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Energetics
Terms modified by Energetics Selected AbstractsEnergetic and exergetic analysis of a domestic water tank with phase change materialINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 3 2008C. Solé Abstract Although water is a cheap and effective medium for thermal energy storage, other options are currently being studied, to increase the storage density or to reduce the cost of the storage. The authors have been developing a system which combines the advantages of stratified sensible heat storage and latent, phase change heat storage; i.e. a hot water storage tank with stratification where a phase change material (PCM) is included into a spiral tube installed in the top of the tank. The PCM used was a granular PCM,graphite compound of about 90 vol.% of sodium acetate trihydrate and 10 vol.% graphite. This paper presents the results of an experimental investigation of the performance of the new storage concept, and of a conventional hot water storage tank for comparison. The data are further analysed with respect to the energetic and exergetic performance of the two systems. Copyright © 2007 John Wiley & Sons, Ltd. [source] Energetic, exergetic and thermoeconomic analysis of Bilkent combined cycle cogeneration plantINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 11 2006C. Ozgur Colpan Abstract This paper is a case study of thermodynamics and economics related analyses applied to an existing gas/steam combined cycle cogeneration plant. Basic thermodynamic properties of the plant are determined by energy analysis utilizing main operation conditions. Exergy destructions within the plant and exergy losses to environment are investigated to determine thermodynamic inefficiencies and to assist for guiding future improvements in the plant. Cost balances and auxiliary equations are applied to several subsystems in the plant, hence, cost formation in the plant is observed. Additionally, cost rate of each product of the plant is calculated. Copyright © 2005 John Wiley & Sons, Ltd. [source] Theoretical Studies on ortho -Oxidation of Phenols with Dioxygen Mediated by Dicopper Complex: Hints for a Catalyst with the Phenolase Activity of TyrosinaseADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 4-5 2007Hiroshi Naka Abstract Theoretical studies on the chemo- and regioselective ortho -oxidation reaction of phenols mediated by a biomimetic (,,,2:,2peroxo)dicopper(II) complex were performed using unrestricted hybrid density functional theory (UB3LYP) calculations, with the aim of providing a guide for the development of new bio-inspired catalysts with the phenolase activity of tyrosinase. Energetic, structural, and electronic analyses suggested the involvement of a side-on (,,,2:,2)-Cu2O2 complex as an active intermediate, and a single electron transfer (SET)-induced electrophilic aromatic substitution mechanism is proposed for the rate-determining CO bond forming process; this is consistent with experimental observations. Moreover, the inherent roles of, and requirement for, two copper ions in this reaction have been elucidated. [source] When time is of the essence: choosing a currency for prey-handling costsJOURNAL OF ANIMAL ECOLOGY, Issue 4 2000Francesco Rovero 1.,Heartbeat rate was measured in shore crabs Carcinus maenas (L.) feeding on mussels Mytilus edulis L. in order to estimate the energetic cost of handling prey and to assess the relative importance of energy and time as costing currencies. 2.,Energetic handling costs represented approximately 2% of corresponding gains. 3.,The tendency of profitability (gain per unit handling time) to increase with prey size was weakened by including energetic handling costs. 4.,Time was judged to be a more appropriate currency than energy for costing prey-handling behaviour. 5.,The importance of time as a costing currency, either through the principle of lost opportunity or through exposure to mortality risk, may extend to other behavioural systems, including aggression. [source] Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 moleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2004Maria Del Carmen Michelini Abstract The Density functional theory has been applied to characterize the structural features of Mo1,2NH3,C2H4, and C2H2 compounds. Coordination modes, geometrical structures, and binding energies have been calculated for several spin multiplets. It has been shown that in contrast to the conserved spin cases (Mo1,2NH3), the interaction between Mo (or Mo2) and C2H4 (or C2H2) are the low-spin (MoC2H4 and C2H2) and high-spin (Mo2C2H4 and C2H2) complexes. In the ground state of Mo1,2C2H4 and C2H2, the metal-center always reacts with the CC center. The spontaneous formation of the global minima is found to be possible due to the crossing between the potential energy surfaces (ground and excited states with respect to the metallic center). The bonding characterization has been performed using the topological analysis of the Electron Localization Function. It has been shown that the most stable electronic structure for a ,-acceptor ligand correlates with a maximum charge transfer from the metal center to the CC bond of the unsaturated hydrocarbons, resulting in the formation of two new basins located on the carbon atoms (away from hydrogen atoms) and the reduction of the number of attractors of the CC basin. The interaction between Mo1,2 and C2H4 (or C2H2) should be considered as a chemical reaction, which causes the multiplicity change. Contrarily, there is no charge transfer between Mo1,2 and NH3, and the partners are bound by an electrostatic interaction. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1647,1655, 2004 [source] Energetic, Low-Melting Salts of Simple HeterocyclesPROPELLANTS, EXPLOSIVES, PYROTECHNICS, Issue 4 2003Gregory Drake The synthesis of three new families of heterocyclic-based salts was undertaken and accomplished. Three triazole systems, 1H-1,2,4-triazole, 4-amino-1,2,4-triazole, and 1H-1,2,3-triazole, were used as proton bases with nitric (HNO3), perchloric (HClO4), and dinitramidic (HN(NO2)2) acid systems. In all cases, stable salts were recovered and fully characterized by vibrational spectra (IR, Raman), multinuclear NMR spectroscopy, material balance, density measurements, and elemental analyses, as well as DSC, TGA and initial safety testing (impact). Many of these salts have melting points well below 100,°C, yet high decomposition onsets, defining them as new, highly energetic members of the well known class of materials identified as ionic liquids. Additionally, the single crystal X-ray diffraction study of 1,2,4-triazolium perchlorate was investigated, revealing the expected structure. [source] Dynamics of multiple intertidal bars over semi-diurnal and lunar tidal cycles, North Lincolnshire, EnglandEARTH SURFACE PROCESSES AND LANDFORMS, Issue 10 2008Selma van Houwelingen Abstract Multiple intertidal bars are common features of wave-dominated sandy beaches, yet their short-term (<1 month) and small-scale (<1 km) morphology and dynamics remain poorly understood. This study describes the morphodynamics of multiple intertidal bars in North Lincolnshire, England, during single and lunar tidal cycles under two contrasting conditions , first when significant wave height was <0·5 m and second when significant wave height frequently exceeded 1 m. The relative importance of swash, surf and shoaling processes in determining morphological change was examined using detailed field observations and a numerical model. The beach featured four intertidal bars and both cross-shore and longshore bar morphology evolved during the field investigation, particularly under medium to high wave-energy conditions. Numerical modelling suggests shoaling processes are most common on the seaward two bars under calm wave conditions (Hs < 0·5 m) and that surf zone processes become more common during neap tides and under more energetic (Hs < 0·5 m) conditions. Surf processes dominate the inner two bars, though swash influence increases in a landward direction. The numerical modelling results combined with low tide survey data and high-resolution morphological measurements strongly suggest changes in the intertidal bar morphology are accomplished by surf zone processes rather than by shoaling wave or swash processes. This is because shoaling waves do not induce significant sediment transport to have any morphological effect, whereas swash action generally does not have enough scope to act as the swash zone is much narrower than the surf zone. It was found, however, that the absolute rate of morphological change under swash action and surfzone processes are of similar magnitudes and that swash action may induce a significant amount of local morphological change when the high tide mark is located on the upper bar, making this process important for bar morphodynamics. Copyright © 2007 John Wiley & Sons, Ltd. [source] CALORIE RESTRICTION AND AGING: A LIFE-HISTORY ANALYSISEVOLUTION, Issue 3 2000Daryl P. Shanley Abstract., The disposable soma theory suggests that aging occurs because natural selection favors a strategy in which fewer resources are invested in somatic maintenance than are necessary for indefinite survival. However, laboratory rodents on calorie-restricted diets have extended life spans and retarded aging. One hypothesis is that this is an adaptive response involving a shift of resources during short periods of famine away from reproduction and toward increased somatic maintenance. The potential benefit is that the animal gains an increased chance of survival with a reduced intrinsic rate of senescence, thereby permitting reproductive value to be preserved for when the famine is over. We describe a mathematical life-history model of dynamic resource allocation that tests this idea. Senescence is modeled as a change in state that depends on the resources allocated to maintenance. Individuals are assumed to allocate the available resources to maximize the total number of descendants. The model shows that the evolutionary hypothesis is plausible and identifies two factors, both likely to exist, that favor this conclusion. These factors are that survival of juveniles is reduced during periods of famine and that the organism needs to pay an energetic "overhead" before any litter of offspring can be produced. If neither of these conditions holds, there is no evolutionary advantage to be gained from switching extra resources to maintenance. The model provides a basis to evaluate whether the life-extending effects of calorie-restriction might apply in other species, including humans. [source] Copper Azide Confined Inside Templated Carbon NanotubesADVANCED FUNCTIONAL MATERIALS, Issue 18 2010Valarie Pelletier Abstract The currently used primary explosives, such as lead azide and lead styphnate, present serious health hazards due to the toxicity of lead. There is a need to replace them with equally energetic but safer-to-handle and more environmentally friendly materials. Copper azide is more environmentally acceptable, but very sensitive and detonates easily from electrostatic charges during handling. If the highly sensitive copper azide is encapsulated within conducting containers, such as anodic aluminum oxide (AAO)-templated carbon nanotubes (CNTs), its sensitivity can be tamed. This work describes a technique for confining energetic copper azide within CNTs. ,5 nm colloidal copper oxide nanoparticles are synthesized and filled into the 200 nm diameter CNTs, produced by template synthesis. The Cu-O inside the CNTs is reduced in hydrogen to copper, and reacted with hydrazoic acid gas to produce copper azide. Upon initiation, the 60 ,m long straight, open-ended CNTs guide decomposition gases along the tube channel without fracturing the nanotube walls. These novel materials have potential for applications as nano-detonators and green primary explosives; they also offer new opportunities for understanding the physics of detonation at the nanoscale. [source] Energetic trade-off between maintenance costs and flight capacity in the sand cricket (Gryllus firmus)FUNCTIONAL ECOLOGY, Issue 4 2008R. F. Nespolo Summary 1Energetic trade-offs are those compromises that appear when the energy budget of an individual's life history closely matches or exceeds the net available energy in the environment in a given moment. In these situations, two or more functions can compete and organisms face physiological decisions in order to survive and reproduce. 2In insects, one of the most costly investments is flight capacity, which increases dispersal capacity but is energetically expensive. Adult sand crickets (Gryllus firmus) can vary drastically in this capacity, being macropterous or micropterous depending on whether they exhibit flight-capable wings. However, this binary phenotype has a continuous subjacent determinant in the macropterous morph which is the mass of the muscles that power flight, the dorso-longitudinal muscles (DLM). 3Using respirometric measurements, we studied a potential trade-off between body parts, the mass of the DLM and energy metabolism (including both maximum and average metabolism). By recording the metabolic rate of c. 180 crickets and then dissecting and weighing their body parts, we took advantage of the correlational structure to infer associations between energetic and morphological variables. We found that the residual mass of the DLM shows a quadratic relationship with residual resting and average metabolism: at low DLM mass there is a negative relationship, which becomes positive at higher DLM mass. 4We suggest that this pattern of covariance is a consequence of the negative correlation between DLM mass and gonad mass, and the relative contribution of functional vs. non-functional DLM. Then, by using energetics and a combination of multivariate and correlational statistics we were able to show how two important life-history functions (i.e. Dispersal and fecundity) compete for the same resources in an insect species. [source] Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognitionGENES TO CELLS, Issue 5 2000Masayuki Oda Thermodynamic and kinetic analyses of biomolecular interactions reveal details of the energetic and dynamic features of molecular recognition processes, and complement structural analyses of the free and complexed conformations. The recent improvements in both isothermal titration calorimetry and surface plasmon resonance sensoring provide powerful tools for analysing biomolecular interactions in thermodynamic and kinetic approaches. The thermodynamic and kinetic parameters obtained for binding between protein and DNA indicate the mechanism of specific DNA recognition, in the high-resolution structures of the protein,DNA complexes. The effects of temperature and ionic strength reflect the conformational changes of the protein and DNA molecules upon complex formation, including important contributions of water and solutes. When combined with mutational studies, the interactions can be reduced to several energetic contributions from individual contacts. These studies should be useful to determine general features of protein functions in genetic regulation. [source] Convection in the Earth's core driven by lateral variations in the core,mantle boundary heat fluxGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 2 2000Steven John Gibbons Summary Moving core fluid maintains an isothermal core,mantle boundary (CMB), so lateral variations in the CMB heat flow result from mantle convection. Such variations will drive thermal winds, even if the top of the core is stably stratified. These flows may contribute to the magnetic secular variation and are investigated here using a simple, non-magnetic numerical model of the core. The results depend on the equatorial symmetry of the boundary heat flux variation. Large-scale equatorially symmetric (ES) heat flux variations at the outer surface of a rapidly rotating spherical shell drive deeply penetrating flows that are strongly suppressed in stratified fluid. Smaller-scale ES heat flux variations drive flows less dominated by rotation and so less inhibited by stratification. Equatorially anti-symmetric flux variations drive flows an order of magnitude less energetic than those driven by ES patterns but, due to the nature of the Coriolis force, are less suppressed by stratification. The response of the rotating core fluid to a general CMB heat flow pattern will then depend strongly on the subadiabatic temperature profile. Imposing a lateral heat flux variation linearly related to a model of seismic tomography in the lowermost mantle drives flow in a density stratified fluid that reproduces some features found in flows inverted from geomagnetic data. [source] Nitrogen-Rich Compounds of the Lanthanoids: The 5,5,-Azobis[1H -tetrazol-1-ides] of some Yttric Earths (Tb, Dy, Ho, Er, Tm, Yb, and Lu)HELVETICA CHIMICA ACTA, Issue 7 2009Georg Steinhauser Abstract A set of N-rich salts, 3,9, of the heavy lanthanoids (terbium, 3; dysprosium, 4; holmium 5; erbium, 6; thulium, 7; ytterbium, 8; lutetium, 9) based on the energetic 5,5,-azobis[1H -tetrazole] (H2ZT) was synthesized and characterized by elemental analysis, vibrational (IR and Raman) spectroscopy, and X-ray structure determination. The synthesis of the lanthanoid salts 3,9 was performed by crystallization from concentrated aqueous solutions of disodium 5,5,-azobis[1H -tetrazol-1-ide] dihydrate (Na2ZT,2,H2O; 1) and the respective Ln(NO3)3,5,H2O and yielded large rhombic crystals of the type [Ln(H2O)8]2(ZT)3,6,H2O in ca. 70% of the theoretical yield. The compounds 3,9 are isostructural (triclinic space group P) to the previously published yttrium salt 2; they show, however, a clear lanthanoid contraction of several crystallographic parameters, e.g., the cell volume or the LnO bond lengths of the Ln3+ ions and the coordinating H2O molecules. The lanthanoid contraction influences the strengths of the H-bonds, which can be observed as a red shift by 4,cm,1 in the characteristic IR band, in particular from 3595,cm,1 (3) to 3599,cm,1 (9). In good agreement with previous works, 2,9 are purely salt-like compounds without a coordinative bond between the tetrazolide anion and the Ln3+ cation. [source] Modafinil and nicotine interactions in abstinent smokersHUMAN PSYCHOPHARMACOLOGY: CLINICAL AND EXPERIMENTAL, Issue 1 2008Mehmet Sofuoglu Abstract In this study, we examined the effects of a wakefulness-promoting medication, modafinil, alone and with the nicotine lozenge, on subjective, physiological and cognitive measures as well as on nicotine withdrawal in overnight abstinent cigarette smokers. Nineteen smokers, 13 male and 6 female, participated in a double-blind, placebo-controlled, crossover study. In each of three experimental sessions, subjects were treated orally with a single 200,mg or 400,mg dose of modafinil or placebo. Two hours and 10 min following the medication treatment, subjects received a single 2,mg nicotine lozenge. Both doses of modafinil alone increased the rating of elated-depressed on the Profile of Mood States (POMS) subscale in the direction of depressed and increased ratings of negative affect on the Positive and Negative Affect Schedule (PANAS). In contrast, the 200,mg modafinil dose combined with a 2,mg nicotine lozenge, increased the rating of energetic-tired in the direction of energetic on the POMS subscale. Modafinil attenuated self-reported rating of ,drug strength' in response to the nicotine lozenge. Modafinil, alone or in combination with the nicotine lozenge, did not affect tobacco withdrawal symptoms. There was an increase in baseline heart rate and systolic blood pressure under modafinil treatment. In addition, modafinil speeded reaction times on a modified Stroop task. The clinical utility of modafinil for smoking cessation needs to be determined in future studies. Copyright © 2007 John Wiley & Sons, Ltd. [source] A variational r -adaption and shape-optimization method for finite-deformation elasticityINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 1 2004P. Thoutireddy Abstract This paper is concerned with the formulation of a variational r -adaption method for finite-deformation elastostatic problems. The distinguishing characteristic of the method is that the variational principle simultaneously supplies the solution, the optimal mesh and, in problems of shape optimization, the equilibrium shapes of the system. This is accomplished by minimizing the energy functional with respect to the nodal field values as well as with respect to the triangulation of the domain of analysis. Energy minimization with respect to the referential nodal positions has the effect of equilibrating the energetic or configurational forces acting on the nodes. We derive general expressions for the configurational forces for isoparametric elements and non-linear, possibly anisotropic, materials under general loading. We illustrate the versatility and convergence characteristics of the method by way of selected numerical tests and applications, including the problem of a semi-infinite crack in linear and non-linear elastic bodies; and the optimization of the shape of elastic inclusions. Copyright © 2004 John Wiley & Sons, Ltd. [source] Dynamic energy and exergy analyses of an industrial cogeneration systemINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 4 2010Yilmaz Yoru Abstract The study deals with the energetic and exergetic analyses of a cogeneration (combined heat and power, CHP) system installed in a ceramic factory, located in Izmir, Turkey. This system has three gas turbines with a total capacity of 13,MW, six spray dryers and two heat exchangers. In the analysis, actual operational data over one-month period are utilized. The so-called CogeNNexT code is written in C++ and developed to analyze energetic and exergetic data from a database. This code is also used to analyze turbines, spray dryers and heat exchangers in this factory. Specifications of some parts of system components have been collected from the factory. Based on the 720,h data pattern (including 43,200 data), the mean energetic and exergetic efficiency values of the cogeneration system are found to be 82.3 and 34.7%, respectively. Copyright © 2009 John Wiley & Sons, Ltd. [source] Performance and exergetic analysis of vapor compression refrigeration system with an internal heat exchanger using a hydrocarbon, isobutane (R600a)INTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 9 2008Ahmet Kabul Abstract Hydrocarbons (HCs) are excellent refrigerants in many ways such as energy efficiency, critical point, solubility, transport and heat transfer properties, but they are also flammable, which causes the need for changes in standards, production and product. There are increasing number of scientists and engineers who believe that an alternative solution, which has been overlooked, may be provided by using HCs. The main objective of this study is to perform energy and exergy analyses for a vapor compression refrigeration system with an internal heat exchanger using a HC, isobutene (R600a). For a refrigeration capacity of 1 kW and cold chamber temperature of 0°C, energy and exergy balances are taken into account to determine the performance of the refrigeration system. Energy and exergy fluxes are determined, and irreversibility rates are calculated for every component of the system. It is seen that the compressor has the highest irreversibility rate, and the heat exchanger has the lowest. Also from the result of the analysis, it is found that condenser and evaporator temperatures have strong effects on energetic and exergetic performances of the system such as coefficient of performance (COP), efficiency ratio (,), exergetic efficiency (,) and irreversibility rate. Copyright © 2008 John Wiley & Sons, Ltd. [source] Energetic and exergetic analysis of a domestic water tank with phase change materialINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 3 2008C. Solé Abstract Although water is a cheap and effective medium for thermal energy storage, other options are currently being studied, to increase the storage density or to reduce the cost of the storage. The authors have been developing a system which combines the advantages of stratified sensible heat storage and latent, phase change heat storage; i.e. a hot water storage tank with stratification where a phase change material (PCM) is included into a spiral tube installed in the top of the tank. The PCM used was a granular PCM,graphite compound of about 90 vol.% of sodium acetate trihydrate and 10 vol.% graphite. This paper presents the results of an experimental investigation of the performance of the new storage concept, and of a conventional hot water storage tank for comparison. The data are further analysed with respect to the energetic and exergetic performance of the two systems. Copyright © 2007 John Wiley & Sons, Ltd. [source] Modeling dioxygen binding to the non-heme iron-containing enzymesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2006A. V. Nemukhin Abstract The structures and properties of the complexes formed upon binding the oxygen molecule to the iron sites in non-heme 2-oxoglutarate-dependent enzymes are characterized by QM(CASSCF)/MM and density functional theory (DFT) calculations. Molecular models for the calculations are constructed following the crystal structure of hypoxia-inducible factor asparaginyl hydroxylase (FIH-1). DFT calculations for the 37-atomic cluster have been carried out at the B3LYP(LANL2DZdp) level. The flexible effective fragment potential method is used as a combined quantum mechanical,molecular mechanical (QM/MM) technique to characterize the fragment of the enzymatic system, including 1,758 atoms in the MM part and 27 atoms in the QM part. In these calculations, the CASSCF(LANL2DZdp) approach is applied in the QM subsystem, and AMBER force field parameters are used in the MM subsystem. With both approaches, equilibrium geometry configurations have been located for different spin states of the system. In DFT calculations, the order of the states is as follows: septet, triplet (+7.7 kcal/mol), quintet (+10.7 kcal/mol). Geometry configurations correspond to the end-on structures with no evidences of electron transfer from Fe(II) to molecular oxygen. In contrast, QM(CASSCF)/MM calculations predict the quintet state as the lowest one, while the septet structure has slightly (<2 kcal/mol) higher energy, and the triplet state is considerably more energetic. In QM/MM calculations, in both quintet and septet states, the electronic configurations show considerable electron charge transfer from iron to oxygen, and the oxidation state of iron in the metal binding site can be characterized as Fe(III). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] When time is of the essence: choosing a currency for prey-handling costsJOURNAL OF ANIMAL ECOLOGY, Issue 4 2000Francesco Rovero 1.,Heartbeat rate was measured in shore crabs Carcinus maenas (L.) feeding on mussels Mytilus edulis L. in order to estimate the energetic cost of handling prey and to assess the relative importance of energy and time as costing currencies. 2.,Energetic handling costs represented approximately 2% of corresponding gains. 3.,The tendency of profitability (gain per unit handling time) to increase with prey size was weakened by including energetic handling costs. 4.,Time was judged to be a more appropriate currency than energy for costing prey-handling behaviour. 5.,The importance of time as a costing currency, either through the principle of lost opportunity or through exposure to mortality risk, may extend to other behavioural systems, including aggression. [source] Impaired Energetic Metabolism After Central Leptin Signaling Leads to Massive Appendicular Bone Loss in Hindlimb-Suspended Rats,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 12 2008Aline Martin Abstract We previously showed in rats that the leptin effects on bone were dose dependent. Positive effects were observed when serum leptin concentration was in a physiological range. In contrast, important increases in serum leptin levels led to negative effects on bone formation similar to those reported after intracerebroventricular leptin administration in mice. To clarify whether leptin effects on bone depend on administration route and/or animal model, female rats were hindlimb unloaded or not and treated either with intracerebroventricular infusion of leptin or vehicle for 14 days. By increasing cerebrospinal fluid (CSF) leptin concentration, intracerebroventricular infusion of leptin significantly reduced food intake and consequently body weight, abdominal fat, and lean mass of the animals. Leptin infusion inhibited bone elongation over the 14 days and blunted cortical bone thickening at the femoral diaphysis site. Interestingly, leptin effects were site dependent in the cancellous bone envelopes, because tibia metaphysis BMD was lower and lumbar spine BMD was higher under intracerebroventricular leptin. Treated groups showed reduced bone remodeling independently of hindlimb unloading. Multiple downstream pathways were implicated in the mediation of these negative leptin effects on bone including not only stimulation of the sympathetic nervous system but also a decrease in somatotropic axis activity. Therefore, the intracerebroventricular leptin-induced bone loss could be largely related to the concurrent alteration of energetic and metabolic status. In summary, our study supports the hypothesis of a concentration-dependent balance between peripheral and central control of leptin on bone. [source] Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of proteinJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Huameng Li Abstract Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein,ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] MOPED: Method for optimizing physical energy parameters using decoysJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2003Chaok Seok Abstract We present a method called MOPED for optimizing energetic and structural parameters in computational models, including all-atom energy functions, when native structures and decoys are given. The present method goes beyond previous approaches in treating energy functions that are nonlinear in the parameters and continuous in the degrees of freedom. We illustrate the method by improving solvation parameters in the energy function EEF1, which consists of the CHARMM19 polar hydrogen force field augmented by a Gaussian solvation term. Although the published parameters for EEF1 correctly discriminate the native from decoys in the decoy sets of Levitt et al., they fail on several of the more difficult decoy sets of Baker et al. MOPED successfully finds improved parameters that allow EEF1 to discriminate native from decoy structures on all protein structures that do not have metals or prosthetic groups. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 89,97, 2003 [source] Application of the frozen atom approximation to the GB/SA continuum model for solvation free energyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2002Olgun Guvench Abstract The generalized Born/surface area (GB/SA) continuum model for solvation free energy is a fast and accurate alternative to using discrete water molecules in molecular simulations of solvated systems. However, computational studies of large solvated molecular systems such as enzyme,ligand complexes can still be computationally expensive even with continuum solvation methods simply because of the large number of atoms in the solute molecules. Because in such systems often only a relatively small portion of the system such as the ligand binding site is under study, it becomes less attractive to calculate energies and derivatives for all atoms in the system. To curtail computation while still maintaining high energetic accuracy, atoms distant from the site of interest are often frozen; that is, their coordinates are made invariant. Such frozen atoms do not require energetic and derivative updates during the course of a simulation. Herein we describe methodology and results for applying the frozen atom approach to both the generalized Born (GB) and the solvent accessible surface area (SASA) parts of the GB/SA continuum model for solvation free energy. For strictly pairwise energetic terms, such as the Coulombic and van-der-Waals energies, contributions from pairs of frozen atoms can be ignored. This leaves energetic differences unaffected for conformations that vary only in the positions of nonfrozen atoms. Due to the nonlocal nature of the GB analytical form, however, excluding such pairs from a GB calculation leads to unacceptable inaccuracies. To apply a frozen-atom scheme to GB calculations, a buffer region within the frozen-atom zone is generated based on a user-definable cutoff distance from the nonfrozen atoms. Certain pairwise interactions between frozen atoms in the buffer region are retained in the GB computation. This allows high accuracy in conformational GB comparisons to be maintained while achieving significant savings in computational time compared to the full (nonfrozen) calculation. A similar approach for using a buffer region of frozen atoms is taken for the SASA calculation. The SASA calculation is local in nature, and thus exact SASA energies are maintained. With a buffer region of 8 Ĺ for the frozen-atom cases, excellent agreement in differences in energies for three different conformations of cytochrome P450 with a bound camphor ligand are obtained with respect to the nonfrozen cases. For various minimization protocols, simulations run 2 to 10.5 times faster and memory usage is reduced by a factor of 1.5 to 5. Application of the frozen atom method for GB/SA calculations thus can render computationally tractable biologically and medically important simulations such as those used to study ligand,receptor binding conformations and energies in a solvated environment. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 214,221, 2002 [source] Identifying native-like protein structures using physics-based potentialsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2002Brian N. Dominy Abstract As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pairs of threaded structures from the EMBL database, and find that it is possible to identify the misfolded structures with over 90% accuracy. Further, we find that misfolded states are generally favored by the solvation term due to the mispairing of favorable intramolecular ionic contacts. We also examine 29 sets of 29 misfolded globin sequences from Levitt's "Decoys ,R' Us" database generated using a sequence homology-based method. Again, we find that discrimination is possible with approximately 90% accuracy. Also, even in these less distorted structures, mispairing of ionic contacts results in a more favorable solvation energy for misfolded states. This is also found to be the case for collapsed, partially folded conformations of CspA and protein G taken from folding free energy calculations. We also find that the inclusion of the generalized Born solvation term, in postprocess energy evaluation, improves the correlation between structural similarity and energy in the globin database. This significantly improves the reliability of the hypothesis that more energetically favorable structures are also more similar to the native conformation. Additionally, we examine seven extensive collections of misfolded structures created by Park and Levitt using a four-state reduced model also contained in the "Decoys ,R' Us" database. Results from these large databases confirm those obtained in the EMBL and misfolded globin databases concerning predictive accuracy, the energetic advantage of misfolded proteins regarding the solvation component, and the improved correlation between energy and structural similarity due to implicit solvation. Z-scores computed for these databases are improved by including the generalized Born implicit solvation term, and are found to be comparable to trained and knowledge-based scoring functions. Finally, we briefly explore the dynamic behavior of a misfolded protein relative to properly folded conformations. We demonstrate that the misfolded conformation diverges quickly from its initial structure while the properly folded states remain stable. Proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria. In summary, we demonstrate the utility of physics-based force fields in identifying native-like conformations in a variety of preconstructed structural databases. The details of this discrimination are shown to be dependent on the construction of the structural database. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 147,160, 2002 [source] Mechanism of a plastic phenotypic response: predator-induced shell thickening in the intertidal gastropod Littorina obtusataJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2007J. I. BROOKES Abstract Phenotypic plasticity has been the object of considerable interest over the past several decades, but in few cases are mechanisms underlying plastic responses well understood. For example, it is unclear whether predator-induced changes in gastropod shell morphology represent an active physiological response or a by-product of reduced feeding. We address this question by manipulating feeding and growth of intertidal snails, Littorina obtusata, using two approaches: (i) exposure to predation cues from green crabs Carcinus maenas and (ii) reduced food availability, and quantifying growth in shell length, shell mass, and body mass, as well as production of faecal material and shell micro-structural characteristics (mineralogy and organic fraction) after 96 days. We demonstrate that L. obtusata actively increases calcification rate in response to predation threat, and that this response entails energetic and developmental costs. That this induced response is not strictly tied to the animal's behaviour should enhance its evolutionary potential. [source] A post-SCF quantum chemistry study on local minima of 8-oxo-guanine stacked with all four nucleic acid bases in B-DNA conformationsJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 4 2007Piotr Cysewski The post SCF MP2/6-31G*(d=0.25) method was applied to obtain potential energy surface of 8-oxoguanine stacked with all four canonical DNA bases. The spatial neighbourhood was scanned of stacked complexes found in the native B-DNA. The presented results suggest that the hydroxyl radical modification of guanine at C8 position has significant impact on structural, energetic, orbital and electrostatic properties of stacked complexes with canonical DNA bases. The pair stabilization energy, including electron correlation terms, suggests that the 5,-A/GA-3, pair is the most stable among all of the studied complexes. The 8-oxo-guanine has been found as a source of significant changes in electroaccepting properties compared to stacked pairs formed by canonical guanine since both electron affinities and localization of HOMO orbital were altered. However, electro-donation abilities are not modified after replacement of guanine with 8-oxo-guanine irrespectively on the context of B-DNA bases. [source] The effect of weekly iron supplementation on anaemia and on iron deficiency among female tea pluckers in BangladeshJOURNAL OF HUMAN NUTRITION & DIETETICS, Issue 3 2001D. Gilgen Aim To investigate the effect of weekly iron supplementation on anaemia and iron deficiency among adult, female tea pluckers. Method A randomized double-blind intervention trial was conducted in a tea estate in Bangladesh where a total of 280 women received either weekly iron supplementation (200 mg ferrous fumarate and 200 mg folic acid) for 24 weeks or a matching placebo. Capillary blood samples were drawn at baseline and post-trial to determine haemoglobin, haematocrit and ferritin concentration. Mean corpuscular haemoglobin concentration (MCHC) was calculated using the haemoglobin and haematocrit values. Results The mean haemoglobin concentration in the supplemented group increased by 5.52 g L,1 over the study period, on average, while ferritin values decreased by 0.33 ,g L,1. The control group showed a decrease in both mean haemoglobin (,0.24 g L,1) and ferritin (,5.32 ,g L,1). Those individuals in the supplemented group with the lowest pretrial haemoglobin and ferritin values experienced the greatest improvements post-trial, whereas nonanaemic individuals showed a decrease in both haemoglobin and ferritin concentrations. A total of 62.2% of women in the supplemented group reported feeling better and more energetic compared to 51.1% in the placebo group; 14.4% of the supplemented group and 22.7% of the control group complained about side-effects. Conclusion Weekly iron supplementation was logistically simpler and cheaper than daily supplementation but would have to be continued on a longer term basis in order to combat both anaemia and iron deficiency. [source] Rational design of shape selective separations and catalysis: Lattice relaxation and effective aperture sizeAICHE JOURNAL, Issue 3 2010Chrysanthos E. Gounaris Abstract Gounaris et al. presented a computational method that can be used for the quick screening of zeolite structures and provide predictions regarding which of them have the potential to exhibit high selectivity among a set of molecules of interest. This article builds upon this earlier work and furthers our understanding of diffusion processes in zeolites and other microporous metal oxides. We first present an augmented formulation to account for the flexibility of the zeolitic portal and conduct an analysis to assess the effect of varying the parameters of the associated quadratic potential. We then introduce a methodology to map the energetic landscape, identify all locally optimal conformations, and probabilistically account for the multiplicity of conformers. Finally, we conduct sensitivity analysis on the effective size of the aperture, and show how the methodology can be fine,tuned through experimental observations. A comprehensive database of 290 molecules of industrial interest and a total of 123 different zeolite structures were used in this study. © 2009 American Institute of Chemical Engineers AIChE J, 2010 [source] A PERSPECTIVE ON PHOTOSYNTHESIS IN THE OLIGOTROPHIC OCEANS: HYPOTHESES CONCERNING ALTERNATE ROUTES OF ELECTRON FLOW,JOURNAL OF PHYCOLOGY, Issue 4 2010Arthur R. Grossman Many regions of the open, oligotrophic oceans are depleted of nutrients, especially nitrogen and iron. The biogenesis and the functioning of the photosynthetic apparatus may be specialized and tailored to the various marine habitats. In this minireview, we discuss some new findings with respect to photosynthetic processes in the oceans. We focus on findings that suggest that some cyanobacteria may route electrons derived from the splitting of H2O to the reduction of O2 and H+ in a water-to-water cycle, and that other cyanobacteria that fix nitrogen during the day are likely missing PSII and enzymes involved in the fixation of inorganic carbon. Both of these proposed "variant" forms of photosynthetic electron flow provide new insights into ways in which marine phytoplankton satisfy their energetic and nutritive requirements. [source] | |||||||||||||||||||||||||||||||||||||||||||||||||