SURFACE ALFVEN WAVE DAMPING IN A THREE-DIMENSIONAL SIMULATION OF THE SOLAR WIND

Here we investigate the contribution of surface Alfven wave damping to the heating of the solar wind in minima conditions. These waves are present in the regions of strong inhomogeneities in density or magnetic field (e.g., the border between open and closed magnetic field lines). Using a three-dimensional (3D) magnetohydrodynamics (MHD) model, we calculate the surface Alfven wave damping contribution between 1 and 4 R(circle dot) (solar radii), the region of interest for both acceleration and coronal heating. We consider waves with frequencies lower than those that are damped in the chromosphere and on the order of those dominating the heliosphere: 3 x 10(-6) to 10(-1) Hz. In the region between open and closed field lines, within a few R(circle dot) of the surface, no other major source of damping has been suggested for the low frequency waves we consider here. This work is the first to study surface Alfven waves in a 3D environment without assuming a priori a geometry of field lines or magnetic and density profiles. We demonstrate that projection effects from the plane of the sky to 3D are significant in the calculation of field line expansion. We determine that waves with frequencies >2.8 x 10(-4) Hz are damped between 1 and 4 R(circle dot). In quiet-Sun regions, surface Alfven waves are damped at further distances compared to active regions, thus carrying additional wave energy into the corona. We compare the surface Alfven wave contribution to the heating by a variable polytropic index and find it as an order of magnitude larger than needed for quiet-Sun regions. For active regions, the contribution to the heating is 20%. As it has been argued that a variable gamma acts as turbulence, our results indicate that surface Alfven wave damping is comparable to turbulence in the lower corona. This damping mechanism should be included self-consistently as an energy driver for the wind in global MHD models.

THREE-DIMENSIONAL NUMERICAL SIMULATIONS OF MAGNETIZED WINDS OF SOLAR-LIKE STARS

By means of self-consistent three-dimensional magnetohydrodynamics (MHD) numerical simulations, we analyze magnetized solar-like stellar winds and their dependence on the plasma-beta parameter (the ratio between thermal and magnetic energy densities). This is the first study to perform such analysis solving the fully ideal three-dimensional MHD equations. We adopt in our simulations a heating parameter described by gamma, which is responsible for the thermal acceleration of the wind. We analyze winds with polar magnetic field intensities ranging from 1 to 20 G. We show that the wind structure presents characteristics that are similar to the solar coronal wind. The steady-state magnetic field topology for all cases is similar, presenting a configuration of helmet streamer-type, with zones of closed field lines and open field lines coexisting. Higher magnetic field intensities lead to faster and hotter winds. For the maximum magnetic intensity simulated of 20 G and solar coronal base density, the wind velocity reaches values of similar to 1000 km s(-1) at r similar to 20r(0) and a maximum temperature of similar to 6 x 10(6) K at r similar to 6r(0). The increase of the field intensity generates a larger ""dead zone"" in the wind, i.e., the closed loops that inhibit matter to escape from latitudes lower than similar to 45 degrees extend farther away from the star. The Lorentz force leads naturally to a latitude-dependent wind. We show that by increasing the density and maintaining B(0) = 20 G the system recover back to slower and cooler winds. For a fixed gamma, we show that the key parameter in determining the wind velocity profile is the beta-parameter at the coronal base. Therefore, there is a group of magnetized flows that would present the same terminal velocity despite its thermal and magnetic energy densities, as long as the plasma-beta parameter is the same. This degeneracy, however, can be removed if we compare other physical parameters of the wind, such as the mass-loss rate. We analyze the influence of gamma in our results and we show that it is also important in determining the wind structure.

Numerical prediction of three-dimensional time-dependent viscoelastic extrudate swell using differential and algebraic models

This study investigates the numerical simulation of three-dimensional time-dependent viscoelastic free surface flows using the Upper-Convected Maxwell (UCM) constitutive equation and an algebraic explicit model. This investigation was carried out to develop a simplified approach that can be applied to the extrudate swell problem. The relevant physics of this flow phenomenon is discussed in the paper and an algebraic model to predict the extrudate swell problem is presented. It is based on an explicit algebraic representation of the non-Newtonian extra-stress through a kinematic tensor formed with the scaled dyadic product of the velocity field. The elasticity of the fluid is governed by a single transport equation for a scalar quantity which has dimension of strain rate. Mass and momentum conservations, and the constitutive equation (UCM and algebraic model) were solved by a three-dimensional time-dependent finite difference method. The free surface of the fluid was modeled using a marker-and-cell approach. The algebraic model was validated by comparing the numerical predictions with analytic solutions for pipe flow. In comparison with the classical UCM model, one advantage of this approach is that computational workload is substantially reduced: the UCM model employs six differential equations while the algebraic model uses only one. The results showed stable flows with very large extrudate growths beyond those usually obtained with standard differential viscoelastic models. (C) 2010 Elsevier Ltd. All rights reserved.

Numerical solution of the PTT constitutive equation for unsteady three-dimensional free surface flows

This work deals with the development of a numerical technique for simulating three-dimensional viscoelastic free surface flows using the PTT (Phan-Thien-Tanner) nonlinear constitutive equation. In particular, we are interested in flows possessing moving free surfaces. The equations describing the numerical technique are solved by the finite difference method on a staggered grid. The fluid is modelled by a Marker-and-Cell type method and an accurate representation of the fluid surface is employed. The full free surface stress conditions are considered. The PTT equation is solved by a high order method, which requires the calculation of the extra-stress tensor on the mesh contours. To validate the numerical technique developed in this work flow predictions for fully developed pipe flow are compared with an analytic solution from the literature. Then, results of complex free surface flows using the FIT equation such as the transient extrudate swell problem and a jet flowing onto a rigid plate are presented. An investigation of the effects of the parameters epsilon and xi on the extrudate swell and jet buckling problems is reported. (C) 2010 Elsevier B.V. All rights reserved.

Three-Dimensional Semiautomatic Road Extraction From a High-Resolution Aerial Image by Dynamic-Programming Optimization in the Object Space

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Three-Dimensional Modelling of Honeybee Venom Allergenic Proteases: Relation to Allergenicity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Light microscopy and computer three-dimensional reconstruction of the blood capillaries of the enamel organ of rat molar tooth germs

We performed a light microscope and a computer three-dimensional reconstruction study of serial sections of the molar enamel organ of 3- and 5-day-old rats perfused with Indian ink through the arterial system. The tooth germs were fixed in Bouin's solution, embedded in paraffin, sectioned and stained with haematoxylin and eosin. For the three-dimensional reconstruction, light micrographs of the serial sections were digitized, and aligned using the serial EM Align software downloaded from http://synapses.bu.edu/tools/. After alignment, the boundaries of the India-ink-filled blood vessels were manually traced with a mouse using the software IGL trace (version 1.26b), also downloaded from the above website. After tracing, a three-dimensional representation of the blood vessel contours was generated in a VRML format and visualized with the help of the software Cortona Web3D viewer (version 4.0) downloaded from http://www.parallelgraphics.com/products/cortona. Our results showed that in regions where ameloblasts are polarized the capillaries are arranged in three distinct levels: (1) penetrating and leaving capillaries in relation to the outer enamel epithelium; (2) capillaries crossing and branching inside the stellate reticulum; and (3) capillaries branching and anastomosing profusely within the stratum intermedium, thereby forming an extensive capillary plexus intimately associated with the cells of the stratum intermedium. The existence of a conspicuous capillary plexus intermingled with cells of the stratum intermedium, as shown in our results, suggests that some molecules produced by cells of the stratum intermedium could be released into the capillary plexus and thereafter carried to the dental follicle.

Exact solution for a three-dimensional three-body problem with harmonic interactions

The three-dimensional three-body problem with non-equal masses interacting through pairwise harmonic forces of non-equal strengths is analysed. It is shown that the Jacobi coordinates per se do not decouple this problem but lead to the problem of two coupled three-dimensional harmonic oscillators which becomes exactly soluble through the use of an additional coordinate set.

Three-dimensional reconstruction of fracture surfaces: Area matching algorithms for automatic parallax measurements

This paper describes two solutions for systematic measurement of surface elevation that can be used for both profile and surface reconstructions for quantitative fractography case studies. The first one is developed under Khoros graphical interface environment. It consists of an adaption of the almost classical area matching algorithm, that is based on cross-correlation operations, to the well-known method of parallax measurements from stereo pairs. A normalization function was created to avoid false cross-correlation peaks, driving to the true window best matching solution at each region analyzed on both stereo projections. Some limitations to the use of scanning electron microscopy and the types of surface patterns are also discussed. The second algorithm is based on a spatial correlation function. This solution is implemented under the NIH Image macro programming, combining a good representation for low contrast regions and many improvements on overall user interface and performance. Its advantages and limitations are also presented.

Quantum propagator for some classes of three-dimensional three-body systems

In this work we solve exactly a class of three-body propagators for the most general quadratic interactions in the coordinates, for arbitrary masses and couplings. This is done both for the constant as the time-dependent couplings and masses, by using the Feynman path integral formalism. Finally, the energy spectrum and the eigenfunctions are recovered from the propagators. © 2005 Elsevier Inc. All rights reserved.

Three-dimensional mapping of real environments for cognitive robots navigation

Abstract The development of cognitive robots needs a strong “sensorial” support which should allow it to perceive the real world for interacting with it properly. Therefore the development of efficient visual-processing software to be equipped in effective artificial agents is a must. In this project we study and develop a visual-processing software that will work as the “eyes” of a cognitive robot. This software performs a three-dimensional mapping of the robot’s environment, providing it with the essential information required to make proper decisions during its navigation. Due to the complexity of this objective we have adopted the Scrum methodology in order to achieve an agile development process, which has allowed us to correct and improve in a fast way the successive versions of the product. The present project is structured in Sprints, which cover the different stages of the software development based on the requirements imposed by the robot and its real necessities. We have initially explored different commercial devices oriented to the acquisition of the required visual information, adopting the Kinect Sensor camera (Microsoft) as the most suitable option. Later on, we have studied the available software to manage the obtained visual information as well as its integration with the robot’s software, choosing the high-level platform Matlab as the common nexus to join the management of the camera, the management of the robot and the implementation of the behavioral algorithms. During the last stages the software has been developed to include the fundamental functionalities required to process the real environment, such as depth representation, segmentation, and clustering. Finally the software has been optimized to exhibit real-time processing and a suitable performance to fulfill the robot’s requirements during its operation in real situations.

Three-dimensional spatial distribution of synapses in the neocortex: A dual-beam electron microscopy study

In the cerebral cortex, most synapses are found in the neuropil, but relatively little is known about their 3-dimensional organization. Using an automated dual-beam electron microscope that combines focused ion beam milling and scanning electron microscopy, we have been able to obtain 10 three-dimensional samples with an average volume of 180 µm(3) from the neuropil of layer III of the young rat somatosensory cortex (hindlimb representation). We have used specific software tools to fully reconstruct 1695 synaptic junctions present in these samples and to accurately quantify the number of synapses per unit volume. These tools also allowed us to determine synapse position and to analyze their spatial distribution using spatial statistical methods. Our results indicate that the distribution of synaptic junctions in the neuropil is nearly random, only constrained by the fact that synapses cannot overlap in space. A theoretical model based on random sequential absorption, which closely reproduces the actual distribution of synapses, is also presented.

Congruent Docking of Dimeric Kinesin and ncd into Three-dimensional Electron Cryomicroscopy Maps of Microtubule–Motor ADP Complexes

We present a new map showing dimeric kinesin bound to microtubules in the presence of ADP that was obtained by electron cryomicroscopy and image reconstruction. The directly bound monomer (first head) shows a different conformation from one in the more tightly bound empty state. This change in the first head is amplified as a movement of the second (tethered) head, which tilts upward. The atomic coordinates of kinesin·ADP dock into our map so that the tethered head associates with the bound head as in the kinesin dimer structure seen by x-ray crystallography. The new docking orientation avoids problems associated with previous predictions; it puts residues implicated by proteolysis-protection and mutagenesis studies near the microtubule but does not lead to steric interference between the coiled-coil tail and the microtubule surface. The observed conformational changes in the tightly bound states would probably bring some important residues closer to tubulin. As expected from the homology with kinesin, the atomic coordinates of nonclaret disjunctional protein (ncd)·ADP dock in the same orientation into the attached head in a map of microtubules decorated with dimeric ncd·ADP. Our results support the idea that the observed direct interaction between the two heads is important at some stages of the mechanism by which kinesin moves processively along microtubules.

Analysis of the relation between the sequence and secondary and three-dimensional structures of immunoglobulin molecules.

Methods of structural and statistical analysis of the relation between the sequence and secondary and three-dimensional structures are developed. About 5000 secondary structures of immunoglobulin molecules from the Kabat data base were predicted. Two statistical analyses of amino acids reveal 47 universal positions in strands and loops. Eight universally conservative positions out of the 47 are singled out because they contain the same amino acid in > 90% of all chains. The remaining 39 positions, which we term universally alternative positions, were divided into five groups: hydrophobic, charged and polar, aromatic, hydrophilic, and Gly-Ala, corresponding to the residues that occupied them in almost all chains. The analysis of residue-residue contacts shows that the 47 universal positions can be distinguished by the number and types of contacts. The calculations of contact maps in the 29 antibody structures revealed that residues in 24 of these 47 positions have contacts only with residues of antiparallel beta-strands in the same beta-sheet and residues in the remaining 23 positions always have far-away contacts with residues from other beta-sheets as well. In addition, residues in 6 of the 47 universal positions are also involved in interactions with residues of the other variable or constant domains.

Three-dimensional tracking of motile bacteria near a solid planar surface.

Knowing how motile bacteria move near and along a solid surface is crucial to understanding such diverse phenomena as the migration of infectious bacteria along a catheter, biofilm growth, and the movement of bacteria through the pore spaces of saturated soil, a critical step in the in situ bioremediation of contaminated aquifers. In this study, a tracking microscope is used to record the three-dimensional motion of Escherichia coli near a planar glass surface. Data from the tracking microscope are analyzed to quantify the effects of bacteria-surface interactions on the swimming behavior of bacteria. The speed of cells approaching the surface is found to decrease in agreement with the mathematical model of Ramia et al. [Ramia, M., Tullock, D. L. & Phan-Tien, N. (1993) Biophys J. 65,755-778], which represents the bacteria as spheres with a single polar flagellum rotating at a constant rate. The tendency of cells to swim adjacent to the surface is shown in computer-generated reproductions of cell traces. The attractive interaction potential between the cells and the solid surface is offered as one of several possible explanations for this tendency.