%) have the ability and are interested in utilizing their own forces to design and construct short span bridges. In reviewing the results from HR-365, the research team developed one "new" bridge replacement concept and a modification of a replacement system currently being used. Both of these bridge replacement alternatives were investigated in this study, the results of which are presented in two volumes. This volume (Volume 1) presents the results of Concept 1 - Steel Beam Precast Units. Concept 2 - Modification of the Beam-in-Slab Bridge is presented in Volume 2. Concept 1, involves the fabrication of precast units (two steel beams connected by a concrete slab) by county work forces. Deck thickness is limited so that the units can be fabricated at one site and then transported to the bridge site where they are connected and the remaining portion of the deck placed. Since Concept 1 bridge is primarily intended for use on low-volume roads, the precast units can be constructed with new or used beams. In the experimental part of the investigation, there were three types of static load tests: small scale connector tests, "handling strength" tests, and service and overload tests of a model bridge. Three finite element models for analyzing the bridge in various states of construction were also developed. Small scale connector tests were completed to determine the best method of connecting the precast double-T (PCDT) units. "Handling strength" tests on an individual PCDT unit were performed to determine the strength and behavior of the precast unit in this configuration. The majority of the testing was completed on the model bridge [L=9,750 mm (32 ft), W=6,400 mm (21 ft)] which was fabricated using the precast units developed. Some of the variables investigated in the model bridge tests were number of connectors required to connect adjacent precast units, contribution of diaphragms to load distribution, influence of position of diaphragms on bridge strength and load distribution, and effect of cast-in-place portion of deck on load distribution. In addition to the service load tests, the bridge was also subjected to overload conditions. Using the finite element models developed, one can predict the behavior and strength of bridges similar to the laboratory model as well as design them. Concept 1 has successfully passed all laboratory testing; the next step is to field test it.

Investigation of Two Bridge Alternatives for Low Volume Roads - Phase II Volume 1 of 2 Concept 1: Steel Beam Precast Units, TR-410, 2000

This project continues the research which addresses the numerous bridge problems on the Iowa secondary road system. It is a continuation (Phase 2) of Project HR-382, in which two replacement alternatives (Concept 1: Steel Beam Precast Units and Concept 2: Modification of the Benton County Beam-in-Slab Bridge) were investigated. In previous research for concept 1, a precast unit bridge was developed through laboratory testing. The steel-beam precast unit bridge requires the fabrication of precast double-tee (PCDT) units, each consisting of two steel beams connected by a reinforced concrete deck. The weight of each PCDT unit is minimized by limiting the deck thickness to 4 in., which permits the units to be constructed off-site and then transported to the bridge site. The number of units required is a function of the width of bridge desired. Once the PCDT units are connected, a cast-in-place reinforced concrete deck is cast over the PCDT units and the bridge railing attached. Since the steel beam PCDT unit bridge design is intended primarily for use on low-volume roads, used steel beams can be utilized for a significant cost savings. In previous research for concept 2, an alternate shear connector (ASC) was developed and subjected to static loading. In this investigation, the ASC was subjected to cyclic loading in both pushout specimens and composite beam tests. Based on these tests, the fatigue strength of the ASC was determined to be significantly greater than that required in typical low volume road single span bridges. Based upon the construction and service load testing, the steel-beam precast unit bridge was successfully shown to be a viable low volume road bridge alternative. The construction process utilized standard methods resulting in a simple system that can be completed with a limited staff. Results from the service load tests indicated adequate strength for all legal loads. An inspection of the bridge one year after its construction revealed no change in the bridge's performance. Each of the systems previously described are relatively easy to construct. Use of the ASC rather than the welded studs significantly simplified the work, equipment, and materials required to develop composite action between the steel beams and the concrete deck.

Strengthening of an Existing Continuous-Span, Steel-Beam, Concrete-Deck Bridge by Post-Tensioning, HR-308, 1990

The need to upgrade a large number of understrength and obsolete bridges in the U.S. has been well documented in the literature. Through several Iowa DOT projects, the concept of strengthening simple-span bridges by post-tensioning has been developed. The purpose of the project described in this report was to investigate the use of post-tensioning for strengthening continuous composite bridges. In a previous, successfully completed investigation, the feasibility of strengthening continuous, composite bridges by post-tensioning was demonstrated on a laboratory 1/3-scale-model bridge (3 spans: 41 ft 11 in. x 8 ft 8 in.). This project can thus be considered the implementation phase. The bridge selected for strengthening was in Pocahontas County near Fonda, Iowa, on County Road N28. With finite element analysis, a post-tensioning system was developed that required post-tensioning of the positive moment regions of both the interior and exterior beams. During the summer of 1988, the strengthening system was installed along with instrumentation to determine the bridge's response and behavior. Before and after post-tensioning, the bridge was subjected to truck loading (1 or 2 trucks at various predetermined critical locations) to determine the effectiveness of the strengthening system. The bridge, with the strengthening system in place, was inspected approximately every three months to determine any changes in its appearance or behavior. In 1989, approximately one year after the initial strengthening, the bridge was retested to identify any changes in its behavior. Post-tensioning forces were removed to reveal any losses over the one-year period. Post-tensioning was reapplied to the bridge, and the bridge was tested using the same loading program used in 1988. Except for at a few locations, stresses were reduced in the bridge the desired amount. At a few locations flexural stresses in the steel beams are still above 18 ksi, the allowable inventory stress for A7 steel. Although maximum stresses are above the inventory stress by about 2 ksi, they are about 5 ksi below the allowable operating stress; therefore, the bridge no longer needs to be load-posted.

Strengthening of Existing Single Span Steel Beam and Concrete Deck Bridges, HR-238, Part 1, 1983

The Phase I research, Iowa Department of Transportation (IDOT) Project HR-214, "Feasibility Study of Strengthening Existing Single Span Steel Beam Concrete Deck Bridges," verified that post-tensioning can be used to provide strengthening of the composite bridges under investigation. Phase II research, reported here, involved the strengthening of two full-scale prototype bridges - one a prototype of the model bridge tested during Phase I and the other larger and skewed. In addition to the field work, Phase II also involved a considerable amount of laboratory work. A literature search revealed that only minimal data existed on the angle-plus-bar shear connectors. Thus, several specimens utilizing angle-plus-bar, as well as channels, studs and high strength bolts as shear connectors were fabricated and tested. To obtain additional shear connector information, the bridge model of Phase I was sawed into four composite concrete slab and steel beam specimens. Two of the resulting specimens were tested with the original shear connection, while the other two specimens had additional shear connectors added before testing. Although orthotropic plate theory was shown in Phase I to predict vertical load distribution in bridge decks and to predict approximate distribution of post-tensioning for right-angle bridges, it was questioned whether the theory could also be used on skewed bridges. Thus, a small plexiglas model was constructed and used in vertical load distribution tests and post-tensioning force distribution tests for verification of the theory. Conclusions of this research are as follows: (1) The capacity of existing shear connectors must be checked as part of a bridge strengthening program. Determination of the concrete deck strength in advance of bridge strengthening is also recommended. (2) The ultimate capacity of angle-plus-bar shear connectors can be computed on the basis of a modified AASHTO channel connector formula and an angle-to-beam weld capacity check. (3) Existing shear connector capacity can be augmented by means of double-nut high strength bolt connectors. (4) Post-tensioning did not significantly affect truck load distribution for right angle or skewed bridges. (5) Approximate post-tensioning and truck load distribution for actual bridges can be predicted by orthotropic plate theory for vertical load; however, the agreement between actual distribution and theoretical distribution is not as close as that measured for the laboratory model in Phase I. (6) The right angle bridge exhibited considerable end restraint at what would be assumed to be simple support. The construction details at bridge abutments seem to be the reason for the restraint. (7) The skewed bridge exhibited more end restraint than the right angle bridge. Both skew effects and construction details at the abutments accounted for the restraint. (8) End restraint in the right angle and skewed bridges reduced tension strains in the steel bridge beams due to truck loading, but also reduced the compression strains caused by post-tensioning.

Strengthening of Existing Single Span Steel Beam and Concrete Deck Bridges, HR-238, Part II, 1985

The unifying objective of Phases I and II of this study was to determine the feasibility of the post-tensioning strengthening method and to implement the technique on two composite bridges in Iowa. Following completion of these two phases, Phase III was undertaken and is documented in this report. The basic objectives of Phase III were further monitoring bridge behavior (both during and after post-tensioning) and developing a practical design methodology for designing the strengthening system under investigation. Specific objectives were: to develop strain and force transducers to facilitate the collection of field data; to investigate further the existence and effects of the end restraint on the post-tensioning process; to determine the amount of post-tensioning force loss that occurred during the time between the initial testing and the retesting of the existing bridges; to determine the significance of any temporary temperature-induced post-tensioning force change; and to develop a simplified design methodology that would incorporate various variables such as span length, angle-of-skew, beam spacing, and concrete strength. Experimental field results obtained during Phases II and III were compared to the theoretical results and to each other. Conclusions from this research are as follows: (1) Strengthening single-span composite bridges by post-tensioning is a viable, economical strengthening technique. (2) Behavior of both bridges was similar to the behavior observed from the bridges during field tests conducted under Phase II. (3) The strain transducers were very accurate at measuring mid-span strain. (4) The force transducers gave excellent results under laboratory conditions, but were found to be less effective when used in actual bridge tests. (5) Loss of post-tensioning force due to temperature effects in any particular steel beam post-tensioning tendon system were found to be small. (6) Loss of post-tensioning force over a two-year period was minimal. (7) Significant end restraint was measured in both bridges, caused primarily by reinforcing steel being continuous from the deck into the abutments. This end restraint reduced the effectiveness of the post-tensioning but also reduced midspan strains due to truck loadings. (8) The SAP IV finite element model is capable of accurately modeling the behavior of a post-tensioned bridge, if guardrails and end restraints are included in the model. (9) Post-tensioning distribution should be separated into distributions for the axial force and moment components of an eccentric post-tensioning force. (10) Skews of 45 deg or less have a minor influence on post-tensioning distribution. (11) For typical Iowa three-beam and four-beam composite bridges, simple regression-derived formulas for force and moment fractions can be used to estimate post-tensioning distribution at midspan. At other locations, a simple linear interpolation gives approximately correct results. (12) A simple analytical model can accurately estimate the flexural strength of an isolated post-tensioned composite beam.

Atomic Force Microscopy Stiffness Tomography on Living Arabidopsis thaliana Cells Reveals the Mechanical Properties of Surface and Deep Cell-Wall Layers during Growth.

Cell-wall mechanical properties play a key role in the growth and the protection of plants. However, little is known about genuine wall mechanical properties and their growth-related dynamics at subcellular resolution and in living cells. Here, we used atomic force microscopy (AFM) stiffness tomography to explore stiffness distribution in the cell wall of suspension-cultured Arabidopsis thaliana as a model of primary, growing cell wall. For the first time that we know of, this new imaging technique was performed on living single cells of a higher plant, permitting monitoring of the stiffness distribution in cell-wall layers as a function of the depth and its evolution during the different growth phases. The mechanical measurements were correlated with changes in the composition of the cell wall, which were revealed by Fourier-transform infrared (FTIR) spectroscopy. In the beginning and end of cell growth, the average stiffness of the cell wall was low and the wall was mechanically homogenous, whereas in the exponential growth phase, the average wall stiffness increased, with increasing heterogeneity. In this phase, the difference between the superficial and deep wall stiffness was highest. FTIR spectra revealed a relative increase in the polysaccharide/lignin content.