Role of Quantum Coherence and Energetic Disorder on Exciton Transport in Polymer Films

The cross-over from coherent to incoherent exciton transport in disordered polymer films is studied by computationally solving a modified form of the Redfield equation for the exciton density matrix. This theory models quantum mechanical (ballistic) and incoherent (diffusive) transport as limiting cases. It also reproduces Forster transport for certain parameter regimes. Using model parameters appropriate to polymer thin films it is shown that short-time quantum mechanical coherence increases the exciton diffusion length. It also causes rapid initial energy relaxation and larger line widths. The route to equilibrium is, however, more questionable, as the equilibrium populations of the model do not satisfy the Boltzmann distributions over the site energies. The Redfield equation for the dimer is solved exactly to provide insight into the numerical results.Comment: Accepted for publication in Phys. Rev. B. (July 2006). 19 pages and 8 figure

Thermodynamic limits on oxygenic photosynthesis around M-dwarf stars: Generalized models and strategies for optimization

We explore the feasibility and potential characteristics of photosynthetic light-harvesting on exo-planets orbiting in the habitable zone of low mass stars ($< 1$ M$_{\odot}$). As stellar temperature, $T_{s}$, decreases, the irradiance maximum red-shifts out of the $400 \textrm{nm} \leq \lambda < 750$ nm range of wavelengths that can be utilized by \emph{oxygenic} photosynthesis on Earth. However, limited irradiance in this region does not preclude oxygenic photosynthesis and Earth's plants, algae and cyanobacteria all possess very efficient \emph{light-harvesting antennae} that facilitate photosynthesis in very low light. Here we construct general models of photosynthetic light-harvesting structures to determine how an oxygenic photosystem would perform in different irradiant spectral fluxes. We illustrate that the process of light-harvesting, capturing energy over a large antenna and concentrating it into a small \emph{reaction centre}, must overcome a fundamental \emph{entropic barrier}. We show that a plant-like antenna cannot be adapted to the light from stars of $T_{s}<3400$ K, as increasing antenna size offers diminishing returns on light-harvesting. This can be overcome if one introduces a slight \emph{enthalpic gradient}, to the antenna. Interestingly, this strategy appears to have been adopted by Earth's oxygenic cyanobacteria, and we conclude that \emph{bacterial} oxygenic photosynthesis is feasible around even the lowest mass M-dwarf stars.Comment: 5 Figures, submitted to Astrobiology and awaiting return of revie

Halo mass - concentration relation from weak lensing

We perform a statistical weak lensing analysis of dark matter profiles around tracers of halo mass from galactic- to cluster-size halos. In this analysis we use 170,640 isolated ~L* galaxies split into ellipticals and spirals, 38,236 groups traced by isolated spectroscopic Luminous Red Galaxies (LRGs) and 13,823 MaxBCG clusters from the Sloan Digital Sky Survey (SDSS) covering a wide range of richness. Together these three samples allow a determination of the density profiles of dark matter halos over three orders of magnitude in mass, from 10^{12} M_{sun} to 10^{15} M_{sun}. The resulting lensing signal is consistent with an NFW or Einasto profile on scales outside the central region. We find that the NFW concentration parameter c_{200b} decreases with halo mass, from around 10 for galactic halos to 4 for cluster halos. Assuming its dependence on halo mass in the form of c_{200b} = c_0 [M/(10^{14}M_{sun}/h)]^{\beta}, we find c_0=4.6 +/- 0.7 (at z=0.22) and \beta=0.13 +/- 0.07, with very similar results for the Einasto profile. The slope (\beta) is in agreement with theoretical predictions, while the amplitude is about two standard deviations below the predictions for this mass and redshift, but we note that the published values in the literature differ at a level of 10-20% and that for a proper comparison our analysis should be repeated in simulations. We discuss the implications of our results for the baryonic effects on the shear power spectrum: since these are expected to increase the halo concentration, the fact that we see no evidence of high concentrations on scales above 20% of the virial radius suggests that baryonic effects are limited to small scales, and are not a significant source of uncertainty for the current weak lensing measurements of the dark matter power spectrum. [ABRIDGED]Comment: 17 pages, 5 figures, accepted to JCAP pending minor revisions that are included in v2 here on arXi

Sunyaev Zel'dovich Effect Observations of Strong Lensing Galaxy Clusters: Probing the Over-Concentration Problem

We have measured the Sunyaev Zel'dovich (SZ) effect for a sample of ten strong lensing selected galaxy clusters using the Sunyaev Zel'dovich Array (SZA). The SZA is sensitive to structures on spatial scales of a few arcminutes, while the strong lensing mass modeling constrains the mass at small scales (typically < 30"). Combining the two provides information about the projected concentrations of the strong lensing clusters. The Einstein radii we measure are twice as large as expected given the masses inferred from SZ scaling relations. A Monte Carlo simulation indicates that a sample randomly drawn from the expected distribution would have a larger median Einstein radius than the observed clusters about 3% of the time. The implied overconcentration has been noted in previous studies with smaller samples of lensing clusters. It persists for this sample, with the caveat that this could result from a systematic effect such as if the gas fractions of the strong lensing clusters are substantially below what is expected.Comment: submitte

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL

Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci

Previous studies have successfully identified genetic variants in several genes associated with human iris (eye) color; however, they all used simplified categorical trait information. Here, we quantified continuous eye color variation into hue and saturation values using high-resolution digital full-eye photographs and conducted a genome-wide association study on 5,951 Dutch Europeans from the Rotterdam Study. Three new regions, 1q42.3, 17q25.3, and 21q22.13, were highlighted meeting the criterion for genome-wide statistically significant association. The latter two loci were replicated in 2,261 individuals from the UK and in 1,282 from Australia. The LYST gene at 1q42.3 and the DSCR9 gene at 21q22.13 serve as promising functional candidates. A model for predicting quantitative eye colors explained over 50% of trait variance in the Rotterdam Study. Over all our data exemplify that fine phenotyping is a useful strategy for finding genes involved in human complex traits

An Integrated Microfluidic Device for Monitoring Changes in Nitric Oxide Production in Single T-Lymphocyte (Jurkat) Cells

A considerable amount of attention has been focused on the analysis of single cells in an effort to better understand cell heterogeneity in cancer and neurodegenerative diseases. Although microfluidic devices have several advantages for single cell analysis, few papers have actually demonstrated the ability of these devices to monitor chemical changes in perturbed biological systems. In this paper, a new microfluidic channel manifold is described that integrates cell transport, lysis, injection, electrophoretic separation, and fluorescence detection into a single device, making it possible to analyze individual cells at a rate of 10 cells/min in an automated fashion. The system was employed to measure nitric oxide (NO) production in single T-lymphocytes (Jurkat cells) using a fluorescent marker, 4-amino-5-methylamino-2',7'-difluorofluorescein diacetate (DAF-FM DA). The cells were also labeled with 6-carboxyfluorescein diacetate (6-CFDA) as an internal standard. The NO production by control cells was compared to that of cells stimulated using lipopolysaccharide (LPS), which is known to cause the expression of inducible nitric oxide synthase (iNOS) in immune-type cells. Statistical analysis of the resulting electropherograms from a population of cells indicated a twofold increase in NO production in the induced cells. These results compare nicely to a recently published bulk cell analysis of NO

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts