Phase-space Lagrangian derivation of electrostatic gyrokinetics in general geometry

Gyrokinetic theory is based on an asymptotic expansion in the small parameter $\epsilon$, defined as the ratio of the gyroradius and the characteristic length of variation of the magnetic field. In this article, this ordering is strictly implemented to compute the electrostatic gyrokinetic phase-space Lagrangian in general magnetic geometry to order $\epsilon^2$. In particular, a new expression for the complete second-order gyrokinetic Hamiltonian is provided, showing that in a rigorous treatment of gyrokinetic theory magnetic geometry and turbulence cannot be dealt with independently. The new phase-space gyrokinetic Lagrangian gives a Vlasov equation accurate to order $\epsilon^2$ and a Poisson equation accurate to order $\epsilon$. The final expressions are explicit and can be implemented into any simulation without further computations.Comment: 55 pages. Version with typo in equation (135) corrected. The second term in the second line of (135) was missing the subindex that indicates that only the perpendicular component of the gradient enters this ter

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

Less constrained omnigeneous stellarators

A stellarator is said to be omnigeneous if all particles have vanishing average radial drifts. In omnigeneous stellarators, particles are perfectly confined in the absence of turbulence and collisions, whereas in non-omnigeneous configurations, particle can drift large radial distances. One of the consequences of omnigeneity is that the unfavorable inverse scaling with collisionality of the stellarator neoclassical fluxes disappears. In the pioneering and influential article [Cary~J~R and Shasharina~S~G 1997 {\it Phys. Plasmas} {\bf 4} 3323], the conditions that the magnetic field of a stellarator must satisfy to be omnigeneous are derived. However, reference [Cary~J~R and Shasharina~S~G 1997 {\it Phys. Plasmas} {\bf 4} 3323] only considered omnigeneous stellarators in which all the minima of the magnetic field strength on a flux surface must have the same value. The same is assumed for the maxima. We show that omnigenenous magnetic fields can have local minima and maxima with different values. Thus, the parameter space in which omnigeneous stellarators are possible is larger than previously expected. The analysis presented in this article is only valid for orbits with vanishing radial width, and in principle it is not applicable to energetic particles. However, one would expect that improving neoclassical confinement would improve energetic particle confinement.Comment: 10 pages, 5 figure

Intrinsic rotation with gyrokinetic models

The generation of intrinsic rotation by turbulence and neoclassical effects in tokamaks is considered. To obtain the complex dependences observed in experiments, it is necessary to have a model of the radial flux of momentum that redistributes the momentum within the tokamak in the absence of a preexisting velocity. When the lowest order gyrokinetic formulation is used, a symmetry of the model precludes this possibility, making small effects in the gyroradius over scale length expansion necessary. These effects that are usually small become important for momentum transport because the symmetry of the lowest order gyrokinetic formulation leads to the cancellation of the lowest order momentum flux. The accuracy to which the gyrokinetic equation needs to be obtained to retain all the physically relevant effects is discussed

Caracterización clínica, microbiológica y ecocardiográfica de pacientes con Endocarditis infecciosa en la Fundación Cardioinfantil 2002-2012

Introducción: La endocarditis infecciosa es una infección microbiana del endocardio poco estudiada en nuestro país, la cual se asocia con múltiples complicaciones clínicas, y que presenta una mortalidad importante, que no ha disminuido a lo largo del tiempo sin importar los cambios epidemiológicos, de tratamiento y el aumento de la cirugía valvular que se presentan en la actualidad. Metodología: Se realizó la búsqueda de los pacientes adultos con diagnóstico de endocarditis infecciosa entre los años 2002 a 2012 en la Fundación Cardioinfantil para la revisión de los registros médicos y la descripción de las características clínicas, microbiológicas y ecocardiográficas. Resultados: se detectaron 144 pacientes hallando un predominio de la lesión de válvula nativa y el compromiso de válvula aórtica, encontrando como germen más común el S. aureus, sin embargo una tasa de 32.6% de hemocultivos negativos. La mortalidad intrahospitalaria fue de 22.2%. Discusión: los datos hallados en general son semejantes a los descritos en la literatura mundial con excepción de algunas variables discordantes en cuanto a la válvula aórtica mayormente comprometida y factores asociados a la endocarditis tricuspidea. Conclusión: la epidemiología de la endocarditis infecciosa de nuestra serie es muy semejante a la de la literatura actual de los países industrializados, aunque con algunas excepciones, requiriéndose la implementación y profundización del estudio de esta patología a nivel nacional.Background: Infective endocarditis is an endocardial microbial infection poorly studied in our country that is related with multiple complications with an important mortality burden regardless the epidemiology changes in time, the treatment and the increasing number in valve surgery nowadays. Methods: we search adult patients with diagnosis of infective endocarditis between 2002-2012 in the cardioinfantil foundation clinic for the review of the clinical records to get a clinical, microbiologic and echocardiographic description of this population. Results: we found 144 patients that show a predominant native valve affection and aortic valve lesions with S. aureus as the most frequent isolated bacteria, nevertheless the blood culture was negative in 32.6% of cases; in-hospital mortality was 22.2%. Discussion: our data are similar to the international publications although some variables are discordant as the aortic lesion predominance and the factors related to the tricuspid valve endocarditis. Conclusions: the epidemiology of infective endocarditis in our series was comparable to the international epidemiology of industrialized countries with some little exceptions. We need an implementation and consolidation in the national study of this pathology

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

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