Effects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2

A general approach to the design of accurate classical potentials for protein folding is described. It includes the introduction of a meaningful statistical measure of the differences between approximations of the same potential energy, the definition of a set of Systematic and Approximately Separable and Modular Internal Coordinates (SASMIC), much convenient for the simulation of general branched molecules, and the imposition of constraints on the most rapidly oscillating degrees of freedom. All these tools are used to study the effects of constraints in the Conformational Equilibrium Distribution (CED) of the model dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of the correcting terms to the naive CED based in the Potential Energy Surface (PES) without any simplifying assumption. These terms are related to mass-metric tensors determinants and also occur in the Fixman's compensating potential. We show that some of the corrections are non-negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.Comment: 8 pages, 1 figure, LaTeX, aipproc style (included

Necesidad de la Terapia Miofuncional en el tratamiento de la Deglución Atípica

la importancia de la deglución atípica se ha visto incrementada en los últimos años debido a sus posibles consecuencias negativas, y a la que se le presta mayor atención desde el ámbito logopédico y ortodóncico. La deglución atípica es un movimiento inadecuado y una posición incorrecta de la lengua en relación al resto de las estructuras orales en la primera fase del proceso deglutorio. De etiología diversa, oscilando desde un desequilibrio del control nervioso hasta malos hábitos como la respiración bucal, provoca alteraciones a nivel anatómico y funcional con consecuencias perjudiciales para el correcto desarrollo anatomofisiológico del individuo. En la mayoría de las ocasiones la deglución atípica aparece vinculada a problemas de oclusiones, actuando una de ellas como causa y la otra como consecuencia, por lo que cobra especial importancia la puesta en práctica de un tratamiento multidisciplinar, el cual radicará en una intervención logopédica utilizando la terapia miofuncional como metodología de intervención junto con una intervención odontológica haciendo uso de la ortodoncia como mecanismo rehabilitador. El presente documento incluye una revisión sistemática tanto de la deglución atípica partiendo del proceso anatomofisiológico adecuado de la deglución como de la terapia miofuncional como mecanismo de intervención más efectivo desde el ámbito logopédico para corregir el mal posicionamiento lingual. También se hace referencia a los hábitos miofuncionales, Además, se incluye un programa de intervención logopédica diseñado para un caso prototípico de deglución atípica.Grado en Logopedi

Las fuerzas productivas de Peñafiel a mediados del siglo XVIII a través del catastro de Ensenada

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When omnigeneity fails

A generic non-symmetric magnetic field does not confine magnetized charged particles for long times due to secular magnetic drifts. Stellarator magnetic fields should be omnigeneous (that is, designed such that the secular drifts vanish), but perfect omnigeneity is technically impossible. There always are small deviations from omnigeneity that necessarily have large gradients. The amplification of the energy flux caused by a deviation of size $\epsilon$ is calculated and it is shown that the scaling with $\epsilon$ of the amplification factor can be as large as linear. In opposition to common wisdom, most of the transport is not due to particles trapped in ripple wells, but to the perturbed motion of particles trapped in the omnigeneous magnetic wells around their bounce points.Comment: 6 pages, 2 figure

Flow damping in stellarators close to quasisymmetry

Quasisymmetric stellarators are a type of optimized stellarators for which flows are undamped to lowest order in an expansion in the normalized Larmor radius. However, perfect quasisymmetry is impossible. Since large flows may be desirable as a means to reduce turbulent transport, it is important to know when a stellarator can be considered to be sufficiently close to quasisymmetry. The answer to this question depends strongly on the size of the spatial gradients of the deviation from quasisymmetry and on the collisionality regime. Recently, formal criteria for closeness to quasisymmetry have been derived in a variety of situations. In particular, the case of deviations with large gradients was solved in the $1/\nu$ regime. Denoting by $\alpha$ a parameter that gives the size of the deviation from quasisymmetry, it was proven that particle fluxes do not scale with $\alpha^{3/2}$, as typically claimed, but with $\alpha$. It was also shown that ripple wells are not necessarily the main cause of transport. This paper reviews those works and presents a new result in another collisionality regime, in which particles trapped in ripple wells are collisional and the rest are collisionless.Comment: 14 pages, 2 figures. To appear in Plasma Physics and Controlled Fusio

Optimizing stellarators for large flows

Plasma flow is damped in stellarators because they are not intrinsically ambipolar, unlike tokamaks, in which the flux-surface averaged radial electric current vanishes for any value of the radial electric field. Only quasisymmetric stellarators are intrinsically ambipolar, but exact quasisymmetry is impossible to achieve in non-axisymmetric toroidal configurations. By calculating the violation of intrinsic ambipolarity due to deviations from quasisymmetry, one can derive criteria to assess when a stellarator can be considered quasisymmetric in practice, i.e. when the flow damping is weak enough. Let us denote by $\alpha$ a small parameter that controls the size of a perturbation to an exactly quasisymmetric magnetic field. Recently, it has been shown that if the gradient of the perturbation is sufficiently small, the flux-surface averaged radial electric current scales as $\alpha^2$ for any value of the collisionality. It was also argued that when the gradient of the perturbation is large, the quadratic scaling is replaced by a more unfavorable one. In this paper, perturbations with large gradients are rigorously treated. In particular, it is proven that for low collisionality a perturbation with large gradient yields, at best, an $O(|\alpha|)$ deviation from quasisymmetry. Heuristic estimations in the literature incorrectly predicted an $O(|\alpha|^{3/2})$ deviation.Comment: 24 pages, 2 figures. To appear in Plasma Physics and Controlled Fusio

The effect of tangential drifts on neoclassical transport in stellarators close to omnigeneity

In general, the orbit-averaged radial magnetic drift of trapped particles in stellarators is non-zero due to the three-dimensional nature of the magnetic field. Stellarators in which the orbit-averaged radial magnetic drift vanishes are called omnigeneous, and they exhibit neoclassical transport levels comparable to those of axisymmetric tokamaks. However, the effect of deviations from omnigeneity cannot be neglected in practice. For sufficiently low collision frequencies (below the values that define the $1/\nu$ regime), the components of the drifts tangential to the flux surface become relevant. This article focuses on the study of such collisionality regimes in stellarators close to omnigeneity when the gradient of the non-omnigeneous perturbation is small. First, it is proven that closeness to omnigeneity is required to preserve radial locality in the drift-kinetic equation for collisionalities below the $1/\nu$ regime. Then, it is shown that neoclassical transport is determined by two layers in phase space. One of the layers corresponds to the $\sqrt{\nu}$ regime and the other to the superbanana-plateau regime. The importance of the superbanana-plateau layer for the calculation of the tangential electric field is emphasized, as well as the relevance of the latter for neoclassical transport in the collisionality regimes considered in this paper. In particular, the tangential electric field is essential for the emergence of a new subregime of superbanana-plateau transport when the radial electric field is small. A formula for the ion energy flux that includes the $\sqrt{\nu}$ regime and the superbanana-plateau regime is given. The energy flux scales with the square of the size of the deviation from omnigeneity. Finally, it is explained why below a certain collisionality value the formulation presented in this article ceases to be valid.Comment: 36 pages. Version to be published in Plasma Physics and Controlled Fusio

Time-dependent patterns in quasivertical cylindrical binary convection

This paper reports on numerical investigations of the effect of a slight inclination a on pattern formation in a shallow vertical cylindrical cell heated from below for binary mixtures with a positive value of the Soret coefficient. By using direct numerical simulation of the three-dimensional Boussinesq equations with Soret effect in cylindrical geometry, we show that a slight inclination of the cell in the range a˜0.036rad=2° strongly influences pattern selection. The large-scale shear flow (LSSF) induced by the small tilt of gravity overcomes the squarelike arrangements observed in noninclined cylinders in the Soret regime, stratifies the fluid along the direction of inclination, and produces an enhanced separation of the two components of the mixture. The competition between shear effects and horizontal and vertical buoyancy alters significantly the dynamics observed in noninclined convection. Additional unexpected time-dependent patterns coexist with the basic LSSF. We focus on an unsual periodic state recently discovered in an experiment, the so-called superhighway convection state (SHC), in which ascending and descending regions of fluid move in opposite directions. We provide numerical confirmation that Boussinesq Navier-Stokes equations with standard boundary conditions contain the essential ingredients that allow for the existence of such a state. Also, we obtain a persistent heteroclinic structure where regular oscillations between a SHC pattern and a state of nearly stationary longitudinal rolls take place. We characterize numerically these time-dependent patterns and investigate the dynamics around the threshold of convection.Postprint (author's final draft

Generación de cuestionarios Moodle con R + exams + Sweave

El paquete exams de R tiene como objetivo la generación automática de cuestionarios. Cada cuestionario se caracteriza por tener variantes –tantas como elija el equipo docente- que comparten un enunciado común pero disponen de diferentes datos. El código fuente se redacta en formato Sweave, es decir, una combinación de instrucciones LaTeX y código R mientras que el formato de salida incluye, entre otros, PDF, HTML y XML. El taller se centra en este último formato que permite de forma relativamente sencilla generar actividades para la plataforma de aprendizaje Moodle. En la sesión se practican los tres pasos necesarios para generar un quiz: 1) elaboración del código fuente, 2) obtención del fichero XML, 3) importación a Moodle y configuración del cuestionario. A partir de ejemplos de complejidad creciente se muestra la potencialidad de esta herramienta para implementar actividades on-line en un rango de asignaturas de estadística que abarca desde primer ciclo hasta máster