[{"author":[{"full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","last_name":"Burnett","first_name":"Laura"}],"date_updated":"2023-04-05T10:59:04Z","date_created":"2023-03-08T15:19:45Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"doi":"10.15479/at:ista:12716","supervisor":[{"last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Circuits of Visual Attention","grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"file":[{"access_level":"closed","file_name":"Burnett_Thesis_2023.docx","creator":"lburnett","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":23029260,"file_id":"12717","relation":"source_file","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z"},{"relation":"main_file","file_id":"12718","date_created":"2023-03-08T15:08:46Z","date_updated":"2023-03-08T15:08:46Z","checksum":"cebc77705288bf4382db9b3541483cd0","success":1,"file_name":"Burnett_Thesis_2023_pdfA.pdf","access_level":"open_access","content_type":"application/pdf","file_size":11959869,"creator":"lburnett"}],"oa_version":"Published Version","_id":"12716","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["599","573"],"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","abstract":[{"lang":"eng","text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-03-10T00:00:00Z","citation":{"ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716."},"page":"178","day":"10","has_accepted_license":"1","article_processing_charge":"No"},{"ec_funded":1,"file_date_updated":"2023-04-25T06:58:36Z","license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","year":"2023","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","last_name":"Chalupa"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"volume":13994,"date_updated":"2023-04-25T07:02:43Z","date_created":"2023-04-20T08:22:53Z","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"],"eisbn":["9783031308208"]},"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"quality_controlled":"1","doi":"10.1007/978-3-031-30820-8_32","conference":{"end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12854","intvolume":" 13994","title":"Bubaak: Runtime monitoring of program verifiers","ddc":["000"],"status":"public","file":[{"file_id":"12864","relation":"main_file","success":1,"checksum":"120d2c2a38384058ad0630fdf8288312","date_updated":"2023-04-25T06:58:36Z","date_created":"2023-04-25T06:58:36Z","access_level":"open_access","file_name":"2023_LNCS_Chalupa.pdf","creator":"dernst","file_size":16096413,"content_type":"application/pdf"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"20","citation":{"chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In Tools and Algorithms for the Construction and Analysis of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540.","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32"},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","page":"535-540","date_published":"2023-04-20T00:00:00Z"},{"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"title":"Area formula for spherical polygons via prequantization","publication_status":"submitted","status":"public","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","_id":"12846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","oa_version":"Preprint","date_updated":"2023-04-25T06:51:21Z","date_created":"2023-04-18T19:16:06Z","author":[{"full_name":"Chern, Albert","first_name":"Albert","last_name":"Chern"},{"first_name":"Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige"}],"type":"preprint","article_number":"2303.14555","abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"citation":{"ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","short":"A. Chern, S. Ishida, ArXiv (n.d.).","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.14555"}],"oa":1,"external_id":{"arxiv":["2303.14555"]},"publication":"arXiv","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2303.14555","date_published":"2023-03-25T00:00:00Z","article_processing_charge":"No","day":"25","month":"03"},{"oa_version":"Published Version","file":[{"date_updated":"2023-04-25T07:16:36Z","date_created":"2023-04-25T07:16:36Z","checksum":"17a7c8e08be609cf2408d37ea55e322c","success":1,"relation":"main_file","file_id":"12865","file_size":580828,"content_type":"application/pdf","creator":"dernst","file_name":"2023_LNCS_ChalupaM.pdf","access_level":"open_access"}],"_id":"12856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13991","ddc":["000"],"status":"public","title":"Vamos: Middleware for best-effort third-party monitoring","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2023-04-20T00:00:00Z","citation":{"ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15."},"publication":"Fundamental Approaches to Software Engineering","page":"260-281","article_processing_charge":"No","has_accepted_license":"1","day":"20","related_material":{"record":[{"id":"12407","status":"public","relation":"earlier_version"}]},"author":[{"last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"full_name":"Mühlböck, Fabian","last_name":"Mühlböck","first_name":"Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425"},{"last_name":"Muroya Lei","first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"volume":13991,"date_created":"2023-04-20T08:29:42Z","date_updated":"2023-04-25T07:19:07Z","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2023-04-25T07:16:36Z","doi":"10.1007/978-3-031-30826-0_15","conference":{"name":"FASE: Fundamental Approaches to Software Engineering","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"quality_controlled":"1","publication_identifier":{"isbn":["9783031308253"],"eissn":["1611-3349"],"eisbn":["9783031308260"],"issn":["0302-9743"]},"month":"04"},{"publication_identifier":{"eissn":["2664-1690"]},"month":"01","doi":"10.15479/AT:ISTA:12407","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"ec_funded":1,"file_date_updated":"2023-01-27T03:18:34Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"12856"}]},"author":[{"first_name":"Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","first_name":"Fabian"},{"full_name":"Muroya Lei, Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","last_name":"Muroya Lei","first_name":"Stefanie"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"date_updated":"2023-04-25T07:19:06Z","date_created":"2023-01-27T03:18:08Z","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"27","keyword":["runtime monitoring","best effort","third party"],"date_published":"2023-01-27T00:00:00Z","citation":{"mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407"},"page":"38","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":662409,"creator":"fmuehlbo","file_name":"main.pdf","access_level":"open_access","date_created":"2023-01-27T03:18:34Z","date_updated":"2023-01-27T03:18:34Z","checksum":"55426e463fdeafe9777fc3ff635154c7","success":1,"relation":"main_file","file_id":"12408"}],"_id":"12407","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["005"],"status":"public","title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring"},{"status":"public","publication_status":"published","title":"Altered childhood brain development in autism and epilepsy","editor":[{"full_name":"Halpern-Felsher, Bonnie","last_name":"Halpern-Felsher","first_name":"Bonnie"}],"publisher":"Elsevier","department":[{"_id":"TiVo"}],"year":"2023","_id":"12866","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-04-25T07:52:43Z","date_updated":"2023-04-25T09:25:40Z","oa_version":"None","author":[{"full_name":"Currin, Christopher","last_name":"Currin","first_name":"Christopher","orcid":"0000-0002-4809-5059","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9"},{"first_name":"Chad","last_name":"Beyer","full_name":"Beyer, Chad"}],"edition":"1","alternative_title":["Vol. 1: Biological Development and Physical Health"],"type":"book_chapter","abstract":[{"text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain.","lang":"eng"}],"quality_controlled":"1","page":"86-98","publication":"Encyclopedia of Child and Adolescent Health","citation":{"ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health. 1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1","ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98.","apa":"Currin, C., & Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1.","short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1."},"language":[{"iso":"eng"}],"doi":"10.1016/b978-0-12-818872-9.00129-1","date_published":"2023-02-01T00:00:00Z","month":"02","day":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9780128188736"]}},{"date_published":"2023-04-06T00:00:00Z","citation":{"ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023."},"page":"115","day":"06","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","file":[{"checksum":"35b5997d2b0acb461f9d33d073da0df5","date_updated":"2023-04-07T06:16:06Z","date_created":"2023-04-07T06:16:06Z","relation":"main_file","embargo":"2024-04-07","file_id":"12814","file_size":9881969,"content_type":"application/pdf","creator":"cchlebak","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf"},{"relation":"source_file","file_id":"12815","checksum":"81198f63c294890f6d58e8b29782efdc","date_created":"2023-04-07T06:17:11Z","date_updated":"2023-04-07T06:17:11Z","access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","file_size":44201583,"content_type":"application/pdf","creator":"cchlebak"},{"creator":"cchlebak","file_size":84731244,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final.docx","checksum":"0317bf7f457bb585f99d453ffa69eb53","date_created":"2023-04-07T06:18:05Z","date_updated":"2023-04-07T06:18:05Z","file_id":"12816","relation":"source_file"}],"_id":"12809","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"status":"public","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","abstract":[{"lang":"eng","text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:12809","supervisor":[{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["2663 - 337X"]},"author":[{"id":"3A96634C-F248-11E8-B48F-1D18A9856A87","first_name":"Catarina","last_name":"Alcarva","full_name":"Alcarva, Catarina"}],"date_updated":"2023-04-26T12:16:56Z","date_created":"2023-04-06T07:54:09Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"file_date_updated":"2023-04-07T06:18:05Z"},{"pmid":1,"year":"2023","publisher":"Springer Nature","department":[{"_id":"XiFe"}],"publication_status":"published","author":[{"last_name":"Zhao","first_name":"Long","full_name":"Zhao, Long"},{"full_name":"Yang, Yiman","first_name":"Yiman","last_name":"Yang"},{"first_name":"Jinchao","last_name":"Chen","full_name":"Chen, Jinchao"},{"full_name":"Lin, Xuelei","first_name":"Xuelei","last_name":"Lin"},{"last_name":"Zhang","first_name":"Hao","full_name":"Zhang, Hao"},{"first_name":"Hao","last_name":"Wang","full_name":"Wang, Hao"},{"full_name":"Wang, Hongzhe","last_name":"Wang","first_name":"Hongzhe"},{"full_name":"Bie, Xiaomin","first_name":"Xiaomin","last_name":"Bie"},{"full_name":"Jiang, Jiafu","last_name":"Jiang","first_name":"Jiafu"},{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"},{"full_name":"Fu, Xiangdong","last_name":"Fu","first_name":"Xiangdong"},{"full_name":"Zhang, Xiansheng","last_name":"Zhang","first_name":"Xiansheng"},{"last_name":"Du","first_name":"Zhuo","full_name":"Du, Zhuo"},{"full_name":"Xiao, Jun","last_name":"Xiao","first_name":"Jun"}],"volume":24,"date_created":"2023-02-23T09:13:49Z","date_updated":"2023-05-08T10:52:49Z","article_number":"7","extern":"1","external_id":{"pmid":["36639687"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"quality_controlled":"1","doi":"10.1186/s13059-022-02844-2","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1474-760X"]},"month":"01","_id":"12668","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","status":"public","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"citation":{"chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2"},"publication":"Genome Biology","article_type":"original","date_published":"2023-01-13T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"13"},{"oa":1,"main_file_link":[{"url":"https://doi.org/10.1002/chem.202202967","open_access":"1"}],"quality_controlled":"1","doi":"10.1002/chem.202202967","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"year":"2023","publication_status":"published","publisher":"Wiley","author":[{"last_name":"Traxler","first_name":"Michael","full_name":"Traxler, Michael"},{"full_name":"Reischauer, Susanne","first_name":"Susanne","last_name":"Reischauer"},{"full_name":"Vogl, Sarah","first_name":"Sarah","last_name":"Vogl"},{"full_name":"Roeser, Jérôme","first_name":"Jérôme","last_name":"Roeser"},{"last_name":"Rabeah","first_name":"Jabor","full_name":"Rabeah, Jabor"},{"full_name":"Penschke, Christopher","first_name":"Christopher","last_name":"Penschke"},{"full_name":"Saalfrank, Peter","first_name":"Peter","last_name":"Saalfrank"},{"full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X"},{"last_name":"Thomas","first_name":"Arne","full_name":"Thomas, Arne"}],"date_created":"2023-05-08T08:25:34Z","date_updated":"2023-05-15T08:39:24Z","volume":29,"article_number":"e202202967","extern":"1","publication":"Chemistry – A European Journal","citation":{"chicago":"Traxler, Michael, Susanne Reischauer, Sarah Vogl, Jérôme Roeser, Jabor Rabeah, Christopher Penschke, Peter Saalfrank, Bartholomäus Pieber, and Arne Thomas. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal. Wiley, 2023. https://doi.org/10.1002/chem.202202967.","short":"M. Traxler, S. Reischauer, S. Vogl, J. Roeser, J. Rabeah, C. Penschke, P. Saalfrank, B. Pieber, A. Thomas, Chemistry – A European Journal 29 (2023).","mla":"Traxler, Michael, et al. “Programmable Photocatalytic Activity of Multicomponent Covalent Organic Frameworks Used as Metallaphotocatalysts.” Chemistry – A European Journal, vol. 29, no. 4, e202202967, Wiley, 2023, doi:10.1002/chem.202202967.","ieee":"M. Traxler et al., “Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts,” Chemistry – A European Journal, vol. 29, no. 4. Wiley, 2023.","apa":"Traxler, M., Reischauer, S., Vogl, S., Roeser, J., Rabeah, J., Penschke, C., … Thomas, A. (2023). Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. Wiley. https://doi.org/10.1002/chem.202202967","ista":"Traxler M, Reischauer S, Vogl S, Roeser J, Rabeah J, Penschke C, Saalfrank P, Pieber B, Thomas A. 2023. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 29(4), e202202967.","ama":"Traxler M, Reischauer S, Vogl S, et al. Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts. Chemistry – A European Journal. 2023;29(4). doi:10.1002/chem.202202967"},"article_type":"original","date_published":"2023-01-18T00:00:00Z","scopus_import":"1","keyword":["General Chemistry","Catalysis","Organic Chemistry"],"day":"18","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12920","status":"public","title":"Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts","intvolume":" 29","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The multicomponent approach allows to incorporate several functionalities into a single covalent organic framework (COF) and consequently allows the construction of bifunctional materials for cooperative catalysis. The well-defined structure of such multicomponent COFs is furthermore ideally suited for structure-activity relationship studies. We report a series of multicomponent COFs that contain acridine- and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives. The acridine motif is responsible for broad light absorption, while the bipyridine unit enables complexation of nickel catalysts. These features enable the usage of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings. Variation of the node units shows that the catalytic activity correlates to the keto-enamine tautomer isomerism. This allows switching between high charge-carrier mobility and persistent, localized charge-separated species depending on the nodes, a tool to tailor the materials for specific reactions. Moreover, nickel-loaded COFs are recyclable and catalyze cross-couplings even using red light irradiation.","lang":"eng"}],"issue":"4"},{"publication_identifier":{"eissn":["1867-3899"],"issn":["1867-3880"]},"month":"04","doi":"10.1002/cctc.202201583","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1002/cctc.202201583","open_access":"1"}],"quality_controlled":"1","extern":"1","article_number":"e202201583","author":[{"first_name":"Amiera","last_name":"Madani","full_name":"Madani, Amiera"},{"first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"}],"volume":15,"date_created":"2023-05-08T08:25:55Z","date_updated":"2023-05-15T08:35:48Z","year":"2023","publisher":"Wiley","publication_status":"published","article_processing_charge":"No","day":"06","scopus_import":"1","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Catalysis"],"date_published":"2023-04-06T00:00:00Z","citation":{"chicago":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202201583.","short":"A. Madani, B. Pieber, ChemCatChem 15 (2023).","mla":"Madani, Amiera, and Bartholomäus Pieber. “In Situ Reaction Monitoring in Photocatalytic Organic Synthesis.” ChemCatChem, vol. 15, no. 7, e202201583, Wiley, 2023, doi:10.1002/cctc.202201583.","ieee":"A. Madani and B. Pieber, “In situ reaction monitoring in photocatalytic organic synthesis,” ChemCatChem, vol. 15, no. 7. Wiley, 2023.","apa":"Madani, A., & Pieber, B. (2023). In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202201583","ista":"Madani A, Pieber B. 2023. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 15(7), e202201583.","ama":"Madani A, Pieber B. In situ reaction monitoring in photocatalytic organic synthesis. ChemCatChem. 2023;15(7). doi:10.1002/cctc.202201583"},"publication":"ChemCatChem","article_type":"original","issue":"7","abstract":[{"lang":"eng","text":"Visible-light photocatalysis provides numerous useful methodologies for synthetic organic chemistry. However, the mechanisms of these reactions are often not fully understood. Common mechanistic experiments mainly aim to characterize excited state properties of photocatalysts and their interaction with other species. Recently, in situ reaction monitoring using dedicated techniques was shown to be well-suited for the identification of intermediates and to obtain kinetic insights, thereby providing more holistic pictures of the reactions of interest. This minireview surveys these technologies and discusses selected examples where reaction monitoring was used to elucidate the mechanism of photocatalytic reactions."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12921","intvolume":" 15","status":"public","title":"In situ reaction monitoring in photocatalytic organic synthesis"},{"doi":"10.1055/a-1979-5933","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1437-210X"],"issn":["0039-7881"]},"month":"05","author":[{"full_name":"Murakami, Sho","last_name":"Murakami","first_name":"Sho"},{"last_name":"Brudy","first_name":"Cosima","full_name":"Brudy, Cosima"},{"full_name":"Bachmann, Moritz","first_name":"Moritz","last_name":"Bachmann"},{"full_name":"Takemoto, Yoshiji","last_name":"Takemoto","first_name":"Yoshiji"},{"full_name":"Pieber, Bartholomäus","last_name":"Pieber","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726"}],"volume":55,"date_updated":"2023-05-15T08:43:50Z","date_created":"2023-05-08T08:25:08Z","year":"2023","publisher":"Georg Thieme Verlag","publication_status":"published","extern":"1","date_published":"2023-05-01T00:00:00Z","citation":{"ama":"Murakami S, Brudy C, Bachmann M, Takemoto Y, Pieber B. Photocatalytic cleavage of trityl protected thiols and alcohols. Synthesis. 2023;55(09):1367-1374. doi:10.1055/a-1979-5933","ista":"Murakami S, Brudy C, Bachmann M, Takemoto Y, Pieber B. 2023. Photocatalytic cleavage of trityl protected thiols and alcohols. Synthesis. 55(09), 1367–1374.","ieee":"S. Murakami, C. Brudy, M. Bachmann, Y. Takemoto, and B. Pieber, “Photocatalytic cleavage of trityl protected thiols and alcohols,” Synthesis, vol. 55, no. 09. Georg Thieme Verlag, pp. 1367–1374, 2023.","apa":"Murakami, S., Brudy, C., Bachmann, M., Takemoto, Y., & Pieber, B. (2023). Photocatalytic cleavage of trityl protected thiols and alcohols. Synthesis. Georg Thieme Verlag. https://doi.org/10.1055/a-1979-5933","mla":"Murakami, Sho, et al. “Photocatalytic Cleavage of Trityl Protected Thiols and Alcohols.” Synthesis, vol. 55, no. 09, Georg Thieme Verlag, 2023, pp. 1367–74, doi:10.1055/a-1979-5933.","short":"S. Murakami, C. Brudy, M. Bachmann, Y. Takemoto, B. Pieber, Synthesis 55 (2023) 1367–1374.","chicago":"Murakami, Sho, Cosima Brudy, Moritz Bachmann, Yoshiji Takemoto, and Bartholomäus Pieber. “Photocatalytic Cleavage of Trityl Protected Thiols and Alcohols.” Synthesis. Georg Thieme Verlag, 2023. https://doi.org/10.1055/a-1979-5933."},"publication":"Synthesis","page":"1367-1374","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Organic Chemistry","Catalysis"],"oa_version":"None","_id":"12919","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 55","status":"public","title":"Photocatalytic cleavage of trityl protected thiols and alcohols","issue":"09","abstract":[{"lang":"eng","text":"We report the visible light photocatalytic cleavage of trityl thioethers or ethers under pH-neutral conditions. The method results in the formation of the respective symmetrical disulfides and alcohols in moderate to excellent yield. The protocol only requires the addition of a suitable photocatalyst and light rendering it orthogonal to several functionalities, including acid labile protective groups. The same conditions can be used to directly convert trityl-protected thiols into unsymmetrical disulfides or selenosulfides, and to cleave trityl resins in solid phase organic synthesis."}],"type":"journal_article"},{"type":"conference","abstract":[{"lang":"eng","text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis."}],"_id":"13048","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","status":"public","oa_version":"Preprint","article_processing_charge":"No","day":"02","citation":{"ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Orlando, FL, United States, 2023, pp. 1768–1776.","apa":"Lieutier, A., & Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In Proceedings of the 55th Annual ACM Symposium on Theory of Computing (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3564246.3585113","ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: Proceedings of the 55th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2023:1768-1776. doi:10.1145/3564246.3585113","chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In Proceedings of the 55th Annual ACM Symposium on Theory of Computing, 1768–76. Association for Computing Machinery, 2023. https://doi.org/10.1145/3564246.3585113.","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–76, doi:10.1145/3564246.3585113.","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776."},"publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","page":"1768-1776","date_published":"2023-06-02T00:00:00Z","ec_funded":1,"acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073.","year":"2023","publisher":"Association for Computing Machinery","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"},{"full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-05-22T08:02:02Z","date_updated":"2023-05-22T08:15:19Z","publication_identifier":{"isbn":["9781450399135"]},"month":"06","external_id":{"arxiv":["2303.04014"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.04014"}],"oa":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073"}],"quality_controlled":"1","doi":"10.1145/3564246.3585113","conference":{"start_date":"2023-06-20","location":"Orlando, FL, United States","end_date":"2023-06-23","name":"STOC: Symposium on Theory of Computing"},"language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL ."}],"ec_funded":1,"type":"conference","date_updated":"2023-06-01T12:54:45Z","date_created":"2023-05-23T11:36:18Z","oa_version":"Preprint","author":[{"full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste","first_name":"Elena-Alexandra"},{"full_name":"Vladu, Adrian","first_name":"Adrian","last_name":"Vladu"},{"full_name":"Kurtic, Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar","last_name":"Kurtic"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13074"}]},"publication_status":"accepted","title":"CrAM: A Compression-Aware Minimizer","status":"public","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"_id":"13053","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","month":"05","article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2023-05-05","start_date":"2023-05-01","location":"Kigali, Rwanda "},"date_published":"2023-05-01T00:00:00Z","quality_controlled":"1","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication":"11th International Conference on Learning Representations ","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=_eTZBs-yedr"}],"external_id":{"arxiv":["2207.14200"]},"oa":1,"citation":{"ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations .","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d."}},{"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/238"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-31368-4_19","conference":{"name":"PKC: Public-Key Cryptography","location":"Atlanta, GA, United States","start_date":"2023-05-07","end_date":"2023-05-10"},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031313677"]},"month":"05","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2023","acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","volume":13940,"date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:03:37Z","author":[{"first_name":"Charlotte","last_name":"Hoffmann","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","full_name":"Hoffmann, Charlotte"},{"first_name":"Pavel","last_name":"Hubáček","full_name":"Hubáček, Pavel"},{"full_name":"Kamath, Chethan","last_name":"Kamath","first_name":"Chethan"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"page":"530-553","citation":{"apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Pietrzak, K. Z. (2023). Certifying giant nonprimes. In Public-Key Cryptography - PKC 2023 (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-31368-4_19","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in Public-Key Cryptography - PKC 2023, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: Public-Key Cryptography - PKC 2023. Vol 13940. Springer Nature; 2023:530-553. doi:10.1007/978-3-031-31368-4_19","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In Public-Key Cryptography - PKC 2023, 13940:530–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-31368-4_19.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553.","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19."},"publication":"Public-Key Cryptography - PKC 2023","date_published":"2023-05-02T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"02","intvolume":" 13940","status":"public","title":"Certifying giant nonprimes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13143","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality."}]},{"file_date_updated":"2023-06-19T08:29:30Z","ec_funded":1,"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:30:54Z","volume":13993,"month":"04","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308222"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"doi":"10.1007/978-3-031-30823-9_1","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13142","ddc":["000"],"status":"public","title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","intvolume":" 13993","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_LNCS_Chatterjee.pdf","file_size":528455,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13150","checksum":"3d8a8bb24d211bc83360dfc2fd744307","success":1,"date_updated":"2023-06-19T08:29:30Z","date_created":"2023-06-19T08:29:30Z"}],"scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","citation":{"apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_1","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in Tools and Algorithms for the Construction and Analysis of Systems , Paris, France, 2023, vol. 13993, pp. 3–25.","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems . Vol 13993. Springer Nature; 2023:3-25. doi:10.1007/978-3-031-30823-9_1","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In Tools and Algorithms for the Construction and Analysis of Systems , 13993:3–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_1.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” Tools and Algorithms for the Construction and Analysis of Systems , vol. 13993, Springer Nature, 2023, pp. 3–25, doi:10.1007/978-3-031-30823-9_1."},"page":"3-25","date_published":"2023-04-22T00:00:00Z"},{"date_updated":"2023-06-19T08:49:46Z","date_created":"2023-06-18T22:00:47Z","volume":13994,"author":[{"full_name":"Anand, Ashwani","last_name":"Anand","first_name":"Ashwani"},{"last_name":"Mallik","first_name":"Kaushik","orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","full_name":"Mallik, Kaushik"},{"first_name":"Satya Prakash","last_name":"Nayak","full_name":"Nayak, Satya Prakash"},{"last_name":"Schmuck","first_name":"Anne Kathrin","full_name":"Schmuck, Anne Kathrin"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"year":"2023","file_date_updated":"2023-06-19T08:43:21Z","language":[{"iso":"eng"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27"},"doi":"10.1007/978-3-031-30820-8_15","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"04","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"]},"oa_version":"Published Version","file":[{"file_name":"2023_LNCS_Anand.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":521425,"file_id":"13151","relation":"main_file","date_updated":"2023-06-19T08:43:21Z","date_created":"2023-06-19T08:43:21Z","success":1,"checksum":"60dcafc1b4f6f070be43bad3fe877974"}],"title":"Computing adequately permissive assumptions for synthesis","status":"public","ddc":["000"],"intvolume":" 13994","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13141","abstract":[{"text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2023-04-20T00:00:00Z","page":"211-228","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","citation":{"apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228.","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15","chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15."},"day":"20","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"date_published":"2023-04-18T00:00:00Z","citation":{"apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826."},"page":"106","day":"18","has_accepted_license":"1","article_processing_charge":"No","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"Thesis_Pokusaeva.docx","file_size":14507243,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"vpokusae","relation":"source_file","file_id":"12857","checksum":"5f589a9af025f7eeebfd0c186209913e","date_updated":"2023-04-20T09:26:51Z","date_created":"2023-04-20T09:14:38Z"},{"date_created":"2023-04-20T09:14:44Z","date_updated":"2023-04-20T09:14:44Z","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"relation":"main_file","file_id":"12858","file_size":10090711,"content_type":"application/pdf","creator":"vpokusae","file_name":"Thesis_Pokusaeva.pdf","access_level":"open_access"}],"_id":"12826","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","ddc":["570","571"],"status":"public","abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:12826","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["2663 - 337X"]},"author":[{"orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria","full_name":"Pokusaeva, Victoria"}],"date_created":"2023-04-14T14:56:04Z","date_updated":"2023-06-23T09:47:36Z","year":"2023","publication_status":"published","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-04-20T09:26:51Z","ec_funded":1},{"ec_funded":1,"file_date_updated":"2023-01-20T10:02:48Z","volume":85,"date_created":"2022-09-11T22:01:57Z","date_updated":"2023-06-27T12:53:43Z","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F"}],"publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","year":"2023","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/s00453-022-01027-6","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000846967100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12322","date_created":"2023-01-20T10:02:48Z","date_updated":"2023-01-20T10:02:48Z","checksum":"71685ca5121f4c837f40c3f8eb50c915","success":1,"file_name":"2023_Algorithmica_Edelsbrunner.pdf","access_level":"open_access","content_type":"application/pdf","file_size":911017,"creator":"dernst"}],"intvolume":" 85","status":"public","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","ddc":["510"],"_id":"12086","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","page":"277-295","article_type":"original","citation":{"chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6"},"publication":"Algorithmica"},{"month":"01","publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000906214600004"]},"isi":1,"quality_controlled":"1","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces"},{"name":"Gradient flow techniques for quantum Markov semigroups","grant_number":"ESP156_N","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"doi":"10.1007/s00028-022-00859-7","language":[{"iso":"eng"}],"article_number":"9","file_date_updated":"2023-01-20T10:45:06Z","ec_funded":1,"year":"2023","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"author":[{"full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","orcid":"0000-0002-9881-6870"},{"full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","last_name":"Wirth","first_name":"Melchior"}],"date_created":"2023-01-08T23:00:53Z","date_updated":"2023-06-28T11:54:35Z","volume":23,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Evolution Equations","citation":{"ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023)."},"article_type":"original","date_published":"2023-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces."}],"issue":"1","_id":"12104","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","ddc":["510"],"intvolume":" 23","file":[{"date_created":"2023-01-20T10:45:06Z","date_updated":"2023-01-20T10:45:06Z","success":1,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","file_id":"12325","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":422612,"file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","access_level":"open_access"}],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11434","intvolume":" 60","status":"public","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall."}],"citation":{"short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics, vol. 60, Springer Nature, 2023, pp. 427–42, doi:10.1007/s00382-022-06337-7.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics. Springer Nature, 2023. https://doi.org/10.1007/s00382-022-06337-7.","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 2023;60:427-442. doi:10.1007/s00382-022-06337-7","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-022-06337-7","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” Climate Dynamics, vol. 60. Springer Nature, pp. 427–442, 2023.","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442."},"publication":"Climate Dynamics","page":"427-442","article_type":"original","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","year":"2023","department":[{"_id":"CaMu"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"relation":"erratum","url":" https://doi.org/10.1007/s00382-022-06401-2"}]},"author":[{"full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","first_name":"Bidyut B","last_name":"Goswami"}],"volume":60,"date_updated":"2023-06-28T11:49:58Z","date_created":"2022-06-05T22:01:50Z","external_id":{"isi":["000803119400002"]},"quality_controlled":"1","isi":1,"doi":"10.1007/s00382-022-06337-7","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0894"],"issn":["0930-7575"]},"month":"01"},{"page":"349-370","citation":{"short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370."},"publication":"26th International Conference Foundations of Software Science and Computation Structures","date_published":"2023-04-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"21","intvolume":" 13992","ddc":["000"],"status":"public","title":"Quantitative safety and liveness","_id":"12467","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_created":"2023-01-31T07:22:21Z","date_updated":"2023-01-31T07:22:21Z","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"relation":"main_file","file_id":"12468","content_type":"application/pdf","file_size":449027,"creator":"esarac","file_name":"qsl.pdf","access_level":"open_access"},{"relation":"main_file","file_id":"13153","date_updated":"2023-06-19T10:28:09Z","date_created":"2023-06-19T10:28:09Z","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","success":1,"file_name":"2023_LNCS_HenzingerT.pdf","access_level":"open_access","file_size":1048171,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states."}],"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2301.11175"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30829-1_17","conference":{"name":"FOSSACS: Foundations of Software Science and Computation Structures","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"},"publication_identifier":{"isbn":["9783031308284"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"04","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_status":"published","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","year":"2023","volume":13992,"date_updated":"2023-07-14T11:20:27Z","date_created":"2023-01-31T07:23:56Z","author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi"},{"last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"ec_funded":1,"file_date_updated":"2023-06-19T10:28:09Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1145/3591230","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2475-1421"]},"month":"06","year":"2023","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery ","publication_status":"published","author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","first_name":"Nikita"},{"last_name":"Khalanskiy","first_name":"Dmitry","full_name":"Khalanskiy, Dmitry"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"volume":7,"date_created":"2023-07-02T22:00:43Z","date_updated":"2023-07-17T08:43:19Z","article_number":"116","file_date_updated":"2023-07-03T13:09:39Z","citation":{"mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages, vol. 7, 116, Association for Computing Machinery , 2023, doi:10.1145/3591230.","short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery , 2023. https://doi.org/10.1145/3591230.","ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230"},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","date_published":"2023-06-06T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"06","_id":"13179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","title":"CQS: A formally-verified framework for fair and abortable synchronization","ddc":["000"],"status":"public","file":[{"file_size":1266773,"content_type":"application/pdf","creator":"alisjak","access_level":"open_access","file_name":"2023_ACMProgram.Lang._Koval.pdf","checksum":"5dba6e73f0ed79adbdae14d165bc2f68","success":1,"date_updated":"2023-07-03T13:09:39Z","date_created":"2023-07-03T13:09:39Z","relation":"main_file","file_id":"13187"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives."}]},{"scopus_import":"1","day":"26","article_processing_charge":"No","publication":"Involve","citation":{"apa":"Browning, T. D., Lyczak, J., & Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. Involve. Mathematical Sciences Publishers. https://doi.org/10.2140/involve.2023.16.331","ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” Involve, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342.","ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. Involve. 2023;16(2):331-342. doi:10.2140/involve.2023.16.331","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/involve.2023.16.331.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:10.2140/involve.2023.16.331."},"article_type":"original","page":"331-342","date_published":"2023-05-26T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface"}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13180","title":"Local solubility for a family of quadrics over a split quadric surface","status":"public","intvolume":" 16","oa_version":"Preprint","month":"05","publication_identifier":{"issn":["1944-4176"],"eissn":["1944-4184"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.06881"}],"oa":1,"external_id":{"arxiv":["2203.06881"]},"quality_controlled":"1","doi":"10.2140/involve.2023.16.331","language":[{"iso":"eng"}],"year":"2023","publication_status":"published","publisher":"Mathematical Sciences Publishers","department":[{"_id":"TiBr"}],"author":[{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D","full_name":"Browning, Timothy D"},{"last_name":"Lyczak","first_name":"Julian","id":"3572849A-F248-11E8-B48F-1D18A9856A87","full_name":"Lyczak, Julian"},{"first_name":"Roman","last_name":"Sarapin","full_name":"Sarapin, Roman"}],"date_updated":"2023-07-17T08:39:19Z","date_created":"2023-07-02T22:00:43Z","volume":16},{"month":"07","day":"01","article_processing_charge":"No","has_accepted_license":"1","quality_controlled":"1","page":"42-42","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.","apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (n.d.). Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 42–42.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :42-42.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC, n.d.","mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 42–42."},"language":[{"iso":"eng"}],"conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","end_date":"2023-06-15","location":"Maribor, Slovenia","start_date":"2023-06-12"},"date_published":"2023-07-01T00:00:00Z","type":"conference_abstract","file_date_updated":"2023-07-18T09:28:30Z","status":"public","publication_status":"accepted","ddc":["000"],"title":"Cryo-EM software packages: A sys-admins point of view","department":[{"_id":"ScienComp"}],"publisher":"EuroCC","_id":"13162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","date_created":"2023-06-23T11:03:18Z","date_updated":"2023-07-18T09:32:16Z","file":[{"file_id":"13250","relation":"main_file","success":1,"checksum":"0ab6173cd5c5634ed773cd37ff012681","date_updated":"2023-07-18T09:28:30Z","date_created":"2023-07-18T09:28:30Z","access_level":"open_access","file_name":"2023_ASHPC_Elefante.pdf","creator":"dernst","content_type":"application/pdf","file_size":380354}],"oa_version":"Submitted Version","author":[{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","last_name":"Stadlbauer","first_name":"Stephan","full_name":"Stadlbauer, Stephan"},{"id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Alexander","first_name":"Michael F","full_name":"Alexander, Michael F"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"}]},{"citation":{"apa":"Schlögl, A., Elefante, S., & Hodirnau, V.-V. (n.d.). Running Windows-applications on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting 2023 (pp. 59–59). Maribor, Slovenia: EuroCC.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting 2023, Maribor, Slovenia, pp. 59–59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023. EuroCC; :59-59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian HPC Meeting 2023, 59–59. EuroCC, n.d.","short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, n.d., pp. 59–59.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC, pp. 59–59."},"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","page":"59-59","date_published":"2023-07-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13161","ddc":["000"],"status":"public","title":"Running Windows-applications on a Linux HPC cluster using WINE","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"13249","date_created":"2023-07-18T09:18:55Z","date_updated":"2023-07-18T09:18:55Z","checksum":"ec8e4295d54171032cdd1b01423eb4a6","success":1,"file_name":"2023_ASHPC_Schloegl.pdf","access_level":"open_access","content_type":"application/pdf","file_size":316959,"creator":"dernst"}],"type":"conference_abstract","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","conference":{"start_date":"2023-06-13","location":"Maribor, Slovenia","end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting"},"language":[{"iso":"eng"}],"month":"07","acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","year":"2023","department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publisher":"EuroCC","publication_status":"inpress","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","last_name":"Elefante","full_name":"Elefante, Stefano"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"}],"date_created":"2023-06-23T11:01:23Z","date_updated":"2023-07-18T09:30:54Z","file_date_updated":"2023-07-18T09:18:55Z"},{"keyword":["General Materials Science","Physical and Theoretical Chemistry"],"day":"05","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"original","page":"6309-6314","publication":"The Journal of Physical Chemistry Letters","citation":{"ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158."},"date_published":"2023-07-05T00:00:00Z","type":"journal_article","abstract":[{"text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.","lang":"eng"}],"issue":"27","ddc":["530"],"title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","status":"public","intvolume":" 14","_id":"13251","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":2121252,"creator":"dernst","file_name":"2023_JourPhysChemistry_Wei.pdf","access_level":"open_access","date_created":"2023-07-19T06:55:39Z","date_updated":"2023-07-19T06:55:39Z","checksum":"c0c040063f06a51b9c463adc504f1a23","success":1,"relation":"main_file","file_id":"13253"}],"oa_version":"Published Version","month":"07","publication_identifier":{"eissn":["1948-7185"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001022811500001"],"arxiv":["2304.14198"]},"language":[{"iso":"eng"}],"doi":"10.1021/acs.jpclett.3c01158","file_date_updated":"2023-07-19T06:55:39Z","ec_funded":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"year":"2023","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","date_updated":"2023-07-19T06:59:19Z","date_created":"2023-07-18T11:13:17Z","volume":14,"author":[{"orcid":"0000-0001-8913-9719","id":"0c5ff007-2600-11ee-b896-98bd8d663294","last_name":"Wei","first_name":"Yujing","full_name":"Wei, Yujing"},{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"first_name":"Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"last_name":"Zhumekenov","first_name":"Ayan A.","full_name":"Zhumekenov, Ayan A."},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek"}]},{"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.03447"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2023-07-10","location":"Paderborn, Germany","end_date":"2023-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2023.129","month":"07","publication_identifier":{"isbn":["9783959772785"],"eissn":["1868-8969"]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","date_updated":"2023-07-31T08:38:38Z","date_created":"2023-07-24T15:11:41Z","volume":261,"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Kebis, Pavol","last_name":"Kebis","first_name":"Pavol"},{"full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac"}],"file_date_updated":"2023-07-24T15:11:05Z","ec_funded":1,"page":"129:1--129:20","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129"},"date_published":"2023-07-05T00:00:00Z","day":"05","article_processing_charge":"Yes","has_accepted_license":"1","title":"Regular methods for operator precedence languages","ddc":["000"],"status":"public","intvolume":" 261","_id":"13292","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"13293","relation":"main_file","success":1,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2","date_updated":"2023-07-24T15:11:05Z","date_created":"2023-07-24T15:11:05Z","access_level":"open_access","file_name":"icalp23.pdf","creator":"esarac","content_type":"application/pdf","file_size":859379}],"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}]},{"type":"journal_article","abstract":[{"text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results.","lang":"eng"}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13277","title":"Stochastic representation of the quantum quartic oscillator","status":"public","ddc":["530"],"intvolume":" 6","oa_version":"Published Version","file":[{"file_name":"2023_SciPostPhysCore_Tucci.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":523236,"file_id":"13329","relation":"main_file","date_updated":"2023-07-31T09:02:27Z","date_created":"2023-07-31T09:02:27Z","success":1,"checksum":"b472bc82108747eda5d52adf9e2ac7f3"}],"keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"day":"14","has_accepted_license":"1","article_processing_charge":"No","publication":"SciPost Physics Core","citation":{"mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029.","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029"},"article_type":"original","date_published":"2023-04-14T00:00:00Z","article_number":"029","file_date_updated":"2023-07-31T09:02:27Z","ec_funded":1,"acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","year":"2023","publication_status":"published","publisher":"SciPost Foundation","department":[{"_id":"MaSe"}],"author":[{"full_name":"Tucci, Gennaro","last_name":"Tucci","first_name":"Gennaro"},{"orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87","last_name":"De Nicola","first_name":"Stefano","full_name":"De Nicola, Stefano"},{"full_name":"Wald, Sascha","last_name":"Wald","first_name":"Sascha"},{"first_name":"Andrea","last_name":"Gambassi","full_name":"Gambassi, Andrea"}],"date_updated":"2023-07-31T09:03:28Z","date_created":"2023-07-24T10:47:46Z","volume":6,"month":"04","publication_identifier":{"issn":["2666-9366"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2211.01923"]},"quality_controlled":"1","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.21468/scipostphyscore.6.2.029","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["2949-804X"]},"month":"04","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2202.04603"]},"language":[{"iso":"eng"}],"doi":"10.21468/scipostphyscodeb.12","article_number":"12","ec_funded":1,"file_date_updated":"2023-07-31T09:09:23Z","publisher":"SciPost Foundation","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2023","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","date_updated":"2023-07-31T09:16:02Z","date_created":"2023-07-24T10:47:15Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"13275"}]},"author":[{"first_name":"Lukas","last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas"},{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"}],"article_processing_charge":"No","has_accepted_license":"1","day":"19","article_type":"original","citation":{"short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12.","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12."},"publication":"SciPost Physics Codebases","date_published":"2023-04-19T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","status":"public","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13276","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"13330","checksum":"f583a70fe915d2208c803f5afb426daa","success":1,"date_created":"2023-07-31T09:09:23Z","date_updated":"2023-07-31T09:09:23Z","access_level":"open_access","file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","file_size":551418,"content_type":"application/pdf","creator":"dernst"}]},{"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"oa":1,"citation":{"ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0.","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0"}],"date_published":"2023-04-19T00:00:00Z","doi":"10.21468/scipostphyscodeb.12-r1.0","article_processing_charge":"No","month":"04","day":"19","publisher":"SciPost Foundation","department":[{"_id":"MiLe"}],"title":"Codebase release 1.0 for FermiFCI","status":"public","ddc":["530"],"_id":"13275","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2023-07-24T10:46:23Z","date_updated":"2023-07-31T09:16:02Z","related_material":{"record":[{"id":"13276","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Rammelmüller","first_name":"Lukas","full_name":"Rammelmüller, Lukas"},{"last_name":"Huber","first_name":"David","full_name":"Huber, David"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"type":"research_data_reference","ec_funded":1,"abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}]},{"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_status":"published","year":"2023","date_created":"2023-07-23T22:01:12Z","date_updated":"2023-07-31T10:54:32Z","author":[{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov"},{"full_name":"Hashemi, Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","first_name":"Diba","last_name":"Hashemi"},{"id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"file_date_updated":"2023-07-31T10:53:08Z","quality_controlled":"1","external_id":{"arxiv":["2304.09331"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3558481.3591082","conference":{"end_date":"2023-06-19","start_date":"2023-06-17","location":"Orlando, FL, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"publication_identifier":{"isbn":["9781450395458"]},"month":"06","ddc":["000"],"status":"public","title":"Provably-efficient and internally-deterministic parallel Union-Find","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13262","file":[{"file_name":"2023_SPAA_Fedorov.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2087937,"creator":"dernst","relation":"main_file","file_id":"13334","date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-31T10:53:08Z","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1}],"oa_version":"Published Version","type":"conference","abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"page":"261-271","citation":{"ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271."},"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","date_published":"2023-06-17T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"17"},{"publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publication_status":"published","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","year":"2023","volume":16,"date_created":"2022-07-03T22:01:33Z","date_updated":"2023-08-01T12:25:44Z","author":[{"last_name":"De Jode","first_name":"Aurélien","full_name":"De Jode, Aurélien"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"}],"file_date_updated":"2023-02-27T07:10:17Z","isi":1,"quality_controlled":"1","external_id":{"isi":["000815663700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/eva.13428","publication_identifier":{"eissn":["1752-4571"]},"month":"02","intvolume":" 16","ddc":["576"],"title":"Ten years of demographic modelling of divergence and speciation in the sea","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11479","file":[{"file_name":"2023_EvolutionaryApplications_DeJode.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2269822,"creator":"dernst","relation":"main_file","file_id":"12685","date_updated":"2023-02-27T07:10:17Z","date_created":"2023-02-27T07:10:17Z","checksum":"d4d6fa9ddf36643af994a6a757919afb","success":1}],"oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"page":"542-559","article_type":"original","citation":{"chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428"},"publication":"Evolutionary Applications","date_published":"2023-02-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"date_updated":"2023-08-01T12:31:40Z","date_created":"2023-01-22T23:00:55Z","volume":13,"author":[{"full_name":"Gómez, Arturo","last_name":"Gómez","first_name":"Arturo"},{"id":"58abbde8-f455-11eb-a497-98c8fd71b905","first_name":"Goncalo","last_name":"Oliveira","full_name":"Oliveira, Goncalo"}],"publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","file_date_updated":"2023-01-23T07:53:23Z","article_number":"468","language":[{"iso":"eng"}],"doi":"10.1038/s41598-022-19827-9","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001003345000051"]},"month":"01","publication_identifier":{"eissn":["2045-2322"]},"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2167792,"creator":"dernst","file_name":"2023_ScientificReports_Gomez.pdf","access_level":"open_access","date_updated":"2023-01-23T07:53:23Z","date_created":"2023-01-23T07:53:23Z","checksum":"a8b83739f4a951e83e0b2a778f03b327","success":1,"relation":"main_file","file_id":"12336"}],"status":"public","title":"New approaches to epidemic modeling on networks","ddc":["510"],"intvolume":" 13","_id":"12329","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection."}],"type":"journal_article","date_published":"2023-01-10T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9."},"day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Oxford Academic","acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","year":"2023","date_updated":"2023-08-01T12:23:55Z","date_created":"2021-01-22T09:31:09Z","volume":2023,"author":[{"full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425","last_name":"Wilsch","first_name":"Florian Alexander"}],"month":"04","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"external_id":{"isi":["000773116000001"],"arxiv":["1901.08503"]},"language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnac048","type":"journal_article","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"issue":"8","status":"public","title":"Integral points of bounded height on a log Fano threefold","intvolume":" 2023","_id":"9034","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","day":"01","article_processing_charge":"No","article_type":"original","page":"6780-6808","publication":"International Mathematics Research Notices","citation":{"mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023."},"date_published":"2023-04-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management."}],"type":"journal_article","file":[{"file_size":4866332,"content_type":"application/pdf","creator":"dernst","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","access_level":"open_access","date_updated":"2023-04-17T07:49:09Z","date_created":"2023-04-17T07:49:09Z","checksum":"cd52292963acce1111634d9fac08c699","success":1,"relation":"main_file","file_id":"12843"}],"oa_version":"Published Version","_id":"12469","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","ddc":["570"],"status":"public","intvolume":" 14","day":"16","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-03-16T00:00:00Z","publication":"Frontiers in Microbiology","citation":{"mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023."},"article_type":"original","file_date_updated":"2023-04-17T07:49:09Z","article_number":"1119002","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias","full_name":"Fürst, Matthias"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"last_name":"Jurvansuu","first_name":"Jaana","full_name":"Jurvansuu, Jaana"},{"full_name":"Oh, Jinook","last_name":"Oh","first_name":"Jinook","orcid":"0000-0001-7425-2372","id":"403169A4-080F-11EA-9993-BF3F3DDC885E"},{"full_name":"Tolonen, Lassi","first_name":"Lassi","last_name":"Tolonen"},{"full_name":"Eder, Thomas","first_name":"Thomas","last_name":"Eder"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"date_updated":"2023-08-01T12:39:58Z","date_created":"2023-01-31T08:13:40Z","volume":14,"acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","year":"2023","pmid":1,"publication_status":"published","publisher":"Frontiers","department":[{"_id":"SyCr"}],"month":"03","publication_identifier":{"eissn":["1664-302X"]},"doi":"10.3389/fmicb.2023.1119002","language":[{"iso":"eng"}],"external_id":{"pmid":["PPR559293 "],"isi":["000961542100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FWF","name":"Viral pathogens and social immunity in ants","grant_number":"M02076","_id":"25DF61D8-B435-11E9-9278-68D0E5697425"}]},{"ec_funded":1,"file_date_updated":"2023-02-02T11:01:10Z","volume":69,"date_updated":"2023-08-01T12:47:32Z","date_created":"2023-01-16T10:04:06Z","author":[{"last_name":"Boissonnat","first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel"},{"last_name":"Dyer","first_name":"Ramsay","full_name":"Dyer, Ramsay"},{"full_name":"Ghosh, Arijit","last_name":"Ghosh","first_name":"Arijit"},{"last_name":"Wintraecken","first_name":"Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs"}],"publisher":"Springer Nature","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","year":"2023","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/s00454-022-00431-7","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000862193600001"]},"abstract":[{"lang":"eng","text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","file_size":582850,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12488","checksum":"46352e0ee71e460848f88685ca852681","success":1,"date_updated":"2023-02-02T11:01:10Z","date_created":"2023-02-02T11:01:10Z"}],"intvolume":" 69","title":"Local criteria for triangulating general manifolds","ddc":["510"],"status":"public","_id":"12287","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"scopus_import":"1","date_published":"2023-01-01T00:00:00Z","page":"156-191","article_type":"original","citation":{"ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7."},"publication":"Discrete & Computational Geometry"},{"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","year":"2023","date_created":"2023-01-12T12:10:18Z","date_updated":"2023-08-01T12:50:48Z","volume":5,"author":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"month":"01","publication_identifier":{"eissn":["2522-5820"]},"isi":1,"quality_controlled":"1","external_id":{"isi":["000890148700002"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42254-022-00539-y","type":"journal_article","abstract":[{"text":"It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective.","lang":"eng"}],"status":"public","title":"Directed percolation and the transition to turbulence","intvolume":" 5","_id":"12165","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","keyword":["General Physics and Astronomy"],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"62-72","publication":"Nature Reviews Physics","citation":{"ama":"Hof B. Directed percolation and the transition to turbulence. Nature Reviews Physics. 2023;5:62-72. doi:10.1038/s42254-022-00539-y","ista":"Hof B. 2023. Directed percolation and the transition to turbulence. Nature Reviews Physics. 5, 62–72.","ieee":"B. Hof, “Directed percolation and the transition to turbulence,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 62–72, 2023.","apa":"Hof, B. (2023). Directed percolation and the transition to turbulence. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-022-00539-y","mla":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 62–72, doi:10.1038/s42254-022-00539-y.","short":"B. Hof, Nature Reviews Physics 5 (2023) 62–72.","chicago":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-022-00539-y."},"date_published":"2023-01-01T00:00:00Z"},{"publication_identifier":{"issn":["0300-5127"],"eissn":["1470-8752"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1042/bst20220221","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000926043100001"]},"file_date_updated":"2023-03-16T07:58:16Z","volume":51,"date_updated":"2023-08-01T12:55:32Z","date_created":"2023-01-27T10:08:19Z","author":[{"first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"first_name":"Manjunath","last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","full_name":"Javoor, Manjunath"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"department":[{"_id":"FlSc"}],"publisher":"Portland Press","publication_status":"published","year":"2023","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["Biochemistry"],"scopus_import":"1","date_published":"2023-02-01T00:00:00Z","page":"87-99","article_type":"original","citation":{"chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221"},"publication":"Biochemical Society Transactions","issue":"1","abstract":[{"lang":"eng","text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","content_type":"application/pdf","file_size":10045006,"creator":"dernst","relation":"main_file","file_id":"12728","checksum":"4e7069845e3dad22bb44fb71ec624c60","success":1,"date_updated":"2023-03-16T07:58:16Z","date_created":"2023-03-16T07:58:16Z"}],"oa_version":"Published Version","intvolume":" 51","status":"public","ddc":["570"],"title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","_id":"12421","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"abstract":[{"lang":"eng","text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion."}],"type":"journal_article","file":[{"success":1,"checksum":"9224f987caefe5dd85a70814d3cce65c","date_updated":"2023-02-02T12:34:54Z","date_created":"2023-02-02T12:34:54Z","file_id":"12489","relation":"main_file","creator":"dernst","file_size":1931647,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_JourFluidMechanics_Marensi.pdf"}],"oa_version":"Published Version","ddc":["530"],"title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","status":"public","intvolume":" 954","_id":"12105","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"10","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2023-01-10T00:00:00Z","article_type":"original","publication":"Journal of Fluid Mechanics","citation":{"ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023).","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001."},"file_date_updated":"2023-02-02T12:34:54Z","article_number":"A10","date_created":"2023-01-08T23:00:53Z","date_updated":"2023-08-01T12:53:23Z","volume":954,"author":[{"id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","first_name":"Elena","full_name":"Marensi, Elena"},{"full_name":"Yalniz, Gökhan","last_name":"Yalniz","first_name":"Gökhan","orcid":"0000-0002-8490-9312","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","first_name":"Nazmi B","last_name":"Budanur","full_name":"Budanur, Nazmi B"}],"publication_status":"published","publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"year":"2023","acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","month":"01","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2022.1001","isi":1,"quality_controlled":"1","project":[{"grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2101.07516"],"isi":["000903336600001"]}},{"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","volume":77,"date_updated":"2023-08-01T12:58:30Z","date_created":"2023-02-05T23:00:59Z","author":[{"full_name":"Bolnick, Daniel I.","last_name":"Bolnick","first_name":"Daniel I."},{"first_name":"Amanda K.","last_name":"Hund","full_name":"Hund, Amanda K."},{"last_name":"Nosil","first_name":"Patrik","full_name":"Nosil, Patrik"},{"last_name":"Peng","first_name":"Foen","full_name":"Peng, Foen"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"first_name":"Swapna","last_name":"Subramanian","full_name":"Subramanian, Swapna"},{"first_name":"Jochen B.W.","last_name":"Wolf","full_name":"Wolf, Jochen B.W."},{"first_name":"Roman","last_name":"Yukilevich","full_name":"Yukilevich, Roman"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"external_id":{"pmid":["36622661"],"isi":["001021686300024"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/evolut/qpac004","publication_identifier":{"eissn":["1558-5646"]},"month":"01","intvolume":" 77","status":"public","title":"A multivariate view of the speciation continuum","_id":"12514","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model."}],"page":"318-328","article_type":"original","citation":{"chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004.","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004"},"publication":"Evolution: International journal of organic evolution","date_published":"2023-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"month":"02","publication_identifier":{"eisbn":["9798350346091"],"eissn":["2375-9259"]},"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000971492200145"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2022-12-01","start_date":"2022-11-28","location":"Orlando, FL, United States","name":"ICDMW: Conference on Data Mining Workshops"},"doi":"10.1109/icdmw58026.2022.00093","article_number":"00093","file_date_updated":"2023-02-14T07:58:26Z","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Institute of Electrical and Electronics Engineers","year":"2023","date_updated":"2023-08-01T13:15:48Z","date_created":"2023-02-14T07:56:21Z","author":[{"full_name":"Forghani, Mohammad","first_name":"Mohammad","last_name":"Forghani"},{"full_name":"Claramunt, Christophe","last_name":"Claramunt","first_name":"Christophe"},{"last_name":"Karimipour","first_name":"Farid","orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","full_name":"Karimipour, Farid"},{"last_name":"Heiler","first_name":"Georg","full_name":"Heiler, Georg"}],"day":"08","has_accepted_license":"1","article_processing_charge":"No","publication":"2022 IEEE International Conference on Data Mining Workshops","citation":{"chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093"},"date_published":"2023-02-08T00:00:00Z","type":"conference","abstract":[{"text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts.","lang":"eng"}],"ddc":["600"],"title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12548","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"12549","checksum":"c253bee25e6dfe484f96662daa119cb6","success":1,"date_updated":"2023-02-14T07:58:26Z","date_created":"2023-02-14T07:58:26Z","access_level":"open_access","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","file_size":1183339,"content_type":"application/pdf","creator":"fkarimip"}]},{"issue":"1","abstract":[{"text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12563","intvolume":" 52","title":"Topology and adjunction in promise constraint satisfaction","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["General Mathematics","General Computer Science"],"date_published":"2023-01-01T00:00:00Z","citation":{"short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223.","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79."},"publication":"SIAM Journal on Computing","page":"38-79","article_type":"original","ec_funded":1,"author":[{"first_name":"Andrei","last_name":"Krokhin","full_name":"Krokhin, Andrei"},{"full_name":"Opršal, Jakub","orcid":"0000-0003-1245-3456","id":"ec596741-c539-11ec-b829-c79322a91242","last_name":"Opršal","first_name":"Jakub"},{"full_name":"Wrochna, Marcin","last_name":"Wrochna","first_name":"Marcin"},{"full_name":"Živný, Stanislav","first_name":"Stanislav","last_name":"Živný"}],"volume":52,"date_updated":"2023-08-01T13:11:30Z","date_created":"2023-02-16T07:03:52Z","year":"2023","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","department":[{"_id":"UlWa"}],"publisher":"Society for Industrial & Applied Mathematics","publication_status":"published","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"01","doi":"10.1137/20m1378223","language":[{"iso":"eng"}],"external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2003.11351","open_access":"1"}],"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"isi":1,"quality_controlled":"1"},{"oa_version":"Preprint","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","status":"public","intvolume":" 107","_id":"12545","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front."}],"issue":"1","type":"journal_article","date_published":"2023-01-24T00:00:00Z","article_type":"original","publication":"Physical Review E","citation":{"ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023)."},"day":"24","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-08-01T13:09:45Z","date_created":"2023-02-12T23:00:59Z","volume":107,"author":[{"full_name":"Rojas Vega, Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","last_name":"Rojas Vega","first_name":"Mauricio Nicolas"},{"first_name":"Pablo","last_name":"De Castro","full_name":"De Castro, Pablo"},{"full_name":"Soto, Rodrigo","first_name":"Rodrigo","last_name":"Soto"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GradSch"}],"acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","year":"2023","article_number":"014608","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.107.014608","isi":1,"quality_controlled":"1","external_id":{"arxiv":["2301.01856"],"isi":["000963909800006"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01856","open_access":"1"}],"oa":1,"month":"01","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]}},{"abstract":[{"text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12427","title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","status":"public","intvolume":" 151","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","publication":"Proceedings of the American Mathematical Society","citation":{"ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239","ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914.","short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914.","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239.","chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239."},"article_type":"original","page":"907-914","author":[{"last_name":"Balestrieri","first_name":"Francesca","id":"3ACCD756-F248-11E8-B48F-1D18A9856A87","full_name":"Balestrieri, Francesca"}],"date_updated":"2023-08-01T13:03:32Z","date_created":"2023-01-29T23:00:58Z","volume":151,"year":"2023","publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"American Mathematical Society","month":"01","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"doi":"10.1090/proc/15239","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03013498/"}],"oa":1,"external_id":{"isi":["000898440000001"]},"quality_controlled":"1","isi":1},{"date_updated":"2023-08-01T13:10:27Z","date_created":"2023-02-12T23:00:58Z","volume":111,"author":[{"id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","orcid":"0000-0002-5615-5277","first_name":"Ana","last_name":"Villalba Requena","full_name":"Villalba Requena, Ana"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}],"year":"2023","language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2023.01.006","isi":1,"quality_controlled":"1","external_id":{"isi":["000994473300001"]},"month":"02","publication_identifier":{"eissn":["1097-4199"]},"oa_version":"None","status":"public","title":"Going back in time with TEMPO","intvolume":" 111","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12542","abstract":[{"text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2023-02-01T00:00:00Z","article_type":"letter_note","page":"291-293","publication":"Neuron","citation":{"short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293.","mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006.","chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006.","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006","apa":"Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006","ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023.","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"type":"journal_article","abstract":[{"text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations.","lang":"eng"}],"issue":"3","status":"public","title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","ddc":["570"],"intvolume":" 24","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12567","file":[{"file_name":"2023_IJMS_Mrestani.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2823025,"file_id":"12569","relation":"main_file","date_created":"2023-02-20T07:09:27Z","date_updated":"2023-02-20T07:09:27Z","success":1,"checksum":"69a35dcd3e0249f902ab881b06ee2e58"}],"oa_version":"Published Version","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128."},"date_published":"2023-01-21T00:00:00Z","article_number":"2128","file_date_updated":"2023-02-20T07:09:27Z","publication_status":"published","publisher":"MDPI","department":[{"_id":"PeJo"}],"acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","year":"2023","date_created":"2023-02-19T23:00:56Z","date_updated":"2023-08-01T13:16:36Z","volume":24,"author":[{"last_name":"Mrestani","first_name":"Achmed","full_name":"Mrestani, Achmed"},{"first_name":"Katharina","last_name":"Lichter","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","full_name":"Lichter, Katharina"},{"first_name":"Anna Leena","last_name":"Sirén","full_name":"Sirén, Anna Leena"},{"full_name":"Heckmann, Manfred","first_name":"Manfred","last_name":"Heckmann"},{"first_name":"Mila M.","last_name":"Paul","full_name":"Paul, Mila M."},{"full_name":"Pauli, Martin","first_name":"Martin","last_name":"Pauli"}],"month":"01","publication_identifier":{"eissn":["1422-0067"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000930324700001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/ijms24032128"},{"type":"journal_article","issue":"2","abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12566","intvolume":" 948","status":"public","title":"Wait-free approximate agreement on graphs","ddc":["000"],"file":[{"relation":"main_file","file_id":"12570","date_updated":"2023-02-20T07:30:20Z","date_created":"2023-02-20T07:30:20Z","checksum":"b27c5290f2f1500c403494364ee39c9f","success":1,"file_name":"2023_TheoreticalCompScience_Alistarh.pdf","access_level":"open_access","content_type":"application/pdf","file_size":602333,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"28","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733","ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023."},"publication":"Theoretical Computer Science","article_type":"original","date_published":"2023-02-28T00:00:00Z","article_number":"113733","ec_funded":1,"file_date_updated":"2023-02-20T07:30:20Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","year":"2023","department":[{"_id":"DaAl"}],"publisher":"Elsevier","publication_status":"published","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Ellen","first_name":"Faith","full_name":"Ellen, Faith"},{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel"}],"volume":948,"date_updated":"2023-08-01T13:17:20Z","date_created":"2023-02-19T23:00:55Z","publication_identifier":{"issn":["0304-3975"]},"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000934262700001"]},"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605","call_identifier":"H2020","name":"Coordination in constrained and natural distributed systems"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.tcs.2023.113733","language":[{"iso":"eng"}]},{"file_date_updated":"2023-02-27T09:23:02Z","year":"2023","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","department":[{"_id":"BjHo"}],"publisher":"Annual Reviews","publication_status":"published","author":[{"last_name":"Dubief","first_name":"Yves","full_name":"Dubief, Yves"},{"first_name":"Vincent E.","last_name":"Terrapon","full_name":"Terrapon, Vincent E."},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"volume":55,"date_updated":"2023-08-01T13:19:47Z","date_created":"2023-02-26T23:01:01Z","publication_identifier":{"eissn":["1545-4479"],"issn":["0066-4189"]},"month":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000915418100026"]},"isi":1,"quality_controlled":"1","doi":"10.1146/annurev-fluid-032822-025933","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12681","intvolume":" 55","title":"Elasto-inertial turbulence","status":"public","ddc":["530"],"file":[{"creator":"dernst","content_type":"application/pdf","file_size":4036706,"file_name":"2023_AnnReviewFluidMech_Dubief.pdf","access_level":"open_access","date_updated":"2023-02-27T09:23:02Z","date_created":"2023-02-27T09:23:02Z","success":1,"checksum":"2666aa3af2a25252d35eb8681d3edff7","file_id":"12690","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"19","citation":{"chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.","short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","apa":"Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933"},"publication":"Annual Review of Fluid Mechanics","page":"675-705","article_type":"original","date_published":"2023-01-19T00:00:00Z"},{"type":"journal_article","abstract":[{"text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.","lang":"eng"}],"status":"public","ddc":["530"],"title":"Transition to turbulence in pipe flow","intvolume":" 55","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12682","file":[{"relation":"main_file","file_id":"12691","date_updated":"2023-02-27T09:35:52Z","date_created":"2023-02-27T09:35:52Z","checksum":"f99ef30f76cabc9e5e1946b380c16db4","success":1,"file_name":"2023_AnnReviewFluidMech_Avila.pdf","access_level":"open_access","file_size":4769537,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","day":"19","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"575-602","publication":"Annual Review of Fluid Mechanics","citation":{"ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","apa":"Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957."},"date_published":"2023-01-19T00:00:00Z","file_date_updated":"2023-02-27T09:35:52Z","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Annual Reviews","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.).","year":"2023","date_created":"2023-02-26T23:01:01Z","date_updated":"2023-08-01T13:20:30Z","volume":55,"author":[{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"},{"full_name":"Barkley, Dwight","first_name":"Dwight","last_name":"Barkley"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"month":"01","publication_identifier":{"issn":["0066-4189"]},"quality_controlled":"1","isi":1,"project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000915418100023"]},"language":[{"iso":"eng"}],"doi":"10.1146/annurev-fluid-120720-025957"},{"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"month":"02","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2204.10059"],"isi":["000940388100001"]},"language":[{"iso":"eng"}],"doi":"10.1039/d2sm01562e","ec_funded":1,"file_date_updated":"2023-03-07T09:19:41Z","publisher":"Royal Society of Chemistry","department":[{"_id":"AnSa"}],"publication_status":"published","year":"2023","acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","volume":19,"date_updated":"2023-08-01T13:28:39Z","date_created":"2023-03-05T23:01:06Z","author":[{"last_name":"Araújo","first_name":"Nuno A.M.","full_name":"Araújo, Nuno A.M."},{"last_name":"Janssen","first_name":"Liesbeth M.C.","full_name":"Janssen, Liesbeth M.C."},{"full_name":"Barois, Thomas","last_name":"Barois","first_name":"Thomas"},{"full_name":"Boffetta, Guido","last_name":"Boffetta","first_name":"Guido"},{"last_name":"Cohen","first_name":"Itai","full_name":"Cohen, Itai"},{"full_name":"Corbetta, Alessandro","last_name":"Corbetta","first_name":"Alessandro"},{"full_name":"Dauchot, Olivier","first_name":"Olivier","last_name":"Dauchot"},{"full_name":"Dijkstra, Marjolein","last_name":"Dijkstra","first_name":"Marjolein"},{"full_name":"Durham, William M.","last_name":"Durham","first_name":"William M."},{"full_name":"Dussutour, Audrey","first_name":"Audrey","last_name":"Dussutour"},{"full_name":"Garnier, Simon","last_name":"Garnier","first_name":"Simon"},{"last_name":"Gelderblom","first_name":"Hanneke","full_name":"Gelderblom, Hanneke"},{"full_name":"Golestanian, Ramin","first_name":"Ramin","last_name":"Golestanian"},{"first_name":"Lucio","last_name":"Isa","full_name":"Isa, Lucio"},{"full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H.","last_name":"Koenderink"},{"full_name":"Löwen, Hartmut","first_name":"Hartmut","last_name":"Löwen"},{"first_name":"Ralf","last_name":"Metzler","full_name":"Metzler, Ralf"},{"first_name":"Marco","last_name":"Polin","full_name":"Polin, Marco"},{"first_name":"C. Patrick","last_name":"Royall","full_name":"Royall, C. Patrick"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"full_name":"Sengupta, Anupam","last_name":"Sengupta","first_name":"Anupam"},{"full_name":"Sykes, Cécile","last_name":"Sykes","first_name":"Cécile"},{"full_name":"Trianni, Vito","last_name":"Trianni","first_name":"Vito"},{"full_name":"Tuval, Idan","last_name":"Tuval","first_name":"Idan"},{"last_name":"Vogel","first_name":"Nicolas","full_name":"Vogel, Nicolas"},{"full_name":"Yeomans, Julia M.","last_name":"Yeomans","first_name":"Julia M."},{"first_name":"Iker","last_name":"Zuriguel","full_name":"Zuriguel, Iker"},{"full_name":"Marin, Alvaro","last_name":"Marin","first_name":"Alvaro"},{"first_name":"Giorgio","last_name":"Volpe","full_name":"Volpe, Giorgio"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","page":"1695-1704","article_type":"original","citation":{"chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","ieee":"N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e"},"publication":"Soft Matter","date_published":"2023-02-06T00:00:00Z","type":"journal_article","abstract":[{"text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.","lang":"eng"}],"intvolume":" 19","title":"Steering self-organisation through confinement","ddc":["540"],"status":"public","_id":"12708","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12711","checksum":"af95aa18b9b01e32fb8f13477c0e2687","success":1,"date_created":"2023-03-07T09:19:41Z","date_updated":"2023-03-07T09:19:41Z","access_level":"open_access","file_name":"2023_SoftMatter_Araujo.pdf","file_size":3581939,"content_type":"application/pdf","creator":"cchlebak"}]},{"date_published":"2023-02-27T00:00:00Z","article_type":"original","citation":{"chicago":"Cheng, Bingqing, Sebastien Hamel, and Mandy Bethkenhagen. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-36841-1.","short":"B. Cheng, S. Hamel, M. Bethkenhagen, Nature Communications 14 (2023).","mla":"Cheng, Bingqing, et al. “Thermodynamics of Diamond Formation from Hydrocarbon Mixtures in Planets.” Nature Communications, vol. 14, 1104, Springer Nature, 2023, doi:10.1038/s41467-023-36841-1.","ieee":"B. Cheng, S. Hamel, and M. Bethkenhagen, “Thermodynamics of diamond formation from hydrocarbon mixtures in planets,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Cheng, B., Hamel, S., & Bethkenhagen, M. (2023). Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-36841-1","ista":"Cheng B, Hamel S, Bethkenhagen M. 2023. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 14, 1104.","ama":"Cheng B, Hamel S, Bethkenhagen M. Thermodynamics of diamond formation from hydrocarbon mixtures in planets. Nature Communications. 2023;14. doi:10.1038/s41467-023-36841-1"},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"27","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"12713","relation":"main_file","success":1,"checksum":"5ff61ad21511950c15abb73b18613883","date_created":"2023-03-07T10:58:00Z","date_updated":"2023-03-07T10:58:00Z","access_level":"open_access","file_name":"2023_NatComm_Cheng.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":1946443}],"intvolume":" 14","ddc":["540"],"status":"public","title":"Thermodynamics of diamond formation from hydrocarbon mixtures in planets","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12702","abstract":[{"text":"Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-36841-1","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000939678300002"],"pmid":["36843123"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"02","volume":14,"date_updated":"2023-08-01T13:36:11Z","date_created":"2023-03-05T23:01:04Z","author":[{"last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"full_name":"Hamel, Sebastien","first_name":"Sebastien","last_name":"Hamel"},{"first_name":"Mandy","last_name":"Bethkenhagen","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy"}],"publisher":"Springer Nature","department":[{"_id":"BiCh"}],"publication_status":"published","pmid":1,"acknowledgement":"BC thanks Daan Frenkel for stimulating discussions. We thank Aleks Reinhardt, Daan Frenkel, Marius Millot, Federica Coppari, Rhys Bunting, and Chris J. Pickard for critically reading the manuscript and providing useful suggestions. BC acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. SH acknowledges support from LDRD 19-ERD-031 and computing support from the Lawrence Livermore National Laboratory (LLNL) Institutional Computing Grand Challenge program. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. MB acknowledges support by the European Horizon 2020 program within the Marie Skłodowska-Curie actions (xICE grant number 894725), funding from the NOMIS foundation and computational resources at the North-German Supercomputing Alliance (HLRN) facilities.","year":"2023","file_date_updated":"2023-03-07T10:58:00Z","article_number":"1104"},{"article_number":"12","file_date_updated":"2023-03-14T10:29:47Z","department":[{"_id":"MaRo"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We are grateful to all the families who took part, the general practitioners, and the Scottish School of Primary Care for their help in recruiting them and the whole GS team that includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists, healthcare assistants, and nurses.","year":"2023","volume":15,"date_created":"2023-03-12T23:01:02Z","date_updated":"2023-08-01T13:38:12Z","author":[{"first_name":"Elena","last_name":"Bernabeu","full_name":"Bernabeu, Elena"},{"full_name":"Mccartney, Daniel L.","last_name":"Mccartney","first_name":"Daniel L."},{"full_name":"Gadd, Danni A.","last_name":"Gadd","first_name":"Danni A."},{"full_name":"Hillary, Robert F.","last_name":"Hillary","first_name":"Robert F."},{"last_name":"Lu","first_name":"Ake T.","full_name":"Lu, Ake T."},{"full_name":"Murphy, Lee","first_name":"Lee","last_name":"Murphy"},{"full_name":"Wrobel, Nicola","last_name":"Wrobel","first_name":"Nicola"},{"full_name":"Campbell, Archie","last_name":"Campbell","first_name":"Archie"},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"full_name":"Liewald, David","last_name":"Liewald","first_name":"David"},{"full_name":"Hayward, Caroline","last_name":"Hayward","first_name":"Caroline"},{"last_name":"Sudlow","first_name":"Cathie","full_name":"Sudlow, Cathie"},{"full_name":"Cox, Simon R.","first_name":"Simon R.","last_name":"Cox"},{"full_name":"Evans, Kathryn L.","first_name":"Kathryn L.","last_name":"Evans"},{"full_name":"Horvath, Steve","last_name":"Horvath","first_name":"Steve"},{"full_name":"Mcintosh, Andrew M.","last_name":"Mcintosh","first_name":"Andrew M."},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard"},{"full_name":"Vallejos, Catalina A.","last_name":"Vallejos","first_name":"Catalina A."},{"full_name":"Marioni, Riccardo E.","first_name":"Riccardo E.","last_name":"Marioni"}],"publication_identifier":{"eissn":["1756-994X"]},"month":"02","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000940286600001"]},"language":[{"iso":"eng"}],"doi":"10.1186/s13073-023-01161-y","type":"journal_article","abstract":[{"text":"Background\r\nEpigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.\r\n\r\nMethods\r\nFirst, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).\r\n\r\nResults\r\nThrough the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.\r\n\r\nConclusions\r\nThe integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.","lang":"eng"}],"intvolume":" 15","ddc":["570"],"title":"Refining epigenetic prediction of chronological and biological age","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12719","file":[{"success":1,"checksum":"833b837910c4db42fb5f0f34125f77a7","date_updated":"2023-03-14T10:29:47Z","date_created":"2023-03-14T10:29:47Z","file_id":"12722","relation":"main_file","creator":"cchlebak","file_size":4275987,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_GenomeMed_Bernabeu.pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"28","article_type":"original","citation":{"chicago":"Bernabeu, Elena, Daniel L. Mccartney, Danni A. Gadd, Robert F. Hillary, Ake T. Lu, Lee Murphy, Nicola Wrobel, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01161-y.","short":"E. Bernabeu, D.L. Mccartney, D.A. Gadd, R.F. Hillary, A.T. Lu, L. Murphy, N. Wrobel, A. Campbell, S.E. Harris, D. Liewald, C. Hayward, C. Sudlow, S.R. Cox, K.L. Evans, S. Horvath, A.M. Mcintosh, M.R. Robinson, C.A. Vallejos, R.E. Marioni, Genome Medicine 15 (2023).","mla":"Bernabeu, Elena, et al. “Refining Epigenetic Prediction of Chronological and Biological Age.” Genome Medicine, vol. 15, 12, Springer Nature, 2023, doi:10.1186/s13073-023-01161-y.","apa":"Bernabeu, E., Mccartney, D. L., Gadd, D. A., Hillary, R. F., Lu, A. T., Murphy, L., … Marioni, R. E. (2023). Refining epigenetic prediction of chronological and biological age. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01161-y","ieee":"E. Bernabeu et al., “Refining epigenetic prediction of chronological and biological age,” Genome Medicine, vol. 15. Springer Nature, 2023.","ista":"Bernabeu E, Mccartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, Mcintosh AM, Robinson MR, Vallejos CA, Marioni RE. 2023. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 15, 12.","ama":"Bernabeu E, Mccartney DL, Gadd DA, et al. Refining epigenetic prediction of chronological and biological age. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01161-y"},"publication":"Genome Medicine","date_published":"2023-02-28T00:00:00Z"},{"file_date_updated":"2023-03-07T12:22:23Z","acknowledgement":"We thank Christoph Lampert for inspiring this work. The\r\nviews and conclusions contained in this document are those of\r\nthe authors and should not be interpreted as representing the\r\nofficial policies, either expressed or implied, of the United States\r\nAir Force or the U.S. Government. The U.S. Government is\r\nauthorized to reproduce and distribute reprints for Government\r\npurposes notwithstanding any copyright notation herein.","year":"2023","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Institute of Electrical and Electronics Engineers","author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner"},{"full_name":"Amini, Alexander","first_name":"Alexander","last_name":"Amini"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"11366","relation":"earlier_version","status":"public"}]},"date_updated":"2023-08-01T13:36:50Z","date_created":"2023-03-05T23:01:04Z","volume":8,"month":"03","publication_identifier":{"eissn":["2377-3766"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2204.07373"],"isi":["000936534100012"]},"quality_controlled":"1","isi":1,"doi":"10.1109/LRA.2023.3240930","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.","lang":"eng"}],"issue":"3","_id":"12704","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["000"],"status":"public","title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","intvolume":" 8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12714","date_updated":"2023-03-07T12:22:23Z","date_created":"2023-03-07T12:22:23Z","checksum":"5a75dcd326ea66685de2b1aaec259e85","success":1,"file_name":"2023_IEEERobAutLetters_Lechner.pdf","access_level":"open_access","content_type":"application/pdf","file_size":944052,"creator":"cchlebak"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"IEEE Robotics and Automation Letters","citation":{"chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LRA.2023.3240930.","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, IEEE Robotics and Automation Letters 8 (2023) 1595–1602.","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” IEEE Robotics and Automation Letters, vol. 8, no. 3, Institute of Electrical and Electronics Engineers, 2023, pp. 1595–602, doi:10.1109/LRA.2023.3240930.","apa":"Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (2023). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LRA.2023.3240930","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” IEEE Robotics and Automation Letters, vol. 8, no. 3. Institute of Electrical and Electronics Engineers, pp. 1595–1602, 2023.","ista":"Lechner M, Amini A, Rus D, Henzinger TA. 2023. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 8(3), 1595–1602.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. IEEE Robotics and Automation Letters. 2023;8(3):1595-1602. doi:10.1109/LRA.2023.3240930"},"article_type":"original","page":"1595-1602","date_published":"2023-03-01T00:00:00Z"},{"issue":"11","abstract":[{"text":"The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 62","status":"public","title":"Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals","_id":"12737","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2023-03-08T00:00:00Z","page":"4625-4636","article_type":"original","citation":{"chicago":"García-Romero, Álvaro, Jessica E. Waters, Rajesh B Jethwa, Andrew D. Bond, Annie L. Colebatch, Raúl García-Rodríguez, and Dominic S. Wright. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry. American Chemical Society, 2023. https://doi.org/10.1021/acs.inorgchem.3c00057.","mla":"García-Romero, Álvaro, et al. “Highly Adaptive Nature of Group 15 Tris(Quinolyl) Ligands─studies with Coinage Metals.” Inorganic Chemistry, vol. 62, no. 11, American Chemical Society, 2023, pp. 4625–36, doi:10.1021/acs.inorgchem.3c00057.","short":"Á. García-Romero, J.E. Waters, R.B. Jethwa, A.D. Bond, A.L. Colebatch, R. García-Rodríguez, D.S. Wright, Inorganic Chemistry 62 (2023) 4625–4636.","ista":"García-Romero Á, Waters JE, Jethwa RB, Bond AD, Colebatch AL, García-Rodríguez R, Wright DS. 2023. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 62(11), 4625–4636.","apa":"García-Romero, Á., Waters, J. E., Jethwa, R. B., Bond, A. D., Colebatch, A. L., García-Rodríguez, R., & Wright, D. S. (2023). Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. American Chemical Society. https://doi.org/10.1021/acs.inorgchem.3c00057","ieee":"Á. García-Romero et al., “Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals,” Inorganic Chemistry, vol. 62, no. 11. American Chemical Society, pp. 4625–4636, 2023.","ama":"García-Romero Á, Waters JE, Jethwa RB, et al. Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals. Inorganic Chemistry. 2023;62(11):4625-4636. doi:10.1021/acs.inorgchem.3c00057"},"publication":"Inorganic Chemistry","volume":62,"date_updated":"2023-08-01T13:42:59Z","date_created":"2023-03-19T23:00:59Z","author":[{"last_name":"García-Romero","first_name":"Álvaro","full_name":"García-Romero, Álvaro"},{"full_name":"Waters, Jessica E.","first_name":"Jessica E.","last_name":"Waters"},{"last_name":"Jethwa","first_name":"Rajesh B","orcid":"0000-0002-0404-4356","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","full_name":"Jethwa, Rajesh B"},{"last_name":"Bond","first_name":"Andrew D.","full_name":"Bond, Andrew D."},{"full_name":"Colebatch, Annie L.","first_name":"Annie L.","last_name":"Colebatch"},{"last_name":"García-Rodríguez","first_name":"Raúl","full_name":"García-Rodríguez, Raúl"},{"first_name":"Dominic S.","last_name":"Wright","full_name":"Wright, Dominic S."}],"department":[{"_id":"StFr"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"acknowledgement":"The authors thank the Walters-Kundert Studentship of Selwyn College (scholarship for J.E.W.), the Leverhulme Trust (R.G.-R. and D.S.W., grant RPG-2017-146), the Australian Research Council (A.L.C., DE200100450), the Spanish Ministry of Science and Innovation (MCI) and the Spanish Ministry of Science, Innovation and Universities (MCIU) (R.G.-R., PID2021-124691NB-I00, funded by MCIN/AEI/10.13039/501100011033/FEDER, UE and PGC2018-096880-A-I00, MCIU/AEI/FEDER), The University of Valladolid and Santander Bank (Fellowship for A.G.-R.), and the U.K. EPSRC and The Royal Dutch Shell plc. (I-Case award for R.B.J., EP/R511870/1) for financial support. Calculations were carried out on an in-house Odyssey HPC cluster (Cambridge), and the authors are grateful for the calculation time used.","year":"2023","publication_identifier":{"eissn":["1520-510X"],"issn":["0020-1669"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1021/acs.inorgchem.3c00057","quality_controlled":"1","isi":1,"external_id":{"isi":["000956110300001"],"pmid":["36883367"]}},{"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"03","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2203.09443"}],"oa":1,"external_id":{"isi":["000982435900002"],"arxiv":["2203.09443"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.130.106901","article_number":"106901","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","year":"2023","volume":130,"date_updated":"2023-08-01T13:39:04Z","date_created":"2023-03-14T13:11:59Z","author":[{"full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"full_name":"Shiva Kumar, Abhishek","id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek","last_name":"Shiva Kumar"},{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"id":"e32c111f-f6e0-11ea-865d-eb955baea334","first_name":"Younes","last_name":"Ashourishokri","full_name":"Ashourishokri, Younes"},{"first_name":"Ayan A.","last_name":"Zhumekenov","full_name":"Zhumekenov, Ayan A."},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek"}],"keyword":["General Physics and Astronomy"],"scopus_import":"1","article_processing_charge":"No","day":"10","article_type":"original","citation":{"ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 2023;130(10). doi:10.1103/physrevlett.130.106901","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.106901","ieee":"A. Volosniev et al., “Spin-electric coupling in lead halide perovskites,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:10.1103/physrevlett.130.106901.","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.106901."},"publication":"Physical Review Letters","date_published":"2023-03-10T00:00:00Z","type":"journal_article","issue":"10","abstract":[{"text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.","lang":"eng"}],"intvolume":" 130","status":"public","title":"Spin-electric coupling in lead halide perovskites","_id":"12723","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint"},{"date_created":"2023-03-14T13:13:05Z","date_updated":"2023-08-01T13:39:47Z","volume":107,"author":[{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"},{"id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek","last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek"},{"full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ashourishokri","first_name":"Younes","id":"e32c111f-f6e0-11ea-865d-eb955baea334","full_name":"Ashourishokri, Younes"},{"full_name":"Zhumekenov, Ayan","first_name":"Ayan","last_name":"Zhumekenov"},{"first_name":"Osman M.","last_name":"Bakr","full_name":"Bakr, Osman M."},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"year":"2023","article_number":"125201","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.107.125201","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"external_id":{"isi":["000972602200006"],"arxiv":["2204.04022"]},"month":"03","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"oa_version":"Preprint","status":"public","title":"Effective model for studying optical properties of lead halide perovskites","intvolume":" 107","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12724","abstract":[{"text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.","lang":"eng"}],"issue":"12","type":"journal_article","date_published":"2023-03-15T00:00:00Z","article_type":"original","publication":"Physical Review B","citation":{"chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.107.125201.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” Physical Review B, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:10.1103/physrevb.107.125201.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.107.125201","ieee":"A. Volosniev et al., “Effective model for studying optical properties of lead halide perovskites,” Physical Review B, vol. 107, no. 12. American Physical Society, 2023.","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 2023;107(12). doi:10.1103/physrevb.107.125201"},"day":"15","article_processing_charge":"No","scopus_import":"1"},{"publication_identifier":{"eissn":["1932-6203"]},"month":"03","doi":"10.1371/journal.pone.0277148","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001024737400001"]},"oa":1,"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"2696E7FE-B435-11E9-9278-68D0E5697425","grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2023-03-27T06:51:09Z","article_number":"e0277148","author":[{"first_name":"Jason Seth","last_name":"Rothman","full_name":"Rothman, Jason Seth"},{"last_name":"Borges Merjane","first_name":"Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","full_name":"Borges Merjane, Carolina"},{"first_name":"Noemi","last_name":"Holderith","full_name":"Holderith, Noemi"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"},{"last_name":"Angus Silver","first_name":"R.","full_name":"Angus Silver, R."}],"volume":18,"date_updated":"2023-08-01T13:46:39Z","date_created":"2023-03-26T22:01:07Z","year":"2023","acknowledgement":"We thank the IST Austria Electron Microscopy Facility for technical support, and Diccon Coyle, Andrea Lőrincz and Zoltan Nusser for their helpful comments and discussions.\r\nFunding for JSR and RAS was from the Wellcome Trust (203048; 224499; https://\r\nwellcome.org/). RAS is in receipt of a Wellcome Trust Principal Research Fellowship (224499).\r\nFunding for CBM and PJ was from Fond zur Förderung der Wissenschaftlichen Forschung (V\r\n739-B27 Elise-Richter Programme to CBM, Z 312-B27 Wittgenstein Award to PJ; \r\nhttps://www.fwf.ac.at). PJ received funding from the European Research Council (ERC; https://erc.europa.eu) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692). NH was supported by a European\r\nResearch Council Advanced Grant (ERC-AG787157).","publisher":"Public Library of Science","department":[{"_id":"PeJo"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","date_published":"2023-03-17T00:00:00Z","citation":{"ista":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. 2023. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 18(3 March), e0277148.","ieee":"J. S. Rothman, C. Borges Merjane, N. Holderith, P. M. Jonas, and R. Angus Silver, “Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy,” PLoS ONE, vol. 18, no. 3 March. Public Library of Science, 2023.","apa":"Rothman, J. S., Borges Merjane, C., Holderith, N., Jonas, P. M., & Angus Silver, R. (2023). Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0277148","ama":"Rothman JS, Borges Merjane C, Holderith N, Jonas PM, Angus Silver R. Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy. PLoS ONE. 2023;18(3 March). doi:10.1371/journal.pone.0277148","chicago":"Rothman, Jason Seth, Carolina Borges Merjane, Noemi Holderith, Peter M Jonas, and R. Angus Silver. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0277148.","mla":"Rothman, Jason Seth, et al. “Validation of a Stereological Method for Estimating Particle Size and Density from 2D Projections with High Accuracy.” PLoS ONE, vol. 18, no. 3 March, e0277148, Public Library of Science, 2023, doi:10.1371/journal.pone.0277148.","short":"J.S. Rothman, C. Borges Merjane, N. Holderith, P.M. Jonas, R. Angus Silver, PLoS ONE 18 (2023)."},"publication":"PLoS ONE","article_type":"original","issue":"3 March","abstract":[{"lang":"eng","text":"Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density."}],"type":"journal_article","file":[{"success":1,"checksum":"2380331ec27cc87808826fc64419ac1c","date_updated":"2023-03-27T06:51:09Z","date_created":"2023-03-27T06:51:09Z","file_id":"12770","relation":"main_file","creator":"dernst","file_size":7290413,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_PLoSOne_Rothman.pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12759","intvolume":" 18","ddc":["570"],"title":"Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy","status":"public"},{"day":"17","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-03-17T00:00:00Z","publication":"Science Advances","citation":{"ieee":"F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science Advances, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224","ista":"Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.","ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.ade5224."},"article_type":"original","abstract":[{"lang":"eng","text":"ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling."}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12768","checksum":"6d7dbe9ed86a116c8a002d62971202c5","success":1,"date_created":"2023-03-27T06:24:49Z","date_updated":"2023-03-27T06:24:49Z","access_level":"open_access","file_name":"2023_ScienceAdvances_Hurtig.pdf","file_size":1826471,"content_type":"application/pdf","creator":"dernst"}],"_id":"12756","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","intvolume":" 9","month":"03","publication_identifier":{"eissn":["2375-2548"]},"doi":"10.1126/sciadv.ade5224","language":[{"iso":"eng"}],"external_id":{"isi":["000968083500010"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"file_date_updated":"2023-03-27T06:24:49Z","ec_funded":1,"article_number":"eade5224","author":[{"first_name":"Fredrik","last_name":"Hurtig","full_name":"Hurtig, Fredrik"},{"last_name":"Burgers","first_name":"Thomas C.Q.","full_name":"Burgers, Thomas C.Q."},{"first_name":"Alice","last_name":"Cezanne","full_name":"Cezanne, Alice"},{"full_name":"Jiang, Xiuyun","first_name":"Xiuyun","last_name":"Jiang"},{"first_name":"Frank N.","last_name":"Mol","full_name":"Mol, Frank N."},{"first_name":"Jovan","last_name":"Traparić","full_name":"Traparić, Jovan"},{"first_name":"Andre Arashiro","last_name":"Pulschen","full_name":"Pulschen, Andre Arashiro"},{"first_name":"Tim","last_name":"Nierhaus","full_name":"Nierhaus, Tim"},{"first_name":"Gabriel","last_name":"Tarrason-Risa","full_name":"Tarrason-Risa, Gabriel"},{"full_name":"Harker-Kirschneck, Lena","first_name":"Lena","last_name":"Harker-Kirschneck"},{"full_name":"Löwe, Jan","first_name":"Jan","last_name":"Löwe"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Vlijm, Rifka","first_name":"Rifka","last_name":"Vlijm"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"}],"date_created":"2023-03-26T22:01:06Z","date_updated":"2023-08-01T13:45:54Z","volume":9,"acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","year":"2023","publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"American Association for the Advancement of Science"},{"month":"03","publication_identifier":{"eissn":["1932-6203"]},"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000985134400106"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0282689","article_number":"e0282689","file_date_updated":"2023-03-27T07:09:08Z","publication_status":"published","department":[{"_id":"FyKo"},{"_id":"MaRo"}],"publisher":"Public Library of Science","acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","year":"2023","date_updated":"2023-08-01T13:47:14Z","date_created":"2023-03-26T22:01:07Z","volume":18,"author":[{"full_name":"Pak, Marina A.","last_name":"Pak","first_name":"Marina A."},{"full_name":"Markhieva, Karina A.","first_name":"Karina A.","last_name":"Markhieva"},{"full_name":"Novikova, Mariia S.","last_name":"Novikova","first_name":"Mariia S."},{"full_name":"Petrov, Dmitry S.","last_name":"Petrov","first_name":"Dmitry S."},{"full_name":"Vorobyev, Ilya S.","first_name":"Ilya S.","last_name":"Vorobyev"},{"full_name":"Maksimova, Ekaterina","first_name":"Ekaterina","last_name":"Maksimova","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"last_name":"Ivankov","first_name":"Dmitry N.","full_name":"Ivankov, Dmitry N."}],"scopus_import":"1","day":"16","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"PLoS ONE","citation":{"chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.","ieee":"M. A. Pak et al., “Using AlphaFold to predict the impact of single mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3. Public Library of Science, 2023.","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689","ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689"},"date_published":"2023-03-16T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"issue":"3","ddc":["570"],"status":"public","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","intvolume":" 18","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12758","file":[{"access_level":"open_access","file_name":"2023_PLoSOne_Pak.pdf","creator":"dernst","content_type":"application/pdf","file_size":856625,"file_id":"12771","relation":"main_file","success":1,"checksum":"0281bdfccf8d76c4e08dd011c603f6b6","date_updated":"2023-03-27T07:09:08Z","date_created":"2023-03-27T07:09:08Z"}],"oa_version":"Published Version"},{"volume":480,"date_updated":"2023-08-01T13:45:12Z","date_created":"2023-03-26T22:01:06Z","author":[{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"}],"publisher":"Portland Press","department":[{"_id":"LeSa"}],"publication_status":"published","pmid":1,"year":"2023","language":[{"iso":"eng"}],"doi":"10.1042/BCJ20210285","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1042/BCJ20210285","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36920092"],"isi":["000957065700001"]},"oa":1,"publication_identifier":{"issn":["0264-6021"],"eissn":["1470-8728"]},"month":"03","oa_version":"Published Version","intvolume":" 480","title":"From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12757","issue":"5","abstract":[{"text":"My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.","lang":"eng"}],"type":"journal_article","date_published":"2023-03-15T00:00:00Z","page":"319-333","article_type":"review","citation":{"mla":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal, vol. 480, no. 5, Portland Press, 2023, pp. 319–33, doi:10.1042/BCJ20210285.","short":"L.A. Sazanov, The Biochemical Journal 480 (2023) 319–333.","chicago":"Sazanov, Leonid A. “From the ‘black Box’ to ‘Domino Effect’ Mechanism: What Have We Learned from the Structures of Respiratory Complex I.” The Biochemical Journal. Portland Press, 2023. https://doi.org/10.1042/BCJ20210285.","ama":"Sazanov LA. From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 2023;480(5):319-333. doi:10.1042/BCJ20210285","ista":"Sazanov LA. 2023. From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. 480(5), 319–333.","ieee":"L. A. Sazanov, “From the ‘black box’ to ‘domino effect’ mechanism: What have we learned from the structures of respiratory complex I,” The Biochemical Journal, vol. 480, no. 5. Portland Press, pp. 319–333, 2023.","apa":"Sazanov, L. A. (2023). From the “black box” to “domino effect” mechanism: What have we learned from the structures of respiratory complex I. The Biochemical Journal. Portland Press. https://doi.org/10.1042/BCJ20210285"},"publication":"The Biochemical Journal","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1"},{"acknowledgement":"J.S. and K.C. acknowledge support from the ERC CoG 863818 (ForM-SMArt)","year":"2023","publication_status":"published","publisher":"The Royal Society","department":[{"_id":"KrCh"}],"author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub","full_name":"Svoboda, Jakub"},{"first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"full_name":"Kaveh, Kamran","last_name":"Kaveh","first_name":"Kamran"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://doi.org/10.6084/m9.figshare.21261771.v1","relation":"research_data"}]},"date_created":"2023-04-02T22:01:09Z","date_updated":"2023-08-01T13:58:34Z","volume":479,"article_number":"20220685","file_date_updated":"2023-04-03T06:25:29Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000957125500002"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"doi":"10.1098/rspa.2022.0685","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1471-2946"],"issn":["1364-5021"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12787","status":"public","title":"Coexistence times in the Moran process with environmental heterogeneity","ddc":["000"],"intvolume":" 479","file":[{"relation":"main_file","file_id":"12796","checksum":"13953d349fbefcb5d21ccc6b303297eb","success":1,"date_updated":"2023-04-03T06:25:29Z","date_created":"2023-04-03T06:25:29Z","access_level":"open_access","file_name":"2023_ProceedingsRoyalSocietyA_Svoboda.pdf","content_type":"application/pdf","file_size":827784,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Populations evolve in spatially heterogeneous environments. While a certain trait might bring a fitness advantage in some patch of the environment, a different trait might be advantageous in another patch. Here, we study the Moran birth–death process with two types of individuals in a population stretched across two patches of size N, each patch favouring one of the two types. We show that the long-term fate of such populations crucially depends on the migration rate μ\r\n between the patches. To classify the possible fates, we use the distinction between polynomial (short) and exponential (long) timescales. We show that when μ is high then one of the two types fixates on the whole population after a number of steps that is only polynomial in N. By contrast, when μ is low then each type holds majority in the patch where it is favoured for a number of steps that is at least exponential in N. Moreover, we precisely identify the threshold migration rate μ⋆ that separates those two scenarios, thereby exactly delineating the situations that support long-term coexistence of the two types. We also discuss the case of various cycle graphs and we present computer simulations that perfectly match our analytical results.","lang":"eng"}],"issue":"2271","publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","citation":{"chicago":"Svoboda, Jakub, Josef Tkadlec, Kamran Kaveh, and Krishnendu Chatterjee. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society, 2023. https://doi.org/10.1098/rspa.2022.0685.","short":"J. Svoboda, J. Tkadlec, K. Kaveh, K. Chatterjee, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 479 (2023).","mla":"Svoboda, Jakub, et al. “Coexistence Times in the Moran Process with Environmental Heterogeneity.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271, 20220685, The Royal Society, 2023, doi:10.1098/rspa.2022.0685.","ieee":"J. Svoboda, J. Tkadlec, K. Kaveh, and K. Chatterjee, “Coexistence times in the Moran process with environmental heterogeneity,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 479, no. 2271. The Royal Society, 2023.","apa":"Svoboda, J., Tkadlec, J., Kaveh, K., & Chatterjee, K. (2023). Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. The Royal Society. https://doi.org/10.1098/rspa.2022.0685","ista":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. 2023. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479(2271), 20220685.","ama":"Svoboda J, Tkadlec J, Kaveh K, Chatterjee K. Coexistence times in the Moran process with environmental heterogeneity. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2023;479(2271). doi:10.1098/rspa.2022.0685"},"article_type":"original","date_published":"2023-03-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","has_accepted_license":"1"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.07067","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2206.07067"],"isi":["000957635500003"]},"project":[{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevLett.130.103202","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"03","year":"2023","acknowledgement":"M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","related_material":{"link":[{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/topology-of-rotating-molecules/"}]},"author":[{"full_name":"Karle, Volker","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle","first_name":"Volker"},{"full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"}],"volume":130,"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T14:02:06Z","article_number":"103202","ec_funded":1,"citation":{"apa":"Karle, V., Ghazaryan, A., & Lemeshko, M. (2023). Topological charges of periodically kicked molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.130.103202","ieee":"V. Karle, A. Ghazaryan, and M. Lemeshko, “Topological charges of periodically kicked molecules,” Physical Review Letters, vol. 130, no. 10. American Physical Society, 2023.","ista":"Karle V, Ghazaryan A, Lemeshko M. 2023. Topological charges of periodically kicked molecules. Physical Review Letters. 130(10), 103202.","ama":"Karle V, Ghazaryan A, Lemeshko M. Topological charges of periodically kicked molecules. Physical Review Letters. 2023;130(10). doi:10.1103/PhysRevLett.130.103202","chicago":"Karle, Volker, Areg Ghazaryan, and Mikhail Lemeshko. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.130.103202.","short":"V. Karle, A. Ghazaryan, M. Lemeshko, Physical Review Letters 130 (2023).","mla":"Karle, Volker, et al. “Topological Charges of Periodically Kicked Molecules.” Physical Review Letters, vol. 130, no. 10, 103202, American Physical Society, 2023, doi:10.1103/PhysRevLett.130.103202."},"publication":"Physical Review Letters","article_type":"original","date_published":"2023-03-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10","_id":"12788","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 130","status":"public","title":"Topological charges of periodically kicked molecules","oa_version":"Preprint","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"We show that the simplest of existing molecules—closed-shell diatomics not interacting with one another—host topological charges when driven by periodic far-off-resonant laser pulses. A periodically kicked molecular rotor can be mapped onto a “crystalline” lattice in angular momentum space. This allows us to define quasimomenta and the band structure in the Floquet representation, by analogy with the Bloch waves of solid-state physics. Applying laser pulses spaced by 1/3 of the molecular rotational period creates a lattice with three atoms per unit cell with staggered hopping. Within the synthetic dimension of the laser strength, we discover Dirac cones with topological charges. These Dirac cones, topologically protected by reflection and time-reversal symmetry, are reminiscent of (although not equivalent to) that seen in graphene. They—and the corresponding edge states—are broadly tunable by adjusting the laser strength and can be observed in present-day experiments by measuring molecular alignment and populations of rotational levels. This paves the way to study controllable topological physics in gas-phase experiments with small molecules as well as to classify dynamical molecular states by their topological invariants."}]},{"date_published":"2023-03-01T00:00:00Z","article_type":"original","citation":{"short":"A. Ghazaryan, T. Holder, E. Berg, M. Serbyn, Physical Review B 107 (2023).","mla":"Ghazaryan, Areg, et al. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B, vol. 107, no. 10, 104502, American Physical Society, 2023, doi:10.1103/PhysRevB.107.104502.","chicago":"Ghazaryan, Areg, Tobias Holder, Erez Berg, and Maksym Serbyn. “Multilayer Graphenes as a Platform for Interaction-Driven Physics and Topological Superconductivity.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.104502.","ama":"Ghazaryan A, Holder T, Berg E, Serbyn M. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 2023;107(10). doi:10.1103/PhysRevB.107.104502","apa":"Ghazaryan, A., Holder, T., Berg, E., & Serbyn, M. (2023). Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.104502","ieee":"A. Ghazaryan, T. Holder, E. Berg, and M. Serbyn, “Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity,” Physical Review B, vol. 107, no. 10. American Physical Society, 2023.","ista":"Ghazaryan A, Holder T, Berg E, Serbyn M. 2023. Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity. Physical Review B. 107(10), 104502."},"publication":"Physical Review B","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 107","title":"Multilayer graphenes as a platform for interaction-driven physics and topological superconductivity","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12790","issue":"10","abstract":[{"text":"Motivated by the recent discoveries of superconductivity in bilayer and trilayer graphene, we theoretically investigate superconductivity and other interaction-driven phases in multilayer graphene stacks. To this end, we study the density of states of multilayer graphene with up to four layers at the single-particle band structure level in the presence of a transverse electric field. Among the considered structures, tetralayer graphene with rhombohedral (ABCA) stacking reaches the highest density of states. We study the phases that can arise in ABCA graphene by tuning the carrier density and transverse electric field. For a broad region of the tuning parameters, the presence of strong Coulomb repulsion leads to a spontaneous spin and valley symmetry breaking via Stoner transitions. Using a model that incorporates the spontaneous spin and valley polarization, we explore the Kohn-Luttinger mechanism for superconductivity driven by repulsive Coulomb interactions. We find that the strongest superconducting instability is in the p-wave channel, and occurs in proximity to the onset of Stoner transitions. Interestingly, we find a range of densities and transverse electric fields where superconductivity develops out of a strongly corrugated, singly connected Fermi surface in each valley, leading to a topologically nontrivial chiral p+ip superconducting state with an even number of copropagating chiral Majorana edge modes. Our work establishes ABCA-stacked tetralayer graphene as a promising platform for observing strongly correlated physics and topological superconductivity.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.107.104502","quality_controlled":"1","isi":1,"external_id":{"arxiv":["2211.02492"],"isi":["000945526400003"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.02492","open_access":"1"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"03","volume":107,"date_created":"2023-04-02T22:01:10Z","date_updated":"2023-08-01T13:59:29Z","related_material":{"link":[{"relation":"press_release","description":"News on the ISTA website","url":"https://ista.ac.at/en/news/reaching-superconductivity-layer-by-layer/"}]},"author":[{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","last_name":"Holder","full_name":"Holder, Tobias"},{"last_name":"Berg","first_name":"Erez","full_name":"Berg, Erez"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"department":[{"_id":"MaSe"},{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","year":"2023","article_number":"104502"},{"publication":"The European Physical Journal E","citation":{"chicago":"Clark Di Leoni, Patricio, Lokahith N Agasthya, Michele Buzzicotti, and Luca Biferale. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00276-9.","mla":"Clark Di Leoni, Patricio, et al. “Reconstructing Rayleigh–Bénard Flows out of Temperature-Only Measurements Using Physics-Informed Neural Networks.” The European Physical Journal E, vol. 46, no. 3, 16, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00276-9.","short":"P. Clark Di Leoni, L.N. Agasthya, M. Buzzicotti, L. Biferale, The European Physical Journal E 46 (2023).","ista":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. 2023. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 46(3), 16.","ieee":"P. Clark Di Leoni, L. N. Agasthya, M. Buzzicotti, and L. Biferale, “Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks,” The European Physical Journal E, vol. 46, no. 3. Springer Nature, 2023.","apa":"Clark Di Leoni, P., Agasthya, L. N., Buzzicotti, M., & Biferale, L. (2023). Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00276-9","ama":"Clark Di Leoni P, Agasthya LN, Buzzicotti M, Biferale L. Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks. The European Physical Journal E. 2023;46(3). doi:10.1140/epje/s10189-023-00276-9"},"article_type":"original","date_published":"2023-03-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12791","status":"public","title":"Reconstructing Rayleigh–Bénard flows out of temperature-only measurements using Physics-Informed Neural Networks","intvolume":" 46","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We investigate the capabilities of Physics-Informed Neural Networks (PINNs) to reconstruct turbulent Rayleigh–Bénard flows using only temperature information. We perform a quantitative analysis of the quality of the reconstructions at various amounts of low-passed-filtered information and turbulent intensities. We compare our results with those obtained via nudging, a classical equation-informed data assimilation technique. At low Rayleigh numbers, PINNs are able to reconstruct with high precision, comparable to the one achieved with nudging. At high Rayleigh numbers, PINNs outperform nudging and are able to achieve satisfactory reconstruction of the velocity fields only when data for temperature is provided with high spatial and temporal density. When data becomes sparse, the PINNs performance worsens, not only in a point-to-point error sense but also, and contrary to nudging, in a statistical sense, as can be seen in the probability density functions and energy spectra.","lang":"eng"}],"issue":"3","external_id":{"isi":["000956387200001"],"arxiv":["2301.07769"]},"oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2301.07769","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1140/epje/s10189-023-00276-9","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1292-895X"],"issn":["1292-8941"]},"year":"2023","acknowledgement":"This project has received partial funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 882340))","publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"Springer Nature","author":[{"last_name":"Clark Di Leoni","first_name":"Patricio","full_name":"Clark Di Leoni, Patricio"},{"full_name":"Agasthya, Lokahith N","id":"cd100965-0804-11ed-9c55-f4878ff4e877","last_name":"Agasthya","first_name":"Lokahith N"},{"first_name":"Michele","last_name":"Buzzicotti","full_name":"Buzzicotti, Michele"},{"last_name":"Biferale","first_name":"Luca","full_name":"Biferale, Luca"}],"date_created":"2023-04-02T22:01:11Z","date_updated":"2023-08-01T14:03:47Z","volume":46,"article_number":"16"},{"file_date_updated":"2023-04-17T07:41:25Z","ec_funded":1,"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publisher":"Elsevier","acknowledgement":"We thank Andrea Pauli (IMP) and Edouard Hannezo (ISTA) for fruitful discussions and support with the SPIM experiments; the Heisenberg group, and especially Feyza Nur Arslan and Alexandra Schauer, for discussions and feedback; Michaela Jović (ISTA) for help with the quantitative real-time PCR protocol; the bioimaging and zebrafish facilities of ISTA for continuous support; Stephan Preibisch (Janelia Research Campus) for support with the SPIM data analysis; and Nobuhiro Nakamura (Tokyo Institute of Technology) for sharing α1-Na+/K+-ATPase antibody. This work was supported by funding from the European Union (European Research Council Advanced grant 742573 to C.-P.H.), postdoctoral fellowships from EMBO (LTF-850-2017) and HFSP (LT000429/2018-L2) to D.P., and a PhD fellowship from the Studienstiftung des deutschen Volkes to F.P.","year":"2023","date_updated":"2023-08-01T14:10:38Z","date_created":"2023-04-16T22:01:07Z","volume":58,"author":[{"full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla","last_name":"Huljev"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"},{"full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","first_name":"Diana C","last_name":"Nunes Pinheiro"},{"first_name":"Friedrich","last_name":"Preusser","full_name":"Preusser, Friedrich"},{"full_name":"Steccari, Irene","first_name":"Irene","last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Naik, Suyash","orcid":"0000-0001-8421-5508","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","last_name":"Naik","first_name":"Suyash"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"month":"04","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"LT000429","_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000982111800001"]},"oa":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2023.02.016","type":"journal_article","abstract":[{"text":"Interstitial fluid (IF) accumulation between embryonic cells is thought to be important for embryo patterning and morphogenesis. Here, we identify a positive mechanical feedback loop between cell migration and IF relocalization and find that it promotes embryonic axis formation during zebrafish gastrulation. We show that anterior axial mesendoderm (prechordal plate [ppl]) cells, moving in between the yolk cell and deep cell tissue to extend the embryonic axis, compress the overlying deep cell layer, thereby causing IF to flow from the deep cell layer to the boundary between the yolk cell and the deep cell layer, directly ahead of the advancing ppl. This IF relocalization, in turn, facilitates ppl cell protrusion formation and migration by opening up the space into which the ppl moves and, thereby, the ability of the ppl to trigger IF relocalization by pushing against the overlying deep cell layer. Thus, embryonic axis formation relies on a hydraulic feedback loop between cell migration and IF relocalization.","lang":"eng"}],"issue":"7","ddc":["570"],"status":"public","title":"A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish","intvolume":" 58","_id":"12830","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2023_DevelopmentalCell_Huljev.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":7925886,"file_id":"12842","relation":"main_file","date_updated":"2023-04-17T07:41:25Z","date_created":"2023-04-17T07:41:25Z","success":1,"checksum":"c80ca2ebc241232aacdb5aa4b4c80957"}],"oa_version":"Published Version","scopus_import":"1","day":"10","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","page":"582-596.e7","publication":"Developmental Cell","citation":{"apa":"Huljev, K., Shamipour, S., Nunes Pinheiro, D. C., Preusser, F., Steccari, I., Sommer, C. M., … Heisenberg, C.-P. J. (2023). A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.02.016","ieee":"K. Huljev et al., “A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish,” Developmental Cell, vol. 58, no. 7. Elsevier, p. 582–596.e7, 2023.","ista":"Huljev K, Shamipour S, Nunes Pinheiro DC, Preusser F, Steccari I, Sommer CM, Naik S, Heisenberg C-PJ. 2023. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 58(7), 582–596.e7.","ama":"Huljev K, Shamipour S, Nunes Pinheiro DC, et al. A hydraulic feedback loop between mesendoderm cell migration and interstitial fluid relocalization promotes embryonic axis formation in zebrafish. Developmental Cell. 2023;58(7):582-596.e7. doi:10.1016/j.devcel.2023.02.016","chicago":"Huljev, Karla, Shayan Shamipour, Diana C Nunes Pinheiro, Friedrich Preusser, Irene Steccari, Christoph M Sommer, Suyash Naik, and Carl-Philipp J Heisenberg. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.02.016.","short":"K. Huljev, S. Shamipour, D.C. Nunes Pinheiro, F. Preusser, I. Steccari, C.M. Sommer, S. Naik, C.-P.J. Heisenberg, Developmental Cell 58 (2023) 582–596.e7.","mla":"Huljev, Karla, et al. “A Hydraulic Feedback Loop between Mesendoderm Cell Migration and Interstitial Fluid Relocalization Promotes Embryonic Axis Formation in Zebrafish.” Developmental Cell, vol. 58, no. 7, Elsevier, 2023, p. 582–596.e7, doi:10.1016/j.devcel.2023.02.016."},"date_published":"2023-04-10T00:00:00Z"},{"citation":{"ama":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 2023;158(13). doi:10.1063/5.0135893","ista":"Zeng Z, Yakaboylu E, Lemeshko M, Shi T, Schmidt R. 2023. Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. 158(13), 134301.","ieee":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, and R. Schmidt, “Variational theory of angulons and their rotational spectroscopy,” The Journal of Chemical Physics, vol. 158, no. 13. American Institute of Physics, 2023.","apa":"Zeng, Z., Yakaboylu, E., Lemeshko, M., Shi, T., & Schmidt, R. (2023). Variational theory of angulons and their rotational spectroscopy. The Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0135893","mla":"Zeng, Zhongda, et al. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics, vol. 158, no. 13, 134301, American Institute of Physics, 2023, doi:10.1063/5.0135893.","short":"Z. Zeng, E. Yakaboylu, M. Lemeshko, T. Shi, R. Schmidt, The Journal of Chemical Physics 158 (2023).","chicago":"Zeng, Zhongda, Enderalp Yakaboylu, Mikhail Lemeshko, Tao Shi, and Richard Schmidt. “Variational Theory of Angulons and Their Rotational Spectroscopy.” The Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0135893."},"publication":"The Journal of Chemical Physics","article_type":"original","date_published":"2023-04-07T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"07","_id":"12831","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 158","title":"Variational theory of angulons and their rotational spectroscopy","status":"public","ddc":["530"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12841","date_updated":"2023-04-17T07:28:38Z","date_created":"2023-04-17T07:28:38Z","checksum":"8d801babea4df48e08895c76571bb19e","success":1,"file_name":"2023_JourChemicalPhysics_Zeng.pdf","access_level":"open_access","content_type":"application/pdf","file_size":7388057,"creator":"dernst"}],"type":"journal_article","issue":"13","abstract":[{"lang":"eng","text":"The angulon, a quasiparticle formed by a quantum rotor dressed by the excitations of a many-body bath, can be used to describe an impurity rotating in a fluid or solid environment. Here, we propose a coherent state ansatz in the co-rotating frame, which provides a comprehensive theoretical description of angulons. We reveal the quasiparticle properties, such as energies, quasiparticle weights, and spectral functions, and show that our ansatz yields a persistent decrease in the impurity’s rotational constant due to many-body dressing, which is consistent with experimental observations. From our study, a picture of the angulon emerges as an effective spin interacting with a magnetic field that is self-consistently generated by the molecule’s rotation. Moreover, we discuss rotational spectroscopy, which focuses on the response of rotating molecules to a laser perturbation in the linear response regime. Importantly, we take into account initial-state interactions that have been neglected in prior studies and reveal their impact on the excitation spectrum. To examine the angulon instability regime, we use a single-excitation ansatz and obtain results consistent with experiments, in which a broadening of spectral lines is observed while phonon wings remain highly suppressed due to initial-state interactions."}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2211.08070"],"isi":["000970038800001"]},"project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"doi":"10.1063/5.0135893","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"]},"month":"04","year":"2023","acknowledgement":"We thank Ignacio Cirac, Christian Schmauder, and Henrik Stapelfeldt for their valuable discussions. We acknowledge support by the Max Planck Society and the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2181/1—390900948 (the Heidelberg STRUCTURES Excellence Cluster). M.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.S. is supported by the National Key Research and Development Program of China (Grant No. 2017YFA0718304) and the National Natural Science Foundation of China (Grant Nos. 11974363, 12135018, and 12047503).","publisher":"American Institute of Physics","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"full_name":"Zeng, Zhongda","last_name":"Zeng","first_name":"Zhongda"},{"full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"full_name":"Shi, Tao","last_name":"Shi","first_name":"Tao"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"}],"volume":158,"date_created":"2023-04-16T22:01:07Z","date_updated":"2023-08-01T14:08:47Z","article_number":"134301","ec_funded":1,"file_date_updated":"2023-04-17T07:28:38Z"},{"date_published":"2023-03-07T00:00:00Z","article_type":"original","citation":{"ama":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 2023;13(1). doi:10.1103/PhysRevX.13.011033","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033.","ieee":"M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” Physical Review X, vol. 13, no. 1. American Physical Society, 2023.","apa":"Ljubotina, M., Desaules, J. Y., Serbyn, M., & Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.011033","mla":"Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:10.1103/PhysRevX.13.011033.","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).","chicago":"Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.011033."},"publication":"Physical Review X","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":1958523,"creator":"dernst","access_level":"open_access","file_name":"2023_PhysReviewX_Ljubotina.pdf","checksum":"ee060cea609af79bba7af74b1ce28078","success":1,"date_created":"2023-04-17T08:36:53Z","date_updated":"2023-04-17T08:36:53Z","relation":"main_file","file_id":"12845"}],"oa_version":"Published Version","intvolume":" 13","title":"Superdiffusive energy transport in kinetically constrained models","ddc":["530"],"status":"public","_id":"12839","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"1","abstract":[{"text":"Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevX.13.011033","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000957625700001"]},"publication_identifier":{"eissn":["2160-3308"]},"month":"03","volume":13,"date_updated":"2023-08-01T14:11:28Z","date_created":"2023-04-16T22:01:09Z","author":[{"full_name":"Ljubotina, Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko","last_name":"Ljubotina"},{"last_name":"Desaules","first_name":"Jean Yves","full_name":"Desaules, Jean Yves"},{"full_name":"Serbyn, Maksym","last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54].","year":"2023","ec_funded":1,"file_date_updated":"2023-04-17T08:36:53Z","article_number":"011033"},{"month":"04","publication_identifier":{"eissn":["2405-8297"]},"quality_controlled":"1","isi":1,"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"external_id":{"isi":["000967601700001"]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.ensm.2023.03.022","publication_status":"published","publisher":"Elsevier","department":[{"_id":"MaIb"}],"acknowledgement":"The authors thank the support from the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación. The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581 and 2021 SGR 00457. ICN2 acknowledges the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. Part of the present work has been performed in the frameworks of Universitat de Barcelona Nanoscience PhD program. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF). S. Lee. and M. Ibáñez acknowledge funding by IST Austria and the Werner Siemens Foundation. J. Llorca is a Serra Húnter Fellow and is grateful to ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2017 SGR 128. L. L.Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). Z. F. Liang acknowledges funding from MINECO SO-FPT PhD grant (SEV-2013-0295-17-1). J. W. Chen and Y. Xu thank the support from The Key Research and Development Program of Hebei Province (No. 20314305D) and the cooperative scientific research project of the “Chunhui Program” of the Ministry of Education (2018-7). This work was supported by the Natural Science Foundation of Sichuan province (NSFSC) and funded by the Science and Technology Department of Sichuan Province (2022NSFSC1229).","year":"2023","date_updated":"2023-08-01T14:08:02Z","date_created":"2023-04-16T22:01:07Z","volume":58,"author":[{"first_name":"Ren","last_name":"He","full_name":"He, Ren"},{"full_name":"Yang, Linlin","first_name":"Linlin","last_name":"Yang"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"first_name":"Xiang","last_name":"Wang","full_name":"Wang, Xiang"},{"full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","id":"BB243B88-D767-11E9-B658-BC13E6697425","last_name":"Lee","first_name":"Seungho"},{"first_name":"Ting","last_name":"Zhang","full_name":"Zhang, Ting"},{"full_name":"Li, Lingxiao","last_name":"Li","first_name":"Lingxiao"},{"full_name":"Liang, Zhifu","last_name":"Liang","first_name":"Zhifu"},{"last_name":"Chen","first_name":"Jingwei","full_name":"Chen, Jingwei"},{"first_name":"Junshan","last_name":"Li","full_name":"Li, Junshan"},{"first_name":"Ahmad","last_name":"Ostovari Moghaddam","full_name":"Ostovari Moghaddam, Ahmad"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Xu, Ying","last_name":"Xu","first_name":"Ying"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"287-298","publication":"Energy Storage Materials","citation":{"chicago":"He, Ren, Linlin Yang, Yu Zhang, Xiang Wang, Seungho Lee, Ting Zhang, Lingxiao Li, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials. Elsevier, 2023. https://doi.org/10.1016/j.ensm.2023.03.022.","short":"R. He, L. Yang, Y. Zhang, X. Wang, S. Lee, T. Zhang, L. Li, Z. Liang, J. Chen, J. Li, A. Ostovari Moghaddam, J. Llorca, M. Ibáñez, J. Arbiol, Y. Xu, A. Cabot, Energy Storage Materials 58 (2023) 287–298.","mla":"He, Ren, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” Energy Storage Materials, vol. 58, no. 4, Elsevier, 2023, pp. 287–98, doi:10.1016/j.ensm.2023.03.022.","apa":"He, R., Yang, L., Zhang, Y., Wang, X., Lee, S., Zhang, T., … Cabot, A. (2023). A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. Elsevier. https://doi.org/10.1016/j.ensm.2023.03.022","ieee":"R. He et al., “A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance,” Energy Storage Materials, vol. 58, no. 4. Elsevier, pp. 287–298, 2023.","ista":"He R, Yang L, Zhang Y, Wang X, Lee S, Zhang T, Li L, Liang Z, Chen J, Li J, Ostovari Moghaddam A, Llorca J, Ibáñez M, Arbiol J, Xu Y, Cabot A. 2023. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 58(4), 287–298.","ama":"He R, Yang L, Zhang Y, et al. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 2023;58(4):287-298. doi:10.1016/j.ensm.2023.03.022"},"date_published":"2023-04-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2.","lang":"eng"}],"issue":"4","status":"public","title":"A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance","intvolume":" 58","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12832","oa_version":"None"},{"publication_status":"published","department":[{"_id":"JePa"}],"publisher":"Wiley","acknowledgement":"Army Research Office. Grant Number: W911NF-20-1-0112","year":"2023","date_updated":"2023-08-01T14:06:50Z","date_created":"2023-04-12T08:30:03Z","volume":5,"author":[{"full_name":"Martinet, Quentin","first_name":"Quentin","last_name":"Martinet","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab"},{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A"}],"article_number":"2200129","file_date_updated":"2023-04-17T06:44:17Z","quality_controlled":"1","isi":1,"external_id":{"isi":["000852291200001"],"arxiv":["2201.03333"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/aisy.202200129","month":"01","publication_identifier":{"issn":["2640-4567"]},"title":"Rotation control, interlocking, and self‐positioning of active cogwheels","ddc":["530"],"status":"public","intvolume":" 5","_id":"12822","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_size":2414125,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_AdvancedIntelligentSystems_Martinet.pdf","checksum":"d48fc41d39892e7fa0d44cb352dd46aa","success":1,"date_created":"2023-04-17T06:44:17Z","date_updated":"2023-04-17T06:44:17Z","relation":"main_file","file_id":"12840"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Gears and cogwheels are elemental components of machines. They restrain degrees of freedom and channel power into a specified motion. Building and powering small-scale cogwheels are key steps toward feasible micro and nanomachinery. Assembly, energy injection, and control are, however, a challenge at the microscale. In contrast with passive gears, whose function is to transmit torques from one to another, interlocking and untethered active gears have the potential to unveil dynamics and functions untapped by externally driven mechanisms. Here, it is shown the assembly and control of a family of self-spinning cogwheels with varying teeth numbers and study the interlocking of multiple cogwheels. The teeth are formed by colloidal microswimmers that power the structure. The cogwheels are autonomous and active, showing persistent rotation. Leveraging the angular momentum of optical vortices, we control the direction of rotation of the cogwheels. The pairs of interlocking and active cogwheels that roll over each other in a random walk and have curvature-dependent mobility are studied. This behavior is leveraged to self-position parts and program microbots, demonstrating the ability to pick up, direct, and release a load. The work constitutes a step toward autonomous machinery with external control as well as (re)programmable microbots and matter."}],"issue":"1","article_type":"original","publication":"Advanced Intelligent Systems","citation":{"ama":"Martinet Q, Aubret A, Palacci JA. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 2023;5(1). doi:10.1002/aisy.202200129","apa":"Martinet, Q., Aubret, A., & Palacci, J. A. (2023). Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. Wiley. https://doi.org/10.1002/aisy.202200129","ieee":"Q. Martinet, A. Aubret, and J. A. Palacci, “Rotation control, interlocking, and self‐positioning of active cogwheels,” Advanced Intelligent Systems, vol. 5, no. 1. Wiley, 2023.","ista":"Martinet Q, Aubret A, Palacci JA. 2023. Rotation control, interlocking, and self‐positioning of active cogwheels. Advanced Intelligent Systems. 5(1), 2200129.","short":"Q. Martinet, A. Aubret, J.A. Palacci, Advanced Intelligent Systems 5 (2023).","mla":"Martinet, Quentin, et al. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems, vol. 5, no. 1, 2200129, Wiley, 2023, doi:10.1002/aisy.202200129.","chicago":"Martinet, Quentin, Antoine Aubret, and Jérémie A Palacci. “Rotation Control, Interlocking, and Self‐positioning of Active Cogwheels.” Advanced Intelligent Systems. Wiley, 2023. https://doi.org/10.1002/aisy.202200129."},"date_published":"2023-01-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"abstract":[{"lang":"eng","text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues."}],"type":"journal_article","file":[{"file_name":"2023_NatureComm_Brandstaetter.pdf","access_level":"open_access","creator":"dernst","file_size":4146777,"content_type":"application/pdf","file_id":"12821","relation":"main_file","date_created":"2023-04-11T06:27:00Z","date_updated":"2023-04-11T06:27:00Z","success":1,"checksum":"54f06f9eee11d43bab253f3492c983ba"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12818","status":"public","ddc":["570"],"title":"Curvature induces active velocity waves in rotating spherical tissues","intvolume":" 14","day":"24","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-03-24T00:00:00Z","publication":"Nature Communications","citation":{"ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 2023;14. doi:10.1038/s41467-023-37054-2","ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature, 2023, doi:10.1038/s41467-023-37054-2.","chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2."},"article_type":"original","file_date_updated":"2023-04-11T06:27:00Z","article_number":"1643","author":[{"first_name":"Tom","last_name":"Brandstätter","full_name":"Brandstätter, Tom"},{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner","full_name":"Brückner, David"},{"last_name":"Han","first_name":"Yu Long","full_name":"Han, Yu Long"},{"full_name":"Alert, Ricard","first_name":"Ricard","last_name":"Alert"},{"last_name":"Guo","first_name":"Ming","full_name":"Guo, Ming"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."}],"date_updated":"2023-08-01T14:05:30Z","date_created":"2023-04-09T22:01:00Z","volume":14,"acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","year":"2023","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"month":"03","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-37054-2","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["36964141"],"isi":["000959887700008"]},"quality_controlled":"1","isi":1},{"title":"Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling","status":"public","intvolume":" 107","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12819","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Reaching a high cavity population with a coherent pump in the strong-coupling regime of a single-atom laser is impossible due to the photon blockade effect. In this Letter, we experimentally demonstrate that in a single-atom maser based on a transmon strongly coupled to two resonators, it is possible to pump over a dozen photons into the system. The first high-quality resonator plays the role of a usual lasing cavity, and the second one presents a controlled dissipation channel, bolstering population inversion, and modifies the energy-level structure to lift the blockade. As confirmation of the lasing action, we observe conventional laser features such as a narrowing of the emission linewidth and external signal amplification. Additionally, we report unique single-atom features: self-quenching and several lasing thresholds.","lang":"eng"}],"issue":"3","article_type":"letter_note","publication":"Physical Review A","citation":{"chicago":"Sokolova, Alesya, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L031701.","mla":"Sokolova, Alesya, et al. “Overcoming Photon Blockade in a Circuit-QED Single-Atom Maser with Engineered Metastability and Strong Coupling.” Physical Review A, vol. 107, no. 3, L031701, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L031701.","short":"A. Sokolova, D.A. Kalacheva, G.P. Fedorov, O.V. Astafiev, Physical Review A 107 (2023).","ista":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. 2023. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 107(3), L031701.","apa":"Sokolova, A., Kalacheva, D. A., Fedorov, G. P., & Astafiev, O. V. (2023). Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L031701","ieee":"A. Sokolova, D. A. Kalacheva, G. P. Fedorov, and O. V. Astafiev, “Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling,” Physical Review A, vol. 107, no. 3. American Physical Society, 2023.","ama":"Sokolova A, Kalacheva DA, Fedorov GP, Astafiev OV. Overcoming photon blockade in a circuit-QED single-atom maser with engineered metastability and strong coupling. Physical Review A. 2023;107(3). doi:10.1103/PhysRevA.107.L031701"},"date_published":"2023-03-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","year":"2023","acknowledgement":"We thank N.N. Abramov for assistance with the experimental setup. The sample was fabricated using equipment of MIPT Shared Facilities Center. This research was supported by Russian Science Foundation, grant no. 21-72-30026.","date_updated":"2023-08-01T14:06:05Z","date_created":"2023-04-09T22:01:00Z","volume":107,"author":[{"full_name":"Sokolova, Alesya","first_name":"Alesya","last_name":"Sokolova","id":"2d0a0600-edfb-11eb-afb5-c0f5fa7f4f3a","orcid":"0000-0002-8308-4144"},{"full_name":"Kalacheva, D. A.","first_name":"D. A.","last_name":"Kalacheva"},{"full_name":"Fedorov, G. P.","first_name":"G. P.","last_name":"Fedorov"},{"full_name":"Astafiev, O. V.","last_name":"Astafiev","first_name":"O. V."}],"article_number":"L031701","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2209.05165","open_access":"1"}],"oa":1,"external_id":{"isi":["000957799000006"],"arxiv":["2209.05165"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.107.L031701","month":"03","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]}},{"file":[{"access_level":"open_access","file_name":"2023_NatureComm_Schmid.pdf","creator":"dernst","content_type":"application/pdf","file_size":1786475,"file_id":"12868","relation":"main_file","success":1,"checksum":"a4b3b7b36fbef068cabf4fb99501fef6","date_updated":"2023-04-25T09:13:53Z","date_created":"2023-04-25T09:13:53Z"}],"oa_version":"Published Version","ddc":["000"],"title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","status":"public","intvolume":" 14","_id":"12861","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations."}],"type":"journal_article","date_published":"2023-04-12T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023).","mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications, vol. 14, 2086, Springer Nature, 2023, doi:10.1038/s41467-023-37817-x.","chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37817-x.","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 2023;14. doi:10.1038/s41467-023-37817-x","apa":"Schmid, L., Ekbatani, F., Hilbe, C., & Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37817-x","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086."},"day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-08-01T14:15:57Z","date_created":"2023-04-23T22:01:03Z","volume":14,"author":[{"full_name":"Schmid, Laura","last_name":"Schmid","first_name":"Laura","orcid":"0000-0002-6978-7329","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ekbatani, Farbod","first_name":"Farbod","last_name":"Ekbatani"},{"full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","year":"2023","pmid":1,"file_date_updated":"2023-04-25T09:13:53Z","ec_funded":1,"article_number":"2086","language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-37817-x","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001003644100020"],"pmid":["37045828"]},"month":"04","publication_identifier":{"eissn":["2041-1723"]}},{"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1010983","quality_controlled":"1","isi":1,"external_id":{"isi":["000962668700002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1553-7358"]},"month":"04","volume":19,"date_updated":"2023-08-01T14:15:16Z","date_created":"2023-04-23T22:01:03Z","related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"author":[{"last_name":"Safavi","first_name":"Shervin","full_name":"Safavi, Shervin"},{"last_name":"Panagiotaropoulos","first_name":"Theofanis I.","full_name":"Panagiotaropoulos, Theofanis I."},{"last_name":"Kapoor","first_name":"Vishal","full_name":"Kapoor, Vishal"},{"first_name":"Juan F","last_name":"Ramirez Villegas","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","full_name":"Ramirez Villegas, Juan F"},{"full_name":"Logothetis, Nikos K.","last_name":"Logothetis","first_name":"Nikos K."},{"full_name":"Besserve, Michel","first_name":"Michel","last_name":"Besserve"}],"publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"publication_status":"published","acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","year":"2023","file_date_updated":"2023-04-25T08:59:18Z","article_number":"e1010983","date_published":"2023-04-01T00:00:00Z","article_type":"original","citation":{"ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 2023;19(4). doi:10.1371/journal.pcbi.1010983","ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., & Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010983","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” PLoS Computational Biology, vol. 19, no. 4. Public Library of Science, 2023.","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1010983.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1010983."},"publication":"PLoS Computational Biology","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","file_size":4737671,"content_type":"application/pdf","file_name":"2023_PLoSCompBio_Safavi.pdf","access_level":"open_access","date_updated":"2023-04-25T08:59:18Z","date_created":"2023-04-25T08:59:18Z","success":1,"checksum":"edeb9d09f3e41ba7c0251308b9e372e7","file_id":"12867","relation":"main_file"}],"intvolume":" 19","title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","status":"public","ddc":["570"],"_id":"12862","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"4","abstract":[{"text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings.","lang":"eng"}],"type":"journal_article"},{"_id":"12879","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Physics-inspired machine learning of localized intensive properties","status":"public","ddc":["000","540"],"file":[{"date_created":"2023-05-02T07:17:05Z","date_updated":"2023-05-02T07:17:05Z","checksum":"5eeec69a51e192dcd94b955d84423836","success":1,"relation":"main_file","file_id":"12883","file_size":1515446,"content_type":"application/pdf","creator":"dernst","file_name":"2023_ChemialScience_Chen.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations.","lang":"eng"}],"citation":{"chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sc00841j.","mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” Chemical Science, Royal Society of Chemistry, 2023, doi:10.1039/d3sc00841j.","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science.","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” Chemical Science. Royal Society of Chemistry, 2023.","apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., & Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. Chemical Science. Royal Society of Chemistry. https://doi.org/10.1039/d3sc00841j","ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. Chemical Science. 2023. doi:10.1039/d3sc00841j"},"publication":"Chemical Science","article_type":"original","date_published":"2023-04-10T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"10","acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","year":"2023","publisher":"Royal Society of Chemistry","department":[{"_id":"BiCh"}],"publication_status":"published","author":[{"full_name":"Chen, Ke","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","first_name":"Ke","last_name":"Chen"},{"full_name":"Kunkel, Christian","last_name":"Kunkel","first_name":"Christian"},{"full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Reuter, Karsten","first_name":"Karsten","last_name":"Reuter"},{"last_name":"Margraf","first_name":"Johannes T.","full_name":"Margraf, Johannes T."}],"date_created":"2023-04-30T22:01:06Z","date_updated":"2023-08-01T14:18:10Z","file_date_updated":"2023-05-02T07:17:05Z","license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000971508100001"]},"quality_controlled":"1","isi":1,"doi":"10.1039/d3sc00841j","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"month":"04"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12878","status":"public","title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","intvolume":" 115","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components."}],"issue":"1","publication":"Plant Journal","citation":{"mla":"Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:10.1111/tpj.16218.","short":"L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174.","chicago":"Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” Plant Journal. Wiley, 2023. https://doi.org/10.1111/tpj.16218.","ama":"Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 2023;115(1):155-174. doi:10.1111/tpj.16218","ista":"Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174.","apa":"Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. Wiley. https://doi.org/10.1111/tpj.16218","ieee":"L. Jiang et al., “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” Plant Journal, vol. 115, no. 1. Wiley, pp. 155–174, 2023."},"article_type":"original","page":"155-174","date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","acknowledgement":"The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","author":[{"full_name":"Jiang, Lihui","last_name":"Jiang","first_name":"Lihui"},{"first_name":"Baolin","last_name":"Yao","full_name":"Yao, Baolin"},{"full_name":"Zhang, Xiaoyan","last_name":"Zhang","first_name":"Xiaoyan"},{"full_name":"Wu, Lixia","first_name":"Lixia","last_name":"Wu"},{"full_name":"Fu, Qijing","first_name":"Qijing","last_name":"Fu"},{"full_name":"Zhao, Yiting","first_name":"Yiting","last_name":"Zhao"},{"last_name":"Cao","first_name":"Yuxin","full_name":"Cao, Yuxin"},{"full_name":"Zhu, Ruomeng","first_name":"Ruomeng","last_name":"Zhu"},{"full_name":"Lu, Xinqi","first_name":"Xinqi","last_name":"Lu"},{"last_name":"Huang","first_name":"Wuying","full_name":"Huang, Wuying"},{"first_name":"Jianping","last_name":"Zhao","full_name":"Zhao, Jianping"},{"first_name":"Kuixiu","last_name":"Li","full_name":"Li, Kuixiu"},{"last_name":"Zhao","first_name":"Shuanglu","full_name":"Zhao, Shuanglu"},{"full_name":"Han, Li","last_name":"Han","first_name":"Li"},{"full_name":"Zhou, Xuan","last_name":"Zhou","first_name":"Xuan"},{"last_name":"Luo","first_name":"Chongyu","full_name":"Luo, Chongyu"},{"full_name":"Zhu, Haiyan","last_name":"Zhu","first_name":"Haiyan"},{"full_name":"Yang, Jing","last_name":"Yang","first_name":"Jing"},{"full_name":"Huang, Huichuan","last_name":"Huang","first_name":"Huichuan"},{"full_name":"Zhu, Zhengge","first_name":"Zhengge","last_name":"Zhu"},{"last_name":"He","first_name":"Xiahong","full_name":"He, Xiahong"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"Zhongkai","last_name":"Zhang","full_name":"Zhang, Zhongkai"},{"full_name":"Liu, Changning","last_name":"Liu","first_name":"Changning"},{"last_name":"Du","first_name":"Yunlong","full_name":"Du, Yunlong"}],"date_updated":"2023-08-01T14:16:33Z","date_created":"2023-04-30T22:01:06Z","volume":115,"external_id":{"pmid":["37025008 "],"isi":["000971861400001"]},"isi":1,"quality_controlled":"1","doi":"10.1111/tpj.16218","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]}},{"article_number":"btad158","ec_funded":1,"file_date_updated":"2023-05-02T07:39:04Z","pmid":1,"acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","year":"2023","department":[{"_id":"ToHe"}],"publisher":"Oxford Academic","publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"author":[{"first_name":"Nikola","last_name":"Beneš","full_name":"Beneš, Nikola"},{"last_name":"Brim","first_name":"Luboš","full_name":"Brim, Luboš"},{"last_name":"Huvar","first_name":"Ondřej","full_name":"Huvar, Ondřej"},{"last_name":"Pastva","first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel"},{"full_name":"Šafránek, David","last_name":"Šafránek","first_name":"David"}],"volume":39,"date_created":"2023-04-30T22:01:05Z","date_updated":"2023-08-01T14:27:28Z","publication_identifier":{"eissn":["1367-4811"]},"month":"04","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"quality_controlled":"1","isi":1,"doi":"10.1093/bioinformatics/btad158","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data."}],"_id":"12876","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 39","ddc":["000"],"status":"public","title":"Boolean network sketches: A unifying framework for logical model inference","file":[{"file_size":478740,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_Bioinformatics_Benes.pdf","checksum":"2cb90ddf781baefddf47eac4b54e2a03","success":1,"date_updated":"2023-05-02T07:39:04Z","date_created":"2023-05-02T07:39:04Z","relation":"main_file","file_id":"12886"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03","citation":{"apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad158","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” Bioinformatics, vol. 39, no. 4. Oxford Academic, 2023.","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 2023;39(4). doi:10.1093/bioinformatics/btad158","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad158.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” Bioinformatics, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:10.1093/bioinformatics/btad158."},"publication":"Bioinformatics","article_type":"original","date_published":"2023-04-03T00:00:00Z"},{"ddc":["570"],"title":"Lamin B1 overexpression alters chromatin organization and gene expression","status":"public","intvolume":" 14","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12880","file":[{"relation":"main_file","file_id":"12884","date_updated":"2023-05-02T07:24:55Z","date_created":"2023-05-02T07:24:55Z","checksum":"8e707eda84f64dbad7f03545ae0a83ef","success":1,"file_name":"2023_Nucleus_Kaneshiro.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3811113,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1."}],"issue":"1","article_type":"original","publication":"Nucleus","citation":{"mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus, vol. 14, no. 1, 2202548, Taylor & Francis, 2023, doi:10.1080/19491034.2023.2202548.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” Nucleus. Taylor & Francis, 2023. https://doi.org/10.1080/19491034.2023.2202548.","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 2023;14(1). doi:10.1080/19491034.2023.2202548","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","apa":"Kaneshiro, J. M., Capitanio, J. S., & Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. Taylor & Francis. https://doi.org/10.1080/19491034.2023.2202548","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” Nucleus, vol. 14, no. 1. Taylor & Francis, 2023."},"date_published":"2023-04-18T00:00:00Z","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Taylor & Francis","department":[{"_id":"MaHe"}],"year":"2023","acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","pmid":1,"date_updated":"2023-08-01T14:18:46Z","date_created":"2023-04-30T22:01:06Z","volume":14,"author":[{"first_name":"Jeanae M.","last_name":"Kaneshiro","full_name":"Kaneshiro, Jeanae M."},{"last_name":"Capitanio","first_name":"Juliana S.","full_name":"Capitanio, Juliana S."},{"full_name":"Hetzer, Martin W","first_name":"Martin W","last_name":"Hetzer","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"article_number":"2202548","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2023-05-02T07:24:55Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["37071033"],"isi":["000971629400001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1080/19491034.2023.2202548","month":"04","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]}},{"author":[{"first_name":"Fumika","last_name":"Suzuki","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","orcid":"0000-0003-4982-5970","full_name":"Suzuki, Fumika"},{"full_name":"Unruh, William G.","first_name":"William G.","last_name":"Unruh"}],"volume":107,"date_created":"2023-05-07T22:01:03Z","date_updated":"2023-08-01T14:33:21Z","acknowledgement":"We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done.","year":"2023","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","ec_funded":1,"article_number":"042216","doi":"10.1103/PhysRevA.107.042216","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2207.13130"}],"external_id":{"arxiv":["2207.13130"],"isi":["000975799300006"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"month":"04","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12914","intvolume":" 107","status":"public","title":"Numerical quantum clock simulations for measuring tunneling times","issue":"4","abstract":[{"lang":"eng","text":"We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier."}],"type":"journal_article","date_published":"2023-04-20T00:00:00Z","citation":{"chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.042216.","mla":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” Physical Review A, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:10.1103/PhysRevA.107.042216.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).","ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216.","ieee":"F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” Physical Review A, vol. 107, no. 4. American Physical Society, 2023.","apa":"Suzuki, F., & Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.042216","ama":"Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 2023;107(4). doi:10.1103/PhysRevA.107.042216"},"publication":"Physical Review A","article_type":"original","article_processing_charge":"No","day":"20","scopus_import":"1"},{"doi":"10.1038/s41467-023-38005-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000979744000004"],"pmid":["37100775"]},"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"month":"04","author":[{"first_name":"J.","last_name":"Díez-Mérida","full_name":"Díez-Mérida, J."},{"last_name":"Díez-Carlón","first_name":"A.","full_name":"Díez-Carlón, A."},{"last_name":"Yang","first_name":"S. Y.","full_name":"Yang, S. Y."},{"full_name":"Xie, Y. M.","last_name":"Xie","first_name":"Y. M."},{"first_name":"X. J.","last_name":"Gao","full_name":"Gao, X. J."},{"first_name":"Jorden L","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L"},{"full_name":"Watanabe, K.","last_name":"Watanabe","first_name":"K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"last_name":"Lu","first_name":"X.","full_name":"Lu, X."},{"last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"first_name":"K. T.","last_name":"Law","full_name":"Law, K. T."},{"full_name":"Efetov, Dmitri K.","last_name":"Efetov","first_name":"Dmitri K."}],"volume":14,"date_updated":"2023-08-01T14:34:00Z","date_created":"2023-05-07T22:01:03Z","pmid":1,"acknowledgement":"We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.","year":"2023","department":[{"_id":"AnHi"}],"publisher":"Springer Nature","publication_status":"published","file_date_updated":"2023-05-08T07:26:40Z","article_number":"2396","date_published":"2023-04-26T00:00:00Z","citation":{"mla":"Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications, vol. 14, 2396, Springer Nature, 2023, doi:10.1038/s41467-023-38005-7.","short":"J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023).","chicago":"Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38005-7.","ama":"Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 2023;14. doi:10.1038/s41467-023-38005-7","ista":"Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396.","apa":"Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38005-7","ieee":"J. Díez-Mérida et al., “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” Nature Communications, vol. 14. Springer Nature, 2023."},"publication":"Nature Communications","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12917","checksum":"a778105665c10beb2354c92d2b295115","success":1,"date_created":"2023-05-08T07:26:40Z","date_updated":"2023-05-08T07:26:40Z","access_level":"open_access","file_name":"2023_NatureComm_DiezMerida.pdf","file_size":1405588,"content_type":"application/pdf","creator":"dernst"}],"_id":"12913","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 14","status":"public","ddc":["530"],"title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","abstract":[{"lang":"eng","text":"The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices."}],"type":"journal_article"},{"month":"06","publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2109.12019"],"isi":["001002343400002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00332-023-09926-w","article_number":"66","file_date_updated":"2023-06-19T07:33:53Z","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","acknowledgement":"We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz.","year":"2023","date_created":"2021-12-16T12:15:35Z","date_updated":"2023-08-01T14:40:33Z","volume":33,"author":[{"first_name":"Klemens","last_name":"Fellner","full_name":"Fellner, Klemens"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"},{"full_name":"Kniely, Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","first_name":"Michael","last_name":"Kniely"},{"last_name":"Tang","first_name":"Bao Quoc","full_name":"Tang, Bao Quoc"}],"scopus_import":"1","day":"07","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Journal of Nonlinear Science","citation":{"ama":"Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w","ista":"Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66.","ieee":"K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.","apa":"Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w","mla":"Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023).","chicago":"Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature, 2023. https://doi.org/10.1007/s00332-023-09926-w."},"date_published":"2023-06-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter."}],"status":"public","title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","ddc":["510"],"intvolume":" 33","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10550","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"13149","checksum":"f3f0f0886098e31c81116cff8183750b","success":1,"date_created":"2023-06-19T07:33:53Z","date_updated":"2023-06-19T07:33:53Z","access_level":"open_access","file_name":"2023_JourNonlinearScience_Fellner.pdf","content_type":"application/pdf","file_size":742315,"creator":"dernst"}]},{"scopus_import":"1","day":"20","has_accepted_license":"1","article_processing_charge":"No","publication":"Interfaces and Free Boundaries","citation":{"ama":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 2023;25(1):37-107. doi:10.4171/IFB/484","ista":"Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107.","apa":"Hensel, S., & Laux, T. (2023). Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. EMS Press. https://doi.org/10.4171/IFB/484","ieee":"S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” Interfaces and Free Boundaries, vol. 25, no. 1. EMS Press, pp. 37–107, 2023.","mla":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries, vol. 25, no. 1, EMS Press, 2023, pp. 37–107, doi:10.4171/IFB/484.","short":"S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.","chicago":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” Interfaces and Free Boundaries. EMS Press, 2023. https://doi.org/10.4171/IFB/484."},"article_type":"original","page":"37-107","date_published":"2023-04-20T00:00:00Z","type":"journal_article","abstract":[{"text":"We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction\r\nof a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting along triple junctions.","lang":"eng"}],"issue":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13043","ddc":["510"],"status":"public","title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","intvolume":" 25","oa_version":"Published Version","file":[{"file_id":"13045","relation":"main_file","success":1,"checksum":"622422484810441e48f613e968c7e7a4","date_updated":"2023-05-22T07:24:13Z","date_created":"2023-05-22T07:24:13Z","access_level":"open_access","file_name":"2023_Interfaces_Hensel.pdf","creator":"dernst","file_size":867876,"content_type":"application/pdf"}],"month":"04","publication_identifier":{"issn":["1463-9963"],"eissn":["1463-9971"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2108.01733"],"isi":["000975817300002"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"doi":"10.4171/IFB/484","language":[{"iso":"eng"}],"file_date_updated":"2023-05-22T07:24:13Z","ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.","year":"2023","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"EMS Press","author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"}],"related_material":{"record":[{"id":"10013","relation":"earlier_version","status":"public"}]},"date_created":"2023-05-21T22:01:06Z","date_updated":"2023-08-01T14:43:29Z","volume":25},{"publication":"The Journal of Chemical Physics","citation":{"mla":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:10.1063/5.0146711.","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” The Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0146711.","ama":"Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 2023;158(16). doi:10.1063/5.0146711","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","ieee":"R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” The Journal of Chemical Physics, vol. 158, no. 16. AIP Publishing, 2023.","apa":"Schmid, R., & Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0146711"},"article_type":"original","date_published":"2023-04-24T00:00:00Z","scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","_id":"12912","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["540"],"title":"Computing chemical potentials of adsorbed or confined fluids","status":"public","intvolume":" 158","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12918","checksum":"4ab8c965f2fa4e17920bfa846847f137","success":1,"date_updated":"2023-05-08T07:44:49Z","date_created":"2023-05-08T07:44:49Z","access_level":"open_access","file_name":"2023_JourChemicalPhysics_Schmid.pdf","file_size":6499468,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.","lang":"eng"}],"issue":"16","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2302.01297"],"pmid":["37093149"],"isi":["001010676000010"]},"isi":1,"quality_controlled":"1","doi":"10.1063/5.0146711","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["1089-7690"]},"acknowledgement":"We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"BiCh"}],"publisher":"AIP Publishing","author":[{"full_name":"Schmid, Rochus","first_name":"Rochus","last_name":"Schmid"},{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"related_material":{"link":[{"url":"https://github.com/BingqingCheng/mu-adsorption","relation":"software"},{"relation":"software","url":"https://github.com/BingqingCheng/S0"}]},"date_updated":"2023-08-01T14:34:49Z","date_created":"2023-05-07T22:01:03Z","volume":158,"article_number":"161101 ","file_date_updated":"2023-05-08T07:44:49Z"},{"department":[{"_id":"BeBi"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 715767 – MATERIALIZABLE), and FWF Lise Meitner (Grant M 3319). We thank the anonymous reviewers for their insightful feedback; Solal Pirelli, Shardul Chiplunkar, and Paola Mejia for proofreading; everyone in the visual computing group at ISTA for inspiring lunch and coffee breaks; Thibault Tricard for help producing the results of Phasor Noise.","year":"2023","volume":42,"date_updated":"2023-08-01T14:47:05Z","date_created":"2023-05-16T08:47:25Z","author":[{"full_name":"Liu, Zhenyuan","last_name":"Liu","first_name":"Zhenyuan","orcid":"0000-0001-9200-5690","id":"70f0d7cf-ae65-11ec-a14f-89dfc5505b19"},{"full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","last_name":"Piovarci","first_name":"Michael"},{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian"},{"last_name":"Charrondiere","first_name":"Raphael","id":"a3a24133-2cc7-11ec-be88-8ddaf6f464b1","full_name":"Charrondiere, Raphael"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2023-05-16T08:28:37Z","project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["001000062600033"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/cgf.14770 ","conference":{"start_date":"2023-05-08","location":"Saarbrucken, Germany","end_date":"2023-05-12","name":"EG: Eurographics"},"publication_identifier":{"issn":["1467-8659"]},"month":"05","intvolume":" 42","ddc":["004"],"status":"public","title":"Directionality-aware design of embroidery patterns","_id":"12972","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":24003702,"content_type":"application/pdf","creator":"mpiovarc","access_level":"open_access","file_name":"Zhenyuan2023.pdf","checksum":"4c188c2be4745467a8790bbf5d6491aa","success":1,"date_updated":"2023-05-16T08:28:37Z","date_created":"2023-05-16T08:28:37Z","relation":"main_file","file_id":"12974"}],"oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Embroidery is a long-standing and high-quality approach to making logos and images on textiles. Nowadays, it can also be performed via automated machines that weave threads with high spatial accuracy. A characteristic feature of the appearance of the threads is a high degree of anisotropy. The anisotropic behavior is caused by depositing thin but long strings of thread. As a result, the stitched patterns convey both color and direction. Artists leverage this anisotropic behavior to enhance pure color images with textures, illusions of motion, or depth cues. However, designing colorful embroidery patterns with prescribed directionality is a challenging task, one usually requiring an expert designer. In this work, we propose an interactive algorithm that generates machine-fabricable embroidery patterns from multi-chromatic images equipped with user-specified directionality fields.We cast the problem of finding a stitching pattern into vector theory. To find a suitable stitching pattern, we extract sources and sinks from the divergence field of the vector field extracted from the input and use them to trace streamlines. We further optimize the streamlines to guarantee a smooth and connected stitching pattern. The generated patterns approximate the color distribution constrained by the directionality field. To allow for further artistic control, the trade-off between color match and directionality match can be interactively explored via an intuitive slider. We showcase our approach by fabricating several embroidery paths."}],"page":"397-409","article_type":"original","citation":{"ista":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. 2023. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 42(2), 397–409.","apa":"Liu, Z., Piovarci, M., Hafner, C., Charrondiere, R., & Bickel, B. (2023). Directionality-aware design of embroidery patterns. Computer Graphics Forum. Saarbrucken, Germany: Wiley. https://doi.org/10.1111/cgf.14770 ","ieee":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, and B. Bickel, “Directionality-aware design of embroidery patterns,” Computer Graphics Forum, vol. 42, no. 2. Wiley, pp. 397–409, 2023.","ama":"Liu Z, Piovarci M, Hafner C, Charrondiere R, Bickel B. Directionality-aware design of embroidery patterns. Computer Graphics Forum. 2023;42(2):397-409. doi:10.1111/cgf.14770 ","chicago":"Liu, Zhenyuan, Michael Piovarci, Christian Hafner, Raphael Charrondiere, and Bernd Bickel. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum. Wiley, 2023. https://doi.org/10.1111/cgf.14770 .","mla":"Liu, Zhenyuan, et al. “Directionality-Aware Design of Embroidery Patterns.” Computer Graphics Forum, vol. 42, no. 2, Wiley, 2023, pp. 397–409, doi:10.1111/cgf.14770 .","short":"Z. Liu, M. Piovarci, C. Hafner, R. Charrondiere, B. Bickel, Computer Graphics Forum 42 (2023) 397–409."},"publication":"Computer Graphics Forum","date_published":"2023-05-08T00:00:00Z","keyword":["embroidery","design","directionality","density","image"],"has_accepted_license":"1","article_processing_charge":"No","day":"08"},{"date_published":"2023-05-17T00:00:00Z","article_type":"original","publication":"Scientific Reports","citation":{"chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35162-z.","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” Scientific Reports, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:10.1038/s41598-023-35162-z.","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., & Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35162-z","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” Scientific Reports, vol. 13, no. 1. Springer Nature, 2023.","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 2023;13(1). doi:10.1038/s41598-023-35162-z"},"day":"17","article_processing_charge":"No","has_accepted_license":"1","keyword":["Multidisciplinary"],"scopus_import":"1","file":[{"file_id":"13047","relation":"main_file","date_updated":"2023-05-22T07:57:37Z","date_created":"2023-05-22T07:57:37Z","success":1,"checksum":"8c1b769693ff4288df8376e59ad1176d","file_name":"2023_ScientificReports_Zavadakova.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3055077}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","intvolume":" 13","_id":"13033","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases."}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/s41598-023-35162-z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000995271600104"]},"month":"05","publication_identifier":{"issn":["2045-2322"]},"date_created":"2023-05-19T11:12:25Z","date_updated":"2023-08-01T14:46:06Z","volume":13,"author":[{"full_name":"Zavadakova, Anna","last_name":"Zavadakova","first_name":"Anna"},{"last_name":"Vistejnova","first_name":"Lucie","full_name":"Vistejnova, Lucie"},{"full_name":"Belinova, Tereza","id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","first_name":"Tereza","last_name":"Belinova"},{"last_name":"Tichanek","first_name":"Filip","full_name":"Tichanek, Filip"},{"full_name":"Bilikova, Dagmar","first_name":"Dagmar","last_name":"Bilikova"},{"full_name":"Mouton, Peter R.","first_name":"Peter R.","last_name":"Mouton"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-023-37265-z","relation":"erratum"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"Bio"}],"year":"2023","acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","file_date_updated":"2023-05-22T07:57:37Z","article_number":"7959"},{"date_published":"2023-05-04T00:00:00Z","article_type":"original","page":"10700–10711","publication":"Journal of the American Chemical Society","citation":{"mla":"Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:10.1021/jacs.3c01200.","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711.","chicago":"Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200.","ama":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200","ista":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711.","apa":"Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c01200","ieee":"L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” Journal of the American Chemical Society, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023."},"day":"04","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2023_JACS_Troussicot.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6719299,"creator":"dernst","relation":"main_file","file_id":"13098","date_created":"2023-05-30T07:05:28Z","date_updated":"2023-05-30T07:05:28Z","checksum":"0758a930ef21c62fc91b14e657479f83","success":1}],"title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","status":"public","ddc":["540"],"intvolume":" 145","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13095","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.","lang":"eng"}],"issue":"19","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1021/jacs.3c01200","quality_controlled":"1","isi":1,"external_id":{"isi":["000985907400001"],"pmid":["37140345"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"05","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"date_created":"2023-05-28T22:01:04Z","date_updated":"2023-08-01T14:48:09Z","volume":145,"author":[{"last_name":"Troussicot","first_name":"Laura","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3","full_name":"Troussicot, Laura"},{"full_name":"Vallet, Alicia","last_name":"Vallet","first_name":"Alicia"},{"full_name":"Molin, Mikael","first_name":"Mikael","last_name":"Molin"},{"full_name":"Burmann, Björn M.","first_name":"Björn M.","last_name":"Burmann"},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"related_material":{"record":[{"id":"12820","status":"public","relation":"research_data"}]},"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"PaSc"}],"year":"2023","acknowledgement":"We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. ","pmid":1,"file_date_updated":"2023-05-30T07:05:28Z"},{"publication_identifier":{"eissn":["1077-8926"]},"month":"05","doi":"10.37236/11471","language":[{"iso":"eng"}],"external_id":{"isi":["000988285500001"],"arxiv":["2105.13828"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2023-05-22T07:43:19Z","article_number":"P2.21","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos","full_name":"Anastos, Michael"}],"volume":30,"date_created":"2023-05-21T22:01:05Z","date_updated":"2023-08-01T14:44:52Z","acknowledgement":"We would like to thank the reviewers for their helpful comments and remarks.","year":"2023","department":[{"_id":"MaKw"}],"publisher":"Electronic Journal of Combinatorics","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"05","scopus_import":"1","date_published":"2023-05-05T00:00:00Z","citation":{"chicago":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2023. https://doi.org/10.37236/11471.","mla":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” Electronic Journal of Combinatorics, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics, 2023, doi:10.37236/11471.","short":"M. Anastos, Electronic Journal of Combinatorics 30 (2023).","ista":"Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21.","apa":"Anastos, M. (2023). A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/11471","ieee":"M. Anastos, “A note on long cycles in sparse random graphs,” Electronic Journal of Combinatorics, vol. 30, no. 2. Electronic Journal of Combinatorics, 2023.","ama":"Anastos M. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 2023;30(2). doi:10.37236/11471"},"publication":"Electronic Journal of Combinatorics","article_type":"original","issue":"2","abstract":[{"text":"Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for c>20, thus extending a result of Frieze and the author to smaller values of c. Thereafter, for c>20, we determine the limit of the probability that G(n, c/n)contains cycles of every length between the length of its shortest and its longest cycles as n→∞.","lang":"eng"}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":448736,"file_name":"2023_JourCombinatorics_Anastos.pdf","access_level":"open_access","date_created":"2023-05-22T07:43:19Z","date_updated":"2023-05-22T07:43:19Z","success":1,"checksum":"6269ed3b3eded6536d3d9d6baad2d5b9","file_id":"13046","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13042","intvolume":" 30","status":"public","ddc":["510"],"title":"A note on long cycles in sparse random graphs"},{"date_published":"2023-04-18T00:00:00Z","doi":"10.15479/AT:ISTA:12820","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"citation":{"mla":"Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820.","short":"P. Schanda, (2023).","chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.","ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820","ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820","ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023."},"month":"04","day":"18","has_accepted_license":"1","article_processing_charge":"No","author":[{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13095"}]},"contributor":[{"last_name":"Troussicot","contributor_type":"researcher","first_name":"Laura"},{"first_name":"Björn M.","contributor_type":"researcher","last_name":"Burmann"}],"date_created":"2023-04-10T05:55:56Z","date_updated":"2023-08-01T14:48:08Z","file":[{"date_updated":"2023-04-14T09:39:33Z","date_created":"2023-04-14T09:39:33Z","checksum":"54a619605e44c871214fb0e07b05c6bf","success":1,"relation":"main_file","file_id":"12823","file_size":54184807,"content_type":"application/zip","creator":"pschanda","file_name":"data_deposition.zip","access_level":"open_access"},{"content_type":"application/octet-stream","file_size":4978,"creator":"pschanda","access_level":"open_access","file_name":"README","checksum":"8dede9fc78399d13144eb05c62bf5750","success":1,"date_updated":"2023-04-14T09:39:58Z","date_created":"2023-04-14T09:39:58Z","relation":"main_file","file_id":"12824"}],"oa_version":"Published Version","year":"2023","_id":"12820","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","ddc":["570"],"department":[{"_id":"PaSc"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript","lang":"eng"}],"file_date_updated":"2023-04-14T09:39:58Z","type":"research_data"},{"publication":"Physical Review B","citation":{"short":"M. French, M. Bethkenhagen, A. Ravasio, J.A. Hernandez, Physical Review B 107 (2023).","mla":"French, Martin, et al. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B, vol. 107, no. 13, 134109, American Physical Society, 2023, doi:10.1103/PhysRevB.107.134109.","chicago":"French, Martin, Mandy Bethkenhagen, Alessandra Ravasio, and Jean Alexis Hernandez. “Ab Initio Calculation of the Reflectivity of Molecular Fluids under Shock Compression.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.134109.","ama":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 2023;107(13). doi:10.1103/PhysRevB.107.134109","apa":"French, M., Bethkenhagen, M., Ravasio, A., & Hernandez, J. A. (2023). Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.134109","ieee":"M. French, M. Bethkenhagen, A. Ravasio, and J. A. Hernandez, “Ab initio calculation of the reflectivity of molecular fluids under shock compression,” Physical Review B, vol. 107, no. 13. American Physical Society, 2023.","ista":"French M, Bethkenhagen M, Ravasio A, Hernandez JA. 2023. Ab initio calculation of the reflectivity of molecular fluids under shock compression. Physical Review B. 107(13), 134109."},"article_type":"original","date_published":"2023-04-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13039","title":"Ab initio calculation of the reflectivity of molecular fluids under shock compression","status":"public","intvolume":" 107","oa_version":"None","type":"journal_article","abstract":[{"text":"We calculate reflectivities of dynamically compressed water, water-ethanol mixtures, and ammonia at infrared and optical wavelengths with density functional theory and molecular dynamics simulations. The influence of the exchange-correlation functional on the results is examined in detail. Our findings indicate that the consistent use of the HSE hybrid functional reproduces experimental results much better than the commonly used PBE functional. The HSE functional offers not only a more accurate description of the electronic band gap but also shifts the onset of molecular dissociation in the molecular dynamics simulations to significantly higher pressures. We also highlight the importance of using accurate reference standards in reflectivity experiments and reanalyze infrared and optical reflectivity data from recent experiments. Thus, our combined theoretical and experimental work explains and resolves lingering discrepancies between calculations and measurements for the investigated molecular substances under shock compression.","lang":"eng"}],"issue":"13","external_id":{"isi":["000974672600001"]},"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevB.107.134109","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"acknowledgement":"We thank R. Redmer for helpful discussions. M.F. acknowledges support by the Deutsche Forschungsgemeinschaft (DFG) within the FOR 2440. M.B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Skłodowska-Curie actions (xICE Grant No. 894725) and the NOMIS foundation. A.R. and J.-A.H. acknowledge support form the French National Research Agency (ANR) through the projects POMPEI (Grant No. ANR-16-CE31-0008) and SUPER-ICES (Grant No. ANR-15-CE30-008-01). The ab initio calculations were performed at the NorthGerman Supercomputing Alliance (HLRN) facilities. ","year":"2023","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BiCh"}],"author":[{"last_name":"French","first_name":"Martin","full_name":"French, Martin"},{"first_name":"Mandy","last_name":"Bethkenhagen","id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","full_name":"Bethkenhagen, Mandy"},{"full_name":"Ravasio, Alessandra","first_name":"Alessandra","last_name":"Ravasio"},{"full_name":"Hernandez, Jean Alexis","last_name":"Hernandez","first_name":"Jean Alexis"}],"date_created":"2023-05-21T22:01:04Z","date_updated":"2023-08-01T14:45:25Z","volume":107,"article_number":"134109"},{"external_id":{"pmid":["37141543"],"isi":["000985497900001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"}],"doi":"10.1021/acsami.3c00625","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"year":"2023","acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). We thank Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X., and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial support from IST Austria.","pmid":1,"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"author":[{"last_name":"Nan","first_name":"Bingfei","full_name":"Nan, Bingfei"},{"full_name":"Song, Xuan","last_name":"Song","first_name":"Xuan"},{"full_name":"Chang, Cheng","last_name":"Chang","first_name":"Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"last_name":"Xiao","first_name":"Ke","full_name":"Xiao, Ke"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Yang, Linlin","first_name":"Linlin","last_name":"Yang"},{"full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"last_name":"Lim","first_name":"Khak Ho","full_name":"Lim, Khak Ho"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"date_created":"2023-05-28T22:01:03Z","date_updated":"2023-08-01T14:50:09Z","volume":15,"file_date_updated":"2023-05-30T07:38:44Z","publication":"ACS Applied Materials and Interfaces","citation":{"mla":"Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces, vol. 15, no. 19, American Chemical Society, 2023, pp. 23380–23389, doi:10.1021/acsami.3c00625.","short":"B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H. Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389.","chicago":"Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c00625.","ama":"Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 2023;15(19):23380–23389. doi:10.1021/acsami.3c00625","ista":"Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 15(19), 23380–23389.","ieee":"B. Nan et al., “Bottom-up synthesis of SnTe-based thermoelectric composites,” ACS Applied Materials and Interfaces, vol. 15, no. 19. American Chemical Society, pp. 23380–23389, 2023.","apa":"Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023). Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c00625"},"article_type":"original","page":"23380–23389","date_published":"2023-05-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","has_accepted_license":"1","_id":"13092","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["540"],"status":"public","title":"Bottom-up synthesis of SnTe-based thermoelectric composites","intvolume":" 15","oa_version":"Published Version","file":[{"file_size":5640829,"content_type":"application/pdf","creator":"dernst","file_name":"2023_ACSAppliedMaterials_Nan.pdf","access_level":"open_access","date_updated":"2023-05-30T07:38:44Z","date_created":"2023-05-30T07:38:44Z","checksum":"23893be46763c4c78daacddd019de821","success":1,"relation":"main_file","file_id":"13099"}],"type":"journal_article","abstract":[{"text":"There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe.","lang":"eng"}],"issue":"19"},{"type":"journal_article","abstract":[{"text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states.","lang":"eng"}],"issue":"10","ddc":["540"],"status":"public","title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","intvolume":" 23","_id":"13094","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2023_NanoLetters_Azadbakht.pdf","access_level":"open_access","file_size":3654910,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13100","date_created":"2023-05-30T07:55:31Z","date_updated":"2023-05-30T07:55:31Z","checksum":"9734d4c617bab3578ef62916b764547a","success":1}],"oa_version":"Published Version","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"No","article_type":"letter_note","page":"4267–4273","publication":"Nano Letters","citation":{"ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375."},"date_published":"2023-05-04T00:00:00Z","file_date_updated":"2023-05-30T07:55:31Z","ec_funded":1,"publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"American Chemical Society","acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","year":"2023","pmid":1,"date_updated":"2023-08-01T14:51:25Z","date_created":"2023-05-28T22:01:03Z","volume":23,"author":[{"last_name":"Azadbakht","first_name":"Ali","full_name":"Azadbakht, Ali"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","first_name":"Billie","last_name":"Meadowcroft","full_name":"Meadowcroft, Billie"},{"full_name":"Varkevisser, Thijs","last_name":"Varkevisser","first_name":"Thijs"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"last_name":"Kraft","first_name":"Daniela J.","full_name":"Kraft, Daniela J."}],"month":"05","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37141427"],"isi":["000985481400001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.3c00375"},{"publication_status":"epub_ahead","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"year":"2023","acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). B.N., M.L., Y.Z., K.X., and X.H. thank the China Scholarship Council (CSC) for the scholarship support. C.C. received funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. M.I. acknowledges the financial support from ISTA and the Werner Siemens Foundation. ICN2 acknowledges funding from Generalitat de Catalunya 2021SGR00457 and project NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/. ICN2 was supported by the Severo Ochoa program from Spanish MCIN/AEI (Grant No.: CEX2021-001214-S) and was funded by the CERCA Programme/Generalitat de Catalunya. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and 2021 SGR 01061. K.H.L. acknowledges support from the National Natural Science Foundation of China (22208293). This study is part of the Advanced Materials programme and was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat de Catalunya.","date_updated":"2023-08-01T14:50:48Z","date_created":"2023-05-28T22:01:03Z","author":[{"full_name":"Nan, Bingfei","last_name":"Nan","first_name":"Bingfei"},{"first_name":"Mengyao","last_name":"Li","full_name":"Li, Mengyao"},{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"},{"full_name":"Chang, Cheng","last_name":"Chang","first_name":"Cheng","orcid":"0000-0002-9515-4277","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"first_name":"Yong","last_name":"Zuo","full_name":"Zuo, Yong"},{"first_name":"Junshan","last_name":"Li","full_name":"Li, Junshan"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"month":"05","publication_identifier":{"eissn":["2637-6113"]},"isi":1,"quality_controlled":"1","project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889"},{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsaelm.3c00055"}],"oa":1,"external_id":{"isi":["000986859000001"]},"language":[{"iso":"eng"}],"doi":"10.1021/acsaelm.3c00055","type":"journal_article","abstract":[{"text":"The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated.","lang":"eng"}],"title":"Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature","status":"public","_id":"13093","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","scopus_import":"1","day":"05","article_processing_charge":"No","article_type":"original","publication":"ACS Applied Electronic Materials","citation":{"apa":"Nan, B., Li, M., Zhang, Y., Xiao, K., Lim, K. H., Chang, C., … Cabot, A. (2023). Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. American Chemical Society. https://doi.org/10.1021/acsaelm.3c00055","ieee":"B. Nan et al., “Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature,” ACS Applied Electronic Materials. American Chemical Society, 2023.","ista":"Nan B, Li M, Zhang Y, Xiao K, Lim KH, Chang C, Han X, Zuo Y, Li J, Arbiol J, Llorca J, Ibáñez M, Cabot A. 2023. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials.","ama":"Nan B, Li M, Zhang Y, et al. Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature. ACS Applied Electronic Materials. 2023. doi:10.1021/acsaelm.3c00055","chicago":"Nan, Bingfei, Mengyao Li, Yu Zhang, Ke Xiao, Khak Ho Lim, Cheng Chang, Xu Han, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaelm.3c00055.","short":"B. Nan, M. Li, Y. Zhang, K. Xiao, K.H. Lim, C. Chang, X. Han, Y. Zuo, J. Li, J. Arbiol, J. Llorca, M. Ibáñez, A. Cabot, ACS Applied Electronic Materials (2023).","mla":"Nan, Bingfei, et al. “Engineering of Thermoelectric Composites Based on Silver Selenide in Aqueous Solution and Ambient Temperature.” ACS Applied Electronic Materials, American Chemical Society, 2023, doi:10.1021/acsaelm.3c00055."},"date_published":"2023-05-05T00:00:00Z"},{"publication_identifier":{"eissn":["1944-7833"],"issn":["1937-0652"]},"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000996014700004"],"arxiv":["1810.06882"]},"project":[{"name":"Between rational and integral points","_id":"26A8D266-B435-11E9-9278-68D0E5697425","grant_number":"EP-P026710-2"}],"quality_controlled":"1","isi":1,"doi":"10.2140/ant.2023.17.719","language":[{"iso":"eng"}],"file_date_updated":"2023-05-30T08:05:22Z","acknowledgement":"The authors are grateful to Paul Nelson, Per Salberger and Jason Starr for useful comments. While working on this paper the first author was supported by EPRSC grant EP/P026710/1. The research was partially conducted during the period the second author served as a Clay Research Fellow, and partially conducted during the period he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zurich Foundation.","year":"2023","publisher":"Mathematical Sciences Publishers","department":[{"_id":"TiBr"}],"publication_status":"published","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"full_name":"Sawin, Will","last_name":"Sawin","first_name":"Will"}],"volume":17,"date_created":"2023-05-28T22:01:02Z","date_updated":"2023-08-01T14:51:57Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"12","citation":{"chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/ant.2023.17.719.","short":"T.D. Browning, W. Sawin, Algebra and Number Theory 17 (2023) 719–748.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Curves on Low Degree Hypersurfaces and the Circle Method.” Algebra and Number Theory, vol. 17, no. 3, Mathematical Sciences Publishers, 2023, pp. 719–48, doi:10.2140/ant.2023.17.719.","apa":"Browning, T. D., & Sawin, W. (2023). Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. Mathematical Sciences Publishers. https://doi.org/10.2140/ant.2023.17.719","ieee":"T. D. Browning and W. Sawin, “Free rational curves on low degree hypersurfaces and the circle method,” Algebra and Number Theory, vol. 17, no. 3. Mathematical Sciences Publishers, pp. 719–748, 2023.","ista":"Browning TD, Sawin W. 2023. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 17(3), 719–748.","ama":"Browning TD, Sawin W. Free rational curves on low degree hypersurfaces and the circle method. Algebra and Number Theory. 2023;17(3):719-748. doi:10.2140/ant.2023.17.719"},"publication":"Algebra and Number Theory","page":"719-748","article_type":"original","date_published":"2023-04-12T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We use a function field version of the Hardy–Littlewood circle method to study the locus of free rational curves on an arbitrary smooth projective hypersurface of sufficiently low degree. On the one hand this allows us to bound the dimension of the singular locus of the moduli space of rational curves on such hypersurfaces and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin conjecture in terms of slopes with respect to the tangent bundle."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13091","intvolume":" 17","status":"public","ddc":["510"],"title":"Free rational curves on low degree hypersurfaces and the circle method","file":[{"file_name":"2023_AlgebraNumberTheory_Browning.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1430719,"file_id":"13101","relation":"main_file","date_created":"2023-05-30T08:05:22Z","date_updated":"2023-05-30T08:05:22Z","success":1,"checksum":"5d5d67b235905650e33cf7065d7583b4"}],"oa_version":"Published Version"},{"ec_funded":1,"file_date_updated":"2023-06-06T07:31:20Z","article_number":"2998","volume":14,"date_updated":"2023-08-02T06:10:26Z","date_created":"2023-06-04T22:01:02Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"13124"}]},"author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"full_name":"Poshakinskiy, Alexander V.","first_name":"Alexander V.","last_name":"Poshakinskiy"},{"full_name":"Sett, Riya","first_name":"Riya","last_name":"Sett","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander N.","last_name":"Poddubny","full_name":"Poddubny, Alexander N."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"}],"department":[{"_id":"JoFi"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"The authors thank W.D. Oliver for discussions, L. Drmic and P. Zielinski for software development, and the MIBA workshop and the IST nanofabrication facility for technical support. This work was supported by the Austrian Science Fund (FWF) through BeyondC (F7105) and IST Austria. E.R. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. and M.Z. acknowledge support from the European Research Council under grant agreement No 758053 (ERC StG QUNNECT) and a NOMIS foundation research grant. The work of A.N.P. and A.V.P. has been supported by the Russian Science Foundation under the grant No 20-12-00194.","year":"2023","publication_identifier":{"eissn":["2041-1723"]},"month":"05","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"doi":"10.1038/s41467-023-38761-6","project":[{"name":"Integrating superconducting quantum circuits","call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"name":"Controllable Collective States of Superconducting Qubit Ensembles","_id":"26B354CA-B435-11E9-9278-68D0E5697425"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2205.03293"],"isi":["001001099700002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"lang":"eng","text":"The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"13123","date_updated":"2023-06-06T07:31:20Z","date_created":"2023-06-06T07:31:20Z","checksum":"a857df40f0882859c48a1ff1e2001ec2","success":1,"file_name":"2023_NaturePhysics_Redchenko.pdf","access_level":"open_access","file_size":1654389,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 14","title":"Tunable directional photon scattering from a pair of superconducting qubits","status":"public","ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13117","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","date_published":"2023-05-24T00:00:00Z","article_type":"original","citation":{"ieee":"E. Redchenko, A. V. Poshakinskiy, R. Sett, M. Zemlicka, A. N. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Redchenko, E., Poshakinskiy, A. V., Sett, R., Zemlicka, M., Poddubny, A. N., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38761-6","ista":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 14, 2998.","ama":"Redchenko E, Poshakinskiy AV, Sett R, Zemlicka M, Poddubny AN, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. Nature Communications. 2023;14. doi:10.1038/s41467-023-38761-6","chicago":"Redchenko, Elena, Alexander V. Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander N. Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38761-6.","short":"E. Redchenko, A.V. Poshakinskiy, R. Sett, M. Zemlicka, A.N. Poddubny, J.M. Fink, Nature Communications 14 (2023).","mla":"Redchenko, Elena, et al. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Nature Communications, vol. 14, 2998, Springer Nature, 2023, doi:10.1038/s41467-023-38761-6."},"publication":"Nature Communications"},{"oa_version":"Preprint","intvolume":" 380","title":"Entangling microwaves with light","status":"public","_id":"13106","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"6646","abstract":[{"text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification.","lang":"eng"}],"type":"journal_article","date_published":"2023-05-18T00:00:00Z","page":"718-721","article_type":"original","citation":{"chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adg3812.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721.","mla":"Sahu, Rishabh, et al. “Entangling Microwaves with Light.” Science, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:10.1126/science.adg3812.","ieee":"R. Sahu et al., “Entangling microwaves with light,” Science, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., & Fink, J. M. (2023). Entangling microwaves with light. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg3812","ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721.","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. Science. 2023;380(6646):718-721. doi:10.1126/science.adg3812"},"publication":"Science","article_processing_charge":"No","day":"18","keyword":["Multidisciplinary"],"volume":380,"date_created":"2023-05-31T11:39:24Z","date_updated":"2023-08-02T06:08:57Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"13122"}],"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/"}]},"author":[{"full_name":"Sahu, Rishabh","last_name":"Sahu","first_name":"Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Liu","last_name":"Qiu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu"},{"last_name":"Hease","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","full_name":"Hease, William J"},{"full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Y.","last_name":"Minoguchi","full_name":"Minoguchi, Y."},{"full_name":"Rabl, P.","first_name":"P.","last_name":"Rabl"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"}],"department":[{"_id":"JoFi"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2023","acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1126/science.adg3812","project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07105","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Integrating superconducting quantum circuits"},{"grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Quantum readout techniques and technologies"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["2301.03315"],"isi":["000996515200004"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.03315"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"month":"05"},{"publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]},"month":"05","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10208-023-09613-y"}],"oa":1,"external_id":{"isi":["000999623100001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10208-023-09613-y","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","publication_status":"epub_ahead","year":"2023","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","date_created":"2023-06-11T22:00:40Z","date_updated":"2023-08-02T06:12:39Z","author":[{"first_name":"Nicolas","last_name":"Clozeau","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas"},{"full_name":"Josien, Marc","first_name":"Marc","last_name":"Josien"},{"last_name":"Otto","first_name":"Felix","full_name":"Otto, Felix"},{"last_name":"Xu","first_name":"Qiang","full_name":"Xu, Qiang"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"30","article_type":"original","citation":{"ista":"Clozeau N, Josien M, Otto F, Xu Q. 2023. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics.","apa":"Clozeau, N., Josien, M., Otto, F., & Xu, Q. (2023). Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-023-09613-y","ieee":"N. Clozeau, M. Josien, F. Otto, and Q. Xu, “Bias in the representative volume element method: Periodize the ensemble instead of its realizations,” Foundations of Computational Mathematics. Springer Nature, 2023.","ama":"Clozeau N, Josien M, Otto F, Xu Q. Bias in the representative volume element method: Periodize the ensemble instead of its realizations. Foundations of Computational Mathematics. 2023. doi:10.1007/s10208-023-09613-y","chicago":"Clozeau, Nicolas, Marc Josien, Felix Otto, and Qiang Xu. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s10208-023-09613-y.","mla":"Clozeau, Nicolas, et al. “Bias in the Representative Volume Element Method: Periodize the Ensemble Instead of Its Realizations.” Foundations of Computational Mathematics, Springer Nature, 2023, doi:10.1007/s10208-023-09613-y.","short":"N. Clozeau, M. Josien, F. Otto, Q. Xu, Foundations of Computational Mathematics (2023)."},"publication":"Foundations of Computational Mathematics","date_published":"2023-05-30T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩\r\n, we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩\r\n of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function."}],"status":"public","title":"Bias in the representative volume element method: Periodize the ensemble instead of its realizations","ddc":["510"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13129","oa_version":"Published Version"},{"publisher":"Zenodo","department":[{"_id":"JoFi"}],"title":"Tunable directional photon scattering from a pair of superconducting qubits","status":"public","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13124","year":"2023","oa_version":"Published Version","date_created":"2023-06-06T07:36:50Z","date_updated":"2023-08-02T06:10:25Z","related_material":{"record":[{"id":"13117","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"last_name":"Poshakinskiy","first_name":"Alexander","full_name":"Poshakinskiy, Alexander"},{"id":"2E6D040E-F248-11E8-B48F-1D18A9856A87","last_name":"Sett","first_name":"Riya","full_name":"Sett, Riya"},{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka"},{"full_name":"Poddubny, Alexander","last_name":"Poddubny","first_name":"Alexander"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"}],"type":"research_data_reference","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","mla":"Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567.","chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567."},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7858567","open_access":"1"}],"doi":"10.5281/ZENODO.7858567","date_published":"2023-04-28T00:00:00Z","article_processing_charge":"No","day":"28","month":"04"},{"date_published":"2023-03-31T00:00:00Z","doi":"10.5281/ZENODO.7789417","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7789418","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417.","mla":"Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417.","short":"R. Sahu, (2023).","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417.","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417","ama":"Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417"},"oa":1,"month":"03","day":"31","article_processing_charge":"No","author":[{"first_name":"Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh"}],"related_material":{"record":[{"id":"13106","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-08-02T06:08:56Z","date_created":"2023-06-06T06:46:16Z","oa_version":"Published Version","_id":"13122","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","status":"public","title":"Entangling microwaves with light","publisher":"Zenodo","department":[{"_id":"JoFi"}],"abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"type":"research_data_reference"},{"type":"journal_article","abstract":[{"text":"Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans.","lang":"eng"}],"intvolume":" 13","ddc":["570"],"title":"The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization","status":"public","_id":"13166","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"baddf6b2fa9adf88263d4a3b0998f0f2","date_updated":"2023-06-26T09:58:53Z","date_created":"2023-06-26T09:58:53Z","file_id":"13170","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4844149,"access_level":"open_access","file_name":"2023_ScientificReports_Vetrova.pdf"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"09","article_type":"original","citation":{"short":"A.A. Vetrova, D.M. Kupaeva, A. Kizenko, T.S. Lebedeva, P. Walentek, N. Tsikolia, S.V. Kremnyov, Scientific Reports 13 (2023).","mla":"Vetrova, Alexandra A., et al. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports, vol. 13, 9382, Springer Nature, 2023, doi:10.1038/s41598-023-35979-8.","chicago":"Vetrova, Alexandra A., Daria M. Kupaeva, Alena Kizenko, Tatiana S. Lebedeva, Peter Walentek, Nikoloz Tsikolia, and Stanislav V. Kremnyov. “The Evolutionary History of Brachyury Genes in Hydrozoa Involves Duplications, Divergence, and Neofunctionalization.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-023-35979-8.","ama":"Vetrova AA, Kupaeva DM, Kizenko A, et al. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 2023;13. doi:10.1038/s41598-023-35979-8","apa":"Vetrova, A. A., Kupaeva, D. M., Kizenko, A., Lebedeva, T. S., Walentek, P., Tsikolia, N., & Kremnyov, S. V. (2023). The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-023-35979-8","ieee":"A. A. Vetrova et al., “The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization,” Scientific Reports, vol. 13. Springer Nature, 2023.","ista":"Vetrova AA, Kupaeva DM, Kizenko A, Lebedeva TS, Walentek P, Tsikolia N, Kremnyov SV. 2023. The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization. Scientific Reports. 13, 9382."},"publication":"Scientific Reports","date_published":"2023-06-09T00:00:00Z","article_number":"9382","file_date_updated":"2023-06-26T09:58:53Z","publisher":"Springer Nature","department":[{"_id":"GradSch"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank N.A. Pertsov White Sea Biological Station of Moscow State University for the help and support in obtaining samples and providing access to all required facilities and equipment of the “Center of Microscopy WSBS MSU”. We are grateful to Dr. Amro Hamdoun for pCS2+8 plasmid (Addgene plasmid # 34931).\r\nWork in the Walentek lab is supported by the Deutsche Forschungsgemeinschaft (DFG) under the Emmy Noether Programme (grant WA3365/2-2) and under Germany’s Excellence Strategy (CIBSS-EXC-2189-Project ID 390939984). SK is supported by the project No. 0088-2021-0009 of the Koltzov Institute of Developmental Biology of the RAS. The study of molecular patterning of D. pumila colony was funded by RFBR, project number 20-04-00978a (to S.K.).","year":"2023","volume":13,"date_created":"2023-06-25T22:00:46Z","date_updated":"2023-08-02T06:17:18Z","author":[{"last_name":"Vetrova","first_name":"Alexandra A.","full_name":"Vetrova, Alexandra A."},{"first_name":"Daria M.","last_name":"Kupaeva","full_name":"Kupaeva, Daria M."},{"full_name":"Kizenko, Alena","id":"a521c60b-0815-11ed-9b02-b8bd522477c8","first_name":"Alena","last_name":"Kizenko"},{"first_name":"Tatiana S.","last_name":"Lebedeva","full_name":"Lebedeva, Tatiana S."},{"last_name":"Walentek","first_name":"Peter","full_name":"Walentek, Peter"},{"full_name":"Tsikolia, Nikoloz","first_name":"Nikoloz","last_name":"Tsikolia"},{"full_name":"Kremnyov, Stanislav V.","first_name":"Stanislav V.","last_name":"Kremnyov"}],"publication_identifier":{"eissn":["2045-2322"]},"month":"06","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37296138"],"isi":["001006690200045"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-023-35979-8"},{"article_number":"184312","acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","year":"2023","department":[{"_id":"GradSch"}],"publisher":"American Physical Society","publication_status":"published","author":[{"last_name":"Orlov","first_name":"Pavel","full_name":"Orlov, Pavel"},{"full_name":"Tiutiakina, Anastasiia","last_name":"Tiutiakina","first_name":"Anastasiia"},{"first_name":"Rustem","last_name":"Sharipov","full_name":"Sharipov, Rustem"},{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","first_name":"Elena","last_name":"Petrova","full_name":"Petrova, Elena"},{"full_name":"Gritsev, Vladimir","first_name":"Vladimir","last_name":"Gritsev"},{"full_name":"Kurlov, Denis V.","first_name":"Denis V.","last_name":"Kurlov"}],"volume":107,"date_updated":"2023-08-02T06:16:02Z","date_created":"2023-06-18T22:00:46Z","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"05","external_id":{"isi":["001003686900004"],"arxiv":["2303.00729"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2303.00729","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1103/PhysRevB.107.184312","language":[{"iso":"eng"}],"type":"journal_article","issue":"18","abstract":[{"lang":"eng","text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain."}],"_id":"13138","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 107","title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 2023;107(18). doi:10.1103/PhysRevB.107.184312","ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., & Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.107.184312","ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” Physical Review B, vol. 107, no. 18. American Physical Society, 2023.","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:10.1103/PhysRevB.107.184312.","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023).","chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.107.184312."},"publication":"Physical Review B","article_type":"original","date_published":"2023-05-01T00:00:00Z"},{"article_type":"original","page":"2243-2260","publication":"Plant Physiology","citation":{"chicago":"Chen, C, Y Zhang, J Cai, Y Qiu, L Li, C Gao, Y Gao, et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology. American Society of Plant Biologists, 2023. https://doi.org/10.1093/plphys/kiad207.","mla":"Chen, C., et al. “Multi-Copper Oxidases SKU5 and SKS1 Coordinate Cell Wall Formation Using Apoplastic Redox-Based Reactions in Roots.” Plant Physiology, vol. 192, no. 3, American Society of Plant Biologists, 2023, pp. 2243–60, doi:10.1093/plphys/kiad207.","short":"C. Chen, Y. Zhang, J. Cai, Y. Qiu, L. Li, C. Gao, Y. Gao, M. Ke, S. Wu, C. Wei, J. Chen, T. Xu, J. Friml, J. Wang, R. Li, D. Chao, B. Zhang, X. Chen, Z. Gao, Plant Physiology 192 (2023) 2243–2260.","ista":"Chen C, Zhang Y, Cai J, Qiu Y, Li L, Gao C, Gao Y, Ke M, Wu S, Wei C, Chen J, Xu T, Friml J, Wang J, Li R, Chao D, Zhang B, Chen X, Gao Z. 2023. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 192(3), 2243–2260.","apa":"Chen, C., Zhang, Y., Cai, J., Qiu, Y., Li, L., Gao, C., … Gao, Z. (2023). Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiad207","ieee":"C. Chen et al., “Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots,” Plant Physiology, vol. 192, no. 3. American Society of Plant Biologists, pp. 2243–2260, 2023.","ama":"Chen C, Zhang Y, Cai J, et al. Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots. Plant Physiology. 2023;192(3):2243-2260. doi:10.1093/plphys/kiad207"},"date_published":"2023-07-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1","title":"Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots","ddc":["575"],"status":"public","intvolume":" 192","_id":"13213","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"5492e1d18ac3eaf202633d210fa0fb75","success":1,"date_created":"2023-07-13T13:26:33Z","date_updated":"2023-07-13T13:26:33Z","relation":"main_file","file_id":"13220","content_type":"application/pdf","file_size":2076977,"creator":"cchlebak","access_level":"open_access","file_name":"2023_PlantPhys_Chen.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth.","lang":"eng"}],"issue":"3","quality_controlled":"1","isi":1,"external_id":{"pmid":["37010107"],"isi":["000971795800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/plphys/kiad207","month":"07","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"acknowledgement":"We thank Dong liu for offering iron staining technique; ZhiChang Chen and Zhenbiao Yang for discussion; Dandan Zheng for earlier attempt; Liwen Jiang and Dingquan Huang for initial tests of the TEM experiment; John C. Sedbrook for a donation of sku5 and pSKU5::SKU5-GFP seeds; Catherine Perrot-Rechenmann and Ke Zhou for the donation of sks1, sks2, and sku5 sks1 seeds; Zengyu Liu and Zhongquan Lin for live-imaging microscopy assistance. We are grateful to Can Peng, and Xixia Li for helping with sample preparation, and taking TEM images, at the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science.","year":"2023","pmid":1,"date_created":"2023-07-12T07:32:58Z","date_updated":"2023-08-02T06:27:55Z","volume":192,"author":[{"full_name":"Chen, C","last_name":"Chen","first_name":"C"},{"last_name":"Zhang","first_name":"Y","full_name":"Zhang, Y"},{"full_name":"Cai, J","last_name":"Cai","first_name":"J"},{"full_name":"Qiu, Y","last_name":"Qiu","first_name":"Y"},{"full_name":"Li, L","last_name":"Li","first_name":"L"},{"full_name":"Gao, C","last_name":"Gao","first_name":"C"},{"first_name":"Y","last_name":"Gao","full_name":"Gao, Y"},{"full_name":"Ke, M","last_name":"Ke","first_name":"M"},{"full_name":"Wu, S","first_name":"S","last_name":"Wu"},{"last_name":"Wei","first_name":"C","full_name":"Wei, C"},{"first_name":"J","last_name":"Chen","full_name":"Chen, J"},{"full_name":"Xu, T","last_name":"Xu","first_name":"T"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Wang, J","first_name":"J","last_name":"Wang"},{"first_name":"R","last_name":"Li","full_name":"Li, R"},{"full_name":"Chao, D","last_name":"Chao","first_name":"D"},{"last_name":"Zhang","first_name":"B","full_name":"Zhang, B"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"},{"last_name":"Gao","first_name":"Z","full_name":"Gao, Z"}],"file_date_updated":"2023-07-13T13:26:33Z"}]