--- _id: '11059' abstract: - lang: eng text: The genome is packaged and organized nonrandomly within the 3D space of the nucleus to promote efficient gene expression and to faithfully maintain silencing of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope membrane, which contains a set of proteins that actively participate in chromatin organization and gene regulation. Technological advances are providing views of genome organization at unprecedented resolution and are beginning to reveal the ways that cells co-opt the structures of the nuclear periphery for nuclear organization and gene regulation. These genome regulatory roles of proteins of the nuclear periphery have important influences on development, disease and ageing. article_processing_charge: No article_type: review author: - first_name: Abigail full_name: Buchwalter, Abigail last_name: Buchwalter - first_name: Jeanae M. full_name: Kaneshiro, Jeanae M. last_name: Kaneshiro - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: 'Buchwalter A, Kaneshiro JM, Hetzer M. Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. 2019;20(1):39-50. doi:10.1038/s41576-018-0063-5' apa: 'Buchwalter, A., Kaneshiro, J. M., & Hetzer, M. (2019). Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. Springer Nature. https://doi.org/10.1038/s41576-018-0063-5' chicago: 'Buchwalter, Abigail, Jeanae M. Kaneshiro, and Martin Hetzer. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” Nature Reviews Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41576-018-0063-5.' ieee: 'A. Buchwalter, J. M. Kaneshiro, and M. Hetzer, “Coaching from the sidelines: The nuclear periphery in genome regulation,” Nature Reviews Genetics, vol. 20, no. 1. Springer Nature, pp. 39–50, 2019.' ista: 'Buchwalter A, Kaneshiro JM, Hetzer M. 2019. Coaching from the sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics. 20(1), 39–50.' mla: 'Buchwalter, Abigail, et al. “Coaching from the Sidelines: The Nuclear Periphery in Genome Regulation.” Nature Reviews Genetics, vol. 20, no. 1, Springer Nature, 2019, pp. 39–50, doi:10.1038/s41576-018-0063-5.' short: A. Buchwalter, J.M. Kaneshiro, M. Hetzer, Nature Reviews Genetics 20 (2019) 39–50. date_created: 2022-04-07T07:44:45Z date_published: 2019-01-01T00:00:00Z date_updated: 2024-10-14T11:18:54Z day: '01' doi: 10.1038/s41576-018-0063-5 extern: '1' external_id: pmid: - '30356165' intvolume: ' 20' issue: '1' keyword: - Genetics (clinical) - Genetics - Molecular Biology language: - iso: eng month: '01' oa_version: None page: 39-50 pmid: 1 publication: Nature Reviews Genetics publication_identifier: eissn: - 1471-0064 issn: - 1471-0056 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Coaching from the sidelines: The nuclear periphery in genome regulation' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ... --- _id: '11060' abstract: - lang: eng text: The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs. article_number: e49796 article_processing_charge: No article_type: original author: - first_name: Abigail full_name: Buchwalter, Abigail last_name: Buchwalter - first_name: Roberta full_name: Schulte, Roberta last_name: Schulte - first_name: Hsiao full_name: Tsai, Hsiao last_name: Tsai - first_name: Juliana full_name: Capitanio, Juliana last_name: Capitanio - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 2019;8. doi:10.7554/elife.49796 apa: Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.49796 chicago: Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.49796. ieee: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress,” eLife, vol. 8. eLife Sciences Publications, 2019. ista: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 8, e49796. mla: Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife, vol. 8, e49796, eLife Sciences Publications, 2019, doi:10.7554/elife.49796. short: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019). date_created: 2022-04-07T07:45:02Z date_published: 2019-10-10T00:00:00Z date_updated: 2024-10-14T12:08:36Z day: '10' ddc: - '570' doi: 10.7554/elife.49796 extern: '1' external_id: pmid: - '31599721' file: - access_level: open_access checksum: 1e8672a1e9c3dc0a2d3d0dad89673616 content_type: application/pdf creator: dernst date_created: 2022-04-08T08:18:01Z date_updated: 2022-04-08T08:18:01Z file_id: '11138' file_name: 2019_eLife_Buchwalter.pdf file_size: 6984654 relation: main_file success: 1 file_date_updated: 2022-04-08T08:18:01Z has_accepted_license: '1' intvolume: ' 8' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' related_material: record: - id: '13079' relation: research_data status: public scopus_import: '1' status: public title: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2019' ... --- _id: '11061' abstract: - lang: eng text: Many adult tissues contain postmitotic cells as old as the host organism. The only organelle that does not turn over in these cells is the nucleus, and its maintenance represents a formidable challenge, as it harbors regulatory proteins that persist throughout adulthood. Here we developed strategies to visualize two classes of such long-lived proteins, histones and nucleoporins, to understand the function of protein longevity in nuclear maintenance. Genome-wide mapping of histones revealed specific enrichment of long-lived variants at silent gene loci. Interestingly, nuclear pores are maintained by piecemeal replacement of subunits, resulting in mosaic complexes composed of polypeptides with vastly different ages. In contrast, nondividing quiescent cells remove old nuclear pores in an ESCRT-dependent manner. Our findings reveal distinct molecular strategies of nuclear maintenance, linking lifelong protein persistence to gene regulation and nuclear integrity. article_processing_charge: No article_type: original author: - first_name: Brandon H. full_name: Toyama, Brandon H. last_name: Toyama - first_name: Rafael full_name: Arrojo e Drigo, Rafael last_name: Arrojo e Drigo - first_name: Varda full_name: Lev-Ram, Varda last_name: Lev-Ram - first_name: Ranjan full_name: Ramachandra, Ranjan last_name: Ramachandra - first_name: Thomas J. full_name: Deerinck, Thomas J. last_name: Deerinck - first_name: Claude full_name: Lechene, Claude last_name: Lechene - first_name: Mark H. full_name: Ellisman, Mark H. last_name: Ellisman - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Toyama BH, Arrojo e Drigo R, Lev-Ram V, et al. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. 2019;218(2):433-444. doi:10.1083/jcb.201809123 apa: Toyama, B. H., Arrojo e Drigo, R., Lev-Ram, V., Ramachandra, R., Deerinck, T. J., Lechene, C., … Hetzer, M. (2019). Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201809123 chicago: Toyama, Brandon H., Rafael Arrojo e Drigo, Varda Lev-Ram, Ranjan Ramachandra, Thomas J. Deerinck, Claude Lechene, Mark H. Ellisman, and Martin Hetzer. “Visualization of Long-Lived Proteins Reveals Age Mosaicism within Nuclei of Postmitotic Cells.” Journal of Cell Biology. Rockefeller University Press, 2019. https://doi.org/10.1083/jcb.201809123. ieee: B. H. Toyama et al., “Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells,” Journal of Cell Biology, vol. 218, no. 2. Rockefeller University Press, pp. 433–444, 2019. ista: Toyama BH, Arrojo e Drigo R, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene C, Ellisman MH, Hetzer M. 2019. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. 218(2), 433–444. mla: Toyama, Brandon H., et al. “Visualization of Long-Lived Proteins Reveals Age Mosaicism within Nuclei of Postmitotic Cells.” Journal of Cell Biology, vol. 218, no. 2, Rockefeller University Press, 2019, pp. 433–44, doi:10.1083/jcb.201809123. short: B.H. Toyama, R. Arrojo e Drigo, V. Lev-Ram, R. Ramachandra, T.J. Deerinck, C. Lechene, M.H. Ellisman, M. Hetzer, Journal of Cell Biology 218 (2019) 433–444. date_created: 2022-04-07T07:45:11Z date_published: 2019-02-04T00:00:00Z date_updated: 2024-10-14T11:19:21Z day: '04' ddc: - '570' doi: 10.1083/jcb.201809123 extern: '1' external_id: pmid: - '30552100' file: - access_level: open_access checksum: 7964ebbf833b0b35f9fba840eea9531d content_type: application/pdf creator: dernst date_created: 2022-04-08T08:26:32Z date_updated: 2022-04-08T08:26:32Z file_id: '11139' file_name: 2019_JCB_Toyama.pdf file_size: 2503838 relation: main_file success: 1 file_date_updated: 2022-04-08T08:26:32Z has_accepted_license: '1' intvolume: ' 218' issue: '2' keyword: - Cell Biology language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '02' oa: 1 oa_version: Published Version page: 433-444 pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 218 year: '2019' ... --- _id: '11062' abstract: - lang: eng text: Most neurons are not replaced during an animal’s lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization. article_processing_charge: No article_type: original author: - first_name: Rafael full_name: Arrojo e Drigo, Rafael last_name: Arrojo e Drigo - first_name: Varda full_name: Lev-Ram, Varda last_name: Lev-Ram - first_name: Swati full_name: Tyagi, Swati last_name: Tyagi - first_name: Ranjan full_name: Ramachandra, Ranjan last_name: Ramachandra - first_name: Thomas full_name: Deerinck, Thomas last_name: Deerinck - first_name: Eric full_name: Bushong, Eric last_name: Bushong - first_name: Sebastien full_name: Phan, Sebastien last_name: Phan - first_name: Victoria full_name: Orphan, Victoria last_name: Orphan - first_name: Claude full_name: Lechene, Claude last_name: Lechene - first_name: Mark H. full_name: Ellisman, Mark H. last_name: Ellisman - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 2019;30(2):343-351.e3. doi:10.1016/j.cmet.2019.05.010 apa: Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T., Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult tissues. Cell Metabolism. Elsevier. https://doi.org/10.1016/j.cmet.2019.05.010 chicago: Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra, Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism. Elsevier, 2019. https://doi.org/10.1016/j.cmet.2019.05.010. ieee: R. Arrojo e Drigo et al., “Age mosaicism across multiple scales in adult tissues,” Cell Metabolism, vol. 30, no. 2. Elsevier, p. 343–351.e3, 2019. ista: Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3. mla: Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult Tissues.” Cell Metabolism, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3, doi:10.1016/j.cmet.2019.05.010. short: R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E. Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism 30 (2019) 343–351.e3. date_created: 2022-04-07T07:45:21Z date_published: 2019-08-06T00:00:00Z date_updated: 2025-12-15T10:02:11Z day: '06' department: - _id: MaHe doi: 10.1016/j.cmet.2019.05.010 extern: '1' external_id: pmid: - '31178361' intvolume: ' 30' issue: '2' keyword: - Cell Biology - Molecular Biology - Physiology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cmet.2019.05.010 month: '08' oa: 1 oa_version: Published Version page: 343-351.e3 pmid: 1 publication: Cell Metabolism publication_identifier: issn: - 1550-4131 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Age mosaicism across multiple scales in adult tissues type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2019' ... --- _id: '10354' abstract: - lang: eng text: "Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems." acknowledgement: We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation. article_number: '82' article_processing_charge: No article_type: original author: - first_name: Lena full_name: Harker-Kirschneck, Lena last_name: Harker-Kirschneck - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 2019;17(1). doi:10.1186/s12915-019-0700-2 apa: Harker-Kirschneck, L., Baum, B., & Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0700-2 chicago: Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology. Springer Nature, 2019. https://doi.org/10.1186/s12915-019-0700-2. ieee: L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” BMC Biology, vol. 17, no. 1. Springer Nature, 2019. ista: Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82. mla: Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology, vol. 17, no. 1, 82, Springer Nature, 2019, doi:10.1186/s12915-019-0700-2. short: L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019). date_created: 2021-11-26T11:25:03Z date_published: 2019-10-22T00:00:00Z date_updated: 2021-11-26T11:54:29Z day: '22' ddc: - '570' doi: 10.1186/s12915-019-0700-2 extern: '1' external_id: pmid: - '31640700' file: - access_level: open_access checksum: 31d8bae55a376d30925f53f7e1a02396 content_type: application/pdf creator: cchlebak date_created: 2021-11-26T11:37:54Z date_updated: 2021-11-26T11:37:54Z file_id: '10356' file_name: 2019_BMCBio_Harker_Kirschneck.pdf file_size: 1648926 relation: main_file success: 1 file_date_updated: 2021-11-26T11:37:54Z has_accepted_license: '1' intvolume: ' 17' issue: '1' keyword: - cell biology language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/559898 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Biology publication_identifier: issn: - 1741-7007 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 17 year: '2019' ... --- _id: '10355' abstract: - lang: eng text: The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments. acknowledgement: We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations. article_processing_charge: No article_type: original author: - first_name: Anne E full_name: Hafner, Anne E last_name: Hafner - first_name: Johannes full_name: Krausser, Johannes last_name: Krausser - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018 apa: Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018 chicago: Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018. ieee: A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019. ista: Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52. mla: Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018. short: A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52. date_created: 2021-11-26T11:33:21Z date_published: 2019-06-18T00:00:00Z date_updated: 2021-11-26T11:54:25Z day: '18' doi: 10.1016/j.sbi.2019.05.018 extern: '1' external_id: pmid: - '31226513' intvolume: ' 58' keyword: - molecular biology - structural biology language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.09349 month: '06' oa: 1 oa_version: Preprint page: 43-52 pmid: 1 publication: Current Opinion in Structural Biology publication_identifier: issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Minimal coarse-grained models for molecular self-organisation in biology type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 58 year: '2019' ... --- _id: '105' abstract: - lang: eng text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.' acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.' article_processing_charge: No article_type: original author: - first_name: Ashley full_name: Marsh, Ashley last_name: Marsh - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Paul full_name: Lockhart, Paul last_name: Lockhart - first_name: Richard full_name: Leventer, Richard last_name: Leventer citation: ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2 apa: Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2 chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2. ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019. ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166. mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2. short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166. date_created: 2018-12-11T11:44:39Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:28:24Z day: '01' department: - _id: GaNo doi: 10.1038/s41431-018-0231-2 external_id: isi: - '000454111500019' pmid: - '30089829' intvolume: ' 27' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41431-018-0231-2 month: '01' oa: 1 oa_version: Published Version page: 161-166 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Springer Nature publist_id: '7949' quality_controlled: '1' scopus_import: '1' status: public title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2019' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '21095' abstract: - lang: eng text: 'Inspired by DNA mimic proteins, we have introduced aromatic foldamers bearing phosphonate groups as synthetic mimics of the charge surface of B-DNA and competitive inhibitors of some therapeutically relevant DNA-binding enzymes: the human DNA Topoisomerase 1 (Top1) and the human HIV-1 integrase (HIV-1 IN). We now report on variants of these anionic foldamers bearing carboxylates instead of phosphonates. Several new monomers have been synthesized with protecting groups suitable for solid phase synthesis (SPS). Six hexadecaamides have been prepared using SPS. Proof of their resemblance to B-DNA was brought by the first crystal structure of one of these DNA-mimic foldamers in its polyanionic form. While some of the foldamers were found to be as active as, or even more active than, the original phosphonate oligomers, others had no activity at all or could even stimulate enzyme activity in vitro. Some foldamers were found to have differential inhibitory effects on the two enzymes. These results demonstrate a strong dependence of inhibitory activity on foldamer structure and charge distribution. They open broad avenues for the development of new classes of derivatives that could inhibit the interaction of specific proteins with their DNA target thereby influencing the cellular pathways in which they are involved.' article_processing_charge: No article_type: original author: - first_name: Valentina full_name: Corvaglia, Valentina last_name: Corvaglia - first_name: Daniel full_name: Carbajo, Daniel last_name: Carbajo - first_name: Panchami full_name: Prabhakaran, Panchami last_name: Prabhakaran - first_name: Krzysztof full_name: Ziach, Krzysztof last_name: Ziach - first_name: Pradeep K full_name: Mandal, Pradeep K id: 6a3def15-d4b4-11ef-9fa9-a24c1f545ec3 last_name: Mandal orcid: 0000-0001-5996-956X - first_name: Victor Dos full_name: Santos, Victor Dos last_name: Santos - first_name: Carole full_name: Legeay, Carole last_name: Legeay - first_name: Rachel full_name: Vogel, Rachel last_name: Vogel - first_name: Vincent full_name: Parissi, Vincent last_name: Parissi - first_name: Philippe full_name: Pourquier, Philippe last_name: Pourquier - first_name: Ivan full_name: Huc, Ivan last_name: Huc citation: ama: 'Corvaglia V, Carbajo D, Prabhakaran P, et al. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins. Nucleic Acids Research. 2019;47(11):5511-5521. doi:10.1093/nar/gkz352' apa: 'Corvaglia, V., Carbajo, D., Prabhakaran, P., Ziach, K., Mandal, P. K., Santos, V. D., … Huc, I. (2019). Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkz352' chicago: 'Corvaglia, Valentina, Daniel Carbajo, Panchami Prabhakaran, Krzysztof Ziach, Pradeep K Mandal, Victor Dos Santos, Carole Legeay, et al. “Carboxylate-Functionalized Foldamer Inhibitors of HIV-1 Integrase and Topoisomerase 1: Artificial Analogues of DNA Mimic Proteins.” Nucleic Acids Research. Oxford University Press, 2019. https://doi.org/10.1093/nar/gkz352.' ieee: 'V. Corvaglia et al., “Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins,” Nucleic Acids Research, vol. 47, no. 11. Oxford University Press, pp. 5511–5521, 2019.' ista: 'Corvaglia V, Carbajo D, Prabhakaran P, Ziach K, Mandal PK, Santos VD, Legeay C, Vogel R, Parissi V, Pourquier P, Huc I. 2019. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins. Nucleic Acids Research. 47(11), 5511–5521.' mla: 'Corvaglia, Valentina, et al. “Carboxylate-Functionalized Foldamer Inhibitors of HIV-1 Integrase and Topoisomerase 1: Artificial Analogues of DNA Mimic Proteins.” Nucleic Acids Research, vol. 47, no. 11, Oxford University Press, 2019, pp. 5511–21, doi:10.1093/nar/gkz352.' short: V. Corvaglia, D. Carbajo, P. Prabhakaran, K. Ziach, P.K. Mandal, V.D. Santos, C. Legeay, R. Vogel, V. Parissi, P. Pourquier, I. Huc, Nucleic Acids Research 47 (2019) 5511–5521. date_created: 2026-01-29T21:17:15Z date_published: 2019-06-20T00:00:00Z date_updated: 2026-02-23T09:56:28Z day: '20' doi: 10.1093/nar/gkz352 extern: '1' has_accepted_license: '1' intvolume: ' 47' issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1093/nar/gkz352 month: '06' oa: 1 oa_version: Published Version page: 5511-5521 publication: Nucleic Acids Research publication_identifier: eissn: - 1362-4962 issn: - 0305-1048 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: 'Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: Artificial analogues of DNA mimic proteins' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2019' ... --- _id: '170' abstract: - lang: eng text: Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ . arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Efthymios full_name: Sofos, Efthymios last_name: Sofos citation: ama: Browning TD, Sofos E. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 2019;373(3-4):977-1016. doi:10.1007/s00208-018-1716-6 apa: Browning, T. D., & Sofos, E. (2019). Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-018-1716-6 chicago: Browning, Timothy D, and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen. Springer Nature, 2019. https://doi.org/10.1007/s00208-018-1716-6. ieee: T. D. Browning and E. Sofos, “Counting rational points on quartic del Pezzo surfaces with a rational conic,” Mathematische Annalen, vol. 373, no. 3–4. Springer Nature, pp. 977–1016, 2019. ista: Browning TD, Sofos E. 2019. Counting rational points on quartic del Pezzo surfaces with a rational conic. Mathematische Annalen. 373(3–4), 977–1016. mla: Browning, Timothy D., and Efthymios Sofos. “Counting Rational Points on Quartic Del Pezzo Surfaces with a Rational Conic.” Mathematische Annalen, vol. 373, no. 3–4, Springer Nature, 2019, pp. 977–1016, doi:10.1007/s00208-018-1716-6. short: T.D. Browning, E. Sofos, Mathematische Annalen 373 (2019) 977–1016. date_created: 2018-12-11T11:44:59Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '01' ddc: - '510' doi: 10.1007/s00208-018-1716-6 extern: '1' external_id: arxiv: - '1609.09057' file: - access_level: open_access checksum: 4061dc2fe99bee25d9adf2d2018cf608 content_type: application/pdf creator: dernst date_created: 2019-05-23T07:53:27Z date_updated: 2020-07-14T12:45:12Z file_id: '6479' file_name: 2019_MathAnnalen_Browning.pdf file_size: 712847 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 373' issue: 3-4 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 977-1016 publication: Mathematische Annalen publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Counting rational points on quartic del Pezzo surfaces with a rational conic tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 373 year: '2019' ... --- _id: '175' abstract: - lang: eng text: An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points. article_processing_charge: No arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Daniel full_name: Loughran, Daniel last_name: Loughran citation: ama: Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514 apa: Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514 chicago: Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514. ieee: T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019. ista: Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785. mla: Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514. short: T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785. date_created: 2018-12-11T11:45:01Z date_published: 2019-04-15T00:00:00Z date_updated: 2025-07-10T11:51:20Z day: '15' department: - _id: TiBr doi: 10.1090/tran/7514 external_id: arxiv: - '1705.01999' isi: - '000464034200019' intvolume: ' 371' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.01999 month: '04' oa: 1 oa_version: Preprint page: 5757-5785 publication: Transactions of the American Mathematical Society publication_identifier: eissn: - 1088-6850 issn: - 0002-9947 publication_status: published publisher: American Mathematical Society publist_id: '7746' quality_controlled: '1' scopus_import: '1' status: public title: Sieving rational points on varieties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 371 year: '2019' ... --- _id: '17506' abstract: - lang: eng text: Sandboxing is a common technique that allows low-level, untrusted components to safely interact with trusted code. However, previous work has only investigated the low-level memory isolation guarantees of sandboxing, leaving open the question of the end-to-end guarantees that sandboxing affords programmers. In this paper, we fill this gap by showing that sandboxing enables reasoning about the known concept of robust safety, i.e., safety of the trusted code even in the presence of arbitrary untrusted code. To do this, we first present an idealized operational semantics for a language that combines trusted code with untrusted code. Sandboxing is built into our semantics. Then, we prove that safety properties of the trusted code (as enforced through a rich type system) are upheld in the presence of arbitrary untrusted code, so long as all interactions with untrusted code occur at the “any” type (a type inhabited by all values). Finally, to alleviate the burden of having to interact with untrusted code at only the “any” type, we formalize and prove safe several wrappers, which automatically convert values between the “any” type and much richer types. All our results are mechanized in the Coq proof assistant. article_processing_charge: No article_type: original author: - first_name: Michael Joachim full_name: Sammler, Michael Joachim id: 510d3901-2a03-11ee-914d-d9ae9011f0a7 last_name: Sammler - first_name: Deepak full_name: Garg, Deepak last_name: Garg - first_name: Derek full_name: Dreyer, Derek last_name: Dreyer - first_name: Tadeusz full_name: Litak, Tadeusz last_name: Litak citation: ama: Sammler MJ, Garg D, Dreyer D, Litak T. The high-level benefits of low-level sandboxing. Proceedings of the ACM on Programming Languages. 2019;4(POPL):1-32. doi:10.1145/3371100 apa: Sammler, M. J., Garg, D., Dreyer, D., & Litak, T. (2019). The high-level benefits of low-level sandboxing. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3371100 chicago: Sammler, Michael Joachim, Deepak Garg, Derek Dreyer, and Tadeusz Litak. “The High-Level Benefits of Low-Level Sandboxing.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2019. https://doi.org/10.1145/3371100. ieee: M. J. Sammler, D. Garg, D. Dreyer, and T. Litak, “The high-level benefits of low-level sandboxing,” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL. Association for Computing Machinery, pp. 1–32, 2019. ista: Sammler MJ, Garg D, Dreyer D, Litak T. 2019. The high-level benefits of low-level sandboxing. Proceedings of the ACM on Programming Languages. 4(POPL), 1–32. mla: Sammler, Michael Joachim, et al. “The High-Level Benefits of Low-Level Sandboxing.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, Association for Computing Machinery, 2019, pp. 1–32, doi:10.1145/3371100. short: M.J. Sammler, D. Garg, D. Dreyer, T. Litak, Proceedings of the ACM on Programming Languages 4 (2019) 1–32. date_created: 2024-09-05T08:36:52Z date_published: 2019-12-20T00:00:00Z date_updated: 2024-09-10T09:58:57Z day: '20' doi: 10.1145/3371100 extern: '1' intvolume: ' 4' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3371100 month: '12' oa: 1 oa_version: Published Version page: 1-32 publication: Proceedings of the ACM on Programming Languages publication_identifier: issn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: The high-level benefits of low-level sandboxing type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 4 year: '2019' ... --- _id: '17510' abstract: - lang: eng text: Weak lensing surveys are reaching sensitivities at which uncertainties in the galaxy redshift distributions n(z) from photo-z errors degrade cosmological constraints. We use ray-tracing simulations and a simple treatment of photo-z errors to assess cosmological parameter biases from uncertainties in n(z) in an LSST-like survey. We use lensing peak counts and the power spectrum to infer cosmological parameters, and find that the latter is somewhat more resilient to photo-z errors. We place conservative lower limits on the survey size at which different types of photo-z errors significantly degrade (${\sim }50{{\ \rm per\ cent}}$) ΛCDM (cold dark matter, wCDM) parameter constraints. A residual constant photo-z bias of |δz| &lt; 0.003(1 + z), the current LSST requirement, does not significantly degrade surveys smaller than ≈1300 (≈490) deg2 using peaks and ≈6500 (≈4900) deg2 using the power spectrum. Surveys smaller than ≈920 (≈450) deg2 and ≈4600 (≈4000) deg2 avoid 25 per cent degradation. Adopting a recent prediction for LSST’s full photo-z probability distribution function (PDF), we find that simply approximating n(z) with the photo-z galaxy distribution computed from this PDF significantly degrades surveys as small as ≈60 (≈65) deg2 using peaks or the power spectrum. If the centroid bias in each tomographic bin is removed from the photo-z galaxy distribution, using peaks or the power spectrum still significantly degrades surveys larger than ≈200 (≈255) or ≈248 (≈315) deg2; 25 per cent degradations occur at survey sizes of ≈140 (≈180) deg2 or ≈165 (≈210) deg2. These results imply that the expected broad photo-z PDF significantly biases parameters, which must be further mitigated using more sophisticated photo-z treatments. article_processing_charge: No article_type: original author: - first_name: Matthew W full_name: Abruzzo, Matthew W last_name: Abruzzo - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: ama: Abruzzo MW, Haiman Z. The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. Monthly Notices of the Royal Astronomical Society. 2019;486(2):2730-2753. doi:10.1093/mnras/stz1016 apa: Abruzzo, M. W., & Haiman, Z. (2019). The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz1016 chicago: Abruzzo, Matthew W, and Zoltán Haiman. “The Impact of Photometric Redshift Errors on Lensing Statistics in Ray-Tracing Simulations.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz1016. ieee: M. W. Abruzzo and Z. Haiman, “The impact of photometric redshift errors on lensing statistics in ray-tracing simulations,” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2. Oxford University Press, pp. 2730–2753, 2019. ista: Abruzzo MW, Haiman Z. 2019. The impact of photometric redshift errors on lensing statistics in ray-tracing simulations. Monthly Notices of the Royal Astronomical Society. 486(2), 2730–2753. mla: Abruzzo, Matthew W., and Zoltán Haiman. “The Impact of Photometric Redshift Errors on Lensing Statistics in Ray-Tracing Simulations.” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2, Oxford University Press, 2019, pp. 2730–53, doi:10.1093/mnras/stz1016. short: M.W. Abruzzo, Z. Haiman, Monthly Notices of the Royal Astronomical Society 486 (2019) 2730–2753. date_created: 2024-09-05T08:49:24Z date_published: 2019-04-18T00:00:00Z date_updated: 2024-09-10T12:49:04Z day: '18' doi: 10.1093/mnras/stz1016 extern: '1' intvolume: ' 486' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz1016 month: '04' oa: 1 oa_version: Published Version page: 2730-2753 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The impact of photometric redshift errors on lensing statistics in ray-tracing simulations type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 486 year: '2019' ... --- _id: '17511' article_number: '019' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Gabriela A. full_name: Marques, Gabriela A. last_name: Marques - first_name: Jia full_name: Liu, Jia last_name: Liu - first_name: José Manuel Zorrilla full_name: Matilla, José Manuel Zorrilla last_name: Matilla - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Armando full_name: Bernui, Armando last_name: Bernui - first_name: Camila P. full_name: Novaes, Camila P. last_name: Novaes citation: ama: Marques GA, Liu J, Matilla JMZ, Haiman Z, Bernui A, Novaes CP. Constraining neutrino mass with weak lensing Minkowski Functionals. Journal of Cosmology and Astroparticle Physics. 2019;2019(06). doi:10.1088/1475-7516/2019/06/019 apa: Marques, G. A., Liu, J., Matilla, J. M. Z., Haiman, Z., Bernui, A., & Novaes, C. P. (2019). Constraining neutrino mass with weak lensing Minkowski Functionals. Journal of Cosmology and Astroparticle Physics. IOP Publishing. https://doi.org/10.1088/1475-7516/2019/06/019 chicago: Marques, Gabriela A., Jia Liu, José Manuel Zorrilla Matilla, Zoltán Haiman, Armando Bernui, and Camila P. Novaes. “Constraining Neutrino Mass with Weak Lensing Minkowski Functionals.” Journal of Cosmology and Astroparticle Physics. IOP Publishing, 2019. https://doi.org/10.1088/1475-7516/2019/06/019. ieee: G. A. Marques, J. Liu, J. M. Z. Matilla, Z. Haiman, A. Bernui, and C. P. Novaes, “Constraining neutrino mass with weak lensing Minkowski Functionals,” Journal of Cosmology and Astroparticle Physics, vol. 2019, no. 06. IOP Publishing, 2019. ista: Marques GA, Liu J, Matilla JMZ, Haiman Z, Bernui A, Novaes CP. 2019. Constraining neutrino mass with weak lensing Minkowski Functionals. Journal of Cosmology and Astroparticle Physics. 2019(06), 019. mla: Marques, Gabriela A., et al. “Constraining Neutrino Mass with Weak Lensing Minkowski Functionals.” Journal of Cosmology and Astroparticle Physics, vol. 2019, no. 06, 019, IOP Publishing, 2019, doi:10.1088/1475-7516/2019/06/019. short: G.A. Marques, J. Liu, J.M.Z. Matilla, Z. Haiman, A. Bernui, C.P. Novaes, Journal of Cosmology and Astroparticle Physics 2019 (2019). date_created: 2024-09-05T08:50:20Z date_published: 2019-06-07T00:00:00Z date_updated: 2024-09-10T13:10:34Z day: '07' doi: 10.1088/1475-7516/2019/06/019 extern: '1' external_id: arxiv: - '1812.08206' intvolume: ' 2019' issue: '06' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1812.08206' month: '06' oa: 1 oa_version: Preprint publication: Journal of Cosmology and Astroparticle Physics publication_identifier: issn: - 1475-7516 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Constraining neutrino mass with weak lensing Minkowski Functionals type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 2019 year: '2019' ... --- _id: '17512' abstract: - lang: eng text: 'The localization of stellar-mass binary black hole mergers using gravitational waves is critical in understanding the properties of the binaries’ host galaxies, observing possible electromagnetic emission from the mergers, or using them as a cosmological distance ladder. The precision of this localization can be substantially increased with prior astrophysical information about the binary system. In particular, constraining the inclination of the binary can reduce the distance uncertainty of the source. Here, we present the first realistic set of localizations for binary black hole mergers, including different prior constraints on the binaries’ inclinations. We find that prior information on the inclination can reduce the localization volume by a factor of 3. We discuss two astrophysical scenarios of interest: (i) follow-up searches for beamed electromagnetic/neutrino counterparts and (ii) mergers in the accretion discs of active galactic nuclei.' article_processing_charge: No article_type: original author: - first_name: K Rainer full_name: Corley, K Rainer last_name: Corley - first_name: Imre full_name: Bartos, Imre last_name: Bartos - first_name: Leo P full_name: Singer, Leo P last_name: Singer - first_name: Andrew R full_name: Williamson, Andrew R last_name: Williamson - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Bence full_name: Kocsis, Bence last_name: Kocsis - first_name: Samaya full_name: Nissanke, Samaya last_name: Nissanke - first_name: Zsuzsa full_name: Márka, Zsuzsa last_name: Márka - first_name: Szabolcs full_name: Márka, Szabolcs last_name: Márka citation: ama: Corley KR, Bartos I, Singer LP, et al. Localization of binary black hole mergers with known inclination. Monthly Notices of the Royal Astronomical Society. 2019;488(3):4459-4463. doi:10.1093/mnras/stz2072 apa: Corley, K. R., Bartos, I., Singer, L. P., Williamson, A. R., Haiman, Z., Kocsis, B., … Márka, S. (2019). Localization of binary black hole mergers with known inclination. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz2072 chicago: Corley, K Rainer, Imre Bartos, Leo P Singer, Andrew R Williamson, Zoltán Haiman, Bence Kocsis, Samaya Nissanke, Zsuzsa Márka, and Szabolcs Márka. “Localization of Binary Black Hole Mergers with Known Inclination.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz2072. ieee: K. R. Corley et al., “Localization of binary black hole mergers with known inclination,” Monthly Notices of the Royal Astronomical Society, vol. 488, no. 3. Oxford University Press, pp. 4459–4463, 2019. ista: Corley KR, Bartos I, Singer LP, Williamson AR, Haiman Z, Kocsis B, Nissanke S, Márka Z, Márka S. 2019. Localization of binary black hole mergers with known inclination. Monthly Notices of the Royal Astronomical Society. 488(3), 4459–4463. mla: Corley, K. Rainer, et al. “Localization of Binary Black Hole Mergers with Known Inclination.” Monthly Notices of the Royal Astronomical Society, vol. 488, no. 3, Oxford University Press, 2019, pp. 4459–63, doi:10.1093/mnras/stz2072. short: K.R. Corley, I. Bartos, L.P. Singer, A.R. Williamson, Z. Haiman, B. Kocsis, S. Nissanke, Z. Márka, S. Márka, Monthly Notices of the Royal Astronomical Society 488 (2019) 4459–4463. date_created: 2024-09-05T08:51:22Z date_published: 2019-07-30T00:00:00Z date_updated: 2024-09-10T13:26:28Z day: '30' doi: 10.1093/mnras/stz2072 extern: '1' intvolume: ' 488' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz2072 month: '07' oa: 1 oa_version: Published Version page: 4459-4463 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Localization of binary black hole mergers with known inclination type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 488 year: '2019' ... --- _id: '17530' abstract: - lang: eng text: Based on the cosmic shear data from the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS), Kilbinger et al. (2013) obtained a constraint on the amplitude of matter fluctuations of σ8(Ωm/0.27)0.6=0.79±0.03 from the two-point correlation function (2PCF). This is ≈3σ lower than the value 0.89±0.01 derived from Planck data on cosmic microwave background (CMB) anisotropies. On the other hand, based on the same CFHTLenS data, but using the power spectrum, and performing a different analysis, Liu et al. (2015) obtained the higher value of σ8(Ωm/0.27)0.64=0.87+0.05−0.06. We here investigate the origin of this difference, by performing a fair side-by-side comparison of the 2PCF and power spectrum analyses on CFHTLenS data. We find that these two statistics indeed deliver different results, even when applied to the same data in an otherwise identical procedure. We identify excess power in the data on small scales (ℓ>5,000) driving the larger values inferred from the power spectrum. We speculate on the possible origin of this excess small-scale power. More generally, our results highlight the utility of analysing the 2PCF and the power spectrum in tandem, to discover (and to help control) systematic errors. article_processing_charge: No article_type: original author: - first_name: Tianhuan full_name: Lu, Tianhuan last_name: Lu - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: ama: Lu T, Haiman Z. The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data. Monthly Notices of the Royal Astronomical Society. 2019;490(4):5033-5042. doi:10.1093/mnras/stz2931 apa: Lu, T., & Haiman, Z. (2019). The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz2931 chicago: Lu, Tianhuan, and Zoltán Haiman. “The Matter Fluctuation Amplitude Inferred from the Weak Lensing Power Spectrum and Correlation Function in CFHTLenS Data.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz2931. ieee: T. Lu and Z. Haiman, “The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data,” Monthly Notices of the Royal Astronomical Society, vol. 490, no. 4. Oxford University Press, pp. 5033–5042, 2019. ista: Lu T, Haiman Z. 2019. The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data. Monthly Notices of the Royal Astronomical Society. 490(4), 5033–5042. mla: Lu, Tianhuan, and Zoltán Haiman. “The Matter Fluctuation Amplitude Inferred from the Weak Lensing Power Spectrum and Correlation Function in CFHTLenS Data.” Monthly Notices of the Royal Astronomical Society, vol. 490, no. 4, Oxford University Press, 2019, pp. 5033–42, doi:10.1093/mnras/stz2931. short: T. Lu, Z. Haiman, Monthly Notices of the Royal Astronomical Society 490 (2019) 5033–5042. date_created: 2024-09-05T09:37:20Z date_published: 2019-10-18T00:00:00Z date_updated: 2024-09-11T08:01:58Z day: '18' doi: 10.1093/mnras/stz2931 extern: '1' intvolume: ' 490' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz2931 month: '10' oa: 1 oa_version: Published Version page: 5033-5042 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/mnras/stad1748 scopus_import: '1' status: public title: The matter fluctuation amplitude inferred from the weak lensing power spectrum and correlation function in CFHTLenS data type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 490 year: '2019' ... --- _id: '17533' abstract: - lang: eng text: "The origins of the stellar-mass black hole mergers discovered by LIGO/Virgo are still unknown. Here we show that if migration traps develop in the accretion disks of active galactic nuclei (AGNs) and promote the mergers of their captive black holes, the majority of black holes within disks will undergo hierarchical mergers—with one of the black holes being the remnant of a previous merger. 40% of AGN-assisted mergers detected by LIGO/Virgo will include a black hole with mass ≳50⁢\U0001D440⊙, the mass limit from stellar core collapse. Hierarchical mergers at traps in AGNs will exhibit black hole spins (anti)aligned with the binary’s orbital axis, a distinct property from other hierarchical channels. Our results suggest, although not definitively (with odds ratio of ∼1), that LIGO’s heaviest merger so far, GW170729, could have originated from this channel." article_number: '181101' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Y. full_name: Yang, Y. last_name: Yang - first_name: I. full_name: Bartos, I. last_name: Bartos - first_name: V. full_name: Gayathri, V. last_name: Gayathri - first_name: K. E. S. full_name: Ford, K. E. S. last_name: Ford - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: S. full_name: Klimenko, S. last_name: Klimenko - first_name: B. full_name: Kocsis, B. last_name: Kocsis - first_name: S. full_name: Márka, S. last_name: Márka - first_name: Z. full_name: Márka, Z. last_name: Márka - first_name: B. full_name: McKernan, B. last_name: McKernan - first_name: R. full_name: O’Shaughnessy, R. last_name: O’Shaughnessy citation: ama: Yang Y, Bartos I, Gayathri V, et al. Hierarchical black hole mergers in active galactic nuclei. Physical Review Letters. 2019;123(18). doi:10.1103/physrevlett.123.181101 apa: Yang, Y., Bartos, I., Gayathri, V., Ford, K. E. S., Haiman, Z., Klimenko, S., … O’Shaughnessy, R. (2019). Hierarchical black hole mergers in active galactic nuclei. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.181101 chicago: Yang, Y., I. Bartos, V. Gayathri, K. E. S. Ford, Zoltán Haiman, S. Klimenko, B. Kocsis, et al. “Hierarchical Black Hole Mergers in Active Galactic Nuclei.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.181101. ieee: Y. Yang et al., “Hierarchical black hole mergers in active galactic nuclei,” Physical Review Letters, vol. 123, no. 18. American Physical Society, 2019. ista: Yang Y, Bartos I, Gayathri V, Ford KES, Haiman Z, Klimenko S, Kocsis B, Márka S, Márka Z, McKernan B, O’Shaughnessy R. 2019. Hierarchical black hole mergers in active galactic nuclei. Physical Review Letters. 123(18), 181101. mla: Yang, Y., et al. “Hierarchical Black Hole Mergers in Active Galactic Nuclei.” Physical Review Letters, vol. 123, no. 18, 181101, American Physical Society, 2019, doi:10.1103/physrevlett.123.181101. short: Y. Yang, I. Bartos, V. Gayathri, K.E.S. Ford, Z. Haiman, S. Klimenko, B. Kocsis, S. Márka, Z. Márka, B. McKernan, R. O’Shaughnessy, Physical Review Letters 123 (2019). date_created: 2024-09-05T09:39:53Z date_published: 2019-11-01T00:00:00Z date_updated: 2024-09-11T14:39:29Z day: '1' doi: 10.1103/physrevlett.123.181101 extern: '1' external_id: arxiv: - '1906.09281' intvolume: ' 123' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1906.09281' month: '11' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: issn: - 0031-9007 - 1079-7114 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Hierarchical black hole mergers in active galactic nuclei type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 123 year: '2019' ... --- _id: '17541' abstract: - lang: eng text: 'In recent years, the discovery of massive quasars at z~7 has provided a striking challenge to our understanding of the origin and growth of supermassive black holes in the early Universe. Mounting observational and theoretical evidence indicates the viability of massive seeds, formed by the collapse of supermassive stars, as a progenitor model for such early, massive accreting black holes. Although considerable progress has been made in our theoretical understanding, many questions remain regarding how (and how often) such objects may form, how they live and die, and how next generation observatories may yield new insight into the origin of these primordial titans. This review focusses on our present understanding of this remarkable formation scenario, based on discussions held at the Monash Prato Centre from November 20--24, 2017, during the workshop "Titans of the Early Universe: The Origin of the First Supermassive Black Holes."' article_number: e027 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Tyrone E. full_name: Woods, Tyrone E. last_name: Woods - first_name: Bhaskar full_name: Agarwal, Bhaskar last_name: Agarwal - first_name: Volker full_name: Bromm, Volker last_name: Bromm - first_name: Andrew full_name: Bunker, Andrew last_name: Bunker - first_name: Ke-Jung full_name: Chen, Ke-Jung last_name: Chen - first_name: Sunmyon full_name: Chon, Sunmyon last_name: Chon - first_name: Andrea full_name: Ferrara, Andrea last_name: Ferrara - first_name: Simon C. O. full_name: Glover, Simon C. O. last_name: Glover - first_name: Lionel full_name: Haemmerlé, Lionel last_name: Haemmerlé - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Tilman full_name: Hartwig, Tilman last_name: Hartwig - first_name: Alexander full_name: Heger, Alexander last_name: Heger - first_name: Shingo full_name: Hirano, Shingo last_name: Hirano - first_name: Takashi full_name: Hosokawa, Takashi last_name: Hosokawa - first_name: Kohei full_name: Inayoshi, Kohei last_name: Inayoshi - first_name: Ralf S. full_name: Klessen, Ralf S. last_name: Klessen - first_name: Chiaki full_name: Kobayashi, Chiaki last_name: Kobayashi - first_name: Filippos full_name: Koliopanos, Filippos last_name: Koliopanos - first_name: Muhammad A. full_name: Latif, Muhammad A. last_name: Latif - first_name: Yuexing full_name: Li, Yuexing last_name: Li - first_name: Lucio full_name: Mayer, Lucio last_name: Mayer - first_name: Mar full_name: Mezcua, Mar last_name: Mezcua - first_name: Priyamvada full_name: Natarajan, Priyamvada last_name: Natarajan - first_name: Fabio full_name: Pacucci, Fabio last_name: Pacucci - first_name: Martin J. full_name: Rees, Martin J. last_name: Rees - first_name: John A. full_name: Regan, John A. last_name: Regan - first_name: Yuya full_name: Sakurai, Yuya last_name: Sakurai - first_name: Stefania full_name: Salvadori, Stefania last_name: Salvadori - first_name: Raffaella full_name: Schneider, Raffaella last_name: Schneider - first_name: Marco full_name: Surace, Marco last_name: Surace - first_name: Takamitsu L. full_name: Tanaka, Takamitsu L. last_name: Tanaka - first_name: Daniel J. full_name: Whalen, Daniel J. last_name: Whalen - first_name: Naoki full_name: Yoshida, Naoki last_name: Yoshida citation: ama: 'Woods TE, Agarwal B, Bromm V, et al. Titans of the early universe: The prato statement on the origin of the first supermassive black holes. Publications of the Astronomical Society of Australia. 2019;36. doi:10.1017/pasa.2019.14' apa: 'Woods, T. E., Agarwal, B., Bromm, V., Bunker, A., Chen, K.-J., Chon, S., … Yoshida, N. (2019). Titans of the early universe: The prato statement on the origin of the first supermassive black holes. Publications of the Astronomical Society of Australia. Cambridge University Press. https://doi.org/10.1017/pasa.2019.14' chicago: 'Woods, Tyrone E., Bhaskar Agarwal, Volker Bromm, Andrew Bunker, Ke-Jung Chen, Sunmyon Chon, Andrea Ferrara, et al. “Titans of the Early Universe: The Prato Statement on the Origin of the First Supermassive Black Holes.” Publications of the Astronomical Society of Australia. Cambridge University Press, 2019. https://doi.org/10.1017/pasa.2019.14.' ieee: 'T. E. Woods et al., “Titans of the early universe: The prato statement on the origin of the first supermassive black holes,” Publications of the Astronomical Society of Australia, vol. 36. Cambridge University Press, 2019.' ista: 'Woods TE, Agarwal B, Bromm V, Bunker A, Chen K-J, Chon S, Ferrara A, Glover SCO, Haemmerlé L, Haiman Z, Hartwig T, Heger A, Hirano S, Hosokawa T, Inayoshi K, Klessen RS, Kobayashi C, Koliopanos F, Latif MA, Li Y, Mayer L, Mezcua M, Natarajan P, Pacucci F, Rees MJ, Regan JA, Sakurai Y, Salvadori S, Schneider R, Surace M, Tanaka TL, Whalen DJ, Yoshida N. 2019. Titans of the early universe: The prato statement on the origin of the first supermassive black holes. Publications of the Astronomical Society of Australia. 36, e027.' mla: 'Woods, Tyrone E., et al. “Titans of the Early Universe: The Prato Statement on the Origin of the First Supermassive Black Holes.” Publications of the Astronomical Society of Australia, vol. 36, e027, Cambridge University Press, 2019, doi:10.1017/pasa.2019.14.' short: T.E. Woods, B. Agarwal, V. Bromm, A. Bunker, K.-J. Chen, S. Chon, A. Ferrara, S.C.O. Glover, L. Haemmerlé, Z. Haiman, T. Hartwig, A. Heger, S. Hirano, T. Hosokawa, K. Inayoshi, R.S. Klessen, C. Kobayashi, F. Koliopanos, M.A. Latif, Y. Li, L. Mayer, M. Mezcua, P. Natarajan, F. Pacucci, M.J. Rees, J.A. Regan, Y. Sakurai, S. Salvadori, R. Schneider, M. Surace, T.L. Tanaka, D.J. Whalen, N. Yoshida, Publications of the Astronomical Society of Australia 36 (2019). date_created: 2024-09-05T09:57:20Z date_published: 2019-08-06T00:00:00Z date_updated: 2024-09-12T13:20:41Z day: '06' doi: 10.1017/pasa.2019.14 extern: '1' external_id: arxiv: - '1810.12310' intvolume: ' 36' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1810.12310' month: '08' oa: 1 oa_version: Preprint publication: Publications of the Astronomical Society of Australia publication_identifier: issn: - 1323-3580 - 1448-6083 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Titans of the early universe: The prato statement on the origin of the first supermassive black holes' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 36 year: '2019' ... --- _id: '17543' abstract: - lang: eng text: 'Massive black-hole (MBH) binaries, which are expected to form following the merger of their parent galaxies, produce gravitational waves which will be detectable by Pulsar Timing Arrays at nanohertz frequencies (year periods). While no confirmed, compact MBH binary systems have been seen in electromagnetic observations, a large number of candidates have recently been identified in optical surveys of AGN variability. Using a combination of cosmological, hydrodynamic simulations; comprehensive, semi-analytic binary merger models; and analytic AGN spectra and variability prescriptions; we calculate the expected electromagnetic detection rates of MBH binaries as periodically variable AGN. In particular, we consider two independent variability models: (i) Doppler boosting due to large orbital velocities, and (ii) hydrodynamic variability in which the fueling of MBH accretion disks is periodically modulated by the companion. Our models predict that numerous MBH binaries should be present and distinguishable in the existing data. In particular, our fiducial models produce an expectation value of 0.2 (Doppler) and 5 (hydrodynamic) binaries to be identifiable in CRTS, while 20 and 100 are expected after five years of LSST observations. The brightness variations in most systems are too small to be distinguishable, but almost 1% of AGN at redshifts z≲0.6 could be in massive binaries. We analyze the predicted binary parameters of observable systems and their selection biases, and include an extensive discussion of our model parameters and uncertainties.' article_processing_charge: No article_type: original author: - first_name: Luke Zoltan full_name: Kelley, Luke Zoltan last_name: Kelley - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: Alberto full_name: Sesana, Alberto last_name: Sesana - first_name: Lars full_name: Hernquist, Lars last_name: Hernquist citation: ama: Kelley LZ, Haiman Z, Sesana A, Hernquist L. Massive BH binaries as periodically variable AGN. Monthly Notices of the Royal Astronomical Society. 2019;485(2):1579-1594. doi:10.1093/mnras/stz150 apa: Kelley, L. Z., Haiman, Z., Sesana, A., & Hernquist, L. (2019). Massive BH binaries as periodically variable AGN. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz150 chicago: Kelley, Luke Zoltan, Zoltán Haiman, Alberto Sesana, and Lars Hernquist. “Massive BH Binaries as Periodically Variable AGN.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz150. ieee: L. Z. Kelley, Z. Haiman, A. Sesana, and L. Hernquist, “Massive BH binaries as periodically variable AGN,” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 2. Oxford University Press, pp. 1579–1594, 2019. ista: Kelley LZ, Haiman Z, Sesana A, Hernquist L. 2019. Massive BH binaries as periodically variable AGN. Monthly Notices of the Royal Astronomical Society. 485(2), 1579–1594. mla: Kelley, Luke Zoltan, et al. “Massive BH Binaries as Periodically Variable AGN.” Monthly Notices of the Royal Astronomical Society, vol. 485, no. 2, Oxford University Press, 2019, pp. 1579–94, doi:10.1093/mnras/stz150. short: L.Z. Kelley, Z. Haiman, A. Sesana, L. Hernquist, Monthly Notices of the Royal Astronomical Society 485 (2019) 1579–1594. date_created: 2024-09-05T09:59:54Z date_published: 2019-01-30T00:00:00Z date_updated: 2024-09-18T08:52:07Z day: '30' doi: 10.1093/mnras/stz150 extern: '1' intvolume: ' 485' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz150 month: '01' oa: 1 oa_version: Published Version page: 1579-1594 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Massive BH binaries as periodically variable AGN type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 485 year: '2019' ... --- _id: '17556' abstract: - lang: eng text: The abundance of molecular hydrogen (H2), the primary coolant in primordial gas, is critical for the thermodynamic evolution and star-formation histories in early protogalaxies. Determining the photodissociation rate of H2 by an incident Lyman-Werner (LW) flux is thus crucial, but prohibitively expensive to calculate on the fly in simulations. The rate is sensitive to the H2 rovibrational distribution, which in turn depends on the gas density, temperature, and incident LW radiation field. We use the publicly available cloudy package to model primordial gas clouds and compare exact photodissociation rate calculations to commonly-used fitting formulae. We find the fit from Wolcott-Green et al. (2011) is most accurate for moderate densities n~10^3 cm^{-3} and temperatures, T~10^3K, and we provide a new fit, which captures the increase in the rate at higher densities and temperatures, owing to the increased excited rovibrational populations in this regime. Our new fit has typical errors of a few percent percent up to n =<10^7 cm^{-3}, T =< 8000K, and H2 column density NH2 =<10^{17} cm^{-2}, and can be easily utilized in simulations. We also show that pumping of the excited rovibrational states of H2 by a strong LW flux further modifies the level populations when the gas density is low, and noticeably decreases self-shielding for J_21 > 10^3 and n < 10^2 cm^{-3}. This may lower the "critical flux" at which primordial gas remains H2-poor in some protogalaxies, enabling massive black hole seed formation. article_processing_charge: No article_type: original author: - first_name: J full_name: Wolcott-Green, J last_name: Wolcott-Green - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: ama: 'Wolcott-Green J, Haiman Z. H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies. Monthly Notices of the Royal Astronomical Society. 2019;484(2):2467-2473. doi:10.1093/mnras/sty3280' apa: 'Wolcott-Green, J., & Haiman, Z. (2019). H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty3280' chicago: 'Wolcott-Green, J, and Zoltán Haiman. “H2 Self-Shielding with Non-LTE Rovibrational Populations: Implications for Cooling in Protogalaxies.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/sty3280.' ieee: 'J. Wolcott-Green and Z. Haiman, “H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies,” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 2. Oxford University Press, pp. 2467–2473, 2019.' ista: 'Wolcott-Green J, Haiman Z. 2019. H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies. Monthly Notices of the Royal Astronomical Society. 484(2), 2467–2473.' mla: 'Wolcott-Green, J., and Zoltán Haiman. “H2 Self-Shielding with Non-LTE Rovibrational Populations: Implications for Cooling in Protogalaxies.” Monthly Notices of the Royal Astronomical Society, vol. 484, no. 2, Oxford University Press, 2019, pp. 2467–73, doi:10.1093/mnras/sty3280.' short: J. Wolcott-Green, Z. Haiman, Monthly Notices of the Royal Astronomical Society 484 (2019) 2467–2473. date_created: 2024-09-05T10:24:40Z date_published: 2019-01-16T00:00:00Z date_updated: 2024-09-18T12:00:29Z day: '16' doi: 10.1093/mnras/sty3280 extern: '1' intvolume: ' 484' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/sty3280 month: '01' oa: 1 oa_version: Published Version page: 2467-2473 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'H2 self-shielding with non-LTE rovibrational populations: Implications for cooling in protogalaxies' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 484 year: '2019' ... --- _id: '17565' abstract: - lang: eng text: 'The coalescence of a compact object with a 104−107M⊙ supermassive black hole (SMBH) produces mHz gravitational waves (GWs) detectable by the future Laser Interferometer Space Antenna (LISA). If such an inspiral occurs in the accretion disc of an active galactic nucleus (AGN), the gas torques imprint a small deviation in the GW waveform. Here we present two-dimensional hydrodynamical simulations with the moving-mesh code DISCO of a BH inspiraling at the GW rate in a binary system with a mass ratio q=M2/M1=10−3, embedded in an accretion disc. We assume a locally isothermal equation of state for the gas (with Mach number M=20) and implement a standard α-prescription for its viscosity (with α=0.03). We find disc torques on the binary that are weaker than in previous semi-analytic toy models, and are in the opposite direction: the gas disc slows down, rather than speeds up the inspiral. We compute the resulting deviations in the GW waveform, which scale linearly with the mass of the disc. The SNR of these deviations accumulates mostly at high frequencies, and becomes detectable in a 5-year LISA observation if the total phase shift exceeds a few radians. We find that this occurs if the disc surface density exceeds Σ0≳102−3gcm−2, as may be the case in thin discs with near-Eddington accretion rates. Since the characteristic imprint on the GW signal is strongly dependent on disc parameters, a LISA detection of an intermediate mass ratio inspiral would probe the physics of AGN discs and migration.' article_processing_charge: No article_type: original author: - first_name: A M full_name: Derdzinski, A M last_name: Derdzinski - first_name: D full_name: D’Orazio, D last_name: D’Orazio - first_name: P full_name: Duffell, P last_name: Duffell - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman - first_name: A full_name: MacFadyen, A last_name: MacFadyen citation: ama: 'Derdzinski AM, D’Orazio D, Duffell P, Haiman Z, MacFadyen A. Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc. Monthly Notices of the Royal Astronomical Society. 2019;486(2):2754-2765. doi:10.1093/mnras/stz1026' apa: 'Derdzinski, A. M., D’Orazio, D., Duffell, P., Haiman, Z., & MacFadyen, A. (2019). Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stz1026' chicago: 'Derdzinski, A M, D D’Orazio, P Duffell, Zoltán Haiman, and A MacFadyen. “Probing Gas Disc Physics with LISA: Simulations of an Intermediate Mass Ratio Inspiral in an Accretion Disc.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2019. https://doi.org/10.1093/mnras/stz1026.' ieee: 'A. M. Derdzinski, D. D’Orazio, P. Duffell, Z. Haiman, and A. MacFadyen, “Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc,” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2. Oxford University Press, pp. 2754–2765, 2019.' ista: 'Derdzinski AM, D’Orazio D, Duffell P, Haiman Z, MacFadyen A. 2019. Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc. Monthly Notices of the Royal Astronomical Society. 486(2), 2754–2765.' mla: 'Derdzinski, A. M., et al. “Probing Gas Disc Physics with LISA: Simulations of an Intermediate Mass Ratio Inspiral in an Accretion Disc.” Monthly Notices of the Royal Astronomical Society, vol. 486, no. 2, Oxford University Press, 2019, pp. 2754–65, doi:10.1093/mnras/stz1026.' short: A.M. Derdzinski, D. D’Orazio, P. Duffell, Z. Haiman, A. MacFadyen, Monthly Notices of the Royal Astronomical Society 486 (2019) 2754–2765. date_created: 2024-09-05T12:05:43Z date_published: 2019-09-05T00:00:00Z date_updated: 2024-09-18T11:01:36Z day: '05' doi: 10.1093/mnras/stz1026 extern: '1' intvolume: ' 486' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/mnras/stz1026 month: '09' oa: 1 oa_version: Published Version page: 2754-2765 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1093/mnras/stz2435 scopus_import: '1' status: public title: 'Probing gas disc physics with LISA: simulations of an intermediate mass ratio inspiral in an accretion disc' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 486 year: '2019' ...