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.

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.

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.

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].

Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework.

Decentralized Sustainable Energy Planning of Tumkur District, India

Present work shows the feasibility of decentralized energy options for the Tumkur district in India. Decentralized energy planning (DEP) involves scaling down energy planning to subnational or regional scales. The important aspect of the energy planning at decentralized level would be to prepare an area-based DEP to meet energy needs and development of alternate energy sources at least-cost to the economy and environment. The geographical coverage and scale reflects the level at which the analysis takes place, which is an important factor in determining the structure of models. In the present work, DEP modeling under different scenarios has been carried out for Tumkur district of India for the year 2020. DEP model is suitably scaled for obtaining the optimal mix of energy resources and technologies using a computer-based goal programming technique. The rural areas of the Tumkur district have different energy needs. Results show that electricity needs can be met by biomass gasifier technology, using biomass feedstock produced by allocating only 12% of the wasteland in the district at 8 t/ha/yr of biomass productivity. Surplus electricity can be produced by adopting the option of biomass power generation from energy plantations. The surplus electricity generated can be supplied to the grid. The sustainable development scenario is a least cost scenario apart from promoting self-reliance, local employment, and environmental benefits. (C) 2010 American Institute of Chemical Engineers Environ Prog, 30: 248-258, 2011

Smart applications for energy harvested WSNs

A Wireless Sensor Network (WSN) powered using harvested energies is limited in its operation by instantaneous power. Since energy availability can be different across nodes in the network, network setup and collaboration is a non trivial task. At the same time, in the event of excess energy, exciting node collaboration possibilities exist; often not feasible with battery driven sensor networks. Operations such as sensing, computation, storage and communication are required to achieve the common goal for any sensor network. In this paper, we design and implement a smart application that uses a Decision Engine, and morphs itself into an energy matched application. The results are based on measurements using IRIS motes running on solar energy. We have done away with batteries; instead used low leakage super capacitors to store harvested energy. The Decision Engine utilizes two pieces of data to provide its recommendations. Firstly, a history based energy prediction model assists the engine with information about in-coming energy. The second input is the energy cost database for operations. The energy driven Decision Engine calculates the energy budgets and recommends the best possible set of operations. Under excess energy condition, the Decision Engine, promiscuously sniffs the neighborhood looking for all possible data from neighbors. This data includes neighbor's energy level and sensor data. Equipped with this data, nodes establish detailed data correlation and thus enhance collaboration such as filling up data gaps on behalf of nodes hibernating under low energy conditions. The results are encouraging. Node and network life time of the sensor nodes running the smart application is found to be significantly higher compared to the base application.

Profile-Based Load Scheduling in Wireless Energy Harvesting Sensors for Data Rate Maximization

In this paper, power management algorithms for energy harvesting sensors (EHS) that operate purely based on energy harvested from the environment are proposed. To maintain energy neutrality, EHS nodes schedule their utilization of the harvested power so as to save/draw energy into/from an inefficient battery during peak/low energy harvesting periods, respectively. Under this constraint, one of the key system design goals is to transmit as much data as possible given the energy harvesting profile. For implementational simplicity, it is assumed that the EHS transmits at a constant data rate with power control, when the channel is sufficiently good. By converting the data rate maximization problem into a convex optimization problem, the optimal load scheduling (power management) algorithm that maximizes the average data rate subject to energy neutrality is derived. Also, the energy storage requirements on the battery for implementing the proposed algorithm are calculated. Further, robust schemes that account for the insufficiency of battery storage capacity, or errors in the prediction of the harvested power are proposed. The superior performance of the proposed algorithms over conventional scheduling schemes are demonstrated through computations using numerical data from solar energy harvesting databases.