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

An intercomparison of subtropical cut-off lows in the Southern Hemisphere using recent reanalyses: ERA-Interim, NCEP-CFRS, MERRA-2, JRA-55, and JRA-25

Four recent reanalysis products ERA-Interim, NCEP-CFSR, MERRA-2 and JRA-55 are evaluated and compared to an older reanalysis JRA-25, to quantify their confidence in representing Cut-off lows (COLs) in the Southern Hemisphere. The climatology of COLs based on the minima of 300-hPa vorticity (ξ300) and 300-hPa geopotential (Z300) provides different perspectives of COLs and contributes to the understanding of the discrepancies observed in the literature regarding their numbers and seasonality. The COLs compare better among the newest reanalyses than compared to the older reanalysis JRA-25. The difference in number between the latest reanalyses are generally small for both ξ300 and, with more COLs identified in ξ300 than in Z300 for all reanalyses. The spatial differences observed between the newest reanalyses are mainly due to differences in the track lengths, which is larger in ERA-Interim and JRA-55 than in NCEP-CFSR and MERRA-2, resulting in disparities in the track density. This is likely due to the difference in the assimilation data system used in each reanalysis product. The largest differences in intensities occur in the ξ300, because this field is very sensitive to the reanalysis resolution. The mean separation distance of the COLs that match between the latest reanalyses are generally small, while the older JRA-25 has a broader distribution and larger number of matches with relatively large distances, indicating larger uncertainties in location of COLs. The results show significant improvements for the most recent reanalyses compared to the older JRA-25 reanalysis, indicating a progress in representing the COL properties

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

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

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

Cuando de salud se trata, ¿a dónde acuden las personas?

Cartel presentado en la Segunda Conferencia Internacional de Comunicación en Salud, celebrada el 23 de octubre de 2015 en la Universidad Carlos III de MadridEsta investigación pretendió conocer las relaciones vecinales y sociales de los/as habitantes de dos de los barrios de la localidad de Bosa y de la localidad de Engativá (Bogotá) con las droguerías como instituciones de respuesta a las situaciones de salud, y si éstas pueden ser consideradas consideradas como lugares en donde se suple la falencia del servicio de salud y asimismo, se instauran relaciones sociales que van más allá de la venta de un producto. Asimismo, conocer las razones por las que los/las habitantes de las localidades de Bosa y Engativá, en dos de sus barrios acuden a las droguerías antes que a las entidades de salud; y qué tipo de población acude con más frecuencia. De acuerdo con lo anterior, se consideró como objetivo general analizar las relaciones sociales y vecinales generadas por los servicios de salud que prestan las droguerías de las dos localidades en su zona central respectivamente como instituciones de respuesta a las situaciones o crisis de salud en estas zonas específicas. Esta investigación tuvo un enfoque hermenéutico interpretativo y tuvo tres etapas: Diagnóstico: A través de observación participante en las droguerías seleccionadas; Trabajo de campo: aplicando las técnicas de entrevista a farmaceutas de las droguerías seleccionadas y encuestas escritas a los clientes consumidores de la farmacia y a habitantes de sus alrededores; Sistematización mediante la recopilación de datos e información y análisis de los mismos, obteniendo como principal respuesta a las preguntas de investigación que las personas prefieren las droguerías antes que los establecimiento de salud como EPS y hospitales por la cercanía, confianza, mejor atención, efectividad en diagnóstico y formulación ya que estando las droguerías dentro de los barrios, y su cercanía con la comunidad, se convierten en un espacio de interrelaciones vecinales

Electrostatic potential variations on stellarator magnetic surfaces in low collisionality regimes

The component of the neoclassical electrostatic potential that is non-constant on the magnetic surface, that we denote by $\tilde\varphi$, can affect radial transport of highly charged impurities, and this has motivated its inclusion in some modern neoclassical codes. The number of neoclassical simulations in which $\tilde\varphi$ is calculated is still scarce, partly because they are usually demanding in terms of computational resources, especially at low collisionality. In this paper the size, the scaling with collisionality and with aspect ratio, and the structure of $\tilde\varphi$ on the magnetic surface are analytically derived in the $1/\nu$, $\sqrt{\nu}$ and superbanana-plateau regimes of stellarators close to omnigeneity; i. e. stellarators that have been optimized for neoclassical transport. It is found that the largest $\tilde\varphi$ that the neoclassical equations admit scales linearly with the inverse aspect ratio and with the size of the deviation from omnigeneity. Using a model for a perturbed omnigeneous configuration, the analytical results are verified and illustrated with calculations by the code KNOSOS. The techniques, results and numerical tools employed in this paper can be applied to neoclassical transport problems in tokamaks with broken axisymmetry.Comment: 30 pages, 12 figures, 1 table. Published versio

Cooler and bigger than thought? Planetary host stellar parameters from the InfraRed Flux Method

Effective temperatures and radii for 92 planet-hosting stars as determined from the InfraRed Flux Method (IRFM) are presented and compared with those given by other authors using different approaches. The IRFM temperatures we have derived are systematically lower than those determined from the spectroscopic condition of excitation equilibrium, the mean difference being as large as 110 K. They are, however, consistent with previous IRFM studies and with the colors derived from Kurucz and MARCS model atmospheres. Comparison with direct measurements of stellar diameters for 7 dwarf stars, which approximately cover the range of temperatures of the planet-hosting stars, suggest that the IRFM radii and temperatures are reliable in an absolute scale. A better understanding of the fundamental properties of the stars with planets will be achieved once this discrepancy between the IRFM and the spectroscopic temperature scales is resolved.Comment: 15 pages, 4 figures. Accepted for publication in Ap