942 resultados para Weather simulations


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Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-dependent transcription factors, hormone binding regulates ER transcriptional activity. Nevertheless, the mechanisms by which ligands enter and leave ERs and other nuclear receptors remain poorly understood. Here, we report results of locally enhanced sampling molecular dynamics simulations to identify dissociation pathways of two ER ligands [the natural hormone 17 beta-estradiol (E-2) and the selective ER modulator raloxifene (RAL)] from the human ER alpha ligand-binding domain in monomeric and dimeric forms. E-2 dissociation occurs via three different pathways in ER monomers. One resembles the mousetrap mechanism (Path I), involving repositioning of helix 12 (H12), others involve the separation of H8 and H11 (Path II), and a variant of this pathway at the bottom of the ligand-binding domain (Path II`). RAL leaves the receptor through Path I and a Path I variant in which the ligand leaves the receptor through the loop region between H11 and H12 (Path I`). Remarkably, ER dimerization strongly suppresses Paths II and II` for E-2 dissociation and modifies RAL escape routes. We propose that differences in ligand release pathways detected in the simulations for ER monomers and dimers provide an explanation for previously observed effects of ER quaternary state on ligand dissociation rates and suggest that dimerization may play an important, and hitherto unexpected, role in regulation of ligand dissociation rates throughout the nuclear receptor family.

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Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

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Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

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We present an efficient numerical methodology for the 31) computation of incompressible multi-phase flows described by conservative phase-field models We focus here on the case of density matched fluids with different viscosity (Model H) The numerical method employs adaptive mesh refinements (AMR) in concert with an efficient semi-implicit time discretization strategy and a linear, multi-level multigrid to relax high order stability constraints and to capture the flow`s disparate scales at optimal cost. Only five linear solvers are needed per time-step. Moreover, all the adaptive methodology is constructed from scratch to allow a systematic investigation of the key aspects of AMR in a conservative, phase-field setting. We validate the method and demonstrate its capabilities and efficacy with important examples of drop deformation, Kelvin-Helmholtz instability, and flow-induced drop coalescence (C) 2010 Elsevier Inc. All rights reserved

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The pressure dependence of the glass-transition temperature, T(g)(P), of the ionic glass-former 2Ca(NO(3))(2) center dot 3KNO(3), CKN, has been obtained by molecular dynamics (MD) simulations The liquid-glass difference of thermal expansivity, Delta alpha, heat capacity, Delta C(p), and isothermal compressibility, Delta kappa, have been calculated as a function of pressure. It has been found that the Ehrenfest relation dT(g)/dP = TV Delta alpha/Delta C(p) predicts the pressure dependence of T, but the other Ehrenfest relation, dT(g)/dP = Delta kappa/Delta alpha, does not. Consequently, the Prigogine-Defay ratio, Pi = Delta C(p)Delta kappa/TV Delta alpha(2), is Pi similar to 1.2 at low pressures, but increases 1 order of magnitude at high pressures. The pressure dependence of the Prigogine-Defay ratio is interpreted in light of recent explanations for the finding Pi > 1.

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The viscosity of ionic liquids based on quaternary ammonium cations is reduced when one of the alkyl chains is replaced by an alkoxy chain (Zhou et al. Chem. Eur. J. 2005, 11, 752.). A microscopic picture of the role played by the ether function in decreasing the viscosity of quaternary ammonium ionic liquids is provided here by molecular dynamics (MD) simulations. A model for the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide, MOENM(2)E TFSI, is compared to the tetraalky-lammonium counterpart. The alkoxy derivative has lower viscosity, higher ionic diffusion coefficients, and higher conductivity than the tetraalkyl system at the same density and temperature. A clear signature of the ether function on the liquid structure is observed in cation-cation correlations, but not in anion-anion or anion-cation correlations. In both the alkyl and the alkoxy ionic liquids, there is aggregation of long chains of neighboring cations within micelle-like structures. The MD simulations indicate that the less effective assembly between the more flexible alkoxy chains, in comparison to alkyl chains, is the structural reason for higher ionic mobility in MOENM(2)E TFSI.

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Canonical Monte Carlo simulations for the Au(210)/H(2)O interface, using a force field recently proposed by us, are reported. The results exhibit the main features normally observed in simulations of water molecules in contact with different noble metal surfaces. The calculations also assess the influence of the surface topography on the structural aspects of the adsorbed water and on the distribution of the water molecules in the direction normal to the metal surface plane. The adsorption process is preferential at sites in the first layer of the metal. The analysis of the density profiles and dipole moment distributions points to two predominant orientations. Most of the molecules are adsorbed with the molecular plane parallel to surface, while others adsorb with one of the O-H bonds parallel to the surface and the other bond pointing towards the bulk liquid phase. There is also evidence of hydrogen bond formation between the first and second solvent layers at the interface. (c) 2007 Elsevier B.V. All rights reserved.

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We report in this work the study of the interaction between formic acid and an oxidized platinum surface under open circuit conditions. The investigation was carried out with the aid of in situ infrared spectroscopy, and results analyzed in terms of a mathematical model and numerical simulations. It has been found that during the first seconds of the interaction a small amount of CO(2) is produced and absolutely no adsorbed CO was observed. A sudden drop in potential then follows, which is accompanied by a steep increase first of CO(2) production and then by adsorbed CO. The steep transient was rationalized in terms of an autocatalytic production of free platinum sites which enhances the overall rate of reaction. Modeling and simulation showed nearly quantitative agreement with the experimental observations and provided further insight into some experimentally inaccessible variables such as surface free sites. Finally, based on the understanding provided from the combined experimental and theoretical approach, we discuss the general aspects influencing the open circuit transient.

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The study reported here is part of a large project for evaluation of the Thermo-Chemical Accumulator (TCA), a technology under development by the Swedish company ClimateWell AB. The studies concentrate on the use of the technology for comfort cooling. This report concentrates on measurements in the laboratory, modelling and system simulation. The TCA is a three-phase absorption heat pump that stores energy in the form of crystallised salt, in this case Lithium Chloride (LiCl) with water being the other substance. The process requires vacuum conditions as with standard absorption chillers using LiBr/water. Measurements were carried out in the laboratories at the Solar Energy Research Center SERC, at Högskolan Dalarna as well as at ClimateWell AB. The measurements at SERC were performed on a prototype version 7:1 and showed that this prototype had several problems resulting in poor and unreliable performance. The main results were that: there was significant corrosion leading to non-condensable gases that in turn caused very poor performance; unwanted crystallisation caused blockages as well as inconsistent behaviour; poor wetting of the heat exchangers resulted in relatively high temperature drops there. A measured thermal COP for cooling of 0.46 was found, which is significantly lower than the theoretical value. These findings resulted in a thorough redesign for the new prototype, called ClimateWell 10 (CW10), which was tested briefly by the authors at ClimateWell. The data collected here was not large, but enough to show that the machine worked consistently with no noticeable vacuum problems. It was also sufficient for identifying the main parameters in a simulation model developed for the TRNSYS simulation environment, but not enough to verify the model properly. This model was shown to be able to simulate the dynamic as well as static performance of the CW10, and was then used in a series of system simulations. A single system model was developed as the basis of the system simulations, consisting of a CW10 machine, 30 m2 flat plate solar collectors with backup boiler and an office with a design cooling load in Stockholm of 50 W/m2, resulting in a 7.5 kW design load for the 150 m2 floor area. Two base cases were defined based on this: one for Stockholm using a dry cooler with design cooling rate of 30 kW; one for Madrid with a cooling tower with design cooling rate of 34 kW. A number of parametric studies were performed based on these two base cases. These showed that the temperature lift is a limiting factor for cooling for higher ambient temperatures and for charging with fixed temperature source such as district heating. The simulated evacuated tube collector performs only marginally better than a good flat plate collector if considering the gross area, the margin being greater for larger solar fractions. For 30 m2 collector a solar faction of 49% and 67% were achieved for the Stockholm and Madrid base cases respectively. The average annual efficiency of the collector in Stockholm (12%) was much lower than that in Madrid (19%). The thermal COP was simulated to be approximately 0.70, but has not been possible to verify with measured data. The annual electrical COP was shown to be very dependent on the cooling load as a large proportion of electrical use is for components that are permanently on. For the cooling loads studied, the annual electrical COP ranged from 2.2 for a 2000 kWh cooling load to 18.0 for a 21000 kWh cooling load. There is however a potential to reduce the electricity consumption in the machine, which would improve these figures significantly. It was shown that a cooling tower is necessary for the Madrid climate, whereas a dry cooler is sufficient for Stockholm although a cooling tower does improve performance. The simulation study was very shallow and has shown a number of areas that are important to study in more depth. One such area is advanced control strategy, which is necessary to mitigate the weakness of the technology (low temperature lift for cooling) and to optimally use its strength (storage).

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The aim of this study was to investigate electricity supply solutions for an educationalcenter that is being built in Chonyonyo Tanzania. Off-grid power generation solutions andfurther optimization possibilities were studied for the case.The study was done for Engineers Without Borders in Sweden. Who are working withMavuno Project on the educational center. The school is set to start operating in year 2015with 40 girl students in the beginning. The educational center will help to improve genderequality by offering high quality education in a safe environment for girls in rural area.It is important for the system to be economically and environmentally sustainable. Thearea has great potential for photovoltaic power generation. Thus PV was considered as theprimary power generation and a diesel generator as a reliable backup. The system sizeoptimization was done with HOMER. For the simulations HOMER required componentdata, weather data and load data. Common components were chose with standardproperties, the loads were based on load estimations from year 2011 and the weather datawas acquired from NASA database. The system size optimization result for this base casewas a system with 26 kW PW; 5.5 kW diesel generator, 15 kW converter and 112 T-105batteries. The initial cost of the system was 55 875 €, the total net present cost 92 121 €and the levelized cost of electricity 0.264 €/kWh.In addition three optimization possibilities were studied. First it was studied how thesystem should be designed and how it would affect the system size to have night loads(security lights) use DC and could the system then be extended in blocks. As a result it wasfound out that the system size could be decreased as the inverter losses would be avoided.Also the system extension in blocks was found to be possible. The second study was aboutinverter stacking where multiple inverters can work as one unit. This type of connectionallows only the required number of inverters to run while shutting down the excess ones.This would allow the converter-unit to run with higher efficiency and lower powerconsumption could be achieved. In future with higher loads the system could be easilyextendable by connecting more inverters either in parallel or series depending on what isneeded. Multiple inverters would also offer higher reliability than using one centralizedinverter. The third study examined how the choice of location for a centralized powergeneration affects the cable sizing for the system. As a result it was found that centralizedpower generation should be located close to high loads in order to avoid long runs of thickcables. Future loads should also be considered when choosing the location. For theeducational center the potential locations for centralized power generation were found outto be close to the school buildings and close to the dormitories.

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The demand for cooling and air-conditioning of building is increasingly ever growing. This increase is mostly due to population and economic growth in developing countries, and also desire for a higher quality of thermal comfort. Increase in the use of conventional cooling systems results in larger carbon footprint and more greenhouse gases considering their higher electricity consumption, and it occasionally creates peaks in electricity demand from power supply grid. Solar energy as a renewable energy source is an alternative to drive the cooling machines since the cooling load is generally high when solar radiation is high. This thesis examines the performance of PV/T solar collector manufactured by Solarus company in a solar cooling system for an office building in Dubai, New Delhi, Los Angeles and Cape Town. The study is carried out by analyzing climate data and the requirements for thermal comfort in office buildings. Cooling systems strongly depend on weather conditions and local climate. Cooling load of buildings depend on many parameters such as ambient temperature, indoor comfort temperature, solar gain to the building and internal gains including; number of occupant and electrical devices. The simulations were carried out by selecting a suitable thermally driven chiller and modeling it with PV/T solar collector in Polysun software. Fractional primary energy saving and solar fraction were introduced as key figures of the project to evaluate the performance of cooling system. Several parametric studies and simulations were determined according to PV/T aperture area and hot water storage tank volume. The fractional primary energy saving analysis revealed that thermally driven chillers, particularly adsorption chillers are not suitable to be utilizing in small size of solar cooling systems in hot and tropic climates such as Dubai and New Delhi. Adsorption chillers require more thermal energy to meet the cooling load in hot and dry climates. The adsorption chillers operate in their full capacity and in higher coefficient of performance when they run in a moderate climate since they can properly reject the exhaust heat. The simulation results also indicated that PV/T solar collector have higher efficiency in warmer climates, however it requires a larger size of PV/T collectors to supply the thermally driven chillers for providing cooling in hot climates. Therefore using an electrical chiller as backup gives much better results in terms of primary energy savings, since PV/T electrical production also can be used for backup electrical chiller in a net metering mechanism.