Numerical corrections to the strong coupling effective Polyakov-line action for finite T Yang-Mills theory

We consider a three-dimensional effective theory of Polyakov lines derived previously from lattice Yang-Mills theory and QCD by means of a resummed strong coupling expansion. The effective theory is useful for investigations of the phase structure, with a sign problem mild enough to allow simulations also at finite density. In this work we present a numerical method to determine improved values for the effective couplings directly from correlators of 4d Yang-Mills theory. For values of the gauge coupling up to the vicinity of the phase transition, the dominant short range effective coupling are well described by their corresponding strong coupling series. We provide numerical results also for the longer range interactions, Polyakov lines in higher representations as well as four-point interactions, and discuss the growing significance of non-local contributions as the lattice gets finer. Within this approach the critical Yang-Mills coupling β c is reproduced to better than one percent from a one-coupling effective theory on N τ = 4 lattices while up to five couplings are needed on N τ = 8 for the same accuracy.

Modeling immune functions of the mouse blood-cerebrospinal fluid barrier in vitro: primary rather than immortalized mouse choroid plexus epithelial cells are suited to study immune cell migration across this brain barrier.

BACKGROUND The blood-cerebrospinal fluid barrier (BCSFB) established by the choroid plexus (CP) epithelium has been recognized as a potential entry site of immune cells into the central nervous system during immunosurveillance and neuroinflammation. The location of the choroid plexus impedes in vivo analysis of immune cell trafficking across the BCSFB. Thus, research on cellular and molecular mechanisms of immune cell migration across the BCSFB is largely limited to in vitro models. In addition to forming contact-inhibited epithelial monolayers that express adhesion molecules, the optimal in vitro model must establish a tight permeability barrier as this influences immune cell diapedesis. METHODS We compared cell line models of the mouse BCSFB derived from the Immortomouse(®) and the ECPC4 line to primary mouse choroid plexus epithelial cell (pmCPEC) cultures for their ability to establish differentiated and tight in vitro models of the BCSFB. RESULTS We found that inducible cell line models established from the Immortomouse(®) or the ECPC4 tumor cell line did not express characteristic epithelial proteins such as cytokeratin and E-cadherin and failed to reproducibly establish contact-inhibited epithelial monolayers that formed a tight permeability barrier. In contrast, cultures of highly-purified pmCPECs expressed cytokeratin and displayed mature BCSFB characteristic junctional complexes as visualized by the junctional localization of E-cadherin, β-catenin and claudins-1, -2, -3 and -11. pmCPECs formed a tight barrier with low permeability and high electrical resistance. When grown in inverted filter cultures, pmCPECs were suitable to study T cell migration from the basolateral to the apical side of the BCSFB, thus correctly modelling in vivo migration of immune cells from the blood to the CSF. CONCLUSIONS Our study excludes inducible and tumor cell line mouse models as suitable to study immune functions of the BCSFB in vitro. Rather, we introduce here an in vitro inverted filter model of the primary mouse BCSFB suited to study the cellular and molecular mechanisms mediating immune cell migration across the BCSFB during immunosurveillance and neuroinflammation.

Modeling the sensitivity of precipitation oxygen isotopes to the Last Glacial Maximum boundary conditions: A study using Community Atmosphere Model (CAM3.0)

To understand the validity of d18O proxy records as indicators of past temperature change, a series of experiments was conducted using an atmospheric general circulation model fitted with water isotope tracers (Community Atmosphere Model version 3.0, IsoCAM). A pre-industrial simulation was performed as the control experiment, as well as a simulation with all the boundary conditions set to Last Glacial Maximum (LGM) values. Results from the pre-industrial and LGM simulations were compared to experiments in which the influence of individual boundary conditions (greenhouse gases, ice sheet albedo and topography, sea surface temperature (SST), and orbital parameters) were changed each at a time to assess their individual impact. The experiments were designed in order to analyze the spatial variations of the oxygen isotopic composition of precipitation (d18Oprecip) in response to individual climate factors. The change in topography (due to the change in land ice cover) played a significant role in reducing the surface temperature and d18Oprecip over North America. Exposed shelf areas and the ice sheet albedo reduced the Northern Hemisphere surface temperature and d18Oprecip further. A global mean cooling of 4.1 °C was simulated with combined LGM boundary conditions compared to the control simulation, which was in agreement with previous experiments using the fully coupled Community Climate System Model (CCSM3). Large reductions in d18Oprecip over the LGM ice sheets were strongly linked to the temperature decrease over them. The SST and ice sheet topography changes were responsible for most of the changes in the climate and hence the d18Oprecip distribution among the simulations.

Selectivity of diacylhydrazine insecticides to the predatory bug Orius laevigatus: In vivo and modeling/docking experiments

BACKGROUND: Knowledge of pesticide selectivity to natural enemies is necessary for a successful implementation of biological and chemical control methods in integrated pest management (IPM) programs. Diacylhydrazine (DAH)-based ecdysone agonists also known as molting-accelerating compounds (MACs) are considered a selective group of insecticides, and their compatibility with predatory Heteroptera, which are used as biological control agents, is known. However, their molecular mode of action has not been explored in beneficial insects such as Orius laevigatus (Fieber) (Hemiptera: Anthocoridae). RESULTS: In this project in vivo toxicity assays demonstrated that the DAH-based RH-5849, tebufenozide and methoxyfenozide have no toxic effect against O. laevigatus. The ligand-binding domain (LBD) of the ecdysone receptor (EcR) of O. laevigatus was sequenced and a homology protein model was constructed which confirmed a cavity structure with 12 ?-helixes, harboring the natural insect molting hormone 20-hydroxyecdysone. However, docking studies showed that a steric clash occurred for the DAH-based insecticides due to a restricted extent of the ligand-binding cavity of the EcR of O. laevigatus. CONCLUSIONS: The insect toxicity assays demonstrated that MACs are selective for O. laevigatus. The modeling/docking experiments are indications that these pesticides do not bind with the LBD-EcR of O. laevigatus and support that they show no biological effects in the predatory bug. These data help in explaining the compatible use of MACs together with predatory bugs in IPM programs. Keywords: Orius laevigatus, selectivity, diacylhydrazine insecticides, ecdysone receptor, homology modelling, docking studies.

Damage assessment on building structures subjected to the recent near-fault earthquake in Lorca (Spain)

The city of Lorca (Spain) was hit on May 11th 2011 by two consecutive earthquakes with 4.6 and 5.2 Mw respectively, causing casualties and important damage in buildings. Lorca is located in the south-east region of Spain and settled on the trace of the Murcia-Totana-Lorca fault. Although the magnitudes of these ground motions were not severe, the damage observed was considerable over a great amount of buildings. More than 300 of them have been demolished and many others are being retrofitted. This paper reports a field study on the damage caused by these earthquakes. The observed damage is related with the structural typology. Further, prototypes of the damaged buildings are idealized with nonlinear numerical models and their seismic behavior and proneness to damage concentration is further investigated through dynamic response analyses.

Mathematical and Numerical Modeling in Maritime Geomechanics

A theoretical and numerical framework to model the foundation of marine offshore structures is presented. The theoretical model is composed by a system of partial differential equations describing coupling between seabed solid skeleton and pore fluids (water, air, oil,…) combined with a system of ordinary differential equations describing the specific constitutive relation of the seabed soil skeleton. Once the theoretical model is described, the finite element numerical procedure to achieve an approximate solution of the governing equations is outlined. In order to validate the proposed theoretical and numerical framework the seaward tilt mechanism induced by the action of breaking waves over a vertical breakwater is numerically reproduced. The results numerically attained are in agreement with the main conclusions drawn from the literature associated with this failure mechanism

A robust numerical framework to the analysis of material failure of fibre reinforced soft tissue

In this work, robustness and stability of continuum damage models applied to material failure in soft tissues are addressed. In the implicit damage models equipped with softening, the presence of negative eigenvalues in the tangent elemental matrix degrades the condition number of the global matrix, leading to a reduction of the computational performance of the numerical model. Two strategies have been adapted from literature to improve the aforementioned computational performance degradation: the IMPL-EX integration scheme [Oliver,2006], which renders the elemental matrix contribution definite positive, and arclength-type continuation methods [Carrera,1994], which allow to capture the unstable softening branch in brittle ruptures. The IMPL-EX integration scheme has as a major drawback the need to use small time steps to keep numerical error below an acceptable value. A convergence study, limiting the maximum allowed increment of internal variables in the damage model, is presented. Finally, numerical simulation of failure problems with fibre reinforced materials illustrates the performance of the adopted methodology.

A numerical study into the influence of quantum dot size on the sub-bandgap interband photocurrent in intermediate band solar cells

A numerical study is presented of the sub-bandgap interband photon absorption in quantum dot intermediate band solar cells. Absorption coefficients and photocurrent densities are calculated for the valence band to intermediate band transitions using a four-band k · p method. It is found that reducing the quantum dot width in the plane perpendicular to the growth direction increases the photocurrent from the valence band to the intermediate-band ground state if the fractional surface coverage of quantum dots is conserved. This provides a path to increase the sub-bandgap photocurrent in intermediate band solar cells.

Multimodal integration of functional and structural brain connectivity. An application to the characterization of Mild Cognitive Impairment

La investigación para el conocimiento del cerebro es una ciencia joven, su inicio se remonta a Santiago Ramón y Cajal en 1888. Desde esta fecha a nuestro tiempo la neurociencia ha avanzado mucho en el desarrollo de técnicas que permiten su estudio. Desde la neurociencia cognitiva hoy se explican muchos modelos que nos permiten acercar a nuestro entendimiento a capacidades cognitivas complejas. Aun así hablamos de una ciencia casi en pañales que tiene un lago recorrido por delante. Una de las claves del éxito en los estudios de la función cerebral ha sido convertirse en una disciplina que combina conocimientos de diversas áreas: de la física, de las matemáticas, de la estadística y de la psicología. Esta es la razón por la que a lo largo de este trabajo se entremezclan conceptos de diferentes campos con el objetivo de avanzar en el conocimiento de un tema tan complejo como el que nos ocupa: el entendimiento de la mente humana. Concretamente, esta tesis ha estado dirigida a la integración multimodal de la magnetoencefalografía (MEG) y la resonancia magnética ponderada en difusión (dMRI). Estas técnicas son sensibles, respectivamente, a los campos magnéticos emitidos por las corrientes neuronales, y a la microestructura de la materia blanca cerebral. A lo largo de este trabajo hemos visto que la combinación de estas técnicas permiten descubrir sinergias estructurofuncionales en el procesamiento de la información en el cerebro sano y en el curso de patologías neurológicas. Más específicamente en este trabajo se ha estudiado la relación entre la conectividad funcional y estructural y en cómo fusionarlas. Para ello, se ha cuantificado la conectividad funcional mediante el estudio de la sincronización de fase o la correlación de amplitudes entre series temporales, de esta forma se ha conseguido un índice que mide la similitud entre grupos neuronales o regiones cerebrales. Adicionalmente, la cuantificación de la conectividad estructural a partir de imágenes de resonancia magnética ponderadas en difusión, ha permitido hallar índices de la integridad de materia blanca o de la fuerza de las conexiones estructurales entre regiones. Estas medidas fueron combinadas en los capítulos 3, 4 y 5 de este trabajo siguiendo tres aproximaciones que iban desde el nivel más bajo al más alto de integración. Finalmente se utilizó la información fusionada de MEG y dMRI para la caracterización de grupos de sujetos con deterioro cognitivo leve, la detección de esta patología resulta relevante en la identificación precoz de la enfermedad de Alzheimer. Esta tesis está dividida en seis capítulos. En el capítulos 1 se establece un contexto para la introducción de la connectómica dentro de los campos de la neuroimagen y la neurociencia. Posteriormente en este capítulo se describen los objetivos de la tesis, y los objetivos específicos de cada una de las publicaciones científicas que resultaron de este trabajo. En el capítulo 2 se describen los métodos para cada técnica que fue empleada: conectividad estructural, conectividad funcional en resting state, redes cerebrales complejas y teoría de grafos y finalmente se describe la condición de deterioro cognitivo leve y el estado actual en la búsqueda de nuevos biomarcadores diagnósticos. En los capítulos 3, 4 y 5 se han incluido los artículos científicos que fueron producidos a lo largo de esta tesis. Estos han sido incluidos en el formato de la revista en que fueron publicados, estando divididos en introducción, materiales y métodos, resultados y discusión. Todos los métodos que fueron empleados en los artículos están descritos en el capítulo 2 de la tesis. Finalmente, en el capítulo 6 se concluyen los resultados generales de la tesis y se discuten de forma específica los resultados de cada artículo. ABSTRACT In this thesis I apply concepts from mathematics, physics and statistics to the neurosciences. This field benefits from the collaborative work of multidisciplinary teams where physicians, psychologists, engineers and other specialists fight for a common well: the understanding of the brain. Research on this field is still in its early years, being its birth attributed to the neuronal theory of Santiago Ramo´n y Cajal in 1888. In more than one hundred years only a very little percentage of the brain functioning has been discovered, and still much more needs to be explored. Isolated techniques aim at unraveling the system that supports our cognition, nevertheless in order to provide solid evidence in such a field multimodal techniques have arisen, with them we will be able to improve current knowledge about human cognition. Here we focus on the multimodal integration of magnetoencephalography (MEG) and diffusion weighted magnetic resonance imaging. These techniques are sensitive to the magnetic fields emitted by the neuronal currents and to the white matter microstructure, respectively. The combination of such techniques could bring up evidences about structural-functional synergies in the brain information processing and which part of this synergy fails in specific neurological pathologies. In particular, we are interested in the relationship between functional and structural connectivity, and how two integrate this information. We quantify the functional connectivity by studying the phase synchronization or the amplitude correlation between time series obtained by MEG, and so we get an index indicating similarity between neuronal entities, i.e. brain regions. In addition we quantify structural connectivity by performing diffusion tensor estimation from the diffusion weighted images, thus obtaining an indicator of the integrity of the white matter or, if preferred, the strength of the structural connections between regions. These quantifications are then combined following three different approaches, from the lowest to the highest level of integration, in chapters 3, 4 and 5. We finally apply the fused information to the characterization or prediction of mild cognitive impairment, a clinical entity which is considered as an early step in the continuum pathological process of dementia. The dissertation is divided in six chapters. In chapter 1 I introduce connectomics within the fields of neuroimaging and neuroscience. Later in this chapter we describe the objectives of this thesis, and the specific objectives of each of the scientific publications that were produced as result of this work. In chapter 2 I describe the methods for each of the techniques that were employed, namely structural connectivity, resting state functional connectivity, complex brain networks and graph theory, and finally, I describe the clinical condition of mild cognitive impairment and the current state of the art in the search for early biomarkers. In chapters 3, 4 and 5 I have included the scientific publications that were generated along this work. They have been included in in their original format and they contain introduction, materials and methods, results and discussion. All methods that were employed in these papers have been described in chapter 2. Finally, in chapter 6 I summarize all the results from this thesis, both locally for each of the scientific publications and globally for the whole work.

Some recent applications of non-linear models to the engineering practice

The Department of Structural Analysis of the University of Santander has been for a longtime involved in the solution of the country´s practical engineering problems. Some of these have required the use of non-conventional methods of analysis, in order to achieve adequate engineering answers. As an example of the increasing application of non-linear computer codes in the nowadays engineering practice, some cases will be briefly presented. In each case, only the main features of the problem involved and the solution used to solve it will be shown

Application of the homogenization techniques to the determination of the effective flexure constants of plate structural systems

A Mindlin plate with periodically distributed ribs patterns is analyzed by using homogenization techniques based on asymptotic expansion methods. The stiffness matrix of the homogenized plate is found to be dependent on the geometrical characteristics of the periodical cell, i.e. its skewness, plan shape, thickness variation etc. and on the plate material elastic constants. The computation of this plate stiffness matrix is carried out by averaging over the cell domain some solutions of different periodical boundary value problems. These boundary value problems are defined in variational form by linear first order differential operators on the cell domain and the boundary conditions of the variational equation correspond to a periodic structural problem. The elements of the stiffness matrix of homogenized plate are obtained by linear combinations of the averaged solution functions of the above mentioned boundary value problems. Finally, an illustrative example of application of this homogenization technique to hollowed plates and plate structures with ribs patterns regularly arranged over its area is shown. The possibility of using in the profesional practice the present procedure to the actual analysis of floors of typical buildings is also emphasized.

Correlation of the structural and functional domains in the membrane protein Vpu from HIV-1

Vpu is an 81-residue membrane protein encoded by the HIV-1 genome. NMR experiments show that the protein folds into two distinct domains, a transmembrane hydrophobic helix and a cytoplasmic domain with two in-plane amphipathic α-helices separated by a linker region. Resonances in one-dimensional solid-state NMR spectra of uniformly 15N labeled Vpu are clearly segregated into two bands at chemical shift frequencies associated with NH bonds in a transmembrane α-helix, perpendicular to the membrane surface, and with NH bonds in the cytoplasmic helices parallel to the membrane surface. Solid-state NMR spectra of truncated Vpu2–51 (residues 2–51), which contains the transmembrane α-helix and the first amphipathic helix of the cytoplasmic domain, and of a construct Vpu28–81 (residues 28–81), which contains only the cytoplasmic domain, support this structural model of Vpu in the membrane. Full-length Vpu (residues 2–81) forms discrete ion-conducting channels of heterogeneous conductance in lipid bilayers. The most frequent conductances were 22 ± 3 pS and 12 ± 3 pS in 0.5 M KCl and 29 ± 3 pS and 12 ± 3 pS in 0.5 M NaCl. In agreement with the structural model, truncated Vpu2–51, which has the transmembrane helix, forms discrete channels in lipid bilayers, whereas the cytoplasmic domain Vpu28–81, which lacks the transmembrane helix, does not. This finding shows that the channel activity is associated with the transmembrane helical domain. The pattern of channel activity is characteristic of the self-assembly of conductive oligomers in the membrane and is compatible with the structural and functional findings.

Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements

The parasitic bacterium Mycoplasma genitalium has a small, reduced genome with close to a basic set of genes. As a first step toward determining the families of protein domains that form the products of these genes, we have used the multiple sequence programs psi-blast and geanfammer to match the sequences of the 467 gene products of M. genitalium to the sequences of the domains that form proteins of known structure [Protein Data Bank (PDB) sequences]. PDB sequences (274) match all of 106 M. genitalium sequences and some parts of another 85; thus, 41% of its total sequences are matched in all or part. The evolutionary relationships of the PDB domains that match M. genitalium are described in the structural classification of proteins (SCOP) database. Using this information, we show that the domains in the matched M. genitalium sequences come from 114 superfamilies and that 58% of them have arisen by gene duplication. This level of duplication is more than twice that found by using pairwise sequence comparisons. The PDB domain matches also describe the domain structure of the matched sequences: just over a quarter contain one domain and the rest have combinations of two or more domains.

Copper binding to the prion protein: Structural implications of four identical cooperative binding sites

Evidence is growing to support a functional role for the prion protein (PrP) in copper metabolism. Copper ions appear to bind to the protein in a highly conserved octapeptide repeat region (sequence PHGGGWGQ) near the N terminus. To delineate the site and mode of binding of Cu(II) to the PrP, the copper-binding properties of peptides of varying lengths corresponding to 2-, 3-, and 4-octarepeat sequences have been probed by using various spectroscopic techniques. A two-octarepeat peptide binds a single Cu(II) ion with Kd ≈ 6 μM whereas a four-octarepeat peptide cooperatively binds four Cu(II) ions. Circular dichroism spectra indicate a distinctive structuring of the octarepeat region on Cu(II) binding. Visible absorption, visible circular dichroism, and electron spin resonance spectra suggest that the coordination sphere of the copper is identical for 2, 3, or 4 octarepeats, consisting of a square-planar geometry with three nitrogen ligands and one oxygen ligand. Consistent with the pH dependence of Cu(II) binding, proton NMR spectroscopy indicates that the histidine residues in each octarepeat are coordinated to the Cu(II) ion. Our working model for the structure of the complex shows the histidine residues in successive octarepeats bridged between two copper ions, with both the Nɛ2 and Nδ1 imidazole nitrogen of each histidine residue coordinated and the remaining coordination sites occupied by a backbone amide nitrogen and a water molecule. This arrangement accounts for the cooperative nature of complex formation and for the apparent evolutionary requirement for four octarepeats in the PrP.