Computational Efficiency of Frequency-- and Time--Domain Calculations of Extreme Mass--Ratio Binaries: Equatorial Orbits

Gravitational waveforms and fluxes from extreme mass--ratio inspirals can be computed using time--domain methods with accuracy that is fast approaching that of frequency--domain methods. We study in detail the computational efficiency of these methods for equatorial orbits of fast spinning Kerr black holes, and find the number of modes needed in either method --as functions of the orbital parameters-- in order to achieve a desired accuracy level. We then estimate the total computation time and argue that for high eccentricity orbits the time--domain approach is more efficient computationally. We suggest that in practice low--$m$ modes are computed using the frequency--domain approach, and high--$m$ modes are computed using the time--domain approach, where $m$ is the azimuthal mode number.Comment: 19 figures, 6 table

Statistical Topology of Cellular Networks in Two and Three Dimensions

Cellular networks may be found in a variety of natural contexts, from soap foams to biological tissues to grain boundaries in a polycrystal, and the characterization of these structures is therefore a subject of interest to a range of disciplines. An approach to describe the topology of a cellular network in two and three dimensions is presented. This allows for the quantification of a variety of features of the cellular network, including a quantification of topological disorder and a robust measure of the statistical similarity or difference of a set of structures. The results of this analysis are presented for numerous simulated systems including the Poisson-Voronoi and the steady-state grain growth structures in two and three dimensions

Distribution of Topological Types in Grain-Growth Microstructures

An open question in studying normal grain growth concerns the asymptotic state to which microstructures converge. In particular, the distribution of grain topologies is unknown. We introduce a thermodynamic-like theory to explain these distributions in two- and three-dimensional systems. In particular, a bending-like energy $E_i$ is associated to each grain topology $t_i$, and the probability of observing that particular topology is proportional to $\frac{1}{s(t_i)}e^{-\beta E_i}$, where $s(t_i)$ is the order of an associated symmetry group and $\beta$ is a thermodynamic-like constant. We explain the physical origins of this approach, and provide numerical evidence in support.Comment: 6 pages, 5 figure

Complete topology of cells, grains, and bubbles in three-dimensional microstructures

We introduce a general, efficient method to completely describe the topology of individual grains, bubbles, and cells in three-dimensional polycrystals, foams, and other multicellular microstructures. This approach is applied to a pair of three-dimensional microstructures that are often regarded as close analogues in the literature: one resulting from normal grain growth (mean curvature flow) and another resulting from a random Poisson-Voronoi tessellation of space. Grain growth strongly favors particular grain topologies, compared with the Poisson-Voronoi model. Moreover, the frequencies of highly symmetric grains are orders of magnitude higher in the the grain growth microstructure than they are in the Poisson-Voronoi one. Grain topology statistics provide a strong, robust differentiator of different cellular microstructures and provide hints to the processes that drive different classes of microstructure evolution.Comment: 5 pages, 6 figures, 5 supplementary page

Differential expression of interferon responsive genes in rodent models of transmissible spongiform encephalopathy disease

BACKGROUND: The pathological hallmarks of transmissible spongiform encephalopathy (TSE) diseases are the deposition of a misfolded form of a host-encoded protein (PrP(res)), marked astrocytosis, microglial activation and spongiosis. The development of powerful gene based technologies has permitted increased levels of pro-inflammatory cytokines to be demonstrated. However, due to the use of assays of differing sensitivities and typically the analysis of a single model system it remained unclear whether this was a general feature of these diseases or to what extent different model systems and routes of infection influenced the relative levels of expression. Similarly, it was not clear whether the elevated levels of cytokines observed in the brain were accompanied by similar increases in other tissues that accumulate PrP(res), such as the spleen. RESULTS: The level of expression of the three interferon responsive genes, Eif2ak2, 2'5'-OAS, and Mx2, was measured in the brains of Syrian hamsters infected with scrapie 263K, VM mice infected with bovine spongiform encephalopathy and C57BL/6 mice infected with the scrapie strain ME7. Glial fibrillary acidic expression confirmed the occurrence of astrocytosis in all models. When infected intracranially all three models showed a similar pattern of increased expression of the interferon responsive genes at the onset of clinical symptoms. At the terminal stage of the disease the level and pattern of expression of the three genes was mostly unchanged in the mouse models. In contrast, in hamsters infected by either the intracranial or intraperitoneal routes, both the level of expression and the expression of the three genes relative to one another was altered. Increased interferon responsive gene expression was not observed in a transgenic mouse model of Alzheimer's disease or the spleens of C57BL/6 mice infected with ME7. Concurrent increases in TNFα, TNFR1, Fas/ApoI receptor, and caspase 8 expression in ME7 infected C57BL/6 mice were observed. CONCLUSION: The identification of increased interferon responsive gene expression in the brains of three rodent models of TSE disease at two different stages of disease progression suggest that this may be a general feature of the disease in rodents. In addition, it was determined that the increased interferon responsive gene expression was confined to the CNS and that the TSE model system and the route of infection influenced the pattern and extent of the increased expression. The concurrent increase in initiators of Eif2ak2 mediated apoptotic pathways in C57BL/6 mice infected with ME7 suggested one mechanism by which increased interferon responsive gene expression may enhance disease progression

Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver

BACKGROUND: Metabolic homeostasis in mammals critically depends on the regulation of fasting-induced genes by CREB in the liver. Previous genome-wide analysis has shown that only a small percentage of CREB target genes are induced in response to fasting-associated signaling pathways. The precise molecular mechanisms by which CREB specifically targets these genes in response to alternating hormonal cues remain to be elucidated. RESULTS: We performed chromatin immunoprecipitation coupled to high-throughput sequencing of CREB in livers from both fasted and re-fed mice. In order to quantitatively compare the extent of CREB-DNA interactions genome-wide between these two physiological conditions we developed a novel, robust analysis method, termed the ‘single sample independence’ (SSI) test that greatly reduced the number of false-positive peaks. We found that CREB remains constitutively bound to its target genes in the liver regardless of the metabolic state. Integration of the CREB cistrome with expression microarrays of fasted and re-fed mouse livers and ChIP-seq data for additional transcription factors revealed that the gene expression switches between the two metabolic states are associated with co-localization of additional transcription factors at CREB sites. CONCLUSIONS: Our results support a model in which CREB is constitutively bound to thousands of target genes, and combinatorial interactions between DNA-binding factors are necessary to achieve the specific transcriptional response of the liver to fasting. Furthermore, our genome-wide analysis identifies thousands of novel CREB target genes in liver, and suggests a previously unknown role for CREB in regulating ER stress genes in response to nutrient influx

WIVERN: a laboratory experiment for testing novel laser-based wavefront sensing techniques

WIVERN is a testbed for laboratory experiments in laser-based wavefront sensing. It emulates laser uplink from a 4m telescope with 1.6 arcsec seeing and laser back-scattering from up to 20 km. Currently there are three current wavefront sensing capabilities. The first two are from a wide-field of view (1.0 arcmin) Shack Hartmann wavefront sensor observing a constellation of point sources at infinity (reference targets, star-oriented wavefront sensing), or an image from emulated back-scattering (wide-field correlation wavefront sensing). The third is based on the PPPP concept. Other sub-systems are laser projection replicating a pupil launch, a 7x7 pupil-conjugate deformable mirror (DM), and a wide-field camera for PSF analysis. A 500 Hz rate accumulates sufficient data for statistical and machine-learning analysis over hour timescales. It is a compact design (2.1m2) with mostly commercial dioptric components. The sub-system optical interfaces are identical: a flat focal plane for easy bench reconfiguration. The end-to-end design is diffraction-limited with ≤ 1% pupil distortion for wavelengths λ=633–750 nm