Biological water: Femtosecond dynamics of macromolecular hydration

The unique features of a macromolecule and water as a solvent make the issue of solvation unconventional, with questions about the static versus dynamic nature of hydration and the, physics of orientational and translational diffusion at the boundary. For proteins, the hydration shell that covers the surface is critical to the stability of its structure and function. Dynamically speaking, the residence time of water at the surface is a signature of its mobility and binding. With femtosecond time resolution it is possible to unravel the shortest residence times which are key for the description of the hydration layer, static or dynamic. In this article we review these issues guided by experimental studies, from this laboratory, of polar hydration dynamics at the surfaces of two proteins (Subtilisin Carlsberg (SC) and Monellin). The natural probe tryptophan amino acid was used for the interrogation of the dynamics, and for direct comparison we also studied the behavior in bulk water - a complete hydration in 1 ps. We develop a theoretical description of solvation and relate the theory to the experimental observations. In this - theoretical approach, we consider the dynamical equilibrium in the hydration shell, defining the rate processes for breaking and making the transient hydrogen bonds, and the effective friction in the layer which is defined by the translational and orientational motions of water molecules. The relationship between the residence time of water molecules and the observed slow component in solvation dynamics is a direct one. For the two proteins studied, we observed a "bimodal decay" for the hydration correlation function, with two primary relaxation times: ultrafast, typically 1 ps or less, and longer, typically 15-40 ps, and both are related to the residence time at the protein surface, depending on the binding energies. We end by making extensions to studies of the denatured state of the protein, random coils, and the biomimetic micelles, and conclude with our thoughts on the relevance of the dynamics of native structures to their functions.

Assessment of treatment capabilities of Varthur Lake, Bangalore, India

Manmade waterbodies have traditionally been used for domestic and irrigation purposes. Unplanned urbanization and ad-hoc approaches have led to these waterbodies receiving untreated sewage. This enriches and eutrophies the waterbody. A physicochemical and biological analysis of sewage-fed Varthur Lake in Bangalore was carried out and its treatment capabilities in terms of BOD removal, nutrient assimilation and self-remediation were assessed. Anaerobic conditions (0 mg/L) prevail at the inlet which improves towards the outlets due to algal aeration. This removed > 50% BOD in the monsoon season but was inhibited by floating macrophytes in all other seasons. Alkalinity, TDS, conductivity and hardness values were higher when compared to earlier studies. This study shows the lake behaves as an anaerobic~aerobic lagoon with a residence time of 4.8 d treating the wastewater to a considerable extent. Further research is required to optimise the system performance.

Tar characterisation in new generation agro-residue gasifiers - Cyclone and downdraft open top twin air entry systems

This paper deals with the characterisation of tar from two configurations of bioresidue thermochemical conversion reactors designed for producer gas based power generation systems. The pulverised fuel reactor is a cyclone system (R1) and the solid bioresidue reactor (denoted R2) is an open top twin air entry system both at 75-90 kg/h capacity (to generate electricity similar to 100 kVA). The reactor, R2, has undergone rigorous test in a major Indo-Swiss programme for the tar quantity at various conditions. The former is a recent technology development. Tars collected from these systems by a standard tar collection apparatus at the laboratory at Indian Institute of Science have been analysed at the Royal Institute of Technology (KTH), Sweden. The results of these analyses show that these thermochemical conversion reactors behave differently from the earlier reactors reported in literature in so far as tar generation is concerned. The extent of tar in hot gas is about 700-800 ppm for R1 and 70-100 ppm for R2. The amounts of the major compounds - naphthalene and phenol-are much lower that what is generally understood to happen in the gasifiers in Europe. It is suggested that the longer residence times at high temperatures allowed for in these reactors is responsible for this behavior. It is concluded the new generation reactor concepts extensively tried out at lower power levels hold promise for high power atmospheric gasification systems for woody as well as pulverisable bioresidues.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Effect of pressure on the ionic conductivity of Li+ and Cl- ions in water

A molecular dynamics simulation study of aqueous solution of LiCl is reported as a function of pressure. Experimental measurements of conductivity of Li+ ion as a function of pressure shows an increase in conductivity with pressure. Our simulations are able to reproduce the observed trend in conductivity. A number of relevant properties have been computed in order to understand the reasons for the increase in conductivity with pressure. These include radial distribution function, void and neck distributions, hydration or coordination numbers, diffusivity, velocity autocorrelation functions, angles between ion-oxygen and dipole of water as well as OH vector, mean residence time for water in the hydration shell, etc. These show that the increase in pressure acts as a structure breaker. The decay of the self part of the intermediate scattering function at small wave number k shows a bi-exponential decay at 1 bar which changes to single exponential decay at higher pressures. The k dependence of the ratio of the self part of the full width at half maximum of the dynamic structure factor to 2Dk(2) exhibits trends which suggest that the void structure of water is playing a role. These support the view that the changes in void and neck distributions in water can account for changes in conductivity or diffusivity of Li+ with pressure. These results can be understood in terms of the levitation effect. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4756909]

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.

Treatment efficacy of algae-based sewage treatment plants

Lagoons have been traditionally used in India for decentralized treatment of domestic sewage. These are cost effective as they depend mainly on natural processes without any external energy inputs. This study focuses on the treatment efficiency of algae-based sewage treatment plant (STP) of 67.65 million liters per day (MLD) capacity considering the characteristics of domestic wastewater (sewage) and functioning of the treatment plant, while attempting to understand the role of algae in the treatment. STP performance was assessed by diurnal as well as periodic investigations of key water quality parameters and algal biota. STP with a residence time of 14.3 days perform moderately, which is evident from the removal of total chemical oxygen demand (COD) (60 %), filterable COD (50 %), total biochemical oxygen demand (BOD) (82 %), and filterable BOD (70 %) as sewage travels from the inlet to the outlet. Furthermore, nitrogen content showed sharp variations with total Kjeldahl nitrogen (TKN) removal of 36 %; ammonium N (NH4-N) removal efficiency of 18 %, nitrate (NO3-N) removal efficiency of 22 %, and nitrite (NO2-N) removal efficiency of 57.8 %. The predominant algae are euglenoides (in facultative lagoons) and chlorophycean members (maturation ponds). The drastic decrease of particulates and suspended matter highlights heterotrophy of euglenoides in removing particulates.

Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Influence of surface area to volume ratio of fuel particles on gasification process in a fixed bed

The paper addresses the effect of particle size on tar generation in a fixed bed gasification system. Pyrolysis, a diffusion limited process, depends on the heating rate and the surface area of the particle influencing the release of the volatile fraction leaving behind residual char. The flaming time has been estimated for different biomass samples. It is found that the flaming time for wood flakes is almost one fourth than that of coconut shells for same equivalent diameter fuel samples. The particle density of the coconut shell is more than twice that of wood spheres, and almost four times compared with wood flakes; having a significant influence on the flaming time. The ratio of the particle surface area to that of an equivalent diameter is nearly two times higher for flakes compared with wood pieces. Accounting for the density effect, on normalizing with density of the particle, the flaming rate is double in the case of wood flakes or coconut shells compared with the wood sphere for an equivalent diameter. This is due to increased surface area per unit volume of the particle. Experiments are conducted on estimation of tar content in the raw gas for wood flakes and standard wood pieces. It is observed that the tar level in the raw gas is about 80% higher in the case of wood flakes compared with wood pieces. The analysis suggests that the time for pyrolysis is lower with a higher surface area particle and is subjected to fast pyrolysis process resulting in higher tar fraction with low char yield. Increased residence time with staged air flow has a better control on residence time and lower tar in the raw gas. (C) 2014 International Energy Initiative. Published by Elsevier Inc. All rights reserved.

The interaction of N-trifluoroacetylgalactosamine and its derivatives with winged bean (Psophocarpus tetragonolobus) basic agglutinin reveals differential mechanism of their recognition: a fluorine-19 nuclear magnetic resonance study

Here, we show the binding results of a leguminosae lectin, winged bean basic agglutinin (WBA I) to N-trifluoroacetylgalactosamine (NTFAGalN), methyl-alpha-N-trifluoroacetylgalactosamine (Me alpha NTFAGalN) and methyl-beta-tifluoroacetylgalactosamine (Me beta NTFAGalN) using (19) F NMR spectroscopy. No chemical shift difference between the free and bound states for NTFAGalN and Me beta NTFAGalN, and 0.01-ppm chemical shift change for Me alpha NTFAGalN, demonstrate that the Me alpha NTFAGalN has a sufficiently long residence time on the protein binding site as compared to Me beta NTFAGalN and the free anomers of NTFAGalN. The sugar anomers were found in slow exchange with the binding site of agglutinin. Consequently, we obtained their binding parameters to the protein using line shape analyses. Aforementioned analyses of the activation parameters for the interactions of these saccharides indicate that the binding of alpha and beta anomers of NTFAGalN and Me alpha NTFAGalN is controlled enthalpically, while that of Me beta NTFAGalN is controlled entropically. This asserts the sterically constrained nature of the interaction of the Me beta NTFAGalN with WBA I. These studies thus highlight a significant role of the conformation of the monosaccharide ligands for their recognition by WBA I.

An integral fluctuation theorem for systems with unidirectional transitions

The fluctuations of a Markovian jump process with one or more unidirectional transitions, where R-ij > 0 but R-ji = 0, are studied. We find that such systems satisfy an integral fluctuation theorem. The fluctuating quantity satisfying the theorem is a sum of the entropy produced in the bidirectional transitions and a dynamical contribution, which depends on the residence times in the states connected by the unidirectional transitions. The convergence of the integral fluctuation theorem is studied numerically and found to show the same qualitative features as systems exhibiting microreversibility.

An ultrastable conjugate of silver nanoparticles and protein formed through weak interactions

In recent years, silver nanoparticles (AgNPs) have attracted significant attention owing to their unique physicochemical, optical, conductive and antimicrobial properties. One of the properties of AgNPs which is crucial for all applications is their stability. In the present study we unravel a mechanism through which silver nanoparticles are rendered ultrastable in an aqueous solution in complex with the protein ubiquitin (Ubq). This involves a dynamic and reversible association and dissociation of ubiquitin from the surface of AgNP. The exchange occurs at a rate much greater than 25 s(-1) implying a residence time of <40 ms for the protein. The AgNP-Ubq complex remains stable for months due to steric stabilization over a wide pH range compared to unconjugated AgNPs. NMR studies reveal that the protein molecules bind reversibly to AgNP with an approximate dissociation constant of 55 mu M and undergo fast exchange. At pH > 4 the positively charged surface of the protein comes in contact with the citrate capped AgNP surface. Further, NMR relaxation-based experiments suggest that in addition to the dynamic exchange, a conformational rearrangement of the protein takes place upon binding to AgNP. The ultrastability of the AgNP-Ubq complex was found to be useful for its anti-microbial activity, which allowed the recycling of this complex multiple times without the loss of stability. Altogether, the study provides new insights into the mechanism of protein-silver nanoparticle interactions and opens up new avenues for its application in a wide range of systems.

Influence of a Counterion on the Ion Atmosphere of an Anion: A Molecular Dynamics Study of LiX and CsX (X = F-, Cl-, I-) in Methanol

We report molecular dynamics (MD) simulations to explore the influence of a counterion on the structure and dynamics of cationic and anionic solvation shells for various ions in methanol at 298 K. We show that the variation in ionic size of either the cation or the anion in an ion pair influences the solvation structure of the other ion as well as the diffusivity in an electrolyte solution of methanol. The extent of ionic association between the cation and its counteranion of different ionic sizes has been investigated by analyzing the radial distribution functions (RDFs) and the orientation of methanol molecules in the first solvation shell (FSS) of ions. It is shown that the methanol in the FSS of the anion as well the cation exhibit quite different radial and orientational structures as compared to methanol which lie in the FSS of either the anion or the cation but not both. We find that the coordination number (CN) of F-, Cr-, and I- ions decreases with increasing size of the anion which is contrary to the trend reported for the anions in H2O. The mean residence time (MRT) of methanol molecules in the FSS of ions has been calculated using the stable states picture (SSP) approach. It is seen that the ion-counterion interaction has a considerable influence on the MRT of methanol molecules in the FSS of ions. We also discuss the stability order of the ion-counterion using the potentials of mean force (PMFs) for ion pairs with ions of different sizes. The PMF plots reveal that the Li+-F- pair (small-small) is highly stable and the Li+-I- pair is least stable (small-large) in electrolyte solutions.

La normativa hispano medieval y su aplicación en Indias : condición femenina dentro del marco penal y procesal

Resumen: El intercambio de culturas con ocasión de la residencia de los nuevos pobladores en tierras americanas, trajo como consecuencia la implantación de diferentes normativas provenientes de la Hispania medieval, pero también un grave desajuste en la aplicación de dichas costumbres para las mujeres, según fuera su estatus social. En ocasiones, indígenas, mestizas y españolas lograron alcanzar posturas flexibles –de parte de las autoridades canónicas y civiles– a la hora de ser multadas o castigadas por la ley; otras veces, su peso caía con todo el rigor sin atender a ningún tipo de diferenciación entre las mujeres.

La investigación comercial como instrumento básico para el conocimiento de las actitudes del electorado: un estudio empírico en la Universidad del País Vasco

[ES] Hoy en día, cualquier partido político debe utilizar el marketing para analizar su mercado y posicionarse en el mismo con una estrategia adecuada. Para ello, el papel de la investigación comercial resulta fundamental, dado que nos permite detectar las necesidades y deseos de los electores, pudiendo el partido adoptar decisiones tendentes a satisfacerlas.