Microscopic modelling of adsorption and the generalised surface layer hypothesis

Two- and three-state models for the adsorption of organic compounds at the electrodelelectrolyte interface are proposed. Different size requirements, if any, for the neutral molecule and the adsorbing solvent are also considered. It is shown how the empirical, generalised surface layer (GSL) relationship (between the potential difference and the electrode charge) formulated by Damaskin et a / . can be understood at the molecular level.

Adsorption isotherms-microscopic modelling

The phenomenon of adsorption is governed by the various interactions among the constituents of the interface and the forms of adsorption isotherms hold the clue to the nature of the se in teractions. An understanding of this phenomenon may be said to be complete only when the parameters occurring in such expres - sions for isotherms are interpretable in terms of molecular/electronic interactions.This objective viz. expressing the composition of the isotherm parameters through a microscopic modelling is by no means a simple one. Such a task is particularly made difficult in the case of charged interfaces where idealisation is difficult to make and, when made, not so easy to justify.

Hierarchical modelling of acclimatory processesstar, open

The term acclimation has been used with several connotations in the field of acclimatory physiology. An attempt has been made, in this paper, to define precisely the term “acclimation” for effective modelling of acclimatory processes. Acclimation is defined with respect to a specific variable, as cumulative experience gained by the organism when subjected to a step change in the environment. Experimental observations on a large number of variables in animals exposed to sustained stress, show that after initial deviation from the basal value (defined as “growth”), the variables tend to return to basal levels (defined as “decay”). This forms the basis for modelling biological responses in terms of their growth and decay. Hierarchical systems theory as presented by Mesarovic, Macko & Takahara (1970) facilitates modelling of complex and partially characterized systems. This theory, in conjunction with “growth-decay” analysis of biological variables, is used to model temperature regulating system in animals exposed to cold. This approach appears to be applicable at all levels of biological organization. Regulation of hormonal activity which forms a part of the temperature regulating system, and the relationship of the latter with the “energy” system of the animal of which it forms a part, are also effectively modelled by this approach. It is believed that this systematic approach would eliminate much of the current circular thinking in the area of acclimatory physiology.

New structural insights and molecular-modelling studies of 4-methyl-5-beta-hydroxyethylthiazole kinase from Pyrococcus horikoshii OT3 (PhThiK)

4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyses the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole. This work reports the first crystal structure of an archaeal ThiK: that from Pyrococcus horikoshii OT3 (PhThiK) at 1.85 angstrom resolution with a phosphate ion occupying the position of the beta-phosphate of the nucleotide. The topology of this enzyme shows the typical ribokinase fold of an alpha/beta protein. The overall structure of PhThiK is similar to those of Bacillus subtilis ThiK (BsThiK) and Enterococcus faecalis V583 ThiK (EfThiK). Sequence analysis of ThiK enzymes from various sources indicated that three-quarters of the residues involved in interfacial regions are conserved. It also revealed that the amino-acid residues in the nucleotide-binding, magnesium ion-binding and substrate-binding sites are conserved. Binding of the nucleotide and substrate to the ThiK enzyme do not influence the quaternary association (trimer) as revealed by the crystal structure of PhThiK.

Assimilation of remote sensing and hydrological data using adaptive filtering techniques for watershed modelling

The knowledge of hydrological variables (e. g. soil moisture, evapotranspiration) are of pronounced importance in various applications including flood control, agricultural production and effective water resources management. These applications require the accurate prediction of hydrological variables spatially and temporally in watershed/basin. Though hydrological models can simulate these variables at desired resolution (spatial and temporal), often they are validated against the variables, which are either sparse in resolution (e. g. soil moisture) or averaged over large regions (e. g. runoff). A combination of the distributed hydrological model (DHM) and remote sensing (RS) has the potential to improve resolution. Data assimilation schemes can optimally combine DHM and RS. Retrieval of hydrological variables (e. g. soil moisture) from remote sensing and assimilating it in hydrological model requires validation of algorithms using field studies. Here we present a review of methodologies developed to assimilate RS in DHM and demonstrate the application for soil moisture in a small experimental watershed in south India.

Contribution of geophysical surveys to groundwater modelling of a porous aquifer in semiarid Niger: An overview

Subsurface geophysical surveys were carried out using a large range of methods in an unconfined sandstone aquifer in semiarid south-western Niger for improving both the conceptual model of water flow through the unsaturated zone and the parameterization of numerical a groundwater model of the aquifer. Methods included: electromagnetic mapping, electrical resistivity tomography (ERT), resistivity logging, time domain electromagnetic sounding (TDEM), and magnetic resonance sounding (MRS). Analyses of electrical conductivities, complemented by geochemical measurements, allowed us to identify preferential pathways for infiltration and drainage beneath gullies and alluvial fans. The mean water content estimated by MRS (13%) was used for computing the regional groundwater recharge from long-term change in the water table. The ranges in permeability and water content obtained with MRS allowed a reduction of the degree of freedom of aquifer parameters used in groundwater modelling.

Modelling heterogeneity of concrete using 2D lattice network for concrete fracture and comparison with AE study

In this paper, numerical modelling of fracture in concrete using two-dimensional lattice model is presented and also a few issues related to lattice modelling technique applicable to concrete fracture are reviewed. A comparison is made with acoustic emission (AE) events with the number of fractured elements. To implement the heterogeneity of the plain concrete, two methods namely, by generating grain structure of the concrete using Fuller's distribution and the concrete material properties are randomly distributed following Gaussian distribution are used. In the first method, the modelling of the concrete at meso level is carried out following the existing methods available in literature. The shape of the aggregates present in the concrete are assumed as perfect spheres and shape of the same in two-dimensional lattice network is circular. A three-point bend (TPB) specimen is tested in the experiment under crack mouth opening displacement (CMOD) control at a rate of 0.0004 mm/sec and the fracture process in the same TPB specimen is modelled using regular triangular 2D lattice network. Load versus crack mouth opening isplacement (CMOD) plots thus obtained by using both the methods are compared with experimental results. It was observed that the number of fractured elements increases near the peak load and beyond the peak load. That is once the crack starts to propagate. AE hits also increase rapidly beyond the peak load. It is compulsory here to mention that although the lattice modelling of concrete fracture used in this present study is very similar to those already available in literature, the present work brings out certain finer details which are not available explicitly in the earlier works.

Water balance modelling in a tropical watershed under deciduous forest (Mule Hole, India): Regolith matric storage buffers the groundwater recharge process

Accurate estimations of water balance are needed in semi-arid and sub-humid tropical regions, where water resources are scarce compared to water demand. Evapotranspiration plays a major role in this context, and the difficulty to quantify it precisely leads to major uncertainties in the groundwater recharge assessment, especially in forested catchments. In this paper, we propose to assess the importance of deep unsaturated regolith and water uptake by deep tree roots on the groundwater recharge process by using a lumped conceptual model (COMFORT). The model is calibrated using a 5 year hydrological monitoring of an experimental watershed under dry deciduous forest in South India (Mule Hole watershed). The model was able to simulate the stream discharge as well as the contrasted behaviour of groundwater table along the hillslope. Water balance simulated for a 32 year climatic time series displayed a large year-to-year variability, with alternance of dry and wet phases with a time period of approximately 14 years. On an average, input by the rainfall was 1090 mm year(-1) and the evapotranspiration was about 900 mm year(-1) out of which 100 mm year(-1) was uptake from the deep saprolite horizons. The stream flow was 100 mm year(-1) while the groundwater underflow was 80 mm year(-1). The simulation results suggest that (i) deciduous trees can uptake a significant amount of water from the deep regolith, (ii) this uptake, combined with the spatial variability of regolith depth, can account for the variable lag time between drainage events and groundwater rise observed for the different piezometers and (iii) water table response to recharge is buffered due to the long vertical travel time through the deep vadose zone, which constitutes a major water reservoir. This study stresses the importance of long term observations for the understanding of hydrological processes in tropical forested ecosystems. (C) 2009 Elsevier B.V. All rights reserved.

Modelling of solute transport in a mild heterogeneous porous medium using stochastic finite element method: Effects of random source conditions

Randomness in the source condition other than the heterogeneity in the system parameters can also be a major source of uncertainty in the concentration field. Hence, a more general form of the problem formulation is necessary to consider randomness in both source condition and system parameters. When the source varies with time, the unsteady problem, can be solved using the unit response function. In the case of random system parameters, the response function becomes a random function and depends on the randomness in the system parameters. In the present study, the source is modelled as a random discrete process with either a fixed interval or a random interval (the Poisson process). In this study, an attempt is made to assess the relative effects of various types of source uncertainties on the probabilistic behaviour of the concentration in a porous medium while the system parameters are also modelled as random fields. Analytical expressions of mean and covariance of concentration due to random discrete source are derived in terms of mean and covariance of unit response function. The probabilistic behaviour of the random response function is obtained by using a perturbation-based stochastic finite element method (SFEM), which performs well for mild heterogeneity. The proposed method is applied for analysing both the 1-D as well as the 3-D solute transport problems. The results obtained with SFEM are compared with the Monte Carlo simulation for 1-D problems.

Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria

We have recently implicated heat shock protein 90 from Plasmodium falciparum (PfHsp90) as a potential drug target against malaria. Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory effects on development of malarial parasite in human erythrocytes. To gain better understanding of the vital role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length structure of yeast Hsp90. Sequence similarity found between PfHsp90 and yeast Hsp90 allowed us to model the core structure with high confidence. The superimposition of the predicted structure with that of the template yeast Hsp90 structure reveals an RMSD of 3.31 angstrom. The N-terminal and middle domains showed the least RMSD (1.76 angstrom) while the more divergent C-terminus showed a greater RMSD (2.84 angstrom) with respect to the template. The structure shows overall conservation of domains involved in nucleotide binding, ATPase activity, co-chaperone binding as well as inter-subunit interactions. Important co-chaperones known to modulate Hsp90 function in other eukaryotes are conserved in malarial parasite as well. An acidic stretch of amino acids found in the linker region, which is uniquely extended in PfHsp90 could not be modeled in this structure suggesting a flexible conformation. Our results provide a basis to compare the overall structure and functional pathways dependent on PfHsp90 in malarial parasite. Further analysis of differences found between human and parasite Hsp90 may make it possible to design inhibitors targeted specifically against malaria.

Ion channel formation by zervamicin-IIB. A molecular modelling study.

Zervamicin-IIB (Zrv-IIB) is a 16 residue peptaibol which forms voltage-activated, multiple conductance level channels in planar lipid bilayers. A molecular model of Zrv-IIB channels is presented. The structure of monomeric Zrv-IIB is based upon the crystal structure of Zervamicin-Leu. The helical backbone is kinked by a hydroxyproline residue at position 10. Zrv-IIB channels are modelled as helix bundles of from 4 to 8 parallel helices surrounding a central pore. The monomers are packed with their C-terminal helical segments in close contact, and the bundles are stabilized by hydrogen bonds between glutamine 11 and hydroxyproline 10 of adjacent helices. Interaction energy profiles for movement of three different probes species (K+, Cl- and water) through the central pore are analyzed. The conformations of: (a) the sidechain of glutamine 3; (b) the hydroxyl group of hydroxyproline 10; and (c) the C-terminal hydroxyl group are "optimized" in order to maximize favourable interactions between the channel and the probes, resulting in favourable interaction energy profiles for all three. This suggests that conformational flexibility of polar sidechains enables the channel lining to mimic an aqueous environment.

Computer modelling approach to study the modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein

The modes of binding of alpha- and beta-anomers of D-galactose, D-fucose and D-glucose to L-arabinose-binding protein (ABP) have been studied by energy minimization using the low resolution (2.4 A) X-ray data of the protein. These studies suggest that these sugars preferentially bind in the alpha-form to ABP, unlike L-arabinose where both alpha- and beta-anomers bind almost equally. The best modes of binding of alpha- and beta-anomers of D-galactose and D-fucose differ slightly in the nature of the possible hydrogen bonds with the protein. The residues Arg 151 and Asn 232 of ABP from bidentate hydrogen bonds with both L-arabinose and D-galactose, but not with D-fucose or D-glucose. However in the case of L-arabinose, Arg 151 forms hydrogen bonds with the hydroxyl group at the C-4 atom and the ring oxygen, whereas in case of D-galactose it forms bonds with the hydroxyl groups at the C-4 and C-6 atoms of the pyranose ring. The calculated conformational energies also predict that D-galactose is a better inhibitor than D-fucose and D-glucose, in agreement with kinetic studies. The weak inhibitor D-glucose binds preferentially to one domain of ABP leading to the formation of a weaker complex. Thus these studies provide information about the most probable binding modes of these sugars and also provide a theoretical explanation for the observed differences in their binding affinities.

Modelling of void initiation and breaking phenomena in a packed bed

Void breaking and formation in a packed bed are important phenomena in stabilising and optimising the performance of reactors such as the blast furnace, spouted bed and catalytic regenerator. These phenomena have been studied using a mathematical model. The model is based on a previously published force balance approach to predict the cavity size. Limited numbers of experiments, at room temperature, have been carried out in order to compare the experimental results with theory. A good agreement has been found between the experimental and theoretical results. In addition, the predictions have been compared with published data, which give reasonable agreement. The role of various forces (friction, pressure and bed weight) on void initiation and breaking has been investigated. The effect of bed height, particle diameter and density, void fraction, as well as gas flow rate on void formation and breaking has also been studied.

Modelling of symmetric laminates under extension

A higher-order theory of laminated composites under in-plane loads is developed. The displacement field is expanded in terms of the thickness co-ordinate, satisfying the zero shear stress condition at the surfaces of the laminate. Using the principle of virtual displacement, the governing equations and boundary conditions are established. Numerical results for interlaminar stresses arising in the case of symmetric laminates under uniform extension have been obtained and are compared with similar results available in the literature.

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.