Mechanisms of variability and predictability of the tropical coupled ocean-atmosphere system

A conceptual model is proposed to explain the observed aperiodicity in the short term climate fluctuations of the tropical coupled ocean-atmosphere system. This is based on the evidence presented here that the tropical coupled ocean-atmosphere system sustains a low frequency inter-annual mode and a host of higher frequency intra-seasonal unstable modes. At long wavelengths, the low frequency mode is dominant while at short wavelengths, the high frequency modes are dominant resulting in the co-existence of a long wave low frequency mode with some short wave intra-seasonal modes in the tropical coupled system. It is argued that due to its long wavelength, the low frequency mode would behave like a linear oscillator while the higher frequency short wave modes would be nonlinear. The conceptual model envisages that an interaction between the low frequency linear oscillator and the high frequency nonlinear oscillations results in the observed aperiodicity of the tropical coupled system. This is illustrated by representing the higher frequency intra-seasonal oscillations by a nonlinear low order model which is then coupled to a linear oscillator with a periodicity of four years. The physical mechanism resulting in the aperiodicity in the low frequency oscillations and implications of these results on the predictability of the coupled system are discussed.

Dynamics of zeolite cage and its effect on the diffusion properties of sorbate: persistence of diffusion anomaly in NaA zeolite

Recent computer simulations on zeolites Y and A have found that the diffusion coefficient and the rate of intercage diffusion exhibit, apart from a linear dependence on the reciprocal of the square of the sorbate diameter, an anomalous peak as sorbate diameter approaches the window diameter. Here we report molecular dynamics simulations of zeolite NaA incorporating framework flexibility as a function of sorbate diameter in order to verify the existence of anomalous diffusion. Results suggest persistence of anomalous diffusion or ring effect. This suggests that the anomalous behavior is a general effect characteristic of zeolites Y and A. The barrier for diffusion across the eight-ring window is seen to be negative and is found to decrease with sorbate size. The effect of sorbate on the cage motion has also been investigated. Results suggest that the window expands during intercage migration only if the sorbate size is comparable to the window diameter. Flexible cage simulations yield a higher value for the diffusion coefficient and also the rate of intercage diffusion. This increase has been shown to be due to an increase in the intercage diffusions via the centralized diffusion mode rather than the surface-mediated mode. It is shown that this increase arises from an increase in the single particle density distribution in the region near the cage center.

Quantum theoretical study of molecular mechanisms of mutation and cancer - A review

Several endogenous and exogenous chemical species, particularly the so-called reactive oxygen species (ROS) and reactive nitrogen oxide species (RNOS), attack deoxyribonucleic acid (DNA) in biological systems producing DNA lesions which hamper normal cell functioning and cause various diseases including mutation and cancer. The guanine (G) base of DNA among all the bases is most susceptible and certain modified guanines get involved in mispairing with other bases during DNA replication. The biological system repairs the abnormal base pairs, but those that are still left cause mutation and cancer. Anti-oxidants present in biological systems can scavenge the ROS and RNOS. Thus three types of molecular events occur in biological media: (i) DNA damage, (ii) DNA repair, and (iii) prevention of DNA damage by scavenging ROS and RNOS. Quantum mechanical methods may be used to unravel molecular mechanisms of such phenomena. Some recent quantum theoretical results obtained on these problems are reviewed here.

Structural basis for the functional and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Plasmodium falciparum

The beta-hydroxyacyl-acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) catalyzes the third and important reaction of the fatty acid elongation cycle. The crystal structure of PfFabZ is available in hexameric (active) and dimeric (inactive) forms. However, PfFabZ has not been crystallized with any bound inhibitors until now. We have designed a new condition to crystallize PfFabZ with its inhibitors bound in the active site, and determined the crystal structures of four of these complexes. This is the first report on any FabZ enzyme with active site inhibitors that interact directly with the catalytic residues. Inhibitor binding not only stabilized the substrate binding loop but also revealed that the substrate binding tunnel has an overall shape of ``U''. In the crystal structures, residue Phe169 located in the middle of the tunnel was found to be in two different conformations, open and closed. Thus, Phe169, merely by changing its side chain conformation, appears to be controlling the length of the tunnel to make it suitable for accommodating longer substrates. The volume of the substrate binding tunnel is determined by the sequence as well as by the conformation of the substrate binding loop region and varies between organisms for accommodating fatty acids of different chain lengths. This report on the crystal structures of the complexes of PfFabZ provides the structural basis of the inhibitory mechanism of the enzyme that could be used to improve the potency of inhibitors against an important component of fatty acid synthesis common to many infectious organisms. (C) 2011 Elsevier Inc. All rights reserved.

Mechanisms of summer intraseasonal sea surface temperature oscillations in the Bay of Bengal

Intraseasonal variations (ISV) of sea surface temperature (SST) in the Bay of Bengal (BoB) is highest in its northwestern part. An Indian Ocean model forced by QuikSCAT winds and climatological river discharge (QR run) reproduces ISV of SST, albeit with weaker magnitude. Air-sea fluxes, in the presence of a shallow mixed layer, efficiently effect intraseasonal SST fluctuations. Warming during intraseasonal events is smaller (<1°C) for June - July period and larger (1.5° to 2°C) during September, the latter due to a thinner mixed layer. To examine the effect of salinity on ISV, the model was run by artificially increasing the salinity (NORR run) and by decreasing it (MAHA10 run). In NORR, both rainfall and river discharge were switched off and in MAHA10 the discharge by river Mahanadi was increased tenfold. The spatial pattern of ISV as well as its periodicity was similar in QR, NORR and MAHA10. The ISV was stronger in NORR and weaker in MAHA10, compared to QR. In NORR, both intraseasonal warming and cooling were higher than in QR, the former due to reduced air-sea heat loss as the mean SST was lower, and the latter due to enhanced subsurface processes resulting from weaker stratification. In MAHA10, both warming and cooling were lower than in QR, the former due to higher air-sea heat loss owing to higher mean SST, and the latter due to weak subsurface processes resulting from stronger stratification. These model experiments suggest that salinity effects are crucial in determining amplitudes of intraseasonal SST variations in the BoB.

Some mechanisms of tribofilm formation in metal/metal and ceramic/metal sliding interactions

Tribological interaction often generates new structures and materials which form the interface between the sliding pair. The new material designated tribofilm here may be protective or tribologically deleterious. The tribofilm plays a major role in determining the friction and wear of the interaction. Here, we give three examples: mechanically mixed, chemically generated and thermally activated, of tribofilms formed in three different tribological systems and speculate on the mechanism of their formation.

Distinct mechanisms of DNA repair in mycobacteria and their implications in attenuation of the pathogen growth

About a third of the human population is estimated to be infected with Mycobacterium tuberculosis. Emergence of drug resistant strains and the protracted treatment strategies have compelled the scientific community to identify newer drug targets, and to develop newer vaccines. In the host macrophages, the bacterium survives within an environment rich in reactive nitrogen and oxygen species capable of damaging its genome. Therefore, for its successful persistence in the host, the pathogen must need robust DNA repair mechanisms. Analysis of M. tuberculosis genome sequence revealed that it lacks mismatch repair pathway suggesting a greater role for other DNA repair pathways such as the nucleotide excision repair, and base excision repair pathways. In this article, we summarize the outcome of research involving these two repair pathways in mycobacteria focusing primarily on our own efforts. Our findings, using Mycobacterium smegmatis model, suggest that deficiency of various DNA repair functions in single or in combinations severely compromises their DNA repair capacity and attenuates their growth under conditions typically encountered in macrophages. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Study on important diffusion parameters of binary Ni3Sn4 phase

Important diffusion parameters, such as-parabolic growth constant, integrated diffusivity, ratio of intrinsic diffusivities of species Ni and Sn, Kirkendall marker velocity and the activation energy for diffusion kinetics of binary Ni3Sn4 phase have been investigated with the help of incremental diffusion couple technique (Sn/Ni0.57Sn0.43) in the temperature range 200-150 degrees C. Low activation energy extracted from Arrhenius plot indicates grain boundary controlled diffusion process. The species Sn is three times faster than Ni at 200 degrees C. Further, the activation energy of Sn tracer diffusivity is greater than that of Ni.

Microstructure-Wear Resistance Correlation and Wear Mechanisms of Spark Plasma Sintered Cu-Pb Nanocomposites

The dispersion of a softer phase in a metallic matrix reduces the coefficient of friction (COF), often at the expense of an increased wear rate at the tribological contact. To address this issue, unlubricated fretting wear tests were performed on spark plasma sintered Cu-Pb nanocomposites against bearing steel. The sintering temperature and the Pb content as well as the fretting parameters were judiciously selected and varied to investigate the role of microstructure (grain size, second-phase content) on the wear resistance properties of Cu-Pb nanocomposites. A combination of the lowest wear rate (similar to 1.5 x 10(-6) mm(3)/Nm) and a modest COF (similar to 0.4) was achieved for Cu-15 wt pct Pb nanocomposites. The lower wear rate of Cu-Pb nanocomposites with respect to unreinforced Cu is attributed to high hardness (similar to 2 to 3.5 GPa) of the matrix, Cu2O/Fe2O3-rich oxide layer formation at tribological interface, and exuding of softer Pb particles. The wear properties are discussed in reference to the characteristics of transfer layer on worn surface as well as subsurface damage probed using focused ion beam microscopy. Interestingly, the flash temperature has been found to have insignificant effect on the observed oxidative wear, and alternative mechanisms are proposed. Importantly, the wear resistance properties of the nanocomposites reveal a weak Hall-Petch-like relationship with grain size of nanocrystalline Cu. (C) The Minerals, Metals & Materials Society and ASM International 2013

In vitro/In vivo assessment and mechanisms of toxicity of bioceramic materials and its wear particulates

With the progress in modern technological research, novel biomaterials are being largely developed for various biomedical applications. Over the past two decades, most of the research focuses on the development of a new generation of bioceramics as substitutes for hard tissue replacement. In reference to their application in different anatomical locations of a patient, newly developed bioceramic materials can potentially induce a toxic/harmful effect to the host tissues. Therefore, prior to clinical testing, relevant biochemical screening assays are to be performed at the cellular and molecular level, to address the issues of biocompatibility and long term performance of the implants. Along with testing strategies in the bulk material toxicity, a detailed evaluation should also be conducted to determine the toxicity of the wear products of the potential bioceramics. This is important as the bioceramics are intended to be implanted in patients with longer life expectancy and notwithstanding, the material will eventually release finer (mostly nanosized) sized debris particles due to continuous wear at articulating surfaces in the hostile corrosive environment of the human body. The wear particulates generated from a biocompatible bioceramic may act in a different way, inducing early/late aseptic loosening at the implant site, resulting in osteolysis and inflammation. Hence, a study on the chronic effects of the wear particulates, in terms of local and systemic toxicity becomes the major criteria in the toxicity evaluation of implantable bioceramics. In this broad perspective, this article summarizes some of the currently used techniques and knowledge in assessing the in vitro and in vivo cytotoxicity and genotoxicity of bioceramic implant materials. It also addresses the need to conduct a broad evaluation before claiming the biocompatibility and clinical feasibility of any new biomaterial. This review also emphasizes some of the case studies based on the experimental designs that are currently followed and its importance in the context of clinical applications.

Wallner lines, crack velocity and mechanisms of crack nucleation and growth in a brittle bulk metallic glass

Mode I fracture experiments were conducted on brittle bulk metallic glass (BMG) samples and the fracture surface features were analyzed in detail to understand the underlying physical processes. Wollner lines, which result from the interaction between the propagating crack front and shear waves emanating from a secondary source, were observed on the fracture surface and geometric analysis of them indicates that the maximum crack velocity is similar to 800 m s(-1), which corresponds to similar to 0.32 times the shear wave speed. Fractography reveals that the sharp crack nucleation at the notch tip occurs at the mid-section of the specimens with the observation of flat and half-penny-shaped cracks. On this basis, we conclude that the crack initiation in brittle BMGs is stress-controlled and occurs through hydrostatic stress-assisted cavity nucleation ahead of the notch tip. High magnification scanning electron and atomic force microscopies of the dynamic crack growth regions reveal highly organized, nanoscale periodic patterns with a spacing of similar to 79 nm. Juxtaposition of the crack velocity with this spacing suggests that the crack takes similar to 10(-10) s for peak-to-peak propagation. This, and the estimated adiabatic temperature rise ahead of the propagating crack tip that suggests local softening, is utilized to critically discuss possible causes for the nanocorrugation formation. Taylor's fluid meniscus instability is unequivocally ruled out. Then, two other possible mechanisms, viz. (a) crack tip blunting and resharpening through nanovoid nucleation and growth ahead of the crack tip and eventual coalescence, and (b) dynamic oscillation of the crack in a thin slab of softened zone ahead of the crack-tip, are critically discussed. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.