On the relationship between finger width, velocity, and fluxes in thermohaline convection

Double-diffusive finger convection occurs in many natural processes.The theories for double-diffusive phenomena that exist at present consider systems with linear stratification in temperature and salinity. The double-diffusive systems with step change in salinity and temperature are, however, not amenable to simple stability analysis. Hence factors that control the width of the finger, velocity, and fluxes in systems that have step change in temperature and salinity have not been understood so far. In this paper we provide new physical insight regarding factors that influence finger convection in two-layer double-diffusive system through two-dimensional numerical simulations. Simulations have been carried out for density stability ratios (R-rho) from 1.5 to 10. For each density stability ratio, the thermal Rayleigh number (Ra-T) has been systematically varied from 7x10(3) to 7x10(8). Results from these simulations show how finger width, velocity, and flux ratios in finger convection are interrelated and the influence of governing parameters such as density stability ratio and the thermal Rayleigh number. The width of the incipient fingers at the time of onset of instability has been shown to vary as Ra-T-1/3. Velocity in the finger varies as Ra(T)1/3/R-rho. Results from simulation agree with the scale analysis presented in the paper. Our results demonstrate that wide fingers have lower velocities and flux ratios compared to those in narrow fingers. This result contradicts present notions about the relation between finger width and flux ratio. A counterflow heat-exchanger analogy is used in understanding the dependence of flux ratio on finger width and velocity.

Approximate potential-distance relationship for clays

The conventional procedure of determining the surface potential of clay platelet and the variation of potential with distance is lengthy and time consuming. Simplified graphical procedures using Gouy theory have been developed and presented. The new procedures are simple, accurate and very much less time consuming.

GEODERM: geometric shape design system using an entity-relationship model

GEODERM, a microcomputer-based solid modeller, which incorporates the parametric object model, is discussed. The entity-relationship model, which is used to describe the conceptual schema of the geometric database, is also presented. Three of the four modules of GEODERM, which have been implemented are described in some detail. They are the Solid Definition Language (SDL), the Solid Manipulation Language (SML) and the User-System Interface.

Use of protein A gene fusions for the analysis of structure-function relationship of the transactivator protein C of bacteriophage Mu

A sensitive dimerization assay for DNA binding proteins has been developed using gene fusion technology. For this purpose, we have engineered a gene fusion using protein A gene of Staphylococcus aureus and C gene, the late gene transactivator of bacteriophage Mu. The C gene was fused to the 3' end of the gene for protein A to generate an A- C fusion. The overexpressed fusion protein was purified in a single step using immunoglobulin affinity chromatography. Purified fusion protein exhibits DNA binding activity as demonstrated by electrophoretic mobility shift assays. When the fusion protein A-C was mixed with C and analyzed for DNA binding, in addition to C and A-C specific complexes, a single intermediate complex comprising of a heterodimer of C and A-C fusion proteins was observed. Further, the protein A moiety in the fusion protein A-C does not contribute to DNA binding as demonstrated by proteolytic cleavage and circular dichroism (CD) analysis. The assay has also been applied to analyze the DNA binding domain of C protein by generating fusions between protein A and N- and C-terminal deletion mutants of C. The results indicate a role for the region towards the carboxy terminal of the protein in DNA binding. The general applicability of this method is discussed.

On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation

Prediction of thermodynamic parameters of protein-protein and antigen-antibody complex formation from high resolution structural parameters has recently received much attention, since an understanding of the contributions of different fundamental processes like hydrophobic interactions, hydrogen bonding, salt bridge formation, solvent reorganization etc. to the overall thermodynamic parameters and their relations with the structural parameters would lead to rational drug design. Using the results of the dissolution of hydrocarbons and other model compounds the changes in heat capacity (DeltaCp), enthalpy (DeltaH) and entropy (DeltaS) have been empirically correlated with the polar and apolar surface areas buried during the process of protein folding/unfolding and protein-ligand complex formation. In this regard, the polar and apolar surfaces removed from the solvent in a protein-ligand complex have been calculated from the experimentally observed values of changes in heat capacity (DeltaCp) and enthalpy (DeltaH) for protein-ligand complexes for which accurate thermodynamic and high resolution structural data are available, and the results have been compared with the x-ray crystallographic observations. Analyses of the available results show poor correlation between the thermodynamic and structural parameters. Probable reasons for this discrepancy are mostly related with the reorganization of water accompanying the reaction which is indeed proven by the analyses of the energetics of the binding of the wheat germ agglutinin to oligosaccharides.

O6-Methylguanine Repair by O6-Alkylguanine-DNA Alkyltransferase

O6-Alkylguanine-DNA alkyltransferase (AGT) repairs O6-methylguanine (O6mG) in DNA that is known to cause Mutation and cancer. On the basis of Calculations performed using density functional theory involving the active site of AGT, a mechanism for catalytic demethylation of O6mG to guanine has been proposed. In this mechanism, roles of six amino acids, i.e., Cys145, His 146, Glu172, Tyr114, Lys165, and Ser159 in catalytic demethylation of O6mG are involved. This mechanism has three steps as follows. At the first step, Cys145 in the Cys145-water-His146-Glu172 tetrad is converted to cysteine thiolate anion while at the second step, abstraction of the Tyr114 proton by the N3 site of O6mG occurs in a barrierless manner. In the third step, abstraction of Lys165 proton by deprotonated Tyr114 and transfer of the methyl group of O6mG to the thiolate group of Cys145 anion Occur simultaneously. As AGT is a major target in cancer therapy, identification of the roles of the different amino acids in demethylation of O6mG is expected to be useful in designing efficient AGT inhibitors.

Two-level k-means clustering algorithm for k-tau relationship establishment and linear-time classification

Partitional clustering algorithms, which partition the dataset into a pre-defined number of clusters, can be broadly classified into two types: algorithms which explicitly take the number of clusters as input and algorithms that take the expected size of a cluster as input. In this paper, we propose a variant of the k-means algorithm and prove that it is more efficient than standard k-means algorithms. An important contribution of this paper is the establishment of a relation between the number of clusters and the size of the clusters in a dataset through the analysis of our algorithm. We also demonstrate that the integration of this algorithm as a pre-processing step in classification algorithms reduces their running-time complexity.

Mycobacterial Stress Regulation: The Dps ``Twin Sister'' Defense Mechanism and Structure-Function Relationship

In this work, we have tried to emphasize the connection between mycobacterial growth and regulation of gene expression. Utilization of multiple carbon sources and diauxic growth helps bacteria to regulate gene expression at an optimum level so that the inhospitable conditions encountered during nutrient depletion can be circumvented. These aspects will be discussed with respect to mycobacterial growth in subsequent sections. Identification and characterization of genes induced under such conditions is helpful to understand the physiology of the bacterium. Although it is necessary to compare the total expression profile of proteins as they transit from vegetative growth to stationary phase, at times a lot of insights can be deciphered from the expression pattern of one or two proteins. We have compared the protein expression and sigma factor selectivity of two such proteins in M. smegmatis to understand the differential regulation of genes playing diverse function in the same species. Some newer insights on the structure and function of one of the Dps proteins are also explained.

Relationship between annual rainfall and tree mortality in a tropical dry forest: Results of a 19-year study at Mudumalai, southern India

Variability in rainfall is known to be a major influence on the dynamics of tropical forests, especially rates and patterns of tree mortality. In tropical dry forests a number of contributing factors to tree mortality, including dry season fire and herbivory by large herbivorous mammals, could be related to rainfall patterns, while loss of water potential in trees during the dry season or a wet season drought could also result in enhanced rates of death. While tree mortality as influenced by severe drought has been examined in tropical wet forests there is insufficient understanding of this process in tropical dry forests. We examined these causal factors in relation to inter-annual differences in rainfall in causing tree mortality within a 50-ha Forest Dynamics Plot located in the tropical dry deciduous forests of Mudumalai, southern India, that has been monitored annually since 1988. Over a 19-year period (1988-2007) mean annual mortality rate of all stems >1 cm dbh was 6.9 +/- 4.6% (range = 1.5-17.5%); mortality rates broadly declined from the smaller to the larger size classes with the rates in stems >30 cm dbh being among the lowest recorded in tropical forest globally. Fire was the main agent of mortality in stems 1-5 cm dbh, elephant-herbivory in stems 5-10 cm dbh, and other natural causes in stems > 10 cm dbh. Elephant-related mortality did not show any relationship to rainfall. On the other hand, fire-related mortality was significantly negatively correlated to quantity of rainfall during the preceding year. Mortality due to other causes in the larger stem sizes was significantly negatively correlated to rainfall with a 2-3-year lag, suggesting that water deficit from mild or prolonged drought enhanced the risk of death but only with a time lag that was greater than similar lags in tree mortality observed in other forest types. In this respect, tropical dry forests growing in regions of high rainfall variability may have evolved greater resistance to rainfall deficit as compared to tropical moist or temperate forests but are still vulnerable to drought-related mortality.

Trace element nutrition of the silkwormBombyx mori L. II. Relationship between cobalt, vitamin B12, benzimidazole and purines

Benzimidazole is toxic to silkworms due to its antagonistic action to purines. Cobalt and copper possess the capacity to reverse its toxicity because of their ability to form complexes with benzimidazole. For reasons unknown cobalt exerts a favourable effect in its free form rather than in the vitamin form on the insect growth.

Adhesively-bonded Patch Repair with Composites

Adhesively-bonded composite patch repairs over cracked or corrosion-damaged metallic aircraft structures have shown great promise for extending life of ageing structures. This study presents the numerical investigation into the interface behaviour of adhesively-bonded cracked aluminum alloy substrate patched with fibre-reinforced composite material. The adhesive is modelled as an elasto-plastic bilinear material to characterise the debond behaviour, while the defective substrate is regarded as linear elastic continuum. Two typical patch shapes were selected based on information available in the literature. Geometric and material nonlinear analyses for square and octagonal patches were performed to capture peel and shear stresses developed between the substrate and the patch to examine the possibility of interface delamination/debonding. Parametric studies on adhesive thickness and patch thickness were carried out to predict their infuence on damage tolerance of repaired structures.

Relationship between Low Strain Shear Modulus and Standard Penetration Test N Values

A low strain shear modulus plays a fundamental role in the estimation of site response parameters In this study an attempt has been made to develop the relationships between standard penetration test (SPT) N values with the low strain shear modulus (G(max)) For this purpose, field experiments SPT and multichannel analysis of surface wave data from 38 locations in Bangalore, India, have been used, which were also used for seismic microzonation project The in situ density of soil layer was evaluated using undisturbed soil samples from the boreholes Shear wave velocity (V-s) profiles with depth were obtained for the same locations or close to the boreholes The values for low strain shear modulus have been calculated using measured V-s and soil density About 215 pairs of SPT N and G(max) values are used for regression analysis The differences between fitted regression relations using measured and corrected values were analyzed It is found that an uncorrected value of N and modulus gives the best fit with a high regression coefficient when compared to corrected N and corrected modulus values This study shows better correlation between measured values of N and G(max) when compared to overburden stress corrected values of N and G(max)

Adhesively-bonded Patch Repair with Composites

Adhesively-bonded composite patch repairs over cracked or corrosion-damaged metallic aircraft structures have shown great promise for extending life of ageing structures. This study presents the numerical investigation into the interface behaviour of adhesively-bonded cracked aluminum alloy substrate patched with fibre-reinforced composite material. The adhesive is modelled as an elasto-plastic bilinear material to characterise the debond behaviour, while the defective substrate is regarded as linear elastic continuum. Two typical patch shapes were selected based on information available in the literature. Geometric and material nonlinear analyses for square and octagonal patches were performed to capture peel and shear stresses developed between the substrate and the patch to examine the possibility of interface delamination/debonding. Parametric studies on adhesive thickness and patch thickness were carried out to predict their infuence on damage tolerance of repaired structures.

Molecular structure-activity relationship study of some non-steroidal antiinflammatory agents using electrostatic potential mapping

A series of 6,11-dihydro-11-oxodibenz[b,e]oxepin-2-acetic acids (DOAA) which are known to be anti-inflammatory agents were studied. The geometries of some of the molecules obtained from X-ray crystallography were used in the calculations as such while the geometries of their derivatives were obtained by local, partial geometry optimization around the Sites of substitution employing the AMI method, keeping the remaining parts of the geometries the same as those in the parent molecules. Molecular electrostatic potential (MEP) mapping was performed for the molecules using optimized hybridization displacement charges (HDC) combined with Lowdin charges, as this charge distribution has been shown earlier to yield near ab initio quality results. A good correlation has been found between the MEP values near the oxygen atoms of the hydroxyl groups of the carboxy groups of the molecules and their anti-inflammatory activities. The result is broadly in agreement with the model proposed earlier by other authors regarding the structure-activity relationship for other similar molecules.