The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Synthesis, spectral characterization and in vitro microbiological evaluation of novel glyoxal, biacetyl and benzil bis-hydrazone macrocyclic Schiff bases and their Co(II), Ni(II) and Cu(II) complexes

A series of binuclear Co(II), Ni(II) and Cu(II) complexes were synthesized by the template condensation of glyoxal, biacetyl or benzil bis-hydrazide, 2,6-diformyl-4-methylphenol and Co(11), Ni(II) or Cu(II) chloride in a 2:2:2 M ratio in ethanol. These 22-membered macrocyclic complexes were characterized by elemental analyses, magnetic, molar conductance, spectral, thermal and fluorescence studies. Elemental analyses suggest the complexes have a 2:1 stoichiometry of the type (M2LX2]center dot nH(2)O and Ni(2)LX(2)2H(2)O]center dot nH(2)O (where M = Co(II) and Cu(II); L = H2L1, H2L2 and H2L3; X = Cl; n = 2). From the spectroscopic and magnetic studies, it has been concluded that the Co(11) and Cu(11) complexes display a five coordinated square pyramidal geometry and the Ni(II) complexes have a six coordinated octahedral geometry. The Schiff bases and their metal complexes have also been screened for their antibacterial and antifungal activities by the MIC method. (C) 2011 Elsevier Ltd. All rights reserved.

Potassium titanyl phosphate and its isomorphs: Growth, properties, and applications

Potassium titanyl phosphate (KTP) and its isomorphs have received enormous attention in the last 2 decades. In particular, KTP assumes importance due to its large nonlinear optic and electrooptic coefficients together with the broad thermal and angular acceptance for second harmonic generation. This article provides an overview of the material aspects, structural, physical, and chemical properties and device feasibility of the KTP family of crystals. Some of the current areas of research and development along with their significance in understanding the physical properties as well as device applications are addressed. Optical waveguide fabrication processes and characteristics with their relevance to the present-day technology are highlighted. Studies performed so far have enabled us to understand the fundamental aspects of these materials and what needs to be pursued vigorously is the exploitation of their device applications to the maximum extent.

FE analysis of piezo-laminate composites under thermal loads

A shear flexible 4-noded finite element formulation, having five mechanical degrees of freedom per node, is presented for modeling the dynamic as well as the static thermal response of laminated composites containing distributed piezoelectric layers. This element has been developed to have one electrical degree of freedom per piezoelectric layer. The mass, stiffness and thermo-electro-mechanical coupling effects on the actuator and sensor layers have been considered. Numerical studies have been conducted to investigate both the sensory and active responses on piezoelectric composite beam and plate structures. It is. concluded that both the thermal and pyroelectric effects are important and need to be considered in the precision distributed control of intelligent structures.

Composition tunable memory and threshold switching in Al20As xTe80− x semiconducting glasses

I-V studies indicate a composition dependent switching behavior (Memory or Threshold) in bulk Al20AsxTe80−x glasses, which is determined by the coordination and composition of aluminum. Investigations on temperature and thickness dependence of switching and structural studies on switched samples suggest thermal and electronic mechanisms of switching for the memory and threshold samples, respectively. The present results also show that these samples have a wider composition range of threshold behavior with lower threshold voltages compared to other threshold samples.

Effects of phase inhomogeneity and boundary conditions on the dynamic response of SMA wire actuators

This paper reports the simulation results from the dynamic analysis of a Shape Memory Alloy (SMA) actuator. The emphasis is on understanding the dynamic behavior under various loading rates and boundary conditions, resulting in complex scenarios such as thermal and stress gradients. Also, due to the polycrystalline nature of SMA wires, presence of microstructural inhomogeneity is inevitable. Probing the effect of inhomogeneity on the dynamic behavior can facilitate the prediction of life and characteristics of SMA wire actuator under varieties of boundary and loading conditions. To study the effect of these factors, an initial boundary value problem of SMA wire is formulated. This is subsequently solved using finite element method. The dynamic response of the SMA wire actuator is analyzed under mechanical loading and results are reported. Effect of loading rate, micro-structural inhomogeneity and thermal boundary conditions on the dynamic response of SMA wire actuator is investigated and the simulation results are reported.

Numerical Study Of Heat Transfer From Pin Fin Heat Sink Using Steady And Pulsated Impinging Jets

The work reported in this thesis is an attempt to enhance heat transfer in electronic devices with the use of impinging air jets on pin-finned heat sinks. The cooling per-formance of electronic devices has attracted increased attention owing to the demand of compact size, higher power densities and demands on system performance and re-liability. Although the technology of cooling has greatly advanced, the main cause of malfunction of the electronic devices remains overheating. The problem arises due to restriction of space and also due to high heat dissipation rates, which have increased from a fraction of a W/cm2to 100s of W /cm2. Although several researchers have at-tempted to address this at the design stage, unfortunately the speed of invention of cooling mechanism has not kept pace with the ever-increasing requirement of heat re- moval from electronic chips. As a result, efficient cooling of electronic chip remains a challenge in thermal engineering. Heat transfer can be enhanced by several ways like air cooling, liquid cooling, phase change cooling etc. However, in certain applications due to limitations on cost and weight, eg. air borne application, air cooling is imperative. The heat transfer can be increased by two ways. First, increasing the heat transfer coefficient (forced convec- tion), and second, increasing the surface area of heat transfer (finned heat sinks). From previous literature it was established that for a given volumetric air flow rate, jet im-pingement is the best option for enhancing heat transfer coefficient and for a given volume of heat sink material pin-finned heat sinks are the best option because of their high surface area to volume ratio. There are certain applications where very high jet velocities cannot be used because of limitations of noise and presence of delicate components. This process can further be improved by pulsating the jet. A steady jet often stabilizes the boundary layer on the surface to be cooled. Enhancement in the convective heat transfer can be achieved if the boundary layer is broken. Disruptions in the boundary layer can be caused by pulsating the impinging jet, i.e., making the jet unsteady. Besides, the pulsations lead to chaotic mixing, i.e., the fluid particles no more follow well defined streamlines but move unpredictably through the stagnation region. Thus the flow mimics turbulence at low Reynolds number. The pulsation should be done in such a way that the boundary layer can be disturbed periodically and yet adequate coolant is made available. So, that there is not much variation in temperature during one pulse cycle. From previous literature it was found that square waveform is most effective in enhancing heat transfer. In the present study the combined effect of pin-finned heat sink and impinging slot jet, both steady and unsteady, has been investigated for both laminar and turbulent flows. The effect of fin height and height of impingement has been studied. The jets have been pulsated in square waveform to study the effect of frequency and duty cycle. This thesis attempts to increase our understanding of the slot jet impingement on pin-finned heat sinks through numerical investigations. A systematic study is carried out using the finite-volume code FLUENT (Version 6.2) to solve the thermal and flow fields. The standard k-ε model for turbulence equations and two layer zonal model in wall function are used in the problem Pressure-velocity coupling is handled using the SIMPLE algorithm with a staggered grid. The parameters that affect the heat transfer coefficient are: height of the fins, total height of impingement, jet exit Reynolds number, frequency of the jet and duty cycle (percentage time the jet is flowing during one complete cycle of the pulse). From the studies carried out it was found that: a) beyond a certain height of the fin the rate of enhancement of heat transfer becomes very low with further increase in height, b) the heat transfer enhancement is much more sensitive to any changes at low Reynolds number than compared to high Reynolds number, c) for a given total height of impingement the use of fins and pulsated jet, increases the effective heat transfer coefficient by almost 200% for the same average Reynolds number, d) for all the cases it was observed that the optimum frequency of impingement is around 50 − 100 Hz and optimum duty cycle around 25-33.33%, e) in the case of turbulent jets the enhancement in heat transfer due to pulsations is very less compared to the enhancement in case of laminar jets.

Groundwater Management in India:Physical, Institutional and Policy Alternatives

Groundwater constitutes a vital natural resource for sustaining India’s agricultural economy and meeting the country’s social, ecological and environmental goals. It is a unique resource, widely available, providing security against droughts and yet it is closely linked to surface-water resources and the hydrological cycle. Its availability depends on geo-hydrological conditions and characteristics of aquifers, from deep to alluvium, sediment crystalline rocks to basalt formations; and agro-climate from humid to subhumid and semi-arid to arid. Its reliable supply, uniform quality and temperature, relative turbidity, pollution-safe, minimal evaporation losses, and low cost of development are attributes making groundwater more attractive compared to other resources. It plays a key role in the provision of safe drinking water to rural populations. For example, already almost 80% of domestic water use in rural areas in India is groundwater-supplied, and much of it is being supplied to farms, villages and small towns. Inadequate control of the use of groundwater, indiscriminate application of agrochemicals and unrestrained pollution of the rural environment by other human activities make groundwater usage unsustainable, necessitating proper management in the face of the twin demand for water of good quality for domestic supply and adequate supply for irrigation, ensuring equity, efficiency and sustainability of the resource. Groundwater irrigation has overtaken surface irrigation in the early 1980s, supported by well energization. It is estimated that there are about 24 million energised wells and tube wells now and it is driven by demand rather than availability, evident through the greater occurrence of wells in districts with high population densities. Apart from aquifer characteristics, land fragmentation and landholding size are the factors that decide the density of wells. The ‘rise and fall’ of local economies dependent on groundwater can be summarized as: the green revolution of 1980s, groundwaterbased agrarian boom, early symptoms of groundwater overdraft, and decline of the groundwater socio-ecology. The social characteristics and policy interventions typical of each stage provide a fascinating insight into the human-resource dynamics. This book is a compilation of nine research papers discussing various aspects of groundwater management. It attempts to integrate knowledge about the physical system, the socio-economic system, the institutional set-up and the policy environment to come out with a more realistic analysis of the situation with regard to the nature, characteristics and intensity of resource use, the size of the economy the use generates, and the negative socioeconomic consequences. Complex variables addressed in this regard focusing on northern Gujarat are the stock of groundwater available in the region, its hydrodynamics, its net outflows against inflows, the economics of its intensive use (particularly irrigation in semi-arid and arid regions), its criticality in the regional hydroecological regime, ethical aspects and social aspects of its use. The first chapter by Dinesh Kumar and Singh, dwells on complex groundwater socio-ecology of India, while emphasizing the need for policy measures to address indiscriminate over-exploitation of dwindling resources. The chapter also explores the nature of groundwater economy and the role of electricity prices on it. The next chapter on groundwater issue in north Gujarat provides a description of groundwater resource characteristics followed by a detailed analysis of the groundwater depletion and quality deterioration problems in the region and their undesirable consequences on the economy, ecosystem health and the society. Considering water-buyers and wellowning farmers individually, a methodology for economic valuation of groundwater in regions where its primary usage is in agriculture, and as assessment of the groundwater economy based on case studies from north Gujarat is presented in the fourth chapter. The next chapter focuses on the extent of dependency of milk production on groundwater, which includes the water embedded in green and dry fodder and animal feed. The study made a realistic estimate of irrigation water productivity in terms of the physics and economics of milk production. The sixth chapter analyses the extent of reduction in water usage, increase in yield and overall increase in physical productivity of alfalfa with the use of the drip irrigation system. The chapter also provides a detailed synthesis of the costs and benefits associated with the use of drip irrigation systems. A linear programmingbased optimization model with the objective to minimize groundwater use taking into account the interaction between two distinct components – farming and dairying under the constraints of food security and income stability for different scenarios, including shift in cropping pattern, introduction of water-efficient crops, water- saving technologies in addition to the ‘business as usual’ scenario is presented in the seventh chapter. The results show that sustaining dairy production in the region with reduced groundwater draft requires crop shifts and adoption of water-saving technologies. The eighth chapter provides evidences to prove that the presence of adequate economic incentive would encourage farmers to adopt water-saving irrigation devices, based on the findings of market research with reference to the level of awareness among farmers of technologies and the factors that decide the adoption of water-saving technologies. However, now the marginal cost of using electricity for agricultural pumping is almost zero. The economic incentives are strong and visible only when the farmers are either water-buyers or have to manage irrigation with limited water from tube-well partnerships. The ninth chapter explores the socio-economic viability of increasing the power tariff and inducing groundwater rationing as a tool for managing energy and groundwater demand, considering the current estimate of the country’s annual economic loss of Rs 320 billion towards electricity subsidy in the farm sector. The tenth chapter suggests private tradable property rights and development of water markets as the institutional tool for achieving equity, efficiency and sustainability of groundwater use. It identifies the externalities for local groundwater management and emphasizes the need for managing groundwater by local user groups, supported by a thorough analysis of groundwater socio-ecology in India. An institutional framework for managing the resource based on participatory approach that is capable of internalizing the externalities, comprising implementation of institutional and technical alternatives for resource management is also presented. Major findings of the analyses and key arguments in each chapter are summarized in the concluding chapter. Case studies of the social and economic benefits of groundwater use, where that use could be described as unsustainable, are interesting. The benefits of groundwater use are outlined and described with examples of social and economic impacts of groundwater and the negative aspects of groundwater development with the compilation of environmental problems based on up-to-date research results. This publication with a well-edited compilation of case studies is informative and constitutes a useful publication for students and professionals.

Stability of domain structures in multi-domain proteins

Multi-domain proteins have many advantages with respect to stability and folding inside cells. Here we attempt to understand the intricate relationship between the domain-domain interactions and the stability of domains in isolation. We provide quantitative treatment and proof for prevailing intuitive ideas on the strategies employed by nature to stabilize otherwise unstable domains. We find that domains incapable of independent stability are stabilized by favourable interactions with tethered domains in the multi-domain context. Stability of such folds to exist independently is optimized by evolution. Specific residue mutations in the sites equivalent to inter-domain interface enhance the overall solvation, thereby stabilizing these domain folds independently. A few naturally occurring variants at these sites alter communication between domains and affect stability leading to disease manifestation. Our analysis provides safe guidelines for mutagenesis which have attractive applications in obtaining stable fragments and domain constructs essential for structural studies by crystallography and NMR.

Alloy/Oxide Equilibria in Iron--Vanadium--Oxygen and Iron--Niobium--Oxygen Systems

An experimental characterization of three-phase equilibria in Fe--V--O and Fe--Nb--O systems at 1823, 1873 and 1923K has been carried out using a solid state cell and by analysis of quenched samples. The oxygen potentials corresponding to these three-phase equilibria were monitored by a solid state cell incorporating Y sub 2 O sub 3 doped ThO sub 2 with Cr + Cr sub 2 O sub 3 as reference electrode. Similar measurements were carried out for Fe--Nb--O alloys in equilibrium with a mixture of FeNb sub 2 O sub 6 and NbO sub 2 . These measurements permit evaluation of interaction parameters (e exp V sub O = --6590/T + 2.892 and e exp Nb sub O = --4066/T + 1.502) and activity coefficients of vanadiun and niobium in dilute solution (ln gamma exp O sub V = --35 320/T + 12.68 and ln gamma sub Nb exp O = --12 386/T + 4.34) in liquid iron. The results obtained in this study resolve a number of discrepancies in thermodynamic data reported in the literature, especially regarding the activity coefficients of V and Nb and the stability ranges for V sub 2 O sub 3 and VO sub 1+x . 18 ref.--AA

Thermodynamics of Al(1-x)Ga(x)N solid solution: Inclination for phase separation and ordering

Although Al(1-x)Ga(x)N semiconductors are used in lighting, displays and high-power amplifiers, there is no experimental thermodynamic information on nitride solid solutions. Thermodynamic data are useful for assessing the intrinsic stability of the solid solution with respect to phase separation and extrinsic stability in relation to other phases such as metallic contacts. The activity of GaN in Al(1-x)Ga(x)N solid solution is determined at 1100 K using a solid-state electrochemical cell: Ga + Al(1-x)Ga(x)N/Fe, Ca(3)N(2)//CaF(2)//Ca(3)N(2), N(2) (0.1 MPa), Fe. The solid-state cell is based on single crystal CaF(2) as the electrolyte and Ca(3)N(2) as the auxiliary electrode to convert the nitrogen chemical potential established by the equilibrium between Ga and Al(1-x)Ga(x)N solid solution into an equivalent fluorine potential. Excess Gibbs free energy of mixing of the solid solution is computed from the results. Results suggest an unusual mixing behavior: a mild tendency for ordering at three discrete compositions (x = 0.25, 0.5 and 0.75) superimposed on predominantly positive deviation from ideality. The lattice parameters exhibit slight deviation from Vegard's law, with the a-parameter showing positive and the c-parameter negative deviation. Although the solid solution is stable in the full range of compositions at growth temperatures, thermodynamic instability is indicated at temperatures below 410 K in the composition range 0.26 <= x <= 0.5. At 355 K, two biphasic regions appear, with terminal solid solutions stable only for 0 <= x <= 0.26 and 0.66 <= x <= 1. The range of terminal solid solubility reduces with decreasing temperature. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

ZnFe(2)O(4): Rapid and sub-100 degrees C synthesis and anneal-tuned magnetic properties

Nanocrystalline zinc ferrite (ZFO) has been synthesized from metal acetylacetonates by microwave irradiation for 5 min in the presence of a surfactant. The as-prepared material is ZFO and has been subjected in air to conventional furnace annealing and to rapid annealing at different temperatures. Both annealing protocols lead to well-crystallized ZFO, with crystallite sizes in the range similar to 8-20 nm, which is ferrimagnetic, even at room temperature, with magnetization attaining saturation. While the magnetization M(S) of conventionally annealed ZFO varies with crystallite size in the expected manner, rapid annealing leads to high M(S) even when the crystallite size is relatively large. The coercivity is greater in the conventionally annealed ZFO. Thermal and magnetic measurements suggest that the inhomogeneous site cationic distribution within each crystallite caused by rapid annealing can be used to tailor the magnetic behaviour of nanocrystalline ferrites.

Atomic layer deposition of ZrO2 thin films: Study of growth kinetics and dielectric behaviour

Thin films of ZrO2 have been deposited by ALD on Si(100) and SIMOX using two different metalorganic complexes of Zr as precursors. These films are characterized by X-ray diffraction, transmission and scanning electron microscopies, infrared spectroscopy, and electrical measurements. These show that amorphous ZrO2 films of high dielectric quality may be grown on Si(100) starting about 400degreesC. As the growth temperature is raised, the films become crystalline, the phase formed and the microstructure depending on precursor molecular structure. The phase of ZrO2 formed depends also on the relative duration of the precursor and oxygen pulses. XPS and IR spectroscopy show that films grown at low temperatures contain chemically unbound carbon, its extent depending on the precursor. C-V measurements show that films grown on Si(100) have low interface state density, low leakage current, a hysteresis width of only 10-250 mV and a dielectric constant of similar to16-25.

Synthesis, spectroscopic properties and biological evaluation of transition metal complexes of salicylhydrazone of anthranilhydrazide: X-ray crystal structure of copper complex

The transition metal complexes of salicylhydrazone of anthranilhydrazide (H2L) were synthesised. The structures of metal complexes were characterized by various spectroscopic [IR, NMR, UV-Vis, EPR], thermal and other physicochemical methods. The single-crystal X-ray diffraction study of [Cu(HL)Cl]center dot H2O reveal its orthorhombic system with space group P2(1)2(1)2 and Z=4. The copper center has a distorted square planar geometry with ONO and Cl as the donor atoms. The ligand and its metal chelates have been screened for their antimicrobial and anti-tubercular activities using serial dilution method. Metal complexes in general have exhibited better antibacterial and antifungal activity than the free ligand and in few cases better than the standard used. Among the bacterial strains used, the complexes are highly potent against Gram-positive strains compared to Gram-negative. Anti-tubercular activity exhibited by the Co(II) complex is comparable with the standard used. (C) 2011 Elsevier B. V. All rights reserved.

Novel algorithm for online voltage stability assessment based on feed forward neural network

This paper presents an artificial feed forward neural network (FFNN) approach for the assessment of power system voltage stability. A novel approach based on the input-output relation between real and reactive power, as well as voltage vectors for generators and load buses is used to train the neural net (NN). The input properties of the feed forward network are generated from offline training data with various simulated loading conditions using a conventional voltage stability algorithm based on the L-index. The neural network is trained for the L-index output as the target vector for each of the system loads. Two separate trained NN, corresponding to normal loading and contingency, are investigated on the 367 node practical power system network. The performance of the trained artificial neural network (ANN) is also investigated on the system under various voltage stability assessment conditions. As compared to the computationally intensive benchmark conventional software, near accurate results in the value of L-index and thus the voltage profile were obtained. Proposed algorithm is fast, robust and accurate and can be used online for predicting the L-indices of all the power system buses. The proposed ANN approach is also shown to be effective and computationally feasible in voltage stability assessment as well as potential enhancements within an overall energy management system in order to determining local and global stability indices