A spatially explicit model for competition among specialists and generalists in a heterogeneous environment

Competition is a major force in structuring ecological communities. The strength of competition can be measured using the concept of a niche. A niche comprises the set of requirements of an organism in terms of habitat, environment and functional role. The more niches overlap, the stronger competition is. The niche breadth is a measure of specialization: the smaller the niche space of an organism, the more specialized the organism is. It follows that, everything else being equal, generalists tend to be more competitive than specialists. In this paper, we compare the outcome of competition among generalists and specialists in a spatial versus a nonspatial habitat in a heterogeneous environment. Generalists can utilize the entire habitat, whereas specialists are restricted to their preferred habitat type. We find that although competitiveness decreases with specialization, specialists are more competitive in a spatial than in a nonspatial habitat as patchiness increases.Comment: Published at http://dx.doi.org/10.1214/105051606000000394 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Spatially explicit non-Mendelian diploid model

We introduce a spatially explicit model for the competition between type $a$ and type $b$ alleles. Each vertex of the $d$-dimensional integer lattice is occupied by a diploid individual, which is in one of three possible states or genotypes: $aa$, $ab$ or $bb$. We are interested in the long-term behavior of the gene frequencies when Mendel's law of segregation does not hold. This results in a voter type model depending on four parameters; each of these parameters measures the strength of competition between genes during meiosis. We prove that with or without a spatial structure, type $a$ and type $b$ alleles coexist at equilibrium when homozygotes are poor competitors. The inclusion of a spatial structure, however, reduces the parameter region where coexistence occurs.Comment: Published in at http://dx.doi.org/10.1214/09-AAP598 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Stochastic spatial models of host-pathogen and host-mutualist interactions I

Mutualists and pathogens, collectively called symbionts, are ubiquitous in plant communities. While some symbionts are highly host-specific, others associate with multiple hosts. The outcomes of multispecies host-symbiont interactions with different degrees of specificity are difficult to predict at this point due to a lack of a general conceptual framework. Complicating our predictive power is the fact that plant populations are spatially explicit, and we know from past research that explicit space can profoundly alter plant-plant interactions. We introduce a spatially explicit, stochastic model to investigate the role of explicit space and host-specificity in multispecies host-symbiont interactions. We find that in our model, pathogens can significantly alter the spatial structure of plant communities, promoting coexistence, whereas mutualists appear to have only a limited effect. Effects are more pronounced the more host-specific symbionts are.Comment: Published at http://dx.doi.org/10.1214/105051605000000782 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Error-resistant Single Qubit Gates with Trapped Ions

Coherent operations constitutive for the implementation of single and multi-qubit quantum gates with trapped ions are demonstrated that are robust against variations in experimental parameters and intrinsically indeterministic system parameters. In particular, pulses developed using optimal control theory are demonstrated for the first time with trapped ions. Their performance as a function of error parameters is systematically investigated and compared to composite pulses.Comment: 5 pages 5 figure

Rotation periods of Post-T Tauri stars in Lindroos systems

We present a rotational study of Post-T Tauri stars (PTTSs) in Lindroos systems, defined as binaries with early type primaries on the main-sequence (MS) and late-type secondaries on the pre-main-sequence (PMS) phase. The importance of this study in comparison with previous ones is that the Lindroos sample is not X-ray selected so we avoid a possible bias towards fast rotators. In this preliminary study we have monitored eleven stars in the UBVRI bands during two campaigns of ten consecutive nights each. Eight of the observed PTTSs show periodic modulations in their lightcurves and the derived periods range from 1.9d to 8.0d. The comparison of these results with theoretical rotational tracks based on disk-star locking theory shows that star-disk decoupling times of 1-20 Myr could reproduce the rotational properties of the targets, assuming an initial rotation period of ~8d and a mass of 1 Mo. We have studied the rotation-activity relations of Lindroos PTTSs and compared them with those found in other groups of PMS and zero-age main-sequence (ZAMS) ~1 Mo stars. The Lindroos sample displays activity-rotation relations very similar to those found in TTSs. It contains a mixture of very active stars, with Lx/Lbol ratios close to the saturation level of -3, and less active (unsaturated) stars. This could be the result of different star-disk decoupling times. Future monitoring of a larger and unbiased sample of PTTS will be important to confirm the significance of these results

How genealogies are affected by the speed of evolution

In a series of recent works it has been shown that a class of simple models of evolving populations under selection leads to genealogical trees whose statistics are given by the Bolthausen-Sznitman coalescent rather than by the well known Kingman coalescent in the case of neutral evolution. Here we show that when conditioning the genealogies on the speed of evolution, one finds a one parameter family of tree statistics which interpolates between the Bolthausen-Sznitman and Kingman's coalescents. This interpolation can be calculated explicitly for one specific version of the model, the exponential model. Numerical simulations of another version of the model and a phenomenological theory indicate that this one-parameter family of tree statistics could be universal. We compare this tree structure with those appearing in other contexts, in particular in the mean field theory of spin glasses

System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap

Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell Proteomics 10, 10.1074/mcp.M110.003699). Here we couple an ultra high pressure liquid chromatography system to a novel bench top Orbitrap mass spectrometer (Q Exactive) with the goal of nearly complete, rapid, and robust analysis of the yeast proteome. Single runs of filter-aided sample preparation (FASP)-prepared and LysC-digested yeast cell lysates identified an average of 3923 proteins. Combined analysis of six single runs improved these values to more than 4000 identified proteins/run, close to the total number of proteins expressed under standard conditions, with median sequence coverage of 23%. Because of the absence of fractionation steps, only minuscule amounts of sample are required. Thus the yeast model proteome can now largely be covered within a few hours of measurement time and at high sensitivity. Median coverage of proteins in Kyoto Encyclopedia of Genes and Genomes pathways with at least 10 members was 88%, and pathways not covered were not expected to be active under the conditions used. To study perturbations of the yeast proteome, we developed an external, heavy lysine-labeled SILAC yeast standard representing different proteome states. This spike-in standard was employed to measure the heat shock response of the yeast proteome. Bioinformatic analysis of the heat shock response revealed that translation-related functions were down-regulated prominently, including nucleolar processes. Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities

Composite absorbing potentials

The multiple scattering interferences due to the addition of several contiguous potential units are used to construct composite absorbing potentials that absorb at an arbitrary set of incident momenta or for a broad momentum interval.Comment: 9 pages, Revtex, 2 postscript figures. Accepted in Phys. Rev. Let

The spectacular evolution of Supernova 1996al over 15 years: a low energy explosion of a stripped massive star in a highly structured environment

Spectrophotometry of SN 1996al carried out throughout 15 years is presented. The early photometry suggests that SN 1996al is a Linear type-II supernova, with an absolute peak of Mv ~ -18.2 mag. Early spectra present broad, asymmetric Balmer emissions, with super-imposed narrow lines with P-Cygni profile, and He I features with asymmetric, broad emission components. The analysis of the line profiles shows that the H and He broad components form in the same region of the ejecta. By day +142, the Halpha profile dramatically changes: the narrow P-Cygni profile disappears, and the Halpha is fitted by three emission components, that will be detected over the remaining 15 yrs of the SN monitoring campaign. Instead, the He I emissions become progressively narrower and symmetric. A sudden increase in flux of all He I lines is observed between 300 and 600 days. Models show that the supernova luminosity is sustained by the interaction of low mass (~1.15 Msun) ejecta, expelled in a low kinetic energy (~ 1.6 x 10^50 erg) explosion, with highly asymmetric circumstellar medium. The detection of Halpha emission in pre-explosion archive images suggests that the progenitor was most likely a massive star (~25 Msun ZAMS) that had lost a large fraction of its hydrogen envelope before explosion, and was hence embedded in a H-rich cocoon. The low-mass ejecta and modest kinetic energy of the explosion are explained with massive fallback of material into the compact remnant, a 7-8 Msun black hole.Comment: 27 pages, 23 figures, Accepted for publication in MNRA