A computationally efficient shear deformable beam element for large deformation multibody applications

In this paper, a new two-dimensional shear deformable beam element based on the absolute nodal coordinate formulation is proposed. The nonlinear elastic forces of the beam element are obtained using a continuum mechanics approach without employing a local element coordinate system. In this study, linear polynomials are used to interpolate both the transverse and longitudinal components of the displacement. This is different from other absolute nodal-coordinate-based beam elements where cubic polynomials are used in the longitudinal direction. The accompanying defects of the phenomenon known as shear locking are avoided through the adoption of selective integration within the numerical integration method. The proposed element is verified using several numerical examples, and the results are compared to analytical solutions and the results for an existing shear deformable beam element. It is shown that by using the proposed element, accurate linear and nonlinear static deformations, as well as realistic dynamic behavior, can be achieved with a smaller computational effort than by using existing shear deformable two-dimensional beam elements.

Study of biomacromolecule conformational changes by Scanning Force Microscopy

L?objectif de ce travail de thèse est l?étude des changements conformationels des biomacromolecules à l?échelle d?une molécule unique. Pour cela on a utilisé la Microscopie à Force Atomique (AFM) appliqué à l?étude des protéines et des acides nucléiques déposés sur une surface. Dans ce type de microscopie, une pointe très fine attachée à l?extrémité d?un levier est balayée au dessus d?une surface. L?interaction de la pointe avec la surface de l?échantillon induit la déflection du levier et ce phénomène permet de reconstruire la topographie de l?échantillon. Très importante dans cette technique est la possibilité de travailler en liquide. Cela permet de étudier les biomolécules en conditions quasi-physiologiques sans qu?elles perdent leur activité. On a étudié GroEL, la chaperonin de E.coli, qui est un homo oligomère avec une structure à double anneau qui joue un rôle très important dans le repliement des protéines dénaturées et celles qui viennent d?être synthétisées. En particulier on a focalisé notre attention sur la stabilité mécanique et sur les changements conformationels qui ont lieu pendant l?activité de GroEL. Une analyse détaillée des changements dans la stabilité mécanique et des effets produits par la liaison et l?hydrolyse de l?ATP est présentée dans ce travail. On a montré que le point le plus faible dans la structure de GroEL est l?interface entre les deux anneaux et que l?étape critique dans l?affaiblissement de la structure est l?hydrolyse de l?ATP. En ce qui concerne le changement conformationel, le passage d?une surface hydrophobe à hydrophile, induit par l?hydrolyse de l?ATP, a été montré. Ensuite on a étudié le changement dans la conformation et dans la topologie de l?ADN résultant de l?interaction avec des molécules spécifiques et en réponse à l?exposition des cellules de E.coli à des conditions de stress. Le niveau de surenroulement est un paramètre très sensible, de façon variée, à tous ces facteurs. Les cellules qui ont crus à de températures plus élevées que leur température optimale ont la tendance à diminuer le nombre de surenroulements négatif pour augmenter la stabilité thermique de leur plasmides. L?interaction avec des agents intercalant induit une transition d?un surenroulement négatif à un surenroulement positif d?une façon dépendante de la température. Finalement, l?effet de l?interaction de l?ADN avec des surfaces différentes a été étudié et une application pratique sur les noeuds d?ADN est présentée.<br/><br/>The aim of the present thesis work is to study the conformational changes of biomacromolecules at the single molecule level. To that end, Atomic Force Microcopy (AFM) imaging was performed on proteins and nucleic acids adsorbed onto a surface. In this microcopy technique a very sharp tip attached at the end of a soft cantilever is scanned over a surface, the interaction of the tip with the sample?s surface will induce the deflection of the cantilever and thus it will make possible to reconstruct the topography. A very important feature of AFM is the possibility to operate in liquid, it means with the sample immersed in a buffer solution. This allows one to study biomolecules in quasi-physiological conditions without loosing their activity. We have studied GroEL, the chaperonin of E.coli, which is a double-ring homooligomer which pays a very important role in the refolding of unfolded and newly synthetized polypeptides. In particular we focus our attention on its mechanical stability and on the conformational change that it undergoes during its activity cycle. A detailed analysis of the change in mechanical stability and how it is affected by the binding and hydrolysis of nucleotides is presented. It has been shown that the weak point of the chaperonin complex is the interface between the two rings and that the critical step to weaken the structure is the hydrolysis of ATP. Concerning the conformational change we have directly measured, with a nanometer scale resolution, the switching from a hydrophobic surface to a hydrophilic one taking place inside its cavity induced by the ATP hydrolysis. We have further studied the change in the DNA conformation and topology as a consequence of the interaction with specific DNA-binding molecules and the exposition of the E.coli cells to stress conditions. The level of supercoiling has been shown to be a very sensitive parameter, even if at different extents, to all these factors. Cells grown at temperatures higher than their optimum one tend to decrease the number of the negative superhelical turns in their plasmids in order to increase their thermal stability. The interaction with intercalating molecules induced a transition from positive to negative supercoiling in a temperature dependent way. The effect of the interaction of the DNA with different surfaces has been investigated and a practical application to DNA complex knots is reported.<br/><br/>Observer les objets biologiques en le touchant Schématiquement le Microscope a Force Atomique (AFM) consiste en une pointe très fine fixée a l?extrémité d?un levier Lors de l?imagerie, la pointe de l?AFM gratte la surface de l?échantillon, la topographie de celui-ci induit des déflections du levier qui sont enregistrées au moyen d?un rayon laser réfléchi par le levier. Ces donnés sont ensuit utilisés par un ordinateur pour reconstituer en 3D la surface de l?échantillon. La résolution de l?instrument est fonction entre autre de la dureté, de la rugosité de l?échantillon et de la forme de la pointe. Selon l?échantillon et la pointe utilisée la résolution de l?AFM peut aller de 0.1 A (sur des cristaux) a quelque dizaine de nanomètres (sur des cellules). Cet instrument est particulierment intéressant en biologie en raison de sa capacité à imager des échantillons immergés dans un liquide, c?est à dire dans des conditions quasiphysiologiques. Dans le cadre de ce travail nous avons étudié les changements conformationels de molécules biologiques soumises à des stimulations externes. Nous avons essentielment concentré notre attention sur des complexes protéiques nommé Chaperons Moléculaires et sur des molécules d?ADN circulaire (plasmides). Les Chaperons sont impliqués entre autre dans la résistance des organismes vivants aux stress thermiques et osmotiques. Leur activité consiste essentielment à aider les autres protéines à être bien pliés dans leur conformation finale et, en conséquence, à eviter que ils soient dénaturées et que ils puissent s?agréger. L?ADN, quant à lui est la molécule qui conserve, dans sa séquence, l?information génétique de tous les organismes vivants. Ce travail a spécifiquement concerné l?étude des changements conformationels des chaperonins suit a leur activation par l?ATP. Ces travaux ont montrés a l?échelle de molécule unique la capacité de ces protéines de changer leur surface de hydrophobique a hydrophilique. Nous avons également utilisé l?AFM pour étudier le changement du nombre des surenroulements des molécules d?ADN circulaire lors d?une exposition à un changement de température et de force ionique. Ces travaux ont permis de montrer comment la cellule regle le nombre de surenroulements dans ces molécules pour répondre et contrôler l?expression génétique même dans de conditions extrêmes. Pour les deux molécules en général, c?était très important d?avoir la possibilité de observer leur transitions d?une conformation a l?autre directement a l?échelle d?une seul molécule et, surtout, avec une résolution largement au dessous des la longueur d?onde de la lumière visible que représente le limite pour l?imagerie optique.

Theoretical Analysis and Simulations of Vertically Vibrated Granular Materials

The dynamical properties ofshaken granular materials are important in many industrial applications where the shaking is used to mix, segregate and transport them. In this work asystematic, large scale simulation study has been performed to investigate the rheology of dense granular media, in the presence of gas, in a three dimensional vertical cylinder filled with glass balls. The base wall of the cylinder is subjected to sinusoidal oscillation in the vertical direction. The viscoelastic behavior of glass balls during a collision, have been studied experimentally using a modified Newton's Cradle device. By analyzing the results of the measurements, using numerical model based on finite element method, the viscous damping coefficient was determinedfor the glass balls. To obtain detailed information about the interparticle interactions in a shaker, a simplified model for collision between particles of a granular material was proposed. In order to simulate the flow of surrounding gas, a formulation of the equations for fluid flow in a porous medium including particle forces was proposed. These equations are solved with Large Eddy Simulation (LES) technique using a subgrid-model originally proposed for compressible turbulent flows. For a pentagonal prism-shaped container under vertical vibrations, the results show that oscillon type structures were formed. Oscillons are highly localized particle-like excitations of the granular layer. This self-sustaining state was named by analogy with its closest large-scale analogy, the soliton, which was first documented by J.S. Russell in 1834. The results which has been reportedbyBordbar and Zamankhan(2005b)also show that slightly revised fluctuation-dissipation theorem might apply to shaken sand, which appears to be asystem far from equilibrium and could exhibit strong spatial and temporal variations in quantities such as density and local particle velocity. In this light, hydrodynamic type continuum equations were presented for describing the deformation and flow of dense gas-particle mixtures. The constitutive equation used for the stress tensor provides an effective viscosity with a liquid-like character at low shear rates and a gaseous-like behavior at high shear rates. The numerical solutions were obtained for the aforementioned hydrodynamic equations for predicting the flow dynamics ofdense mixture of gas and particles in vertical cylindrical containers. For a heptagonal prism shaped container under vertical vibrations, the model results were found to predict bubbling behavior analogous to those observed experimentally. This bubbling behavior may be explained by the unusual gas pressure distribution found in the bed. In addition, oscillon type structures were found to be formed using a vertically vibrated, pentagonal prism shaped container in agreement with computer simulation results. These observations suggest that the pressure distribution plays a key rolein deformation and flow of dense mixtures of gas and particles under vertical vibrations. The present models provide greater insight toward the explanation of poorly understood hydrodynamic phenomena in the field of granular flows and dense gas-particle mixtures. The models can be generalized to investigate the granular material-container wall interactions which would be an issue of high interests in the industrial applications. By following this approach ideal processing conditions and powder transport can be created in industrial systems.

Comprehensive Study of Crystal Growth from Solution

Crystal growth is an essential phase in crystallization kinetics. The rate of crystal growth provides significant information for the design and control of crystallization processes; nevertheless, obtaining accurate growth rate data is still challenging due to a number of factors that prevail in crystal growth. In industrial crystallization, crystals are generally grown from multi-componentand multi-particle solutions under complicated hydrodynamic conditions; thus, it is crucial to increase the general understanding of the growth kinetics in these systems. The aim of this work is to develop a model of the crystal growth rate from solution. An extensive literature review of crystal growth focuses on themodelling of growth kinetics and thermodynamics, and new measuring techniques that have been introduced in the field of crystallization. The growth of a singlecrystal is investigated in binary and ternary systems. The binary system consists of potassium dihydrogen phosphate (KDP, crystallizing solute) and water (solvent), and the ternary system includes KDP, water and an organic admixture. The studied admixtures, urea, ethanol and 1-propanol, are employed at relatively highconcentrations (of up to 5.0 molal). The influence of the admixtures on the solution thermodynamics is studied using the Pitzer activity coefficient model. Theprediction method of the ternary solubility in the studied systems is introduced and verified. The growth rate of the KDP (101) face in the studied systems aremeasured in the growth cell as a function of supersaturation, the admixture concentration, the solution velocity over a crystal and temperature. In addition, the surface morphology of the KDP (101) face is studied using ex situ atomic force microscopy (AFM). The crystal growth rate in the ternary systems is modelled on the basis of the two-step growth model that contains the Maxwell-Stefan (MS) equations and a surface-reaction model. This model is used together with measuredcrystal growth rate data to develop a new method for the evaluation of the model parameters. The validation of the model is justified with experiments. The crystal growth rate in an imperfectly mixed suspension crystallizer is investigatedusing computational fluid dynamics (CFD). A solid-liquid suspension flow that includes multi-sized particles is described by the multi-fluid model as well as by a standard k-epsilon turbulence model and an interface momentum transfer model. The local crystal growth rate is determined from calculated flow information in a diffusion-controlled crystal growth regime. The calculated results are evaluated experimentally.

Unplanned complex suicide by self-strangulation associated with multiple sharp force injuries: a case report.

In cases of ligature strangulation, the importance of distinguishing self-inflicted death from homicide is crucial. This entails objective scene investigation, autopsy and anamnesis in order to elucidate the manner of death correctly. The authors report a case of unplanned complex suicide by means of self-strangulation and multiple sharp force injury. The use of more than one suicide method, consecutively--termed unplanned complex suicide--gives this case particular significance. A brief discussion on this uncommon method of suicide is presented, particularly relevant to the attending forensic physician. In addition, a short overview of the entity of complex suicide is given.

Efeito do extrato de alho na quebra de dormência de gemas de videiras e no controle in vitro do agente causal da antracnose (Elsinoe ampelina Shear)

Considerando a redução ou eliminação do uso de substâncias sintéticas que preconizam os sistemas sustentáveis de produção de frutas, este trabalho teve como objetivo a busca de novas alternativas para a quebra de dormência e o controle de doenças em videiras. Estacas de videira contendo uma gema foram pulverizadas com os seguintes tratamentos: 1) testemunha; 2) OV (óleo vegetal) 1%; 3) extrato de alho (EA) 3%; 4) EA 3% + OV 1%. Posteriormente, as estacas foram mantidas em câmara de crescimento (25±2.5ºC) por 56 dias. O único tratamento que estimulou a brotação das estacas de videira cv. Isabel Precoce foi o EA 3% + OV 1%, que atingiu 35% de brotação, diferindo estatisticamente dos tratamentos- testemunha (12,5%), OV 1% (17,5%) e EA 3% (15,0%). Provavelmente, o estádio de endodormência profunda das gemas, após apenas 90 horas de frio ( < 7,0ºC), impediu melhores resultados dos tratamentos para quebra de dormência. Três experimentos, foram conduzidos in vitro, com diferentes doses de extrato de alho, com o objetivo de avaliar o controle do fungo Elsinoe ampelina. Em todos os experimentos, houve efeito quadrático no crescimento micelial, sem ter havido diferenças entre os tratamentos com extrato de alho, evidenciando o seu efeito fungicida, mesmo na dose mais baixa de EA (0,0615%).