FISH: A 3D parallel MHD code for astrophysical applications

FISH is a fast and simple ideal magneto-hydrodynamics code that scales to ~10 000 processes for a Cartesian computational domain of ~1000^3 cells. The simplicity of FISH has been achieved by the rigorous application of the operator splitting technique, while second order accuracy is maintained by the symmetric ordering of the operators. Between directional sweeps, the three-dimensional data is rotated in memory so that the sweep is always performed in a cache-efficient way along the direction of contiguous memory. Hence, the code only requires a one-dimensional description of the conservation equations to be solved. This approach also enable an elegant novel parallelisation of the code that is based on persistent communications with MPI for cubic domain decomposition on machines with distributed memory. This scheme is then combined with an additional OpenMP parallelisation of different sweeps that can take advantage of clusters of shared memory. We document the detailed implementation of a second order TVD advection scheme based on flux reconstruction. The magnetic fields are evolved by a constrained transport scheme. We show that the subtraction of a simple estimate of the hydrostatic gradient from the total gradients can significantly reduce the dissipation of the advection scheme in simulations of gravitationally bound hydrostatic objects. Through its simplicity and efficiency, FISH is as well-suited for hydrodynamics classes as for large-scale astrophysical simulations on high-performance computer clusters. In preparation for the release of a public version, we demonstrate the performance of FISH in a suite of astrophysically orientated test cases.Comment: 27 pages, 11 figure

Cell line-specific efficacy of thermoradiotherapy in human and canine cancer cells in vitro

Objective Aims were to investigate sensitivity of various human and canine cancer cell lines to hyperthermia and the influence of particular treatment conditions, and to analyze the DNA-damage response and mode of cell death in cell line radiosensitized by hyperthermia. Additionally, we were interested in the involvement of HSP70 in radiosensitization. Methods Radiosensitization by hyperthermia was determined in a panel of human and canine cancer cell lines using clonogenic cell survival assay, as well as levels of heat shock proteins (HSPs) using immunoblotting. The influence of the hyperthermia-radiotherapy time gap, different temperatures and the order of treatments on clonogenicity of hyperthermia-sensitive A549 cells was investigated. Additionally, DNA damage and cell death were assessed by Comet assay and an apoptosis/necrosis assay. Further we induced transient knockdown in A549 cells to test HSP70’s involvement in radiosensitization. Results Out of eight cell lines tested, only two (A549 and Abrams) showed significant decrease in clonogenic cell survival when pre-treated with hyperthermia at 42˚C. Strong induction of HSP70 upon thermoradiotherapy (HT-RT) treatment was found in all cell lines. Transient knockdown of HSP70 in A549 cells did not result in decrease of clonogenic cell survival in response to HT-RT. Conclusion Tumor cell-type, temperature and order of treatment play an important role in radiosensitization by hyperthermia. However, hyperthermia has limited potency to radiosensitize canine cancer cells grown in a 2D cell culture setting presented here. DNA damage and apoptosis/necrosis did not increase upon combined treatment and cytosolic levels of HSP70 appear not to play critical role in the radiosensitization of A549 cells

Directed Fixed Energy Sandpile Model

We numerically study the directed version of the fixed energy sandpile. On a closed square lattice, the dynamical evolution of a fixed density of sand grains is studied. The activity of the system shows a continuous phase transition around a critical density. While the deterministic version has the set of nontrivial exponents, the stochastic model is characterized by mean field like exponents.Comment: 5 pages, 6 figures, to be published in Phys. Rev.

Interface Equations for Capillary Rise in Random Environment

We consider the influence of quenched noise upon interface dynamics in 2D and 3D capillary rise with rough walls by using phase-field approach, where the local conservation of mass in the bulk is explicitly included. In the 2D case the disorder is assumed to be in the effective mobility coefficient, while in the 3D case we explicitly consider the influence of locally fluctuating geometry along a solid wall using a generalized curvilinear coordinate transformation. To obtain the equations of motion for meniscus and contact lines, we develop a systematic projection formalism which allows inclusion of disorder. Using this formalism, we derive linearized equations of motion for the meniscus and contact line variables, which become local in the Fourier space representation. These dispersion relations contain effective noise that is linearly proportional to the velocity. The deterministic parts of our dispersion relations agree with results obtained from other similar studies in the proper limits. However, the forms of the noise terms derived here are quantitatively different from the other studies

Energy and momentum of cylindrical gravitational waves. II

Recently Nathan Rosen and the present author obtained the energy and momentum densities of cylindrical gravitational waves in Einstein's prescription and found them to be finite and reasonable. In the present paper we calculate the same in prescriptions of Tolman as well as Landau and Lifshitz and discuss the results.Comment: 8 pages, LaTex, To appear in Pramana- J. Physic

Stalagmite water content as a proxy for drip water supply in tropical and subtropical areas

In this pilot study water was extracted from samples of two Holocene stalagmites from Socotra Island, Yemen, and one Eemian stalagmite from southern continental Yemen. The amount of water extracted per unit mass of stalagmite rock, termed "water yield" hereafter, serves as a measure of its total water content. Based on direct correlation plots of water yields and δ18Ocalcite and on regime shift analyses, we demonstrate that for the studied stalagmites the water yield records vary systematically with the corresponding oxygen isotopic compositions of the calcite (δ18Ocalcite). Within each stalagmite lower δ18Ocalcite values are accompanied by lower water yields and vice versa. The δ18Ocalcite records of the studied stalagmites have previously been interpreted to predominantly reflect the amount of rainfall in the area; thus, water yields can be linked to drip water supply. Higher, and therefore more continuous drip water supply caused by higher rainfall rates, supports homogeneous deposition of calcite with low porosity and therefore a small fraction of water-filled inclusions, resulting in low water yields of the respective samples. A reduction of drip water supply fosters irregular growth of calcite with higher porosity, leading to an increase of the fraction of water-filled inclusions and thus higher water yields. The results are consistent with the literature on stalagmite growth and supported by optical inspection of thin sections of our samples. We propose that for a stalagmite from a dry tropical or subtropical area, its water yield record represents a novel paleo-climate proxy recording changes in drip water supply, which can in turn be interpreted in terms of associated rainfall rates

A transition from river networks to scale-free networks

A spatial network is constructed on a two dimensional space where the nodes are geometrical points located at randomly distributed positions which are labeled sequentially in increasing order of one of their co-ordinates. Starting with $N$ such points the network is grown by including them one by one according to the serial number into the growing network. The $t$-th point is attached to the $i$-th node of the network using the probability: $\pi_i(t) \sim k_i(t)\ell_{ti}^{\alpha}$ where $k_i(t)$ is the degree of the $i$-th node and $\ell_{ti}$ is the Euclidean distance between the points $t$ and $i$. Here $\alpha$ is a continuously tunable parameter and while for $\alpha=0$ one gets the simple Barab\'asi-Albert network, the case for $\alpha \to -\infty$ corresponds to the spatially continuous version of the well known Scheidegger's river network problem. The modulating parameter $\alpha$ is tuned to study the transition between the two different critical behaviors at a specific value $\alpha_c$ which we numerically estimate to be -2.Comment: 5 pages, 5 figur