Modelling of Fe2 + oxidation by Thiobacillus ferrooxidans

The kinetics of oxidation of aqueous acidic ferrous sulphate by Thiobacillus ferrooxidans has been studied in a batch reactor. The contribution of cell wall envelopes to the oxidation rate has been shown to be negligible. A model which accounts for the oxidation of Fe2 +, death of bacteria due to Fe3 + poisoning, existence of an optimal pH and precipitation of Fe3 + has been proposed. The model is able to predict the concentration of Fe2 + and pH quite satisfactorily. The predictions of Fe3 + are not so accurate because of simplifying assumptions made about its precipitation.

Nature of Cl center dot center dot center dot Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis:Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl center dot center dot center dot Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.

Relaxation system based sub-grid scale modelling for large eddy simulation of Burgers' equation

An implicit sub-grid scale model for large eddy simulation is presented by utilising the concept of a relaxation system for one dimensional Burgers' equation in a novel way. The Burgers' equation is solved for three different unsteady flow situations by varying the ratio of relaxation parameter (epsilon) to time step. The coarse mesh results obtained with a relaxation scheme are compared with the filtered DNS solution of the same problem on a fine mesh using a fourth-order CWENO discretisation in space and third-order TVD Runge-Kutta discretisation in time. The numerical solutions obtained through the relaxation system have the same order of accuracy in space and time and they closely match with the filtered DNS solutions.

Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes

Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.

Modelling and analysis of the variance in parallelism in parallel computations

In this paper, we introduce an analytical technique based on queueing networks and Petri nets for making a performance analysis of dataflow computations when executed on the Manchester machine. This technique is also applicable for the analysis of parallel computations on multiprocessors. We characterize the parallelism in dataflow computations through a four-parameter characterization, namely, the minimum parallelism, the maximum parallelism, the average parallelism and the variance in parallelism. We observe through detailed investigation of our analytical models that the average parallelism is a good characterization of the dataflow computations only as long as the variance in parallelism is small. However, significant difference in performance measures will result when the variance in parallelism is comparable to or higher than the average parallelism.

Modelling multiple disulphide loop containing polypeptides by random conformation generation. The test cases of α-conotoxin GI and edothelin I

A general procedure for arriving at 3-D models of disulphiderich olypeptide systems based on the covalent cross-link constraints has been developed. The procedure, which has been coded as a computer program, RANMOD, assigns a large number of random, permitted backbone conformations to the polypeptide and identifies stereochemically acceptable structures as plausible models based on strainless disulphide bridge modelling. Disulphide bond modelling is performed using the procedure MODIP developed earlier, in connection with the choice of suitable sites where disulphide bonds could be engineered in proteins (Sowdhamini,R., Srinivasan,N., Shoichet,B., Santi,D.V., Ramakrishnan,C. and Balaram,P. (1989) Protein Engng, 3, 95-103). The method RANMOD has been tested on small disulphide loops and the structures compared against preferred backbone conformations derived from an analysis of putative disulphide subdatabase and model calculations. RANMOD has been applied to disulphiderich peptides and found to give rise to several stereochemically acceptable structures. The results obtained on the modelling of two test cases, a-conotoxin GI and endothelin I, are presented. Available NMR data suggest that such small systems exhibit conformational heterogeneity in solution. Hence, this approach for obtaining several distinct models is particularly attractive for the study of conformational excursions.

Integrated modelling approaches to analysis of climate change impacts on forests and forest management

This paper reviews integrated economic and ecological models that address impacts and adaptation to climate change in the forest sector. Early economic model studies considered forests as one out of many possible impacts of climate change, while ecological model studies tended to limit the economic impacts to fixed price-assumptions. More recent studies include broader representations of both systems, but there are still few studies which can be regarded fully integrated. Full integration of ecological and economic models is needed to address forest management under climate change appropriately. The conclusion so far is that there are vast uncertainties about how climate change affects forests. This is partly due to the limited knowledge about the global implications of the social and economical adaptation to the effects of climate change on forests.

Excitation and correlation of N-14 overtone transitions and measurement of heteronuclear dipolar coupling using DAPT

For studying systems containing nitrogen, limited use of N-14 NMR spectroscopy has been made because of the large quadrupolar interaction experienced by the N-14 nucleus and the absence of a central transition. To overcome the above problem, use of overtone spectroscopy has been suggested. Though this approach has limited applicability for powder samples due to second order quadrupole broadening, it is useful for studying oriented samples and single crystals. Here, we demonstrate the use of the recently proposed dipolar assisted polarization transfer (DAPT) pulse scheme for exciting the overtone transitions. The pulse sequence may also be utilized as a two-dimensional experiment to obtain H-1-N-14 dipolar couplings and H-1 chemical shifts. (C) 2010 Elsevier B.V. All rights reserved.

Fracture Properties of Concrete-Concrete Interfaces Using Digital Image Correlation

The mode I and mode II fracture toughness and the critical strain energy release rate for different concrete-concrete jointed interfaces are experimentally determined using the Digital Image Correlation technique. Concrete beams having different compressive strength materials on either side of a centrally placed vertical interface are prepared and tested under three-point bending in a closed loop servo-controlled testing machine under crack mouth opening displacement control. Digital images are captured before loading (undeformed state) and at different instances of loading. These images are analyzed using correlation techniques to compute the surface displacements, strain components, crack opening and sliding displacements, load-point displacement, crack length and crack tip location. It is seen that the CMOD and vertical load-point displacement computed using DIC analysis matches well with those measured experimentally.

Design, modelling and simulation of vibratory micromachined gyroscopes

Among various MEMS sensors, a rate gyroscope is one of the most complex sensors from the design point of view. The gyro normally consists of a proof mass suspended by an elaborate assembly of beams that allow the system to vibrate in two transverse modes. The structure is normally analysed and designed using commercial FEM packages such as ANSYS or MEMS specific commercial tools such as Coventor or Intellisuite. In either case, the complexity in analysis rises manyfolds when one considers the etch hole topography and the associated fluid flow calculation for damping. In most cases, the FEM analysis becomes prohibitive and one resorts to equivalent electrical circuit simulations using tools like SABER in Coventor. Here, we present a simplified lumped parameter model of the tuning fork gyro and show how easily it can be implemented using a generic tool like SIMULINK. The results obtained are compared with those obtained from more elaborate and intense simulations in Coventor. The comparison shows that lumped parameter SIMULINK model gives equally good results with fractional effort in modelling and computation. Next, the performance of a symmetric and decoupled vibratory gyroscope structure is also evaluated using this approach and a few modifications are made in this design to enhance the sensitivity of the device.

Characterization of substrate UpA binding to RNase A--computer modelling and energetics approach.

In the past two decades RNase A has been the focus of diverse investigations in order to understand the nature of substrate binding and to know the mechanism of enzyme action. Although this system is reasonably well characterized from the view point of some of the binding sites, the details of interactions in the second base binding (B2) site is insufficient. Further, the nature of ligand-protein interaction is elucidated generally by studies on RNase A-substrate analog complexes (mainly with the help of X-ray crystallography). Hence, the details of interactions at atomic level arising due to substrates are inferred indirectly. In the present paper, the dinucleotide substrate UpA is fitted into the active site of RNase A Several possible substrate conformations are investigated and the binding modes have been selected based on Contact Criteria. Thus identified RNase A-UpA complexes are energy minimized in coordinate space and are analysed in terms of conformations, energetics and interactions. The best possible ligand conformations for binding to RNase A are identified by experimentally known interactions and by the energetics. Upon binding of UpA to RNase A the changes associated,with protein back bone, Side chains in general and at the binding sites in particular are described. Further, the detailed interactions between UpA and RNase A are characterized in terms of hydrogen bonds and energetics. An extensive study has helped in interpreting the diverse results obtained from a number of experiments and also in evaluating the extent of changes the protein and the substrate undergo in order to maximize their interactions.

Correlation filtering: a terrain correction method for aeromagnetic maps with application

In correlation filtering we attempt to remove that component of the aeromagnetic field which is closely related to the topography. The magnetization vector is assumed to be spatially variable, but it can be successively estimated under the additional assumption that the magnetic component due to topography is uncorrelated with the magnetic signal of deeper origin. The correlation filtering was tested against a synthetic example. The filtered field compares very well with the known signal of deeper origin. We have also applied this method to real data from the south Indian shield. It is demonstrated that the performance of the correlation filtering is superior in situations where the direction of magnetization is variable, for example, where the remnant magnetization is dominant.

Correlation of seasonal changes in sperm output with endocrinological changes in the adult male bonnet monkey, Macaca radiata

We have examined the monthly variations in sperm output and attempted to correlate the profiles of endocrine hormones secreted with the sperm counts throughout the ,year in the adult male bonnet monkey. As previously reported, there was a distinct spurt in sperm output beginning September through December months. A concomitant increase in serum testosterone and prolactin concentrations were also noted during September through November (mid and post-monsoon season). Although there was a marked increase in gonadotropin releasing hormone stimulated testosterone secretion, the peak testosterone concentrations post gonadotropin releasing hormone injection did not vary significantly (P>0.05) throughout the year. Basal serum follicle stimulating hormone concentrations did not vary significantly (P>0.05) during April to June months compared to September-November months. Serum inhibin concentration remained unaltered throughout the year, except in the month of March. The results of this study provide evidence for annual rhythms in prolactin and testosterone secretion and a distinct seasonality in the sperm output of the adult male bonnet monkey, but the pituitary responsiveness to exogenous gonadotropin releasing hormone remains unaltered throughout the year. Because of the existence of seasonality as noted in the present study, future studies which utilize the adult male bonnet monkey as an experimental model need to take into consideration the seasonal effects on reproductive function in this species.

A novel property of an Auto-Correlation Sequence and some Applications

In this article, we use some spectral properties of polynomials presented in 1] and map an auto-correlation sequence to a set of Line Spectral Frequencies(LSFs) and reflection coefficients. This novel characterization of an auto-correlation sequence is used to obtain a lattice structure of a Linear-Phase(LP) FIR filter.