Detection of Water Vapor in the Thermal Spectrum of the Non-Transiting Hot Jupiter upsilon Andromedae b

The upsilon Andromedae system was the first multi-planet system discovered orbiting a main sequence star. We describe the detection of water vapor in the atmosphere of the innermost non-transiting gas giant ups~And~b by treating the star-planet system as a spectroscopic binary with high-resolution, ground-based spectroscopy. We resolve the signal of the planet's motion and break the mass-inclination degeneracy for this non-transiting planet via deep combined flux observations of the star and the planet. In total, seven epochs of Keck NIRSPEC $L$ band observations, three epochs of Keck NIRSPEC short wavelength $K$ band observations, and three epochs of Keck NIRSPEC long wavelength $K$ band observations of the ups~And~system were obtained. We perform a multi-epoch cross correlation of the full data set with an atmospheric model. We measure the radial projection of the Keplerian velocity ($K_P$ = 55 $\pm$ 9 km/s), true mass ($M_b$ = 1.7 $^{+0.33}_{-0.24}$ $M_J$), and orbital inclination \big($i_b$ = 24 $\pm$ 4$^{\circ}$\big), and determine that the planet's opacity structure is dominated by water vapor at the probed wavelengths. Dynamical simulations of the planets in the ups~And~system with these orbital elements for ups~And~b show that stable, long-term (100 Myr) orbital configurations exist. These measurements will inform future studies of the stability and evolution of the ups~And~system, as well as the atmospheric structure and composition of the hot Jupiter.Comment: Accepted to A

How the Choice of Force-Field Affects the Stability and Self-Assembly Process of Supramolecular CTA Fibers

[Image: see text] In recent years, computational methods have become an essential element of studies focusing on the self-assembly process. Although they provide unique insights, they face challenges, from which two are the most often mentioned in the literature: the temporal and spatial scale of the self-assembly. A less often mentioned issue, but not less important, is the choice of the force-field. The repetitive nature of the supramolecular structure results in many similar interactions. Consequently, even a small deviation in these interactions can lead to significant energy differences in the whole structure. However, studies comparing different force-fields for self-assembling systems are scarce. In this article, we compare molecular dynamics simulations for trifold hydrogen-bonded fibers performed with different force-fields, namely GROMOS, CHARMM General Force Field (CGenFF), CHARMM Drude, General Amber Force-Field (GAFF), Martini, and polarized Martini. Briefly, we tested the force-fields by simulating: (i) spontaneous self-assembly (none form a fiber within 500 ns), (ii) stability of the fiber (observed for CHARMM Drude, GAFF, MartiniP), (iii) dimerization (observed for GROMOS, GAFF, and MartiniP), and (iv) oligomerization (observed for CHARMM Drude and MartiniP). This system shows that knowledge of the force-field behavior regarding interactions in oligomer and larger self-assembled structures is crucial for designing efficient simulation protocols for self-assembling systems

Simulating the Multi-Epoch Direct Detection Technique to Isolate the Thermal Emission of the Non-Transiting Hot Jupiter HD187123B

We report the 6.5$\sigma$ detection of water from the hot Jupiter HD187123b with a Keplerian orbital velocity $K_p$ of 53 $\pm$ 13 km/s. This high confidence detection is made using a multi-epoch, high resolution, cross correlation technique, and corresponds to a planetary mass of 1.4$^{+0.5}_{-0.3}$ $M_J$ and an orbital inclination of 21 $\pm$ 5$^{\circ}$. The technique works by treating the planet/star system as a spectroscopic binary and obtaining high signal-to-noise, high resolution observations at multiple points across the planet's orbit to constrain the system's binary dynamical motion. All together, seven epochs of Keck/NIRSPEC $L$-band observations were obtained, with five before the instrument upgrade and two after. Using high resolution SCARLET planetary and PHOENIX stellar spectral models, along with a line-by-line telluric absorption model, we were able to drastically increase the confidence of the detection by running simulations that could reproduce, and thus remove, the non-random structured noise in the final likelihood space well. The ability to predict multi-epoch results will be extremely useful for furthering the technique. Here, we use these simulations to compare three different approaches to combining the cross correlations of high resolution spectra and find that the Zucker 2003 log(L) approach is least affected by unwanted planet/star correlation for our HD187123 data set. Furthermore, we find that the same total S/N spread across an orbit in many, lower S/N epochs rather than fewer, higher S/N epochs could provide a more efficient detection. This work provides a necessary validation of multi-epoch simulations which can be used to guide future observations and will be key to studying the atmospheres of further separated, non-transiting exoplanets.Comment: Accepted to AJ, 14 pages, 10 figure

Ground- and Space-based Detection of the Thermal Emission Spectrum of the Transiting Hot Jupiter KELT-2Ab

We describe the detection of water vapor in the atmosphere of the transiting hot Jupiter KELT-2Ab by treating the star-planet system as a spectroscopic binary with high-resolution, ground-based spectroscopy. We resolve the signal of the planet's motion with deep combined flux observations of the star and the planet. In total, six epochs of Keck NIRSPEC $L$-band observations were obtained, and the full data set was subjected to a cross correlation analysis with a grid of self-consistent atmospheric models. We measure a radial projection of the Keplerian velocity, $K_P$, of 148 $\pm$ 7 km s$^{-1}$, consistent with transit measurements, and detect water vapor at 3.8$\sigma$. We combine NIRSPEC $L$-band data with $Spitzer$ IRAC secondary eclipse data to further probe the metallicity and carbon-to-oxygen ratio of KELT-2Ab's atmosphere. While the NIRSPEC analysis provides few extra constraints on the $Spitzer$ data, it does provide roughly the same constraints on metallicity and carbon-to-oxygen ratio. This bodes well for future investigations of the atmospheres of non-transiting hot Jupiters.Comment: accepted to A

Evidence for the Direct Detection of the Thermal Spectrum of the Non-Transiting Hot Gas Giant HD 88133 b

We target the thermal emission spectrum of the non-transiting gas giant HD 88133 b with high-resolution near-infrared spectroscopy, by treating the planet and its host star as a spectroscopic binary. For sufficiently deep summed flux observations of the star and planet across multiple epochs, it is possible to resolve the signal of the hot gas giant's atmosphere compared to the brighter stellar spectrum, at a level consistent with the aggregate shot noise of the full data set. To do this, we first perform a principal component analysis to remove the contribution of the Earth's atmosphere to the observed spectra. Then, we use a cross-correlation analysis to tease out the spectra of the host star and HD 88133 b to determine its orbit and identify key sources of atmospheric opacity. In total, six epochs of Keck NIRSPEC L band observations and three epochs of Keck NIRSPEC K band observations of the HD 88133 system were obtained. Based on an analysis of the maximum likelihood curves calculated from the multi-epoch cross correlation of the full data set with two atmospheric models, we report the direct detection of the emission spectrum of the non-transiting exoplanet HD 88133 b and measure a radial projection of the Keplerian orbital velocity of 40 $\pm$ 15 km/s, a true mass of 1.02$^{+0.61}_{-0.28}M_J$, a nearly face-on orbital inclination of 15${^{+6}_{-5}}^{\circ}$, and an atmosphere opacity structure at high dispersion dominated by water vapor. This, combined with eleven years of radial velocity measurements of the system, provides the most up-to-date ephemeris for HD 88133.Comment: 9 pages, 6 figures; accepted for publication in Ap

Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and Opportunities

[Image: see text] Self-assembled metallo-organic cages have emerged as promising biomimetic platforms that can encapsulate whole substrates akin to an enzyme active site. Extensive experimental work has enabled access to a variety of structures, with a few notable examples showing catalytic behavior. However, computational investigations of metallo-organic cages are scarce, not least due to the challenges associated with their modeling and the lack of accurate and efficient protocols to evaluate these systems. In this review, we discuss key molecular principles governing the design of functional metallo-organic cages, from the assembly of building blocks through binding and catalysis. For each of these processes, computational protocols will be reviewed, considering their inherent strengths and weaknesses. We will demonstrate that while each approach may have its own specific pitfalls, they can be a powerful tool for rationalizing experimental observables and to guide synthetic efforts. To illustrate this point, we present several examples where modeling has helped to elucidate fundamental principles behind molecular recognition and reactivity. We highlight the importance of combining computational and experimental efforts to speed up supramolecular catalyst design while reducing time and resources

Genome-Wide Comparison of PU.1 and Spi-B Binding Sites in a Mouse B Lymphoma Cell Line

Background Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, roles in B cell development. PU.1 and Spi-B are both expressed in B cells, and have been demonstrated to redundantly activate transcription of genes required for B cell differentiation and function. It was hypothesized that Spi-B and PU.1 occupy a similar set of regions within the genome of a B lymphoma cell line. Results To compare binding regions of Spi-B and PU.1, murine WEHI-279 lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Anti-FLAG chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) was performed. Analysis for high-stringency enriched genomic regions demonstrated that PU.1 occupied 4528 regions and Spi-B occupied 3360 regions. The majority of regions occupied by Spi-B were also occupied by PU.1. Regions bound by Spi-B and PU.1 were frequently located immediately upstream of genes associated with immune response and activation of B cells. Motif-finding revealed that both transcription factors were predominantly located at the ETS core domain (GGAA), however, other unique motifs were identified when examining regions associated with only one of the two factors. Motifs associated with unique PU.1 binding included POU2F2, while unique motifs in the Spi-B regions contained a combined ETS-IRF motif. Conclusions Our results suggest that complementary biological functions of PU.1 and Spi-B may be explained by their interaction with a similar set of regions in the genome of B cells. However, sites uniquely occupied by PU.1 or Spi-B provide insight into their unique functions

P53 IMMUNOHISTOCHEMISTRY AS A SURROGATE FOR TP53 MUTATIONAL ANALYSIS IN ENDOMETRIAL CANCER BIOPSIES

Meeting abstract from 17th Biennial Meeting of the International Gynecologic Cancer Society Kyoto, Japan September 14-16, 201