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 Nconditions. We present the evolution of SMS method, 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.

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.

A panel method free-wake code for aeroelastic rotor predictions

A panel method free-wake model to analyse the rotor flapping is presented. The aerodynamic model consists of a panel method, which takes into account the three-dimensional rotor geometry, and a free-wake model, to determine the wake shape. The main features of the model are the wake division into a near-wake sheet and a far wake represented by a single tip vortex, and the modification of the panel method formulation to take into account this particular wake description. The blades are considered rigid with a flap degree of freedom. The problem solution is approached using a relaxation method, which enforces periodic boundary conditions. Finally, several code validations against helicopter and wind turbine experimental data are performed, showing good agreement

Numerical and experimental study of appendages in racing yachts and their influence on the free surface

Las prestaciones de un velero de regatas se estiman por medio de los Programas de Predicción de Velocidad (VPP) que incluyen las características de estabilidad y modelos aero e hidrodinámico del barco. Por esta razón, es importante tener una evaluación adecuada de las fuerzas en apéndices y de su variación en diferentes condiciones de navegación, escora y deriva. Además, para el cálculo de las fuerzas en los apéndices es importante conocer sus características hidrodinámicas cuando trabajan conjuntamente en un campo fluido fuertemente modificado por la carena. Por esta razón, se han utilizado una serie de ensayos realizados en el Canal de Ensayos de la ETSIN con el objetivo de validar códigos numéricos que permiten una evaluación más rápida y focalizada en los distintos fenómenos que se producen. Dichos ensayos se han realizado de forma que pudiera medirse independientemente las fuerzas hidrodinámicas en cada apéndice, lo que permitirá evaluar el reparto de fuerzas en diferentes condiciones de navegación para poder profundizar en las interacciones entre carena, quilla y timón. Las técnicas numéricas permiten capturar detalles que difícilmente se pueden visualizar en ensayos experimentales. En este sentido, se han probado las últimas técnicas utilizadas en los últimos workshops y se ha enfocado el estudio a un nuevo método con el objetivo de mostrar una metodologia más rápida que pueda servir a la industria para este tipo de aproximación al problema. ABSTRACT The performances of a racing sailboat are estimated by means of the speed prediction programs (VPP), which include the ship stability characteristics and the aero and hydrodynamic models. For this reason, it is important to have an adequate evaluation of the forces in appendices and its variation in different sailing conditions, heel and leeway Moreover, for the analysis of the forces in the appendices, it is important to know their hydrodynamic characteristics when they work together in a fluid field strongly modified by the canoe body. For this reason, several tests have been done in the ETSIN towing tank with the aim to validate numeric codes that allowing faster analysis and they permit to focus on the different phenomena that occur there. Such tests have been done in a way that the hydrodynamic forces in each appendage could be measured independently allowing assessing the distribution of forces in different sailing conditions to be able to deepen the interactions between the canoe body, the keel and the rudder. Numerical techniques allow capturing details that can hardly be displayed in experimental tests. In this sense, the latest techniques used in the recent workshops have been reviewed and the study has been focused to propose a new model with the aim to show a new faster methodology which serves the industry for this type of approach to the problem.

Rapid treadmilling of brain microtubules free of microtubule-associated proteins in vitro and its suppression by tau

We have determined the treadmilling rate of brain microtubules (MTs) free of MT-associated proteins (MAPs) at polymer mass steady state in vitro by using [3H]GTP-exchange. We developed buffer conditions that suppressed dynamic instability behavior by ≈10-fold to minimize the contribution of dynamic instability to total tubulin-GTP exchange. The MTs treadmilled rapidly under the suppressed dynamic instability conditions, at a minimum rate of 0.2 μm/min. Thus, rapid treadmilling is an intrinsic property of MAP-free MTs. Further, we show that tau, an axonal stabilizing MAP involved in Alzheimer’s disease, strongly suppresses the treadmilling rate. These results indicate that tau’s function in axons might involve suppression of axonal MT treadmilling. We describe mathematically how treadmilling and dynamic instability are mechanistically distinct MT behaviors. Finally, we present a model that explains how small changes in the critical tubulin subunit concentration at MT minus ends, caused by intrinsic differences in rate constants or regulatory proteins, could produce large changes in the treadmilling rate.

Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7

We investigated the relative free energies of hapten binding to the germ line and mature forms of the 48G7 antibody Fab fragments by applying a continuum model to structures sampled from molecular dynamics simulations in explicit solvent. Reasonable absolute and very good relative free energies were obtained. As a result of nine somatic mutations that do not contact the hapten, the affinity-matured antibody binds the hapten >104 tighter than the germ line antibody. Energetic analysis reveals that van der Waals interactions and nonpolar contributions to solvation are similar and drive the formations of both the germ line and mature antibody–hapten complexes. Affinity maturation of the 48G7 antibody therefore appears to occur through reorganization of the combining site geometry in a manner that optimizes the balance of gaining favorable electrostatic interactions with the hapten and losing those with solvent during the binding process. As reflected by lower rms fluctuations in the antibody–hapten complex, the mature complex undergoes more restricted fluctuations than the germ line complex. The dramatically increased affinity of the 48G7 antibody over its germ line precursor is thus made possible by electrostatic optimization.

Identification of protein–protein interfaces by decreased amide proton solvent accessibility

Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry was used to identify peptic fragments from protein complexes that retained deuterium under hydrogen exchange conditions due to decreased solvent accessibility at the interface of the complex. Short deuteration times allowed preferential labeling of rapidly exchanging surface amides so that primarily solvent accessibility changes and not conformational changes were detected. A single mass spectrum of the peptic digest mixture was analyzed to determine the deuterium content of all proteolytic fragments of the protein. The protein–protein interface was reliably indicated by those peptides that retained more deuterons in the complex compared with control experiments in which only one protein was present. The method was used to identify the kinase inhibitor [PKI(5–24)] and ATP-binding sites in the cyclic-AMP-dependent protein kinase. Three overlapping peptides identified the ATP-binding site, three overlapping peptides identified the glycine-rich loop, and two peptides identified the PKI(5–24)-binding site. A complex of unknown structure also was analyzed, human α-thrombin bound to an 83-aa fragment of human thrombomodulin [TMEGF(4–5)]. Five peptides from thrombin showed significantly decreased solvent accessibility in the complex. Three peptides identified the anion-binding exosite I, confirming ligand competition experiments. Two peptides identified a new region of thrombin near the active site providing a potential mechanism of how thrombomodulin alters thrombin substrate specificity.

A meanfield approach to the thermodynamics of a protein-solvent system with application to the oligomerization of the tumor suppressor p53

The thermodynamic stability and oligomerization status of the tumor suppressor p53 tetramerization domain have been studied experimentally and theoretically. A series of hydrophilic mutations at Met-340 and Leu-344 of human p53 were designed to disrupt the hydrophobic dimer–dimer interface of the tetrameric oligomerization domain of p53 (residues 325–355). Meanfield calculations of the free energy of the solvated mutants as a function of interdimer distance were compared with experimental data on the thermal stability and oligomeric state (tetramer, dimer, or equilibrium mixture of both) of each mutant. The calculations predicted a decreasing stability and oligomeric state for the following amino acids at residue 340: Met (tetramer) > Ser Asp, His, Gln, > Glu, Lys (dimer), whereas the experimental results showed the following order: Met (tetramer) > Ser > Gln > His, Lys > Asp, Glu (dimers). For residue 344, the calculated trend was Leu (tetramer) > Ala > Arg, Gln, Lys (dimer), and the experimental trend was Leu (tetramer) > Ala, Arg, Gln, Lys (dimer). The discrepancy for the lysine side chain at residue 340 is attributed to the dual nature of lysine, both hydrophobic and charged. The incorrect prediction of stability of the mutant with Asp at residue 340 is attributed to the fact that within the meanfield approach, we use the wild-type backbone configuration for all mutants, but low melting temperatures suggest a softening of the α-helices at the dimer–dimer interface. Overall, this initial application of meanfield theory toward a protein-solvent system is encouraging for the application of the theoretical model to more complex systems.

Genetic recombination of poliovirus in a cell-free system

Genetic recombination of plus-strand RNA viruses is an important process for promoting genetic variation. By using genetically marked poliovirus RNAs, we have demonstrated that genetic recombination can occur in a cell-free system that generates infective virus from added poliovirus RNA. Recombinant polioviruses were isolated, and the region of crossing over was roughly mapped. Recombinants could be isolated even under conditions where the yield of viruses from one of the parental RNAs was depressed to levels comparable to or less than the yield of recombinant viruses, an observation suggesting that only one of the recombining RNAs needs to be replication-competent. The generation of poliovirus recombinants in a cell-free system offers new possibilities for studying recombination and evolution of RNA viruses.

Destabilization of Ca2+-free gelsolin may not be responsible for proteolysis in Familial Amyloidosis of Finnish Type

Mutations at position 187 in secreted gelsolin enable aberrant proteolysis at the 172–173 and 243–244 amide bonds, affording the 71-residue amyloidogenic peptide deposited in Familial Amyloidosis of Finnish Type (FAF). Thermodynamic comparisons of two different domain 2 constructs were carried out to study possible effects of the mutations on proteolytic susceptibility. In the construct we consider to be most representative of domain 2 in the context of the full-length protein (134–266), the D187N FAF variant is slightly destabilized relative to wild type (WT) under the conditions of urea denaturation, but exhibits a Tm identical to WT. The D187Y variant is less stable to intermediate urea concentrations and exhibits a Tm that is estimated to be ≈5°C lower than WT (pH 7.4, Ca2+-free). Although the thermodynamic data indicate that the FAF mutations may slightly destabilize domain 2, these changes are probably not sufficient to shift the native to denatured state equilibrium enough to enable the proteolysis leading to FAF. Biophysical data indicate that these two FAF variants may have different native state structures and possibly different pathways of amyloidosis.

Thermal unfolding of human high-density apolipoprotein A-1: implications for a lipid-free molten globular state.

Apolipoprotein A-1 (apoA-1) in complex with high-density lipoprotein is critically involved in the transport and metabolism of cholesterol and in the pathogenesis of atherosclerosis. We reexamined the thermal unfolding of lipid-free apoA-1 in low-salt solution at pH approximately 7, by using differential scanning calorimetry and circular dichroism. At protein concentrations <5 mg/ml, thermal unfolding of apoA-1 is resolved as an extended peak (25 degrees C-90 degrees C) that can be largely accounted for by a single reversible non-two-state transition with midpoint Tm 57 +/- 1 degree C, calorimetric enthalpy deltaH(Tm)= 200 +/- 20 kcal/mol (1 kcal = 4.18 kJ), van't Hoff enthalpy deltaHv(Tm) approximately 32.5 kcal/mol, and cooperativity deltaHv(Tm)/deltaH(Tm) approximately 0.16. The enthalpy deltaH(Tm) can be accounted for by melting of the alpha-helical structure that is inferred by CD to constitute approximately 60% of apoA-1 amino acids. Farand near-UV CD spectra reveal noncoincident melting of the secondary and tertiary structural elements and indicate a well-defined secondary structure but a largely melted tertiary structure for apoA-1 at approximately 37 degrees C and pH 7. This suggests a molten globular-like state for lipid-free apoA-1 under near-physiological conditions. Our results suggest that in vivo lipid binding by apoA-1 may be mediated via the molten globular apolipoprotein state in plasma.

Long-term in vivo expression of the human glucocerebrosidase gene in nonhuman primates after CD34+ hematopoietic cell transduction with cell-free retroviral vector preparations.

Successful gene transfer into stem cells would provide a potentially useful therapeutic modality for treatment of inherited and acquired disorders affecting hematopoietic tissues. Coculture of primate bone marrow cells with retroviral producer cells, autologous stroma, or an engineered stromal cell line expressing human stem cell factor has resulted in a low efficiency of gene transfer as reflected by the presence of 0.1-5% of genetically modified cells in the blood of reconstituted animals. Our experiments in a nonhuman primate model were designed to explore various transduction protocols that did not involve coculture in an effort to define clinically useful conditions and to enhance transduction efficiency of repopulating cells. We report the presence of genetically modified cells at levels ranging from 0.1% (granulocytes) to 14% (B lymphocytes) more than 1 year following reconstitution of myeloablated animals with CD34+ immunoselected cells transduced in suspension culture with cytokines for 4 days with a retrovirus containing the glucocerebrosidase gene. A period of prestimulation for 7 days in the presence of autologous stroma separated from the CD34+ cells by a porous membrane did not appear to enhance transduction efficiency. Infusion of transduced CD34+ cells into animals without myeloablation resulted in only transient appearance of genetically modified cells in peripheral blood. Our results document that retroviral transduction of primate repopulating cells can be achieved without coculture with stroma or producer cells and that the proportion of genetically modified cells may be highest in the B-lymphoid lineage under the given transduction conditions.

Evaluation of hectorites, synthesized in different conditions, as soot combustion catalysts after impregnation with copper

Two microporous hectorites were prepared by conventional and microwave heating, and a delaminated mesoporous hectorite by an ultrasound-assisted synthesis. These three hectorites were impregnated with copper. The characterization techniques used were XRD, N2 adsorption, TEM and H2 reduction after selective surface copper oxidation by N2O (to determine copper dispersion). The catalytic activity for soot combustion of the copper-free and the copper-containing hectorites was tested under a gas mixture of 500 ppm NOx/5% O2/N2 (and 5% O2/N2 in some cases), evaluating their stability through three consecutive soot combustion experiments. The delaminated hectorite showed the highest surface area (353 m2/g) allowing the highest dispersion of copper. This copper-containing catalyst was the most active for soot combustion among those prepared and tested in this study. We have also concluded that the Cu/hectorite-catalyzed soot combustion mechanism is based on the activation of the O2 molecule and not on the NO2-assisted soot combustion.

In Search of a Feasible EU-Mercosul Free Trade Agreement. CEPS Working Document No. 378, 25 February 2013

This paper aims at identifying ways to pursue the EU–Mercosul negotiations leading to a free trade agreement (FTA). After reviewing their already long history, it outlines a basic framework, in goods, services and other themes, judged possible. The main point is that, given the prevailing conditions on both sides, an agreement to be signed within a reasonable time must be modest, i.e. along the described lines. It then clearly sets up the decisions confronting the negotiators: either to pursue the modest, feasible option or to terminate negotiations under the FTA heading. The latter, however, does not imply an end to the dialogue. Many actions and measures may be taken – which are easier to discuss and fix – that could pave the way for, in due time, a closer-to-ideal FTA to be considered again. These are the subjects of a last section.

Metal-free catalysts derived from lignin for efficient wet peroxide oxidation

In this work, a wheat and hemp lignin (Sarkanda, Granit S.A.) has been used as raw material for the development of metal-free activated carbons. These materials were tested in the catalytic wet peroxide oxidation (CWPO) of 4-nitrophenol (4-NP; 5 g L-1) during 24 h experiments conducted at relatively mild operating conditions (p = 1 atm, t = 50 °C, pH = 3, catalyst load = 2.5 g L-1 and [H2O2]0 = 17.8 g L-1). First, the lignin was carbonized under N2 atmosphere followed by the activation of the obtained non-porous carbon (LG) under air atmosphere at different temperatures (150 to 350 ºC), leading to the generation of significant porosity.