X-Pro peptides. A theoretical study of the hydrogen bonded conformations of (alpha-aminoisobutyryl-L -prolyl)n sequences

Intramolecularly hydrogen bonded conformations of (Aib-Pro)n sequences have been analysed theoretically. Both 4-1 (C10 and 3-1 (C7 hydrogen bonded regular structures are shown to be stereochemically feasible. Conformational energies for the helical structures have been estimated using classical potential energy methods. Both C10 and C7 conformations have very similar energies. Pyrrolidine ring puckering has a pronounced effect on the energies, and only Cv-endo puckered Pro residues can be accommodated. The theoretical calculations using spectroscopic data suggest that the recently proposed novel 310 helical conformation for benzyloxycarbonyl(Aib-Pro)4-methyl ester is in solution, is indeed energetically and stereochemically favourable.

X-Pro peptides. A theoretical study of the hydrogen bonded conformations of (a-aminoisobutyryl-L -prolyl)n sequences

Intramolecularly hydrogen bonded conformations of (Aib-Pro)n sequences have been analysed theoretically. Both 4�1 (C10 and 3�1 (C7 hydrogen bonded regular structures are shown to be stereochemically feasible. Conformational energies for the helical structures have been estimated using classical potential energy methods. Both C10 and C7 conformations have very similar energies. Pyrrolidine ring puckering has a pronounced effect on the energies, and only Cγ-endo puckered Pro residues can be accommodated. The theoretical calculations using spectroscopic data suggest that the recently proposed novel 310 helical conformation for benzyloxycarbonyl(Aib-Pro)4-methyl ester is in solution, is indeed energetically and stereochemically favourable.

Determination of size-independent specific fracture energy of concrete mixes by two methods

The RILEM work-of-fracture method for measuring the specific fracture energy of concrete from notched three-point bend specimens is still the most common method used throughout the world, despite the fact that the specific fracture energy so measured is known to vary with the size and shape of the test specimen. The reasons for this variation have also been known for nearly two decades, and two methods have been proposed in the literature to correct the measured size-dependent specific fracture energy (G(f)) in order to obtain a size-independent value (G(F)). It has also been proved recently, on the basis of a limited set of results on a single concrete mix with a compressive strength of 37 MPa, that when the size-dependent G(f) measured by the RILEM method is corrected following either of these two methods, the resulting specific fracture energy G(F) is very nearly the same and independent of the size of the specimen. In this paper, we will provide further evidence in support of this important conclusion using extensive independent test results of three different concrete mixes ranging in compressive strength from 57 to 122 MPa. (c) 2013 Elsevier Ltd. All rights reserved.

Rural energy consumption patterns - A field study

This paper is a condensed version of the final report of a detailed field study of rural energy consumption patterns in six villages located west of Bangalore in the dry belt of Karnataka State in India. The study was carried out in two phases; first, a pilot study of four villages and second, the detailed study of six villages, the populations of which varied from around 350 to about 950. The pilot survey ended in late 1976, and most of the data was collected for the main project in 1977. Processing of the collected data was completed in 1980. The aim was to carry out a census survey, rather than a sample study. Hence, considerable effort was expended in production of both a suitable questionnaire, ensuring that all respondents were contacted, and devising methods which would accurately reflect the actual energy use in various energy-utilising activities. In the end, 560 households out of 578 (97%) were surveyed. The following ranking was found for the various energy sources in order of average percentage contribution to the annual total energy requirement: firewood, 81·6%; human energy, 7·7%; animal energy, 2·7%; kerosene, 2·1%; electricity, 0·6% and all other sources (rice husks, agro-wastes, coal and diesel fuel), 5·3%. In other words commercial fuels made only a small contribution to the overall energy use. It should be noted that dung cakes are not burned in this region. The average energy use pattern, sector by sector, again on a percentage basis, was as follows: domestic, 88·3%; industry, 4·7%; agriculture, 4·3%; lighting, 2·2% and transport, 0·5%. The total annual per capita energy consumption was 12·6 ± 1·2 GJ, giving an average annual household consumption of around 78·6 GJ.

Rural energy consumption patterns - A field study

This paper is a condensed version of the final report of a detailed field study of rural energy consumption patterns in six villages located west of Bangalore in the dry belt of Karnataka State in India. The study was carried out in two phases; first, a pilot study of four villages and second, the detailed study of six villages, the populations of which varied from around 350 to about 950. The pilot survey ended in late 1976, and most of the data was collected for the main project in 1977. Processing of the collected data was completed in 1980. The aim was to carry out a census survey, rather than a sample study. Hence, considerable effort was expended in production of both a suitable questionnaire, ensuring that all respondents were contacted, and devising methods which would accurately reflect the actual energy use in various energy-utilising activities. In the end, 560 households out of 578 (97%) were surveyed. The following ranking was found for the various energy sources in order of average percentage contribution to the annual total energy requirement: firewood, 81A·6%; human energy, 7A·7%; animal energy, 2A·7%; kerosene, 2A·1%; electricity, 0A·6% and all other sources (rice husks, agro-wastes, coal and diesel fuel), 5A·3%. In other words commercial fuels made only a small contribution to the overall energy use. It should be noted that dung cakes are not burned in this region. The average energy use pattern, sector by sector, again on a percentage basis, was as follows: domestic, 88A·3%; industry, 4A·7%; agriculture, 4A·3%; lighting, 2A·2% and transport, 0A·5%. The total annual per capita energy consumption was 12A·6 A± 1A·2 GJ, giving an average annual household consumption of around 78A·6 GJ.

Application of optimization methods to vibration control of stretched strings

In this paper, non-linear programming techniques are applied to the problem of controlling the vibration pattern of a stretched string. First, the problem of finding the magnitudes of two control forces applied at two points l1 and l2 on the string to reduce the energy of vibration over the interval (l1, l2) relative to the energy outside the interval (l1, l2) is considered. For this problem the relative merits of various methods of non-linear programming are compared. The more complicated problem of finding the positions and magnitudes of two control forces to obtain the desired energy pattern is then solved by using the slack unconstrained minimization technique with the Fletcher-Powell search. In the discussion of the results it is shown that the position of the control force is very important in controlling the energy pattern of the string.

Crystallization kinetics of SrBi2B2O7 glasses by non-isothermal methods

Transparent glasses of SrBi2B2O7 (SBBO) were fabricated via the conventional melt-quenching technique. The amorphous and the glassy nature of the as-quenched samples were, respectively, confirmed by X-ray powder diffraction (XRD) and differential scanning calorimetry (DSC). The glass transition (T (g)) and the crystallization parameters [crystallization activation energy (E (cr)) and Avrami exponent (n)] were evaluated under non-isothermal conditions using DSC. There was a close agreement between the activation energies for the crystallization process determined by Augis and Bennet and Kissinger methods. The variation of local activation energy [E (c)(x)] that was determined by Ozawa method, decreased with the fraction of crystallization (x). The Avrami exponent (n(x)) increased with the increase in fraction of crystallization (x) suggesting that there was a change over in the crystallization process from the surface to the bulk.

A Search for Energy Minimized Sequences of Proteins

In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10(-7). In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.

Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks

The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of llostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side-chains and then to compute the ligand-induced population shift. Finally, we obtain the free-energy landscape of the protein in equilibrium, characterizing the free-energy minima accessed by the protein complexes. We have chosen human tryptophanyl-tRNA synthetase (hTrpRS), a protein esponsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure.

High energy oxygen ion induced modifications in lead based perovskite thin films

The lead based ferroelectric PbZr0.53Ti0.47O3 (PZT), (Pb0.90La0.10)TiO3 (PLT10) and (Pb0.80La0.20)TiO3 (PLT20) thin films, prepared by pulsed laser ablation technique, were studied for their response to the 70 MeV oxygen ion irradiation. The dielectric analysis, capacitance-voltage (C- V) and DC leakage current measurements were performed before and after the irradiation to high-energy oxygen ions. The irradiation produced considerable changes in the dielectric, C-V, leakage characteristics and induced some amount of amorphization. The PZT films showed partial recrystallization after a thermal annealing at 400 degrees C for 10 min. The phase transition temperature [T-c] of PLT20 increased from 115 degrees C to 120 degrees C. The DC conductivity measurements showed a shift in the onset of non-linear conduction region. The current density decreased by two orders of magnitude after irradiation. After annealing the irradiated films at a temperature of 400 degrees C for 10 min, the films partially regained the dielectric and electrical properties. The results are discussed in terms of the irradiation-induced amorphization, the pinning of the ferroelectric domains by trapped charges and the thermal annealing of the defects generated during the irradiation. (C) 2007 Elsevier B.V. All rights reserved.

Impedance studies on high energy Li3+ irradiated PZT thin films

The ferroelectric Pb(Zr0.48Ti0.52)O-3 (PZT) thin films prepared by the pulsed laser deposition technique were studied for their response to high energy lithium ion irradiation through impedance spectroscopy. The Debye peaks, observed in the impedance and modulus plots of irradiatedfilms, shifts towards higher frequencies compared to those of unirradiated films. This is equivalent to the trend observed with increase in temperature in the unirradiated films due to the dielectric relaxation. The irradiated films showed a decrease in the grain resistance compared to the unirradiated films. The activation energy of dielectric relaxation increases from 1.25 eV of unirradiated film to 1.62 eV of irradiated film. The observed modifications in the irradiated film were ascribed to the modifications in the grain structure due to the high value of electronic energy loss.

Studies on the ionic transport and structural investigations of La0.5Li0.5TiO3 perovskite synthesized by wet chemical methods and the effect of Ce, Zr substitution at Ti site

La0.5Li0.5TiO3 perovskite was synthesized by various wet chemical methods. By adopting low temperature methods of preparation lithium loss from the material is prevented. La0.5Li0.5TiO3 (LLTO) was formed with cubic symmetry at 1473 K. LLTO was formed at relatively lower temperature by using hydrothermal preparation method. PVA gel-decomposition route yield tetragonal LLTO on annealing the dried gel at 1473 K. By using gel-carbonate route LiTi2O4 minor phase was found to remain even after heat-treatment at 1473 K. The hydroxylation of LLTO was done in deionized water as well as in dilute acetic acid medium. By hydroxylation process incorporation of hydroxyls and leaching out of Li+ was observed from the material. The Li+ concentration of these compositions was examined by AAS. The electrical conductivities of these compositions were measured by dc and ac impedance techniques at elevated temperatures. The activation energies of electrical conduction for these compositions were estimated from the experimental results. The measured activation energy of Li+ conduction is 0.34 eV. Unhydroxylated samples exhibit only Li+ conduction, whereas, the hydroxylated LLTO show proton conductivity at 298-550 K in addition to Li+ conductivity. The effect of Zr or Ce substitution in place of Ti were attempted. La0.5Li0.5ZrO3 Perovskite was not formed; instead pyrochlore phase (La2Zr2O7) along with monoclinic ZrO2 phases was observed above 1173 K; below 1173 K cubic ZrO2 is stable. (La0.5Li0.5)(2)CeO4 solid solution was formed in the case of Ce substitution at Ti sublattice on heat-treatment up to 1673 K. (c) 2005 Springer Science + Business Media, Inc.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Direct stability evaluation of power systems with detailed generator models using structure-preserving energy functions

Energy-based direct methods for transient stability analysis are potentially useful both as offline tools for planning purposes as well as for online security assessment. In this paper, a novel structure-preserving energy function (SPEF) is developed using the philosophy of structure-preserving model for the system and detailed generator model including flux decay, transient saliency, automatic voltage regulator (AVR), exciter and damper winding. A simpler and yet general expression for the SPEF is also derived which can simplify the computation of the energy function. The system equations and the energy function are derived using the centre-of-inertia (COI) formulation and the system loads are modelled as arbitrary functions of the respective bus voltages. Application of the proposed SPEF to transient stability evaluation of power systems is illustrated with numerical examples.