--- _id: '6877' article_processing_charge: No article_type: original author: - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047 apa: Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047 chicago: Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047. ieee: A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019. ista: Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53. mla: Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047. short: A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53. date_created: 2019-09-15T22:00:46Z date_published: 2019-09-19T00:00:00Z date_updated: 2024-03-27T23:30:40Z day: '19' department: - _id: MiSi doi: 10.1016/j.cell.2019.08.047 external_id: isi: - '000486618500011' pmid: - '31539498' intvolume: ' 179' isi: 1 issue: '1' language: - iso: eng month: '09' oa_version: None page: 51-53 pmid: 1 publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '6891' relation: dissertation_contains status: public scopus_import: '1' status: public title: The neural crest pitches in to remove apoptotic debris type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 179 year: '2019' ... --- _id: '6830' article_processing_charge: No article_type: letter_note author: - first_name: Ximena full_name: Contreras, Ximena id: 475990FE-F248-11E8-B48F-1D18A9856A87 last_name: Contreras - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021 apa: Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021 chicago: Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021. ieee: X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019. ista: Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752. mla: Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021. short: X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752. date_created: 2019-08-25T22:00:50Z date_published: 2019-09-04T00:00:00Z date_updated: 2024-03-27T23:30:41Z day: '04' department: - _id: SiHi doi: 10.1016/j.neuron.2019.08.021 external_id: isi: - '000484400200002' pmid: - '31487522' intvolume: ' 103' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2019.08.021 month: '09' oa: 1 oa_version: Published Version page: 750-752 pmid: 1 publication: Neuron publication_identifier: eissn: - '10974199' issn: - '08966273' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '7902' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Memo1 tiles the radial glial cell grid type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 103 year: '2019' ... --- _id: '6627' abstract: - lang: eng text: Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation. article_number: '3337' article_processing_charge: Yes article_type: original author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337 apa: Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337 chicago: Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337. ieee: M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019. ista: Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337. mla: Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337. short: M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019). date_created: 2019-07-11T12:00:32Z date_published: 2019-07-07T00:00:00Z date_updated: 2024-03-27T23:30:43Z day: '07' ddc: - '580' department: - _id: JiFr doi: 10.3390/ijms20133337 ec_funded: 1 external_id: isi: - '000477041100221' pmid: - '31284661' file: - access_level: open_access checksum: dd9d1cbb933a72ceb666c9667890ac51 content_type: application/pdf creator: dernst date_created: 2019-07-17T06:17:15Z date_updated: 2020-07-14T12:47:34Z file_id: '6645' file_name: 2019_JournalMolecularScience_Adamowski.pdf file_size: 3330291 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 20' isi: 1 issue: '13' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: International Journal of Molecular Sciences publication_identifier: eissn: - 1422-0067 publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public scopus_import: '1' status: public title: Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '7117' abstract: - lang: eng text: We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models. article_number: '157' article_processing_charge: No article_type: original author: - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Christian full_name: Schumacher, Christian last_name: Schumacher - first_name: Espen full_name: Knoop, Espen last_name: Knoop - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Moritz full_name: Bächer, Moritz last_name: Bächer citation: ama: 'Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576' apa: 'Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576' chicago: 'Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.' ieee: 'C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.' ista: 'Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.' mla: 'Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.' short: C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019). date_created: 2019-11-26T14:22:09Z date_published: 2019-11-06T00:00:00Z date_updated: 2024-03-27T23:30:46Z day: '06' ddc: - '000' department: - _id: BeBi doi: 10.1145/3355089.3356576 ec_funded: 1 external_id: isi: - '000498397300007' file: - access_level: open_access checksum: 56a2fb019adcb556d2b022f5e5acb68c content_type: application/pdf creator: bbickel date_created: 2019-11-26T14:24:26Z date_updated: 2020-07-14T12:47:49Z file_id: '7119' file_name: xcad_sup_mat_siga19.pdf file_size: 1673176 relation: supplementary_material title: X-CAD Supplemental Material - access_level: open_access checksum: 5f29d76aceb5102e766cbab9b17d776e content_type: application/pdf creator: bbickel date_created: 2019-11-26T14:24:27Z date_updated: 2020-07-14T12:47:49Z description: This is the author's version of the work. file_id: '7120' file_name: XCAD_authors_version.pdf file_size: 14563618 relation: main_file title: 'X-CAD: Optimizing CAD Models with Extended Finite Elements' - access_level: open_access checksum: 0d31e123286cbec9e28b2001c2bb0d55 content_type: video/mp4 creator: bbickel date_created: 2019-11-26T14:27:37Z date_updated: 2020-07-14T12:47:49Z file_id: '7121' file_name: XCAD_video.mp4 file_size: 259979129 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '12897' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'X-CAD: Optimizing CAD Models with Extended Finite Elements' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 38 year: '2019' ... --- _id: '6189' abstract: - lang: eng text: 'Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations.' article_number: '114502' article_processing_charge: No author: - first_name: Nishchal full_name: Agrawal, Nishchal id: 469E6004-F248-11E8-B48F-1D18A9856A87 last_name: Agrawal - first_name: George H full_name: Choueiri, George H id: 448BD5BC-F248-11E8-B48F-1D18A9856A87 last_name: Choueiri - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502 apa: Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502 chicago: Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502. ieee: N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019. ista: Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502. mla: Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502. short: N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019). date_created: 2019-03-31T21:59:12Z date_published: 2019-03-22T00:00:00Z date_updated: 2024-03-27T23:30:47Z day: '22' department: - _id: BjHo doi: 10.1103/PhysRevLett.122.114502 external_id: arxiv: - '1809.06358' isi: - '000461922000006' intvolume: ' 122' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.06358 month: '03' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: eissn: - '10797114' issn: - '00319007' publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '9728' relation: dissertation_contains status: public scopus_import: '1' status: public title: Transition to turbulence in particle laden flows type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2019' ... --- _id: '6371' abstract: - lang: eng text: "Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \ \r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler citation: ama: Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371 apa: Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371 chicago: Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371. ieee: C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019. ista: Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. mla: Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371. short: C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019. date_created: 2019-05-03T11:55:51Z date_published: 2019-05-03T00:00:00Z date_updated: 2024-02-21T13:45:52Z day: '03' ddc: - '576' - '579' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:6371 file: - access_level: open_access checksum: c0085d47c58c9cbcab1b0a783480f6da content_type: application/pdf creator: cigler date_created: 2019-05-03T11:54:52Z date_updated: 2021-02-11T11:17:13Z embargo: 2020-05-02 file_id: '6373' file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf file_size: 12597663 relation: main_file - access_level: closed checksum: 2eac954de1c8bbf7e6fb35ed0221ae8c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cigler date_created: 2019-05-03T11:54:54Z date_updated: 2020-07-14T12:47:28Z embargo_to: open_access file_id: '6374' file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx file_size: 34644426 relation: source_file file_date_updated: 2021-02-11T11:17:13Z has_accepted_license: '1' keyword: - gene regulation - biophysics - transcription factor binding - bacteria language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '152' project: - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture (DOC Fellowship) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '67' relation: part_of_dissertation status: public - id: '5585' relation: popular_science status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '10286' abstract: - lang: eng text: 'In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.' article_processing_charge: No article_type: original author: - first_name: Elie Noumon full_name: Allini, Elie Noumon last_name: Allini - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski - first_name: Oto full_name: Petura, Oto last_name: Petura - first_name: Florent full_name: Bernard, Florent last_name: Bernard - first_name: Marek full_name: Laban, Marek last_name: Laban - first_name: Viktor full_name: Fischer, Viktor last_name: Fischer citation: ama: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242 apa: Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242 chicago: Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242. ieee: E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018. ista: Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242. mla: Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242. short: E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242. date_created: 2021-11-14T23:01:25Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-11-15T10:48:49Z day: '01' ddc: - '000' department: - _id: KrPi doi: 10.13154/tches.v2018.i3.214-242 file: - access_level: open_access checksum: b816b848f046c48a8357700d9305dce5 content_type: application/pdf creator: cchlebak date_created: 2021-11-15T10:27:29Z date_updated: 2021-11-15T10:27:29Z file_id: '10289' file_name: 2018_IACR_Allini.pdf file_size: 955755 relation: main_file success: 1 file_date_updated: 2021-11-15T10:27:29Z has_accepted_license: '1' intvolume: ' 2018' issue: '3' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 214-242 publication: IACR Transactions on Cryptographic Hardware and Embedded Systems publication_identifier: eissn: - 2569-2925 publication_status: published publisher: International Association for Cryptologic Research quality_controlled: '1' scopus_import: '1' status: public title: Evaluation and monitoring of free running oscillators serving as source of randomness 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: 2018 year: '2018' ... --- _id: '10362' abstract: - lang: eng text: Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties. acknowledgement: We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1). article_processing_charge: No article_type: original author: - first_name: Patrick D. Ellis full_name: Fisher, Patrick D. Ellis last_name: Fisher - first_name: Qi full_name: Shen, Qi last_name: Shen - first_name: Bernice full_name: Akpinar, Bernice last_name: Akpinar - first_name: Luke K. full_name: Davis, Luke K. last_name: Davis - first_name: Kenny Kwok Hin full_name: Chung, Kenny Kwok Hin last_name: Chung - first_name: David full_name: Baddeley, David last_name: Baddeley - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Thomas J. full_name: Melia, Thomas J. last_name: Melia - first_name: Bart W. full_name: Hoogenboom, Bart W. last_name: Hoogenboom - first_name: Chenxiang full_name: Lin, Chenxiang last_name: Lin - first_name: C. Patrick full_name: Lusk, C. Patrick last_name: Lusk citation: ama: Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044 apa: Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.7b08044 chicago: Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044. ieee: P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018. ista: Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518. mla: Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044. short: P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518. date_created: 2021-11-26T15:15:00Z date_published: 2018-01-19T00:00:00Z date_updated: 2021-11-26T15:57:02Z day: '19' doi: 10.1021/acsnano.7b08044 extern: '1' external_id: pmid: - '29350911' intvolume: ' 12' issue: '2' keyword: - general physics and astronomy language: - iso: eng month: '01' oa_version: None page: 1508-1518 pmid: 1 publication: ACS Nano publication_identifier: eissn: - 1936-086X issn: - 1936-0851 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 year: '2018' ... --- _id: '10360' abstract: - lang: eng text: Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation. acknowledgement: We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI). article_processing_charge: No article_type: original author: - first_name: Samuel I. A. full_name: Cohen, Samuel I. A. last_name: Cohen - first_name: Risto full_name: Cukalevski, Risto last_name: Cukalevski - first_name: Thomas C. T. full_name: Michaels, Thomas C. T. last_name: Michaels - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Mattias full_name: Törnquist, Mattias last_name: Törnquist - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Alexander K. full_name: Buell, Alexander K. last_name: Buell - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles - first_name: Sara full_name: Linse, Sara last_name: Linse citation: ama: Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x apa: Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-018-0023-x chicago: Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry. Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x. ieee: S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” Nature Chemistry, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018. ista: Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531. mla: Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x. short: S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531. date_created: 2021-11-26T12:41:38Z date_published: 2018-03-26T00:00:00Z date_updated: 2021-11-26T15:14:00Z day: '26' doi: 10.1038/s41557-018-0023-x extern: '1' external_id: pmid: - '29581486' intvolume: ' 10' issue: '5' keyword: - general chemical engineering - general chemistry language: - iso: eng month: '03' oa_version: None page: 523-531 pmid: 1 publication: Nature Chemistry publication_identifier: eissn: - 1755-4349 issn: - 1755-4330 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 10 year: '2018' ... --- _id: '10357' abstract: - lang: eng text: The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements. acknowledgement: We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions. article_processing_charge: No article_type: original author: - first_name: Alexander J. full_name: Dear, Alexander J. last_name: Dear - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Thomas C. T. full_name: Michaels, Thomas C. T. last_name: Michaels - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles citation: ama: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805 apa: Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.8b07805 chicago: Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805. ieee: A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” The Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018. ista: Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730. mla: Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805. short: A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730. date_created: 2021-11-26T11:55:12Z date_published: 2018-10-18T00:00:00Z date_updated: 2021-11-26T12:40:02Z day: '18' doi: 10.1021/acs.jpcb.8b07805 extern: '1' external_id: pmid: - '30336667' intvolume: ' 122' issue: '49' keyword: - materials chemistry language: - iso: eng month: '10' oa_version: None page: 11721-11730 pmid: 1 publication: The Journal of Physical Chemistry B publication_identifier: eissn: - 1520-5207 issn: - 1520-6106 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Statistical mechanics of globular oligomer formation by protein molecules type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 122 year: '2018' ... --- _id: '10359' abstract: - lang: eng text: Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets. acknowledgement: We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1. article_processing_charge: No article_type: original author: - first_name: Tine full_name: Curk, Tine last_name: Curk - first_name: Peter full_name: Wirnsberger, Peter last_name: Wirnsberger - first_name: Jure full_name: Dobnikar, Jure last_name: Dobnikar - first_name: Daan full_name: Frenkel, Daan last_name: Frenkel - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786 apa: Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786 chicago: Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786. ieee: T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018. ista: Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356. mla: Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:10.1021/acs.nanolett.8b00786. short: T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356. date_created: 2021-11-26T12:15:47Z date_published: 2018-04-18T00:00:00Z date_updated: 2021-11-26T15:14:08Z day: '18' doi: 10.1021/acs.nanolett.8b00786 extern: '1' external_id: pmid: - '29667410' intvolume: ' 18' issue: '9' keyword: - mechanical engineering - condensed matter physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.10147 month: '04' oa: 1 oa_version: Preprint page: 5350-5356 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Controlling cargo trafficking in multicomponent membranes type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 18 year: '2018' ... --- _id: '10358' abstract: - lang: eng text: Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements. acknowledgement: We thank Claudia Flandoli for the help with illustrations. article_processing_charge: No article_type: original author: - first_name: Thomas C. T. full_name: Michaels, Thomas C. T. last_name: Michaels - first_name: Lucie X. full_name: Liu, Lucie X. last_name: Liu - first_name: Samo full_name: Curk, Samo last_name: Curk - first_name: Peter G. full_name: Bolhuis, Peter G. last_name: Bolhuis - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles citation: ama: 'Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280' apa: 'Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., & Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280' chicago: 'Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics. Taylor & Francis, 2018. https://doi.org/10.1080/00268976.2018.1474280.' ieee: 'T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor & Francis, pp. 3055–3065, 2018.' ista: 'Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065.' mla: 'Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22, Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.' short: T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065. date_created: 2021-11-26T12:08:02Z date_published: 2018-05-24T00:00:00Z date_updated: 2021-11-26T12:39:58Z day: '24' doi: 10.1080/00268976.2018.1474280 extern: '1' external_id: arxiv: - '1803.04851' intvolume: ' 116' issue: 21-22 keyword: - physical chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.04851 month: '05' oa: 1 oa_version: Preprint page: 3055-3065 publication: Molecular Physics publication_identifier: eissn: - 1362-3028 issn: - 0026-8976 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: 'Reaction rate theory for supramolecular kinetics: application to protein aggregation' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 116 year: '2018' ... --- _id: '10361' abstract: - lang: eng text: Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation. acknowledgement: "We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969)." article_processing_charge: No article_type: original author: - first_name: Thomas C.T. full_name: Michaels, Thomas C.T. last_name: Michaels - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Johnny full_name: Habchi, Johnny last_name: Habchi - first_name: Sean full_name: Chia, Sean last_name: Chia - first_name: Georg full_name: Meisl, Georg last_name: Meisl - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Tuomas P.J. full_name: Knowles, Tuomas P.J. last_name: Knowles citation: ama: Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322 apa: Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322 chicago: Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews, 2018. https://doi.org/10.1146/annurev-physchem-050317-021322. ieee: T. C. T. Michaels et al., “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” Annual Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018. ista: Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298. mla: Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322. short: T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298. date_created: 2021-11-26T12:52:12Z date_published: 2018-02-28T00:00:00Z date_updated: 2021-11-26T15:58:19Z day: '28' doi: 10.1146/annurev-physchem-050317-021322 extern: '1' external_id: pmid: - '29490200' intvolume: ' 69' issue: '1' keyword: - physical and theoretical chemistry language: - iso: eng month: '02' oa_version: None page: 273-298 pmid: 1 publication: Annual Review of Physical Chemistry publication_identifier: eissn: - 1545-1593 issn: - 0066-426X publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 69 year: '2018' ... --- _id: '10626' abstract: - lang: eng text: "Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4." acknowledgement: We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation. article_number: '226801' article_processing_charge: No article_type: original author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: H. full_name: Zhou, H. last_name: Zhou - first_name: E. M. full_name: Spanton, E. M. last_name: Spanton - first_name: T. full_name: Taniguchi, T. last_name: Taniguchi - first_name: K. full_name: Watanabe, K. last_name: Watanabe - first_name: A. F. full_name: Young, A. F. last_name: Young citation: ama: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801 apa: Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.226801 chicago: Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.226801. ieee: H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22. American Physical Society, 2018. ista: Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801. mla: Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801. short: H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018). date_created: 2022-01-14T12:15:47Z date_published: 2018-11-28T00:00:00Z date_updated: 2022-01-14T13:48:35Z day: '28' doi: 10.1103/physrevlett.121.226801 extern: '1' external_id: arxiv: - '1805.04199' intvolume: ' 121' issue: '22' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.04199 month: '11' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 121 year: '2018' ... --- _id: '10627' abstract: - lang: eng text: We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures. acknowledgement: "We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n" article_number: '184501' article_processing_charge: No article_type: original author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Tyler R. full_name: Naibert, Tyler R. last_name: Naibert - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian citation: ama: Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501 apa: Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.184501 chicago: Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501. ieee: H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” Physical Review B, vol. 97, no. 18. American Physical Society, 2018. ista: Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501. mla: Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:10.1103/physrevb.97.184501. short: H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018). date_created: 2022-01-14T13:48:47Z date_published: 2018-05-08T00:00:00Z date_updated: 2022-01-14T13:58:24Z day: '08' doi: 10.1103/physrevb.97.184501 extern: '1' external_id: arxiv: - '1703.08184' intvolume: ' 97' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.08184 month: '05' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Imaging phase slip dynamics in micron-size superconducting rings type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 97 year: '2018' ... --- _id: '10883' abstract: - lang: eng text: 'Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.' acknowledgement: 'A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.' alternative_title: - EPiC Series in Computing article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Svozil, Alexander last_name: Svozil citation: ama: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k' apa: 'Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k' chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k. ieee: K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253. ista: 'Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.' mla: Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k. short: K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253. conference: end_date: 2018-11-21 location: Awassa, Ethiopia name: 'LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning' start_date: 2018-11-17 date_created: 2022-03-18T12:46:32Z date_published: 2018-10-23T00:00:00Z date_updated: 2022-07-29T09:24:31Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.29007/5z5k ec_funded: 1 external_id: arxiv: - '1909.04983' file: - access_level: open_access checksum: 1229aa8640bd6db610c85decf2265480 content_type: application/pdf creator: dernst date_created: 2022-05-17T07:51:08Z date_updated: 2022-05-17T07:51:08Z file_id: '11392' file_name: 2018_EPiCs_Chatterjee.pdf file_size: 720893 relation: main_file success: 1 file_date_updated: 2022-05-17T07:51:08Z has_accepted_license: '1' intvolume: ' 57' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 233-253 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning publication_identifier: issn: - 2398-7340 publication_status: published publisher: EasyChair quality_controlled: '1' scopus_import: '1' status: public title: Quasipolynomial set-based symbolic algorithms for parity games type: conference user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 57 year: '2018' ... --- _id: '1092' abstract: - lang: eng text: 'A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. ' author: - first_name: Fatemeh full_name: Mohammadi, Fatemeh id: 2C29581E-F248-11E8-B48F-1D18A9856A87 last_name: Mohammadi - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Charles full_name: Wang, Charles last_name: Wang - first_name: Josephine full_name: Yu, Josephine last_name: Yu citation: ama: Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93. doi:10.1137/16M107894X apa: Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. SIAM. https://doi.org/10.1137/16M107894X chicago: Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X. ieee: F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” SIAM Journal on Discrete Mathematics, vol. 32, no. 1. SIAM, pp. 64–93, 2018. ista: Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93. mla: Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:10.1137/16M107894X. short: F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93. date_created: 2018-12-11T11:50:06Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T06:48:13Z day: '01' doi: 10.1137/16M107894X extern: '1' intvolume: ' 32' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.01814 month: '01' oa: 1 oa_version: Preprint page: 64-93 publication: SIAM Journal on Discrete Mathematics publication_status: published publisher: SIAM publist_id: '6284' quality_controlled: '1' status: public title: Generalized permutohedra from probabilistic graphical models type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2018' ... --- _id: '11' abstract: - lang: eng text: We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm. author: - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: Peter full_name: Pickl, Peter last_name: Pickl citation: ama: 'Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9' apa: 'Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9' chicago: Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9. ieee: 'N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.' ista: 'Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.' mla: Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9. short: N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214. conference: end_date: 2017-04-01 location: Munich, Germany name: 'MaLiQS: Macroscopic Limits of Quantum Systems' start_date: 2017-03-30 date_created: 2018-12-11T11:44:08Z date_published: 2018-10-27T00:00:00Z date_updated: 2021-01-12T06:48:16Z day: '27' department: - _id: RoSe doi: 10.1007/978-3-030-01602-9_9 ec_funded: 1 external_id: arxiv: - '1806.10843' intvolume: ' 270' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.10843 month: '10' oa: 1 oa_version: Preprint page: 185 - 214 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication_status: published publisher: Springer publist_id: '8045' quality_controlled: '1' scopus_import: 1 status: public title: Mean-field limits of particles in interaction with quantised radiation fields type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 270 year: '2018' ... --- _id: '11063' abstract: - lang: eng text: The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus. article_processing_charge: No article_type: original author: - first_name: Asako full_name: McCloskey, Asako last_name: McCloskey - first_name: Arkaitz full_name: Ibarra, Arkaitz last_name: Ibarra - 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: McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331. doi:10.1101/gad.315523.118 apa: McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118 chicago: McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development. Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118. ieee: A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” Genes & Development, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018. ista: McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331. mla: McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118. short: A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331. date_created: 2022-04-07T07:45:30Z date_published: 2018-09-18T00:00:00Z date_updated: 2022-07-18T08:32:32Z day: '18' doi: 10.1101/gad.315523.118 extern: '1' external_id: pmid: - '30228202' intvolume: ' 32' issue: 19-20 keyword: - Developmental Biology - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/gad.315523.118 month: '09' oa: 1 oa_version: Published Version page: 1321-1331 pmid: 1 publication: Genes & Development publication_identifier: issn: - 0890-9369 - 1549-5477 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: Tpr regulates the total number of nuclear pore complexes per cell nucleus type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 32 year: '2018' ... --- _id: '11064' abstract: - lang: eng text: Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients. article_number: '221' article_processing_charge: No article_type: original author: - first_name: Jason G. full_name: Fleischer, Jason G. last_name: Fleischer - first_name: Roberta full_name: Schulte, Roberta last_name: Schulte - first_name: Hsiao H. full_name: Tsai, Hsiao H. last_name: Tsai - first_name: Swati full_name: Tyagi, Swati last_name: Tyagi - first_name: Arkaitz full_name: Ibarra, Arkaitz last_name: Ibarra - first_name: Maxim N. full_name: Shokhirev, Maxim N. last_name: Shokhirev - first_name: Ling full_name: Huang, Ling last_name: Huang - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Saket full_name: Navlakha, Saket last_name: Navlakha citation: ama: Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6 apa: Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6 chicago: Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6. ieee: J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018. ista: Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221. mla: Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018, doi:10.1186/s13059-018-1599-6. short: J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018). date_created: 2022-04-07T07:45:40Z date_published: 2018-12-20T00:00:00Z date_updated: 2022-07-18T08:32:34Z day: '20' doi: 10.1186/s13059-018-1599-6 extern: '1' external_id: pmid: - '30567591' intvolume: ' 19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s13059-018-1599-6 month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: issn: - 1474-760X publication_status: published publisher: BioMed Central quality_controlled: '1' scopus_import: '1' status: public title: Predicting age from the transcriptome of human dermal fibroblasts type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 19 year: '2018' ... --- _id: '11508' abstract: - lang: eng text: Distant luminous Lyman-α emitters (LAEs) are excellent targets for spectroscopic observations of galaxies in the epoch of reionisation (EoR). We present deep high-resolution (R = 5000) VLT/X-shooter observations, along with an extensive collection of photometric data of COLA1, a proposed double peaked LAE at z = 6.6. We rule out the possibility that COLA1’s emission line is an [OII] doublet at z = 1.475 on the basis of i) the asymmetric red line-profile and flux ratio of the peaks (blue/red=0.31 ± 0.03) and ii) an unphysical [OII]/Hα ratio ([OII]/Hα >  22). We show that COLA1’s observed B-band flux is explained by a faint extended foreground LAE, for which we detect Lyα and [OIII] at z = 2.142. We thus conclude that COLA1 is a real double-peaked LAE at z = 6.593, the first discovered at z >  6. COLA1 is UV luminous (M1500 = −21.6 ± 0.3), has a high equivalent width (EW0,Lyα = 120−40+50 Å) and very compact Lyα emission (r50,Lyα = 0.33−0.04+0.07 kpc). Relatively weak inferred Hβ+[OIII] line-emission from Spitzer/IRAC indicates an extremely low metallicity of Z <  1/20 Z⊙ or reduced strength of nebular lines due to high escape of ionising photons. The small Lyα peak separation of 220 ± 20 km s−1 implies a low HI column density and an ionising photon escape fraction of ≈15 − 30%, providing the first direct evidence that such galaxies contribute actively to the reionisation of the Universe at z >  6. Based on simple estimates, we find that COLA1 could have provided just enough photons to reionise its own ≈0.3 pMpc (2.3 cMpc) bubble, allowing the blue Lyα line to be observed. However, we also discuss alternative scenarios explaining the detected double peaked nature of COLA1. Our results show that future high-resolution observations of statistical samples of double peaked LAEs at z >  5 are a promising probe of the occurrence of ionised regions around galaxies in the EoR. acknowledgement: JM acknowledges the award of a Huygens PhD fellowship from Leiden University. MG acknowledges support from NASA grant NNX17AK58G. APA, PhD::SPACE fellow, acknowledges support from the FCT through the fellowship PD/BD/52706/2014. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 294.A-5018, 098.A-0819, 099.A-0254 and 0100.A-0213. We are grateful for the excellent data-sets from the COSMOS and UltraVISTA survey teams. This research was supported by the Munich Institute for Astro- and Particle Physics (MIAPP) of the DFG cluster of excellence “Origin and Structure of the Universe”. We thank the referee for their comments that improved the paper. We also thank Christoph Behrens, Len Cowie, Koki Kakiichi, Peter Laursen, Charlotte Mason, Eros Vanzella, Lewis Weinberger and Johannes Zabl for discussions. We have benefited from the public available programming language Python, including the numpy, matplotlib, scipy and astropy packages (Hunter 2007; Astropy Collaboration 2013), the astronomical imaging tools Swarp (Bertin 2010) and ds9 and the Topcat analysis tool (Taylor 2013). article_number: A136 article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Max full_name: Gronke, Max last_name: Gronke - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Mauro full_name: Stefanon, Mauro last_name: Stefanon - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering citation: ama: 'Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201833528' apa: 'Matthee, J. J., Sobral, D., Gronke, M., Paulino-Afonso, A., Stefanon, M., & Röttgering, H. (2018). Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833528' chicago: 'Matthee, Jorryt J, David Sobral, Max Gronke, Ana Paulino-Afonso, Mauro Stefanon, and Huub Röttgering. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833528.' ieee: 'J. J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, and H. Röttgering, “Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.' ista: 'Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. 2018. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 619, A136.' mla: 'Matthee, Jorryt J., et al. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics, vol. 619, A136, EDP Sciences, 2018, doi:10.1051/0004-6361/201833528.' short: J.J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, H. Röttgering, Astronomy & Astrophysics 619 (2018). date_created: 2022-07-06T11:14:23Z date_published: 2018-11-19T00:00:00Z date_updated: 2022-07-19T09:32:08Z day: '19' doi: 10.1051/0004-6361/201833528 extern: '1' external_id: arxiv: - '1805.11621' intvolume: ' 619' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: high-redshift / galaxies: formation / dark ages / reionization / first stars / techniques: spectroscopic / intergalactic medium' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.11621 month: '11' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 619 year: '2018' ... --- _id: '11549' abstract: - lang: eng text: We investigate the clustering properties of ∼7000 H β + [O III] and [O II] narrowband-selected emitters at z ∼ 0.8–4.7 from the High-z Emission Line Survey. We find clustering lengths, r0, of 1.5–4.0 h−1 Mpc and minimum dark matter halo masses of 1010.7–12.1 M⊙ for our z = 0.8–3.2 H β + [O III] emitters and r0 ∼ 2.0–8.3 h−1 Mpc and halo masses of 1011.5–12.6 M⊙ for our z = 1.5–4.7 [O II] emitters. We find r0 to strongly increase both with increasing line luminosity and redshift. By taking into account the evolution of the characteristic line luminosity, L⋆(z), and using our model predictions of halo mass given r0, we find a strong, redshift-independent increasing trend between L/L⋆(z) and minimum halo mass. The faintest H β + [O III] emitters are found to reside in 109.5 M⊙ haloes and the brightest emitters in 1013.0 M⊙ haloes. For [O II] emitters, the faintest emitters are found in 1010.5 M⊙ haloes and the brightest emitters in 1012.6 M⊙ haloes. A redshift-independent stellar mass dependency is also observed where the halo mass increases from 1011 to 1012.5 M⊙ for stellar masses of 108.5 to 1011.5 M⊙, respectively. We investigate the interdependencies of these trends by repeating our analysis in a Lline−Mstar grid space for our most populated samples (H β + [O III] z = 0.84 and [O II] z = 1.47) and find that the line luminosity dependency is stronger than the stellar mass dependency on halo mass. For L > L⋆ emitters at all epochs, we find a relatively flat trend with halo masses of 1012.5–13 M⊙, which may be due to quenching mechanisms in massive haloes that is consistent with a transitional halo mass predicted by models. acknowledgement: We thank the anonymous referee for their useful comments and suggestions that improved this study. AAK thanks Anahita Alavi and Irene Shivaei for useful discussion in the making of this paper. AAK acknowledges that this work was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX16AO92H. DS acknowledges financial support from the Netherlands Organization for Scientific Research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. PNB is grateful for support from STFC via grant STM001229/1. IRS acknowledges support from STFC (ST/L00075X/1), the ERC Advanced Grant DUSTYGAL (321334), and a Royal Society/Wolfson Merit award. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G. article_processing_charge: No article_type: original author: - first_name: A A full_name: Khostovan, A A last_name: Khostovan - first_name: D full_name: Sobral, D last_name: Sobral - first_name: B full_name: Mobasher, B last_name: Mobasher - first_name: P N full_name: Best, P N last_name: Best - first_name: I full_name: Smail, I last_name: Smail - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: B full_name: Darvish, B last_name: Darvish - first_name: H full_name: Nayyeri, H last_name: Nayyeri - first_name: S full_name: Hemmati, S last_name: Hemmati - first_name: J P full_name: Stott, J P last_name: Stott citation: ama: 'Khostovan AA, Sobral D, Mobasher B, et al. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 2018;478(3):2999-3015. doi:10.1093/mnras/sty925' apa: 'Khostovan, A. A., Sobral, D., Mobasher, B., Best, P. N., Smail, I., Matthee, J. J., … Stott, J. P. (2018). The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty925' chicago: 'Khostovan, A A, D Sobral, B Mobasher, P N Best, I Smail, Jorryt J Matthee, B Darvish, H Nayyeri, S Hemmati, and J P Stott. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty925.' ieee: 'A. A. Khostovan et al., “The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3. Oxford University Press, pp. 2999–3015, 2018.' ista: 'Khostovan AA, Sobral D, Mobasher B, Best PN, Smail I, Matthee JJ, Darvish B, Nayyeri H, Hemmati S, Stott JP. 2018. The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass. Monthly Notices of the Royal Astronomical Society. 478(3), 2999–3015.' mla: 'Khostovan, A. A., et al. “The Clustering of H β + [O III] and [O II] Emitters since z ∼ 5: Dependencies with Line Luminosity and Stellar Mass.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 3, Oxford University Press, 2018, pp. 2999–3015, doi:10.1093/mnras/sty925.' short: A.A. Khostovan, D. Sobral, B. Mobasher, P.N. Best, I. Smail, J.J. Matthee, B. Darvish, H. Nayyeri, S. Hemmati, J.P. Stott, Monthly Notices of the Royal Astronomical Society 478 (2018) 2999–3015. date_created: 2022-07-08T11:48:48Z date_published: 2018-08-01T00:00:00Z date_updated: 2022-08-19T06:53:39Z day: '01' doi: 10.1093/mnras/sty925 extern: '1' external_id: arxiv: - '1705.01101' intvolume: ' 478' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: haloes' - 'galaxies: high-redshift' - 'galaxies: star formation' - 'cosmology: observations' - large-scale structure of Universe language: - iso: eng main_file_link: - url: https://arxiv.org/abs/1705.01101 month: '08' oa_version: Published Version page: 2999-3015 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The clustering of H β + [O III] and [O II] emitters since z ∼ 5: Dependencies with line luminosity and stellar mass' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 478 year: '2018' ... --- _id: '11557' abstract: - lang: eng text: Deep narrow-band surveys have revealed a large population of faint Ly α emitters (LAEs) in the distant Universe, but relatively little is known about the most luminous sources (⁠LLyα≳1042.7 erg s−1; LLyα≳L∗Lyα⁠). Here we present the spectroscopic follow-up of 21 luminous LAEs at z ∼ 2–3 found with panoramic narrow-band surveys over five independent extragalactic fields (≈4 × 106 Mpc3 surveyed at z ∼ 2.2 and z ∼ 3.1). We use WHT/ISIS, Keck/DEIMOS, and VLT/X-SHOOTER to study these sources using high ionization UV lines. Luminous LAEs at z ∼ 2–3 have blue UV slopes (⁠β=−2.0+0.3−0.1⁠) and high Ly α escape fractions (⁠50+20−15 per cent) and span five orders of magnitude in UV luminosity (MUV ≈ −19 to −24). Many (70 per cent) show at least one high ionization rest-frame UV line such as C IV, N V, C III], He II or O III], typically blue-shifted by ≈100–200 km s−1 relative to Ly α. Their Ly α profiles reveal a wide variety of shapes, including significant blue-shifted components and widths from 200 to 4000 km s−1. Overall, 60 ± 11  per cent appear to be active galactic nucleus (AGN) dominated, and at LLyα > 1043.3 erg s−1 and/or MUV < −21.5 virtually all LAEs are AGNs with high ionization parameters (log U = 0.6 ± 0.5) and with metallicities of ≈0.5 − 1 Z⊙. Those lacking signatures of AGNs (40 ± 11  per cent) have lower ionization parameters (⁠logU=−3.0+1.6−0.9 and log ξion = 25.4 ± 0.2) and are apparently metal-poor sources likely powered by young, dust-poor ‘maximal’ starbursts. Our results show that luminous LAEs at z ∼ 2–3 are a diverse population and that 2×L∗Lyα and 2×M∗UV mark a sharp transition in the nature of LAEs, from star formation dominated to AGN dominated. acknowledgement: 'We thank the anonymous reviewer for their timely and constructive comments that greatly helped us to improve the manuscript. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. IRS acknowledges support from the ERC Advanced Grant DUSTYGAL (321334), STFC (ST/P000541/1), and a Royal Society/Wolfson Merit Award. PNB is grateful for support from STFC via grant ST/M001229/1. We thank Anne Verhamme, Kimihiko Nakajima, Ryan Trainor, Sangeeta Malhotra, Max Gronke, James Rhoads, Fang Xia An, Matthew Hayes, Takashi Kojima, Mark Dijkstra, and Anne Jaskot for many helpful and engaging discussions, particularly during the SnowCLAW Ly α workshop. We thank Bruno Ribeiro, Stephane Charlot, and Joseph Caruana for comments on the manuscript. The authors would also like to thank Ingrid Tengs, Meg Singleton, Ali Khostovan, and Sara Perez for participating in part of the observations. We also thank Joao Calhau, Leah Morabito, Sergio Santos, and Aayush Saxena for their assistance with the narrow-band observations which allowed to select some of the sour ces. Based on observations obtained with the William Herschel Telescope, program: W16AN004; the Very Large Telescope, programs: 098.A-0819 & 099.A-0254; and the Keck II telescope, program: C267D. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, 092.A-0786, 093.A-0561, 097.A-0943, 098.A-0819, 099.A-0254 and 179.A-2005. The authors acknowledge the award of service time (SW2014b20) on the WHT. WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. The authors would also like to thank all the extremely helpful observatory staff that have greatly contributed towards our observations, particularly Fiona Riddick, Lilian Dominguez, Florencia Jimenez, and Ian Skillen. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2013). This research has made use of the VizieR catalogue access tool, CDS, Strasbourg, France.' article_processing_charge: No article_type: original author: - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: Philip N full_name: Best, Philip N last_name: Best - first_name: Lara full_name: Alegre, Lara last_name: Alegre - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Bahram full_name: Mobasher, Bahram last_name: Mobasher - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Andra full_name: Stroe, Andra last_name: Stroe - first_name: Iván full_name: Oteo, Iván last_name: Oteo citation: ama: 'Sobral D, Matthee JJ, Darvish B, et al. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 2018;477(2):2817-2840. doi:10.1093/mnras/sty782' apa: 'Sobral, D., Matthee, J. J., Darvish, B., Smail, I., Best, P. N., Alegre, L., … Oteo, I. (2018). The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty782' chicago: 'Sobral, David, Jorryt J Matthee, Behnam Darvish, Ian Smail, Philip N Best, Lara Alegre, Huub Röttgering, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty782.' ieee: 'D. Sobral et al., “The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN,” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2. Oxford University Press, pp. 2817–2840, 2018.' ista: 'Sobral D, Matthee JJ, Darvish B, Smail I, Best PN, Alegre L, Röttgering H, Mobasher B, Paulino-Afonso A, Stroe A, Oteo I. 2018. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 477(2), 2817–2840.' mla: 'Sobral, David, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2, Oxford University Press, 2018, pp. 2817–40, doi:10.1093/mnras/sty782.' short: D. Sobral, J.J. Matthee, B. Darvish, I. Smail, P.N. Best, L. Alegre, H. Röttgering, B. Mobasher, A. Paulino-Afonso, A. Stroe, I. Oteo, Monthly Notices of the Royal Astronomical Society 477 (2018) 2817–2840. date_created: 2022-07-12T07:18:02Z date_published: 2018-06-01T00:00:00Z date_updated: 2022-08-19T07:01:08Z day: '01' doi: 10.1093/mnras/sty782 extern: '1' external_id: arxiv: - '1802.10102' intvolume: ' 477' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: active' - 'galaxies: evolution' - 'galaxies: high-redshift' - 'galaxies: ISM' - 'galaxies: starburst' - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.10102 month: '06' oa: 1 oa_version: Preprint page: 2817-2840 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 477 year: '2018' ... --- _id: '11558' abstract: - lang: eng text: We present and explore deep narrow- and medium-band data obtained with the Subaru and the Isaac Newton Telescopes in the ∼2 deg2 COSMOS field. We use these data as an extremely wide, low-resolution (R ∼ 20–80) Integral Field Unit survey to slice through the COSMOS field and obtain a large sample of ∼4000 Ly α emitters (LAEs) from z ∼ 2 to 6 in 16 redshift slices (SC4K). We present new Ly α luminosity functions (LFs) covering a comoving volume of ∼108 Mpc3. SC4K extensively complements ultradeep surveys, jointly covering over 4 dex in Ly α luminosity and revealing a global (2.5 < z < 6) synergy LF with α=−1.93+0.12−0.12⁠, log10Φ∗Lyα=−3.45+0.22−0.29 Mpc−3, and log10L∗Lyα=42.93+0.15−0.11 erg s−1. The Schechter component of the Ly α LF reveals a factor ∼5 rise in L∗Lyα and a ∼7 × decline in Φ∗Lyα from z ∼ 2 to 6. The data reveal an extra power-law (or Schechter) component above LLy α ≈ 1043.3 erg s−1 at z ∼ 2.2–3.5 and we show that it is partially driven by X-ray and radio active galactic nucleus (AGN), as their Ly α LF resembles the excess. The power-law component vanishes and/or is below our detection limits above z > 3.5, likely linked with the evolution of the AGN population. The Ly α luminosity density rises by a factor ∼2 from z ∼ 2 to 3 but is then found to be roughly constant (⁠1.1+0.2−0.2×1040 erg s−1 Mpc−3) to z ∼ 6, despite the ∼0.7 dex drop in ultraviolet (UV) luminosity density. The Ly α/UV luminosity density ratio rises from 4 ± 1 per cent to 30 ± 6 per cent from z ∼ 2.2 to 6. Our results imply a rise of a factor of ≈2 in the global ionization efficiency (ξion) and a factor ≈4 ± 1 in the Ly α escape fraction from z ∼ 2 to 6, hinting for evolution in both the typical burstiness/stellar populations and even more so in the typical interstellar medium conditions allowing Ly α photons to escape. acknowledgement: "We thank the anonymous referee for their constructive comments that helped us improve the manuscript. DS acknowledges the hospitality of the IAC and a Severo Ochoa visiting grant. SS and JC acknowledge studentships from the Lancaster University. JM acknowledges a Huygens PhD fellowship from Leiden University. APA acknowledges financial support from the Science and Technology Foundation (FCT, Portugal) through research grants UID/FIS/04434/2013 and fellowship PD/BD/52706/2014. The authors thank Alyssa Drake, Kimihiko Nakajima, Yuichi Harikane, Max Gronke, Irene Shivaei, Helmut Dannerbauer, Huub Rottgering, ¨ Marius Eide, and Masami Ouchi for many engaging and stimulating discussions. We also thank Sara Perez, Alex Bennett, and Tom Rose for their involvement in the early stages of this project. Based on data products from observations made with European Southern Observatory (ESO) Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 097.A 0943,\r\n098.A-0819, 099.A-0254, and 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Based on observations using the WFC on the 2.5 m INT, as part of programmes 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118, and 2016AN001. The INT is operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France– Hawaii Telescope Legacy Survey (CFHTLS), a collaborative project of NRC and CNRS.\r\nWe are grateful to the CFHTLS, COSMOS-UltraVISTA, and COSMOS survey teams. We are also unmeasurably thankful to the pioneering and continuous work from previous Ly α surveys’ teams. Without these previous Ly α and the wider reach legacy surveys, this research would have been impossible. We also thank the VUDS team for making available spectroscopic redshifts from data obtained with VIMOS at the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Programme 185.A-0791. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY and SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2005). We publicly release a catalogue with all LAEs used in this paper (SC4K), so it can be freely explored by the community (see five example entries in Table A1)." article_processing_charge: No article_type: original author: - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Bruno full_name: Ribeiro, Bruno last_name: Ribeiro - first_name: João full_name: Calhau, João last_name: Calhau - first_name: Ali A full_name: Khostovan, Ali A last_name: Khostovan citation: ama: 'Sobral D, Santos S, Matthee JJ, et al. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 2018;476(4):4725-4752. doi:10.1093/mnras/sty378' apa: 'Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Ribeiro, B., Calhau, J., & Khostovan, A. A. (2018). Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty378' chicago: 'Sobral, David, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Bruno Ribeiro, João Calhau, and Ali A Khostovan. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty378.' ieee: 'D. Sobral et al., “Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6,” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4. Oxford University Press, pp. 4725–4752, 2018.' ista: 'Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Ribeiro B, Calhau J, Khostovan AA. 2018. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 476(4), 4725–4752.' mla: 'Sobral, David, et al. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4, Oxford University Press, 2018, pp. 4725–52, doi:10.1093/mnras/sty378.' short: D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, B. Ribeiro, J. Calhau, A.A. Khostovan, Monthly Notices of the Royal Astronomical Society 476 (2018) 4725–4752. date_created: 2022-07-12T10:41:08Z date_published: 2018-06-01T00:00:00Z date_updated: 2022-08-19T07:04:45Z day: '01' doi: 10.1093/mnras/sty378 extern: '1' external_id: arxiv: - '1712.04451' intvolume: ' 476' issue: '4' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: formation' - 'galaxies: high-redshift' - 'galaxies: luminosity function' - mass function - 'galaxies: statistics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.04451 month: '06' oa: 1 oa_version: Preprint page: 4725-4752 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 476 year: '2018' ... --- _id: '11555' abstract: - lang: eng text: We investigate the morphology of the [C II] emission in a sample of ‘normal’ star-forming galaxies at 5 < z < 7.2 in relation to their UV (rest-frame) counterpart. We use new Atacama Large Millimetre/submillimetre Array (ALMA) observations of galaxies at z ∼ 6–7, as well as a careful re-analysis of archival ALMA data. In total 29 galaxies were analysed, 21 of which are detected in [C II]. For several of the latter the [C II] emission breaks into multiple components. Only a fraction of these [C II] components, if any, is associated with the primary UV systems, while the bulk of the [C II] emission is associated either with fainter UV components, or not associated with any UV counterpart at the current limits. By taking into account the presence of all these components, we find that the L[CII]–SFR (star formation rate) relation at early epochs is fully consistent with the local relation, but it has a dispersion of 0.48 ± 0.07 dex, which is about two times larger than observed locally. We also find that the deviation from the local L[CII]–SFR relation has a weak anticorrelation with the EW(Ly α). The morphological analysis also reveals that [C II] emission is generally much more extended than the UV emission. As a consequence, these primordial galaxies are characterized by a [C II] surface brightness generally much lower than expected from the local Σ[CII]−ΣSFR relation. These properties are likely a consequence of a combination of different effects, namely gas metallicity, [C II] emission from obscured star-forming regions, strong variations of the ionization parameter, and circumgalactic gas in accretion or ejected by these primeval galaxies. acknowledgement: "This paper makes use of the following ALMA data:\r\nADS/JAO.ALMA#2012.1.00719.S, ADS/JAO.ALMA#2012.A.00040.S,\r\nADS/JAO.ALMA#2013.A.00433.S, ADS/JAO.ALMA#2011.0.00115.S,\r\nADS/JAO.ALMA#2012.1.00033.S, ADS/JAO.ALMA#2012.1.00523.S,\r\nADS/JAO.ALMA#2013.1.00815.S, ADS/JAO.ALMA#2015.1.00834.S.,\r\nADS/JAO.ALMA#2015.1.01105.S, AND ADS/JAO.ALMA#2016.1.01240.S\r\nwhich can be retrieved from the ALMA data archive:\r\nhttps://almascience.eso.org/ alma-data/archive. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. We are grateful to G. Jones to for providing his [C II] flux maps. RM and SC acknowledge support by the Science and Technology Facilities Council (STFC). RM acknowledges ERC Advanced Grant 695671 ‘QUENCH’. AF acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120." article_processing_charge: No article_type: original author: - first_name: S full_name: Carniani, S last_name: Carniani - first_name: R full_name: Maiolino, R last_name: Maiolino - first_name: R full_name: Amorin, R last_name: Amorin - first_name: L full_name: Pentericci, L last_name: Pentericci - first_name: A full_name: Pallottini, A last_name: Pallottini - first_name: A full_name: Ferrara, A last_name: Ferrara - first_name: C J full_name: Willott, C J last_name: Willott - first_name: R full_name: Smit, R last_name: Smit - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: D full_name: Sobral, D last_name: Sobral - first_name: P full_name: Santini, P last_name: Santini - first_name: M full_name: Castellano, M last_name: Castellano - first_name: S full_name: De Barros, S last_name: De Barros - first_name: A full_name: Fontana, A last_name: Fontana - first_name: A full_name: Grazian, A last_name: Grazian - first_name: L full_name: Guaita, L last_name: Guaita citation: ama: Carniani S, Maiolino R, Amorin R, et al. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 2018;478(1):1170-1184. doi:10.1093/mnras/sty1088 apa: Carniani, S., Maiolino, R., Amorin, R., Pentericci, L., Pallottini, A., Ferrara, A., … Guaita, L. (2018). Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1088 chicago: Carniani, S, R Maiolino, R Amorin, L Pentericci, A Pallottini, A Ferrara, C J Willott, et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1088. ieee: S. Carniani et al., “Kiloparsec-scale gaseous clumps and star formation at z = 5–7,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1. Oxford University Press, pp. 1170–1184, 2018. ista: Carniani S, Maiolino R, Amorin R, Pentericci L, Pallottini A, Ferrara A, Willott CJ, Smit R, Matthee JJ, Sobral D, Santini P, Castellano M, De Barros S, Fontana A, Grazian A, Guaita L. 2018. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 478(1), 1170–1184. mla: Carniani, S., et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1, Oxford University Press, 2018, pp. 1170–84, doi:10.1093/mnras/sty1088. short: S. Carniani, R. Maiolino, R. Amorin, L. Pentericci, A. Pallottini, A. Ferrara, C.J. Willott, R. Smit, J.J. Matthee, D. Sobral, P. Santini, M. Castellano, S. De Barros, A. Fontana, A. Grazian, L. Guaita, Monthly Notices of the Royal Astronomical Society 478 (2018) 1170–1184. date_created: 2022-07-11T08:05:42Z date_published: 2018-07-01T00:00:00Z date_updated: 2022-08-19T06:58:06Z day: '01' doi: 10.1093/mnras/sty1088 extern: '1' external_id: arxiv: - '1712.03985' intvolume: ' 478' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - 'galaxies: ISM' - 'galaxies: formation' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.03985 month: '07' oa: 1 oa_version: Preprint page: 1170-1184 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Kiloparsec-scale gaseous clumps and star formation at z = 5–7 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 478 year: '2018' ... --- _id: '11584' abstract: - lang: eng text: Observations show that star-forming galaxies reside on a tight 3D plane between mass, gas-phase metallicity, and star formation rate (SFR), which can be explained by the interplay between metal-poor gas inflows, SFR and outflows. However, different metals are released on different time-scales, which may affect the slope of this relation. Here, we use central, star-forming galaxies with Mstar = 109.0–10.5 M⊙ from the EAGLE hydrodynamical simulation to examine 3D relations between mass, SFR, and chemical enrichment using absolute and relative C, N, O, and Fe abundances. We show that the scatter is smaller when gas-phase α-enhancement is used rather than metallicity. A similar plane also exists for stellar α-enhancement, implying that present-day specific SFRs are correlated with long time-scale star formation histories. Between z = 0 and 1, the α-enhancement plane is even more insensitive to redshift than the plane using metallicity. However, it evolves at z > 1 due to lagging iron yields. At fixed mass, galaxies with higher SFRs have star formation histories shifted towards late times, are more α-enhanced, and this α-enhancement increases with redshift as observed. These findings suggest that relations between physical properties inferred from observations may be affected by systematic variations in α-enhancements. acknowledgement: We thank the anonymous referee for their constructive comments. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. We thank Jarle Brinchmann, Rob Crain and David Sobral for discussions. We acknowledge the use of the TOPCAT software (Taylor 2013) for assisting in rapid exploration of multidimensional data sets and the use of PYTHON and its NUMPY, MATPLOTLIB, and PANDAS packages. article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Joop full_name: Schaye, Joop last_name: Schaye citation: ama: 'Matthee JJ, Schaye J. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 2018;479(1):L34-L39. doi:10.1093/mnrasl/sly093' apa: 'Matthee, J. J., & Schaye, J. (2018). Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press. https://doi.org/10.1093/mnrasl/sly093' chicago: 'Matthee, Jorryt J, and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters. Oxford University Press, 2018. https://doi.org/10.1093/mnrasl/sly093.' ieee: 'J. J. Matthee and J. Schaye, “Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement,” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1. Oxford University Press, pp. L34–L39, 2018.' ista: 'Matthee JJ, Schaye J. 2018. Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement. Monthly Notices of the Royal Astronomical Society: Letters. 479(1), L34–L39.' mla: 'Matthee, Jorryt J., and Joop Schaye. “Star-Forming Galaxies Are Predicted to Lie on a Fundamental Plane of Mass, Star Formation Rate, and α-Enhancement.” Monthly Notices of the Royal Astronomical Society: Letters, vol. 479, no. 1, Oxford University Press, 2018, pp. L34–39, doi:10.1093/mnrasl/sly093.' short: 'J.J. Matthee, J. Schaye, Monthly Notices of the Royal Astronomical Society: Letters 479 (2018) L34–L39.' date_created: 2022-07-14T12:49:47Z date_published: 2018-09-01T00:00:00Z date_updated: 2022-08-19T08:35:45Z day: '01' doi: 10.1093/mnrasl/sly093 extern: '1' external_id: arxiv: - '1802.06786' intvolume: ' 479' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: abundances' - 'galaxies: evolution' - 'galaxies: formation' - 'galaxies: star formation' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.06786 month: '09' oa: 1 oa_version: Preprint page: L34 - L39 publication: 'Monthly Notices of the Royal Astronomical Society: Letters' publication_identifier: eissn: - 1745-3933 issn: - 1745-3925 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Star-forming galaxies are predicted to lie on a fundamental plane of mass, star formation rate, and α-enhancement type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 479 year: '2018' ... --- _id: '11619' abstract: - lang: eng text: We report on the confirmation and mass determination of π Men c, the first transiting planet discovered by NASA’s TESS space mission. π Men is a naked-eye (V = 5.65 mag), quiet G0 V star that was previously known to host a sub-stellar companion (π Men b) on a longperiod (Porb = 2091 days), eccentric (e = 0.64) orbit. Using TESS time-series photometry, combined with Gaia data, published UCLES at AAT Doppler measurements, and archival HARPS at ESO-3.6m radial velocities, we found that π Men c is a close-in planet with an orbital period of Porb = 6.27 days, a mass of Mc = 4.52 ± 0.81 M⊕, and a radius of Rc = 2.06 ± 0.03 R⊕. Based on the planet’s orbital period and size, π Men c is a super-Earth located at, or close to, the radius gap, while its mass and bulk density suggest it may have held on to a significant atmosphere. Because of the brightness of the host star, this system is highly suitable for a wide range of further studies to characterize the planetary atmosphere and dynamical properties. We also performed an asteroseismic analysis of the TESS data and detected a hint of power excess consistent with the seismic values expected for this star, although this result depends on the photometric aperture used to extract the light curve. This marginal detection is expected from pre-launch simulations hinting at the asteroseismic potential of the TESS mission for longer, multi-sector observations and/or for more evolved bright stars. article_number: L10 article_processing_charge: No article_type: letter_note author: - first_name: D. full_name: Gandolfi, D. last_name: Gandolfi - first_name: O. full_name: Barragán, O. last_name: Barragán - first_name: J. H. full_name: Livingston, J. H. last_name: Livingston - first_name: M. full_name: Fridlund, M. last_name: Fridlund - first_name: A. B. full_name: Justesen, A. B. last_name: Justesen - first_name: S. full_name: Redfield, S. last_name: Redfield - first_name: L. full_name: Fossati, L. last_name: Fossati - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: S. full_name: Grziwa, S. last_name: Grziwa - first_name: J. full_name: Cabrera, J. last_name: Cabrera - first_name: R. A. full_name: García, R. A. last_name: García - first_name: C. M. full_name: Persson, C. M. last_name: Persson - first_name: V. full_name: Van Eylen, V. last_name: Van Eylen - first_name: A. P. full_name: Hatzes, A. P. last_name: Hatzes - first_name: D. full_name: Hidalgo, D. last_name: Hidalgo - first_name: S. full_name: Albrecht, S. last_name: Albrecht - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: W. D. full_name: Cochran, W. D. last_name: Cochran - first_name: Sz. full_name: Csizmadia, Sz. last_name: Csizmadia - first_name: H. full_name: Deeg, H. last_name: Deeg - first_name: Ph. full_name: Eigmüller, Ph. last_name: Eigmüller - first_name: M. full_name: Endl, M. last_name: Endl - first_name: A. full_name: Erikson, A. last_name: Erikson - first_name: M. full_name: Esposito, M. last_name: Esposito - first_name: E. full_name: Guenther, E. last_name: Guenther - first_name: J. full_name: Korth, J. last_name: Korth - first_name: R. full_name: Luque, R. last_name: Luque - first_name: P. full_name: Montañes Rodríguez, P. last_name: Montañes Rodríguez - first_name: D. full_name: Nespral, D. last_name: Nespral - first_name: G. full_name: Nowak, G. last_name: Nowak - first_name: M. full_name: Pätzold, M. last_name: Pätzold - first_name: J. full_name: Prieto-Arranz, J. last_name: Prieto-Arranz citation: ama: 'Gandolfi D, Barragán O, Livingston JH, et al. TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201834289' apa: 'Gandolfi, D., Barragán, O., Livingston, J. H., Fridlund, M., Justesen, A. B., Redfield, S., … Prieto-Arranz, J. (2018). TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834289' chicago: 'Gandolfi, D., O. Barragán, J. H. Livingston, M. Fridlund, A. B. Justesen, S. Redfield, L. Fossati, et al. “TESS’s First Planet: A Super-Earth Transiting the Naked-Eye Star π Mensae.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201834289.' ieee: 'D. Gandolfi et al., “TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.' ista: 'Gandolfi D, Barragán O, Livingston JH, Fridlund M, Justesen AB, Redfield S, Fossati L, Mathur S, Grziwa S, Cabrera J, García RA, Persson CM, Van Eylen V, Hatzes AP, Hidalgo D, Albrecht S, Bugnet LA, Cochran WD, Csizmadia S, Deeg H, Eigmüller P, Endl M, Erikson A, Esposito M, Guenther E, Korth J, Luque R, Montañes Rodríguez P, Nespral D, Nowak G, Pätzold M, Prieto-Arranz J. 2018. TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae. Astronomy & Astrophysics. 619, L10.' mla: 'Gandolfi, D., et al. “TESS’s First Planet: A Super-Earth Transiting the Naked-Eye Star π Mensae.” Astronomy & Astrophysics, vol. 619, L10, EDP Sciences, 2018, doi:10.1051/0004-6361/201834289.' short: D. Gandolfi, O. Barragán, J.H. Livingston, M. Fridlund, A.B. Justesen, S. Redfield, L. Fossati, S. Mathur, S. Grziwa, J. Cabrera, R.A. García, C.M. Persson, V. Van Eylen, A.P. Hatzes, D. Hidalgo, S. Albrecht, L.A. Bugnet, W.D. Cochran, S. Csizmadia, H. Deeg, P. Eigmüller, M. Endl, A. Erikson, M. Esposito, E. Guenther, J. Korth, R. Luque, P. Montañes Rodríguez, D. Nespral, G. Nowak, M. Pätzold, J. Prieto-Arranz, Astronomy & Astrophysics 619 (2018). date_created: 2022-07-18T14:41:16Z date_published: 2018-11-22T00:00:00Z date_updated: 2022-08-22T07:43:29Z day: '22' doi: 10.1051/0004-6361/201834289 extern: '1' external_id: arxiv: - '1809.07573' intvolume: ' 619' keyword: - Space and Planetary Science - Astronomy and Astrophysics - planetary systems / planets and satellites - detection / planets and satellites - fundamental parameters / planets and satellites - terrestrial planets / stars - fundamental parameters language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.07573 month: '11' oa: 1 oa_version: Preprint publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'TESS’s first planet: A super-Earth transiting the naked-eye star π Mensae' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 619 year: '2018' ... --- _id: '11618' abstract: - lang: eng text: Asteroseismology provides global stellar parameters such as masses, radii, or surface gravities using mean global seismic parameters and effective temperature for thousands of low-mass stars (0.8 M⊙ < M < 3 M⊙). This methodology has been successfully applied to stars in which acoustic modes excited by turbulent convection are measured. Other methods such as the Flicker technique can also be used to determine stellar surface gravities, but only works for log g above 2.5 dex. In this work, we present a new metric called FliPer (Flicker in spectral power density, in opposition to the standard Flicker measurement which is computed in the time domain); it is able to extend the range for which reliable surface gravities can be obtained (0.1 < log g < 4.6 dex) without performing any seismic analysis for stars brighter than Kp < 14. FliPer takes into account the average variability of a star measured in the power density spectrum in a given range of frequencies. However, FliPer values calculated on several ranges of frequency are required to better characterize a star. Using a large set of asteroseismic targets it is possible to calibrate the behavior of surface gravity with FliPer through machine learning. This calibration made with a random forest regressor covers a wide range of surface gravities from main-sequence stars to subgiants and red giants, with very small uncertainties from 0.04 to 0.1 dex. FliPer values can be inserted in automatic global seismic pipelines to either give an estimation of the stellar surface gravity or to assess the quality of the seismic results by detecting any outliers in the obtained νmax values. FliPer also constrains the surface gravities of main-sequence dwarfs using only long-cadence data for which the Nyquist frequency is too low to measure the acoustic-mode properties. acknowledgement: We thank the anonymous referee for the very useful comments. We would also like to thank M. Benbakoura for his help in analyzing the light curves of several binary systems included in our set of stars. L.B. and R.A.G. acknowledge the support from PLATO and GOLF CNES grants. S.M. acknowledges support from the National Aeronautics and Space Administration under Grant NNX15AF13G, the National Science Foundation grant AST-1411685, and the Ramon y Cajal fellowship no. RYC-2015-17697. E.C. is funded by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 664931. O.J.H and B.M.R. acknowledge the support of the UK Science and Technology Facilities Council (STFC). Funding for the Stellar Astrophysics Centre is provided by the Danish National Research Foundation (Grant DNRF106). This research has made use of NASA’s Astrophysics Data System. Data presented in this paper were obtained from the Mikulski Archive for Space Telescopes (MAST). STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555. article_number: A38 article_processing_charge: No article_type: original author: - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: R. A. full_name: García, R. A. last_name: García - first_name: G. R. full_name: Davies, G. R. last_name: Davies - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: E. full_name: Corsaro, E. last_name: Corsaro - first_name: O. J. full_name: Hall, O. J. last_name: Hall - first_name: B. M. full_name: Rendle, B. M. last_name: Rendle citation: ama: 'Bugnet LA, García RA, Davies GR, et al. FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. 2018;620. doi:10.1051/0004-6361/201833106' apa: 'Bugnet, L. A., García, R. A., Davies, G. R., Mathur, S., Corsaro, E., Hall, O. J., & Rendle, B. M. (2018). FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833106' chicago: 'Bugnet, Lisa Annabelle, R. A. García, G. R. Davies, S. Mathur, E. Corsaro, O. J. Hall, and B. M. Rendle. “FliPer: A Global Measure of Power Density to Estimate Surface Gravities of Main-Sequence Solar-like Stars and Red Giants.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833106.' ieee: 'L. A. Bugnet et al., “FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants,” Astronomy & Astrophysics, vol. 620. EDP Sciences, 2018.' ista: 'Bugnet LA, García RA, Davies GR, Mathur S, Corsaro E, Hall OJ, Rendle BM. 2018. FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants. Astronomy & Astrophysics. 620, A38.' mla: 'Bugnet, Lisa Annabelle, et al. “FliPer: A Global Measure of Power Density to Estimate Surface Gravities of Main-Sequence Solar-like Stars and Red Giants.” Astronomy & Astrophysics, vol. 620, A38, EDP Sciences, 2018, doi:10.1051/0004-6361/201833106.' short: L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, E. Corsaro, O.J. Hall, B.M. Rendle, Astronomy & Astrophysics 620 (2018). date_created: 2022-07-18T14:37:39Z date_published: 2018-12-01T00:00:00Z date_updated: 2022-08-22T07:41:07Z day: '01' doi: 10.1051/0004-6361/201833106 extern: '1' external_id: arxiv: - '1809.05105' intvolume: ' 620' keyword: - Space and Planetary Science - Astronomy and Astrophysics - asteroseismology / methods - data analysis / stars - oscillations language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.05105 month: '12' oa: 1 oa_version: Preprint publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'FliPer: A global measure of power density to estimate surface gravities of main-sequence solar-like stars and red giants' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 620 year: '2018' ... --- _id: '11620' abstract: - lang: eng text: We report the discovery and characterization of HD 89345b (K2-234b; EPIC 248777106b), a Saturn-sized planet orbiting a slightly evolved star. HD 89345 is a bright star (V = 9.3 mag) observed by the K2 mission with 1 min time sampling. It exhibits solar-like oscillations. We conducted asteroseismology to determine the parameters of the star, finding the mass and radius to be 1.12+0.04−0.01M⊙ and 1.657+0.020−0.004R⊙⁠, respectively. The star appears to have recently left the main sequence, based on the inferred age, 9.4+0.4−1.3Gyr⁠, and the non-detection of mixed modes. The star hosts a ‘warm Saturn’ (P = 11.8 d, Rp = 6.86 ± 0.14 R⊕). Radial-velocity follow-up observations performed with the FIbre-fed Echelle Spectrograph, HARPS, and HARPS-N spectrographs show that the planet has a mass of 35.7 ± 3.3 M⊕. The data also show that the planet’s orbit is eccentric (e ≈ 0.2). An investigation of the rotational splitting of the oscillation frequencies of the star yields no conclusive evidence on the stellar inclination angle. We further obtained Rossiter–McLaughlin observations, which result in a broad posterior of the stellar obliquity. The planet seems to confirm to the same patterns that have been observed for other sub-Saturns regarding planet mass and multiplicity, orbital eccentricity, and stellar metallicity. acknowledgement: 'We gratefully acknowledge many helpful suggestions by the anonymous referee. Based on observations made with a) the Nordic Optical Telescope, operated by the Nordic Optical Telescope Scientific Association at the Observatorio del Roque de los Muchachos; b) the ESO-3.6m telescope at La Silla Observatory under programme ID 0100.C-0808; c) the Italian Telescopio Nazionale Galileo operated on the island of La Palma by the Fundación Galileo Galilei of the Istituto Nazionale di Astrofisica. NESSI was funded by the NASA Exoplanet Exploration Program and the NASA Ames Research Center. NESSI was built at the Ames Research Center by Steve B. Howell, Nic Scott, Elliott P. Horch, and Emmett Quigley. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 730890. This material reflects only the authors views and the Commission is not liable for any use that may be made of the information contained therein. DG gratefully acknowledges the financial support of the Programma Giovani Ricercatori – Rita Levi Montalcini – Rientro dei Cervelli (2012) awarded by the Italian Ministry of Education, Universities and Research (MIUR). SaM would like to acknowledge support from the Ramon y Cajal fellowship number RYC-2015-17697. AJ, MH, and SA acknowledge support by the Danish Council for Independent Research, through a DFF Sapere Aude Starting Grant nr. 4181-00487B. SzCs, APH, MP, and HR acknowledge the support of the DFG priority program SPP 1992Exploring the Diversity of Extrasolar Planets (grants HA 3279/12-1, PA 525/18-1, PA5 25/19-1 and PA525/20-1, RA 714/14-1) HD, CR, and FPH acknowledge the financial support from MINECO under grants ESP2015-65712-C5-4-R and AYA2016-76378-P. This paper has made use of the IAC Supercomputing facility HTCondor (http://research.cs.wisc.edu/htcondor/), partly financed by the Ministry of Economy and Competitiveness with FEDER funds, code IACA13-3E-2493. MF and CMP gratefully acknowledge the support of the Swedish National Space Board. RAG and StM thanks the support of the CNES PLATO grant. PGB is a postdoctoral fellow in the MINECO-programme ’Juan de la Cierva Incorporacion’ (IJCI-2015-26034). StM acknowledges support from ERC through SPIRE grant (647383) and from ISSI through the ENCELADE 2.0 team. VSA acknowledges support from VILLUM FONDEN (research grant 10118). MNL acknowledges support from the ESA-PRODEX programme. Funding for the Stellar Astrophysics Centre is provided by The Danish National Research Foundation (Grant agreement no.: DNRF106) This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC, https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. This research was made with the use of NASA’s Astrophysics Data System and the NASA Exoplanet Archive, which is operated by the California Institute of Technology, under contract with the National Aeronautics and Space Administration under the Exoplanet Exploration Program.' article_processing_charge: No article_type: original author: - first_name: V full_name: Van Eylen, V last_name: Van Eylen - first_name: F full_name: Dai, F last_name: Dai - first_name: S full_name: Mathur, S last_name: Mathur - first_name: D full_name: Gandolfi, D last_name: Gandolfi - first_name: S full_name: Albrecht, S last_name: Albrecht - first_name: M full_name: Fridlund, M last_name: Fridlund - first_name: R A full_name: García, R A last_name: García - first_name: E full_name: Guenther, E last_name: Guenther - first_name: M full_name: Hjorth, M last_name: Hjorth - first_name: A B full_name: Justesen, A B last_name: Justesen - first_name: J full_name: Livingston, J last_name: Livingston - first_name: M N full_name: Lund, M N last_name: Lund - first_name: F full_name: Pérez Hernández, F last_name: Pérez Hernández - first_name: J full_name: Prieto-Arranz, J last_name: Prieto-Arranz - first_name: C full_name: Regulo, C last_name: Regulo - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: M E full_name: Everett, M E last_name: Everett - first_name: T full_name: Hirano, T last_name: Hirano - first_name: D full_name: Nespral, D last_name: Nespral - first_name: G full_name: Nowak, G last_name: Nowak - first_name: E full_name: Palle, E last_name: Palle - first_name: V full_name: Silva Aguirre, V last_name: Silva Aguirre - first_name: T full_name: Trifonov, T last_name: Trifonov - first_name: J N full_name: Winn, J N last_name: Winn - first_name: O full_name: Barragán, O last_name: Barragán - first_name: P G full_name: Beck, P G last_name: Beck - first_name: W J full_name: Chaplin, W J last_name: Chaplin - first_name: W D full_name: Cochran, W D last_name: Cochran - first_name: S full_name: Csizmadia, S last_name: Csizmadia - first_name: H full_name: Deeg, H last_name: Deeg - first_name: M full_name: Endl, M last_name: Endl - first_name: P full_name: Heeren, P last_name: Heeren - first_name: S full_name: Grziwa, S last_name: Grziwa - first_name: A P full_name: Hatzes, A P last_name: Hatzes - first_name: D full_name: Hidalgo, D last_name: Hidalgo - first_name: J full_name: Korth, J last_name: Korth - first_name: S full_name: Mathis, S last_name: Mathis - first_name: P full_name: Montañes Rodriguez, P last_name: Montañes Rodriguez - first_name: N full_name: Narita, N last_name: Narita - first_name: M full_name: Patzold, M last_name: Patzold - first_name: C M full_name: Persson, C M last_name: Persson - first_name: F full_name: Rodler, F last_name: Rodler - first_name: A M S full_name: Smith, A M S last_name: Smith citation: ama: 'Van Eylen V, Dai F, Mathur S, et al. HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. 2018;478(4):4866-4880. doi:10.1093/mnras/sty1390' apa: 'Van Eylen, V., Dai, F., Mathur, S., Gandolfi, D., Albrecht, S., Fridlund, M., … Smith, A. M. S. (2018). HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1390' chicago: 'Van Eylen, V, F Dai, S Mathur, D Gandolfi, S Albrecht, M Fridlund, R A García, et al. “HD 89345: A Bright Oscillating Star Hosting a Transiting Warm Saturn-Sized Planet Observed by K2.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1390.' ieee: 'V. Van Eylen et al., “HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 4. Oxford University Press, pp. 4866–4880, 2018.' ista: 'Van Eylen V, Dai F, Mathur S, Gandolfi D, Albrecht S, Fridlund M, García RA, Guenther E, Hjorth M, Justesen AB, Livingston J, Lund MN, Pérez Hernández F, Prieto-Arranz J, Regulo C, Bugnet LA, Everett ME, Hirano T, Nespral D, Nowak G, Palle E, Silva Aguirre V, Trifonov T, Winn JN, Barragán O, Beck PG, Chaplin WJ, Cochran WD, Csizmadia S, Deeg H, Endl M, Heeren P, Grziwa S, Hatzes AP, Hidalgo D, Korth J, Mathis S, Montañes Rodriguez P, Narita N, Patzold M, Persson CM, Rodler F, Smith AMS. 2018. HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2. Monthly Notices of the Royal Astronomical Society. 478(4), 4866–4880.' mla: 'Van Eylen, V., et al. “HD 89345: A Bright Oscillating Star Hosting a Transiting Warm Saturn-Sized Planet Observed by K2.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 4, Oxford University Press, 2018, pp. 4866–80, doi:10.1093/mnras/sty1390.' short: V. Van Eylen, F. Dai, S. Mathur, D. Gandolfi, S. Albrecht, M. Fridlund, R.A. García, E. Guenther, M. Hjorth, A.B. Justesen, J. Livingston, M.N. Lund, F. Pérez Hernández, J. Prieto-Arranz, C. Regulo, L.A. Bugnet, M.E. Everett, T. Hirano, D. Nespral, G. Nowak, E. Palle, V. Silva Aguirre, T. Trifonov, J.N. Winn, O. Barragán, P.G. Beck, W.J. Chaplin, W.D. Cochran, S. Csizmadia, H. Deeg, M. Endl, P. Heeren, S. Grziwa, A.P. Hatzes, D. Hidalgo, J. Korth, S. Mathis, P. Montañes Rodriguez, N. Narita, M. Patzold, C.M. Persson, F. Rodler, A.M.S. Smith, Monthly Notices of the Royal Astronomical Society 478 (2018) 4866–4880. date_created: 2022-07-18T14:43:17Z date_published: 2018-08-01T00:00:00Z date_updated: 2022-08-22T07:45:38Z day: '01' doi: 10.1093/mnras/sty1390 extern: '1' external_id: arxiv: - '1805.01860' intvolume: ' 478' issue: '4' keyword: - Space and Planetary Science - Astronomy and Astrophysics - asteroseismology - 'planets and satellites: composition' - 'planets and satellites: formation' - 'planets and satellites: fundamental parameters' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.01860 month: '08' oa: 1 oa_version: Preprint page: 4866-4880 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'HD 89345: A bright oscillating star hosting a transiting warm Saturn-sized planet observed by K2' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 478 year: '2018' ... --- _id: '11631' abstract: - lang: eng text: "The recently launched NASA Transiting Exoplanet Survey Satellite (TESS) mission is going to collect lightcurves for a few hundred million of stars and we expect to increase the number of pulsating stars to analyze compared to the few thousand stars observed by the CoRoT, Kepler and K2 missions. However, most of the TESS targets have not yet been properly classified and characterized. In order to improve the analysis of the TESS data, it is crucial to determine the type of stellar pulsations in a timely manner. We propose an automatic method to classify stars attending to their pulsation properties, in particular, to identify solar-like pulsators among all TESS targets. It relies on the use of the global amount of power contained in the power spectrum (already known as the FliPer method) as a key parameter, along with\r\nthe effective temperature, to feed into a machine learning classifier. Our study, based on TESS simulated datasets, shows that we are able to classify pulsators with a 98% accuracy." article_number: '1811.12140' article_processing_charge: No author: - first_name: Lisa Annabelle full_name: Bugnet, Lisa Annabelle id: d9edb345-f866-11ec-9b37-d119b5234501 last_name: Bugnet orcid: 0000-0003-0142-4000 - first_name: R. A. full_name: García, R. A. last_name: García - first_name: G. R. full_name: Davies, G. R. last_name: Davies - first_name: S. full_name: Mathur, S. last_name: Mathur - first_name: O. J. full_name: Hall, O. J. last_name: Hall - first_name: B. M. full_name: Rendle, B. M. last_name: Rendle citation: ama: 'Bugnet LA, García RA, Davies GR, Mathur S, Hall OJ, Rendle BM. FliPer: Classifying TESS pulsating stars. arXiv. doi:10.48550/arXiv.1811.12140' apa: 'Bugnet, L. A., García, R. A., Davies, G. R., Mathur, S., Hall, O. J., & Rendle, B. M. (n.d.). FliPer: Classifying TESS pulsating stars. arXiv. https://doi.org/10.48550/arXiv.1811.12140' chicago: 'Bugnet, Lisa Annabelle, R. A. García, G. R. Davies, S. Mathur, O. J. Hall, and B. M. Rendle. “FliPer: Classifying TESS Pulsating Stars.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1811.12140.' ieee: 'L. A. Bugnet, R. A. García, G. R. Davies, S. Mathur, O. J. Hall, and B. M. Rendle, “FliPer: Classifying TESS pulsating stars,” arXiv. .' ista: 'Bugnet LA, García RA, Davies GR, Mathur S, Hall OJ, Rendle BM. FliPer: Classifying TESS pulsating stars. arXiv, 1811.12140.' mla: 'Bugnet, Lisa Annabelle, et al. “FliPer: Classifying TESS Pulsating Stars.” ArXiv, 1811.12140, doi:10.48550/arXiv.1811.12140.' short: L.A. Bugnet, R.A. García, G.R. Davies, S. Mathur, O.J. Hall, B.M. Rendle, ArXiv (n.d.). date_created: 2022-07-21T07:05:23Z date_published: 2018-11-29T00:00:00Z date_updated: 2022-08-22T08:41:55Z day: '29' doi: 10.48550/arXiv.1811.12140 extern: '1' external_id: arxiv: - '1811.12140' keyword: - asteroseismology - methods - data analysis - stars - oscillations language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1811.12140' month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'FliPer: Classifying TESS pulsating stars' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '11657' abstract: - lang: eng text: The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weight sum of the cut edges. Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm is based on cluster contraction using label propagation and Padberg and Rinaldi’s contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory parallel implementations of our algorithm. Extensive experiments on both real-world and generated instances show that our algorithm finds the optimal cut on nearly all instances significantly faster than other state-of-the-art exact algorithms, and our error rate is lower than that of other heuristic algorithms. In addition, our parallel algorithm runs a factor 7.5× faster on average when using 32 threads. To further speed up computations, we also give a version of our algorithm that performs random edge contractions as preprocessing. This version achieves a lower running time and better parallel scalability at the expense of a higher error rate. article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Noe, Alexander last_name: Noe - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Darren full_name: Strash, Darren last_name: Strash citation: ama: Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. 2018;23:1-22. doi:10.1145/3274662 apa: Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. Association for Computing Machinery. https://doi.org/10.1145/3274662 chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” ACM Journal of Experimental Algorithmics. Association for Computing Machinery, 2018. https://doi.org/10.1145/3274662. ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” ACM Journal of Experimental Algorithmics, vol. 23. Association for Computing Machinery, pp. 1–22, 2018. ista: Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms. ACM Journal of Experimental Algorithmics. 23, 1–22. mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” ACM Journal of Experimental Algorithmics, vol. 23, Association for Computing Machinery, 2018, pp. 1–22, doi:10.1145/3274662. short: M.H. Henzinger, A. Noe, C. Schulz, D. Strash, ACM Journal of Experimental Algorithmics 23 (2018) 1–22. date_created: 2022-07-27T08:28:26Z date_published: 2018-10-01T00:00:00Z date_updated: 2022-09-09T11:32:52Z day: '01' doi: 10.1145/3274662 extern: '1' external_id: arxiv: - '1708.06127' intvolume: ' 23' keyword: - Theoretical Computer Science language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.06127 month: '10' oa: 1 oa_version: Preprint page: 1-22 publication: ACM Journal of Experimental Algorithmics publication_identifier: eissn: - 1084-6654 issn: - 1084-6654 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Practical minimum cut algorithms type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2018' ... --- _id: '11667' abstract: - lang: eng text: The focus of classic mechanism design has been on truthful direct-revelation mechanisms. In the context of combinatorial auctions, the truthful direct-revelation mechanism that maximizes social welfare is the Vickrey-Clarke-Groves mechanism. For many valuation spaces, computing the allocation and payments of the VCG mechanism, however, is a computationally hard problem. We thus study the performance of the VCG mechanism when bidders are forced to choose bids from a subspace of the valuation space for which the VCG outcome can be computed efficiently. We prove improved upper bounds on the welfare loss for restrictions to additive bids and upper and lower bounds for restrictions to non-additive bids. These bounds show that increased expressiveness can give rise to additional equilibria of poorer efficiency. article_number: '5' article_processing_charge: No article_type: original author: - first_name: Paul full_name: Dütting, Paul last_name: Dütting - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: Dütting P, Henzinger MH, Starnberger M. Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. 2018;6(2). doi:10.1145/3232860 apa: Dütting, P., Henzinger, M. H., & Starnberger, M. (2018). Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. Association for Computing Machinery. https://doi.org/10.1145/3232860 chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Valuation Compressions in VCG-Based Combinatorial Auctions.” ACM Transactions on Economics and Computation. Association for Computing Machinery, 2018. https://doi.org/10.1145/3232860. ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Valuation compressions in VCG-based combinatorial auctions,” ACM Transactions on Economics and Computation, vol. 6, no. 2. Association for Computing Machinery, 2018. ista: Dütting P, Henzinger MH, Starnberger M. 2018. Valuation compressions in VCG-based combinatorial auctions. ACM Transactions on Economics and Computation. 6(2), 5. mla: Dütting, Paul, et al. “Valuation Compressions in VCG-Based Combinatorial Auctions.” ACM Transactions on Economics and Computation, vol. 6, no. 2, 5, Association for Computing Machinery, 2018, doi:10.1145/3232860. short: P. Dütting, M.H. Henzinger, M. Starnberger, ACM Transactions on Economics and Computation 6 (2018). date_created: 2022-07-27T11:46:46Z date_published: 2018-05-01T00:00:00Z date_updated: 2022-09-09T12:04:42Z day: '01' doi: 10.1145/3232860 extern: '1' external_id: arxiv: - '1310.3153' intvolume: ' 6' issue: '2' keyword: - Theory of computation - Algorithmic game theory and mechanism design - Applied computing - Economics - Simplified mechanisms - Combinatorial auctions with item bidding - Price of anarchy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1310.3153 month: '05' oa: 1 oa_version: Preprint publication: ACM Transactions on Economics and Computation publication_identifier: eissn: - 2167-8383 issn: - 2167-8375 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Valuation compressions in VCG-based combinatorial auctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2018' ... --- _id: '11664' abstract: - lang: eng text: "We present a deterministic incremental algorithm for exactly maintaining the size of a minimum cut with O(log3 n log log2 n) amortized time per edge insertion and O(1) query time. This result partially answers an open question posed by Thorup (2007). It also stays in sharp contrast to a polynomial conditional lower bound for the fully dynamic weighted minimum cut problem. Our algorithm is obtained by combining a sparsification technique of Kawarabayashi and Thorup (2015) or its recent improvement by Henzinger, Rao, and Wang (2017), and an exact incremental algorithm of Henzinger (1997).\r\n\r\nWe also study space-efficient incremental algorithms for the minimum cut problem. Concretely, we show that there exists an O(nlog n/ε2) space Monte Carlo algorithm that can process a stream of edge insertions starting from an empty graph, and with high probability, the algorithm maintains a (1+ε)-approximation to the minimum cut. The algorithm has O((α (n) log3 n)/ε 2) amortized update time and constant query time, where α (n) stands for the inverse of Ackermann function." acknowledgement: "We thank the two anonymous reviewers for their suggestions and comments, which improved the\r\nquality of the article." article_number: '17' article_processing_charge: No article_type: original author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Mikkel full_name: Thorup, Mikkel last_name: Thorup citation: ama: Goranci G, Henzinger MH, Thorup M. Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. 2018;14(2). doi:10.1145/3174803 apa: Goranci, G., Henzinger, M. H., & Thorup, M. (2018). Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. Association for Computing Machinery. https://doi.org/10.1145/3174803 chicago: Goranci, Gramoz, Monika H Henzinger, and Mikkel Thorup. “Incremental Exact Min-Cut in Polylogarithmic Amortized Update Time.” ACM Transactions on Algorithms. Association for Computing Machinery, 2018. https://doi.org/10.1145/3174803. ieee: G. Goranci, M. H. Henzinger, and M. Thorup, “Incremental exact min-cut in polylogarithmic amortized update time,” ACM Transactions on Algorithms, vol. 14, no. 2. Association for Computing Machinery, 2018. ista: Goranci G, Henzinger MH, Thorup M. 2018. Incremental exact min-cut in polylogarithmic amortized update time. ACM Transactions on Algorithms. 14(2), 17. mla: Goranci, Gramoz, et al. “Incremental Exact Min-Cut in Polylogarithmic Amortized Update Time.” ACM Transactions on Algorithms, vol. 14, no. 2, 17, Association for Computing Machinery, 2018, doi:10.1145/3174803. short: G. Goranci, M.H. Henzinger, M. Thorup, ACM Transactions on Algorithms 14 (2018). date_created: 2022-07-27T11:29:39Z date_published: 2018-04-01T00:00:00Z date_updated: 2022-09-09T11:38:14Z day: '01' doi: 10.1145/3174803 extern: '1' external_id: arxiv: - '1611.06500' intvolume: ' 14' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.06500 month: '04' oa: 1 oa_version: Preprint publication: ACM Transactions on Algorithms publication_identifier: eissn: - 1549-6333 issn: - 1549-6325 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Incremental exact min-cut in polylogarithmic amortized update time type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '11757' abstract: - lang: eng text: We develop a dynamic version of the primal-dual method for optimization problems, and apply it to obtain the following results. (1) For the dynamic set-cover problem, we maintain an O ( f 2)-approximately optimal solution in O ( f · log(m + n)) amortized update time, where f is the maximum “frequency” of an element, n is the number of sets, and m is the maximum number of elements in the universe at any point in time. (2) For the dynamic b-matching problem, we maintain an O (1)-approximately optimal solution in O (log3 n) amortized update time, where n is the number of nodes in the graph. article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Giuseppe full_name: Italiano, Giuseppe last_name: Italiano citation: ama: Bhattacharya S, Henzinger MH, Italiano G. Dynamic algorithms via the primal-dual method. Information and Computation. 2018;261(08):219-239. doi:10.1016/j.ic.2018.02.005 apa: Bhattacharya, S., Henzinger, M. H., & Italiano, G. (2018). Dynamic algorithms via the primal-dual method. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2018.02.005 chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe Italiano. “Dynamic Algorithms via the Primal-Dual Method.” Information and Computation. Elsevier, 2018. https://doi.org/10.1016/j.ic.2018.02.005. ieee: S. Bhattacharya, M. H. Henzinger, and G. Italiano, “Dynamic algorithms via the primal-dual method,” Information and Computation, vol. 261, no. 08. Elsevier, pp. 219–239, 2018. ista: Bhattacharya S, Henzinger MH, Italiano G. 2018. Dynamic algorithms via the primal-dual method. Information and Computation. 261(08), 219–239. mla: Bhattacharya, Sayan, et al. “Dynamic Algorithms via the Primal-Dual Method.” Information and Computation, vol. 261, no. 08, Elsevier, 2018, pp. 219–39, doi:10.1016/j.ic.2018.02.005. short: S. Bhattacharya, M.H. Henzinger, G. Italiano, Information and Computation 261 (2018) 219–239. date_created: 2022-08-08T11:20:03Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-02-10T07:27:39Z day: '01' doi: 10.1016/j.ic.2018.02.005 extern: '1' intvolume: ' 261' issue: '08' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.ic.2018.02.005 month: '08' oa: 1 oa_version: Published Version page: 219-239 publication: Information and Computation publication_identifier: issn: - 0890-5401 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Dynamic algorithms via the primal-dual method type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 261 year: '2018' ... --- _id: '11828' abstract: - lang: eng text: "We consider the problem of dynamically maintaining (approximate) all-pairs effective resistances in separable graphs, which are those that admit an n^{c}-separator theorem for some c<1. We give a fully dynamic algorithm that maintains (1+epsilon)-approximations of the all-pairs effective resistances of an n-vertex graph G undergoing edge insertions and deletions with O~(sqrt{n}/epsilon^2) worst-case update time and O~(sqrt{n}/epsilon^2) worst-case query time, if G is guaranteed to be sqrt{n}-separable (i.e., it is taken from a class satisfying a sqrt{n}-separator theorem) and its separator can be computed in O~(n) time. Our algorithm is built upon a dynamic algorithm for maintaining approximate Schur complement that approximately preserves pairwise effective resistances among a set of terminals for separable graphs, which might be of independent interest.\r\nWe complement our result by proving that for any two fixed vertices s and t, no incremental or decremental algorithm can maintain the s-t effective resistance for sqrt{n}-separable graphs with worst-case update time O(n^{1/2-delta}) and query time O(n^{1-delta}) for any delta>0, unless the Online Matrix Vector Multiplication (OMv) conjecture is false.\r\nWe further show that for general graphs, no incremental or decremental algorithm can maintain the s-t effective resistance problem with worst-case update time O(n^{1-delta}) and query-time O(n^{2-delta}) for any delta >0, unless the OMv conjecture is false." alternative_title: - LIPIcs article_number: '40' article_processing_charge: No author: - first_name: Gramoz full_name: Goranci, Gramoz last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Pan full_name: Peng, Pan last_name: Peng citation: ama: 'Goranci G, Henzinger MH, Peng P. Dynamic effective resistances and approximate schur complement on separable graphs. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.40' apa: 'Goranci, G., Henzinger, M. H., & Peng, P. (2018). Dynamic effective resistances and approximate schur complement on separable graphs. In 26th Annual European Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.40' chicago: Goranci, Gramoz, Monika H Henzinger, and Pan Peng. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” In 26th Annual European Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.40. ieee: G. Goranci, M. H. Henzinger, and P. Peng, “Dynamic effective resistances and approximate schur complement on separable graphs,” in 26th Annual European Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112. ista: 'Goranci G, Henzinger MH, Peng P. 2018. Dynamic effective resistances and approximate schur complement on separable graphs. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 40.' mla: Goranci, Gramoz, et al. “Dynamic Effective Resistances and Approximate Schur Complement on Separable Graphs.” 26th Annual European Symposium on Algorithms, vol. 112, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.40. short: G. Goranci, M.H. Henzinger, P. Peng, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-08-22 location: Helsinki, Finland name: 'ESA: Annual European Symposium on Algorithms' start_date: 2018-08-20 date_created: 2022-08-12T08:26:42Z date_published: 2018-08-14T00:00:00Z date_updated: 2023-02-16T11:08:08Z day: '14' doi: 10.4230/LIPICS.ESA.2018.40 extern: '1' external_id: arxiv: - '1802.09111' intvolume: ' 112' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2018.40 month: '08' oa: 1 oa_version: Published Version publication: 26th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959770811' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Dynamic effective resistances and approximate schur complement on separable graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2018' ... --- _id: '11827' abstract: - lang: eng text: We study the metric facility location problem with client insertions and deletions. This setting differs from the classic dynamic facility location problem, where the set of clients remains the same, but the metric space can change over time. We show a deterministic algorithm that maintains a constant factor approximation to the optimal solution in worst-case time O~(2^{O(kappa^2)}) per client insertion or deletion in metric spaces while answering queries about the cost in O(1) time, where kappa denotes the doubling dimension of the metric. For metric spaces with bounded doubling dimension, the update time is polylogarithmic in the parameters of the problem. alternative_title: - LIPIcs article_number: '39' article_processing_charge: No author: - first_name: 'Gramoz ' full_name: 'Goranci, Gramoz ' last_name: Goranci - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Dariusz full_name: Leniowski, Dariusz last_name: Leniowski citation: ama: 'Goranci G, Henzinger MH, Leniowski D. A tree structure for dynamic facility location. In: 26th Annual European Symposium on Algorithms. Vol 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.ESA.2018.39' apa: 'Goranci, G., Henzinger, M. H., & Leniowski, D. (2018). A tree structure for dynamic facility location. In 26th Annual European Symposium on Algorithms (Vol. 112). Helsinki, Finland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ESA.2018.39' chicago: Goranci, Gramoz , Monika H Henzinger, and Dariusz Leniowski. “A Tree Structure for Dynamic Facility Location.” In 26th Annual European Symposium on Algorithms, Vol. 112. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ESA.2018.39. ieee: G. Goranci, M. H. Henzinger, and D. Leniowski, “A tree structure for dynamic facility location,” in 26th Annual European Symposium on Algorithms, Helsinki, Finland, 2018, vol. 112. ista: 'Goranci G, Henzinger MH, Leniowski D. 2018. A tree structure for dynamic facility location. 26th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 112, 39.' mla: Goranci, Gramoz, et al. “A Tree Structure for Dynamic Facility Location.” 26th Annual European Symposium on Algorithms, vol. 112, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.ESA.2018.39. short: G. Goranci, M.H. Henzinger, D. Leniowski, in:, 26th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-08-22 location: Helsinki, Finland name: 'ESA: Annual European Symposium on Algorithms' start_date: 2018-08-20 date_created: 2022-08-12T08:20:57Z date_published: 2018-08-14T00:00:00Z date_updated: 2023-02-16T10:50:51Z day: '14' doi: 10.4230/LIPICS.ESA.2018.39 extern: '1' external_id: arxiv: - '1909.06653' intvolume: ' 112' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPIcs.ESA.2018.39 month: '08' oa: 1 oa_version: Published Version publication: 26th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959770811' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: A tree structure for dynamic facility location type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2018' ... --- _id: '11768' abstract: - lang: eng text: "In the decremental single-source shortest paths (SSSP) problem, we want to maintain the distances between a given source node s and every other node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach [16] has been the fastest known algorithm for three decades. At the cost of a (1+ϵ)-approximation factor, the running time was recently improved to n2+o(1) by Bernstein and Roditty [9]. In this article, we bring the running time down to near-linear: We give a (1+ϵ)-approximation algorithm with m1+o(1) expected total update time, thus obtaining near-linear time. Moreover, we obtain m1+o(1) log W time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn) time is the mn0.9 + o(1)-time algorithm by Henzinger et al. [18, 19], which works for directed graphs with quasi-polynomial edge weights. The expected running time bound of our algorithm holds against an oblivious adversary.\r\n\r\nIn contrast to the previous results, which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (h, ϵ)-hop set introduced by Cohen [12] in the PRAM literature. An (h, ϵ)-hop set of a graph G=(V, E) is a set F of weighted edges such that the distance between any pair of nodes in G can be (1+ϵ)-approximated by their h-hop distance (given by a path containing at most h edges) on G′=(V, E ∪ F). Our algorithm can maintain an (no(1), ϵ)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain approximate distances using this hop set, we extend the monotone Even-Shiloach tree of Henzinger et al. [20] and combine it with the bounded-hop SSSP technique of Bernstein [4, 5] and Mądry [27]. These two new tools might be of independent interest." article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. 2018;65(6):1-40. doi:10.1145/3218657 apa: Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2018). Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. Association for Computing Machinery. https://doi.org/10.1145/3218657 chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” Journal of the ACM. Association for Computing Machinery, 2018. https://doi.org/10.1145/3218657. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” Journal of the ACM, vol. 65, no. 6. Association for Computing Machinery, pp. 1–40, 2018. ista: Henzinger MH, Krinninger S, Nanongkai D. 2018. Decremental single-source shortest paths on undirected graphs in near-linear total update time. Journal of the ACM. 65(6), 1–40. mla: Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” Journal of the ACM, vol. 65, no. 6, Association for Computing Machinery, 2018, pp. 1–40, doi:10.1145/3218657. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, Journal of the ACM 65 (2018) 1–40. date_created: 2022-08-08T12:33:17Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-02-21T16:30:41Z day: '01' doi: 10.1145/3218657 extern: '1' external_id: arxiv: - '1512.08148' intvolume: ' 65' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1512.08148 month: '12' oa: 1 oa_version: Preprint page: 1-40 publication: Journal of the ACM publication_identifier: eissn: - 1557-735X issn: - 0004-5411 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '11855' relation: earlier_version status: public scopus_import: '1' status: public title: Decremental single-source shortest paths on undirected graphs in near-linear total update time type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 65 year: '2018' ... --- _id: '11872' abstract: - lang: eng text: We design fast dynamic algorithms for proper vertex and edge colorings in a graph undergoing edge insertions and deletions. In the static setting, there are simple linear time algorithms for (Δ + 1)- vertex coloring and (2Δ – 1)-edge coloring in a graph with maximum degree Δ. It is natural to ask if we can efficiently maintain such colorings in the dynamic setting as well. We get the following three results. (1) We present a randomized algorithm which maintains a (Δ + 1)-vertex coloring with O(log Δ) expected amortized update time. (2) We present a deterministic algorithm which maintains a (1 + o(1)Δ-vertex coloring with O(polylog Δ) amortized update time. (3) We present a simple, deterministic algorithm which maintains a (2Δ – 1)-edge coloring with O(log Δ) worst-case update time. This improves the recent O(Δ)-edge coloring algorithm with worst-case update time [4]. article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Deeparnab full_name: Chakrabarty, Deeparnab last_name: Chakrabarty - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. Dynamic algorithms for graph coloring. In: 29th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2018:1-20. doi:10.1137/1.9781611975031.1' apa: 'Bhattacharya, S., Chakrabarty, D., Henzinger, M. H., & Nanongkai, D. (2018). Dynamic algorithms for graph coloring. In 29th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1–20). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975031.1' chicago: Bhattacharya, Sayan, Deeparnab Chakrabarty, Monika H Henzinger, and Danupon Nanongkai. “Dynamic Algorithms for Graph Coloring.” In 29th Annual ACM-SIAM Symposium on Discrete Algorithms, 1–20. Society for Industrial and Applied Mathematics, 2018. https://doi.org/10.1137/1.9781611975031.1. ieee: S. Bhattacharya, D. Chakrabarty, M. H. Henzinger, and D. Nanongkai, “Dynamic algorithms for graph coloring,” in 29th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2018, pp. 1–20. ista: 'Bhattacharya S, Chakrabarty D, Henzinger MH, Nanongkai D. 2018. Dynamic algorithms for graph coloring. 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1–20.' mla: Bhattacharya, Sayan, et al. “Dynamic Algorithms for Graph Coloring.” 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20, doi:10.1137/1.9781611975031.1. short: S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, D. Nanongkai, in:, 29th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2018, pp. 1–20. conference: end_date: 2018-01-10 location: New Orleans, LA, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2018-01-07 date_created: 2022-08-16T12:07:14Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-02-17T11:39:01Z day: '01' doi: 10.1137/1.9781611975031.1 extern: '1' external_id: arxiv: - '1711.04355' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.04355 month: '01' oa: 1 oa_version: Preprint page: 1 - 20 publication: 29th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-161197503-1 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Dynamic algorithms for graph coloring type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '11882' abstract: - lang: eng text: The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weight sum of the cut edges. Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm is based on cluster contraction using label propagation and Padberg and Rinaldi's contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory parallel implementations of our algorithm. Extensive experiments on both real-world and generated instances show that our algorithm finds the optimal cut on nearly all instances significantly faster than other state-of-the-art exact algorithms, and our error rate is lower than that of other heuristic algorithms. In addition, our parallel algorithm shows good scalability. article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Noe, Alexander last_name: Noe - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Darren full_name: Strash, Darren last_name: Strash citation: ama: 'Henzinger MH, Noe A, Schulz C, Strash D. Practical minimum cut algorithms. In: 20th Workshop on Algorithm Engineering and Experiments. Society for Industrial and Applied Mathematics; 2018:48-61. doi:10.1137/1.9781611975055.5' apa: 'Henzinger, M. H., Noe, A., Schulz, C., & Strash, D. (2018). Practical minimum cut algorithms. In 20th Workshop on Algorithm Engineering and Experiments (pp. 48–61). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611975055.5' chicago: Henzinger, Monika H, Alexander Noe, Christian Schulz, and Darren Strash. “Practical Minimum Cut Algorithms.” In 20th Workshop on Algorithm Engineering and Experiments, 48–61. Society for Industrial and Applied Mathematics, 2018. https://doi.org/10.1137/1.9781611975055.5. ieee: M. H. Henzinger, A. Noe, C. Schulz, and D. Strash, “Practical minimum cut algorithms,” in 20th Workshop on Algorithm Engineering and Experiments, New Orleans, LA, United States, 2018, pp. 48–61. ista: 'Henzinger MH, Noe A, Schulz C, Strash D. 2018. Practical minimum cut algorithms. 20th Workshop on Algorithm Engineering and Experiments. ALENEX: Symposium on Algorithm Engineering and Experiments, 48–61.' mla: Henzinger, Monika H., et al. “Practical Minimum Cut Algorithms.” 20th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018, pp. 48–61, doi:10.1137/1.9781611975055.5. short: M.H. Henzinger, A. Noe, C. Schulz, D. Strash, in:, 20th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2018, pp. 48–61. conference: end_date: 2018-01-08 location: New Orleans, LA, United States name: 'ALENEX: Symposium on Algorithm Engineering and Experiments' start_date: 2018-01-07 date_created: 2022-08-17T07:04:57Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-02-17T14:03:39Z day: '01' doi: 10.1137/1.9781611975055.5 extern: '1' external_id: arxiv: - '1708.06127' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.06127 month: '01' oa: 1 oa_version: Preprint page: 48-61 publication: 20th Workshop on Algorithm Engineering and Experiments publication_identifier: eisbn: - 978-1-61197-505-5 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: Practical minimum cut algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '11890' abstract: - lang: eng text: "We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph \U0001D43A=(\U0001D449,\U0001D438), with |\U0001D449|=\U0001D45B and |\U0001D438|=\U0001D45A, in \U0001D45C(\U0001D45A‾‾√) time per update. In particular, for minimum vertex cover, we provide deterministic data structures for maintaining a (2+\U0001D716) approximation in \U0001D442(log\U0001D45B/\U0001D7162) amortized time per update. For maximum matching, we show how to maintain a (3+\U0001D716) approximation in \U0001D442(min(\U0001D45B√/\U0001D716,\U0001D45A1/3/\U0001D7162) amortized time per update and a (4+\U0001D716) approximation in \U0001D442(\U0001D45A1/3/\U0001D7162) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [in 42nd ACM Symposium on Theory of Computing, Cambridge, MA, ACM, 2010, pp. 457--464]." article_processing_charge: No article_type: original author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Giuseppe F. full_name: Italiano, Giuseppe F. last_name: Italiano citation: ama: Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. 2018;47(3):859-887. doi:10.1137/140998925 apa: Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2018). Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/140998925 chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2018. https://doi.org/10.1137/140998925. ieee: S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” SIAM Journal on Computing, vol. 47, no. 3. Society for Industrial & Applied Mathematics, pp. 859–887, 2018. ista: Bhattacharya S, Henzinger MH, Italiano GF. 2018. Deterministic fully dynamic data structures for vertex cover and matching. SIAM Journal on Computing. 47(3), 859–887. mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” SIAM Journal on Computing, vol. 47, no. 3, Society for Industrial & Applied Mathematics, 2018, pp. 859–87, doi:10.1137/140998925. short: S. Bhattacharya, M.H. Henzinger, G.F. Italiano, SIAM Journal on Computing 47 (2018) 859–887. date_created: 2022-08-17T08:21:23Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-02-21T16:31:30Z day: '01' doi: 10.1137/140998925 extern: '1' external_id: arxiv: - '1412.1318' intvolume: ' 47' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.1318 month: '05' oa: 1 oa_version: Preprint page: 859-887 publication: SIAM Journal on Computing publication_identifier: eissn: - 1095-7111 issn: - 0097-5397 publication_status: published publisher: Society for Industrial & Applied Mathematics quality_controlled: '1' related_material: record: - id: '11875' relation: earlier_version status: public scopus_import: '1' status: public title: Deterministic fully dynamic data structures for vertex cover and matching type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2018' ... --- _id: '11911' abstract: - lang: eng text: It is common knowledge that there is no single best strategy for graph clustering, which justifies a plethora of existing approaches. In this paper, we present a general memetic algorithm, VieClus, to tackle the graph clustering problem. This algorithm can be adapted to optimize different objective functions. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. We instantiate our scheme with local search for modularity and show that our algorithm successfully improves or reproduces all entries of the 10th DIMACS implementation challenge under consideration using a small amount of time. alternative_title: - LIPIcs article_number: '3' article_processing_charge: No author: - first_name: Sonja full_name: Biedermann, Sonja last_name: Biedermann - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Christian full_name: Schulz, Christian last_name: Schulz - first_name: Bernhard full_name: Schuster, Bernhard last_name: Schuster citation: ama: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. Memetic graph clustering. In: 17th International Symposium on Experimental Algorithms. Vol 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.SEA.2018.3' apa: 'Biedermann, S., Henzinger, M. H., Schulz, C., & Schuster, B. (2018). Memetic graph clustering. In 17th International Symposium on Experimental Algorithms (Vol. 103). L’Aquila, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SEA.2018.3' chicago: Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Memetic Graph Clustering.” In 17th International Symposium on Experimental Algorithms, Vol. 103. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.SEA.2018.3. ieee: S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Memetic graph clustering,” in 17th International Symposium on Experimental Algorithms, L’Aquila, Italy, 2018, vol. 103. ista: 'Biedermann S, Henzinger MH, Schulz C, Schuster B. 2018. Memetic graph clustering. 17th International Symposium on Experimental Algorithms. SEA: Symposium on Experimental Algorithms, LIPIcs, vol. 103, 3.' mla: Biedermann, Sonja, et al. “Memetic Graph Clustering.” 17th International Symposium on Experimental Algorithms, vol. 103, 3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.SEA.2018.3. short: S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, 17th International Symposium on Experimental Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-07-29 location: L'Aquila, Italy name: 'SEA: Symposium on Experimental Algorithms' start_date: 2018-07-27 date_created: 2022-08-18T06:49:40Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-02-16T11:45:14Z day: '01' doi: 10.4230/LIPICS.SEA.2018.3 extern: '1' external_id: arxiv: - '1802.07034' intvolume: ' 103' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.SEA.2018.3 month: '07' oa: 1 oa_version: Published Version publication: 17th International Symposium on Experimental Algorithms publication_identifier: isbn: - '9783959770705' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: Memetic graph clustering type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 103 year: '2018' ... --- _id: '11958' abstract: - lang: eng text: Solid reagents, leaching catalysts, and heterogeneous photocatalysts are commonly employed in batch processes but are ill-suited for continuous-flow chemistry. Heterogeneous catalysts for thermal reactions are typically used in packed-bed reactors, which cannot be penetrated by light and thus are not suitable for photocatalytic reactions involving solids. We demonstrate that serial micro-batch reactors (SMBRs) allow for the continuous utilization of solid materials together with liquids and gases in flow. This technology was utilized to develop selective and efficient fluorination reactions using a modified graphitic carbon nitride heterogeneous catalyst instead of costly homogeneous metal polypyridyl complexes. The merger of this inexpensive, recyclable catalyst and the SMBR approach enables sustainable and scalable photocatalysis. article_processing_charge: No article_type: letter_note author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Menny full_name: Shalom, Menny last_name: Shalom - first_name: Markus full_name: Antonietti, Markus last_name: Antonietti - first_name: Peter H. full_name: Seeberger, Peter H. last_name: Seeberger - first_name: Kerry full_name: Gilmore, Kerry last_name: Gilmore citation: ama: Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. 2018;57(31):9976-9979. doi:10.1002/anie.201712568 apa: Pieber, B., Shalom, M., Antonietti, M., Seeberger, P. H., & Gilmore, K. (2018). Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201712568 chicago: Pieber, Bartholomäus, Menny Shalom, Markus Antonietti, Peter H. Seeberger, and Kerry Gilmore. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201712568. ieee: B. Pieber, M. Shalom, M. Antonietti, P. H. Seeberger, and K. Gilmore, “Continuous heterogeneous photocatalysis in serial micro-batch reactors,” Angewandte Chemie International Edition, vol. 57, no. 31. Wiley, pp. 9976–9979, 2018. ista: Pieber B, Shalom M, Antonietti M, Seeberger PH, Gilmore K. 2018. Continuous heterogeneous photocatalysis in serial micro-batch reactors. Angewandte Chemie International Edition. 57(31), 9976–9979. mla: Pieber, Bartholomäus, et al. “Continuous Heterogeneous Photocatalysis in Serial Micro-Batch Reactors.” Angewandte Chemie International Edition, vol. 57, no. 31, Wiley, 2018, pp. 9976–79, doi:10.1002/anie.201712568. short: B. Pieber, M. Shalom, M. Antonietti, P.H. Seeberger, K. Gilmore, Angewandte Chemie International Edition 57 (2018) 9976–9979. date_created: 2022-08-24T10:57:25Z date_published: 2018-07-26T00:00:00Z date_updated: 2023-02-21T10:09:18Z day: '26' doi: 10.1002/anie.201712568 extern: '1' external_id: pmid: - '29377383' intvolume: ' 57' issue: '31' language: - iso: eng month: '07' oa_version: None page: 9976-9979 pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - ' 1521-3773' issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Continuous heterogeneous photocatalysis in serial micro-batch reactors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2018' ... --- _id: '1215' abstract: - lang: eng text: "Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus." acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA. article_processing_charge: Yes (via OA deal) author: - first_name: Franco full_name: Flandoli, Franco last_name: Flandoli - first_name: Francesco full_name: Russo, Francesco last_name: Russo - first_name: Giovanni A full_name: Zanco, Giovanni A id: 47491882-F248-11E8-B48F-1D18A9856A87 last_name: Zanco citation: ama: Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2 apa: Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2 chicago: Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2. ieee: F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018. ista: Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826. mla: Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2. short: F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826. date_created: 2018-12-11T11:50:45Z date_published: 2018-06-01T00:00:00Z date_updated: 2021-01-12T06:49:09Z day: '01' ddc: - '519' department: - _id: JaMa doi: 10.1007/s10959-016-0724-2 file: - access_level: open_access checksum: 47686d58ec21c164540f1a980ff2163f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:13Z date_updated: 2020-07-14T12:44:39Z file_id: '5266' file_name: IST-2016-712-v1+1_s10959-016-0724-2.pdf file_size: 671125 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 31' issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 789-826 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Journal of Theoretical Probability publication_status: published publisher: Springer publist_id: '6119' pubrep_id: '712' quality_controlled: '1' scopus_import: 1 status: public title: Infinite-dimensional calculus under weak spatial regularity of the processes 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2018' ... --- _id: '124' abstract: - lang: eng text: By investigating the in situ chemical and O-isotope compositions of olivine in lightly sintered dust agglomerates from the early Solar System, we constrain their origins and the retention of dust in the protoplanetary disk. The grain sizes of silicates in these agglomeratic olivine (AO) chondrules indicate that the grain sizes of chondrule precursors in the Renazzo-like carbonaceous (CR) chondrites ranged from <1 to 80 µm. We infer this grain size range to be equivalent to the size range for dust in the early Solar System. AO chondrules may contain, but are not solely composed of, recycled fragments of earlier formed chondrules. They also contain 16O-rich olivine related to amoeboid olivine aggregates and represent the best record of chondrule-precursor materials. AO chondrules contain one or more large grains, sometimes similar to FeO-poor (type I) and/or FeO-rich (type II) chondrules, while others contain a type II chondrule core. These morphologies are consistent with particle agglomeration by electrostatic charging of grains during collision, a process that may explain solid agglomeration in the protoplanetary disk in the micrometer size regime. The petrographic, isotopic, and chemical compositions of AO chondrules are consistent with chondrule formation by large-scale shocks, bow shocks, and current sheets. The petrographic, isotopic, and chemical similarities between AO chondrules in CR chondrites and chondrule-like objects from comet 81P/Wild 2 indicate that comets contain AO chondrules. We infer that these AO chondrules likely formed in the inner Solar System and migrated to the comet forming region at least 3 Ma after the formation of the first Solar System solids. Observations made in this study imply that the protoplanetary disk retained a dusty disk at least ∼3.7 Ma after the formation of the first Solar System solids, longer than half of the dusty accretion disks observed around other stars. author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Devin full_name: Schrader, Devin last_name: Schrader - first_name: Kazuhide full_name: Nagashima, Kazuhide last_name: Nagashima - first_name: Jemma full_name: Davidson, Jemma last_name: Davidson - first_name: Timothy full_name: Mccoy, Timothy last_name: Mccoy - first_name: Harold full_name: Conolly Jr, Harold last_name: Conolly Jr - first_name: Dante full_name: Lauretta, Dante last_name: Lauretta citation: ama: 'Waitukaitis SR, Schrader D, Nagashima K, et al. The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. 2018;223:405-421. doi:10.1016/j.gca.2017.12.014' apa: 'Waitukaitis, S. R., Schrader, D., Nagashima, K., Davidson, J., Mccoy, T., Conolly Jr, H., & Lauretta, D. (2018). The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. Elsevier. https://doi.org/10.1016/j.gca.2017.12.014' chicago: 'Waitukaitis, Scott R, Devin Schrader, Kazuhide Nagashima, Jemma Davidson, Timothy Mccoy, Harold Conolly Jr, and Dante Lauretta. “The Retention of Dust in Protoplanetary Disks: Evidence from Agglomeration Olivine Chondrules from the Outer Solar System.” Geochimica et Cosmochimica Acta. Elsevier, 2018. https://doi.org/10.1016/j.gca.2017.12.014.' ieee: 'S. R. Waitukaitis et al., “The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system,” Geochimica et Cosmochimica Acta, vol. 223. Elsevier, pp. 405–421, 2018.' ista: 'Waitukaitis SR, Schrader D, Nagashima K, Davidson J, Mccoy T, Conolly Jr H, Lauretta D. 2018. The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system. Geochimica et Cosmochimica Acta. 223, 405–421.' mla: 'Waitukaitis, Scott R., et al. “The Retention of Dust in Protoplanetary Disks: Evidence from Agglomeration Olivine Chondrules from the Outer Solar System.” Geochimica et Cosmochimica Acta, vol. 223, Elsevier, 2018, pp. 405–21, doi:10.1016/j.gca.2017.12.014.' short: S.R. Waitukaitis, D. Schrader, K. Nagashima, J. Davidson, T. Mccoy, H. Conolly Jr, D. Lauretta, Geochimica et Cosmochimica Acta 223 (2018) 405–421. date_created: 2018-12-11T11:44:45Z date_published: 2018-02-15T00:00:00Z date_updated: 2021-01-12T06:49:19Z day: '15' doi: 10.1016/j.gca.2017.12.014 extern: '1' intvolume: ' 223' language: - iso: eng month: '02' oa_version: None page: 405 - 421 publication: Geochimica et Cosmochimica Acta publication_status: published publisher: Elsevier publist_id: '7930' quality_controlled: '1' status: public title: 'The retention of dust in protoplanetary disks: evidence from agglomeration olivine chondrules from the outer solar system' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 223 year: '2018' ... --- _id: '125' abstract: - lang: eng text: Many fields of study, including medical imaging, granular physics, colloidal physics, and active matter, require the precise identification and tracking of particle-like objects in images. While many algorithms exist to track particles in diffuse conditions, these often perform poorly when particles are densely packed together—as in, for example, solid-like systems of granular materials. Incorrect particle identification can have significant effects on the calculation of physical quantities, which makes the development of more precise and faster tracking algorithms a worthwhile endeavor. In this work, we present a new tracking algorithm to identify particles in dense systems that is both highly accurate and fast. We demonstrate the efficacy of our approach by analyzing images of dense, solid-state granular media, where we achieve an identification error of 5% in the worst evaluated cases. Going further, we propose a parallelization strategy for our algorithm using a GPU, which results in a speedup of up to 10× when compared to a sequential CPU implementation in C and up to 40× when compared to the reference MATLAB library widely used for particle tracking. Our results extend the capabilities of state-of-the-art particle tracking methods by allowing fast, high-fidelity detection in dense media at high resolutions. author: - first_name: Mauricio full_name: Cerda, Mauricio last_name: Cerda - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Cristóbal full_name: Navarro, Cristóbal last_name: Navarro - first_name: Juan full_name: Silva, Juan last_name: Silva - first_name: Nicolás full_name: Mujica, Nicolás last_name: Mujica - first_name: Nancy full_name: Hitschfeld, Nancy last_name: Hitschfeld citation: ama: Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. A high-speed tracking algorithm for dense granular media. Computer Physics Communications. 2018;227:8-16. doi:10.1016/j.cpc.2018.02.010 apa: Cerda, M., Waitukaitis, S. R., Navarro, C., Silva, J., Mujica, N., & Hitschfeld, N. (2018). A high-speed tracking algorithm for dense granular media. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.02.010 chicago: Cerda, Mauricio, Scott R Waitukaitis, Cristóbal Navarro, Juan Silva, Nicolás Mujica, and Nancy Hitschfeld. “A High-Speed Tracking Algorithm for Dense Granular Media.” Computer Physics Communications. Elsevier, 2018. https://doi.org/10.1016/j.cpc.2018.02.010. ieee: M. Cerda, S. R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, and N. Hitschfeld, “A high-speed tracking algorithm for dense granular media,” Computer Physics Communications, vol. 227. Elsevier, pp. 8–16, 2018. ista: Cerda M, Waitukaitis SR, Navarro C, Silva J, Mujica N, Hitschfeld N. 2018. A high-speed tracking algorithm for dense granular media. Computer Physics Communications. 227, 8–16. mla: Cerda, Mauricio, et al. “A High-Speed Tracking Algorithm for Dense Granular Media.” Computer Physics Communications, vol. 227, Elsevier, 2018, pp. 8–16, doi:10.1016/j.cpc.2018.02.010. short: M. Cerda, S.R. Waitukaitis, C. Navarro, J. Silva, N. Mujica, N. Hitschfeld, Computer Physics Communications 227 (2018) 8–16. date_created: 2018-12-11T11:44:45Z date_published: 2018-06-01T00:00:00Z date_updated: 2021-01-12T06:49:23Z day: '01' doi: 10.1016/j.cpc.2018.02.010 extern: '1' intvolume: ' 227' language: - iso: eng month: '06' oa_version: None page: 8 - 16 publication: Computer Physics Communications publication_status: published publisher: Elsevier publist_id: '7928' quality_controlled: '1' status: public title: A high-speed tracking algorithm for dense granular media type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 227 year: '2018' ... --- _id: '126' abstract: - lang: eng text: The Leidenfrost effect occurs when a liquid or stiff sublimable solid near a hot surface creates enough vapor beneath it to lift itself up and float. In contrast, vaporizable soft solids, e.g., hydrogels, have been shown to exhibit persistent bouncing - the elastic Leidenfrost effect. By carefully lowering hydrogel spheres towards a hot surface, we discover that they are also capable of floating. The bounce-to-float transition is controlled by the approach velocity and temperature, analogously to the "dynamic Leidenfrost effect." For the floating regime, we measure power-law scalings for the gap geometry, which we explain with a model that couples the vaporization rate to the spherical shape. Our results reveal that hydrogels are a promising pathway for controlling floating Leidenfrost objects through shape. acknowledgement: We acknowledge funding from the Netherlands Organization for Scientific Research through Grants VICI No. NWO- 680-47-609 (M. v. H. and S. W.) and VENI No. NWO-680- 47-453 (S. W.), and from the German Science Foundation through Grant No. HA8467/1-1 (K. H.). article_number: '048001 ' author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Kirsten full_name: Harth, Kirsten last_name: Harth - first_name: Martin full_name: Van Hecke, Martin last_name: Van Hecke citation: ama: 'Waitukaitis SR, Harth K, Van Hecke M. From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. 2018;121(4). doi:10.1103/PhysRevLett.121.048001' apa: 'Waitukaitis, S. R., Harth, K., & Van Hecke, M. (2018). From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.048001' chicago: 'Waitukaitis, Scott R, Kirsten Harth, and Martin Van Hecke. “From Bouncing to Floating: The Leidenfrost Effect with Hydrogel Spheres.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.048001.' ieee: 'S. R. Waitukaitis, K. Harth, and M. Van Hecke, “From bouncing to floating: the Leidenfrost effect with hydrogel spheres,” Physical Review Letters, vol. 121, no. 4. American Physical Society, 2018.' ista: 'Waitukaitis SR, Harth K, Van Hecke M. 2018. From bouncing to floating: the Leidenfrost effect with hydrogel spheres. Physical Review Letters. 121(4), 048001.' mla: 'Waitukaitis, Scott R., et al. “From Bouncing to Floating: The Leidenfrost Effect with Hydrogel Spheres.” Physical Review Letters, vol. 121, no. 4, 048001, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.048001.' short: S.R. Waitukaitis, K. Harth, M. Van Hecke, Physical Review Letters 121 (2018). date_created: 2018-12-11T11:44:46Z date_published: 2018-07-25T00:00:00Z date_updated: 2021-01-12T06:49:27Z day: '25' doi: 10.1103/PhysRevLett.121.048001 extern: '1' intvolume: ' 121' issue: '4' language: - iso: eng month: '07' oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7927' quality_controlled: '1' status: public title: 'From bouncing to floating: the Leidenfrost effect with hydrogel spheres' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2018' ... --- _id: '127' abstract: - lang: eng text: The ideas of topology are breaking ground in origami-based metamaterials. Experiments now show that certain shapes — doughnuts included — exhibit topological bistability, and can be made to click between different topologically stable states. author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: Waitukaitis SR. Clicks for doughnuts. Nature Physics. 2018;14(8):777-778. doi:10.1038/s41567-018-0160-6 apa: Waitukaitis, S. R. (2018). Clicks for doughnuts. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0160-6 chicago: Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0160-6. ieee: S. R. Waitukaitis, “Clicks for doughnuts,” Nature Physics, vol. 14, no. 8. Nature Publishing Group, pp. 777–778, 2018. ista: Waitukaitis SR. 2018. Clicks for doughnuts. Nature Physics. 14(8), 777–778. mla: Waitukaitis, Scott R. “Clicks for Doughnuts.” Nature Physics, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 777–78, doi:10.1038/s41567-018-0160-6. short: S.R. Waitukaitis, Nature Physics 14 (2018) 777–778. date_created: 2018-12-11T11:44:46Z date_published: 2018-05-28T00:00:00Z date_updated: 2021-01-12T06:49:31Z day: '28' doi: 10.1038/s41567-018-0160-6 extern: '1' intvolume: ' 14' issue: '8' language: - iso: eng month: '05' oa_version: None page: 777 - 778 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7926' status: public title: Clicks for doughnuts type: journal_article user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2018' ... --- _id: '174' abstract: - lang: eng text: We survey recent efforts to quantify failures of the Hasse principle in families of rationally connected varieties. alternative_title: - Proceedings of Symposia in Pure Mathematics article_processing_charge: No author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: 'Browning TD. How often does the Hasse principle hold? In: Vol 97. American Mathematical Society; 2018:89-102. doi:10.1090/pspum/097.2/01700' apa: 'Browning, T. D. (2018). How often does the Hasse principle hold? (Vol. 97, pp. 89–102). Presented at the Algebraic Geometry, Salt Lake City, Utah, USA: American Mathematical Society. https://doi.org/10.1090/pspum/097.2/01700' chicago: Browning, Timothy D. “How Often Does the Hasse Principle Hold?,” 97:89–102. American Mathematical Society, 2018. https://doi.org/10.1090/pspum/097.2/01700. ieee: T. D. Browning, “How often does the Hasse principle hold?,” presented at the Algebraic Geometry, Salt Lake City, Utah, USA, 2018, vol. 97, no. 2, pp. 89–102. ista: Browning TD. 2018. How often does the Hasse principle hold? Algebraic Geometry, Proceedings of Symposia in Pure Mathematics, vol. 97, 89–102. mla: Browning, Timothy D. How Often Does the Hasse Principle Hold? Vol. 97, no. 2, American Mathematical Society, 2018, pp. 89–102, doi:10.1090/pspum/097.2/01700. short: T.D. Browning, in:, American Mathematical Society, 2018, pp. 89–102. conference: end_date: 2015-07-10 location: Salt Lake City, Utah, USA name: Algebraic Geometry start_date: 2015-07-06 date_created: 2018-12-11T11:45:01Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T06:52:54Z day: '01' doi: 10.1090/pspum/097.2/01700 extern: '1' intvolume: ' 97' issue: '2' language: - iso: eng month: '01' oa_version: None page: 89 - 102 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: How often does the Hasse principle hold? type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 97 year: '2018' ... --- _id: '176' abstract: - lang: eng text: For a general class of non-negative functions defined on integral ideals of number fields, upper bounds are established for their average over the values of certain principal ideals that are associated to irreducible binary forms with integer coefficients. article_processing_charge: No article_type: original 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. Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. 2018;15(3):547-567. doi:10.1142/S1793042119500283 apa: Browning, T. D., & Sofos, E. (2018). Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. World Scientific Publishing. https://doi.org/10.1142/S1793042119500283 chicago: Browning, Timothy D, and Efthymios Sofos. “Averages of Arithmetic Functions over Principal Ideals.” International Journal of Nuber Theory. World Scientific Publishing, 2018. https://doi.org/10.1142/S1793042119500283. ieee: T. D. Browning and E. Sofos, “Averages of arithmetic functions over principal ideals,” International Journal of Nuber Theory, vol. 15, no. 3. World Scientific Publishing, pp. 547–567, 2018. ista: Browning TD, Sofos E. 2018. Averages of arithmetic functions over principal ideals. International Journal of Nuber Theory. 15(3), 547–567. mla: Browning, Timothy D., and Efthymios Sofos. “Averages of Arithmetic Functions over Principal Ideals.” International Journal of Nuber Theory, vol. 15, no. 3, World Scientific Publishing, 2018, pp. 547–67, doi:10.1142/S1793042119500283. short: T.D. Browning, E. Sofos, International Journal of Nuber Theory 15 (2018) 547–567. date_created: 2018-12-11T11:45:01Z date_published: 2018-11-16T00:00:00Z date_updated: 2021-01-12T06:53:01Z day: '16' doi: 10.1142/S1793042119500283 extern: '1' external_id: arxiv: - '1706.04331' intvolume: ' 15' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.04331 month: '11' oa: 1 oa_version: Preprint page: 547-567 publication: International Journal of Nuber Theory publication_status: published publisher: World Scientific Publishing status: public title: Averages of arithmetic functions over principal ideals type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 15 year: '2018' ... --- _id: '178' abstract: - lang: eng text: We give an upper bound for the number of rational points of height at most B, lying on a surface defined by a quadratic form Q. The bound shows an explicit dependence on Q. It is optimal with respect to B, and is also optimal for typical forms Q. article_processing_charge: No 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: Roger full_name: Heath-Brown, Roger last_name: Heath-Brown citation: ama: Browning TD, Heath-Brown R. Counting rational points on quadric surfaces. Discrete Analysis. 2018;15:1-29. doi:10.19086/da.4375 apa: Browning, T. D., & Heath-Brown, R. (2018). Counting rational points on quadric surfaces. Discrete Analysis. Alliance of Diamond Open Access Journals. https://doi.org/10.19086/da.4375 chicago: Browning, Timothy D, and Roger Heath-Brown. “Counting Rational Points on Quadric Surfaces.” Discrete Analysis. Alliance of Diamond Open Access Journals, 2018. https://doi.org/10.19086/da.4375. ieee: T. D. Browning and R. Heath-Brown, “Counting rational points on quadric surfaces,” Discrete Analysis, vol. 15. Alliance of Diamond Open Access Journals, pp. 1–29, 2018. ista: Browning TD, Heath-Brown R. 2018. Counting rational points on quadric surfaces. Discrete Analysis. 15, 1–29. mla: Browning, Timothy D., and Roger Heath-Brown. “Counting Rational Points on Quadric Surfaces.” Discrete Analysis, vol. 15, Alliance of Diamond Open Access Journals, 2018, pp. 1–29, doi:10.19086/da.4375. short: T.D. Browning, R. Heath-Brown, Discrete Analysis 15 (2018) 1–29. date_created: 2018-12-11T11:45:02Z date_published: 2018-09-07T00:00:00Z date_updated: 2022-08-26T09:13:02Z day: '07' ddc: - '512' doi: 10.19086/da.4375 extern: '1' external_id: arxiv: - '1801.00979' intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.00979 month: '09' oa: 1 oa_version: Preprint page: 1 - 29 publication: Discrete Analysis publication_identifier: eissn: - 2397-3129 publication_status: published publisher: Alliance of Diamond Open Access Journals quality_controlled: '1' status: public title: Counting rational points on quadric surfaces 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2018' ...