Deterministic shape control in plasma-aided nanotip assembly

The possibility of deterministic plasma-assisted reshaping of capped cylindrical seed nanotips by manipulating the plasma parameter-dependent sheath width is shown. Multiscale hybrid gas phase/solid surface numerical experiments reveal that under the wide-sheath conditions the nanotips widen at the base and when the sheath is narrow, they sharpen up. By combining the wide- and narrow-sheath stages in a single process, it turns out possible to synthesize wide-base nanotips with long- and narrow-apex spikes, ideal for electron microemitter applications. This plasma-based approach is generic and can be applied to a larger number of multipurpose nanoassemblies. © 2005 American Institute of Physics.

Numerical simulation of self-organized nano-islands in plasma-based assembly of quantum dot arrays

This work presents the details of the numerical model used in simulation of self-organization of nano-islands on solid surfaces in plasma-assisted assembly of quantum dot structures. The model includes the near-substrate non-neutral layer (plasma sheath) and a nanostructured solid deposition surface and accounts for the incoming flux of and energy of ions from the plasma, surface temperature-controlled adatom migration about the surface, adatom collisions with other adatoms and nano-islands, adatom inflow to the growing nano-islands from the plasma and from the two-dimensional vapour on the surface, and particle evaporation to the ambient space and the two-dimensional vapour. The differences in surface concentrations of adatoms in different areas within the quantum dot pattern significantly affect the self-organization of the nano-islands. The model allows one to formulate the conditions when certain islands grow, and certain ones shrink or even dissolve and relate them to the process control parameters. Surface coverage by selforganized quantum dots obtained from numerical simulation appears to be in reasonable agreement with the available experimental results.

Low-temperature assembly of ordered carbon nanotip arrays in low-frequency, high-density inductively coupled plasmas

High-density inductively coupled plasma (ICP)-assisted self-assembly of the ordered arrays of various carbon nanostructures (NS) for the electron field emission applications is reported. Carbon-based nano-particles, nanotips, and pyramid-like structures, with the controllable shape, ordering, and areal density are grown under remarkably low process temperatures (260-350 °C) and pressures (below 0.1 Torr), on the same Ni-based catalyst layers, in a DC bias-controlled floating temperature regime. A high degree of positional and directional ordering, elevated sp2 content, and a well-structured graphitic morphology are achieved without the use of pre-patterned or externally heated substrates.

Self-assembly of uniform carbon nanotip structures in chemically active inductively coupled plasmas

Self-assembly of carbon nanotip (CNTP) structures on Ni-based catalyst in chemically active inductively coupled plasmas of CH 4 + H 2 + Ar gas mixtures is reported. By varying the process conditions, it appears possible to control the shape, size, and density of CNTPs, content of the nanocrystalline phase in the films, as well as to achieve excellent crystallinity, graphitization, uniformity and vertical alignment of the resulting nanostructures at substrate temperatures 300-500°C and low gas pressures (below 13.2 Pa). This study provides a simple and efficient plasma-enhanced chemical vapor deposition (PECVD) technique for the fabrication of vertically aligned CNTP arrays for electron field emitters.

Assembly and self-organization of nanomaterials

The increasing interest in nanoscience and nanotechnology has prompted intense investigations into appropriate fabrication techniques. Self-organized, bottom-up growth of nanomaterials using plasma nanofabrication techniques1–10 has proven to be one of the most promising approaches for the construction of precisely tailored nanostructures (i.e., quantum dots,11–13 nanotubes,14–17 nanowires,18–20 etc.) arrays. Thus the primary aim of this chapter is to show how plasmas may be used to achieve a high level of control during the self-organized growth of a range of nanomaterials, from zero-dimensional quantum dots (Section 15.2) to one- and two-dimensional nanomaterials (Section 15.3) to nanostructured films (Section 15.4)...

Structure and assembly of immature HIV

The major structural components of HIV are synthesized as a 55-kDa polyprotein, Gag. Particle formation is driven by the self-assembly of Gag into a curved hexameric lattice, the structure of which is poorly understood. We used cryoelectron tomography and contrast-transfer-function corrected subtomogram averaging to study the structure of the assembled immature Gag lattice to approximate to 17-angstrom resolution. Gag is arranged in the immature virus as a single, continuous, but incomplete hexameric lattice whose curvature is mediated without a requirement for pentameric defects. The resolution of the structure allows positioning of individual protein domains. High-resolution crystal structures were fitted into the reconstruction to locate protein-protein interfaces involved in Gag assembly, and to identify the structural transformations associated with virus maturation. The results of this study suggest a concept for the formation of nonsymmetrical enveloped viruses of variable sizes.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Centrobin regulates the assembly of functional mitotic spindles

The proper function of the spindle is crucial to the high fidelity of chromosome segregation and is indispensable for tumor suppression in humans. Centrobin is a recently identified centrosomal protein that has a role in stabilizing the microtubule structure. Here we functionally characterize the defects in centrosome integrity and spindle assembly in Centrobin-depleted cells. Centrobin-depleted cells show a range of spindle abnormalities including unfocused poles that are not associated with centrosomes, S-shaped spindles and mini spindles. These cells undergo mitotic arrest and subsequently often die by apoptosis, as determined by live cell imaging. Co-depletion of Mad2 relieves the mitotic arrest, indicating that cells arrest due to a failure to silence the spindle checkpoint in metaphase. Consistent with this, Centrobin-depleted metaphase cells stained positive for BubR1 and BubR1 S676. Staining with a panel of centrosome markers showed a loss of centrosome anchoring to the mitotic spindle. Furthermore, these cells show less cold-stable microtubules and a shorter distance between kinetochore pairs. These results show a requirement of Centrobin in maintaining centrosome integrity, which in turn promotes anchoring of mitotic spindle to the centrosomes. Furthermore, this anchoring is required for the stability of microtubule–kinetochore attachments and biogenesis of tension-ridden and properly functioning mitotic spindle.

A normal-distribution based reputation model

Rating systems are used by many websites, which allow customers to rate available items according to their own experience. Subsequently, reputation models are used to aggregate available ratings in order to generate reputation scores for items. A problem with current reputation models is that they provide solutions to enhance accuracy of sparse datasets not thinking of their models performance over dense datasets. In this paper, we propose a novel reputation model to generate more accurate reputation scores for items using any dataset; whether it is dense or sparse. Our proposed model is described as a weighted average method, where the weights are generated using the normal distribution. Experiments show promising results for the proposed model over state-of-the-art ones on sparse and dense datasets.

Exploitation of the menshutkin reaction for the controlled assembly of halogen bonded architectures incorporating 1,2-diiodotetrafluorobenzene and 1,3,5-Triiodotrifluorobenzene

1,4-Diazabicyclo[2.2.2]octane (DABCO) forms well-defined co-crystals with 1,2-diiodotetrafluorobenzene (1,2-DITFB), [(1,2-DITFB)2DABCO], and 1,3,5-triiodotrifluorobenzene, [(1,3,5-TITFB)2DABCO]. Both systems exhibited lower-than-expected supramolecular connectivity, which inspired a search for polymorphs in alternative crystallization solvents. In dichloromethane solution, the Menshutkin reaction was found to occur, generating chloride anions and quaternary ammonium cations through the reaction between the solvent and DABCO. The controlled in situ production of chloride ions facilitated the crystallization of new halogen bonded networks, DABCO–CH2Cl[(1,2-DITFB)Cl] (zigzag X-bonded chains) and (DABCO–CH2Cl)3[(1,3,5-TITFB)2Cl3]·CHCl3 (2D pseudo-trigonal X-bonded nets displaying Borremean entanglement), propagating with charge-assisted C–I···Cl– halogen bonds. The method was found to be versatile, and substitution of DABCO with triethylamine (TEA) gave (TEA-CH2Cl)3[(1,2-DITFB)Cl3]·4(H2O) (mixed halogen bond hydrogen bond network with 2D supramolecular connectivity) and TEA-CH2Cl[(1,3,5-TITFB)Cl] (tightly packed planar trigonal nets). The co-crystals were typically produced in high yield and purity with relatively predictable supramolecular topology, particularly with respect to the connectivity of the iodobenzene molecules. The potential to use this synthetic methodology for crystal engineering of halogen bonded architectures is demonstrated and discussed.

Glutathione transferase activities in renal carcinomas and adjacent normal renal tissues : factors influencing renal carcinogenesis induced by xenobiotics

In general, the biological activation of nephrocarcinogenic chlorinated hydrocarbons proceeds via conjugatiton with glutathione. It has mostly been assamed that the main site of initial conjugation is the liver, followed by a mandatory transfer of intermediates to the kidney. It was therefore of interest to study the enzyme activities of subgroups of glutathione transferases (GSTs) in renal cancers and the surrounding normal renal tissues of the same individuals (n = 21). For genotyping the individuals with respect to known polymorphic GST isozymes the following substrates with differential specificity were used: 1-chloro-2,4-dinitrobenzene for overall GST activity (except GST θ); 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole for GST α; 1,2-dichloro-4-nitro-benzene for GST μ; ethacrynic acid and 4-vinylpyridine for GST π; and methyl chloride for GST θ. In general, the normal tissues were able to metabolize the test substrates. A general decrease in individual GST enzyme activities was apparent in the course of cancerization, and in some (exceptional) cases individual activities, expressed in the normal renal tissue, were lost in the tumour tissue. The GST enzyme activities in tumours were independent of tumour stage, or the age and gender of the patients. There was little influence of known polymorphisms of GSTM1, GSTM3 and GSTP1 upon the activities towards the test substrates, whereas the influence of GSTT1 polymorphism on the activity towads methyl chloride was straightforward. In general, the present findings support the concept that the initial GST-dependent bioactivation step of nephrocarcinogenic chlorinated hydrocarbons may take place in the kidney itself. This should be a consideration in toxicokinetic modelling.

Glutathione transferase Ti and M1 genotype polymorphism in the normal population of Shanghai

Glutathione transferases are known to be important enzymes in the metabolism of xenobiotics. In humans genetic polymorphisms have been reported for the hGSTM1 and hGSTT1 genes leading to individual differences in susceptibility towards toxic effects, such as cancer. This study describes the distribution of the two polymorphisms of hGSTT1 and hGSTM1 in the normal Chinese population of Shanghai. Out of 219 healthy individuals having been genotyped for GSTTI and GSTMI, 108 (49%) were identified to be homozygously deficient for the GSTT1 gene and 107 (49%) for the GSTM1 gene.

Adsorption thermodynamics and kinetics study for the self-assembly of 1,8,15,22-tetraaminophthalocyanatocobalt(II) on glassy carbon surface

Spontaneous adsorption of 1,8,15,22-tetraaminophthalocyanatocobalt(II) (4α-CoIITAPc) on glassy carbon (GC) electrode leads to the formation of a stable self-assembled monolayer (SAM). Since the SAM of 4α-CoIITAPc is redox active, its adsorption on GC electrode was followed by cyclic voltammetry. SAM of 4α-CoIITAPc on GC electrode shows two pairs of well-defined redox peaks corresponding to CoIII/CoII and CoIIIPc−1/CoIIIPc−2. The surface coverage (Γ) value, calculated by integrating the charge under CoII oxidation, was used to study the adsorption thermodynamics and kinetics of 4α-CoIITAPc on GC surface. Cyclic voltammetric studies show that the adsorption of 4α-CoIITAPc on GC electrode has reached the saturation coverage (Γs) within 3 h. The Γs value for the SAM of 4α-CoIITAPc on GC electrode was found to be 2.37 × 10−10 mol cm−2. Gibbs free energy (ΔGads) and adsorption rate constant (kad) for the adsorption of 4α-CoIITAPc on GC surface were found to be −16.76 kJ mol−1 and 7.1 M−1 s−1, respectively. The possible mechanism for the self-assembly of 4α-CoIITAPc on GC surface is through the addition of nucleophilic amines to the olefinic bond on the GC surface in addition to a meager contribution from π stacking. The contribution of π stacking was confirmed from the adsorption of unsubstituted phthalocyanatocobalt(II) (CoPc) on GC electrode. Raman spectra for the SAM of 4α-CoIITAPc on carbon surface shows strong stretching and breathing bands of Pc macrocycle, pyrrole ring and isoindole ring. Raman and CV studies suggest that 4α-CoIITAPc is adopting nearly a flat orientation or little bit tilted orientation.