Modelling water adsorption on Au(210) surfaces: II. Monte Carlo simulations

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.

A Cost Model for the Effect of Setup Time Reduction in Stainless Steel Strip Production

Setup time reduction facilitate the flexibility needed for just-in-time production. An integrated steel mill with meltshop, continuous caster and hot rolling mill is often operated as decoupled processes. Setup time reduction provides the flexibility needed to reduce buffering, shorten lead times and create an integrated process flow. The interdependency of setup times, process flexibility and integration were analysed through system dynamics simulation. The results showed significant reductions of energy consumption and tied capital. It was concluded that setup time reduction in the hot strip mill can aid process integration and hence improve production economy while reducing environmental impact.

Simulação computacional de medidas estereológicas em estruturas de metal duro (WC-Co)

This work focuses on the creation and applications of a dynamic simulation software in order to study the hard metal structure (WC-Co). The technological ground used to increase the GPU hardware capacity was Geforce 9600 GT along with the PhysX chip created to make games more realistic. The software simulates the three-dimensional carbide structure to the shape of a cubic box where tungsten carbide (WC) are modeled as triangular prisms and truncated triangular prisms. The program was proven effective regarding checking testes, ranging from calculations of parameter measures such as the capacity to increase the number of particles simulated dynamically. It was possible to make an investigation of both the mean parameters and distributions stereological parameters used to characterize the carbide structure through cutting plans. Grounded on the cutting plans concerning the analyzed structures, we have investigated the linear intercepts, the intercepts to the area, and the perimeter section of the intercepted grains as well as the binder phase to the structure by calculating the mean value and distribution of the free path. As literature shows almost consensually that the distribution of the linear intercepts is lognormal, this suggests that the grain distribution is also lognormal. Thus, a routine was developed regarding the program which made possible a more detailed research on this issue. We have observed that it is possible, under certain values for the parameters which define the shape and size of the Prismatic grain to find out the distribution to the linear intercepts that approach the lognormal shape. Regarding a number of developed simulations, we have observed that the distribution curves of the linear and area intercepts as well as the perimeter section are consistent with studies on static computer simulation to these parameters.

Non-inclusion complexes between riboflavin and cyclodextrins

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular characterization and phylogenetic analysis of JussuMP-I: A RGD-P-III class hemorrhagic metalloprotease from Bothrops jararacussu snake venom

Snake venom metalloproteases (SVMPs) embody zinc-dependent multidomain enzymes responsible for a relevant pathophysiology in envenomation. including local and systemic hemorrhage. The molecular features responsible for hemorrhagic potency of SVMPs have been associated with their multidomains structures which can target these proteins them to several receptors of different tissues and cellular types. BjussuMP-I. a SVMP isolated from the Bothrops jararacussu venom, has been characterized as a P-III hemorrhagic metalloprotease. The complete cDNA sequence of BjussuMP-I with 1641bp encodes open reading frames of 547 amino acid residues, which conserve the common domains of P-III high molecular weight hemorrhagic metalloproteases: (i) pre-pro-peptide, (ii) metalloprotease, (iii) disintegrin-like and (iv) rich cysteine domain. BjussuMP-I induced lyses in fibrin clots and inhibited collagen- and ADP-induced platelet aggregation. We are reporting, for the first time, the primary structure of an RGD-P-III class snake venom metalloprotease. A phylogenetic analysis of the BjussuMP-1 metalloprotease/catalytic domain was performed to get new insights into the molecular evolution of the metalloproteases. A theoretical molecular model of this domain was built through folding recognition (threading) techniques and refined by molecular dynamics simulation. Then, the final BjussuMP-I catalytic domain model was compared to other SVMPs and Reprolysin family proteins in order to identify eventual structural differences, which could help to understand the biochemical activities of these enzymes. The presence of large hydrophobic areas and some conserved surface charge-positive residues were identified as important features of the SVMPs and other metalloproteases. (C) 2006 Elsevier B.V. All rights reserved.

Structural and functional properties of Bp-LAAO, a new L-amino acid oxidase isolated from Bothrops pauloensis snake venom

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Local order around rare earth ions during the devitrification of oxyfluoride glasses

Erbium L-3-edge extended x-ray absorption fine structure (EXAFS) measurements were performed on rare earth doped fluorosilicate and fluoroborate glasses and glass ceramics. The well known nucleating effects of erbium ions for the crystallization of cubic lead fluoride (based on x-ray diffraction measurements) and the fact that the rare earth ions are present in the crystalline phase (as indicated by Er3+ emission spectra) seem in contradiction with the present EXAFS analysis, which indicates a lack of medium range structural ordering around the Er3+ ions and suggests that the lead fluoride crystallization does not occur in the nearest neighbor distance of the rare earth ion. Molecular dynamics simulations of the devitrification process of a lead fluoride glass doped with Er3+ ions were performed, and results indicate that Er3+ ions lower the devitrification temperature of PbF2, in good agreement with the experimental results. The genuine role of Er3+ ions in the devitrification process of PbF2 has been investigated. Although Er3+ ions could indeed act as seeds for crystallization, as experiments suggest, molecular dynamics simulation results corroborate the experimental EXAFS observation that the devitrification does not occur at its nearest neighbor distance. (c) 2008 American Institute of Physics.

Analysis of agonist and antagonist effects on thyroid hormone receptor conformation by hydrogen/deuterium exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T 3) or antagonist (NH3). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/ deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, Cterminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T 3, but not NH3, increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T 3 but not NH3.Wepresent data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011). Copyright © 2011 by The Endocrine Society.

Biophysical characterization of the recombinant importin-α from neurospora crassa

Neurospora crassa has been widely used as a model organism and contributed to the development of biochemistry and molecular biology by allowing the identification of many metabolic pathways and mechanisms responsible for gene regulation. Nuclear proteins are synthesized in the cytoplasm and need to be translocated to the nucleus to exert their functions which the importin-α receptor has a key role for the classical nuclear import pathway. In an attempt to get structural information of the nuclear transport process in N. crassa, we present herein the cloning, expression, purification and structural studies with N-terminally truncated IMPα from N. crassa (IMPα-Nc). Circular dichroism analysis revealed that the IMPα-Nc obtained is correctly folded and presents a high structural conservation compared to other importins-α. Dynamic light scattering, analytical size-exclusion chromatography experiments and molecular dynamics simulations indicated that the IMPα-Nc unbound to any ligand may present low stability in solution. The IMPα-Nc theoretical model displayed high similarity of its inner concave surface, which binds the cargo proteins containing the nuclear localization sequences, among IMPα from different species. However, the presence of non-conserved amino acids relatively close to the NLS binding region may influence the binding specificity of IMPα-Nc to cargo proteins. Copyright © 2012 Bentham Science Publishers. All Rights Reserved.

Análise conformacional dos petídeos protonectina e protonectina (1-6), isolados e em associação, em mistura TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Interação do peptídeo MP-I com micela de SDS em solução aquosa: um estudo por dinâmica molecular

Pós-graduação em Biofísica Molecular - IBILCE

Estudos conformacionais por dinâmica molecular de peptídeos antimicrobianos da família dos Mastoparanos em misturas de TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo de nanofios de Au e dendrímeros

A primeira parte deste trabalho aborda a simulação computacional de dinâmica molecular clássica da interação de sistemas matriciais constituídos de nanofios paralelos de Au simuladas em função do tempo. Como resultados foram encontrados os tempos de colisões entre os fios da matriz. A segunda parte deste trabalho utiliza dinâmica molecular clássica para simular cinco gerações de dendrímeros PAMAM, cada qual interagindo individualmente com um nanotubo de carbono em função do tempo resultando num motor molecular. Além disso, foram calculados os espectros de absorção deste sistema e foi verificado que eles são nanomotores controlados pela luz. Para todos estes sistemas foram calculadas energias cinética, potencial, total, velocidade, propriedades termodinâmicas como variação de entropia molar, capacidade molar térmica e temperatura in situ. Estas grandezas nos forneceram valiosas informações sobre o comportamento destes sistemas.

Análise do escoamento turbulento por um queimador industrial a gás utilizando dinâmica dos fluidos computacional

Pós-graduação em Engenharia Mecânica - FEG

Numerical modeling of flow through an industrial burner orifice

This paper presents numerical modeling of a turbulent natural gas flow through a non-premixed industrial burner of a slab reheating furnace. The furnace is equipped with diffusion side swirl burners capable of utilizing natural gas or coke oven gas alternatively through the same nozzles. The study is focused on one of the burners of the preheating zone. Computational Fluid Dynamics simulation has been used to predict the burner orifice turbulent flow. Flow rate and pressure at burner upstream were validated by experimental measurements. The outcomes of the numerical modeling are analyzed for the different turbulence models in terms of pressure drop, velocity profiles, and orifice discharge coefficient. The standard, RNG, and Realizable k-epsilon models and Reynolds Stress Model (RSM) have been used. The main purpose of the numerical investigation is to determine the turbulence model that more consistently reproduces the experimental results of the flow through an industrial non-premixed burner orifice. The comparisons between simulations indicate that all the models tested satisfactorily and represent the experimental conditions. However, the Realizable k-epsilon model seems to be the most appropriate turbulence model, since it provides results that are quite similar to the RSM and RNG k-epsilon models, requiring only slightly more computational power than the standard k-epsilon model. (C) 2014 Elsevier Ltd. All rights reserved.