Thermodynamics of water entry in hydrophobic channels of carbon nanotubes

Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermodynamic understanding of this phenomenon, we use the recently developed two phase thermodynamics method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk water and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with that of bulk water shows significant shifts in the positions of the spectral peaks that are directly related to the tube radius. (C) 2011 American Institute of Physics.

Coadsorption of Dioxygen and Water on the Ni(110) Surface: Role of O1--Type Species in the Dissociation of Water

While the adsorption of dioxygen at a clean Ni(110) surface gives rise to two O(1s) features at 531 and 530 eV assigned to O-(a) and O2-(a) type species respectively, coadsorption of dioxygen and water mixtures result in the additional formation of hydroxyl species characterized by an O(1s) peak at 532.3 eV. The latter is attributed to the oxygen induced dissociation of water via a low energy pathway involving the O-(a)-type species. The proportions of the O-(a) and the hydroxyl species are greater for small O-2/H2O ratios and lower temperatures (120 K). With increase in temperature, the relative surface concentrations of the O-(a) and the hydroxyl species decrease while there is an increase in the concentration of the oxidic O2-(a) species. Thus, the surface concentrations of both the hydroxyl and the O2-(a) species depend critically on the presence of O- type species. Above 300K the surface chemistry in the main involves the conversion of O- to O2- species via the hydroxyl species.

Injection cooling of blunt bodies flying at high Mach numbers

A study of transpiration cooling of blunt bodies such as a hemicylinder is made by solving Navier-Stokes equations. An upwind, implicit time-marching code is developed for this purpose. The study is conducted for both perfect-gas and real-gas (chemical equilibrium) flows. Investigations are carried out for a special wall condition that is referred to as no heat flow into the wall condition. The effects of air injection on wall temperature are analyzed. Analyses are carried out for Mach numbers ranging between 6-10 and Reynolds numbers ranging between 10(6)-10(7). Studies are made for spatially constant as well as spatially varying mass injection rate distributions, White cold air injection reduces the wall temperature substantially, transpiration cooling is relatively less effective when the gas is in chemical equilibrium.

Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Observation of Water-Mediated Helix-Terminating Conformation in a Dehydrophenylalanine Peptide: Crystal and Solution Structure of the Octapeptide Ac-.DELTA.Phe-Val-.DELTA.Phe-Phe-Ala-Val-.DELTA.Phe-Gly-OMe

We have synthesised and determined the solution conformation and X-ray crystal structure of the octapeptide Ac-Delta Phe(1)-Val(2)-Delta Phe(3)-Phe(4)-Ala(5)-Val(6)-Delta Phe(7)-Gly(8)-OCH3 (Delta Phe = alpha,beta-dehydrophenylalanine) containing three Delta Phe residues as conformation constraining residues. In the solid state, the peptide folds into (i) an N-terminal (3)10(R)-helical pentapeptide segment, (ii) a middle non-helical segment, and (iii) a C-terminal incipient (3)10(L)-helical segment. The results of H-1 NMR data also suggest that a similar multiple-turn conformation for the peptide is largely maintained in solution. Though the C-terminal helix is incipient, the overall conformation of the octapeptide matches well with the conformation of the hairpins reported. Comparison of the pi-turn seen in the octapeptide molecule with those observed in proteins at the C-terminal end of helixes shows the structural similarity among them. A water molecule mediates the 5 --> 2 hydrogen bond in the pi-turn region. This is the first example of a water-inserted pi-turn in oligopeptides reported so far. Comparison between the present octapeptide and another (3)10(R)-helical dehydro nonapeptide Boc-Val-Delta Phe-Phe-Ala-Phe-Delta Phe-Val-Delta Phe-Gly-OCH3 solved by us recently, demonstrates the possible sequence-dependent conformational variations in alpha,beta-dehydrophenylalanine-containing oligopeptides.

Classification of microwatersheds based on morphological characteristics

Three classification techniques, namely, K-means Cluster Analysis (KCA), Fuzzy Cluster Analysis (FCA), and Kohonen Neural Networks (KNN) were employed to group 25 microwatersheds of Kherthal watershed, Rajasthan into homogeneous groups for formulating the basis for suitable conservation and management practices. Ten parameters, mainly, morphological, namely, drainage density (D-d), bifurcation ratio (R-b), stream frequency (F-u), length of overland flow (L-o), form factor (R-f), shape factor (B-s), elongation ratio (R-e), circulatory ratio (R-c), compactness coefficient (C-c) and texture ratio (T) are used for the classification. Optimal number of groups is chosen, based on two cluster validation indices Davies-Bouldin and Dunn's. Comparative analysis of various clustering techniques revealed that 13 microwatersheds out of 25 are commonly suggested by KCA, FCA and KNN i.e., 52%; 17 microwatersheds out of 25 i.e., 68% are commonly suggested by KCA and FCA whereas these are 16 out of 25 in FCA and KNN (64%) and 15 out of 25 in KNN and CA (60%). It is observed from KNN sensitivity analysis that effect of various number of epochs (1000, 3000, 5000) and learning rates (0.01, 0.1-0.9) on total squared error values is significant even though no fixed trend is observed. Sensitivity analysis studies revealed that microwatershecls have occupied all the groups even though their number in each group is different in case of further increase in the number of groups from 5 to 6, 7 and 8. (C) 2010 International Association of Hydro-environment Engineering and Research, Asia Pacific Division. Published by Elsevier B.V. All rights reserved.

Geochemistry of water and ground water in the Nhecolandia, Pantanal of Mato Grosso, Brazil: Variability and associated processes

A distinctive feature of the Nhecolandia, a sub-region of the Pantanal wetland in Brazil, is the presence of both saline and freshwater lakes. Saline lakes used to be attributed to a past and phase during the Pleistocene. However, recent studies have shown that saline and fresh water lakes are linked by a continuous water table, indicating that saline water could come from a contemporary concentration process. This concentration process could also be responsible for the large chemical variability of the waters observed in the area. A regional water sampling has been conducted in surface and sub-surface water and the water table, and the results of the geochemical and statistical analysis are presented. Based on sodium contents, the concentration shows a 1: 4443 ratio. All the samples belong to the same chemical family and evolve in a sodic alkaline manner. Calcite or magnesian calcite precipitates very early in the process of concentration, probably followed by the precipitation of magnesian silicates. The most concentrated solutions remain under-saturated with respect to the sodium carbonate salt, even if this equilibrium is likely reached around the saline lakes. Apparently, significant amounts of sulfate and chloride are lost simultaneously from the solutions, and this cannot be explained solely by evaporative concentration. This could be attributed to the sorption on reduced minerals in a green sub-surface horizon in the "cordilhieira" areas. In the saline lakes, low potassium, phosphate, magnesium, and sulfate are attributed to algal blooms. Under the influence of evaporation, the concentration of solutions and associated chemical precipitations are identified as the main factors responsible for the geochemical variability in this environment (about 92 % of the variance). Therefore, the saline lakes of Nhecolandia have to be managed as landscape units in equilibrium with the present water flows and not inherited from a past and phase. In order to elaborate hydrochemical tracers for a quantitative estimation of water flows, three points have to be investigated more precisely: (1) the quantification of magnesium involved in the Mg-calcite precipitation; (2) the identification of the precise stoichiometry of the Mg-silicate; and (3) the verification of the loss of chloride and sulfate by sorption onto labile iron minerals.

Optimal crop planning and conjunctive use of water resources in a coastal river basin

Due to increasing trend of intensive rice cultivation in a coastal river basin, crop planning and groundwater management are imperative for the sustainable agriculture. For effective management, two models have been developed viz. groundwater balance model and optimum cropping and groundwater management model to determine optimum cropping pattern and groundwater allocation from private and government tubewells according to different soil types (saline and non-saline), type of agriculture (rainfed and irrigated) and seasons (monsoon and winter). A groundwater balance model has been developed considering mass balance approach. The components of the groundwater balance considered are recharge from rainfall, irrigated rice and non-rice fields, base flow from rivers and seepage flow from surface drains. In the second phase, a linear programming optimization model is developed for optimal cropping and groundwater management for maximizing the economic returns. The models developed were applied to a portion of coastal river basin in Orissa State, India and optimal cropping pattern for various scenarios of river flow and groundwater availability was obtained.

Slow orientational dynamics of water molecules at a micellar surface

The dynamics of water molecules near an aqueous micellar interface is studied in an atomistic molecular dynamics simulation of cesium pentadecafluorooctanoate (CsPFO) in water. The dipolar orientational time correlation function (tcf) and the translational diffusion of the water molecules are investigated. Results show that both the reorientational and the translational motion of water molecules near the micelle are restricted. In particular, the orientational tcf exhibits a very slow component in the long time which is slower than its bulk value by 2 orders of magnitude. This slow decay seems to be related to the slow decay often observed in experiments. The origin of the slow decay is analyzed.

Scalable weak aligning medium for enantiodiscrimination of water soluble chiral molecules

The study reports the first indication of a lyotropic liquid crystalline phase of an aqueous solution of polysaccharide xanthan gum, as a physical parameter dependent scalable and reversible weak alignment medium, for enantiodiscrimination of water soluble chiral molecules.

Biochemistry of water-logged soils. Part IV. Carbon and nitrogen transformations

1. During the fermentation of water-logged soil containing added substances with different carbon-nitrogen ratios, the reaction first turns slightly acid, but soon returns to the original hydrogen-ion concentration (pH 7·6). 2. The quantities of ammonia present in the medium increase up to a point, after which there is steady decrease. 3. There is nitrification only in the case of substances with narrow C/N ratios. The production of nitrate generally commences only after about a month, when the vigour of the initial fermentation has subsided and fairly large quantities of ammonia have accumulated in the medium. 4. The extent of mineralisation of nitrogen is determined chiefly by the C/N ratio, though in the cases of substances like mahua and lantana the presence of other constituents may also influence the processes. The quantities of mineralised nitrogen present in the soil system generally tend to decrease after about two months.

Dynamics of water at the interface of a small protein, enterotoxin

Fully atomistic molecular dynamics simulations have been carried out to investigate the correlation of biological activity with dynamics of water molecules in an aqueous protein solution of the toxic domain of enterotoxin (PDB ID: 1ETN). This is a small protein of 13 amino acid residues. Our study of this water soluble protein clearly reveals that water dynamics slows down in the hydration layer. Despite this general slowing down, water molecules in the vicinity of the second beta turn of this protein exhibit faster dynamics than those near other regions of the protein. Since this beta turn is believed to play a critical role in the receptor binding of this protein, the faster dynamics of water near the beta turn m ay have biological significance. The collective orientational dynamics of the water molecules in the protein solution exhibits a characteristic long time component of 27 ps, which agrees well with dielectric relaxation experiments.

Exploring use of climate information for optimal design of water resources infrastructure

We conducted surveys of fire and fuels managers at local, regional, and national levels to gain insights into decision processes and information flows in wildfire management. Survey results in the form of fire managers’ decision calendars show how climate information needs vary seasonally, over space, and through the organizational network, and help determine optimal points for introducing climate information and forecasts into decision processes. We identified opportunities to use climate information in fire management, including seasonal to interannual climate forecasts at all organizational levels, to improve the targeting of fuels treatments and prescribed burns, the positioning and movement of initial attack resources, and staffing and budgeting decisions. Longer-term (5–10 years) outlooks also could be useful at the national level in setting budget and research priorities. We discuss these opportunities and examine the kinds of organizational changes that could facilitate effective use of existing climate information and climate forecast capabilities.