Synthetic scope and DFT analysis of the chiral binap-gold(I) complex-catalyzed 1,3-dipolar cycloaddition of azlactones with alkenes

he 1,3-dipolar cycloaddition between glycine-derived azlactones with maleimides is efficiently catalyzed by the dimeric chiral complex [(S-a)-Binap.AuTFA](2). The alanine-derived oxazolone only reacts with tert-butyl acrylate giving anomalous regiochemistry, which is explained and supported by Natural Resonance Theory and Nucleus Independent Chemical Shifts calculations. The origin of the high enantiodiscrimination observed with maleimides and tert-butyl acrylate is analyzed using DFT computed at M06/Lanl2dz//ONIOM(b3lyp/Lanl2dz:UFF) level. Several applications of these cycloadducts in the synthesis of new proline derivatives with a 2,5-trans-arrangement and in the preparation of complex fused polycyclic molecules are described.

Image-based delineation and classification of built heritage masonry

[EN]Fundación Zain is developing new built heritage assessment protocols. The goal is to objectivize and standardize the analysis and decision process that leads to determining the degree of protection of built heritage in the Basque Country. The ultimate step in this objectivization and standardization effort will be the development of an information and communication technology (ICT) tool for the assessment of built heritage. This paper presents the ground work carried out to make this tool possible: the automatic, image-based delineation of stone masonry. This is a necessary first step in the development of the tool, as the built heritage that will be assessed consists of stone masonry construction, and many of the features analyzed can be characterized according to the geometry and arrangement of the stones. Much of the assessment is carried out through visual inspection. Thus, this process will be automated by applying image processing on digital images of the elements under inspection. The principal contribution of this paper is the automatic delineation the framework proposed. The other contribution is the performance evaluation of this delineation as the input to a classifier for a geometrically characterized feature of a built heritage object. The element chosen to perform this evaluation is the stone arrangement of masonry walls. The validity of the proposed framework is assessed on real images of masonry walls.

Numerical simulation of a single fluid particle rising in non-Newtonian fluids

In this work, a level set method is developed for simulating the motion of a fluid particle rising in non-Newtonian fluids described by generalized Newtonian as well as viscoelastic model fluids. As the shear-thinning model we use a Carreau-Yasuda model, and the viscoelastic effect can be modeled with Oldroyd-B constitutive equations. The control volume formulation with the SIMPLEC algorithm incorporated is used to solve the governing equations on a staggered Eulerian grid. The level set method is implemented to compute the motion of a bubble in a Newtonian fluid as one of typical examples for validation, and the computational results are in good agreement with the reported experimental data．The level set method is also applied for simulating a Newtonian drop rising in Carreau-Yasuda and Oldroyd-B fluids．Numerical results including noticeably negative wake behind the drop and viscosity field are obtained, and compare satisfactorily with the known literature data.

A Hybrid Scheme Based on Finite Element/Volume Methods for Two Immiscible Fluid Flows

We have successfully extended our implicit hybrid finite element/volume (FE/FV) solver to flows involving two immiscible fluids. The solver is based on the segregated pressure correction or projection method on staggered unstructured hybrid meshes. An intermediate velocity field is first obtained by solving the momentum equations with the matrix-free implicit cell-centered FV method. The pressure Poisson equation is solved by the node-based Galerkin FE method for an auxiliary variable. The auxiliary variable is used to update the velocity field and the pressure field. The pressure field is carefully updated by taking into account the velocity divergence field. This updating strategy can be rigorously proven to be able to eliminate the unphysical pressure boundary layer and is crucial for the correct temporal convergence rate. Our current staggered-mesh scheme is distinct from other conventional ones in that we store the velocity components at cell centers and the auxiliary variable at vertices. The fluid interface is captured by solving an advection equation for the volume fraction of one of the fluids. The same matrix-free FV method, as the one used for momentum equations, is used to solve the advection equation. We will focus on the interface sharpening strategy to minimize the smearing of the interface over time. We have developed and implemented a global mass conservation algorithm that enforces the conservation of the mass for each fluid.

La ley del suelo del País Vasco : un paso más hacia la protección del suelo rural

[ES]La Ley del suelo del País Vasco del 2007 nace con el objeto de favorecer el acceso a una vivienda digna. Sin embargo, en la medida en que apuesta por frenar la especulación y la sostenibilidad del medio legisla sobre el tratamiento que se le ha de aportar al suelo no urbanizable. En este caso, no altera sustancialmente la regulación del suelo rural pero sí incorpora nuevas obligaciones dirigidas a frenar la intensidad de la urbanización en este suelo. Se regula la construcción de nueva vivienda, el desarrollo urbanístico de núcleos y barrios rurales y se obliga a profundizar en la calificación del suelo no urbanizable. La aplicación de los nuevos contenidos quedan en manos de los municipios e instituciones sectoriales y los primeros resultados parecen denotar un cambio de tendencia en municipios que han observado la pérdida de calidad paisajística del medio rural, la creciente especulación y la desagrarización de este entorno.

A Wide Band Strong Acoustic Absorption in a Locally Network Anechoic Coating

Composite materials with interpenetrating network structures usually exhibit unexpected merit due to the cooperative interaction. Locally resonant phononic crystals (LRPC) exhibit excellent sound attenuation performance based on a periodical arrangement of sound wave scatters. Inspired by the interpenetrating network structure and the LRPC concept, we develop a locally network anechoic coating (LNAC) that can achieve a wide band of underwater strong acoustic absorption. The experimental results show that the LNAC possesses an excellent underwater acoustic absorbing capacity in a wide frequency range. Moreover, in order to investigate the impact of the interpenetrating network structure, we fabricate a faultage structure sample and the network is disconnected by hard polyurethane (PU). The experimental comparison between the LNAC and the faultage structure sample shows that the interpenetrating network structure of the LNAC plays an important role in achieving a wide band strong acoustic absorption.

Molecular genetics of the Drosophila eyes absent gene

The Drosophila compound eye has provided a genetic approach to understanding the specification of cell fates during differentiation. The eye is made up of some 750 repeated units or ommatidia, arranged in a lattice. The cellular composition of each ommatidium is identical. The arrangement of the lattice and the specification of cell fates in each ommatidium are thought to occur in development through cellular interactions with the local environment. Many mutations have been studied that disrupt the proper patterning and cell fating in the eye. The eyes absent (eya) mutation, the subject of this thesis, was chosen because of its eyeless phenotype. In eya mutants, eye progenitor cells undergo programmed cell death before the onset of patterning has occurred. The molecular genetic analysis of the gene is presented.

The eye arises from the larval eye-antennal imaginal disc. During the third larval instar, a wave of differentiation progresses across the disc, marked by a furrow. Anterior to the furrow, proliferating cells are found in apparent disarray. Posterior to the furrow, clusters of differentiating cells can be discerned, that correspond to the ommatidia of the adult eye. Analysis of an allelic series of eya mutants in comparison to wild type revealed the presence of a selection point: a wave of programmed cell death that normally precedes the furrow. In eya mutants, an excessive number of eye progenitor cells die at this selection point, suggesting the eya gene influences the distribution of cells between fates of death and differentiation.

In addition to its role in the eye, the eya gene has an embryonic function. The eye function is autonomous to the eye progenitor cells. Molecular maps of the eye and embryonic phenotypes are different. Therefore, the function of eya in the eye can be treated independently of the embryonic function. Cloning of the gene reveals two cDNA's that are identical except for the use of an alternatively-spliced 5' exon. The predicted protein products differ only at the N-termini. Sequence analysis shows these two proteins to be the first of their kind to be isolated. Trangenic studies using the two cDNA's show that either gene product is able to rescue the eye phenotype of eya mutants.

The eya gene exhibits interallelic complementation. This interaction is an example of an "allelic position effect": an interaction that depends on the relative position in the genome of the two alleles, which is thought to be mediated by chromosomal pairing. The interaction at eya is essentially identical to a phenomenon known as transvection, which is an allelic position effect that is sensitive to certain kinds of chromosomal rearrangements. A current model for the mechanism of transvection is the trans action of gene regulatory regions. The eya locus is particularly well suited for the study of transvection because the mutant phenotypes can be quantified by scoring the size of the eye.

The molecular genetic analysis of eya provides a system for uncovering mechanisms underlying differentiation, developmentally regulated programmed cell death, and gene regulation.

Parylene-C as a new piezoelectric material

The goal of this thesis is to develop a proper microelectromechanical systems (MEMS) process to manufacture piezoelectric Parylene-C (PA-C), which is famous for its chemical inertness, mechanical and thermal properties and electrical insulation. Furthermore, piezoelectric PA-C is used to build miniature, inexpensive, non-biased piezoelectric microphones.

These piezoelectric PA-C MEMS microphones are to be used in any application where a conventional piezoelectric and electret microphone can be used, such as in cell phones and hearing aids. However, they have the advantage of a simplified fabrication process compared with existing technology. In addition, as a piezoelectric polymer, PA-C has varieties of applications due to its low dielectric constant, low elastic stiffness, low density, high voltage sensitivity, high temperature stability and low acoustic and mechanical impedance. Furthermore, PA-C is an FDA approved biocompatible material and is able to maintain operate at a high temperature.

To accomplish piezoelectric PA-C, a MEMS-compatible poling technology has been developed. The PA-C film is poled by applying electrical field during heating. The piezoelectric coefficient, -3.75pC/N, is obtained without film stretching.

The millimeter-scale piezoelectric PA-C microphone is fabricated with an in-plane spiral arrangement of two electrodes. The dynamic range is from less than 30 dB to above 110 dB SPL (referenced 20 µPa) and the open-circuit sensitivities are from 0.001 – 0.11 mV/Pa over a frequency range of 1 - 10 kHz. The total harmonic distortion of the device is less than 20% at 110 dB SPL and 1 kHz.

Contribution of women to fisheries development in Kainji Lake basin

The study was carried to examine the contribution of women to fisheries development in the Kainji basin. The sample was drawn in some of the major fishing villages in the sub strata of the basin. A total of 120 respondents were used. The findings revealed that women were involved in fisheries activities most especially in the processing and marketing aspects. Many of the respondents happened to be wives of the fishermen. Few bought fishing equipment with a special arrangement for the supply of fish while some buy from fishermen. This revealed the willingness of the women to be empowered in the economic activities in the area to meet some basic household. Major constrains to the women in this area were the scarcity of fish, no support from the government or private agencies. Recommendations were made on how to enhance women participation in fisheries development

Report of the Inter-American Tropical Tuna Commission for the year 1963

ENGLISH: The Inter-American Tropical Tuna Commission was created by a Convention between the Republic of Costa Rica and the United States of America. The Convention came into force in 1950. One of the provisions of the Convention was that other governments whose nationals participate in the fisheries covered by the Convention could adhere if they so desired and if the existing members agreed. Under this arrangement, the Republic of Panama adhered to the COl1vention in 1953. The Republic of Ecuador adhered in 1961. The Senate of the Republic of Mexico approved adherence in 1963; and the Republic of Colombia has indicated her desire to adhere. Full members during 1963 were Costa Rica, Ecuador, Panama, and the United States. SPANISH: La Comisión Interamericana del Atún Tropical fue creada en virtud de una Convención entre la República de Costa Rica y los Estados Unidos de América. La Convención entró en vigencia en 1950. Una de las estipulaciones de la Convención, permite a los gobiernos de otros países cuyos habitantes participen en las pesquerías a que dicha Convención se refiere, adherirse a ella si así lo desean y si los Gobiernos Miembros están de acuerdo. Acogiéndose a esa estipulación, la República de Panamá se adhirió a la Convención en 1953. La República del Ecuador se adhirió en 1961. El Senado de la República de México aprobó la adhesión en 1963; y la República de Colombia ha manifestado su deseo de adherirse. Durante el año de 1963 han sido miembros Costa Rica, Ecuador, Panamá y los Estados Unidos. (PDF contains 89 pages.)

Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

Interplay of martensitic phase transformation and plastic slip in polycrystals

Inspired by key experimental and analytical results regarding Shape Memory Alloys (SMAs), we propose a modelling framework to explore the interplay between martensitic phase transformations and plastic slip in polycrystalline materials, with an eye towards computational efficiency. The resulting framework uses a convexified potential for the internal energy density to capture the stored energy associated with transformation at the meso-scale, and introduces kinetic potentials to govern the evolution of transformation and plastic slip. The framework is novel in the way it treats plasticity on par with transformation.

We implement the framework in the setting of anti-plane shear, using a staggered implicit/explict update: we first use a Fast-Fourier Transform (FFT) solver based on an Augmented Lagrangian formulation to implicitly solve for the full-field displacements of a simulated polycrystal, then explicitly update the volume fraction of martensite and plastic slip using their respective stick-slip type kinetic laws. We observe that, even in this simple setting with an idealized material comprising four martensitic variants and four slip systems, the model recovers a rich variety of SMA type behaviors. We use this model to gain insight into the isothermal behavior of stress-stabilized martensite, looking at the effects of the relative plastic yield strength, the memory of deformation history under non-proportional loading, and several others.

We extend the framework to the generalized 3-D setting, for which the convexified potential is a lower bound on the actual internal energy, and show that the fully implicit discrete time formulation of the framework is governed by a variational principle for mechanical equilibrium. We further propose an extension of the method to finite deformations via an exponential mapping. We implement the generalized framework using an existing Optimal Transport Mesh-free (OTM) solver. We then model the $\alpha$--$\gamma$ and $\alpha$--$\varepsilon$ transformations in pure iron, with an initial attempt in the latter to account for twinning in the parent phase. We demonstrate the scalability of the framework to large scale computing by simulating Taylor impact experiments, observing nearly linear (ideal) speed-up through 256 MPI tasks. Finally, we present preliminary results of a simulated Split-Hopkinson Pressure Bar (SHPB) experiment using the $\alpha$--$\varepsilon$ model.

Controlling wave propagation through nonlinear engineered granular systems

We study the fundamental dynamic behavior of a special class of ordered granular systems in order to design new, structured materials with unique physical properties. The dynamic properties of granular systems are dictated by the nonlinear, Hertzian, potential in compression and zero tensile strength resulting from the discrete material structure. Engineering the underlying particle arrangement of granular systems allows for unique dynamic properties, not observed in natural, disordered granular media. While extensive studies on 1D granular crystals have suggested their usefulness for a variety of engineering applications, considerably less attention has been given to higher-dimensional systems. The extension of these studies in higher dimensions could enable the discovery of richer physical phenomena not possible in 1D, such as spatial redirection and anisotropic energy trapping. We present experiments, numerical simulation (based on a discrete particle model), and in some cases theoretical predictions for several engineered granular systems, studying the effects of particle arrangement on the highly nonlinear transient wave propagation to develop means for controlling the wave propagation pathways. The first component of this thesis studies the stress wave propagation resulting from a localized impulsive loading for three different 2D particle lattice structures: square, centered square, and hexagonal granular crystals. By varying the lattice structure, we observe a wide range of properties for the propagating stress waves: quasi-1D solitary wave propagation, fully 2D wave propagation with tunable wave front shapes, and 2D pulsed wave propagation. Additionally the effects of weak disorder, inevitably present in real granular systems, are investigated. The second half of this thesis studies the solitary wave propagation through 2D and 3D ordered networks of granular chains, reducing the effective density compared to granular crystals by selectively placing wave guiding chains to control the acoustic wave transmission. The rapid wave front amplitude decay exhibited by these granular networks makes them highly attractive for impact mitigation applications. The agreement between experiments, numerical simulations, and applicable theoretical predictions validates the wave guiding capabilities of these engineered granular crystals and networks and opens a wide range of possibilities for the realization of increasingly complex granular material design.

Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

Estudio de optimización para la implantación de procesos productivos con indicadores de sostenibilidad

[ES]Los constantes cambios tanto en la demanda como en la oferta y la competencia de mercado han incrementado el interés en la optimización de nuestros recursos. Son muchas las empresas que se ven sometidas a un continuo cambio tanto en el tipo de producto como en la cantidad a fabricar, para ello es necesario tener una distribución flexible y capaz de sobrevivir al paso del tiempo. El objetivo de este proyecto es obtener una lista de control mediante la que se pueda analizar la sostenibilidad de una implantación. La lista está formada por 23 indicadores mediante los cuales se logra simplificar y reflejar los aspectos más relevantes de una implantación, permitiendo la obtención de información sobre los puntos débiles y fuertes de la distribución. A través de la evaluación de los resultados, se pueden examinar distintas opciones para reducir los problemas y optimizar el proceso. Además, con el objeto de verificar la fiabilidad del planteamiento se incluye un ejemplo de aplicación sobre una implantación real y su respectivo análisis.