On the Use of Matrix-Free Shift-Invert Strategies For Global Flow Instability Analysis

A novel time-stepping shift-invert algorithm for linear stability analysis of laminar flows in complex geometries is presented. This method, based on a Krylov subspace iteration, enables the solution of complex non-symmetric eigenvalue problems in a matrix-free framework. Validations and comparisons to the classical exponential method have been performed in three different cases: (i) stenotic flow, (ii) backward-facing step and (iii) lid-driven swirling flow. Results show that this new approach speeds up the required Krylov subspace iterations and has the capability of converging to specific parts of the global spectrum. It is shown that, although the exponential method remains the method of choice if leading eigenvalues are sought, the performance of the present method could be dramatically improved with the use of a preconditioner. In addition, as opposed to other methods, this strategy can be directly applied to any time-stepper, regardless of the temporal or spatial discretization of the latter.

Conditions for perfect focusing multiple point sources with the SMS design method

In this work, we demonstrate how it is possible to sharply image multiple object points. The Simultaneous Multiple Surface (SMS) design method has usually been presented as a method to couple N wave-front pairs with N surfaces, but recent findings show that when using N surfaces, we can obtain M image points when Nmethod, from its basics, to imaging two object points through one surface, the transition from two to three objet points obtained by increasing the parallelism, and getting to the designs of six surfaces imaging up to eight object points. These designs are limited with the condition that the surfaces cannot be placed at the aperture stop. In the process of maximizing the object points to sharp image, we try to exhaust the degrees of freedom of aspherics and free-forms. We conjecture that maximal SMS designs are very close to a good solution, hence using them as a starting point for the optimization will lead us faster to a final optical system. We suggest here different optimization strategies which combined with the SMS method are proven to give the best solution. Through the example of imaging with the high aspect ratio, we compare the results obtained optimizing the rotational lens and using a combination of SMS method and optimization, showing that the second approach is giving significantly smaller value of overall RMS spot diameter.

Evaluation of the surface free energy of plant surfaces: toward standardizing the procedure

Plant surfaces have been found to have a major chemical and physical heterogeneity and play a key protecting role against multiple stress factors. During the last decade, there is a raising interest in examining plant surface properties for the development of biomimetic materials. Contact angle measurement of different liquids is a common tool for characterizing synthetic materials, which is just beginning to be applied to plant surfaces. However, some studies performed with polymers and other materials showed that for the same surface, different surface free energy values may be obtained depending on the number and nature of the test liquids analyzed, materials' properties, and surface free energy calculation methods employed. For 3 rough and 3 rather smooth plant materials, we calculated their surface free energy using 2 or 3 test liquids and 3 different calculation methods. Regardless of the degree of surface roughness, the methods based on 2 test liquids often led to the under- or over-estimation of surface free energies as compared to the results derived from the 3-Liquids method. Given the major chemical and structural diversity of plant surfaces, it is concluded that 3 different liquids must be considered for characterizing materials of unknown physico-chemical properties, which may significantly differ in terms of polar and dispersive interactions. Since there are just few surface free energy data of plant surfaces with the aim of standardizing the calculation procedure and interpretation of the results among for instance, different species, organs, or phenological states, we suggest the use of 3 liquids and the mean surface tension values provided in this study.

Dynamic interactions between solids and viscous liquids with free surface = Interacciones dinámicas entre sólidos y líquidos viscosos con superficie libre

En esta tesis se investiga la interacción entre un fluido viscoso y un cuerpo sólido en presencia de una superficie libre. El problema se expresa teóricamente poniendo especial atención a los aspectos de conservación de energía y de la interacción del fluido con el cuerpo. El problema se considera 2D y monofásico, y un desarrollo matemático permite una descomposición de los términos disipativos en términos relacionados con la superficie libre y términos relacionados con la enstrofía. El modelo numérico utilizado en la tesis se basa en el método sin malla Smoothed Particle Hydrodynamics (SPH). De manera análoga a lo que se hace a nivel continuo, las propiedades de conservación se estudian en la tesis con el sistema discreto de partículas. Se tratan también las condiciones de contorno de un cuerpo que se mueve en un flujo viscoso, implementadas con el método ghost-fluid. Se ha desarrollado un algoritmo explícito de interacción fluido / cuerpo. Se han documentado algunos casos de modo detallado con el objetivo de comprobar la capacidad del modelo para reproducir correctamente la disipación de energía y el movimiento del cuerpo. En particular se ha investigado la atenuación de una onda estacionaria, comparando la simulación numérica con predicciones teóricas. Se han realizado otras pruebas para monitorizar la disipación de energía para flujos más violentos que implican la fragmentación de la superficie libre. La cantidad de energía disipada con los diferentes términos se ha evaluado en los casos estudiados con el modelo numérico. Se han realizado otras pruebas numéricas para verificar la técnica de modelización de la interacción fluido / cuerpo, concretamente las fuerzas ejercidas por las olas en cuerpos con formas simples, y el equilibrio de un cuerpo flotante con una forma compleja. Una vez que el modelo numérico ha sido validado, se han realizado simulaciones numéricas para obtener una comprensión más completa de la física implicada en casos (casi) realistas sobre los había aspectos que no se conocían suficientemente. En primer lugar se ha estudiado el el flujo alrededor de un cilindro bajo la superficie libre. El estudio se ha realizado con un número de Reynolds moderado, para un rango de inmersiones del cilindro y números de Froude. La solución numérica permite una investigación de los patrones complejos que se producen. La estela del cilindro interactúa con la superficie libre. Se han identificado algunos inestabilidades características. El segundo estudio se ha realizado sobre el problema de sloshing, tanto experimentalmente como numéricamente. El análisis se restringe a aguas poco profundas y con oscilación horizontal, pero se ha estudiado un gran número de condiciones, lo que lleva a una comprensión bastante completa de los sistemas de onda involucradas. La última parte de la tesis trata también sobre un problema de sloshing pero esta vez el tanque está oscilando con rotación y hay acoplamiento con un sistema mecánico. El sistema se llama pendulum-TLD (Tuned Liquid Damper - con líquido amortiguador). Este tipo de sistema se utiliza normalmente para la amortiguación de las estructuras civiles. El análisis se ha realizado analíticamente, numéricamente y experimentalmente utilizando líquidos con viscosidades diferentes, centrándose en características no lineales y mecanismos de disipación. ABSTRA C T The subject of the present thesis is the interaction between a viscous fluid and a solid body in the presence of a free surface. The problem is expressed first theoretically with a particular focus on the energy conservation and the fluid-body interaction. The problem is considered 2D and monophasic, and some mathematical development allows for a decomposition of the energy dissipation into terms related to the Free Surface and others related to the enstrophy. The numerical model used on the thesis is based on Smoothed Particle Hydrodynamics (SPH): a computational method that works by dividing the fluid into particles. Analogously to what is done at continuum level, the conservation properties are studied on the discrete system of particles. Additionally the boundary conditions for a moving body in a viscous flow are treated and discussed using the ghost-fluid method. An explicit algorithm for handling fluid-body coupling is also developed. Following these theoretical developments on the numerical model, some test cases are devised in order to test the ability of the model to correctly reproduce the energy dissipation and the motion of the body. The attenuation of a standing wave is used to compare what is numerically simulated to what is theoretically predicted. Further tests are done in order to monitor the energy dissipation in case of more violent flows involving the fragmentation of the free-surface. The amount of energy dissipated with the different terms is assessed with the numerical model. Other numerical tests are performed in order to test the fluid/body interaction method: forces exerted by waves on simple shapes, and equilibrium of a floating body with a complex shape. Once the numerical model has been validated, numerical tests are performed in order to get a more complete understanding of the physics involved in (almost) realistic cases. First a study is performed on the flow passing a cylinder under the free surface. The study is performed at moderate Reynolds numbers, for various cylinder submergences, and various Froude numbers. The capacity of the numerical solver allows for an investigation of the complex patterns which occur. The wake from the cylinder interacts with the free surface, and some characteristical flow mechanisms are identified. The second study is done on the sloshing problem, both experimentally and numerically. The analysis is restrained to shallow water and horizontal excitation, but a large number of conditions are studied, leading to quite a complete understanding of the wave systems involved. The last part of the thesis still involves a sloshing problem but this time the tank is rolling and there is coupling with a mechanical system. The system is named pendulum-TLD (Tuned Liquid Damper). This kind of system is normally used for damping of civil structures. The analysis is then performed analytically, numerically and experimentally for using liquids with different viscosities, focusing on non-linear features and dissipation mechanisms.

Design of a Semi-analytical Method to Describe Plasma-Wall Interactions

Electric probes are objects immersed in the plasma with sharp boundaries which collect of emit charged particles. Consequently, the nearby plasma evolves under abrupt imposed and/or naturally emerging conditions. There could be localized currents, different time scales for plasma species evolution, charge separation and absorbing-emitting walls. The traditional numerical schemes based on differences often transform these disparate boundary conditions into computational singularities. This is the case of models using advection-diffusion differential equations with source-sink terms (also called Fokker-Planck equations). These equations are used in both, fluid and kinetic descriptions, to obtain the distribution functions or the density for each plasma species close to the boundaries. We present a resolution method grounded on an integral advancing scheme by using approximate Green's functions, also called short-time propagators. All the integrals, as a path integration process, are numerically calculated, what states a robust grid-free computational integral method, which is unconditionally stable for any time step. Hence, the sharp boundary conditions, as the current emission from a wall, can be treated during the short-time regime providing solutions that works as if they were known for each time step analytically. The form of the propagator (typically a multivariate Gaussian) is not unique and it can be adjusted during the advancing scheme to preserve the conserved quantities of the problem. The effects of the electric or magnetic fields can be incorporated into the iterative algorithm. The method allows smooth transitions of the evolving solutions even when abrupt discontinuities are present. In this work it is proposed a procedure to incorporate, for the very first time, the boundary conditions in the numerical integral scheme. This numerical scheme is applied to model the plasma bulk interaction with a charge-emitting electrode, dealing with fluid diffusion equations combined with Poisson equation self-consistently. It has been checked the stability of this computational method under any number of iterations, even for advancing in time electrons and ions having different time scales. This work establishes the basis to deal in future work with problems related to plasma thrusters or emissive probes in electromagnetic fields.

A time-domain finite element method for seakeeping and wave resistance problems

El objetivo de la tesis es la investigación de algoritmos numéricos para el desarrollo de herramientas numéricas para la simulación de problemas tanto de comportamiento en la mar como de resistencia al avance de buques y estructuras flotantes. La primera herramienta desarrollada resuelve el problema de difracción y radiación de olas. Se basan en el método de los elementos finitos (MEF) para la resolución de la ecuación de Laplace, así como en esquemas basados en MEF, integración a lo largo de líneas de corriente, y en diferencias finitas desarrollados para la condición de superficie libre. Se han desarrollado herramientas numéricas para la resolución de la dinámica de sólido rígido en sistemas multicuerpos con ligaduras. Estas herramientas han sido integradas junto con la herramienta de resolución de olas difractadas y radiadas para la resolución de problemas de interacción de cuerpos con olas. También se han diseñado algoritmos de acoplamientos con otras herramientas numéricas para la resolución de problemas multifísica. En particular, se han realizado acoplamientos con una herramienta numérica basada de cálculo de estructuras con MEF para problemas de interacción fluido-estructura, otra de cálculo de líneas de fondeo, y con una herramienta numérica de cálculo de flujos en tanques internos para problemas acoplados de comportamiento en la mar con “sloshing”. Se han realizado simulaciones numéricas para la validación y verificación de los algoritmos desarrollados, así como para el análisis de diferentes casos de estudio con aplicaciones diversas en los campos de la ingeniería naval, oceánica, y energías renovables marinas. ABSTRACT The objective of this thesis is the research on numerical algorithms to develop numerical tools to simulate seakeeping problems as well as wave resistance problems of ships and floating structures. The first tool developed is a wave diffraction-radiation solver. It is based on the finite element method (FEM) in order to solve the Laplace equation, as well as numerical schemes based on FEM, streamline integration, and finite difference method tailored for solving the free surface boundary condition. It has been developed numerical tools to solve solid body dynamics of multibody systems with body links across them. This tool has been integrated with the wave diffraction-radiation solver to solve wave-body interaction problems. Also it has been tailored coupling algorithms with other numerical tools in order to solve multi-physics problems. In particular, it has been performed coupling with a MEF structural solver to solve fluid-structure interaction problems, with a mooring solver, and with a solver capable of simulating internal flows in tanks to solve couple seakeeping-sloshing problems. Numerical simulations have been carried out to validate and verify the developed algorithms, as well as to analyze case studies in the areas of marine engineering, offshore engineering, and offshore renewable energy.

Two-dimensional isostatic meshes in the finite element method

In a Finite Element (FE) analysis of elastic solids several items are usually considered, namely, type and shape of the elements, number of nodes per element, node positions, FE mesh, total number of degrees of freedom (dot) among others. In this paper a method to improve a given FE mesh used for a particular analysis is described. For the improvement criterion different objective functions have been chosen (Total potential energy and Average quadratic error) and the number of nodes and dof's of the new mesh remain constant and equal to the initial FE mesh. In order to find the mesh producing the minimum of the selected objective function the steepest descent gradient technique has been applied as optimization algorithm. However this efficient technique has the drawback that demands a large computation power. Extensive application of this methodology to different 2-D elasticity problems leads to the conclusion that isometric isostatic meshes (ii-meshes) produce better results than the standard reasonably initial regular meshes used in practice. This conclusion seems to be independent on the objective function used for comparison. These ii-meshes are obtained by placing FE nodes along the isostatic lines, i.e. curves tangent at each point to the principal direction lines of the elastic problem to be solved and they should be regularly spaced in order to build regular elements. That means ii-meshes are usually obtained by iteration, i.e. with the initial FE mesh the elastic analysis is carried out. By using the obtained results of this analysis the net of isostatic lines can be drawn and in a first trial an ii-mesh can be built. This first ii-mesh can be improved, if it necessary, by analyzing again the problem and generate after the FE analysis the new and improved ii-mesh. Typically, after two first tentative ii-meshes it is sufficient to produce good FE results from the elastic analysis. Several example of this procedure are presented.

Blood glutathione synthesis rates in healthy adults receiving a sulfur amino acid-free diet

The availability of cysteine is thought to be the rate limiting factor for synthesis of the tripeptide glutathione (GSH), based on studies in rodents. GSH status is compromised in various disease states and by certain medications leading to increased morbidity and poor survival. To determine the possible importance of dietary cyst(e)ine availability for whole blood glutathione synthesis in humans, we developed a convenient mass spectrometric method for measurement of the isotopic enrichment of intact GSH and then applied it in a controlled metabolic study. Seven healthy male subjects received during two separate 10-day periods an l-amino acid based diet supplying an adequate amino acid intake or a sulfur amino acid (SAA) (methionine and cysteine) free mixture (SAA-free). On day 10, l-[1-13C]cysteine was given as a primed, constant i.v. infusion (3μmol⋅kg−1⋅h−1) for 6 h, and incorporation of label into whole blood GSH determined by GC/MS selected ion monitoring. The fractional synthesis rate (mean ± SD; day-1) of whole blood GSH was 0.65 ± 0.13 for the adequate diet and 0.49 ± 0.13 for the SAA-free diet (P < 0.01). Whole blood GSH was 1,142 ± 243 and 1,216 ± 162 μM for the adequate and SAA-free periods (P > 0.05), and the absolute rate of GSH synthesis was 747 ± 216 and 579 ± 135 μmol⋅liter−1⋅day−1, respectively (P < 0.05). Thus, a restricted dietary supply of SAA slows the rate of whole blood GSH synthesis and diminishes turnover, with maintenance of the GSH concentration in healthy subjects.

A quantitative method for evaluating the stabilities of nucleic acids

We report a general method for screening, in solution, the impact of deviations from canonical Watson-Crick composition on the thermodynamic stability of nucleic acid duplexes. We demonstrate how fluorescence resonance energy transfer (FRET) can be used to detect directly free energy differences between an initially formed “reference” duplex (usually a Watson-Crick duplex) and a related “test” duplex containing a lesion/alteration of interest (e.g., a mismatch, a modified, a deleted, or a bulged base, etc.). In one application, one titrates into a solution containing a fluorescently labeled, FRET-active, reference duplex, an unlabeled, single-stranded nucleic acid (test strand), which may or may not compete successfully to form a new duplex. When a new duplex forms by strand displacement, it will not exhibit FRET. The resultant titration curve (normalized fluorescence intensity vs. logarithm of test strand concentration) yields a value for the difference in stability (free energy) between the newly formed, test strand-containing duplex and the initial reference duplex. The use of competitive equilibria in this assay allows the measurement of equilibrium association constants that far exceed the magnitudes accessible by conventional titrimetric techniques. Additionally, because of the sensitivity of fluorescence, the method requires several orders of magnitude less material than most other solution methods. We discuss the advantages of this method for detecting and characterizing any modification that alters duplex stability, including, but not limited to, mutagenic lesions. We underscore the wide range of accessible free energy values that can be defined by this method, the applicability of the method in probing for a myriad of nucleic acid variations, such as single nucleotide polymorphisms, and the potential of the method for high throughput screening.

Randomised controlled trial of the READER method of critical appraisal in general practice

Objective: To evaluate the READER model for critical reading by comparing it with a free appraisal, and to explore what factors influence different components of the model.

Randomised controlled trial of laparoscopic versus open mesh repair for inguinal hernia: outcome and cost

Objective: To compare tension-free open mesh hernioplasty under local anaesthetic with transabdominal preperitoneal laparoscopic hernia repair under general anaesthetic.

On a psychophysical transformed-rule up and down method converging on a 75% level of correct responses

Tranformed-rule up and down psychophysical methods have gained great popularity, mainly because they combine criterion-free responses with an adaptive procedure allowing rapid determination of an average stimulus threshold at various criterion levels of correct responses. The statistical theory underlying the methods now in routine use is based on sets of consecutive responses with assumed constant probabilities of occurrence. The response rules requiring consecutive responses prevent the possibility of using the most desirable response criterion, that of 75% correct responses. The earliest transformed-rule up and down method, whose rules included nonconsecutive responses, did not contain this limitation but failed to become generally accepted, lacking a published theoretical foundation. Such a foundation is provided in this article and is validated empirically with the help of experiments on human subjects and a computer simulation. In addition to allowing the criterion of 75% correct responses, the method is more efficient than the methods excluding nonconsecutive responses in their rules.

Single photon emission computerized tomography imaging of amphetamine-induced dopamine release in drug-free schizophrenic subjects.

The dopamine hypothesis of schizophrenia proposes that hyperactivity of dopaminergic transmission is associated with this illness, but direct observation of abnormalities of dopamine function in schizophrenia has remained elusive. We used a newly developed single photon emission computerized tomography method to measure amphetamine-induced dopamine release in the striatum of fifteen patients with schizophrenia and fifteen healthy controls. Amphetamine-induced dopamine release was estimated by the amphetamine-induced reduction in dopamine D2 receptor availability, measured as the binding potential of the specific D2 receptor radiotracer [123I] (S)-(-)-3-iodo-2-hydroxy-6-methoxy-N-[(1-ethyl-2-pyrrolidinyl) methyl]benzamide ([123I]IBZM). The amphetamine-induced decrease in [123I]IBZM binding potential was significantly greater in the schizophrenic group (-19.5 +/- 4.1%) compared with the control group (-7.6 +/- 2.1%). In the schizophrenic group, elevated amphetamine effect on [123I]IBZM binding potential was associated with emergence or worsening of positive psychotic symptoms. This result suggests that psychotic symptoms elicited in this experimental setting in schizophrenic patients are associated with exaggerated stimulation of dopaminergic transmission. Such an observation would be compatible with an abnormal responsiveness of dopaminergic neurons in schizophrenia.

A gain-of-function of an amyotrophic lateral sclerosis-associated Cu,Zn-superoxide dismutase mutant: An enhancement of free radical formation due to a decrease in Km for hydrogen peroxide.

Cu,Zn-superoxide dismutase (SOD) is known to be a locus of mutation in familial amyotrophic lateral sclerosis (FALS). Transgenic mice that express a mutant Cu,Zn-SOD, Gly-93--> Ala (G93A), have been shown to develop amyotrophic lateral sclerosis (ALS) symptoms. We cloned the FALS mutant, G93A, and wild-type cDNA of human Cu,Zn-SOD, overexpressed them in Sf9 insect cells, purified the proteins, and studied their enzymic activities for catalyzing the dismutation of superoxide anions and the generation of free radicals with H2O2 as substrate. Our results showed that both enzymes contain one copper ion per subunit and have identical dismutation activity. However, the free radical-generating function of the G93A mutant, as measured by the spin trapping method, is enhanced relative to that of the wild-type enzyme, particularly at lower H2O2 concentrations. This is due to a small, but reproducible, decrease in the value of Km for H2O2 for the G93A mutant, while the kcat is identical for both enzymes. Thus, the ALS symptoms observed in G93A transgenic mice are not caused by the reduction of Cu,Zn-SOD activity with the mutant enzyme; rather, it is induced by a gain-of-function, an enhancement of the free radical-generating function. This is consistent with the x-ray crystallographic studies showing the active channel of the FALS mutant is slightly larger than that of the wild-type enzyme; thus, it is more accessible to H2O2. This gain-of-function, in part, may provide an explanation for the association between ALS and Cu,Zn-SOD mutants.

Thermodynamic parameters for the helix-coil transition of oligopeptides: molecular dynamics simulation with the peptide growth method.

The helix-coil transition equilibrium of polypeptides in aqueous solution was studied by molecular dynamics simulation. The peptide growth simulation method was introduced to generate dynamic models of polypeptide chains in a statistical (random) coil or an alpha-helical conformation. The key element of this method is to build up a polypeptide chain during the course of a molecular transformation simulation, successively adding whole amino acid residues to the chain in a predefined conformation state (e.g., alpha-helical or statistical coil). Thus, oligopeptides of the same length and composition, but having different conformations, can be incrementally grown from a common precursor, and their relative conformational free energies can be calculated as the difference between the free energies for growing the individual peptides. This affords a straightforward calculation of the Zimm-Bragg sigma and s parameters for helix initiation and helix growth. The calculated sigma and s parameters for the polyalanine alpha-helix are in reasonable agreement with the experimental measurements. The peptide growth simulation method is an effective way to study quantitatively the thermodynamics of local protein folding.