Discrete element calculations of the impact of a sand column against rigid structures

Discrete particle simulations of column of an aggregate of identical particles impacting a rigid, fixed target and a rigid, movable target are presented with the aim to understand the interaction of an aggregate of particles upon a structure. In most cases the column of particles is constrained against lateral expansion. The pressure exerted by the particles upon the fixed target (and the momentum transferred) is independent of the co-efficient of restitution and friction co-efficient between the particles but are strongly dependent upon the relative density of the particles in the column. There is a mild dependence on the contact stiffness between the particles which controls the elastic deformation of the densified aggregate of particles. In contrast, the momentum transfer to a movable target is strongly sensitive to the mass ratio of column to target. The impact event can be viewed as an inelastic collision between the sand column and the target with an effective co-efficient of restitution between 0 and 0.35 depending upon the relative density of the column. We present a foam analogy where impact of the aggregate of particles can be modelled by the impact of an equivalent foam projectile. The calculations on the equivalent projectile are significantly less intensive computationally and yet give predictions to within 5% of the full discrete particle calculations. They also suggest that "model" materials can be used to simulate the loading by an aggregate of particles within a laboratory setting. © 2012 Elsevier Ltd. All rights reserved.

In vitro activities of small peptides from snake venom against clinical isolates of drug-resistant Mycobacterium tuberculosis

The recent re-emergence of tuberculosis, especially the multidrug-resistant cases, has highlighted the importance of screening effective novel drugs against Mycobacterium tuberculosis. In this study, the in vitro activities of small peptides isolated from snake venom were investigated against multidrug-resistant M. tuberculosis. Minimum inhibitory concentrations (MICs) were determined by the Bactec TB-460 radiometric method. A small peptide with the amino acid sequence ECYRKSDIVTCEPWQKFCYREVTFFPNHPVYLSGCASECTETNSKWCCTTDKCNRARGG (designated as vgf-1) from Naja atra (isolated from Yunnan province of China) venom had in vitro activity against clinically isolated multidrug-resistant strains of M. tuberculosis. The MIC was 8.5 mg/l. The antimycobacterial domain of this 60aa peptide is under investigation. (C) 2003 Elsevier Science B.V. and the International Society of Chemotherapy. All rights reserved.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Device and circuit-level performance of carbon nanotube field-effect transistor with benchmarking against a nano-MOSFET

The performance of a semiconducting carbon nanotube (CNT) is assessed and tabulated for parameters against those of a metal-oxide-semiconductor field-effect transistor (MOSFET). Both CNT and MOSFET models considered agree well with the trends in the available experimental data. The results obtained show that nanotubes can significantly reduce the drain-induced barrier lowering effect and subthreshold swing in silicon channel replacement while sustaining smaller channel area at higher current density. Performance metrics of both devices such as current drive strength, current on-off ratio (Ion/Ioff), energy-delay product, and power-delay product for logic gates, namely NAND and NOR, are presented. Design rules used for carbon nanotube field-effect transistors (CNTFETs) are compatible with the 45-nm MOSFET technology. The parasitics associated with interconnects are also incorporated in the model. Interconnects can affect the propagation delay in a CNTFET. Smaller length interconnects result in higher cutoff frequency. © 2012 Tan et al.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages.

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation.

Nanobodies raised against monomeric α-synuclein distinguish between fibrils at different maturation stages

Nanobodies are single-domain fragments of camelid antibodies that are emerging as versatile tools in biotechnology. We describe here the interactions of a specific nanobody, NbSyn87, with the monomeric and fibrillar forms of α-synuclein (αSyn), a 140-residue protein whose aggregation is associated with Parkinson's disease. We have characterized these interactions using a range of biophysical techniques, including nuclear magnetic resonance and circular dichroism spectroscopy, isothermal titration calorimetry and quartz crystal microbalance measurements. In addition, we have compared the results with those that we have reported previously for a different nanobody, NbSyn2, also raised against monomeric αSyn. This comparison indicates that NbSyn87 and NbSyn2 bind with nanomolar affinity to distinctive epitopes within the C-terminal domain of soluble αSyn, comprising approximately amino acids 118-131 and 137-140, respectively. The calorimetric and quartz crystal microbalance data indicate that the epitopes of both nanobodies are still accessible when αSyn converts into its fibrillar structure. The apparent affinities and other thermodynamic parameters defining the binding between the nanobody and the fibrils, however, vary significantly with the length of time that the process of fibril formation has been allowed to progress and with the conditions under which formation occurs, indicating that the environment of the C-terminal domain of αSyn changes as fibril assembly takes place. These results demonstrate that nanobodies are able to target forms of potentially pathogenic aggregates that differ from each other in relatively minor details of their structure, such as those associated with fibril maturation. © 2013 Elsevier Ltd.

The impact of sand slugs against beams and plates: Coupled discrete particle/finite element simulations

The impact of a slug of dry sand particles against a metallic sandwich beam or circular sandwich plate is analysed in order to aid the design of sandwich panels for shock mitigation. The sand particles interact via a combined linear-spring-and-dashpot law whereas the face sheets and compressible core of the sandwich beam and plate are treated as rate-sensitive, elastic-plastic solids. The majority of the calculations are performed in two dimensions and entail the transverse impact of end-clamped monolithic and sandwich beams, with plane strain conditions imposed. The sand slug is of rectangular shape and comprises a random loose packing of identical, circular cylindrical particles. These calculations reveal that loading due to the sand is primarily inertial in nature with negligible fluid-structure interaction: the momentum transmitted to the beam is approximately equal to that of the incoming sand slug. For a slug of given incoming momentum, the dynamic deflection of the beam increases with decreasing duration of sand-loading until the impulsive limit is attained. Sandwich beams with thick, strong cores significantly outperform monolithic beams of equal areal mass. This performance enhancement is traced to the "sandwich effect" whereby the sandwich beams have a higher bending strength than that of the monolithic beams. Three-dimensional (3D) calculations are also performed such that the sand slug has the shape of a circular cylindrical column of finite height, and contains spherical sand particles. The 3D slug impacts a circular monolithic plate or sandwich plate and we show that sandwich plates with thick strong cores again outperform monolithic plates of equal areal mass. Finally, we demonstrate that impact by sand particles is equivalent to impact by a crushable foam projectile. The calculations on the equivalent projectile are significantly less intensive computationally, yet give predictions to within 5% of the full discrete particle calculations for the monolithic and sandwich beams and plates. These foam projectile calculations suggest that metallic foam projectiles can be used to simulate the loading by sand particles within a laboratory setting. © 2013 Elsevier Ltd.

Remediation against floatation of underground structures

Underground structures located in liquefiable soil deposits are susceptible to floatation following an earthquake event due to their lower unit weight relative to the surrounding saturated soil. Centrifuge tests have been carried out to assess the effectiveness of existing remediation techniques in reducing the uplift of underground structures, namely in situ densification and the use of coarse sand backfill. The centrifuge test results showed that these methods do reduce the uplift displacement of buoyant structures. Their performance was thereafter linked to the theoretical mechanism of floatation of underground structures. Based on the understanding from preceding tests, a further improvement on the use of the coarse sand backfill was carried out, which produced a greater reduction in the uplift displacement of the structure. Each of these techniques, however, does pose issues when applied in the field, such as possible damage to surrounding structures, construction issues and maintenance problems.

Comparison of ilities for protection against uncertainty in system design

The concepts of reliability, robustness, adaptability, versatility, resilience and flexibility have been used to describe how a system design can mitigate the likely impact of uncertainties without removing their sources. With the increasing number of publications on designing systems to have such ilities, there is a need to clarify the relationships between the different ideas. This short article introduces a framework to compare these different ways in which a system can be insensitive to uncertainty, clarifying their meaning in the context of complex system design. We focus on relationships between the ilities listed above and do not discuss in detail methods to design-for-ilities. © 2013 The Author(s). Published by Taylor & Francis.

Enhanced protection against oxidative stress in an astaxanthin-overproduction Haematococcus mutant (Chlorophyceae)

Many unicellular green algae can become yellow or red in various natural habitats due to mass accumulation of a secondary carotenoid, such as lutein, or astaxanthin. The accumulation of secondary carotenoids is generally thought to be a survival strategy of the algae under photo-oxidative stress or other adverse environmental conditions. The physiological role of the carotenoids in stress response is less well understood at the subcellular or molecular level. In this study, a stable astaxanthin overproduction mutant (MT 2877) was isolated by chemical mutagenesis of a wild type (WT) of the green microalga Haematococcus pluvialis Flotow NIES-144. MT 2877 was identical to the WT with respect to morphology, pigment composition, and growth kinetics during the early vegetative stage of the life cycle. However, it had the ability to synthesize and accumulate about twice the astaxanthin content of the WT under high light, or under high light in the presence of excess amounts of ferrous sulphate and sodium acetate. Under stress, the mutant exhibited higher photosynthetic activities than the WT, based on considerably higher chlorophyll fluorescence induction, chlorophyll autofluorescence intensities, and oxygen evolution rates. Cell mortality caused by stress was reduced by half in the mutant culture compared with the WT. Enhanced protection of the mutant against stress is attributed to its accelerated carotenogenesis and accumulation of astaxanthin. Our results suggest that MT 2877, or other astaxanthin overproduction Haematococcus mutants, may offer dual benefits, as compared with the wild type, by increasing cellular astaxanthin content while reducing cell mortality during stress-induced carotenogenesis.

Generation and characterization of monoclonal antibodies against the flounder Paralichthys olivaceus rhabdovirus

Two MAbs (3C7 and 3C9) against flounder Paralichthys olivaceus rhabdovirus (PORV) were generated with hybridoma cell fusion technology and characterized by an indirect enzyme-linked immunosorbent assay, isotype test, Western blot and immunodot analysis and immunofluorescence assay. Isotyping tests demonstrated that both of the two MAbs belonged to IgM subclass. Western blot analysis showed the MAbs reacted with 42, 30, and 22 kDa viral proteins, which were localized within the cytoplasm of PORV-infected grass carp ovary (GCO) cells analyzed by indirect immunofluorescences tests. The MAb 3C7 was also selected at random for detecting virus antigens in the inoculated grass carp tissues by immunohistochemistry assay. Flow cytometry tests showed that at the 36 h postinfection (0.25 PFU/cell), the 23% PORV-infected GCO cells could be distinguished from the uninfected cells with the MAb 3C7. Such MAbs could be useful for diagnosis and potential treatment of viral infection. (C) 2007 Elsevier B.V. All rights reserved.

The response of antioxidant systems in Nostoc sphaeroides against UV-B radiation and the protective effects of exogenous antioxidants

UV radiation is one of many harmful factors found in space that are detrimental to organisms on earth in space exploration. In the present work, we examined the role of antioxidant system in Nostoc sphaeroides Kutz (Cyanobacterium) and the effects of exogenously applied antioxidant molecules on its photosynthetic rate under UV-B radiation. It was found that UV-B radiation promoted the activity of antioxidant system to protect photosystem 11 (PSII) and exogenously applied antioxidant: sodium nitroprusside (SNP) and N-acetylcysteine (NAC) had an obvious protection on PSII activity under UV-B radiation. The activity of superoxide dismutase (SOD, EC 1.15.1.1), catalase (CAT, EC 1.11.1.6), peroxidase (POD, EC 1.11.1.7) and content of NIDA (malondialdehyde) and ASC (ascorbate) were improved by 0.5 mM and 1 mM SNP, but 0.1 mM SNP decreased the activity of antioxidant system. Addition of exogenous NAC decreased the activity of SOD, POD, CAT and the content MDA and ASC. In contrast, exogenously applied NAC increased GSH content. The results suggest that exogenous SNP and NAC may protect algae by different mechanisms: SNP may play double roles as both sources of reactive free radicals as well as ROS scavengers in mediating the protective role of PSII on algae under UV-B radiation. On the other hand, NAC functions as an antioxidant or precursor of glutathione, which could protect PSII directly from UV-B radiation. (c) 2007 COSPAR, Published by Elsevier Ltd. All rights reserved.

The involvement of the antioxidant system in protection of desert cyanobacterium Nostoc sp against UV-B radiation and the effects of exogenous antioxidants

In this study, we found that UV-B radiation decreased photosynthetic activity and boosted lipid peroxidation of desert Nostoc sp., and exogenous chemicals (ascorbate acid (ASC), N-acetylcysteine (NAC), and sodium nitroprusside (SNP)) had obvious protective effects on photosynthesis and membranes under UV-B radiation. High-concentration SNP boosted the activities of antioxidant enzymes, but low-concentration SNP reduced the activities of antioxidant enzymes. Both NAC and ASC treatments of cells decreased activities of antioxidant enzymes. The results suggested that those chemicals possibly had different mechanisms of protection of algae cells against UV-B radiation. SNP might play double roles as a signal molecule in the formation of algae cell protection of Photosystem 11 under UV-B radiation and as a (reactive oxygen species) scavenger, while NAC and ASC might function as antioxidant reagents or precursors of other antioxidant molecules, which could protect cells directly against ROS initiated by UV-B radiation. (c) 2006 Elsevier Inc. All rights reserved.