MuMax: a new high-performance micromagnetic simulation tool

We present MuMax, a general-purpose micromagnetic simulation tool running on Graphical Processing Units (GPUs). MuMax is designed for high performance computations and specifically targets large simulations. In that case speedups of over a factor 100x can easily be obtained compared to the CPU-based OOMMF program developed at NIST. MuMax aims to be general and broadly applicable. It solves the classical Landau-Lifshitz equation taking into account the magnetostatic, exchange and anisotropy interactions, thermal effects and spin-transfer torque. Periodic boundary conditions can optionally be imposed. A spatial discretization using finite differences in 2 or 3 dimensions can be employed. MuMax is publicly available as open source software. It can thus be freely used and extended by community. Due to its high computational performance, MuMax should open up the possibility of running extensive simulations that would be nearly inaccessible with typical CPU-based simulators.Comment: To be published in JMM

Two Clusters with Radio-quiet Cooling Cores

Radio lobes inflated by active galactic nuclei at the centers of clusters are a promising candidate for halting condensation in clusters with short central cooling times because they are common in such clusters. In order to test the AGN-heating hypothesis, we obtained Chandra observations of two clusters with short central cooling times yet no evidence for AGN activity: Abell 1650 and Abell 2244. The cores of these clusters indeed appear systematically different from cores with more prominent radio emission. They do not have significant central temperature gradients, and their central entropy levels are markedly higher than in clusters with stronger radio emission, corresponding to central cooling times ~ 1 Gigayear. Also, there is no evidence for fossil X-ray cavities produced by an earlier episode of AGN heating. We suggest that either (1) the central gas has not yet cooled to the point at which feedback is necessary to prevent it from condensing, possibly because it is conductively stabilized, or (2) the gas experienced a major heating event $\gtrsim 1$ Gyr in the past and has not required feedback since then. The fact that these clusters with no evident feedback have higher central entropy and therefore longer central cooling times than clusters with obvious AGN feedback strongly suggests that AGNs supply the feedback necessary to suppress condensation in clusters with short central cooling times.Comment: ApJ Letter, in pres

When Should One Substract Background Fluorescence in Two Color Microarrays?

Two color microarrays are a powerful tool for genomic analysis, but have noise components that make inferences regarding gene expression inefficient and potentially misleading. Background fluorescence,whether attributable to non-specific binding or other sources,is an important component of noise. The decision to subtract fluorescence surrounding spots of hybridization from spot fluorescence has been controversial, with no clear criteria for determining circumstances that may favor, or disfavor, background subtraction. While it is generally accepted that subtracting background reduces bias but increases variance in the estimates of the ratios of interest, no formal analysis of the bias-variance trade off of background subtraction has been undertaken. In this paper, we use simulation to systematically examine the bias-variance trade off under a variety of possible experimental conditions. Our simulation is based on data obtained from two self versus self microarray experiments and is free of distributional assumptions. Our results identify factors that are important for determining whether to background subtract, including the correlation of foreground to background intensity ratios. Using these results we develop recommendations for diagnostic visualizations that can help decisions about background subtraction

Simulation Studies of Nanomagnet-Based Architecture

We report a simulation study on interacting ensembles of Co nanomagnets that can perform basic logic operations and propagate logic signals, where the state variable is the magnetization direction. Dipole field coupling between individual nanomagnets drives the logic functionality of the ensemble and coordinated arrangements of the nanomagnets allow for the logic signal to propagate in a predictable way. Problems with the integrity of the logic signal arising from instabilities in the constituent magnetizations are solved by introducing a biaxial anisotropy term to the Gibbs magnetic free energy of each nanomagnet. The enhanced stability allows for more complex components of a logic architecture capable of random combinatorial logic, including horizontal wires, vertical wires, junctions, fanout nodes, and a novel universal logic gate. Our simulations define the focus of scaling trends in nanomagnet-based logic and provide estimates of the energy dissipation and time per nanomagnet reversal

Direct observation of domain wall structures in curved permalloy wires containing an antinotch

The formation and field response of head-to-head domain walls in curved permalloy wires, fabricated to contain a single antinotch, have been investigated using Lorentz microscopy. High spatial resolution maps of the vector induction distribution in domain walls close to the antinotch have been derived and compared with micromagnetic simulations. In wires of 10 nm thickness the walls are typically of a modified asymmetric transverse wall type. Their response to applied fields tangential to the wire at the antinotch location was studied. The way the wall structure changes depends on whether the field moves the wall away from or further into the notch. Higher fields are needed and much more distorted wall structures are observed in the latter case, indicating that the antinotch acts as an energy barrier for the domain wal

Frequent genomic copy number gain and overexpression of GATA-6 in pancreatic carcinoma

Multiple genetic alterations are well recognized as contributing to pancreatic carcinogenesis, although the finding of recurrent copy number changes indicates additional targets remain to be found. The objective of this study was to identify novel targets of genetic alteration that contribute to pancreatic cancer development or progression. We used Representational Oligonucleotide Microarray Analysis (ROMA) to identify copy number changes in pancreatic cancer xenografts, and validated these findings using FISH, quantitative PCR, Western blotting and immunohistochemical labeling. With this approach, we identified a 0.36-Mb amplification at 18q11.2 containing two known genes, GATA-6 and cTAGE1. Using a cutoff value of 3.0 fold compared to haploid controls, copy number gain or amplification was confirmed in 4 of 42 (9.5%) pancreatic carcinomas analyzed. Combined genetic and transcriptional analyses showed consistent overexpression of GATA-6 in all carcinomas with 18q11.2 gain, as well as in the majority of pancreatic cancers examined (17 of 30 cancers, 56.7%) that did not have gain of this region. By contrast, overexpression of cTAGE1 was rare in these same cancers suggesting GATA-6 is the true target of this copy number increase. GATA-6 mRNA overexpression corresponded to robust nuclear protein expression in cancer cell lines and resected tissues consistent with its role as a transcription factor. Intense nuclear labeling was significantly increased in PanIN-3 lesions and infiltrating carcinomas compared to normal duct epithelium (p < 0.000001 and p < 0.003, respectively). Forced overexpression of GATA6 in MiaPaca2 cells resulted in increased proliferation and growth in soft-agar. Gain and overexpression of the development-related transcription factor GATA-6 may play an important and hitherto unrecognized role in pancreatic carcinogenesis

Cooling in the X-ray halo of the rotating, massive early-type galaxy NGC 7049

The relative importance of the physical processes shaping the thermodynamics of the hot gas permeating rotating, massive early-type galaxies is expected to be different from that in non-rotating systems. Here, we report the results of the analysis of XMM-Newton data for the massive, lenticular galaxy NGC 7049. The galaxy harbours a dusty disc of cool gas and is surrounded by an extended hot X-ray emitting gaseous atmosphere with unusually high central entropy. The hot gas in the plane of rotation of the cool dusty disc has a multi-temperature structure, consistent with ongoing cooling. We conclude that the rotational support of the hot gas is likely capable of altering the multiphase condensation regardless of the $t_{\rm cool}/t_{\rm ff}$ ratio, which is here relatively high, $\sim 40$. However, the measured ratio of cooling time and eddy turnover time around unity ($C$-ratio $\approx 1$) implies significant condensation, and at the same time, the constrained ratio of rotational velocity and the velocity dispersion (turbulent Taylor number) ${\rm Ta_t} > 1$ indicates that the condensing gas should follow non-radial orbits forming a disc instead of filaments. This is in agreement with hydrodynamical simulations of massive rotating galaxies predicting a similarly extended multiphase disc.Comment: 11 pages, 12 figures, accepted for publication in MNRA

A Combined MG II/CA II Survey of Stellar Magnetic Activity in the Solar Neighborhood

We use nearly contemporaneus low-resolution IUE observations of Mg II h + k emission and Mount Wilson Observatory Ca II H + K S indices for 33 pairs of observations of lower main sequence stars to formulate a relationship that will permit accurate predictions of S values as a function of (B - V) color and Mg II h + k flux. The resulting relationship is useful because it will extend the set of solar neighborhood stars for which a uniform estimate of chromospheric activity is available to include stars that are not observable from Mount Wilson as well as providing additional estimates of activity levels for stars that are on the Mount Wilson HK Project observing list