Deformation Studies of Tungsten-Gold Contacts at the Nanometer Scale.

The deformation behavior of atomically clean, nanometer sized tungsten / gold contacts was studied at room temperature in ultra-high vacuum. An instrument that combines atomic force microscopy (AFM), scanning tunneling microscopy (STM), and field ion microscopy (FIM) into a single experimental apparatus was designed, constructed, and calibrated. A cross-hair force sensor having a spring constant of - 442 N/m was developed and its motion was monitored during indentation experiments with a differential interferometer. Tungsten tips of controlled size (12.8 nm < tip radius < 2 1.6 nm) were first shaped and characterized using FIM and then indented into a Au (1 10) single crystal to depths ranging from 1.5 nrn to 18 nm using the force sensor. Continuum mechanics models were found to be valid in predicting elastic deformation during initial contact and plastic zone depths despite our small size regime. Multiple discrete yielding events lasting < 1.5 ms were observed during the plastic deformation regime; at the yield points a maximum value for the principal shear stress was measured to be 5 + 1 GPa. During tip withdrawal, "pop-out" events relating to material relaxation within the contact were observed. Adhesion between the tip and sample led to experimental signatures that suggest neck formation prior to the break of contact. STM images of indentation holes revealed various shapes that can be attributed to the (1 1 1 ) (1 10) crystallographic slip system in gold. FIM images of the tip after indentation showed no evidence of tip damage

Geochemical composition of gabbroic rocks from ODP Hole 179-1105A, southwest Indian Ridge

Oxide-free olivine gabbro and gabbro, and oxide olivine gabbro and gabbro make up the bulk of the gabbroic suite recovered from Ocean Drilling Program (ODP) Leg 179 Hole 1105A, which lies 1.2 km away from Hole 735B on the eastern transverse ridge of the Atlantis II Fracture Zone, Southwest Indian Ridge. The rocks recovered during Leg 179 show striking similarities to rocks recovered from the uppermost 500 m of Hole 735B during ODP Leg 118. The rocks of the Atlantis platform were likely unroofed as part of the footwall block of a large detachment fault on the inside corner of the intersection of the Southwest Indian Ridge and the Atlantis II Transform at ~11.5 Ma. We analyzed the lithologic, geochemical, and structural stratigraphy of the section. Downhole lithologic variation allowed division of the core into 141 lithologic intervals and 4 main units subdivided on the basis of predominance of oxide gabbroic vs. oxide-free gabbroic rocks. Detailed analyses of whole-rock chemistry, mineral chemistry, microstructure, and modes of 147 samples are presented and clearly show that the gabbroic rocks are of cumulate origin. These studies also indicate that geochemistry results correlate well with downhole magnetic susceptibility and Formation MicroScanner (FMS) resistivity measurements and images. FMS images show rocks with a well-layered structure and significant numbers of mappable layer contacts or compositional contrasts. Downhole cryptic mineral and whole-rock chemical variations depict both "normal" and inverse fine-scale variations on a scale of 10 m to <2 m with significant compositional variation over a short distance within the 143-m section sampled. A Mg# shift in whole-rock or Fo contents of olivine of as much as 20-30 units over a few meters of section is not atypical of the extreme variation in downhole plots. The products of the earliest stages of basaltic differentiation are not represented by any cumulates, as the maximum Fo content was Fo78. Similarly, the extent of fractionation represented by the gabbroic rocks and scarce granophyres in the section is much greater than that represented in the Atlantis II basalts. The abundance of oxide gabbros is similar to that in Hole 735B, Unit IV, which is tentatively correlated as a similar unit or facies with the oxide gabbroic units of Hole 1105A. Oxide phases are generally present in the most fractionated gabbroic rocks and lacking in more primitive gabbroic rocks, and there is a definite progression of oxide abundance as, for example, the Mg# of clinopyroxene falls below 73-75. Coprecipitation of oxide at such early Mg#s cannot be modeled by perfect fractional crystallization. In situ boundary layer fractionation may offer a more plausible explanation for the complex juxtaposition of oxide- and nonoxide-bearing more primitive gabbroic rocks. The geochemical signal may, in part, be disrupted by the presence of mylonitic shear zones, which strike east-west and dip both to the south and north, but predominantly to the south away from the northern rift valley where they formed. Downhole deformation textures indicate increasing average strain and crystal-plastic deformation in units that contain oxides. Oxide-rich zones may represent zones of rheologic weakness in the cumulate section along which mylonitic and foliated gabbroic shear zones nucleate in the solid state at high temperature, or the oxide may be a symptom of former melt-rich zones and hypersolidus flow, as predicted during study of Hole 735B.

Impact of N on the atomic-scale Sb distribution in quaternary GaAsSbN-capped InAs quantum dots

The use of GaAsSbN capping layers on InAs/GaAs quantum dots (QDs) has recently been proposed for micro- and optoelectronic applications for their ability to independently tailor electron and hole confinement potentials. However, there is a lack of knowledge about the structural and compositional changes associated with the process of simultaneous Sb and N incorporation. In the present work, we have characterized using transmission electron microscopy techniques the effects of adding N in the GaAsSb/InAs/GaAs QD system. Firstly, strain maps of the regions away from the InAs QDs had revealed a huge reduction of the strain fields with the N incorporation but a higher inhomogeneity, which points to a composition modulation enhancement with the presence of Sb-rich and Sb-poor regions in the range of a few nanometers. On the other hand, the average strain in the QDs and surroundings is also similar in both cases. It could be explained by the accumulation of Sb above the QDs, compensating the tensile strain induced by the N incorporation together with an In-Ga intermixing inhibition. Indeed, compositional maps of column resolution from aberration-corrected Z-contrast images confirmed that the addition of N enhances the preferential deposition of Sb above the InAs QD, giving rise to an undulation of the growth front. As an outcome, the strong redshift in the photoluminescence spectrum of the GaAsSbN sample cannot be attributed only to the N-related reduction of the conduction band offset but also to an enhancement of the effect of Sb on the QD band structure.

Probing the Saccharomyces cerevisiae centromeric DNA (CEN DNA)–binding factor 3 (CBF3) kinetochore complex by using atomic force microscopy

Yeast centromeric DNA (CEN DNA) binding factor 3 (CBF3) is a multisubunit protein complex that binds to the essential CDEIII element in CEN DNA. The four CBF3 proteins are required for accurate chromosome segregation and are considered to be core components of the yeast kinetochore. We have examined the structure of the CBF3–CEN DNA complex by atomic force microscopy. Assembly of CBF3–CEN DNA complexes was performed by combining purified CBF3 proteins with a DNA fragment that includes the CEN region from yeast chromosome III. Atomic force microscopy images showed DNA molecules with attached globular bodies. The contour length of the DNA containing the complex is ≈9% shorter than the DNA alone, suggesting some winding of DNA within the complex. The measured location of the single binding site indicates that the complex is located asymmetrically to the right of CDEIII extending away from CDEI and CDEII, which is consistent with previous data. The CEN DNA is bent ≈55° at the site of complex formation. A significant fraction of the complexes are linked in pairs, showing three to four DNA arms, with molecular volumes approximately three times the mean volumes of two-armed complexes. These multi-armed complexes indicate that CBF3 can bind two DNA molecules together in vitro and, thus, may be involved in holding together chromatid pairs during mitosis.

The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase

The crystal structure of an enzyme–substrate complex with histidyl-tRNA synthetase from Escherichia coli, ATP, and the amino acid analog histidinol is described and compared with the previously obtained enzyme–product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the catalytic magnesium ion seen in seryl-tRNA synthetase. When Arg-259 is substituted with histidine, the apparent second order rate constant (kcat/Km) for the pyrophosphate exchange reaction and the aminoacylation reaction decreases 1,000-fold and 500-fold, respectively. Crystals soaked with MnCl2 reveal the existence of two metal binding sites between β- and γ-phosphates; these sites appear to stabilize the conformation of the pyrophosphate. The use of both conserved metal ions and arginine in phosphoryl transfer provides evidence of significant early functional divergence of class II aminoacyl-tRNA synthetases.

Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy

The Escherichia coli protein DbpA is unique in its subclass of DEAD box RNA helicases, because it possesses ATPase-specific activity toward the peptidyl transferase center in 23S rRNA. Although its remarkable ATPase activity had been well defined toward various substrates, its RNA helicase activity remained to be characterized. Herein, we show by using biochemical assays and atomic force microscopy that DbpA exhibits ATP-stimulated unwinding activity of RNA duplex regardless of its primary sequence. This work presents an attempt to investigate the action of DEAD box proteins by a single-molecule visualization methodology. Our atomic force microscopy images enabled us to observe directly the unwinding reaction of a DEAD box helicase on long stretches of double-stranded RNA. Specifically, we could differentiate between the binding of DbpA to RNA in the absence of ATP and the formation of a Y-shaped intermediate after its progression through double-stranded RNA in the presence of ATP. Recent studies have questioned the designation of DbpA, in particular, and DEAD box proteins in general as RNA helicases. However, accumulated evidence and the results reported herein suggest that these proteins are indeed helicases that resemble in many aspects the DNA helicases.

Manganese oxide minerals: Crystal structures and economic and environmental significance

Manganese oxide minerals have been used for thousands of years—by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry.

Imaging ROMK1 inwardly rectifying ATP-sensitive K+ channel protein using atomic force microscopy.

The inwardly rectifying K+ channel ROMK1 has been implicated as being significant in K+ secretion in the distal nephron. ROMK1 has been shown by immunocytochemistry to be expressed in relevant nephron segments. The development of the atomic force microscope has made possible the production of high resolution images of small particles, including a variety of biological macromolecules. Recently, a fusion protein of glutathione S-transferase (GST) and ROMK1 (ROMK1-GST) has been used to produce a polyclonal antibody for immunolocalization of ROMK1. We have used atomic force microscopy to examine ROMK1-GST and the native ROMK1 polypeptide cleaved from GST. Imaging was conducted with the proteins in physiological solutions attached to mica. ROMK1-GST appears in images as a particle composed of two units of similar size. Analyses of images indicate that the two units have volumes of approximately 118 nm3, which is close to the theoretical volume of a globular protein of approximately 65 kDa (the molecular mass of ROMK1-GST). Native GST exists as a dimer, and the images obtained here are consistent with the ROMK1-GST fusion protein's existence as a heterodimer. In experiments on ROMK1 in aqueous solution, single molecules appear to aggregate, but contact to the mica was maintained. Addition of ATP to the solution produced a change in height of the aggregates. This change (which was reversible) suggests that ATP induces a structural change in the ROMK1 protein. The data show that atomic force microscopy is a useful tool for examination of purified protein molecules under near-physiological conditions, and furthermore, that structural alterations in the proteins may be continuously investigated.

Evidence-based nanoscopic and molecular framework for excipient functionality in compressed orally disintegrating tablets

The work investigates the adhesive/cohesive molecular and physical interactions together with nanoscopic features of commonly used orally disintegrating tablet (ODT) excipients microcrystalline cellulose (MCC) and D-mannitol. This helps to elucidate the underlying physico-chemical and mechanical mechanisms responsible for powder densification and optimum product functionality. Atomic force microscopy (AFM) contact mode analysis was performed to measure nano-adhesion forces and surface energies between excipient-drug particles (6-10 different particles per each pair). Moreover, surface topography images (100 nm2-10 μm2) and roughness data were acquired from AFM tapping mode. AFM data were related to ODT macro/microscopic properties obtained from SEM, FTIR, XRD, thermal analysis using DSC and TGA, disintegration testing, Heckel and tabletability profiles. The study results showed a good association between the adhesive molecular and physical forces of paired particles and the resultant densification mechanisms responsible for mechanical strength of tablets. MCC micro roughness was 3 times that of D-mannitol which explains the high hardness of MCC ODTs due to mechanical interlocking. Hydrogen bonding between MCC particles could not be established from both AFM and FTIR solid state investigation. On the contrary, D-mannitol produced fragile ODTs due to fragmentation of surface crystallites during compression attained from its weak crystal structure. Furthermore, AFM analysis has shown the presence of extensive micro fibril structures inhabiting nano pores which further supports the use of MCC as a disintegrant. Overall, excipients (and model drugs) showed mechanistic behaviour on the nano/micro scale that could be related to the functionality of materials on the macro scale. © 2014 Al-khattawi et al.

Elastic and plastic properties of Mo3Si measured by nanoindentation

Single crystal Mo3Si specimens were grown and tested at room temperature using established nanoindentation techniques at various crystallographic orientations. The indentation modulus and hardness were obtained for loads that were large enough to determine bulk properties, yet small enough to avoid cracking in the specimens. From the indentation modulus results, anisotropic elastic constants were determined. As load was initially increased to approximately 1.5 mN, the hardness exhibited a sudden drop that corresponded to a jump in displacement. The resolved shear stress that was determined from initial yielding was 10-15% of the shear modulus, but 3 to 4 times the value obtained from the bulk hardness. Non-contact atomic force microscopy images in the vicinity of indents revealed features consistent with {100}(010) slip.

Arthur Lindo Patterson, his function and element preferences in early crystal structures

In 1934, Arthur Lindo Patterson showed that a map of interatomic vectors is obtainable from measured X-ray diffraction data without phase information. Such maps were interpretable for simple crystal structures, but proliferation and overlapping of peaks caused confusion as the number of atoms increased. Since the peak height of a vector between two particular atoms is related to the product of their atomic numbers, a complicated structure could effectively be reduced to a simple one by including just a few heavy atoms (of high atomic number) since their interatomic vectors would stand out from the general clutter. Once located, these atoms provide approximate phases for Fourier syntheses that reveal the locations of additional atoms. Surveys of small-molecule structures in the Cambridge Structural Database during the periods 1936-1969, when Patterson methods were commonly used, and 1980-2013, dominated by direct methods, demonstrate large differences in the abundance of certain elements. The moderately heavy elements K, Rb, As and Br are the heaviest elements in the structure more than 3 times as often in the early period than in the recent period. Examples are given of three triumphs of the heavy atom method and two initial failures that had to be overcome. © 2014 © 2014 Taylor & Francis.

Influência da superfície do titânio nitretado a plasma em diferentes atmosferas na ativação de plaquetas sanguíneas

This study aimed to analyze the biological response of titanium surfaces modified by plasma Ar + N2 + H2. Titanium disks grade II received different surface treatments Ar + N2 + H2 plasma, constituting seven groups including only polished samples used as standard. Before and after treatment the samples were evaluated in terms of topography, crystal structure and wettability, using atomic force microscopy, X-ray diffraction, Raman spectroscopy and testing of the sessile drop, respectively. Rich plasma (PRP) was applied to the surfaces modified in culture plates. Images obtained by scanning electron microscopy of the adhered platelets were analyzed to verify the behavior of platelets in the different experimental conditions. We verified that the adition of H2 on plasma atmosphere resulted in more rough surfaces, with round tops. These surfaces, in contrast to that surfaces treated with high concentration of N2, are less propense to platelet aggregation and, consequently, to the formation of thrombus when applied in biomedical devices.

Estudo da deposição de filmes finos de BaTi(1-X)Zr(X)O3 por meio de planejamento Box-Behnken

Ferroelectric ceramics with perovskite structure (ABO3) are widely used in solid state memories (FeRAM’s and DRAM's) as well as multilayered capacitors, especially as a thin films. When doped with zirconium ions, BaTiO3-based materials form a solid solution known as barium zirconate titanate (BaTi1-xZrxO3). Also called BZT, this material can undergo significant changes in their electrical properties for a small variation of zirconium content in the crystal lattice. The present work is the study of the effects of deposition parameters of BaTi0,75Zr0,25O3 thin films by spin-coating method on their morphology and physical properties, through an experimental design of the Box-Behnken type. The resin used in the process has been synthesized by the polymeric precursor method (Pechini) and subsequently split into three portions each of which has its viscosity adjusted to 10, 20 and 30 mPa∙s by means of a rotary viscometer. The resins were then deposited on Pt/Ti/SiO2/Si substrates by spin-coating method on 15 different combinations of viscosity, spin speed (3000, 5500 and 8000 rpm) and the number of deposited layers (5, 8 and 11 layers) and then calcined at 800 ° C for 1 h. The phase composition of the films was analyzed by X-ray diffraction (XRD) and indexed with the JCPDS 36-0019. Surface morphology and grain size were observed by atomic force microscopy (AFM) indicating uniform films and average grain size around 40 nm. Images of the cross section of the films were obtained by scanning electron microscopy field emission (SEM-FEG), indicating very uniform thicknesses ranging from 140-700 nm between samples. Capacitance measurements were performed at room temperature using an impedance analyzer. The films presented dielectric constant values of 55-305 at 100kHz and low dielectric loss. The design indicated no significant interaction effects between the deposition parameters on the thickness of the films. The response surface methodology enabled better observes the simultaneous effect of variables.

Single-crystal micro/nanostructures and thin films of lamellar molybdenum oxide by solid-state pyrolysis of organometallic derivatives of a cyclotriphosphazene

The solid-state pyrolysis of organometallic derivatives of a cyclotriphosphazene is demonstrated to be a new, simple and versatile solid-state templating method for obtaining single-crystal micro- and nanocrystals of transition and valve metal oxides. The technique, when applied to Mo-containing organometallics N3P3[OC6H4CH2CN·Mo(CO)5]6 and N3P3[OC6H4CH2CN·Mo(CO)4 py]6, results in stand-alone and surface-deposited lamellar MoO3 single crystals, as determined by electron and atomic force microscopies and X-ray diffraction. The size and morphology of the resulting crystals can be tuned by the composition of the precursor. X-ray photoelectron and infrared spectroscopies indicate that the deposition of highly lamellar MoO3 directly on an oxidized (400 nm SiO2) surface or (100) single-crystal silicon surfaces yields a layered uniphasic single-crystal film formed by cluster diffusion on the surface during pyrolysis of the metal-carbonyl derivatives. For MoO3 in its layered form, this provides a new route to an important intercalation material for high energy density battery materials.

Crystallization on the Mesoscale : Self-Assembly of Iron Oxide Nanocubes into Mesocrystals

Self-assembly of nanoparticles is a promising route to form complex, nanostructured materials with functional properties. Nanoparticle assemblies characterized by a crystallographic alignment of the nanoparticles on the atomic scale, i.e. mesocrystals, are commonly found in nature with outstanding functional and mechanical properties. This thesis aims to investigate and understand the formation mechanisms of mesocrystals formed by self-assembling iron oxide nanocubes. We have used the thermal decomposition method to synthesize monodisperse, oleate-capped iron oxide nanocubes with average edge lengths between 7 nm and 12 nm and studied the evaporation-induced self-assembly in dilute toluene-based nanocube dispersions. The influence of packing constraints on the alignment of the nanocubes in nanofluidic containers has been investigated with small and wide angle X-ray scattering (SAXS and WAXS, respectively). We found that the nanocubes preferentially orient one of their {100} faces with the confining channel wall and display mesocrystalline alignment irrespective of the channel widths.  We manipulated the solvent evaporation rate of drop-cast dispersions on fluorosilane-functionalized silica substrates in a custom-designed cell. The growth stages of the assembly process were investigated using light microscopy and quartz crystal microbalance with dissipation monitoring (QCM-D). We found that particle transport phenomena, e.g. the coffee ring effect and Marangoni flow, result in complex-shaped arrays near the three-phase contact line of a drying colloidal drop when the nitrogen flow rate is high. Diffusion-driven nanoparticle assembly into large mesocrystals with a well-defined morphology dominates at much lower nitrogen flow rates. Analysis of the time-resolved video microscopy data was used to quantify the mesocrystal growth and establish a particle diffusion-based, three-dimensional growth model. The dissipation obtained from the QCM-D signal reached its maximum value when the microscopy-observed lateral growth of the mesocrystals ceased, which we address to the fluid-like behavior of the mesocrystals and their weak binding to the substrate. Analysis of electron microscopy images and diffraction patterns showed that the formed arrays display significant nanoparticle ordering, regardless of the distinctive formation process.  We followed the two-stage formation mechanism of mesocrystals in levitating colloidal drops with real-time SAXS. Modelling of the SAXS data with the square-well potential together with calculations of van der Waals interactions suggests that the nanocubes initially form disordered clusters, which quickly transform into an ordered phase.