Parametric Study of the Device Angle Dependency of a Single Vortex Generator on a Flat Plate

Ponencia presentada en el 10th World Congress on Computational Mechanics (WCCM 2012), Sao Paulo (Brazil).Publicados los abstracts en documento con ISBN: 978-85-86686-69-6.

Nonlinear magnetic vortex dynamics in a circular nanodot excited by spin-polarized current

We investigate analytically and numerically nonlinear vortex spin torque oscillator dynamics in a circular magnetic nanodot induced by a spin-polarized current perpendicular to the dot plane. We use a generalized nonlinear Thiele equation including spin-torque term by Slonczewski for describing the nanosize vortex core transient and steady orbit motions and analyze nonlinear contributions to all forces in this equation. Blue shift of the nano-oscillator frequency increasing the current is explained by a combination of the exchange, magnetostatic, and Zeeman energy contributions to the frequency nonlinear coefficient. Applicability and limitations of the standard nonlinear nano-oscillator model are discussed.

Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

Microwave absorption properties of permalloy nanodots in the vortex and quasi-uniform magnetization states

When the in-plane bias magnetic field acting on a flat circular magnetic dot is smaller than the saturation field, there are two stable competing magnetization configurations of the dot: the vortex and the quasi-uniform (C-state). We measured microwave absorption properties in an array of non-interacting permalloy dots in the frequency range 1-8 GHz when the in-plane bias magnetic field was varied in the region of the dot magnetization state bi-stability. We found that the microwave absorption properties in the vortex and quasi-uniform stable states are substantially different, so that switching between these states in a fixed bias field can be used for the development of reconfigurable microwave magnetic materials.

Higher order vortex gyrotropic modes in circular ferromagnetic nanodots

Magnetic vortex that consists of an in-plane curling magnetization configuration and a needle-like core region with out-of-plane magnetization is known to be the ground state of geometrically confined submicron soft magnetic elements. Here magnetodynamics of relatively thick (50-100 nm) circular Ni80Fe20 dots were probed by broadband ferromagnetic resonance in the absence of external magnetic field. Spin excitation modes related to the thickness dependent vortex core gyrotropic dynamics were detected experimentally in the gigahertz frequency range. Both analytical theory and micromagnetic simulations revealed that these exchange dominated modes are flexure oscillations of the vortex core string with n = 0,1,2 nodes along the dot thickness. The intensity of the mode with n = 1 depends significantly on both dot thickness and diameter and in some cases is higher than the one of the uniform mode with n = 0. This opens promising perspectives in the area of spin transfer torque oscillators.

Self-Similarity and helical symmetry in vortex generator flow simulations

According to experimental observations, the vortices generated by vortex generators have previously been observed to be self-similar for both the axial (u(z)) and azimuthal (u(circle minus)) velocity profiles. Further, the measured vortices have been observed to obey the criteria for helical symmetry. This is a powerful result, since it reduces the highly complex flow to merely four parameters. In the present work, corresponding computer simulations using Reynolds-Averaged Navier-Stokes equations have been carried out and compared to the experimental observations. The main objective of this study is to investigate how well the simulations can reproduce the physics of the flow and if the same analytical model can be applied. Using this model, parametric studies can be significantly reduced and, further, reliable simulations can substantially reduce the costs of the parametric studies themselves.

Computational study of the vortex path variation with the VG height

An extensive range of conventional, vane-type, passive vortex generators (VGs) are in use for successful applications of flow separation control. In most cases, the VG height is designed with the same thickness as the local boundary layer at the VG position. However, in some applications, these conventional VGs may produce excess residual drag. The so-called low-profile VGs can reduce the parasitic drag associated to this kind of passive control devices. As suggested by many authors, low-profile VGs can provide enough momentum transfer over a region several times their own height for effective flow-separation control with much lower drag. The main objective of this work is to study the variation of the path and the development of the primary vortex generated by a rectangular VG mounted on a flat plate with five different device heights h = delta, h(1) = 0.8 delta, h(2) = 0.6 delta, h(3) = 0.4 delta and h(4) = 0.2 delta, where delta is the local boundary layer thickness. For this purpose, computational simulations have been carried out at Reynolds number Re = 1350 based on the height of the conventional VG h = 0.25m with the angle of attack of the vane to the oncoming flow beta = 18.5 degrees. The results show that the VG scaling significantly affects the vortex trajectory and the peak vorticity generated by the primary vortex.

Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase

Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.