{"year":"2021","volume":508,"intvolume":"       508","acknowledgement":"The authors thank the referee for constructive feedback that improved the outcome of this study. We are grateful to Antoinette Songaila Cowie for sharing the ‘NEPLA4’ spectrum with us. This research has made use of NASA’s Astrophysics Data System, and many open source projects such as trident (Hummels et al. 2017), IPython (Pérez & Granger 2007), SciPy (Virtanen et al. 2019), NumPy (Walt et al. 2011), matplotlib (Hunter 2007), pandas (McKinney 2010), and the yt-project (Turk et al. 2011). MG was supported by NASA through the NASA Hubble Fellowship grant HST-HF2-51409 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5-26555. MG acknowledges support from NASA grants HST-GO-15643.017, and HST-AR15797.001 as well as XSEDE grant TG-AST180036. CAM acknowledges support by NASA Headquarters through the NASA Hubble Fellowship grant HST-HF2-51413.001-A. PRS was supported in part by U.S. NSF grant AST-1009799, NASA grant NNX11AE09G, and supercomputer resources from NSF XSEDE grant TG AST090005 and the Texas Advanced Computing Center (TACC) at The University of Texas at Austin. JM acknowledges a Zwicky Prize Fellowship from ETH Zurich. GY acknowledges financial support by MICIU/FEDER under project grant PGC2018-094975-C21. SEIB acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 669253). ITI was supported by the Science and Technology Facilities Council [grants ST/I000976/1, ST/F002858/1, ST/P000525/1, and ST/T000473/1]; and The Southeast Physics Network (SEPNet). KA was supported by NRF2016R1D1A1B04935414 and NRF-2016R1A5A1013277. KA also appreciates APCTP for its hospitality during completion of this work. PO acknowledges support from the French ANR funded project ORAGE (ANR-14-CE33-0016). ND and DA acknowledge funding from the French ANR for project ANR-12-JS05- 0001 (EMMA). The CoDa II simulation was performed at Oak Ridge National Laboratory/Oak Ridge Leadership Computing Facility on the Titan supercomputer (INCITE 2016 award AST031). Processing was performed on the Eos and Rhea clusters. Resolution study simulations were performed on Piz Daint at the Swiss National Supercomputing Center (PRACE Tier 0 award, project id pr37). The authors would like to acknowledge the High Performance Computing center of the University of Strasbourg for supporting this work by providing scientific support and access to computing resources. Part of the computing resources were funded by the Equipex EquipMeso project (Programme Investissements d’Avenir) and the CPER Alsacalcul/Big Data.","keyword":["dark ages","reionization","first stars","intergalactic medium","galaxies: formation"],"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"external_id":{"arxiv":["2004.14496"]},"publication":"Monthly Notices of the Royal Astronomical Society","author":[{"first_name":"Max","last_name":"Gronke","full_name":"Gronke, Max"},{"full_name":"Ocvirk, Pierre","first_name":"Pierre","last_name":"Ocvirk"},{"last_name":"Mason","first_name":"Charlotte","full_name":"Mason, Charlotte"},{"orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"full_name":"Bosman, Sarah E I","last_name":"Bosman","first_name":"Sarah E I"},{"first_name":"Jenny G","last_name":"Sorce","full_name":"Sorce, Jenny G"},{"first_name":"Joseph","last_name":"Lewis","full_name":"Lewis, Joseph"},{"full_name":"Ahn, Kyungjin","last_name":"Ahn","first_name":"Kyungjin"},{"full_name":"Aubert, Dominique","last_name":"Aubert","first_name":"Dominique"},{"full_name":"Dawoodbhoy, Taha","first_name":"Taha","last_name":"Dawoodbhoy"},{"full_name":"Iliev, Ilian T","last_name":"Iliev","first_name":"Ilian T"},{"first_name":"Paul R","last_name":"Shapiro","full_name":"Shapiro, Paul R"},{"full_name":"Yepes, Gustavo","last_name":"Yepes","first_name":"Gustavo"}],"page":"3697-3709","doi":"10.1093/mnras/stab2762","_id":"11522","language":[{"iso":"eng"}],"citation":{"short":"M. Gronke, P. Ocvirk, C. Mason, J.J. Matthee, S.E.I. Bosman, J.G. Sorce, J. Lewis, K. Ahn, D. Aubert, T. Dawoodbhoy, I.T. Iliev, P.R. Shapiro, G. Yepes, Monthly Notices of the Royal Astronomical Society 508 (2021) 3697–3709.","chicago":"Gronke, Max, Pierre Ocvirk, Charlotte Mason, Jorryt J Matthee, Sarah E I Bosman, Jenny G Sorce, Joseph Lewis, et al. “Lyman-α Transmission Properties of the Intergalactic Medium in the CoDaII Simulation.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/mnras/stab2762\">https://doi.org/10.1093/mnras/stab2762</a>.","apa":"Gronke, M., Ocvirk, P., Mason, C., Matthee, J. J., Bosman, S. E. I., Sorce, J. G., … Yepes, G. (2021). Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stab2762\">https://doi.org/10.1093/mnras/stab2762</a>","ista":"Gronke M, Ocvirk P, Mason C, Matthee JJ, Bosman SEI, Sorce JG, Lewis J, Ahn K, Aubert D, Dawoodbhoy T, Iliev IT, Shapiro PR, Yepes G. 2021. Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation. Monthly Notices of the Royal Astronomical Society. 508(3), 3697–3709.","ama":"Gronke M, Ocvirk P, Mason C, et al. Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation. <i>Monthly Notices of the Royal Astronomical Society</i>. 2021;508(3):3697-3709. doi:<a href=\"https://doi.org/10.1093/mnras/stab2762\">10.1093/mnras/stab2762</a>","ieee":"M. Gronke <i>et al.</i>, “Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 508, no. 3. Oxford University Press, pp. 3697–3709, 2021.","mla":"Gronke, Max, et al. “Lyman-α Transmission Properties of the Intergalactic Medium in the CoDaII Simulation.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 508, no. 3, Oxford University Press, 2021, pp. 3697–709, doi:<a href=\"https://doi.org/10.1093/mnras/stab2762\">10.1093/mnras/stab2762</a>."},"article_type":"original","scopus_import":"1","publisher":"Oxford University Press","date_created":"2022-07-07T09:30:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","oa":1,"status":"public","title":"Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation","quality_controlled":"1","date_updated":"2022-08-18T10:45:56Z","month":"12","article_processing_charge":"No","day":"01","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.14496"}],"abstract":[{"lang":"eng","text":"The decline in abundance of Lyman-α (Lyα) emitting galaxies at z ≳ 6 is a powerful and commonly used probe to constrain the progress of cosmic reionization. We use the CODAII simulation, which is a radiation hydrodynamic simulation featuring a box of ∼94 comoving Mpc side length, to compute the Lyα transmission properties of the intergalactic medium (IGM) at z ∼ 5.8 to 7. Our results mainly confirm previous studies, i.e. we find a declining Lyα transmission with redshift and a large sightline-to-sightline variation. However, motivated by the recent discovery of blue Lyα peaks at high redshift, we also analyse the IGM transmission on the blue side, which shows a rapid decline at z ≳ 6 of the blue transmission. This low transmission can be attributed not only to the presence of neutral regions but also to the residual neutral hydrogen within ionized regions, for which a density even as low as nHI∼10−9cm−3 (sometimes combined with kinematic effects) leads to a significantly reduced visibility. Still, we find that ∼1 per cent of sightlines towards M1600AB ∼ −21 galaxies at z ∼ 7 are transparent enough to allow a transmission of a blue Lyα peak. We discuss our results in the context of the interpretation of observations."}],"issue":"3","extern":"1","publication_status":"published","date_published":"2021-12-01T00:00:00Z"}