Role of soil structure and matric suction in collapse of a compacted clay soil

This paper examines the role of microstructure and matric suction in the collapse behavior of a compacted clay soil from Bangalore District in Karnataka State, India. The microstructure of the compacted specimens was examined by mercury intrusion porosimetry (MIP), and the ASTM Filter Paper Method was used to determine their matric suction. The microstructure and matric suction of the compacted specimens were changed by varying their compaction water content, dry density, and clay content (< 2 mum fraction). Experimental results showed that relative abundance of coarse (60 to 6 mum) pores was mainly affected by increasing the dry density of the specimens from 1.49 to 1.77 g/cm(3). The relative abundance of coarse and fine (0.01 to 0.002 mum) pores was affected by increasing the compaction water content from 10.6 to 26.4%. Variations in dry density, compaction water content, and clay contents notably affected the matric suction of the compacted specimens. The collapse behavior of the compacted specimens is explained from analysis of the MIP and matric suction results.

The advection-condensation model and water-vapour probability density functions

The statistically steady humidity distribution resulting from an interaction of advection, modelled as an uncorrelated random walk of moist parcels on an isentropic surface, and a vapour sink, modelled as immediate condensation whenever the specific humidity exceeds a specified saturation humidity, is explored with theory and simulation. A source supplies moisture at the deep-tropical southern boundary of the domain and the saturation humidity is specified as a monotonically decreasing function of distance from the boundary. The boundary source balances the interior condensation sink, so that a stationary spatially inhomogeneous humidity distribution emerges. An exact solution of the Fokker-Planck equation delivers a simple expression for the resulting probability density function (PDF) of the wate-rvapour field and also the relative humidity. This solution agrees completely with a numerical simulation of the process, and the humidity PDF exhibits several features of interest, such as bimodality close to the source and unimodality further from the source. The PDFs of specific and relative humidity are broad and non-Gaussian. The domain-averaged relative humidity PDF is bimodal with distinct moist and dry peaks, a feature which we show agrees with middleworld isentropic PDFs derived from the ERA interim dataset. Copyright (C) 2011 Royal Meteorological Society

Ce(0.67)Fe(0.33)O(2-delta) and Ce(0.65)Fe(0.33)Pt(0.02)O(2-delta): New water gas shift (WGS) catalysts

Ce(0.65)Fe(0.33)Pt(0.02)O(2-delta) and Ce(0.67)Fe(0.33)O(2-delta) have been synthesized by a new low temperature sonochemical method using diethylenetriamine as a complexing agent. Due to the substitution of Fe and Pt ions in CeO(2), lattice oxygen is activated in Ce(0.67)Fe(0.33)O(2-delta) and Ce(0.65)Fe(0.33)Pt(0.02)O(2-delta). Hydrogen uptake studies show strong reduction peaks at 125 C in Ce(0.65)Fe(0.33)Pt(0.02)O(2-delta) against a hydrogen uptake peak at 420 degrees C in Ce(0.67)Fe(0.33)O(2-delta). Fe substituted ceria, Ce(0.67)Fe(0.33)O(2-delta) itself acts as a catalyst for CO oxidation and water gas shift (WGS) reactions at moderate temperatures. The rate of CO conversion in WGS with Pt free Ce(0.65)Fe(0.33)O(2-delta) is 2.8 mu mol g(-1) s(-1) at 450 C and with Pt substituted Ce(0.65)Fe(0.33)Pt(0.02)O(2-delta) is 4.05 mu mol g(-1) s(-1) at 275 degrees C. Due to the synergistic interaction of the Pt ion with Ce and Fe ions in Ce(0.65)Fe(0.33)Pt(0.02)O(2-delta), the catalyst showed much higher activity for CO oxidation and WGS reactions compared to Ce(0.67)Fe(0.33)O(2-delta). A reverse WGS reaction does not occur over Ce(0.65)Fe(0.33)Pt(0.02)O(2-delta). The catalyst also does not deactivate even when operated for a long time. Nearly 100% conversion of CO to CO(2) with 100% H(2) selectivity is observed in WGS reactions even up to 550 degrees C. (C) 2011 Elsevier B.V. All rights reserved.

Non-monotonic, distance-dependent relaxation of water in reverse micelles: Propagation of surface induced frustration along hydrogen bond networks

Layer-wise, distance-dependent orientational relaxation of water confined in reverse micelles (RM) is studied using theoretical and computational tools. We use both a newly constructed ``spins on a ring'' (SOR) Ising-type model (with Shore-Zwanzig rotational dynamics) and atomistic simulations with explicit water. Our study explores the effect of reverse micelle size and role of intermolecular correlations, compromised by the presence of a highly polar surface, on the distance (from the interface) dependence of water relaxation. The ``spins on a ring'' model can capture some aspects of distance dependence of relaxation, such as acceleration of orientational relaxation at intermediate layers. In atomistic simulations, layer-wise decomposition of hydrogen bond formation pattern clearly reveals that hydrogen bond arrangement of water at a certain distance away from the surface can remain frustrated due to the interaction with the polar surface head groups. This layer-wise analysis also reveals the presence of a non-monotonic slow relaxation component which can be attributed to this frustration effect and which is accentuated in small to intermediate size RMs. For large size RMs, the long time component decreases monotonically from the interface to the interior of the RMs with slowest relaxation observed at the interface. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4732095]

Nanostructured Pd modified Ni/CeO2 catalyst for water gas shift and catalytic hydrogen combustion reaction

Nanostructured Pd-modified Ni/CeO2 catalyst was synthesized in a single step by solution combustion method and characterized by XRD, TEM, XPS, TPR and BET surface analyzer techniques. The catalytic performance of this compound was investigated by performing the water gas shift (WGS) and catalytic hydrogen combustion (CHC) reaction. The present compound is highly active and selective (100%) toward H-2 production for the WGS reaction. A lack of CO methanation activity is an important finding of present study and this is attributed to the ionic substitution of Pd and Ni species in CeO2. The creation of oxide vacancies due to ionic substitution of aliovalent ions induces dissociation of H2O that is responsible for the improved catalytic activity for WGS reaction. The combined H-2-TPR and XPS results show a synergism exists among Pd, Ni and ceria support. The redox reaction mechanism was used to correlate experimental data for the WGS reaction and a mechanism involving the interaction of adsorbed H-2 and O-2 through the hydroxyl species was proposed for CHC reaction. The parity plot shows a good correspondence between the experimental and predicted reaction rates. (c) 2012 Elsevier B.V. All rights reserved.

Role of invariant water molecules and water-mediated ionic interactions in D-xylose isomerase from Streptomyces rubiginosus

The enzyme, D-xylose isomerase (D-xylose keto-isomerase; EC 5.3.1.5) is a soluble enzyme that catalyzes the conversion of the aldo-sugar D-xylose to the keto-sugar D-xylulose. A total of 27 subunits of D-xylose isomerase from Streptomyces rubiginosus were analyzed in order to identify the invariant water molecules and their water-mediated ionic interactions. A total of 70 water molecules were found to be invariant. The structural and/or functional roles of these water molecules have been discussed. These invariant water molecules and their ionic interactions may be involved in maintaining the structural stability of the enzyme D-xylose isomerase. Fifty-eight of the 70 invariant water molecules (83%) have at least one interaction with the main chain polar atom.

Cytotoxicity of aluminium oxide nanoparticles towards fresh water algal isolate at low exposure concentrations

The growing commercial applications had brought aluminium oxide nanoparticles under,toxicologists' purview. In the present study, the cytotoxicity of two different sized aluminium oxide nanoparticles (ANP(1), mean hydrodynamic diameter 82.6 +/- 22 nm and ANP(2), mean hydrodynamic diameter 246.9 +/- 39 nm) towards freshwater algal isolate Chlorella ellipsoids at low exposure levels (<= 1 mu g/mL) using sterile lake water as the test medium was assessed. The dissolution of alumina nanoparticles and consequent contribution towards toxicity remained largely unexplored owing to its presumed insoluble nature. Herein, the leached Al3+ ion mediated toxicity has been studied along with direct particulate toxicity to bring out the dynamics of toxicity through colloidal stability, biochemical, spectroscopic and microscopic analyses. The mean hydrodynamic diameter increased with time both for ANP(1) 82.6 +/- 22 nm (0 h) to 246.3 +/- 59 nm (24h), to 1204 +/- 140 nm (72 h)] and ANP(2) 246.9 +/- 39 nm (Oh) to 368.28 +/- 48 nm (24 h), to 1225.96 +/- 186 nm (72 h)] signifying decreased relative abundance of submicron sized particles (<1000 nm). The detailed cytotoxicity assays showed a significant reduction in the viability dependent on dose and exposure. A significant increase in ROS and LDH levels were noted for both ANPs at 1 mu g/mL concentration. The zeta potential and FT-IR analyses suggested surface chemical interaction between nanoparticles and algal cells. The substantial morphological changes and cell wall damage were confirmed through microscopic analyses (SEM, TEM, and CLSM). At 72 h, significant Al3+ ion release in the test medium 0.092 mu g/mL for ANP(1), and 0.19 mu g/mL for ANP(2)] was noted, and the resulting suspension containing leached ions caused significant cytotoxicity, revealing a substantial ionic contribution. This study indicates that both the nano-size and ionic dissolution play a significant role in the cytotoxicity of ANPs towards freshwater algae, and the exposure period largely determines the prevalent mode of nano-toxicity.

Relation Between the Diffusivity, Viscosity, and Ionic Radius of LiCl in Water, Methanol, and Ethylene Glycol: A Molecular Dynamics Simulation

A molecular dynamics (MD) investigation of LiCl in water, methanol, and ethylene glycol (EG) at 298 K is reported. Several; structural and dynamical properties of the ions as well as the solvent such as self-diffusivity, radial distribution functions, void and neck distributions, velocity autocorrelation functions, and mean residence times of solvent in the first solvation shell have been computed. The results show that the reciprocal relationship between the self-diffusivity of the ions and the viscosity is valid in almost all solvents with the exception of water. From an analysis of radial distribution functions and coordination numbers the nature of hydrogen bonding within the solvent and its influence on the void and neck distribution becomes evident. It is seen that the solvent solvent interaction is important in EG while solute solvent interactions dominate in water and methanol. From Voronoi tessellation, it is seen that the voids and necks within methanol are larger as compared to those within water or EG. On the basis of the void and neck distributions obtained from MD simulations and literature experimental data of limiting ion conductivity for various ions of different sizes we show that there is a relation between the void and neck radius on e one hand and dependence of conductivity on the ionic radius on the other. It is shown that the presence of large diameter voids and necks in methanol is responsible for maximum in limiting ion conductivity (lambda(0)) of TMA(+), while in water in EG, the maximum is seen for Rb+. In the case of monovalent anions, maximum in lambda(0) as a function ionic radius is seen for Br- in water EG but for the larger ClO4- ion in methanol. The relation between the void and neck distribution and the variation in lambda(0) with ionic radius arises via the Levitation effect which is discussed. These studies show the importance of the solvent structure and the associated void structure.

Albumin-mediated incorporation of water-insoluble therapeutics in layer-by-layer assembled thin films and microcapsules

The present study demonstrates a method to deliver hydrophobic drugs by incorporation into thin films and microcapsules fabricated via a layer-by-layer assembly approach. The hydrophobic molecule binding properties of albumin have been exploited for solubilization of a water-insoluble molecule, pyrene (model drug), by preparation of non-covalent conjugates with bovine serum albumin (BSA). Conjugation with BSA renders a highly negative zeta potential to the previously uncharged pyrene which favors the assembly formation by electrostatic interaction with a positively charged polyelectrolyte, chitosan (at acidic pH). The growth of the assembly was followed by monitoring pyrene absorbance with successive layer deposition. The thin film assembly was demonstrated to be capable of releasing its hydrophobic cargo under physiological conditions. We demonstrated the applicability of this approach by encapsulating a water-insoluble drug, curcumin. These assemblies were further loaded with the anti-cancer drug Doxorubicin. Biocompatible calcium carbonate microparticles were used for capsule preparation. The porous nature of the microparticles allows for the pre-encapsulation of therapeutic macromolecules like protein. The fabrication of protein encapsulated stable microcapsules with hydrophobic molecules incorporated into the shell of the microcapsules has been demonstrated. The microcapsules were further capable of loading hydrophilic molecules like Rhodamine B. Thus, using the approach described, a multi-agent carrier for hydrophobic and hydrophilic drugs as well as therapeutic macromolecules can be envisioned.

Solvent Sensitivity of Protein Unfolding: Dynamical Study of Chicken Villin Headpiece Subdomain in Water Ethanol Binary Mixture

We carry out a series of long atomistic molecular dynamics simulations to study the unfolding of a small protein, chicken villin headpiece (HP-36), in water-ethanol (EtOH) binary mixture. The prime objective of this work is to explore the sensitivity of protein unfolding dynamics toward increasing concentration of the cosolvent and unravel essential features of intermediates formed in search of a dynamical pathway toward unfolding. In water ethanol binary mixtures, HP-36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as similar to 600 K to denature in pure aqueous solvent. However, an interesting course of pathway is observed to be followed in the process, guided by the formation of unique intermediates. The first step of unfolding is essentially the separation of the cluster formed by three hydrophobic (phenylalanine) residues, namely, Phe-7, Phe-11, and Phe-18, which constitute the hydrophobic core, thereby initiating melting of helix-2 of the protein. The initial steps are similar to temperature-induced unfolding as well as chemical unfolding using DMSO as cosolvent. Subsequent unfolding steps follow a unique path. As water-ethanol shows composition-dependent anomalies, so do the details of unfolding dynamics. With an increase in cosolvent concentration, different partially unfolded intermediates are found to be formed. This is reflected in a remarkable nonmonotonic composition dependence of several order parameters, including fraction of native contacts and protein-solvent interaction energy. The emergence of such partially unfolded states can be attributed to the preferential solvation of the hydrophobic residues by the ethyl groups of ethanol. We further quantify the local dynamics of unfolding by using a Marcus-type theory.

Remarkable role of positional isomers in the design of sensors for the ratiometric detection of copper and mercury ions in water

Cation sensing properties of the three positional isomers of rhodamine based sensors (1-3) are studied in water. The sensors differ only in the position of pyridine's nitrogen. The chemosensor 1, with pyridine nitrogen at ortho-position, showed a selective colorimetric detection of Cu(II) ions in water, at physiological pH 7.4 and also in medium containing BSA (bovine serum albumin) and blood serum. Notably the compound 2 and 3, with pyridine end located at meta-and para-positions did not show any color change with Cu(II) ions, although both the compounds showed turn-on change both in color and fluorescence with Hg(II) ions specifically. All the probes showed ratiometric changes with the specific metal ions. The changing position of nitrogen also changed the complexation pattern of the sensors with the metal ions. Probe 1 showed 2 : 1 complexation with Cu(II), whereas 2 and 3 showed 1 : 1 complexation with Hg(II) ions. The mechanism investigation showed that the change in color upon addition of metal ions is due to the ring-opening of the spirolactam ring of the probes. Cu(II) interacted with ligand 1 through a three-point interaction mode comprising carbonyl oxygen, amido nitrogen and pyridine nitrogen end. But in case of 2 and 3, Hg2+ only interacted through pyridine nitrogen ends. Quantitative estimation of Cu2+ and Hg2+ in complex biological media such as bovine albumin protein (BSA) and human blood serum were performed using these sensors. Rapid on-site detection as well as discrimination of these toxic ions was demonstrated using easily prepared portable test-strips.

Selective and Efficient Detection of Nitro-Aromatic Explosives in Multiple Media including Water, Micelles, Organogel, and Solid Support

Selective detection of nitro-aromatic compounds (NACs) at nanomolar concentration is achieved for the first time in multiple media including water, micelles or in organogels as well as using test strips. Mechanism of interaction of NACs with highly fluorescent p-phenylenevinylene-based molecules has been described as the electron transfer phenomenon from the electron-rich chromophoric probe to the electron deficient NACs. The selectivity in sensing is guided by the pK(a) of the probes as well as the NACs under consideration. TNP-induced selective gel-to-sol transition in THF medium is also observed through the reorganization of molecular self-assembly and the portable test trips are made successfully for rapid on-site detection purpose.

Synthesis, crystal structure, DNA interaction and cleavage activities of mononuclear and trinuclear copper(II) complexes

Mono- and trinuclear copper(II) complexes with 2-1-(2-dimethylamino-ethylamino)-ethyl]-phenol (HL) have been synthesized and structurally characterized. The mononuclear complex Cu(L)(H2O)(ONO2)] (1) crystallizes in monoclinic space group P2(1) /n with a square pyramidal Cu(II) center coordinated by the tridentate Schiff base (L) and a water ligand in the equatorial plane and an oxygen atom from nitrate in the axial position. The trinuclear complex (CuL)(3)(mu(3)-OH)](ClO4)(2)center dot H2O (2) crystallizes in hexagonal space group P6(3); all three copper atoms are five-coordinate with square pyramidal geometries. The interactions of these complexes with calf-thymus DNA have been investigated using absorption spectrophotometry. The mononuclear complex binds more strongly than the trinuclear complex. The DNA cleavage activity of these complexes has been studied on double-stranded pBR 322 plasmid DNA by gel electrophoresis experiments in the absence and in the presence of added oxidant (H2O2). The trinuclear complex cleaves DNA more efficiently than the mononuclear complex in the presence of H2O2.

Conserved water-mediated recognition and dynamics of NAD(+) (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor

Inosine monophosphate dehydrogenase (IMPDH) enzyme involves in GMP biosynthesis pathway. Type I hIMPDH is expressed at lower levels in all cells, whereas type II is especially observed in acute myelogenous leukemia, chronic myelogenous leukemia cancer cells, and 10 ns simulation of the IMP-NAD(+) complex structures (PDB ID. 1B3O and 1JCN) have revealed the presence of a few conserved hydrophilic centers near carboxamide group of NAD(+). Three conserved water molecules (W1, W, and W1 `) in di-nucleotide binding pocket of enzyme have played a significant role in the recognition of carboxamide group (of NAD(+)) to D274 and H93 residues. Based on H-bonding interaction of conserved hydrophilic (water molecular) centers within IMP-NAD(+)-enzyme complexes and their recognition to NAD(+), some covalent modification at carboxamide group of di-nucleotide (NAD(+)) has been made by substituting the -CONH(2)group by -CONHNH2 (carboxyl hydrazide group) using water mimic inhibitor design protocol. The modeled structure of modified ligand may, though, be useful for the development of antileukemic agent or it could be act as better inhibitor for hIMPDH-II.

PLIC: protein-ligand interaction clusters

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein-ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of similar to 68 000 protein-ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein-ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein-ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database-protein-ligand interaction clusters (PLIC).