Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones

Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone. Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of β- and γ-turns. A study of the minimum energy conformationsvis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases. A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families. Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures. The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature.

Electron energy distributions and transport coefficients in N2 in E times B fields

Using the concept of energy-dependent effective field intensity, electron transport coefficients in nitrogen have been determined in E times B fields (E = electric field intensity, B = magnetic flux density) by the numerical solution of the Boltzmann transport equation for the energy distribution of electrons. It has been observed that as the value of B/p (p = gas pressure) is increased from zero, the perpendicular drift velocity increased linearly at first, reaches a maximum value, and then decreases with increasing B/p. In general, the electron mean energy is found to be a function of Eavet/p( Eavet = averaged effective electric field intensity) only, but the other transport coefficients, such as transverse drift velocity, perpendicular drift velocity, and the Townsend ionization coefficient, are functions of both E/p and B/p.

Distance dependence of fluorescence resonance energy transfer

Deviations from the usual R (-6) dependence of the rate of fluorescence resonance energy transfer (FRET) on the distance between the donor and the acceptor have been a common scenario in the recent times. In this paper, we present a critical analysis of the distance dependence of FRET, and try to illustrate the non R (-6) type behaviour of the rate for the case of transfer from a localized electronic excitation on the donor, a dye molecule to three different energy acceptors with delocalized electronic excitations namely, graphene,two-dimensional semiconducting sheet and the case of such a semiconducting sheet rolled to obtain a nanotube. We use simple analytic models to understand the distance dependence in each case.

Universalization of access to modern energy services in Indian households-Economic and policy analysis

Provision of modern energy services for cooking (with gaseous fuels)and lighting (with electricity) is an essential component of any policy aiming to address health, education or welfare issues; yet it gets little attention from policy-makers. Secure, adequate, low-cost energy of quality and convenience is core to the delivery of these services. The present study analyses the energy consumption pattern of Indian domestic sector and examines the urban-rural divide and income energy linkage. A comprehensive analysis is done to estimate the cost for providing modern energy services to everyone by 2030. A public-private partnership-driven business model, with entrepreneurship at the core, is developed with institutional, financing and pricing mechanisms for diffusion of energy services. This approach, termed as EMPOWERS (entrepreneurship model for provision of wholesome energy-related basic services), if adopted, can facilitate large-scale dissemination of energy-efficient and renewable technologies like small-scale biogas/biofuel plants, and distributed power generation technologies to provide clean, safe, reliable and sustainable energy to rural households and urban poor. It is expected to integrate the processes of market transformation and entrepreneurship development involving government, NGOs, financial institutions and community groups as stakeholders. (C) 2009 Elsevier Ltd. All rights reserved.

An Experimental Study on Energy Absorption Behavior of Polyurethane Foams

This article is concerned with a study on the energy absorption behavior of polyurethane (PU) foams such as flexible high resilience (HR), flexible viscoelastic (VE) and semi-rigid (SR) foams as a function of the overall foam density. Foam samples were prepared in the form of cubes by mixing appropriate polyol and isocyanate compounds produced by Huntsman International India Pvt. Ltd. in varying proportions leading to a range of densities for each type of foam. The cubical samples were tested under compressive load in a standard UTM. Based on the measured load-displacement behaviors, variations of peak load and energy-absorption attributes with respect to density are plotted for each type of foam and the possible existence of an optimum foam density is shown.

Thermoelectric power in ultrathin films, quantum wires and carbon nanotubes under classically large magnetic field: Simplified theory and relative comparison

We study the thermoelectric power under classically large magnetic field (TPM) in ultrathin films (UFs), quantum wires (QWs) of non-linear optical materials on the basis of a newly formulated electron dispersion law considering the anisotropies of the effective electron masses, the spin-orbit splitting constants and the presence of the crystal field splitting within the framework of k.p formalism. The results of quantum confined III-V compounds form the special cases of our generalized analysis. The TPM has also been studied for quantum confined II-VI, stressed materials, bismuth and carbon nanotubes (CNs) on the basis of respective dispersion relations. It is found taking quantum confined CdGeAs2, InAs, InSb, CdS, stressed n-InSb and Bi that the TPM increases with increasing film thickness and decreasing electron statistics exhibiting quantized nature for all types of quantum confinement. The TPM in CNs exhibits oscillatory dependence with increasing carrier concentration and the signature of the entirely different types of quantum systems are evident from the plots. Besides, under certain special conditions, all the results for all the materials gets simplified to the well-known expression of the TPM for non-degenerate materials having parabolic energy bands, leading to the compatibility test. (C) 2009 Elsevier B.V. All rights reserved.

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.

Magnetic energy dissipation in force-free jets

It is shown that a magnetic-pressure-dominated, supersonic jet which expands (or contracts) in response to variations in the confining external pressure can dissipate magnetic energy through field-line reconnection as it relaxes to a minimum-energy configuration. In order for a continuous dissipation to take place, the effective reconnection time must be a fraction ɛ ⪉ 1 of the expansion time. The amount of energy dissipation is calculated, and it is concluded that magnetic energy dissipation could, in principle, power the observed synchrotron emission in extragalactic radio jets such as NGC 6251. However, this mechanism is only viable if the reconnection time is substantially shorter than the nominal resistive tearing time in the jet.

Embodied energy in cement stabilised rammed earth walls

Rammed earth walls are low carbon emission and energy efficient alternatives to load bearing walls. Large numbers of rammed earth buildings have been constructed in the recent past across the globe. This paper is focused on embodied energy in cement stabilised rammed earth (CSRE) walls. Influence of soil grading, density and cement content on compaction energy input has been monitored. A comparison between energy content of cement and energy in transportation of materials, with that of the actual energy input during rammed earth compaction in the actual field conditions and the laboratory has been made. Major conclusions of the investigations are (a) compaction energy increases with increase in clay fraction of the soil mix and it is sensitive to density of the CSRE wall, (b) compaction energy varies between 0.033 MJ/m(3) and 0.36 MJ/m(3) for the range of densities and cement contents attempted, (c) energy expenditure in the compaction process is negligible when compared to energy content of the cement and (d) total embodied energy in CSRE walls increases linearly with the increase in cement content and is in the range of 0.4-0.5 GJ/m(3) for cement content in the rage of 6-8%. (C) 2009 Elsevier B.V. All rights reserved.

A universal relation for the cohesive energy of nanoparticles

A universal relation between the cohesive energy and the particle size has been predicted based on the liquid-drop model. The universal relation is well supported by other theoretical models and the available experimental data. The universal relations for intermediate size range as well as for particles with very few atoms are discussed. A comparison of onset temperature of evaporation also establishes a universal relation.

Holomorphic Sobolev spaces, Hermite and special Hermite semigroups and a Paley-Wiener theorem for the windowed Fourier transform

The images of Hermite and Laguerre-Sobolev spaces under the Hermite and special Hermite semigroups (respectively) are characterized. These are used to characterize the image of Schwartz class of rapidly decreasing functions f on R-n and C-n under these semigroups. The image of the space of tempered distributions is also considered and a Paley-Wiener theorem for the windowed (short-time) Fourier transform is proved.