Tomographic Simulations of accretion disks in cataclysmic variables - Flickering and wind

Both continuum and emission line flickering are phenomena directly associated with the mass-accretion process. In this work we simulated accretion-disk Doppler maps, including the effects of winds and flickering flares. Synthetic flickering Doppler maps were calculated and the effect of the flickering parameters on the maps was explored. Jets and winds occur in many astrophysical objects where accretion disks are present. Jets are generally absent among the cataclysmic variables (CVs), but there is evidence of mass loss by wind in many objects. CVs are ideal objects to study accretion disks, and consequently to study the wind associated with these disks. We also present simulations of accretion disks, including the presence of a wind with orbital phase resolution. Synthetic Ha line profiles in the optical region were obtained and their corresponding Doppler maps were calculated. The effect of the wind simulation parameters on the wind line profiles was also explored. From this study we verified that optically thick lines and/or emission by diffuse material into the primary Roche lobe are necessary to generate single peaked line profiles, often seen in CVs. The future accounting of these effects is suggested for interpreting Doppler tomography reconstructions.

SIMULATIONS OF WINDS OF WEAK-LINED T TAURI STARS. II. THE EFFECTS OF A TILTED MAGNETOSPHERE AND PLANETARY INTERACTIONS

Based on our previous work, we investigate here the effects on the wind and magnetospheric structures of weak-lined T Tauri stars due to a misalignment between the axis of rotation of the star and its magnetic dipole moment vector. In such a configuration, the system loses the axisymmetry presented in the aligned case, requiring a fully three-dimensional (3D) approach. We perform 3D numerical magnetohydrodynamic simulations of stellar winds and study the effects caused by different model parameters, namely the misalignment angle theta(t), the stellar period of rotation, the plasma-beta, and the heating index.. Our simulations take into account the interplay between the wind and the stellar magnetic field during the time evolution. The system reaches a periodic behavior with the same rotational period of the star. We show that the magnetic field lines present an oscillatory pattern. Furthermore, we obtain that by increasing theta(t), the wind velocity increases, especially in the case of strong magnetic field and relatively rapid stellar rotation. Our 3D, time-dependent wind models allow us to study the interaction of a magnetized wind with a magnetized extrasolar planet. Such interaction gives rise to reconnection, generating electrons that propagate along the planet`s magnetic field lines and produce electron cyclotron radiation at radio wavelengths. The power released in the interaction depends on the planet`s magnetic field intensity, its orbital radius, and on the stellar wind local characteristics. We find that a close-in Jupiter-like planet orbiting at 0.05 AU presents a radio power that is similar to 5 orders of magnitude larger than the one observed in Jupiter, which suggests that the stellar wind from a young star has the potential to generate strong planetary radio emission that could be detected in the near future with LOFAR. This radio power varies according to the phase of rotation of the star. For three selected simulations, we find a variation of the radio power of a factor 1.3-3.7, depending on theta(t). Moreover, we extend the investigation done in Vidotto et al. and analyze whether winds from misaligned stellar magnetospheres could cause a significant effect on planetary migration. Compared to the aligned case, we show that the timescale tau(w) for an appreciable radial motion of the planet is shorter for larger misalignment angles. While for the aligned case tau(w) similar or equal to 100 Myr, for a stellar magnetosphere tilted by theta(t) = 30 degrees, tau(w) ranges from similar to 40 to 70 Myr for a planet located at a radius of 0.05 AU. Further reduction on tau(w) might occur for even larger misalignment angles and/or different wind parameters.

Hydrodynamical simulations of Galactic fountains - II. Evolution of multiple fountains

The ejection of gas out of the disc in late-type galaxies is related to star formation and is mainly due to the explosion of Type II supernovae (SN II). In a previous paper, we considered the evolution of a single Galactic fountain, that is, a fountain powered by a single SN cluster. Using three-dimensional hydrodynamical simulations, we studied in detail the fountain flow and its dependence with several factors, such as the Galactic rotation, the distance to the Galactic centre and the presence of a hot gaseous halo. As a natural followup, this paper investigates the dynamical evolution of multiple generations of fountains generated by similar to 100 OB associations. We have considered the observed size-frequency distribution of young stellar clusters within the Galaxy in order to appropriately fuel the multiple fountains in our simulations. Most of the results of the previous paper have been confirmed, like for example the formation of intermediate velocity clouds above the disc by the multiple fountains. Also, this work confirms the localized nature of the fountain flows: the freshly ejected metals tend to fall back close to the same Galactocentric region where they are delivered. Therefore, the fountains do not change significantly the radial profile of the disc chemical abundance. The multiple fountain simulations also allowed us to consistently calculate the feedback of the star formation on the halo gas. We found that the hot gas gains about 10 per cent of all the SN II energy produced in the disc. Thus, the SN feedback more than compensate for the halo radiative losses and allow for a quasi steady-state disc-halo circulation to exist. Finally, we have also considered the possibility of mass infall from the intergalactic medium and its interaction with the clouds that are formed by the fountains. Though our simulations are not suitable to reproduce the slow rotational pattern that is typically observed in the haloes around the disc galaxies, they indicate that the presence of an external gas infall may help to slow down the rotation of the gas in the clouds and thus the amount of angular momentum that they transfer to the coronal gas, as previously suggested in the literature.

SIMULATIONS OF WINDS OF WEAK-LINED T TAURI STARS: THE MAGNETIC FIELD GEOMETRY AND THE INFLUENCE OF THE WIND ON GIANT PLANET MIGRATION

By means of numerical simulations, we investigate magnetized stellar winds of pre-main-sequence stars. In particular, we analyze under which circumstances these stars will present elongated magnetic features (e.g., helmet streamers, slingshot prominences, etc). We focus on weak-lined T Tauri stars, as the presence of the tenuous accretion disk is not expected to have strong influence on the structure of the stellar wind. We show that the plasma-beta parameter (the ratio of thermal to magnetic energy densities) is a decisive factor in defining the magnetic configuration of the stellar wind. Using initial parameters within the observed range for these stars, we show that the coronal magnetic field configuration can vary between a dipole-like configuration and a configuration with strong collimated polar lines and closed streamers at the equator (multicomponent configuration for the magnetic field). We show that elongated magnetic features will only be present if the plasma-beta parameter at the coronal base is beta(0) << 1. Using our self-consistent three-dimensional magnetohydrodynamics model, we estimate for these stellar winds the timescale of planet migration due to drag forces exerted by the stellar wind on a hot-Jupiter. In contrast to the findings of Lovelace et al., who estimated such timescales using the Weber and Davis model, our model suggests that the stellar wind of these multicomponent coronae are not expected to have significant influence on hot-Jupiters migration. Further simulations are necessary to investigate this result under more intense surface magnetic field strengths (similar to 2-3 kG) and higher coronal base densities, as well as in a tilted stellar magnetosphere.

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.

Surfactant-nanotube interactions in water and nanotube separation by diameter: atomistic simulations

A non-destructive sorting method to separate single-walled carbon nanotubes (SWNTs) by diameter was recently proposed. By this method, SWNTs are suspended in water by surfactant encapsulation and the separation is carried out by ultracentrifugation in a density gradient. SWNTs of different diameters are distributed according to their densities along the centrifuge tube. A mixture of two anionic surfactants, namely sodium dodecylsulfate (SDS) and sodium cholate (SC), presented the best performance in discriminating nanotubes by diameter. Unexpectedly, small diameter nanotubes are found at the low density part of the centrifuge tube. We present molecular dynamics studies of the water-surfactant-SWNT system to investigate the role of surfactants in the sorting process. We found that surfactants can actually be attracted towards the interior of the nanotube cage, depending on the relationship between the surfactant radius of gyration and the nanotube diameter. The dynamics at room temperature showed that, as the amphiphile moves to the hollow cage, water molecules are dragged together, thereby promoting the nanotube filling. The resulting densities of filled SWNT are in agreement with measured densities.

Computer simulations of copper and gold nanowires and single-wall nanowires

Copper and gold nanowires under tension evolve to form linear atomic chains (LACs), and the study and understanding of this evolution is an important subject for the development of nanocontacts. Here we study the differences and similarities between copper and gold nanowires (NWs) under stress along the [111] crystallographic direction until their rupture using tight-binding molecular dynamics. In both metals, the first significant rearrangement occurs due to one inside atom that goes to the NW` surface. In an attempt to better understand this effect, for both metals we also consider hollow NW`s where the inside atoms were excluded after the initial relaxation to create single-wall NW`s (SWNWs). The dynamical evolution of these SWNWs provides insight on the formation of the constriction that evolves to form LACs. Studying the calculated forces supported by the NW`s we show that SWNWs can sustain larger forces before the first major rearrangement in the copper and gold when compared to the original NW`s.

Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach

Thyroid hormone receptors (TR) are hormone-dependent transcription regulators that play a major role in human health, development, and metabolic functions. The thyroid hormone resistance syndrome, diabetes, obesity, and some types of cancer are just a few examples of important diseases that are related to TR malfunctioning, particularly impaired hormone binding. Ligand binding to and dissociation from the receptor ultimately control gene transcription and, thus, detailed knowledge of binding and release mechanisms are fundamental for the comprehension of the receptor`s biological function and development of pharmaceuticals. In this work, we present the first computational study of ligand entry into the ligand binding domain (LBD) of a nuclear receptor. We report molecular dynamics simulations of ligand binding to TRs using a generalization of the steered molecular dynamics technique designed to perform single-molecule pulling simulations along arbitrarily nonlinear driving pathways. We show that only gentle protein movements and conformational adaptations are required for ligand entry into the LBDs and that the magnitude of the forces applied to assist ligand binding are of the order of the forces involved in ligand dissociation. Our simulations suggest an alternative view for the mechanisms ligand binding and dissociation of ligands from nuclear receptors in which ligands can simply diffuse through the protein surface to reach proper positioning within the binding pocket. The proposed picture indicates that the large-amplitude protein motions suggested by the apo- and holo-RXR alpha crystallographic structures are not required, reconciling conformational changes of LBDs required for ligand entry with other nuclear receptors apo-structures that resemble the ligand-bound LBDs.

Ligand dissociation from estrogen receptor is mediated by receptor dimerization: Evidence from molecular dynamics simulations

Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-dependent transcription factors, hormone binding regulates ER transcriptional activity. Nevertheless, the mechanisms by which ligands enter and leave ERs and other nuclear receptors remain poorly understood. Here, we report results of locally enhanced sampling molecular dynamics simulations to identify dissociation pathways of two ER ligands [the natural hormone 17 beta-estradiol (E-2) and the selective ER modulator raloxifene (RAL)] from the human ER alpha ligand-binding domain in monomeric and dimeric forms. E-2 dissociation occurs via three different pathways in ER monomers. One resembles the mousetrap mechanism (Path I), involving repositioning of helix 12 (H12), others involve the separation of H8 and H11 (Path II), and a variant of this pathway at the bottom of the ligand-binding domain (Path II`). RAL leaves the receptor through Path I and a Path I variant in which the ligand leaves the receptor through the loop region between H11 and H12 (Path I`). Remarkably, ER dimerization strongly suppresses Paths II and II` for E-2 dissociation and modifies RAL escape routes. We propose that differences in ligand release pathways detected in the simulations for ER monomers and dimers provide an explanation for previously observed effects of ER quaternary state on ligand dissociation rates and suggest that dimerization may play an important, and hitherto unexpected, role in regulation of ligand dissociation rates throughout the nuclear receptor family.

Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

Three-dimensional, fully adaptive simulations of phase-field fluid models

We present an efficient numerical methodology for the 31) computation of incompressible multi-phase flows described by conservative phase-field models We focus here on the case of density matched fluids with different viscosity (Model H) The numerical method employs adaptive mesh refinements (AMR) in concert with an efficient semi-implicit time discretization strategy and a linear, multi-level multigrid to relax high order stability constraints and to capture the flow`s disparate scales at optimal cost. Only five linear solvers are needed per time-step. Moreover, all the adaptive methodology is constructed from scratch to allow a systematic investigation of the key aspects of AMR in a conservative, phase-field setting. We validate the method and demonstrate its capabilities and efficacy with important examples of drop deformation, Kelvin-Helmholtz instability, and flow-induced drop coalescence (C) 2010 Elsevier Inc. All rights reserved

Prigogine-Defay Ratio for an Ionic Glass-Former: Molecular Dynamics Simulations

The pressure dependence of the glass-transition temperature, T(g)(P), of the ionic glass-former 2Ca(NO(3))(2) center dot 3KNO(3), CKN, has been obtained by molecular dynamics (MD) simulations The liquid-glass difference of thermal expansivity, Delta alpha, heat capacity, Delta C(p), and isothermal compressibility, Delta kappa, have been calculated as a function of pressure. It has been found that the Ehrenfest relation dT(g)/dP = TV Delta alpha/Delta C(p) predicts the pressure dependence of T, but the other Ehrenfest relation, dT(g)/dP = Delta kappa/Delta alpha, does not. Consequently, the Prigogine-Defay ratio, Pi = Delta C(p)Delta kappa/TV Delta alpha(2), is Pi similar to 1.2 at low pressures, but increases 1 order of magnitude at high pressures. The pressure dependence of the Prigogine-Defay ratio is interpreted in light of recent explanations for the finding Pi > 1.

Alkoxy Chain Effect on the Viscosity of a Quaternary Ammonium Ionic Liquid: Molecular Dynamics Simulations

The viscosity of ionic liquids based on quaternary ammonium cations is reduced when one of the alkyl chains is replaced by an alkoxy chain (Zhou et al. Chem. Eur. J. 2005, 11, 752.). A microscopic picture of the role played by the ether function in decreasing the viscosity of quaternary ammonium ionic liquids is provided here by molecular dynamics (MD) simulations. A model for the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide, MOENM(2)E TFSI, is compared to the tetraalky-lammonium counterpart. The alkoxy derivative has lower viscosity, higher ionic diffusion coefficients, and higher conductivity than the tetraalkyl system at the same density and temperature. A clear signature of the ether function on the liquid structure is observed in cation-cation correlations, but not in anion-anion or anion-cation correlations. In both the alkyl and the alkoxy ionic liquids, there is aggregation of long chains of neighboring cations within micelle-like structures. The MD simulations indicate that the less effective assembly between the more flexible alkoxy chains, in comparison to alkyl chains, is the structural reason for higher ionic mobility in MOENM(2)E TFSI.

Modelling water adsorption on Au(210) surfaces: II. Monte Carlo simulations

Canonical Monte Carlo simulations for the Au(210)/H(2)O interface, using a force field recently proposed by us, are reported. The results exhibit the main features normally observed in simulations of water molecules in contact with different noble metal surfaces. The calculations also assess the influence of the surface topography on the structural aspects of the adsorbed water and on the distribution of the water molecules in the direction normal to the metal surface plane. The adsorption process is preferential at sites in the first layer of the metal. The analysis of the density profiles and dipole moment distributions points to two predominant orientations. Most of the molecules are adsorbed with the molecular plane parallel to surface, while others adsorb with one of the O-H bonds parallel to the surface and the other bond pointing towards the bulk liquid phase. There is also evidence of hydrogen bond formation between the first and second solvent layers at the interface. (c) 2007 Elsevier B.V. All rights reserved.