Hermit Thrush (\u3cem\u3eCatharus guttatus\u3c/em\u3e) and Veery (\u3cem\u3eC. fuscescens\u3c/em\u3e) Breeding Habitat Associations in Southern Appalachian High-Elevation Forests.

The Hermit Thrush is a new breeding bird in the Southern Appalachian high-elevation mountains, having expanded its range southward over the last few decades. Here it is sympatric with the Veery, a congeneric breeding resident. In order to more fully understand why the range expansion took place and to understand more about the local ecology of the newly arrived bird, I measured several habitat variables in 30 Hermit Thrush and 24 Veery territories. Principal Components Analysis and Cluster Analysis brought to light several patterns of habitat preferences for these 2 species. Hermit Thrushes prefer territories with more leaf litter on the ground and less shrub density than Veery territories. Competition between these species should remain low, as their niche differences brought to light in this study should enable them to breed in close proximity to each other in these high-elevation mountains

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a na\"ive user to approach GAMer 2, a mesh generation code written in C++ designed to convert structural datasets to realistic geometric meshes, while preserving the underlying shapes. We present two example cases, 1) mesh generation at the subcellular scale as informed by electron tomography, and 2) meshing a protein with structure from x-ray crystallography. We further demonstrate that the meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.Comment: 6 pages and 4 figures. Supplemental Movie available upon reques

3.6 and 4.5 μ\mum Spitzer{\it Spitzer} Phase Curves of the Highly-Irradiated Hot Jupiters WASP-19b and HAT-P-7b

We analyze full-orbit phase curve observations of the transiting hot Jupiters WASP-19b and HAT-P-7b at 3.6 and 4.5 $\mu$m obtained using the Spitzer Space Telescope. For WASP-19b, we measure secondary eclipse depths of $0.485\%\pm 0.024\%$ and $0.584\%\pm 0.029\%$ at 3.6 and 4.5 $\mu$m, which are consistent with a single blackbody with effective temperature $2372 \pm 60$ K. The measured 3.6 and 4.5 $\mu$m secondary eclipse depths for HAT-P-7b are $0.156\%\pm 0.009\%$ and $0.190\%\pm 0.006\%$, which are well-described by a single blackbody with effective temperature $2667\pm 57$ K. Comparing the phase curves to the predictions of one-dimensional and three-dimensional atmospheric models, we find that WASP-19b's dayside emission is consistent with a model atmosphere with no dayside thermal inversion and moderately efficient day-night circulation. We also detect an eastward-shifted hotspot, suggesting the presence of a superrotating equatorial jet. In contrast, HAT-P-7b's dayside emission suggests a dayside thermal inversion and relatively inefficient day-night circulation; no hotspot shift is detected. For both planets, these same models do not agree with the measured nightside emission. The discrepancies in the model-data comparisons for WASP-19b might be explained by high-altitude silicate clouds on the nightside and/or high atmospheric metallicity, while the very low 3.6 $\mu$m nightside planetary brightness for HAT-P-7b may be indicative of an enhanced global C/O ratio. We compute Bond albedos of 0 ($<0.08$ at $1\sigma$) and $0.38\pm 0.06$ for WASP-19b and HAT-P-7b, respectively. In the context of other planets with thermal phase curve measurements, we show that WASP-19b and HAT-P-7b fit the general trend of decreasing day-night heat recirculation with increasing irradiation.Comment: 22 pages, 29 figures, accepted by Ap

Spitzer Secondary Eclipse Observations of Five Cool Gas Giant Planets and Empirical Trends in Cool Planet Emission Spectra

In this work we present Spitzer 3.6 and 4.5 micron secondary eclipse observations of five new cool (<1200 K) transiting gas giant planets: HAT-P-19b, WASP-6b, WASP-10b, WASP-39b, and WASP-67b. We compare our measured eclipse depths to the predictions of a suite of atmosphere models and to eclipse depths for planets with previously published observations in order to constrain the temperature- and mass-dependent properties of gas giant planet atmospheres. We find that the dayside emission spectra of planets less massive than Jupiter require models with efficient circulation of energy to the night side and/or increased albedos, while those with masses greater than that of Jupiter are consistently best-matched by models with inefficient circulation and low albedos. At these relatively low temperatures we expect the atmospheric methane to CO ratio to vary as a function of metallicity, and we therefore use our observations of these planets to constrain their atmospheric metallicities. We find that the most massive planets have dayside emission spectra that are best-matched by solar metallicity atmosphere models, but we are not able to place strong constraints on metallicities of the smaller planets in our sample. Interestingly, we find that the ratio of the 3.6 and 4.5 micron brightness temperatures for these cool transiting planets is independent of planet temperature, and instead exhibits a tentative correlation with planet mass. If this trend can be confirmed, it would suggest that the shape of these planets' emission spectra depends primarily on their masses, consistent with the hypothesis that lower-mass planets are more likely to have metal-rich atmospheres.Comment: 16 pages, 14 figures, accepted for publication in Ap

Chemical Reaction Dynamics at Surfaces

Contains reports on three research projects.Joint Services Electronics Program (Contract DAAL03-86-K-0002)Joint Services Electronics Program (Contract DAAL03-89-C-0001)National Science Foundation (Grant CHE 85-08734)MIT Energy Laboratory - Synthetic Fuels CenterPetroleum Research Fund (Contract 19014-AC5

Chemical Reaction Dynamics at Surfaces

Contains reports on six research projects.Joint Services Electronics Program Contract DAAL03-89-C-0001MIT Energy Laboratory - Synthetic Fuels CenterNational Science Foundation Grant CHE 85-08734Petroleum Research Fund Contract 19014-AC

A New Sample of Cool Subdwarfs from SDSS: Properties and Kinematics

We present a new sample of M subdwarfs compiled from the 7th data release of the Sloan Digital Sky Survey. With 3517 new subdwarfs, this new sample significantly increases the number of spectroscopically confirmed low-mass subdwarfs. This catalog also includes 905 extreme and 534 ultra sudwarfs. We present the entire catalog including observed and derived quantities, and template spectra created from co-added subdwarf spectra. We show color-color and reduced proper motion diagrams of the three metallicity classes, which are shown to separate from the disk dwarf population. The extreme and ultra subdwarfs are seen at larger values of reduced proper motion as expected for more dynamically heated populations. We determine 3D kinematics for all of the stars with proper motions. The color-magnitude diagrams show a clear separation of the three metallicity classes with the ultra and extreme subdwarfs being significantly closer to the main sequence than the ordinary subdwarfs. All subdwarfs lie below (fainter) and to the left (bluer) of the main sequence. Based on the average $(U,V,W)$ velocities and their dispersions, the extreme and ultra subdwarfs likely belong to the Galactic halo, while the ordinary subdwarfs are likely part of the old Galactic (or thick) disk. An extensive activity analysis of subdwarfs is performed using H$\alpha$ emission and 208 active subdwarfs are found. We show that while the activity fraction of subdwarfs rises with spectral class and levels off at the latest spectral classes, consistent with the behavior of M dwarfs, the extreme and ultra subdwarfs are basically flat.Comment: 66 pages, 23 figures, accepted in Ap

Chemical Reaction Dynamics at Surfaces

Contains reports on two research projects with publication lists in each section.Joint Services Electronics Program Contract DAAL03-89-C-0001MIT Energy Laboratory Synthetic Fuels CenterNational Science Foundation Grant CHE 85-08734Petroleum Research Fund Contract 19014-AC

LHS6343C: A Transiting Field Brown Dwarf Discovered by the Kepler Mission

We report the discovery of a brown dwarf that transits one member of the M+M binary system LHS6343AB every 12.71 days. The transits were discovered using photometric data from the Kelper public data release. The LHS6343 stellar system was previously identified as a single high-proper-motion M dwarf. We use high-contrast imaging to resolve the system into two low-mass stars with masses 0.45 Msun and 0.36 Msun, respectively, and a projected separation of 55 arcsec. High-resolution spectroscopy shows that the more massive component undergoes Doppler variations consistent with Keplerian motion, with a period equal to the transit period and an amplitude consistent with a companion mass of M_C = 62.8 +/- 2.3 Mjup. Based on an analysis of the Kepler light curve we estimate the radius of the companion to be R_C = 0.832 +/- 0.021 Rjup, which is consistent with theoretical predictions of the radius of a > 1 Gyr brown dwarf.Comment: Our previous analysis neglected the dependence of the scaled semimajor axis, a/R, on the transit depth. By not correcting a/R for the third-light contamination, we overestimated the mass of Star A, which led to an overestimate the mass and radius of the LHS6343