From Blackbirds to Black Holes: Investigating Capture-Recapture Methods for Time Domain Astronomy [HEAP]

In time domain astronomy, recurrent transients present a special problem: how to infer total populations from limited observations. Monitoring observations may give a biassed view of the underlying population due to limitations on observing time, visibility and instrumental sensitivity. A similar problem exists in the life sciences, where animal populations (such as migratory birds) or disease prevalence, must be estimated from sparse and incomplete data. The class of methods termed Capture-Recapture is used to reconstruct population estimates from time-series records of encounters with the study population. This paper investigates the performance of Capture-Recapture methods in astronomy via a series of numerical simulations. The Blackbirds code simulates monitoring of populations of transients, in this case accreting binary stars (neutron star or black hole accreting from a stellar companion) under a range of observing strategies. We first generate realistic light-curves for populations of binaries with contrasting orbital period distributions. These models are then randomly sampled at observing cadences typical of existing and planned monitoring surveys. The classical capture-recapture methods, Lincoln-Peterson, Schnabel estimators, related techniques, and newer methods implemented in the Rcapture package are compared. A general exponential model based on the radioactive decay law is introduced, and demonstrated to recover (at 95% confidence) the underlying population abundance and duty cycle, in a fraction of the observing visits (10-50%) required to discover all the sources in the simulation. Capture-Recapture is a promising addition to the toolbox of time domain astronomy, and methods implemented in R by the biostats community can be readily called from within Python.

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S. Laycock
Tue, 17 Jan 17

Comments: Accepted to New Astronomy. 11 pages, 8 figures (refereed version prior to editorial process)

Circular spectropolarimetric sensing of chiral photosystems in decaying leaves [CL]

Circular polarization spectroscopy has proven to be an indispensable tool in photosynthesis research and (bio)-molecular research in general. Oxygenic photosystems typically display an asymmetric Cotton effect around the chlorophyll absorbance maximum with a signal $\leq 1 \%$. In vegetation, these signals are the direct result of the chirality of the supramolecular aggregates. The circular polarization is thus directly influenced by the composition and architecture of the photosynthetic macrodomains, and is thereby linked to photosynthetic functioning. Although ordinarily measured only on a molecular level, we have developed a new spectropolarimetric instrument, TreePol, that allows for both laboratory and in-the-field measurements. Through spectral multiplexing, TreePol is capable of fast measurements with a sensitivity of $\sim 1*10^{-4}$ and is therefore suitable of non-destructively probing the molecular architecture of whole plant leaves. We have measured the chiroptical evolution of \textit{Hedera helix} leaves for a period of 22 days. Spectrally resolved circular polarization measurements (450-900 nm) on whole leaves in transmission exhibit a strong decrease in the polarization signal over time after plucking, which we accredit to the deterioration of chiral macro-aggregates. Chlorophyll \textit{a} levels measured over the same period by means of UV-Vis absorption and fluorescence spectroscopy showed a much smaller decrease. With these results we are able to distinguish healthy from deteriorating leaves. Hereby we indicate the potency of circular polarization spectroscopy on whole and intact leaves as a nondestructive tool for structural and plant stress assessment. Additionally, we underline the establishment of circular polarization signals as remotely accessible means of detecting the presence of extraterrestrial life.

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C. Patty, L. Visser, F. Ariese, et. al.
Fri, 6 Jan 17

Comments: 29 pages, 6 figures

Thermodynamic Explanation for the Cosmic Ubiquity of Organic Pigments [EPA]

There is increasingly more evidence being accumulated for the occurrence of large amounts of organic material in the cosmos, particularly in the form of aromatic compounds. These molecules can be found on the surface of Earth and Mars, in the atmospheres of the larger planets and on many of their satellites, on asteroids, comets, meteorites, the atmospheres of red giant stars, interstellar nebulae, and in the spiral arms of galaxies. Many of these environments are expected to be of low temperature and pressure, implying that the Gibbs free energy for the formation of these complex molecules should be positive and large, suggesting that their existence could only be attributed to non-equilibrium thermodynamic processes. In this article we first review the evidence for the abundance of these molecules in the cosmos and then describe how the ubiquity can be explained from within the framework of non-equilibrium thermodynamics on the basis of the catalytic properties of these pigment molecules in dissipating photons of the ultraviolet and visible emission spectra of neighboring stars, leading to greater local entropy production. A relation between the maximum wavelength of absorption of these organic pigments and the corresponding stellar photon environment, provides a guide to determining which aromatic compounds are most probable in a given stellar neighborhood, a postulate that can be verified on Earth. It is suggested that at least some of the baryonic dark matter may be associated with these molecules which emit in the extreme infrared with many, but weak, emission lines, thus so far escaping detection. This thermodynamic explanation for the ubiquity of these organic molecules also has relevance to the possibility of life, both as we know it, and as we may not know it, throughout the universe.

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K. Michaelian and A. Simeonov
Thu, 1 Sep 16

Comments: 23 pages, no figures

Modeling Stellar Proton Event-induced particle radiation dose on close-in exoplanets [EPA]

Kepler observations have uncovered the existence of a large number of close-in exoplanets and serendipitously of stellar superflares with emissions several orders of magnitude higher than those observed on the Sun. The interaction between the two and its implications on planetary habitability is of great interest to the community. Stellar Proton Events interact with the planetary atmosphere, generate secondary particles and increase the radiation dose on the surface. This effect is amplified for close-in exoplanets and can be a serious threat to potential planetary life. Using Monte Carlo simulations, we model the SPE-induced particle radiation dose on the surface of such exoplanets. We study the dependence of radiation dose on flare energy, planet’s orbital distance, magnetic field strength and atmospheric column density, and discuss its implications on constraining planetary habitability.

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D. Atri
Thu, 23 Jun 16

Comments: N/A

Curvature-induced dissipation [CL]

By inspecting the effect of curvature on a moving fluid, we find that local sources of curvature not only exert inertial forces on the flow, but also generate viscous stresses as a result of the departure of streamlines from the idealized geodesic motion. The curvature-induced viscous forces are shown to cause an indirect and yet appreciable energy dissipation. As a consequence, the flow converges to a stationary equilibrium state solely by virtue of curvature-induced dissipation. In addition, we show that flow through randomly-curved media satisfies a non-linear transport law, resembling Darcy-Forchheimer’s law, due to the viscous forces generated by the spatial curvature. It is further shown that the permeability can be characterized in terms of the average metric perturbation.

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J. Debus, M. Mendoza, S. Succi, et. al.
Fri, 11 Dec 15

Comments: N/A

Parking-garage structures in astrophysics and biophysics [CL]

A striking shape was recently observed for the cellular organelle endoplasmic reticulum consisting of stacked sheets connected by helical ramps. This shape is interesting both for its biological function, to synthesize proteins using an increased surface area for ribosome factories, and its geometric properties that may be insensitive to details of the microscopic interactions. In the present work, we find very similar shapes in our molecular dynamics simulations of the nuclear pasta phases of dense nuclear matter that are expected deep in the crust of neutron stars. There are dramatic differences between nuclear pasta and terrestrial cell biology. Nuclear pasta is 14 orders of magnitude denser than the aqueous environs of the cell nucleus and involves strong interactions between protons and neutrons, while cellular scale biology is dominated by the entropy of water and complex assemblies of biomolecules. Nonetheless the very similar geometry suggests both systems may have similar coarse-grained dynamics and that the shapes are indeed determined by geometrical considerations, independent of microscopic details. Many of our simulations self-assemble into flat sheets connected by helical ramps. These ramps may impact the thermal and electrical conductivities, viscosity, shear modulus, and breaking strain of neutron star crust. The interaction we use, with Coulomb frustration, may provide a simple model system that reproduces many biologically important shapes.

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C. Horowitz, D. Berry, M. Caplan, et. al.
Wed, 2 Sep 15

Comments: 5 pages, 3 figures

The Habitable Zone of Inhabited Planets [EPA]

In this paper we discuss and illustrate the hypothesis that life substantially alters the state of a planetary environment and therefore, modifies the limits of the HZ as estimated for an uninhabited planet. This hypothesis lead to the introduction of the Habitable Zone for Inhabited planets (hereafter InHZ), defined here as the region where the complex interaction between life and its abiotic environment is able to produce plausible equilibrium states with the necessary physical conditions for the existence and persistence of life itself. We support our hypothesis of an InHZ with three theoretical arguments, multiple evidences coming from observations of the Earth system, several conceptual experiments and illustrative numerical simulations. Conceptually the diference between the InHZ and the Abiotic HZ (AHZ) depends on unique and robust properties of life as an emergent physical phenomenon and not necesarily on the particular life forms bearing in the planet. Our aim here is to provide conceptual basis for the development of InHZ models incorporating consistently life-environment interactions. Although previous authors have explored the effects of life on habitability there is a gap in research developing the reasons why life should be systematically included at determining the HZ limits. We do not provide here definitive limits to the InHZ but we show through simple numerical models (as a parable of an inhabited planet) how the limits of the AHZ could be modified by including plausible interactions between biota and its environment. These examples aim also at posing the question that if limits of the HZ could be modified by the presence of life in those simple dynamical systems how will those limits change if life is included in established models of the AHZ.

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J. Zuluaga, J. Salazar, P. Cuartas-Restrepo, et. al.
Tue, 20 May 14

Comments: Accepted for publication in Biogeosciences Discussion; 16 pages, 5 figures. Comments and discussion are welcomed at: this http URL

Real-Space x-ray tomographic reconstruction of randomly oriented objects with sparse data frames [CL]

Schemes for X-ray imaging single protein molecules using new x-ray sources, like x-ray free electron lasers (XFELs), require processing many frames of data that are obtained by taking temporally short snapshots of identical molecules, each with a random and unknown orientation. Due to the small size of the molecules and short exposure times, average signal levels of much less than 1 photon/pixel/frame are expected, much too low to be processed using standard methods. One approach to process the data is to use statistical methods developed in the EMC algorithm (Loh & Elser, Phys. Rev. E, 2009) which processes the data set as a whole. In this paper we apply this method to a real-space tomographic reconstruction using sparse frames of data (below $10^{-2}$ photons/pixel/frame) obtained by performing x-ray transmission measurements of a low-contrast, randomly-oriented object. This extends the work by Philipp et al. (Optics Express, 2012) to three dimensions and is one step closer to the single molecule reconstruction problem.

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Fri, 8 Nov 13