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.

Potential and economics of forestry options for carbon sequestration in India

There is a need to understand the carbon (C) sequestration potential of the forestry option and its financial implications for each country.In India the C emissions from deforestation are estimated to be nearly offset by C sequestration in forests under succession and tree plantations. India has nearly succeeded in stabilizing the area under forests and has adequate forest conservation strategies. Biomass demands for softwood, hardwood and firewood are estimated to double or treble by the year 2020. A set of forestry options were developed to meet the projected biomass needs, and keeping in mind the features of land categories available, three scenarios were developed: potential; demand-driven; and programme-driven scenarios. Adoption of the demand-driven scenario, targeted at meeting the projected biomass needs, is estimated to sequester 78 Mt of C annually after accounting for all emissions resulting from clearfelling and end use of biomass. The demand-driven scenario is estimated to offset 50% of national C emission at 1990 level. The cost per t of C sequestered for forestry options is lower than the energy options considered. The annual investment required for implementing the demand-driven scenario is estimated to be US$ 2.1 billion for six years and is shown to be feasible. Among forestry options, the ranking based on investment cost per t of C sequestered from least cost to highest cost is; natural regeneration-agro-forestry-enhanced natural regeneration (< US$ 2.5/t C)-timber-community-softwood forestry (US$ 3.3 to 7.3 per t of C).

The energy balance in the Ramdas layer

On calm clear nights, air at a height of a few decimetres above bare soil can be cooler than the surface by several degrees in what we shall call the Ramdas layer (Ramdas and Atmanathan, 1932). The authors have recently offered a logical explanation for such a lifted temperature minimum, together with a detailed numerical model. In this paper, we provide physical insight into the phenomenon by a detailed discussion of the energy budget in four typical cases, including one with a lifted minimum. It is shown that the net cooling rate near ground is the small difference between two dominant terms, representing respectively radiative upflux from the ground and from the air layers just above ground. The delicate energy balance that leads to the lifted minimum is upset by turbulent transport, by surface emissivity approaching unity, or by high ground cooling rates. The rapid variation of the flux emissivity of humid air is shown to dominate radiative transport near the ground.

Direct Evaluation Of Transient Stability Improvement With Static Var Compensators Using A Structure Preserving Energy Function

The ability of Static Var Compensators (SVCs) to rapidly and continuously control reactive power in response to changing system conditions can result in the improvement of system stability and also increase the power transfer in the transmission system. This paper concerns the application of strategically located SVCs to enhance the transient stability limits and the direct evaluation of the effect of these SVCs on transient stability using a Structure Preserving Energy Function (SPEF). The SVC control system can be modelled from the steady- state control characteristic to accurately simulate its effect on transient stability. Treating the SVC as a voltage-dependent reactive power load leads to the derivation of a path-independent SPEF for the SVC. Case studies on a 10-machine test system using multiple SVCs illustrate the effects of SVCs on transient stability and its accurate prediction.

Optical studies of SN 2009jf: a Type Ib supernova with an extremely slow decline and aspherical signature

Optical UBVRI photometry and medium-resolution spectroscopy of the Type Ib supernova SN 2009jf, during the period from similar to -15 to +250 d, with respect to the B maximum are reported. The light curves are broad, with an extremely slow decline. The early post-maximum decline rate in the V band is similar to SN 2008D; however, the late-phase decline rate is slower than other Type Ib supernovae studied. With an absolute magnitude of M-V = -17.96 +/- 0.19 at peak, SN 2009jf is a normally bright supernova. The peak bolometric luminosity and the energy deposition rate via the 56Ni -> 56Co chain indicate that similar to 0.17+0.03(-0.03) M-circle dot of 56Ni was ejected during the explosion. The He i 5876 A line is clearly identified in the first spectrum of day similar to -15, at a velocity of similar to 16 000 km s-1. The O i] 6300-6364 A line seen in the nebular spectrum has a multipeaked and asymmetric emission profile, with the blue peak being stronger. The estimated flux in this line implies that greater than or similar to 1.34 M-circle dot oxygen was ejected. The slow evolution of the light curves of SN 2009jf indicates the presence of a massive ejecta. The high expansion velocity in the early phase and broader emission lines during the nebular phase suggest it to be an explosion with a large kinetic energy. A simple qualitative estimate leads to the ejecta mass of M-ej = 4-9 M-circle dot and kinetic energy E-K = 3-8 x 1051 erg. The ejected mass estimate is indicative of an initial main-sequence mass of greater than or similar to 20-25 M-circle dot.

Lopsidedness in WHISP galaxies I. Rotation curves and kinematic lopsidedness

The frequently observed lopsidedness of the distribution of stars and gas in disc galaxies is still considered as a major problem in galaxy dynamics. It is even discussed as an imprint of the formation history of discs and the evolution of baryons in dark matter haloes. Here, we analyse a selected sample of 70 galaxies from the Westerbork Hi Survey of Spiral and Irregular Galaxies. The Hi data allow us to follow the morphology and the kinematics out to very large radii. In the present paper, we present the rotation curves and study the kinematic asymmetry. We extract the rotation curves of the receding and approaching sides separately and show that the kinematic behaviour of disc galaxies can be classified into five different types: symmetric velocity fields where the rotation curves of the receding and approaching sides are almost identical; global distortions where the rotation velocities of the receding and approaching sides have an offset that is constant with radius; local distortions leading to large deviations in the inner and negligible deviations in the outer parts (and vice versa); and distortions that divide the galaxies into two kinematic systems that are visible in terms of the different behaviour of the rotation curves of the receding and approaching sides, which leads to a crossing and a change in side. The kinematic lopsidedness is measured from the maximum rotation velocities, averaged over the plateau of the rotation curves. This gives a good estimate of the global lopsidedness in the outer parts of the sample galaxies. We find that the mean value of the perturbation parameter denoting the lopsided potential as obtained from the kinematic data is 0.056. Altogether, 36% of the sample galaxies are globally lopsided, which can be interpreted as the disc responding to a halo that was distorted by a tidal encounter. In Paper II, we study the morphological lopsidedness of the same sample of galaxies.

Measurement of Gibbs energy of formation of Ca2PbO4 using a solid-state cell with three electrodes

Phase relations in the system Ca-Pb-O at 1100 K have been determined by equilibrating 18 compositions in the ternary and identifying the phases present in quenched samples by X-ray diffraction and energy dispersive X-ray analysis (EDX). Only one ternary compound Ca2PbO4 was found to be present. The compound coexists with CaO and PbO. The intermetallic compounds Ca2Pb, Ca5Pb3 and CaPb and liquid alloys are in equilibrium with CaO. The standard Gibbs energies of formation of Ca2PbO4 (880 - 1100 K) and Pb3O4 (770 - 910 K) were determined using solid-state cells based on yttria-stabilized zirconia as the solid electrolyte. Pure oxygen gas at 0.1 MPa was used as the reference electrode. For measurements on Ca2PbO4, a novel cell design with three electrodes in series, separated by solid electrolyte membranes, was used to avoid polarization of the electrode containing three solid phases. Two three-phase electrodes were used. The first absorbs the electrochemical flux of oxygen from the reference electrode to the measuring electrode. The other three-phase electrode, which is unaffected by the oxygen flux through the solid electrolyte, is used for electromotive force (EMF) measurement. The results from EMF studies were cross-checked using thermogravimetry (TG) under controlled oxygen partial pressures. The stability of Pb3O4 was investigated using a conventional solid-state cell with RuO2 electrodes. The results can be summarized by the following equations: 2CaO + PbO +1/2O(2) --> Ca2PbO4 Delta(r)G degrees/J mol(-1) = (- 128340 + 93.21 T/K) +/- 200 3PbO + 1/2O(2) --> Pb3O4 Delta(r)G degrees/J mol(-1) = (- 70060 + 77.5 T/K) +/- 150

Escape of high mass ions due to initial thermal energy and its implications for axially symmetric RF ion trap mass analyzer design

This paper investigates the loss of high mass ions due to their initial thermal energy in ion trap mass analyzers. It provides an analytical expression for estimating the percentage loss of ions of a given mass at a particular temperature, in a trap operating under a predetermined set of conditions. The expression we developed can be used to study the loss of ions due to its initial thermal energy in traps which have nonlinear fields as well as those which have linear fields. The expression for the percentage of ions lost is shown to be a function of the temperature of the ensemble of ions, ion mass and ion escape velocity. An analytical expression for the escape velocity has also been derived in terms of the trapping field, drive frequency and ion mass. Because the trapping field is determined by trap design parameters and operating conditions, it has been possible to study the influence of these parameters on ion loss. The parameters investigated include ion temperature, magnitude of the initial potential applied to the ring electrode (which determines the low mass cut-off), trap size, dimensions of apertures in the endcap electrodes and RF drive frequency. Our studies demonstrate that ion loss due to initial thermal energy increases with increase in mass and that, in the traps investigated, ion escape occurs in the radial direction. Reduction in the loss of high mass ions is favoured by lower ion temperatures, increasing low mass cut-off, increasing trap size, and higher RF drive frequencies. However, dimensions of the apertures in the endcap electrodes do not influence ion loss in the range of aperture sizes considered. (C) 2010 Elsevier B.V. All rights reserved.

Structural and transport properties of high energy ion irradiated YBCO

The effects of 100 MeV Oxygen and 200 MeV Silver ions on the structural and transport properties of YBCO thin films are reported. Both normal state and superconducting properties were studied on Laser ablated and high pressure oxygen sputtered films. Precise electrical resistance and critical current measurements near T-c were made and the data obtained were analysed in the light of existing models of para-coherence near T-c and the other aspects of radiation damage arising from microstructural studies such as atomic force microscopy (AFM). There was evidence of sputtering by high energy ions from AFM measurement. (C) 1998 Elsevier Science Ltd. All rights reserved.

Giant radio sources

We present multifrequency Very Large Array (VLA) observations of two giant quasars, 0437-244 and 1025-229, from the Molonglo Complete Sample. These sources have well-defined FR II radio structure, possible one-sided jets, no significant depolarization between 1365 and 4935 MHz and low rotation measure (\ RM \ < 20 rad m(-2)). The giant sources are defined to be those with overall projected size greater than or equal to 1 Mpc. We have compiled a sample of about 50 known giant radio sources from the literature, and have compared some of their properties with a complete sample of 3CR radio sources of smaller sizes to investigate the evolution of giant sources, and test their consistency with the unified scheme for radio galaxies and quasars. We find an inverse correlation between the degree of core prominence and total radio luminosity, and show that the giant radio sources have similar core strengths to smaller sources of similar total luminosity. Hence their large sizes are unlikely to be caused by stronger nuclear activity. The degree of collinearity of the giant sources is also similar to that of the sample of smaller sources. The luminosity-size diagram shows that the giant sources are less luminous than our sample of smaller sized 3CR sources, consistent with evolutionary scenarios in which the giants have evolved from the smaller sources, losing energy as they expand to these large dimensions. For the smaller sources, radiative losses resulting from synchrotron radiation are more significant while for the giant sources the equipartition magnetic fields are smaller and inverse Compton lass owing to microwave background radiation is the dominant process. The radio properties of the giant radio galaxies and quasars are consistent with the unified scheme.

Levitation effect and its relationship with the underlying potential energy landscape

Positions of potential energy minima for spherical monatomic sorbates in zeolite NaY have been identified for different sizes of the sorbate. It is found that for small sorbates (sigma less than or equal to 4.96 Angstrom) there are only six adsorption sites per alpha-cage, which are located close to the inner surface of the alpha-cage. For larger sorbates, additional sites of comparable energies appear close to the 12-ring window which forms the bottleneck for intercage diffusion. Minimum energy paths between these sites have been computed. These suggest that the barriers for both intracage and intercage site-to-site migrations are comparable and decrease with increase in sorbate size. Earlier simulation studies on the diffusion of monatomic sorbates in zeolites indicated that there is a dramatic change in the nature of dependence of D on sorbate size around 4.96 Angstrom, for zeolite NaY. Therefore, the present results suggest that the dependence of D on sorbate size and the changes in the potential energy landscape are correlated. The sorbate-zeolite system is characterized by a flatter potential energy landscape when the sorbate size is large. (C) 1999 American Institute of Physics. [S0021-9606(99)51110-0].