Modelling the chemical weathering fluxes at the watershed scale in the Tropics (Mule Hole, South India): Relative contribution of the smectite/kaolinite assemblage versus primary minerals

We investigate the chemical weathering processes and fluxes in a small experimental watershed (SEW) through a modelling approach. The study site is the Mule Hole SEW developed on a gneissic basement located in the climatic gradient of the Western Ghats, South India. The model couples a lumped hydrological model simulating the water budget at the watershed scale to the WITCH model estimating the dissolution/precipitation rates of minerals using laboratory kinetic laws. Forcing functions and parameters of the simulation are defined by the field data. The coupled model is calibrated with stream and groundwater compositions through the testing of a large range of smectite solubility and abundance in the soil horizons. We found that, despite the low abundance of smectite in the dominant soil type of the watershed (4 vol.%), their net dissolution provides 75% of the export of dissolved silica, while primary silicate mineral dissolution releases only 15% of this flux. Overall, smectites (modelled as montmorillonites) are not stable under the present day climatic conditions. Furthermore, the dissolution of trace carbonates in the saprolitic horizon provides 50% of the calcium export at the watershed scale. Modelling results show the contrasted behavior of the two main soil types of the watershed: red soils (88% of the surface) are provider of calcium, while black soils (smectite-rich and characterized by a lower drainage) consumes calcium through overall carbonate precipitation. Our model results stress the key role played by minor/accessory minerals and by the thermodynamic properties of smectite minerals, and by the drainage of the weathering profiles on the weathering budget of a tropical watershed. (C) 2010 Elsevier B.V. All rights reserved.

Computer modelling studies on the mechanism of action of ribonuclease T1

The mechanism of action of ribonuclease (RNase) T1 is still a matter of considerable debate as the results of x-ray, 2-D nmr and site-directed mutagenesis studies disagree regarding the role of the catalytically important residues. Hence computer modelling studies were carried out by energy minimisation of the complexes of RNase T1 and some of its mutants (His40Ala, His40Lys, and Glu58Ala) with the substrate guanyl cytosine (GpC), and of native RNase T1 with the reaction intermediate guanosine 2',3'-cyclic phosphate (G greater than p). The puckering of the guanosine ribose moiety in the minimum energy conformer of the RNase T1-GpC (substrate) complex was found to be O4'-endo and not C3'-endo as in the RNase T1-3'-guanylic acid (inhibitor/product) complex. A possible scheme for the mechanism of action of RNase T1 has been proposed on the basis of the arrangement of the catalytically important amino acid residues His40, Glu58, Arg77, and His92 around the guanosine ribose and the phosphate moiety in the RNase T1-GpC and RNase T1-G greater than p complexes. In this scheme, Glu58 serves as the general base group and His92 as the general acid group in the transphosphorylation step. His40 may be essential for stabilising the negatively charged phosphate moiety in the enzyme-transition state complex.

Electric Field Modelling of Composite High Voltage Insulators

This paper deals with the two-dimensional electric field modelling and electric field stress calculations of different types of composite insulators used in high voltage distribution and transmission systems. The computer simulations are carried out by using a commercially available software package. The potential and electric filed results obtained for the actual insulator profiles for three types of composite/polymeric insulators are discussed and presented.

Modelling, Design and Analysis of Low Frequency Platform for Attenuating Micro-Vibration in Spacecraft

One of the most important factors that affect the pointing of precision payloads and devices in space platforms is the vibration generated due to static and dynamic unbalanced forces of rotary equipments placed in the neighborhood of payload. Generally, such disturbances are of low amplitude, less than 1 kHz, and are termed as ‘micro-vibrations’. Due to low damping in the space structure, these vibrations have long decay time and they degrade the performance of payload. This paper addresses the design, modeling and analysis of a low frequency space frame platform for passive and active attenuation of micro-vibrations. This flexible platform has been designed to act as a mount for devices like reaction wheels, and consists of four folded continuous beams arranged in three dimensions. Frequency and response analysis have been carried out by varying the number of folds, and thickness of vertical beam. Results show that lower frequencies can be achieved by increasing the number of folds and by decreasing the thickness of the blade. In addition, active vibration control is studied by incorporating piezoelectric actuators and sensors in the dynamic model. It is shown using simulation that a control strategy using optimal control is effective for vibration suppression under a wide variety of loading conditions.

Modes of binding of guanosine monophosphates to ribonuclease T1 - A computer modelling study

Computer-modelling studies on the modes of binding of the three guanosine monophosphate inhibitors 2'-GMP, 3'-GMP, and 5'-GMP to ribonuclease (RNase) T1 have been carried out by energy minimization in Cartesian-coordinate space. The inhibitory power was found to decrease in the order 2'-GMP > 3'-GMP > 5'-GMP in agreement with the experimental observations. The ribose moiety was found to form hydrogen bonds with the protein in all the enzyme-inhibitor complexes, indicating that it contributes to the binding energy and does not merely act as a spacer between the base and the phosphate moieties as suggested earlier. 2'-GMP and 5'-GMP bind to RNase T1 in either of the two ribose puckered forms (with C3'-endo more favoured over the C2'-endo) and 3'-GMP binds to RNase T1 predominantly in C3'-endo form. The catalytically important residue His-92 was found to form hydrogen bond with the phosphate moiety in all the enzyme-inhibitor complexes, indicating that this residue may serve as a general acid group during catalysis. Such an interaction was not found in either X-ray or two-dimensional NMR studies.

Macroscopic model of city traffic using bond graph modelling

Modelling of city traffic involves capturing of all the dynamics that exist in real-time traffic. Probabilistic models and queuing theory have been used for mathematical representation of the traffic system. This paper proposes the concept of modelling the traffic system using bond graphs wherein traffic flow is based on energy conservation. The proposed modelling approach uses switched junctions to model complex traffic networks. This paper presents the modelling, simulation and experimental validation aspects.

Modelling studies on neurodegenerative disease causing triplet repeat sequences d(CGG/GCC) and d(CAG/CTG): Duplexes vs Quadruplexes

Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimmer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.

A standard reference frame for the description of Nucleic Acid Base-Pair Geometry

A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures. The different standards used in computer programs created for this purpose give rise to con¯icting interpretations of the same structure.1 For example, parts of a structure that appear ``normal'' according to one computational scheme may be highly unusual according to another and vice versa. It is thus dif®cult to carry out comprehensive comparisons of nucleic acid structures and to pinpoint unique conformational features in individual structures

Molecular modelling of saccharide-lipid interactions

Certain saccharides, including trehalose, sucrose and glucose, stabilize lipid bilayers against dehydration. It has been suggested that these saccharides replace waters of hydration as the system is dried, thereby maintaining the headgroups at their hydrated spacing. The lipid acyl chains consequently have sufficient free volume to remain in the liquid crystallines state, and the processes that disrupt membrane integrity are inhibited. Initial molecular graphic investigations of a model trehalose/DMPC system supported this idea (Chandrasekhar, I. and Gaber, B.P. (1988) J. Biomol. Stereodyn, 5, 1163–1171). We have extended these studies to glucose and sucrose. A set of AMBER potential parameters has been established that reproduce simple saccharide conformations, including the anomeric effect. Extensive energy minimizations have been conducted on all three systems. The saccharide-lipid interaction energies become less stable in the order trehalose

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.

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.

Reference annual atmospheres for midlatitude and tropics

Many aerospace and scientific applications require the specification of the atmospheric properties at various locations, UT and seasons for a range of solar and geomagnetic activity. The nature and mechanisms of the lower and upper atmospheres are different so also their models. Further there is a need to match these models and this is accomplished here in a simple way. In the revision of CIRA 1972 in 1986, the reference middle atmospheres is not yet complete. Two annual reference atmospheres from sea level up to 2000 km for the midlatitude and the tropics is proposed. Other monthly reference atmospheres as also the structure of the atmospheric tables to be provided in the above document is also indicated.