Edge Of Groove Research Articles

Effects of N2,N2-dimethylguanosine on RNA structure and stability: Crystal structure of an RNA duplex with tandem m22G:A pairs

Methylation of the exocyclic amino group of guanine is a relatively common modification in rRNA and tRNA. Single methylation (N(2)-methylguanosine, m(2)G) is the second most frequently encountered nucleoside analog in Escherichia coli rRNAs. The most prominent case of dual methylation (N(2),N(2)-dimethylguanosine, m(2) (2)G) is found in the majority of eukaryotic tRNAs at base pair m(2) (2)G26:A44. The latter modification eliminates the ability of the N(2) function to donate in hydrogen bonds and alters its pairing behavior, notably vis-à-vis C. Perhaps a less obvious consequence of the N(2),N(2)-dimethyl modification is its role in controlling the pairing modes between G and A. We have determined the crystal structure of a 13-mer RNA duplex with central tandem m(2) (2)G:A pairs. In the structure both pairs adopt an imino-hydrogen bonded, pseudo-Watson-Crick conformation. Thus, the sheared conformation frequently seen in tandem G:A pairs is avoided due to a potential steric clash between an N(2)-methyl group and the major groove edge of A. Additionally, for a series of G:A containing self-complementary RNAs we investigated how methylation affects competitive hairpin versus duplex formation based on UV melting profile analysis.

Fabrication of High-Aspect Ratio Micro Holes on Hard Brittle Materials -Study on Electrorheological Fluid-Assisted Micro Ultrasonic Machining-

Ultrasonic machining (USM) is an effective method for machining of hard brittle materials. In this process, the slurry is supplied to the gap between the workpiece and the ultrasonic vibrating tool, and the materials are removed by the impacts of the abrasive grains that are pressurized by an ultrasonic vibrating tool. The purpose of this research is to achieve precise and efficient microfabrication on hard brittle materials by USM. However, in the case of microfabrication, chipping which is generally observed around the edges of machined micro holes and grooves, deteriorates the machining accuracy. In addition, there is another problem in that the machining efficiency decreases with the progress of the machining. Electrorheological fluid-assisted USM has been proposed as a countermeasure to these problems. In the present study, the problems and countermeasures associated with the machining of high-aspect ratio micro holes in hard brittle materials by electrorheological fluid-assisted USM are investigated. By positioning an auxiliary electrode under the workpiece, it becomes possible to keep the electric field high even when the machining depth becomes large. As a result, high-precision and high-aspect ratio micro holes can be machined on hard brittle materials.

Behaviour of Longitudinal Cracks on Slab Surfaces in V‐H Rolling Processes

The behaviour of longitudinal cracks on slab surfaces in multi‐pass vertical‐horizontal rolling processes was simulated by the finite element method (FEM). The influence of friction coefficients and fillet radii of grooved edge rolls on the closure and growth of cracks were analysed in regard to crack shape and crack length elongation ratio. The results indicate that the crack width increases both with increasing friction coefficient and with increasing fillet radii of the grooved edger rolls; the crack length increases as the fillet radii increase in V1 and H1 passes, and decreases as the fillet radii increase in V2 ~ H3 rolling. Moreover, the cracks become longer under a higher friction coefficient. Experiments of the behaviour of longitudinal cracks on slab surfaces in multi‐pass V‐H rolling processes were investigated taking lead as model material for the hot rolling of steel. The calculated results showed similar deformation variations compared to the experimental ones.

A Bridging Water Anchors the Tethered 5-(3-Aminopropyl)-2′-deoxyuridine Amine in the DNA Major Groove Proximate to the N+2 C·G Base Pair: Implications for Formation of Interstrand 5′-GNC-3′ Cross-Links by Nitrogen Mustards,

Site-specific insertion of 5-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7)T (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19)T (20)C (21) Z (22)C (23)G (24))-3' (named DDD (Z10)) and 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7) X (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19) X (20)C (21) Z (22)C (23)G (24))-3' (named DDD (2+Z10)) (X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD (2+Z10) duplex reveals that the tethered cations at base pairs A (5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2+) binding sites located adjacent to N+2 base pairs C (3).Z (22) and Z (10).C (15). Bridging waters located between the tethered amines and either Z (10) or Z (22) O (6) stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD (2+Z10) duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z (10) O (6) and Z (22) O (6). The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating interstrand cross-linking.

Quantitative anatomy of vertebral artery groove on the posterior arch of atlas in relation to spinal surgical procedures

The location of the vertebral artery on a groove on the superior surface of the posterior arch of atlas makes it vulnerable to injury during surgical procedures in this region. Knowledge of the quantitative anatomy of the vertebral artery groove is therefore necessary. In 55 dry adult atlas vertebrae, the distance of the medial edges of the vertebral artery groove were measured from the posterior midline at both the inner and outer cortices of the posterior arch of atlas. In addition, the distance between the vertebral artery grooves on either side as well as the length of the vertebral artery groove was also measured. It was found that a minimum of 1.5 cm of the posterior arch could be safely exposed at both the outer and inner cortices. In addition, with mobilization of the vertebral artery from its groove on both the sides, an additional 1 cm of posterior arch could be exposed on either side. Exposure of the posterior arch of the atlas is an important step in surgical procedures for treatment of diverse conditions of the upper spinal cord and foramen magnum region. Injury to the vertebral artery in its position on the vertebral groove may lead to disastrous complications. The present study reveals that the neurosurgeon can safely expose up to 3.5 cm of the posterior arch of atlas and knowledge of this anatomic fact may help in planning surgical approaches.

Comment on “Enhanced transmission of light through a gold film due to excitation of standing surface-plasmon Bloch waves”

The purpose of this comment is first to correct a misapprehension of the role played by composite wave diffraction on surface-wave generation at subwavelength structures and second to point out that periodic Bloch structures are unnecessary for the efficient production of the surface plasmon polariton (SPP) guided mode either as traveling or standing waves. Guided surface waves originate from simple slit or groove edges illuminated under normal incidence, and one-dimensional (1-D) surface cavities from these standing waves are easily realized.

Fabrication of Micro Ni-W Electroplated Diamond Tools and Their Application to Grooving of Brittle Materials

The present paper intends to improve the tool quality and the machining performance of micro cylindrical Ni-W electroplated diamond tools. From the grooving tests of silicon the following results were obtained. The scatter of diamond grit density on the tool surface can be prevented through the intermittent pouring of electroplating solution into the solution with grit supported by a filter. Ni strike plating before electroplating is useful for extending the tool life, but it can result in the degradation of roughness on groove side surface. Tool wear may result from the removal of bond material due to generated chip and dropped diamond grit, therefore the usage of harder bond material and the heat treatment of bond material are recommended. For a constant tool diameter there exists a suitable grit diameter from the viewpoint of machining efficiency and groove roughness. In grooving of quartz glass, chippings of 10-20μm may occur on the groove edges, which can be prevented by the application of axial ultrasonic vibration to the tool.

Phase shifts and interference in surface plasmon polariton waves

A pi phase shift between the incident wave and surface Plasmon polariton (SPP) waves launched from a one-dimensional (slit or groove) subwavelength structure has been found in numerical simulations and invoked to explain recent measurements of optical transmission in slit arrays. Although groove launchers exhibit an overall phase shift that depends on the groove depth, it is shown here how magnetic field induction at the incident surface, and oscillating dipoles from the accumulated charge at the slit or groove edges on the entrance facet lead to an intrinsic pi phase shift, independent of the groove or slit depth. Destructive interference between the pi-shifted surface wave and the incident wave explains the observed transmission minima when the pitch of an array of slits becomes equal to an integer multiple of the SPP wavelength.

Structuring electrospun polycaprolactone nanofiber tissue scaffolds by femtosecond laser ablation

Meshes of electrospun (ES) polycaprolactone (PCL) and polyethylene terephthalate nanofiber meshes were structured by ablation of linear grooves with a scanned femtosecond laser. Focus spot size, pulse energy, and scanning speed were varied to determine their affects on groove size and the characteristics of the electrospun fiber at the edges of these grooves. The femtosecond laser was seen to be an effective means for flexibly structuring the surface of ES PCL scaffolds. Femtosecond ablation resulted in much more uniformly ablated patterns compared to Q-switched nanosecond pulse laser ablation. Also, the width of the ablated grooves was well controlled by laser energy and focus spot size, although the grooves were significantly larger than the spot size. Also, some melting of fibers was observed at the edges of grooves. These affects were attributed to optical radiation from laser-induced plasma at higher pulse energies and melting of fibers at laser fluences lower than the ablation threshold. The ablation threshold for the PCL mesh was estimated to be significantly larger than that of bulk (solid) PCL, a result attributed to multiple scattering of the laser energy within the volume of the nanofiber mesh.

Tribological analysis of TiN and DLC coated contacts by 3D FEM modelling and stress simulation

Surface coatings, like titanium nitride (TiN) and diamond-like carbon (DLC) coatings, offer high wear resistance and good friction performance for a wide range of applications. With novel advanced techniques like modelling and simulation, the performance of these coatings can be predicted under a wide range of loading conditions. This provides valuable information for the coating design and for the use of coatings in different applications. A previously developed three-dimensional finite element method (FEM) model was used for calculating the first principal stress distribution in a scratch test contact as a spherical diamond tip is moving with increased load on DLC and TiN coated high speed steel surfaces containing no residual stresses. The used three-dimensional model is comprehensive in the sense that it considers elastic and plastic behaviour of the contacting surfaces. The first cracks to appear on the surface are angular cracks on the edge of the scratch groove. This corresponds to the region of high two directional tensile stresses occurring in FEM stress simulations at the edge of the scratch groove. The coating/substrate stiffness ratio influences considerably on the coating behaviour. The TiN coating that had higher Young's modulus compared to the substrate material experienced high tensile stresses when loaded by the diamond stylus. The DLC coating that had lower stiffness compared to substrate material experienced comparatively low tensile stresses. The DLC coatings had maximum tensile stresses in the range of 700–900 MPa. The TiN coatings had tensile stresses in the range 2200–3000 MPa. The coating thickness had only minor effect on the maximum tensile stress level for the 1 and 2 μm thick coatings. The location of the experimentally observed first crack in the surface corresponds to the location of maximum tensile stress concentrations in the stress simulations and the direction of the observed crack corresponds with the stress components in the calculated stress field. The role of residual stresses is discussed.

Close relation between the inferior vena cava ligament and the caudate lobe in the human liver

This study was conducted to clarify the real relation between the inferior vena cava (IVC) ligament and the caudate lobe in the human liver and also to elucidate their surgical importance in liver surgery. Specimens obtained from 20 adult cadaveric livers were submitted for the study. Histological structures of the IVC ligament and its relationship to the caudate lobe and the IVC were microscopically investigated. The IVC ligament was a broad membranous connective tissue bridging the left and right side edges of the caval groove in which the IVC was embedded. At both edges of the caval groove, the IVC ligament was continuously transformed from the Glisson's capsules of the caudate and right lobes. The component of the portal triad, which originated from that of caudate lobe, and lymphatics were distributed in the IVC ligament without exception and ectopic hepatocytes existed in it in 4 of the 20 cases. A close relation between the IVC ligament and the caudate lobe was confirmed. The findings suggested that the IVC ligament is a kind of degenerated hepatic tissue. When dissecting it, surgeons should manipulate it carefully to prevent unexpected bleeding and bile leakage.

The electrostatic characteristics of G{middle dot}U wobble base pairs

G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands.

Channel plasmon-polaritons: modal shape, dispersion, and losses

We theoretically study channel plasmon-polaritons (CPPs) with a geometry similar to that in recent experiments at telecommunication wavelengths [Bozhevolnyi et al., Nature 440, 508 (2006)]. The CPP modal shape, dispersion relation, and losses are simulated by using the multiple multipole method and the finite difference time domain technique. It is shown that, with an increase of the wavelength, the fundamental CPP mode shifts progressively toward the groove opening, ceasing to be guided at the groove bottom and becoming hybridized with wedge plasmon-polaritons running along the groove edges.

Backside etching of fused silica with UV laser pulses using mercury

Laser-induced backside wet etching (LIBWE) is an indirect etching technique that was first demonstrated for fused silica applying a pyrene doped hydrocarbon solution and was recently demonstrated for gallium as a highly absorbing liquid. In this study the etching of fused silica with mercury as liquid absorber is demonstrated using a nanosecond UV laser (excimer laser λ = 248 nm, 25 ns pulses) radiation. The high absorption coefficient of mercury enforces the absorption of the UV laser radiation within a 100 nm region near the solid interface so that, despite the high reflectivity, the threshold for etching was measured to be 0.76 J cm−2. With rising laser fluence the etch rate increases nearly linearly in the whole laser fluence range and reaches a value of 650 nm/pulse at a laser fluence of about 10 J cm−2. The etched surfaces were investigated by scanning electron microscopy, atomic force microscopy and interference microscopy and show well defined etch groove edges and a flat, smooth etched bottom that features an rms roughness of about 2.2 nm. The laser-induced backside etching of fused silica with mercury combines a low etching threshold, high etch rates and a still smooth etching of well-defined patterns into material surfaces.

The effect of shielding gas composition on welding performance and weld properties in hybrid CO2 laser–gas metal arc welding of carbon manganese steel

Metals industries producing large structures currently have a particular interest in hybrid laser welding processes, which possess advantages compared with conventional methods of welding. One major benefit is a reduction in deformation that enables the amount of postweld finishing work to be reduced. Assembly then also becomes simpler because of the greater accuracy that may be achieved. Larger joint tolerances may be accommodated compared with laser welding alone. By using appropriate filler metal, the weld metal composition may be controlled to meet metallurgical criteria. The hybrid CO2 laser–gas metal arc (GMA) welding process was investigated in this study; the aim being to clarify the effects of process gas composition on welding performance, weld cross section, quality, and mechanical properties, when welding carbon manganese steel. Helium, argon, and carbon dioxide were used in varying proportions as shielding gases for welding I-butt and T-butt joints. The composition of the shielding gas was found to affect welding performance, weld quality, and weld cross-section geometry. The best results were obtained by using argon, with a helium content of 40%–50% and a carbon dioxide content of 2%–5%; the exact composition depending on the groove edge quality. Hybrid laser welds of high quality may be produced in carbon manganese steel with a variety of shielding gas compositions, but to maximize productivity, reliability, and quality, while minimizing gas cost, the composition must be selected carefully.

Suppression of Cavitation Instabilities in an Inducer by J-Groove (Control by the Change of Axial Location)

The results of the control of tip leakage vortex cavitation, and cavitation instabilities, are discussed. The control was made by adjusting the axial location of the leading and trailing edges of shallow grooves, called J-grooves, on the casing wall. If the leading edge of the groove is too close to the leading edge to the impeller blade, the tip leakage vortex is trapped by the groove leading edge and the tip leakage vortex cavitation approaches the leading edge of the next blade. A premature severe cavitation surge occurs when the tip leakage vortex cavitation starts to interact with the leading edge. This type of cavitation surge can be avoided by extending the groove leading edge upstream. However, in this case another type of cavitation surge occurs at much lower cavitation number caused by the cavitation between the blade surface and the tip leakage vortex cavitation. Thus, the importance of the tip leakage vortex cavitation for cavitation instability are shown by a series of experiments using J-grooves.

Anneal-Less Domain Wall Displacement Detection of 27 Gbit/in2 Land/Groove Recording Using a Deep Groove Substrate and a Blue Laser

We have studied an anneal-less domain wall displacement detection (DWDD) disk of a land/groove recording on a deep groove substrate using a numerical aperture (NA) 0.65 objective lens and a blue laser diode (LD). The substrates were prepared using a stamper formed by reactive ion etching (RIE) and O2 plasma treatment to realize both steep side-wall angles and smooth surfaces on the substrates. In designing the groove shape, we have clarified three key factors: the groove edge shape, the groove depth and the land width. These factors affected the magnetic film discontinuity at the groove edge and the recording power margin on the land. We have achieved a recording density of 27 Gbit/in2 by optimizing the groove shape.

Ligand Specificity of Human Surfactant Protein D: EXPRESSION OF A MUTANT TRIMERIC COLLECTIN THAT SHOWS ENHANCED INTERACTIONS WITH INFLUENZA A VIRUS

Surfactant protein D is a pattern recognition molecule that plays diverse roles in immune regulation and anti-microbial host defense. Its interactions with known ligands are calcium-dependent and involve binding to the trimeric, C-type carbohydrate recognition domain. Surfactant protein D preferentially binds to glucose and related sugars. However, CL-43, a bovine serum lectin, which evolved through duplication of the surfactant protein D gene in ruminants, prefers mannose and mannose-rich polysaccharides. Surfactant protein D is characterized by two relatively conserved motifs at the binding face, along the edges of the shallow carbohydrate-binding groove. For CL-43, sequence alignments demonstrate a basic insertion, Arg-Ala-Lys (RAK), immediately N-terminal to the first motif. We hypothesized that this insertion contributes to the differences in saccharide selectivity and host defense function and compared the activities of recombinant trimeric neck + carbohydrate recognition domains of human surfactant protein D (NCRD) with CL-43 (RCL-43-NCRD) and selected NCRD mutants. Insertion of the CL-43 RAK sequence or a control Ala-Ala-Ala sequence (AAA) into the corresponding position in NCRD increased the efficiency of binding to mannan and changed the inhibitory potencies of competing saccharides to more closely resemble those of CL-43. In addition, RAK resembled CL-43 in its greater capacity to inhibit the infectivity of influenza A virus and to increase uptake of influenza by neutrophils.

Wetting morphologies at microstructured surfaces

The wetting of microstructured surfaces is studied both experimentally and theoretically. Even relatively simple surface topographies such as grooves with rectangular cross section exhibit a large variety of different wetting morphologies as observed by atomic force microscopy. This polymorphism arises from liquid wedge formation along the groove corners and from contact line pinning along the groove edges. A global morphology diagram is derived that depends only on two system parameters: (i) the aspect ratio of the groove geometry and (ii) The contact angle of the underlying substrate material. For microfluidics, the most interesting shape regimes involve extended liquid filaments, which can grow and shrink in length while their cross section stays essentially constant. Thus, any method by which one can vary the contact angle can be used to switch the length of the filament, as is demonstrated in the context of electrowetting.

Abrasive wear behaviour of Fe, Co and Ni based metallic glasses

Metallic glasses are a different category of materials that are characterized by their amorphous structure and metallic bonds. Owing to their disordered structure, metallic glasses possess several unique properties that make them attractive for tribological applications. This paper deals with an in depth investigation into the two-body abrasive wear behaviour of several compositions of Fe, Co and Ni based metallic glasses while rubbing against metallographic grade SiC abrasive papers. Identical studies have also been carried out on crystalline cold-rolled AISI 304 stainless steel for comparison. Two-body abrasive wear results indicate that wear characteristics of different metallic glasses are marginally superior or similar to that of stainless steel. The wear in Ni based metallic glass MBF 35 is significantly higher than that in stainless steel. This is inspite of the fact that metallic glasses are considerably harder than stainless steel. Scratch indentation and acoustic emission studies (AE) were carried out with a view to understanding the mechanisms of occurrence of two-body abrasive wear in metallic glasses. Scratched surfaces of metallic glasses indicated the presence of arc-like features that in some cases extend well beyond the scratched groove edges. In the case of Ni based metallic glass MBF 35, cracking on the surface was clearly visible. In stainless steel, the grooves formed were neatly cut out and were free from the arc-like features. During scratch tests on metallic glasses, AE signals were obtained but no AE signals were generated during scratch tests on steel. Presence of arc-like features on scratched surfaces in metallic glasses are tensile micro-cracks formed due to brittle fracture owing to their poor ductility in tension. These results revealed that the abrasive wear of metallic glasses is not commensurate to their high hardness and occurrence of micro-cracking results in their poor abrasive wear resistance.