paper.bib

@article{barstow_clouds_2014,
  title = {{{CLOUDS ON THE HOT JUPITER HD189733b}}: {{CONSTRAINTS FROM THE REFLECTION SPECTRUM}}},
  shorttitle = {{{CLOUDS ON THE HOT JUPITER HD189733b}}},
  author = {Barstow, J. K. and Aigrain, S. and Irwin, P. G. J. and Hackler, T. and Fletcher, L. N. and Lee, J. M. and Gibson, N. P.},
  year = {2014},
  month = apr,
  journal = {The Astrophysical Journal},
  volume = {786},
  number = {2},
  pages = {154},
  publisher = {The American Astronomical Society},
  issn = {0004-637X},
  doi = {10.1088/0004-637X/786/2/154},
  urldate = {2023-10-23},
  abstract = {The hot Jupiter HD 189733b is probably the best studied of the known extrasolar planets, with published transit and eclipse spectra covering the near UV to mid-IR range. Recent work on the transmission spectrum has shown clear evidence for the presence of clouds in its atmosphere, which significantly increases the model atmosphere parameter space that must be explored in order to fully characterize this planet. In this work, we apply the NEMESIS atmospheric retrieval code to the recently published HST/STIS reflection spectrum, and also to the dayside thermal emission spectrum in light of new Spitzer/IRAC measurements, as well as our own re-analysis of the HST/NICMOS data. We first use the STIS data to place some constraints on the nature of clouds on HD 189733b and explore solution degeneracy between different cloud properties and the abundance of Na in the atmosphere; as already noted in previous work, absorption due to Na plays a significant role in determining the shape of the reflection spectrum. We then perform a new retrieval of the temperature profile and abundances of H2O, CO2, CO, and CH4 from the dayside thermal emission spectrum. Finally, we investigate the effect of including cloud in the model on this retrieval process. We find that the current quality of data does not warrant the extra complexity introduced by including cloud in the model; however, future data are likely to be of sufficient resolution and signal-to-noise that a more complete model, including scattering particles, will be required.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/F82CBVWX/Barstow et al. - 2014 - CLOUDS ON THE HOT JUPITER HD189733b CONSTRAINTS F.pdf}
}

@article{barstow_comparison_2020,
  title = {A Comparison of Exoplanet Spectroscopic Retrieval Tools},
  author = {Barstow, J. K. and Changeat, Quentin and Garland, Ryan and Line, Michael R and Rocchetto, Marco and Waldmann, Ingo P},
  year = {2020},
  month = apr,
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {493},
  number = {4},
  pages = {4884--4909},
  issn = {0035-8711},
  doi = {10.1093/mnras/staa548},
  urldate = {2022-08-15},
  abstract = {Over the last several years, spectroscopic observations of transiting exoplanets have begun to uncover information about their atmospheres, including atmospheric composition and indications of the presence of clouds and hazes. Spectral retrieval is the leading technique for interpretation of transmission spectra and is employed by several teams using a variety of forward models and parameter estimation algorithms. However, different model suites have mostly been used in isolation and so it is unknown whether the results from each are comparable. As we approach the launch of the James Webb Space Telescope, we anticipate advances in wavelength coverage, precision, and resolution of transit spectroscopic data, so it is important that the tools that will be used to interpret these information-rich spectra are validated. To this end, we present an intermodel comparison of three retrieval suites: TauREx, nemesis, and chimera. We demonstrate that the forward model spectra are in good agreement (residual deviations on the order of 20--40~ppm), and discuss the results of cross-retrievals among the three tools. Generally, the constraints from the cross-retrievals are consistent with each other and with input values to within 1{$\sigma$}. However, for high precision scenarios with error envelopes of order 30~ppm, subtle differences in the simulated spectra result in discrepancies between the different retrieval suites, and inaccuracies in retrieved values of several {$\sigma$}. This can be considered analogous to substantial systematic/astrophysical noise in a real observation, or errors/omissions in a forward model such as molecular line list incompleteness or missing absorbers.},
  file = {/Users/jingxuanyang/Zotero/storage/BMT3AXRQ/Barstow et al. - 2020 - A comparison of exoplanet spectroscopic retrieval .pdf;/Users/jingxuanyang/Zotero/storage/CLCBNAQU/Barstow et al. - 2020 - A comparison of exoplanet spectroscopic retrieval .pdf;/Users/jingxuanyang/Zotero/storage/GFJ2S8VZ/Barstow et al. - 2020 - A comparison of exoplanet spectroscopic retrieval .pdf;/Users/jingxuanyang/Zotero/storage/IVV8ZJS6/Barstow et al. - 2020 - A comparison of exoplanet spectroscopic retrieval .pdf;/Users/jingxuanyang/Zotero/storage/S79M7IIQ/Barstow et al. - 2020 - A comparison of exoplanet spectroscopic retrieval .pdf;/Users/jingxuanyang/Zotero/storage/KAFKUSWE/5780232.html}
}

@article{barstow_consistent_2016,
  title = {A {{CONSISTENT RETRIEVAL ANALYSIS OF}} 10 {{HOT JUPITERS OBSERVED IN TRANSMISSION}}},
  author = {Barstow, J. K. and Aigrain, S. and Irwin, P. G. J. and Sing, D. K.},
  year = {2016},
  month = dec,
  journal = {The Astrophysical Journal},
  volume = {834},
  number = {1},
  pages = {50},
  publisher = {The American Astronomical Society},
  issn = {0004-637X},
  doi = {10.3847/1538-4357/834/1/50},
  urldate = {2024-06-24},
  abstract = {We present a consistent optimal estimation retrieval analysis of 10 hot Jupiter exoplanets, each with transmission spectral data spanning the visible to near-infrared wavelength range. Using the NEMESIS radiative transfer and retrieval tool, we calculate a range of possible atmospheric states for WASP-6b, WASP-12b, WASP-17b, WASP-19b, WASP-31b, WASP-39b, HD 189733b, HD 209458b, HAT-P-1b, and HAT-P-12b. We find that the spectra of all 10 planets are consistent with the presence of some atmospheric aerosol; WASP-6b, WASP-12b, WASP-17b, WASP-19b, HD 189733b, and HAT-P-12b are all fit best by Rayleigh scattering aerosols, whereas WASP-31b, WASP-39b and HD 209458b are better represented by a gray cloud model. HAT-P-1b has solutions that fall into both categories. WASP-6b, HAT-P-12b, HD 189733b, and WASP-12b must have aerosol extending to low atmospheric pressures (below 0.1 mbar). In general, planets with equilibrium temperatures between 1300 and 1700 K are best represented by deeper, gray cloud layers, whereas cooler or hotter planets are better fit using high Rayleigh scattering aerosol. We find little evidence for the presence of molecular absorbers other than H2O. Retrieval methods can provide a consistent picture across a range of hot Jupiter atmospheres with existing data, and will be a powerful tool for the interpretation of James Webb Space Telescope observations.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/CZHFLUXV/Barstow et al. - 2016 - A CONSISTENT RETRIEVAL ANALYSIS OF 10 HOT JUPITERS.pdf}
}

@article{barstow_unveiling_2020,
  title = {Unveiling Cloudy Exoplanets: The Influence of Cloud Model Choices on Retrieval Solutions},
  shorttitle = {Unveiling Cloudy Exoplanets},
  author = {Barstow, J. K.},
  year = {2020},
  month = oct,
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {497},
  number = {4},
  pages = {4183--4195},
  issn = {0035-8711, 1365-2966},
  doi = {10.1093/mnras/staa2219},
  urldate = {2022-12-19},
  abstract = {In recent years, it has become clear that a substantial fraction of transiting exoplanets have some form of aerosol present in their atmospheres. Transit spectroscopy -- mostly of hot Jupiters, but also of some smaller planets -- has provided evidence for this, in the form of steep downward slopes from blue to red in the optical part of the spectrum, and muted gas absorption features throughout. Retrieval studies seeking to constrain the composition of exoplanet atmospheres must therefore account for the presence of aerosols. However, clouds and hazes are complex physical phenomena, and the transit spectra that are currently available allow us to constrain only some of their properties. Therefore, representation of aerosols in retrieval models requires that they are described by only a few parameters, and this has been done in a variety of ways within the literature. Here, I investigate a range of parametrizations for exoplanet aerosol and their effects on retrievals from transmission spectra of hot Jupiters HD 189733b and HD 209458b. I find that results qualitatively agree for the cloud/haze itself regardless of the parametrization used, and indeed using multiple approaches provides a more holistic picture; the retrieved abundance of H2O is also very robust to assumptions about aerosols. I also find strong evidence that aerosol on HD 209458b covers less than half of the terminator region, whilst the picture is less clear for HD 189733b.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/K7KGLIWJ/Barstow - 2020 - Unveiling cloudy exoplanets the influence of clou.pdf}
}

@article{burrows_spectra_2014,
  title = {Spectra as Windows into Exoplanet Atmospheres},
  author = {Burrows, Adam S.},
  year = {2014},
  month = sep,
  journal = {Proceedings of the National Academy of Sciences},
  volume = {111},
  number = {35},
  pages = {12601--12609},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.1304208111},
  urldate = {2022-09-21},
  abstract = {Understanding a planet's atmosphere is a necessary condition for understanding not only the planet itself, but also its formation, structure, evolution, and habitability. This requirement puts a premium on obtaining spectra and developing credible interpretative tools with which to retrieve vital planetary information. However, for exoplanets, these twin goals are far from being realized. In this paper, I provide a personal perspective on exoplanet theory and remote sensing via photometry and low-resolution spectroscopy. Although not a review in any sense, this paper highlights the limitations in our knowledge of compositions, thermal profiles, and the effects of stellar irradiation, focusing on, but not restricted to, transiting giant planets. I suggest that the true function of the recent past of exoplanet atmospheric research has been not to constrain planet properties for all time, but to train a new generation of scientists who, by rapid trial and error, are fast establishing a solid future foundation for a robust science of exoplanets.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/UG5V7F37/Burrows - 2014 - Spectra as windows into exoplanet atmospheres.pdf}
}

@article{chachan_breaking_2023,
  title = {Breaking {{Degeneracies}} in {{Formation Histories}} by {{Measuring Refractory Content}} in {{Gas Giants}}},
  author = {Chachan, Yayaati and Knutson, Heather A. and Lothringer, Joshua and Blake, Geoffrey A.},
  year = {2023},
  month = feb,
  journal = {The Astrophysical Journal},
  volume = {943},
  number = {2},
  pages = {112},
  issn = {0004-637X, 1538-4357},
  doi = {10.3847/1538-4357/aca614},
  urldate = {2023-10-11},
  abstract = {Relating planet formation to atmospheric composition has been a long-standing goal of the planetary science community. So far, most modeling studies have focused on predicting the enrichment of heavy elements and the C/O ratio in giant planet atmospheres. Although this framework provides useful constraints on the potential formation locations of gas giant exoplanets, carbon and oxygen measurements alone are not enough to determine where a given gas giant planet originated. Here, we show that characterizing the abundances of refractory elements (e.g., silicon and iron) can break these degeneracies. Refractory elements are present in the solid phase throughout most of the disk, and their atmospheric abundances therefore reflect the solid-to-gas accretion ratio during formation. We introduce a new framework that parameterizes the atmospheric abundances of gas giant exoplanets in the form of three ratios: Si/H, O/Si, and C/Si. Si/H traces the solid-to-gas accretion ratio of a planet and is loosely equivalent to earlier notions of ``metallicity.'' For O/Si and C/Si, we present a global picture of their variation with distance and time based on what we know from the solar system meteorites and an updated understanding of the variations of thermal processing within protoplanetary disks. We show that ultrahot Jupiters are ideal targets for atmospheric characterization studies using this framework as we can measure the abundances of refractories, oxygen, and carbon in the gas phase. Finally, we propose that hot Jupiters with silicate clouds and low water abundances might have accreted their envelopes between the soot line and the water snow line.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/GF4I8DJE/Chachan et al. - 2023 - Breaking Degeneracies in Formation Histories by Me.pdf}
}

@article{feroz_multimodal_2008,
  title = {Multimodal Nested Sampling: An Efficient and Robust Alternative to {{Markov Chain Monte Carlo}} Methods for Astronomical Data Analyses},
  shorttitle = {Multimodal Nested Sampling},
  author = {Feroz, F. and Hobson, M. P.},
  year = {2008},
  month = feb,
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {384},
  number = {2},
  pages = {449--463},
  issn = {0035-8711},
  doi = {10.1111/j.1365-2966.2007.12353.x},
  urldate = {2022-08-23},
  abstract = {In performing a Bayesian analysis of astronomical data, two difficult problems often emerge. First, in estimating the parameters of some model for the data, the resulting posterior distribution may be multimodal or exhibit pronounced (curving) degeneracies, which can cause problems for traditional Markov Chain Monte Carlo (MCMC) sampling methods. Secondly, in selecting between a set of competing models, calculation of the Bayesian evidence for each model is computationally expensive using existing methods such as thermodynamic integration. The nested sampling method introduced by Skilling, has greatly reduced the computational expense of calculating evidence and also produces posterior inferences as a by-product. This method has been applied successfully in cosmological applications by Mukherjee, Parkinson \& Liddle, but their implementation was efficient only for unimodal distributions without pronounced degeneracies. Shaw, Bridges \& Hobson recently introduced a clustered nested sampling method which is significantly more efficient in sampling from multimodal posteriors and also determines the expectation and variance of the final evidence from a single run of the algorithm, hence providing a further increase in efficiency. In this paper, we build on the work of Shaw et al. and present three new methods for sampling and evidence evaluation from distributions that may contain multiple modes and significant degeneracies in very high dimensions; we also present an even more efficient technique for estimating the uncertainty on the evaluated evidence. These methods lead to a further substantial improvement in sampling efficiency and robustness, and are applied to two toy problems to demonstrate the accuracy and economy of the evidence calculation and parameter estimation. Finally, we discuss the use of these methods in performing Bayesian object detection in astronomical data sets, and show that they significantly outperform existing MCMC techniques. An implementation of our methods will be publicly released shortly.},
  file = {/Users/jingxuanyang/Zotero/storage/D92JDBF4/Feroz and Hobson - 2008 - Multimodal nested sampling an efficient and robus.pdf;/Users/jingxuanyang/Zotero/storage/C72EDEXY/1023701.html}
}

@article{harris_array_2020,
  title = {Array Programming with {{NumPy}}},
  author = {Harris, Charles R. and Millman, K. Jarrod and {van der Walt}, St{\'e}fan J. and Gommers, Ralf and Virtanen, Pauli and Cournapeau, David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and Smith, Nathaniel J. and Kern, Robert and Picus, Matti and Hoyer, Stephan and {van Kerkwijk}, Marten H. and Brett, Matthew and Haldane, Allan and {del R{\'i}o}, Jaime Fern{\'a}ndez and Wiebe, Mark and Peterson, Pearu and {G{\'e}rard-Marchant}, Pierre and Sheppard, Kevin and Reddy, Tyler and Weckesser, Warren and Abbasi, Hameer and Gohlke, Christoph and Oliphant, Travis E.},
  year = {2020},
  month = sep,
  journal = {Nature},
  volume = {585},
  number = {7825},
  pages = {357--362},
  publisher = {Nature Publishing Group},
  issn = {1476-4687},
  doi = {10.1038/s41586-020-2649-2},
  urldate = {2023-10-10},
  abstract = {Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis.},
  copyright = {2020 The Author(s)},
  langid = {english},
  keywords = {Computational neuroscience,Computational science,Computer science,Software,Solar physics},
  file = {/Users/jingxuanyang/Zotero/storage/AY9TCK93/Harris et al. - 2020 - Array programming with NumPy.pdf}
}

@article{hunter_matplotlib_2007,
  title = {Matplotlib: {{A 2D Graphics Environment}}},
  shorttitle = {Matplotlib},
  author = {Hunter, John D.},
  year = {2007},
  month = may,
  journal = {Computing in Science \& Engineering},
  volume = {9},
  number = {3},
  pages = {90--95},
  issn = {1558-366X},
  doi = {10.1109/MCSE.2007.55},
  urldate = {2023-10-10},
  abstract = {Matplotlib is a 2D graphics package used for Python for application development, interactive scripting,and publication-quality image generation across user interfaces and operating systems},
  file = {/Users/jingxuanyang/Zotero/storage/KDMSG98G/4160265.html}
}

@article{irwin_25d_2020,
  title = {2.{{5D}} Retrieval of Atmospheric Properties from Exoplanet Phase Curves: Application to {{WASP-43b}} Observations},
  shorttitle = {2.{{5D}} Retrieval of Atmospheric Properties from Exoplanet Phase Curves},
  author = {Irwin, P. G. J. and Parmentier, Vivien and Taylor, Jake and Barstow, Jo and Aigrain, Suzanne and Lee, Elspeth and Garland, Ryan},
  year = {2020},
  month = mar,
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {493},
  number = {1},
  pages = {106--125},
  issn = {0035-8711, 1365-2966},
  doi = {10.1093/mnras/staa238},
  urldate = {2023-01-03},
  abstract = {We present a novel retrieval technique that attempts to model phase curve observations of exoplanets more realistically and reliably, which we call the 2.5-dimensional (2.5D) approach. In our 2.5D approach we retrieve the vertical temperature profile and mean gaseous abundance of a planet at all longitudes and latitudes simultaneously, assuming that the temperature or composition, x, at a particular longitude and latitude ( , ) is given by x( , ) = x{\textasciimacron} + (x( , 0) - x{\textasciimacron}) cosn , where x{\textasciimacron} is the mean of the morning and evening terminator values of x( , 0), and n is an assumed coefficient. We compare our new 2.5D scheme with the more traditional 1D approach, which assumes the same temperature profile and gaseous abundances at all points on the visible disc of a planet for each individual phase observation, using a set of synthetic phase curves generated from a GCM-based simulation. We find that our 2.5D model fits these data more realistically than the 1D approach, confining the hotter regions of the planet more closely to the dayside. We then apply both models to WASP-43b phase curve observations of HST/WFC3 and Spitzer/IRAC. We find that the dayside of WASP-43b is apparently much hotter than the nightside and show that this could be explained by the presence of a thick cloud on the nightside with a cloud top at pressure {$<$}0.2 bar. We further show that while the mole fraction of water vapour is reasonably well constrained to (1--10) {\texttimes} 10-4, the abundance of CO is very difficult to constrain with these data since it is degenerate with temperature and prone to possible systematic radiometric differences between the HST/WFC3 and Spitzer/IRAC observations. Hence, it is difficult to reliably constrain C/O.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/5CHJV4GX/Irwin et al. - 2020 - 2.5D retrieval of atmospheric properties from exop.pdf;/Users/jingxuanyang/Zotero/storage/ERNR2X3B/Irwin et al. - 2020 - 2.5D retrieval of atmospheric properties from exop.pdf;/Users/jingxuanyang/Zotero/storage/ESIVFPHG/5715917.html}
}

@article{irwin_nemesis_2008,
  title = {The {{NEMESIS}} Planetary Atmosphere Radiative Transfer and Retrieval Tool},
  author = {Irwin, P. G. J. and Teanby, N.A. and {de Kok}, R. and Fletcher, L.N. and Howett, C.J.A. and Tsang, C.C.C. and Wilson, C.F. and Calcutt, S.B. and Nixon, C.A. and Parrish, P.D.},
  year = {2008},
  month = apr,
  journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
  volume = {109},
  number = {6},
  pages = {1136--1150},
  issn = {00224073},
  doi = {10.1016/j.jqsrt.2007.11.006},
  urldate = {2022-09-05},
  abstract = {With the exception of in situ atmospheric probes, the most useful way to study the atmospheres of other planets is to observe their electromagnetic spectra through remote observations, either from ground-based telescopes or from spacecraft. Atmospheric properties most consistent with these observed spectra are then derived with retrieval models. All retrieval models attempt to extract the maximum amount of atmospheric information from finite sets of data, but while the problem to be solved is fundamentally the same for any planetary atmosphere, until now all such models have been assembled ad hoc to address data from individual missions.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/5YFEMYR4/Irwin et al. - 2008 - The NEMESIS planetary atmosphere radiative transfe.pdf}
}

@article{james_temporal_2023,
  title = {The {{Temporal Brightening}} of {{Uranus}}' {{Northern Polar Hood From HST}}/{{WFC3}} and {{HST}}/{{STIS Observations}}},
  author = {James, Arjuna and Irwin, Patrick G. J. and Dobinson, Jack and Wong, Michael H. and Tsubota, Troy K. and Simon, Amy A. and Fletcher, Leigh N. and Roman, Michael T. and Teanby, Nick A. and Toledo, Daniel and Orton, Glenn S.},
  year = {2023},
  month = oct,
  journal = {Journal of Geophysical Research: Planets},
  volume = {128},
  number = {10},
  pages = {e2023JE007904},
  issn = {2169-9097, 2169-9100},
  doi = {10.1029/2023JE007904},
  urldate = {2023-10-11},
  abstract = {Hubble Space Telescope Wide-Field Camera 3 (HST/WFC3) observations spanning 2015 to 2021 confirm a brightening of Uranus' north polar hood feature with time. The vertical aerosol model of Irwin et al. (2023, https://doi.org/10.1038/s41550-023-02047-0) (IRW23), consisting of a deep haze layer based at {$\sim$}5 bar, a 1--2 bar haze layer, and an extended haze rising up from the 1--2 bar layer, was applied to retrievals on HST Space Telescope Imaging Spectrograph (STIS) (HST/STIS) observations (Sromovsky et al., 2014, 2019, https:// doi.org/10.1016/j.icarus.2014.05.016, https://doi.org/10.1016/j.icarus.2018.06.026) revealing a reduction in cloud-top CH4 volume mixing ratio (VMR) (i.e., above the deep {$\sim$}5 bar haze) by an average of 0.0019 {\textpm} 0.0003 between 40--80{$\mkern1mu$}{\textopenbullet}N ({$\sim$}10\% average reduction) from 2012 to 2015. A combination of latitudinal retrievals on the HST/WFC3 and HST/STIS data sets, again employing the IRW23 model, reveal a temporal thickening of the 1--2 bar haze layer to be the main cause of the polar hood brightening, finding an average increase in integrated opacity of 1.09 {\textpm} 0.08 ({$\sim$}33\% increase) at 0.8 {\textmu}m north of {$\sim$}45{$^\circ$}N, concurrent with a decrease in the imaginary refractive index spectrum of the 1--2 bar haze layer north of {$\sim$}40{$^\circ$}N and longwards of {$\sim$}0.7 {\textmu}m. Small contributions to the brightening were found from a thickening of the deep aerosol layer, with an average increase in integrated opacity of 0.6 {\textpm} 0.1 (58\% increase) north of 45{$^\circ$}N between 2012 and 2015, and from the aforementioned decrease in CH4 VMR. Our results are consistent with the slowing of a stratospheric meridional circulation, exhibiting subsidence at the poles.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/YE86HYDX/James et al. - 2023 - The Temporal Brightening of Uranus' Northern Polar.pdf}
}

@article{krissansen-totton_detectability_2018,
  title = {Detectability of {{Biosignatures}} in {{Anoxic Atmospheres}} with the James Webb Space Telescope: {{A TRAPPIST-1e Case Study}}},
  shorttitle = {Detectability of {{Biosignatures}} in {{Anoxic Atmospheres}} with the\${\textbackslash}less\$i\${\textbackslash}greater\${{James Webb Space Telescope}}\${\textbackslash}less\$/I\${\textbackslash}greater\$},
  author = {{Krissansen-Totton}, Joshua and Garland, Ryan and Irwin, Patrick and Catling, David C.},
  year = {2018},
  month = aug,
  journal = {The Astronomical Journal},
  volume = {156},
  number = {3},
  pages = {114},
  publisher = {American Astronomical Society},
  issn = {1538-3881},
  doi = {10.3847/1538-3881/aad564},
  urldate = {2022-08-16},
  abstract = {The James Webb Space Telescope (JWST) may be capable of finding biogenic gases in the atmospheres of habitable exoplanets around low-mass stars. Considerable attention has been given to the detectability of biogenic oxygen, which could be found using an ozone proxy, but ozone detection with JWST will be extremely challenging, even for the most favorable targets. Here, we investigate the detectability of biosignatures in anoxic atmospheres analogous to those that likely existed on the early Earth. Arguably, such anoxic biosignatures could be more prevalent than oxygen biosignatures if life exists elsewhere. Specifically, we simulate JWST retrievals of TRAPPIST-1e to determine whether the methane plus carbon dioxide disequilibrium biosignature pair is detectable in transit transmission. We find that {$\sim$}10 transits using the Near InfraRed Spectrograph prism instrument may be sufficient to detect carbon dioxide and constrain methane abundances sufficiently well to rule out known, nonbiological CH4 production scenarios to {$\sim$}90\% confidence. Furthermore, it might be possible to put an upper limit on carbon monoxide abundances that would help rule out nonbiological methane-production scenarios, assuming the surface biosphere would efficiently draw down atmospheric CO. Our results are relatively insensitive to high-altitude clouds and instrument noise floor assumptions, although stellar heterogeneity and variability may present challenges.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/38AC9LAA/Krissansen-Totton et al. - 2018 - Detectability of Biosignatures in Anoxic Atmospher.pdf}
}

@article{lacis_description_1991,
  title = {A Description of the Correlated {\emph{k}} Distribution Method for Modeling Nongray Gaseous Absorption, Thermal Emission, and Multiple Scattering in Vertically Inhomogeneous Atmospheres},
  author = {Lacis, Andrew A. and Oinas, Valdar},
  year = {1991},
  journal = {Journal of Geophysical Research},
  volume = {96},
  number = {D5},
  pages = {9027},
  issn = {0148-0227},
  doi = {10.1029/90JD01945},
  urldate = {2023-03-28},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/5DJI7QYI/Lacis and Oinas - 1991 - A description of the correlated k distribut.pdf}
}

@inproceedings{lam_numba_2015,
  title = {Numba: A {{LLVM-based Python JIT}} Compiler},
  shorttitle = {Numba},
  booktitle = {Proceedings of the {{Second Workshop}} on the {{LLVM Compiler Infrastructure}} in {{HPC}}},
  author = {Lam, Siu Kwan and Pitrou, Antoine and Seibert, Stanley},
  year = {2015},
  month = nov,
  series = {{{LLVM}} '15},
  pages = {1--6},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  doi = {10.1145/2833157.2833162},
  urldate = {2023-10-11},
  abstract = {Dynamic, interpreted languages, like Python, are attractive for domain-experts and scientists experimenting with new ideas. However, the performance of the interpreter is often a barrier when scaling to larger data sets. This paper presents a just-in-time compiler for Python that focuses in scientific and array-oriented computing. Starting with the simple syntax of Python, Numba compiles a subset of the language into efficient machine code that is comparable in performance to a traditional compiled language. In addition, we share our experience in building a JIT compiler using LLVM[1].},
  isbn = {978-1-4503-4005-2},
  keywords = {compiler,LLVM,Python},
  file = {/Users/jingxuanyang/Zotero/storage/ZCUFB455/Lam et al. - 2015 - Numba a LLVM-based Python JIT compiler.pdf}
}

@article{lee_optimal_2012,
  title = {Optimal Estimation Retrievals of the Atmospheric Structure and Composition of {{HD}} 189733b from Secondary Eclipse Spectroscopy: {{Exoplanet}} Retrieval from Transit Spectroscopy},
  shorttitle = {Optimal Estimation Retrievals of the Atmospheric Structure and Composition of {{HD}} 189733b from Secondary Eclipse Spectroscopy},
  author = {Lee, J.-M. and Fletcher, L. N. and Irwin, P. G. J.},
  year = {2012},
  month = feb,
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {420},
  number = {1},
  pages = {170--182},
  issn = {00358711},
  doi = {10.1111/j.1365-2966.2011.20013.x},
  urldate = {2023-04-04},
  abstract = {Recent spectroscopic observations of transiting hot Jupiters have permitted the derivation of the thermal structure and molecular abundances of H2O, CO2, CO and CH4 in these extreme atmospheres. Here, for the first time, we apply the technique of optimal estimation to determine the thermal structure and composition of an exoplanet by solving the inverse problem. The development of a suite of radiative transfer and retrieval tools for exoplanet atmospheres is described, building upon a retrieval algorithm which is extensively used in the study of our own Solar system. First, we discuss the plausibility of detection of different molecules in the dayside atmosphere of HD 189733b and the best-fitting spectrum retrieved from all publicly available sets of secondary eclipse observations between 1.45 and 24 {\textmu}m. Additionally, we use contribution functions to assess the vertical sensitivity of the emission spectrum to temperatures and molecular composition. Over the altitudes probed by the contribution functions, the retrieved thermal structure shows an isothermal upper atmosphere overlying a deeper adiabatic layer (temperature decreasing with altitude), which is consistent with previously reported dynamical and observational results. The formal uncertainties on retrieved parameters are estimated conservatively using an analysis of the cross-correlation functions and the degeneracy between different atmospheric properties. The formal solution of the inverse problem suggests that the uncertainties on retrieved parameters are larger than suggested in previous studies, and that the presence of CO and CH4 is only marginally supported by the available data. Nevertheless, by including as broad a wavelength range as possible in the retrieval, we demonstrate that available spectra of HD 189733b can constrain a family of potential solutions for the atmospheric structure.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/5F5IZBZI/Lee et al. - 2012 - Optimal estimation retrievals of the atmospheric s.pdf}
}

@article{line_systematic_2013,
  title = {A {{SYSTEMATIC RETRIEVAL ANALYSIS OF SECONDARY ECLIPSE SPECTRA}}. {{I}}. {{A COMPARISON OF ATMOSPHERIC RETRIEVAL TECHNIQUES}}},
  author = {Line, Michael R. and Wolf, Aaron S. and Zhang, Xi and Knutson, Heather and Kammer, Joshua A. and Ellison, Elias and Deroo, Pieter and Crisp, Dave and Yung, Yuk L.},
  year = {2013},
  month = sep,
  journal = {The Astrophysical Journal},
  volume = {775},
  number = {2},
  pages = {137},
  issn = {0004-637X, 1538-4357},
  doi = {10.1088/0004-637X/775/2/137},
  urldate = {2023-01-03},
  abstract = {Exoplanet atmosphere spectroscopy enables us to improve our understanding of exoplanets just as remote sensing in our own solar system has increased our understanding of the solar system bodies. The challenge is to quantitatively determine the range of temperatures and molecular abundances allowed by the data, which is often difficult given the low information content of most exoplanet spectra that commonly leads to degeneracies in the interpretation. A variety of spectral retrieval approaches have been applied to exoplanet spectra, but no previous investigations have sought to compare these approaches. We compare three different retrieval methods: optimal estimation, differential evolution Markov chain Monte Carlo, and bootstrap Monte Carlo on a synthetic water-dominated hot Jupiter. We discuss expectations of uncertainties in abundances and temperatures given current and potential future observations. In general, we find that the three approaches agree for high spectral resolution, high signal-to-noise data expected to come from potential future spaceborne missions, but disagree for low-resolution, low signal-to-noise spectra representative of current observations. We also compare the results from a parameterized temperature profile versus a full classical Level-by-Level approach and discriminate in which situations each of these approaches is applicable. Furthermore, we discuss the implications of our models for the inferred C-to-O ratios of exoplanetary atmospheres. Specifically, we show that in the observational limit of a few photometric points, the retrieved C/O is biased toward values near solar and near one simply due to the assumption of uninformative priors.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/2J2945D9/Line et al. - 2013 - A SYSTEMATIC RETRIEVAL ANALYSIS OF SECONDARY ECLIP.pdf;/Users/jingxuanyang/Zotero/storage/7BEMGI8I/Line et al. - 2013 - A SYSTEMATIC RETRIEVAL ANALYSIS OF SECONDARY ECLIP.pdf;/Users/jingxuanyang/Zotero/storage/DRQV7DKH/Line et al. - 2013 - A SYSTEMATIC RETRIEVAL ANALYSIS OF SECONDARY ECLIP.pdf}
}

@article{macdonald_catalog_2023,
  title = {A {{Catalog}} of {{Exoplanet Atmospheric Retrieval Codes}}},
  author = {MacDonald, Ryan J. and Batalha, Natasha E.},
  year = {2023},
  month = mar,
  journal = {Research Notes of the AAS},
  volume = {7},
  number = {3},
  pages = {54},
  publisher = {The American Astronomical Society},
  issn = {2515-5172},
  doi = {10.3847/2515-5172/acc46a},
  urldate = {2023-03-29},
  abstract = {Exoplanet atmospheric retrieval is a computational technique widely used to infer properties of planetary atmospheres from remote spectroscopic observations. Retrieval codes typically employ Bayesian sampling algorithms or machine learning approaches to explore the range of atmospheric properties (e.g., chemical composition, temperature structure, aerosols) compatible with an observed spectrum. However, despite the wide adoption of exoplanet retrieval techniques, there is currently no systematic summary of exoplanet retrieval codes in the literature. Here, we provide a catalog of the atmospheric retrieval codes published to date, alongside links to their respective code repositories where available. Our catalog will be continuously updated via a Zenodo archive.},
  langid = {english}
}

@article{madhusudhan_atmospheric_2017,
  title = {Atmospheric Signatures of Giant Exoplanet Formation by Pebble Accretion},
  author = {Madhusudhan, N. and Bitsch, Bertram and Johansen, Anders and Eriksson, Linn},
  year = {2017},
  month = aug,
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {469},
  number = {4},
  pages = {4102--4115},
  issn = {0035-8711, 1365-2966},
  doi = {10.1093/mnras/stx1139},
  urldate = {2023-03-29},
  abstract = {Atmospheric chemical abundances of giant planets lead to important constraints on planetary formation and migration. Studies have shown that giant planets that migrate through the protoplanetary disc can accrete substantial amounts of oxygen-rich planetesimals, leading to supersolar metallicities in the envelope and solar or subsolar C/O ratios. Pebble accretion has been demonstrated to play an important role in core accretion and to have growth rates that are consistent with planetary migration. The high pebble accretion rates allow planetary cores to start their growth beyond 10 au and subsequently migrate to cold ( 1 au), warm ({$\sim$}0.1--1 au) or hot ( 0.1 au) orbits. In this work we investigate how the formation of giant planets via pebble accretion influences their atmospheric chemical compositions. We find that under the standard pebble accretion scenario, where the core is isolated from the envelope, the resulting metallicities (O/H and C/H ratios) are subsolar, while the C/O ratios are supersolar. Planets that migrate through the disc to become hot Jupiters accrete substantial amounts of water vapour, but still acquire slightly subsolar O/H and supersolar C/O of 0.7--0.8. The metallicity can be substantially subsolar ({$\sim$}0.2--0.5 {\texttimes} solar) and the C/O can even approach 1.0 if the planet accretes its envelope mostly beyond the CO2 ice line, i.e. cold Jupiters or hot Jupiters that form far out and migrate in by scattering. Allowing for core erosion yields significantly supersolar metallicities and solar or subsolar C/O, which can also be achieved by other means, e.g. photoevaporation and late-stage planetesimal accretion.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/A35XW38A/Madhusudhan et al. - 2017 - Atmospheric signatures of giant exoplanet formatio.pdf}
}

@article{madhusudhan_temperature_2009,
  title = {A {{TEMPERATURE AND ABUNDANCE RETRIEVAL METHOD FOR EXOPLANET ATMOSPHERES}}},
  author = {Madhusudhan, N. and Seager, S.},
  year = {2009},
  month = dec,
  journal = {The Astrophysical Journal},
  volume = {707},
  number = {1},
  pages = {24--39},
  issn = {0004-637X, 1538-4357},
  doi = {10.1088/0004-637X/707/1/24},
  urldate = {2023-01-06},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/PVQFKYSH/Madhusudhan and Seager - 2009 - A TEMPERATURE AND ABUNDANCE RETRIEVAL METHOD FOR E.pdf}
}

@article{mordasini_imprint_2016,
  title = {{{THE IMPRINT OF EXOPLANET FORMATION HISTORY ON OBSERVABLE PRESENT-DAY SPECTRA OF HOT JUPITERS}}},
  author = {Mordasini, C. and {van Boekel}, R. and Molli{\`e}re, P. and Henning, {\relax Th}. and Benneke, Bj{\"o}rn},
  year = {2016},
  month = nov,
  journal = {The Astrophysical Journal},
  volume = {832},
  number = {1},
  pages = {41},
  issn = {1538-4357},
  doi = {10.3847/0004-637X/832/1/41},
  urldate = {2023-03-29},
  abstract = {The composition of a planet's atmosphere is determined by its formation, evolution, and present-day insolation. A planet's spectrum therefore may hold clues on its origins. We present a ``chain'' of models, linking the formation of a planet to its observable present-day spectrum. The chain links include (1) the planet's formation and migration, (2) its long-term thermodynamic evolution, (3) a variety of disk chemistry models, (4) a non-gray atmospheric model, and (5) a radiometric model to obtain simulated spectroscopic observations with James Webb Space Telescope and ARIEL. In our standard chemistry model the inner disk is depleted in refractory carbon as in the Solar System and in white dwarfs polluted by extrasolar planetesimals. Our main findings are: (1) envelope enrichment by planetesimal impacts during formation dominates the final planetary atmospheric composition of hot Jupiters. We investigate two, under this finding, prototypical formation pathways: a formation inside or outside the water iceline, called ``dry'' and ``wet'' planets, respectively. (2) Both the ``dry'' and ``wet'' planets are oxygen-rich (C/O{$<$}1) due to the oxygen-rich nature of the solid building blocks. The ``dry'' planet's C/O ratio is {$<$}0.2 for standard carbon depletion, while the ``wet'' planet has typical C/O values between 0.1 and 0.5 depending mainly on the clathrate formation efficiency. Only non-standard disk chemistries without carbon depletion lead to carbonrich C/O ratios {$>$}1 for the ``dry'' planet. (3) While we consistently find C/O ratios {$<$}1, they still vary significantly. To link a formation history to a specific C/O, a better understanding of the disk chemistry is thus needed.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/2E8VDABF/Mordasini et al. - 2016 - THE IMPRINT OF EXOPLANET FORMATION HISTORY ON OBSE.pdf}
}

@article{teanby_active_2012,
  title = {Active Upper-Atmosphere Chemistry and Dynamics from Polar Circulation Reversal on {{Titan}}},
  author = {Teanby, Nicholas A. and Irwin, Patrick G. J. and Nixon, Conor A. and {de Kok}, Remco and Vinatier, Sandrine and Coustenis, Athena and {Sefton-Nash}, Elliot and Calcutt, Simon B. and Flasar, F. Michael},
  year = {2012},
  month = nov,
  journal = {Nature},
  volume = {491},
  number = {7426},
  pages = {732--735},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/nature11611},
  urldate = {2022-09-05},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/VUU7K52R/Teanby et al. - 2012 - Active upper-atmosphere chemistry and dynamics fro.pdf}
}

@article{virtanen_scipy_2020,
  title = {{{SciPy}} 1.0: Fundamental Algorithms for Scientific Computing in {{Python}}},
  shorttitle = {{{SciPy}} 1.0},
  author = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and {van der Walt}, St{\'e}fan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C. J. and Polat, {\.I}lhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Ant{\^o}nio H. and Pedregosa, Fabian and {van Mulbregt}, Paul},
  year = {2020},
  month = mar,
  journal = {Nature Methods},
  volume = {17},
  number = {3},
  pages = {261--272},
  publisher = {Nature Publishing Group},
  issn = {1548-7105},
  doi = {10.1038/s41592-019-0686-2},
  urldate = {2023-10-10},
  abstract = {SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.},
  copyright = {2020 The Author(s)},
  langid = {english},
  keywords = {Biophysical chemistry,Computational biology and bioinformatics,Technology},
  file = {/Users/jingxuanyang/Zotero/storage/A3VF4PGN/Virtanen et al. - 2020 - SciPy 1.0 fundamental algorithms for scientific c.pdf}
}

@article{yang_simultaneous_2024,
  title = {Simultaneous Retrieval of Orbital Phase Resolved {{JWST}}/{{MIRI}} Emission Spectra of the Hot {{Jupiter WASP-43b}}: {{Evidence}} of Water, Ammonia and Carbon Monoxide},
  shorttitle = {Simultaneous Retrieval of Orbital Phase Resolved {{JWST}}/{{MIRI}} Emission Spectra of the Hot {{Jupiter WASP-43b}}},
  author = {Yang, Jingxuan and Hammond, Mark and Piette, Anjali A A and Blecic, Jasmina and Bell, Taylor J and Irwin, Patrick G J and Parmentier, Vivien and Tsai, Shang-Min and Barstow, Joanna K and Crouzet, Nicolas and Kreidberg, Laura and Mendon{\c c}a, Jo{\~a}o M and Taylor, Jake and Baeyens, Robin and Ohno, Kazumasa and Teinturier, Lucas and Nixon, Matthew C},
  year = {2024},
  month = jun,
  journal = {Monthly Notices of the Royal Astronomical Society},
  pages = {stae1427},
  issn = {0035-8711},
  doi = {10.1093/mnras/stae1427},
  urldate = {2024-06-24},
  abstract = {Spectroscopic phase curves of hot Jupiters measure their emission spectra at multiple orbital phases, thus enabling detailed characterisation of their atmospheres. Precise constraints on the atmospheric composition of these exoplanets offer insights into their formation and evolution. We analyse four phase-resolved emission spectra of the hot Jupiter WASP-43b, generated from a phase curve observed with the MIRI/LRS onboard the JWST, to retrieve its atmospheric properties. Using a parametric 2D temperature model and assuming a chemically homogeneous atmosphere within the observed pressure region, we simultaneously fit the four spectra to constrain the abundances of atmospheric constituents, thereby yielding more precise constraints than previous work that analysed each spectrum independently. Our analysis reveals statistically significant evidence of NH3 (4{$\sigma$}) in a hot Jupiter's emission spectra for the first time, along with evidence of H2O (6.5{$\sigma$}), CO (3.1{$\sigma$}), and a non-detection of CH4. With our abundance constraints, we tentatively estimate the metallicity of WASP-43b at 0.6-6.5 {\texttimes} solar and its C/O ratio at 0.6-0.9. Our findings offer vital insights into the atmospheric conditions and formation history of WASP-43b by simultaneously constraining the abundances of carbon, oxygen, and nitrogen-bearing species.},
  file = {/Users/jingxuanyang/Zotero/storage/G25U5RJZ/Yang et al. - 2024 - Simultaneous retrieval of orbital phase resolved J.pdf;/Users/jingxuanyang/Zotero/storage/XTZS5IHK/7692040.html}
}

@article{yang_testing_2023,
  title = {Testing {{2D}} Temperature Models in {{Bayesian}} Retrievals of Atmospheric Properties from Hot {{Jupiter}} Phase Curves},
  author = {Yang, Jingxuan and Irwin, Patrick G J and Barstow, Joanna K},
  year = {2023},
  month = sep,
  journal = {Monthly Notices of the Royal Astronomical Society},
  volume = {525},
  number = {4},
  pages = {5146--5167},
  issn = {0035-8711, 1365-2966},
  doi = {10.1093/mnras/stad2555},
  urldate = {2023-10-10},
  abstract = {ABSTRACT             Spectroscopic phase curves of transiting hot Jupiters are spectral measurements at multiple orbital phases, giving a set of disc-averaged spectra that probe multiple hemispheres. By fitting model phase curves to observations, we can constrain the atmospheric properties of hot Jupiters, such as molecular abundance, aerosol distribution, and thermal structure, which offer insights into their atmospheric dynamics, chemistry, and formation. We propose a novel 2D temperature parametrization consisting of a dayside and a nightside to retrieve information from near-infrared phase curves and apply the method to phase curves of WASP-43b observed by HST/Wide Field Camera 3 and Spitzer/Infra-Red Array Camera. In our scheme, the temperature is constant on isobars on the nightside and varies with cosn(longitude/{$\epsilon$}) on isobars on the dayside, where n and {$\epsilon$} are free parameters. We fit all orbital phases simultaneously using the radiative transfer package nemesispy coupled to a Bayesian inference code. We first validate the performance of our retrieval scheme with synthetic phase curves generated from a Global Circulation Model and find that our 2D scheme can accurately retrieve the latitudinally averaged thermal structure and constrain the abundance of H2O and CH4. We then apply our 2D scheme to the observed phase curves of WASP-43b and find: (1) The dayside temperature--pressure profiles do not vary strongly with longitude and are non-inverted. (2) The retrieved nightside temperatures are extremely low, suggesting significant nightside cloud coverage. (3) The H2O volume mixing ratio is constrained to 5.6~{\texttimes}~10-5--4.0~{\texttimes}~10-4, and we retrieve an upper bound for CH4 mixing ratio at {$\sim$}10-6.},
  langid = {english},
  file = {/Users/jingxuanyang/Zotero/storage/6V2UDYIS/Yang et al. - 2023 - Testing 2D temperature models in Bayesian retrieva.pdf}
}