The inner regions of protoplanetary disks

To understand how planetary systems form in the dusty disks around pre-main-sequence stars a detailed knowledge of the structure and evolution of these disks is required. While this is reasonably well understood for the regions of the disk beyond about 1 AU, the structure of these disks inward of 1 AU remains a puzzle. This is partly because it is very difficult to spatially resolve these regions with current telescopes. But it is also because the physics of this region, where the disk becomes so hot that the dust starts to evaporate, is poorly understood. With infrared interferometry it has become possible in recent years to directly spatially resolve the inner AU of protoplanetary disks, albeit in a somewhat limited way. These observations have partly confirmed current models of these regions, but also posed new questions and puzzles. Moreover, it has turned out that the numerical modeling of these regions is extremely challenging. In this review we give a rough overview of the history and recent developments in this exciting field of astrophysics.Comment: 45 pages with 14 Figures. to appear in Annual Review of Astronomy and Astrophysics (2010, Vol. 48

A numerical model for multigroup radiation hydrodynamics

We present in this paper a multigroup model for radiation hydrodynamics to account for variations of the gas opacity as a function of frequency. The entropy closure model (M1) is applied to multigroup radiation transfer in a radiation hydrodynamics code. In difference from the previous grey model, we are able to reproduce the crucial effects of frequency-variable gas opacities, a situation omnipresent in physics and astrophysics. We also account for the energy exchange between neighbouring groups which is important in flows with strong velocity divergence. These terms were computed using a finite volume method in the frequency domain. The radiative transfer aspect of the method was first tested separately for global consistency (reversion to grey model) and against a well established kinetic model through Marshak wave tests with frequency dependent opacities. Very good agreement between the multigroup M1 and kinetic models was observed in all tests. The successful coupling of the multigroup radiative transfer to the hydrodynamics was then confirmed through a second series of tests. Finally, the model was linked to a database of opacities for a Xe gas in order to simulate realistic multigroup radiative shocks in Xe. The differences with the previous grey models are discussed.Comment: 27 pages, 11 figures, Accepted for publication in JQSR

Multi-Stage Modeling of the Kinetics of Activation of CaMKII

Ca 2+ /calmodulin-dependent protein kinase 2 (CaMKII) plays an important role in induction of long-term potentiation and formation of memory. It is abundant in dendritic spines, and is activated when Ca 2+ flows into the postsynaptic cytosol through open NMDA-type glutamate receptors. Its function is fine-tuned through interaction with other proteins as well as through subunit interactions and regulatory autophosphorylation. We have undertaken a multi-stage project to study the critical kinetics of activation of CaMKII in the spine by combining modeling and experimental studies. We are using computational modeling and simulations on various platforms, coupled with biochemical experiments in vitro, and eventually in vivo, to understand CaMKII regulation. The project includes the following steps: 1. Determining the parameters governing activation of a monomeric subunit. The CaMKII holoenzyme is a large dodecamer of similar, homologous subunits held together by interactions between the association domains located at the carboxyl end of each subunit. Individual, monomeric subunits can be expressed recombinantly by removing the association domain. Computer simulations of activation of monomeric CaMKII by Ca 2+ /calmodulin at both saturating and non-saturating concentrations in a test tube have helped to identify the binding parameters that are most crucial for modeling of regulation of CaMKII and thus have indicated the most useful biochemical assays to measure those parameters (Pepke et al., 2010). We are using these measurements to fine-tune our model of activation of individual catalytic subunits. 2. Building a model of the holoenzyme. Because a CaMKII holoenzyme contains 12 similar subunits, each of which can exist in several states, the holoenzyme can have a large number of state combinations. Thus, modeling the entire holoenzyme requires a computational framework that avoids the ensuing combinatorial complexity. The stochastic simulator MCell provides an elegant, rule-based way of modeling state changes in the CaMKII holoenzyme. 3. Modeling cooperativity that arises from the dodecameric structure of CaMKII. Autophosphorylation at threonine-286, which activates CaMKII subunits, is an inter-subunit event. Thus, it is greatly facilitated by the close proximity of subunits in the holoenzyme. In addition, the subunits within the holoenzyme are arranged as dimers which appears to result in cooperativity in the binding of Ca 2+ /CaM to individual subunits of the dimer (Chao et al., 2010). An accurate model of activation of subunits in the holoenzyme and their autophosphorylation will allow us to explore the effects of cooperativity on CaMKII activation on various time scales. 4. Modeling CaMKII within the context of a postsynaptic spine CaMKII interacts with a variety of other proteins, both in the postsynaptic density (PSD), close to major sources of Ca 2+ influx, and in other parts of the spine. In the fourth stage of this project we plan to implement kinetic models of activation of CaMKII in the context of an MCell model of Ca 2+ influx into a spine upon activation of NMDA-type glutamate receptors (Keller et al., 2008; Keller et al., 2011, submitted). We will explore the effects of different localization and numbers of CaMKII holoenzymes in the spine on CaMKII activation. References: Pepke, S., Kinzer-Ursem, T., Mihalas, S., and Kennedy, M.B. (2010). A dynamic model of interactions of Ca 2+ , calmodulin, and catalytic subunits of Ca 2+ /calmodulin-dependent protein kinase II. PLoS Comput Biol 6, e1000675. Chao, L.H., Pellicena, P., Deindl, S., Barclay, L.A., Schulman, H., and Kuriyan, J. (2010). Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation. Nat Struct Mol Biol 17, 264-272. Keller, D.X., Franks, K.M., Bartol, T.M., Jr., and Sejnowski, T.J. (2008). Calmodulin activation by calcium transients in the postsynaptic density of dendritic spines. PLoS ONE 3, e2045. Keller, D.X., Bartol, T.M., Kinney, J.P, Kennedy, M.B., Bajaj, C., Harris, K.M., and Sejnowski, T.J. Regulation of synaptic calcium transients in reconstructed dendritic spines of hippocampal CA1 pyramidal neurons, submitted

The structure of line-driven winds

Following procedures pioneered by Castor, Abbott & Klein (1975, [CAK]), spherically-symmetric supersonic winds for O stars are computed for matching to plane-parallel moving reversing layers (RL's) from Paper I (Lucy 2007). In contrast to a CAK wind, each of these solutions is singularity-free, thus allowing its mass-loss rate to be fixed by the regularity condition at the sonic point within the RL. Moreover, information propagation in these winds by radiative-acoustic waves is everywhere outwardly-directed, justifying the implicit assumption in Paper I that transonic flows are unaffected by inwardly-directed wave motions.Comment: Accepted by A&A; 7 pages, 1 table, 4 figure

General Relativistic versus Newtonian: a universality in radiation hydrodynamics

We compare Newtonian and general relativistic descriptions of the stationary accretion of self-gravitating fluids onto compact bodies. Spherical symmetry and thin gas approximation are assumed. Luminosity depends, amongst other factors, on the temperature and the contribution of gas to the total mass, in both -- general relativistic ($L_{GR}$) and Newtonian ($L_N$) -- models. We discover a remarkable universal behaviour for transonic flows: the ratio of respective luminosities $L_{GR}/L_N$ is independent of the fractional mass of the gas and depends on asymptotic temperature. It is close to 1 in the regime of low asymptotic temperatures and can grow by one order of magnitude for high temperatures. These conclusions are valid for a wide range of polytropic equations of state.Comment: 8 pages, 4 figure

Importance of cooling in triggering the collapse of hypermassive neutron stars

The inspiral and merger of a binary neutron star (NSNS) can lead to the formation of a hypermassive neutron star (HMNS). As the HMNS loses thermal pressure due to neutrino cooling and/or centrifugal support due to gravitational wave (GW) emission, and/or magnetic breaking of differential rotation it will collapse to a black hole. To assess the importance of shock-induced thermal pressure and cooling, we adopt an idealized equation of state and perform NSNS simulations in full GR through late inspiral, merger, and HMNS formation, accounting for cooling. We show that thermal pressure contributes significantly to the support of the HMNS against collapse and that thermal cooling accelerates its "delayed" collapse. Our simulations demonstrate explicitly that cooling can induce the catastrophic collapse of a hot hypermassive neutron star formed following the merger of binary neutron stars. Thus, cooling physics is important to include in NSNS merger calculations to accurately determine the lifetime of the HMNS remnant and to extract information about the NS equation of state, cooling mechanisms, bar instabilities and B-fields from the GWs emitted during the transient phase prior to BH formation.Comment: 13 pages, 7 figures, matches published versio

On the Properties of Plastic Ablators in Laser-Driven Material Dynamics Experiments

Radiation hydrodynamics simulations were used to study the effect of plastic ablators in laser-driven shock experiments. The sensitivity to composition and equation of state was found to be 5-10% in ablation pressure. As was found for metals, a laser pulse of constant irradiance gave a pressure history which decreased by several percent per nanosecond. The pressure history could be made more constant by adjusting the irradiance history. The impedance mismatch with the sample gave an increase o(100%) in the pressure transmitted into the sample, for a reduction of several tens of percent in the duration of the peak load applied to the sample, and structured the release history by adding a release step to a pressure close to the ablation pressure. Algebraic relations were found between the laser pulse duration, the ablator thickness, and the duration of the peak pressure applied to the sample, involving quantities calculated from the equations of state of the ablator and sample using shock dynamics.Comment: Typos fixe

SAtlas: Spherical Versions of the Atlas Stellar Atmosphere Program

Context: The current stellar atmosphere programs still cannot match some fundamental observations of the brightest stars, and with new techniques, such as optical interferometry, providing new data for these stars, additional development of stellar atmosphere codes is required. Aims: To modify the open-source model atmosphere program Atlas to treat spherical geometry, creating a test-bed stellar atmosphere code for stars with extended atmospheres. Methods: The plane-parallel Atlas has been changed by introducing the necessary spherical modifications in the pressure structure, in the radiative transfer and in the temperature correction. Results: Several test models show that the spherical program matches the plane-parallel models in the high surface gravity regime, and matches spherical models computed by Phoenix and by MARCS in the low gravity case.Comment: 10 pages, 10 figures, Accepted for publication in A&

General Relativistic Radiant Shock Waves in the Post-Quasistatic Approximation

An evolution of radiant shock wave front is considered in the framework of a recently presented method to study self-gravitating relativistic spheres, whose rationale becomes intelligible and finds full justification within the context of a suitable definition of the post-quasistatic approximation. The spherical matter configuration is divided into two regions by the shock and each side of the interface having a different equation of state and anisotropic phase. In order to simulate dissipation effects due to the transfer of photons and/or neutrinos within the matter configuration, we introduce the flux factor, the variable Eddington factor and a closure relation between them. As we expected the strength of the shock increases the speed of the fluid to relativistic values and for some critical ones is larger than light speed. In addition, we find that energy conditions are very sensible to the anisotropy, specially the strong one. As a special feature of the model, we find that the contribution of the matter and radiation to the radial pressure are the same order of magnitude as in the mant as in the core, moreover, in the core radiation pressure is larger than matter pressure.Comment: To appear in Journal of Physics:Conference Series:"XXIX Spanish Relativity Meeting (ERE 2006): Einstein's Legacy: From the Theoretical Paradise to Astrophysical Observations

Distance-redshift from an optical metric that includes absorption

We show that it is possible to equate the intensity reduction of a light wave caused by weak absorption with a geometrical reduction in intensity caused by a "transverse" conformal transformation of the spacetime metric in which the wave travels. We are consequently able to modify Gordon's optical metric to account for electromagnetic properties of ponderable material whose properties include both refraction and absorption. Unlike refraction alone however, including absorption requires a modification of the optical metric that depends on the eikonal of the wave itself. We derive the distance-redshift relation from the modified optical metric for Friedman-Lema\^itre-Robertson-Walker spacetimes whose cosmic fluid has associated refraction and absorption coefficients. We then fit the current supernovae data and provide an alternate explanation (other than dark energy) of the apparent acceleration of the universe.Comment: 2 figure