[{"issue":"Supplement_1","scopus_import":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Trap spaces of multi-valued networks: Definition, computation, and applications","day":"30","type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/","citation":{"ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. 2023;39(Supplement_1):i513-i522. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>","chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>.","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>, vol. 39, no. Supplement_1, Oxford University Press, 2023, pp. i513–22, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>.","apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., &#38; Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>","ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” <i>Bioinformatics</i>, vol. 39, no. Supplement_1. Oxford University Press, pp. i513–i522, 2023.","short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522."},"date_created":"2023-07-23T22:01:12Z","acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","has_accepted_license":"1","file_date_updated":"2023-07-31T11:09:05Z","abstract":[{"text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models.","lang":"eng"}],"_id":"13263","status":"public","date_published":"2023-06-30T00:00:00Z","department":[{"_id":"ToHe"}],"quality_controlled":"1","date_updated":"2025-05-14T11:07:28Z","oa_version":"Published Version","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"},"publication":"Bioinformatics","publisher":"Oxford University Press","related_material":{"link":[{"relation":"software","url":"https://github.com/giang-trinh/trap-mvn"}]},"year":"2023","file":[{"file_name":"2023_Bioinformatics_Trinh.pdf","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2023-07-31T11:09:05Z","date_updated":"2023-07-31T11:09:05Z","success":1,"file_id":"13335","checksum":"ba3abe1171df1958413b7c7f957f5486","file_size":641736}],"page":"i513-i522","volume":39,"external_id":{"pmid":["37387165"],"isi":["001027457000060"]},"month":"06","ddc":["000"],"intvolume":"        39","article_type":"original","publication_status":"published","author":[{"full_name":"Trinh, Van Giang","first_name":"Van Giang","last_name":"Trinh"},{"first_name":"Belaid","last_name":"Benhamou","full_name":"Benhamou, Belaid"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pastva, Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","last_name":"Pastva","orcid":"0000-0003-1993-0331"}],"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"language":[{"iso":"eng"}],"ec_funded":1,"corr_author":"1","fulldoi":"https://doi.org/10.1093/bioinformatics/btad262","article_processing_charge":"Yes","pmid":1,"oa":1,"publication_identifier":{"issn":["1367-4803"],"eissn":["1367-4811"]},"doi":"10.1093/bioinformatics/btad262"},{"fulldoi":"https://doi.org/10.1145/3575859","arxiv":1,"article_processing_charge":"No","oa":1,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"doi":"10.1145/3575859","intvolume":"        42","publication_status":"published","article_type":"original","month":"03","author":[{"full_name":"Zhong, Fanchao","last_name":"Zhong","first_name":"Fanchao"},{"full_name":"Xu, Yonglai","last_name":"Xu","first_name":"Yonglai"},{"orcid":"0000-0002-6389-1045","first_name":"Haisen","last_name":"Zhao","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","full_name":"Zhao, Haisen"},{"full_name":"Lu, Lin","last_name":"Lu","first_name":"Lin"}],"language":[{"iso":"eng"}],"year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.02374"}],"volume":42,"external_id":{"arxiv":["2201.02374"],"isi":["001018739600002"]},"date_updated":"2023-12-13T11:34:59Z","quality_controlled":"1","oa_version":"Preprint","publication":"ACM Transactions on Graphics","publisher":"Association for Computing Machinery","article_number":"26","status":"public","date_published":"2023-03-17T00:00:00Z","department":[{"_id":"BeBi"}],"acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","_id":"13265","abstract":[{"lang":"eng","text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality."}],"type":"journal_article","citation":{"ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>.","ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>","mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>.","apa":"Zhong, F., Xu, Y., Zhao, H., &#38; Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>","short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).","ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3. Association for Computing Machinery, 2023."},"date_created":"2023-07-23T22:01:13Z","issue":"3","scopus_import":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","day":"17"},{"doi":"10.1111/nph.19123","corr_author":"1","fulldoi":"https://doi.org/10.1111/nph.19123","article_processing_charge":"Yes (via OA deal)","pmid":1,"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"oa":1,"author":[{"full_name":"Qi, Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","first_name":"Linlin","orcid":"0000-0001-5187-8401"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","grant_number":"P37051"}],"language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","intvolume":"       240","ddc":["580"],"month":"10","volume":240,"file":[{"date_created":"2024-01-29T11:21:43Z","file_name":"2023_NewPhytologist_Qi.pdf","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","success":1,"file_id":"14898","checksum":"6d9bbd45b8e7bb3ceee2586d447bacb2","file_size":974464,"date_updated":"2024-01-29T11:21:43Z"}],"external_id":{"pmid":["37434303"],"isi":["001026321500001"]},"page":"489-495","year":"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"},"publication":"New Phytologist","publisher":"Wiley","date_updated":"2024-10-22T12:50:00Z","quality_controlled":"1","oa_version":"Published Version","date_published":"2023-10-01T00:00:00Z","department":[{"_id":"JiFr"}],"status":"public","abstract":[{"text":"The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general.","lang":"eng"}],"_id":"13266","acknowledgement":"We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.","file_date_updated":"2024-01-29T11:21:43Z","has_accepted_license":"1","date_created":"2023-07-23T22:01:13Z","citation":{"mla":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>.","ieee":"L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” <i>New Phytologist</i>, vol. 240, no. 2. Wiley, pp. 489–495, 2023.","short":"L. Qi, J. Friml, New Phytologist 240 (2023) 489–495.","apa":"Qi, L., &#38; Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>","ista":"Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495.","ama":"Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. 2023;240(2):489-495. doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>","chicago":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>."},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tale of cAMP as a second messenger in auxin signaling and beyond","day":"01","issue":"2","scopus_import":"1","isi":1},{"oa":1,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"arxiv":1,"article_processing_charge":"Yes (via OA deal)","corr_author":"1","fulldoi":"https://doi.org/10.1007/s00454-023-00500-5","doi":"10.1007/s00454-023-00500-5","intvolume":"        70","month":"07","ddc":["510"],"publication_status":"published","article_type":"original","language":[{"iso":"eng"}],"author":[{"full_name":"Brunck, Florestan R","id":"6ab6e556-f394-11eb-9cf6-9dfb78f00d8d","last_name":"Brunck","first_name":"Florestan R"}],"year":"2023","volume":70,"external_id":{"arxiv":["2107.04112"],"isi":["001023742800003"]},"page":"1059-1089","file":[{"date_updated":"2024-01-29T11:15:22Z","checksum":"865e68daafdd4edcfc280172ec50f5ea","file_id":"14897","success":1,"file_size":1466020,"file_name":"2023_DiscreteComputGeometry_Brunck.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_created":"2024-01-29T11:15:22Z"}],"oa_version":"Published Version","quality_controlled":"1","date_updated":"2024-10-09T21:06:01Z","publisher":"Springer Nature","publication":"Discrete and Computational Geometry","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"},"status":"public","department":[{"_id":"UlWa"}],"date_published":"2023-07-05T00:00:00Z","file_date_updated":"2024-01-29T11:15:22Z","has_accepted_license":"1","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria).","abstract":[{"lang":"eng","text":"Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0\r\n such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses."}],"_id":"13270","type":"journal_article","date_created":"2023-07-23T22:01:14Z","citation":{"mla":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3, Springer Nature, 2023, pp. 1059–89, doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>.","apa":"Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>","ieee":"F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant curvature,” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3. Springer Nature, pp. 1059–1089, 2023.","short":"F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089.","chicago":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>.","ama":"Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. 2023;70(3):1059-1089. doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>","ista":"Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 70(3), 1059–1089."},"isi":1,"scopus_import":"1","issue":"3","day":"05","title":"Iterated medial triangle subdivision in surfaces of constant curvature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"04","ddc":["530"],"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."}],"_id":"13275","author":[{"last_name":"Rammelmüller","first_name":"Lukas","full_name":"Rammelmüller, Lukas"},{"full_name":"Huber, David","first_name":"David","last_name":"Huber"},{"orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"ec_funded":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.21468/scipostphyscodeb.12-r1.0","corr_author":"1","oa":1,"status":"public","doi":"10.21468/scipostphyscodeb.12-r1.0","date_published":"2023-04-19T00:00:00Z","department":[{"_id":"MiLe"}],"oa_version":"Published Version","date_updated":"2025-04-15T06:54:44Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"SciPost Foundation","day":"19","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"13276"}]},"title":"Codebase release 1.0 for FermiFCI","type":"research_data_reference","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0"}],"date_created":"2023-07-24T10:46:23Z","citation":{"ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","apa":"Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>","mla":"Rammelmüller, Lukas, et al. <i>Codebase Release 1.0 for FermiFCI</i>. SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>.","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>."}},{"month":"04","article_type":"original","ddc":["530"],"publication_status":"published","author":[{"last_name":"Rammelmüller","first_name":"Lukas","full_name":"Rammelmüller, Lukas"},{"last_name":"Huber","first_name":"David","full_name":"Huber, David"},{"first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"ec_funded":1,"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"arxiv":1,"article_processing_charge":"No","corr_author":"1","fulldoi":"https://doi.org/10.21468/scipostphyscodeb.12","publication_identifier":{"issn":["2949-804X"]},"oa":1,"doi":"10.21468/scipostphyscodeb.12","oa_version":"Published Version","date_updated":"2025-04-15T06:54:44Z","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"},"publisher":"SciPost Foundation","related_material":{"record":[{"relation":"research_data","id":"13275","status":"public"}]},"publication":"SciPost Physics Codebases","year":"2023","external_id":{"arxiv":["2202.04603"]},"file":[{"date_updated":"2023-07-31T09:09:23Z","file_size":551418,"checksum":"f583a70fe915d2208c803f5afb426daa","file_id":"13330","success":1,"access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","date_created":"2023-07-31T09:09:23Z"}],"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.","file_date_updated":"2023-07-31T09:09:23Z","has_accepted_license":"1","_id":"13276","abstract":[{"text":"<jats:p>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.</jats:p>","lang":"eng"}],"article_number":"12","status":"public","date_published":"2023-04-19T00:00:00Z","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"19","title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","type":"journal_article","citation":{"apa":"Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. <i>SciPost Physics Codebases</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">https://doi.org/10.21468/scipostphyscodeb.12</a>","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” <i>SciPost Physics Codebases</i>. SciPost Foundation, 2023.","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.” <i>SciPost Physics Codebases</i>, 12, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">10.21468/scipostphyscodeb.12</a>.","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.","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. <i>SciPost Physics Codebases</i>. 2023. doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">10.21468/scipostphyscodeb.12</a>","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” <i>SciPost Physics Codebases</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">https://doi.org/10.21468/scipostphyscodeb.12</a>."},"date_created":"2023-07-24T10:47:15Z"},{"date_created":"2023-07-24T10:47:46Z","citation":{"mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” <i>SciPost Physics Core</i>, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">10.21468/scipostphyscore.6.2.029</a>.","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” <i>SciPost Physics Core</i>, vol. 6, no. 2. SciPost Foundation, 2023.","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","apa":"Tucci, G., De Nicola, S., Wald, S., &#38; Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. <i>SciPost Physics Core</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">https://doi.org/10.21468/scipostphyscore.6.2.029</a>","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. <i>SciPost Physics Core</i>. 2023;6(2). doi:<a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">10.21468/scipostphyscore.6.2.029</a>","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” <i>SciPost Physics Core</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">https://doi.org/10.21468/scipostphyscore.6.2.029</a>."},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stochastic representation of the quantum quartic oscillator","day":"14","issue":"2","scopus_import":"1","date_published":"2023-04-14T00:00:00Z","department":[{"_id":"MaSe"}],"article_number":"029","status":"public","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"abstract":[{"lang":"eng","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."}],"_id":"13277","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. ","has_accepted_license":"1","file_date_updated":"2023-07-31T09:02:27Z","external_id":{"arxiv":["2211.01923"]},"volume":6,"file":[{"date_updated":"2023-07-31T09:02:27Z","file_size":523236,"success":1,"checksum":"b472bc82108747eda5d52adf9e2ac7f3","file_id":"13329","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","file_name":"2023_SciPostPhysCore_Tucci.pdf","date_created":"2023-07-31T09:02:27Z"}],"year":"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"},"publication":"SciPost Physics Core","publisher":"SciPost Foundation","quality_controlled":"1","date_updated":"2025-04-14T07:43:56Z","oa_version":"Published Version","doi":"10.21468/scipostphyscore.6.2.029","corr_author":"1","fulldoi":"https://doi.org/10.21468/scipostphyscore.6.2.029","arxiv":1,"article_processing_charge":"No","oa":1,"publication_identifier":{"issn":["2666-9366"]},"author":[{"full_name":"Tucci, Gennaro","last_name":"Tucci","first_name":"Gennaro"},{"orcid":"0000-0002-4842-6671","first_name":"Stefano","last_name":"De Nicola","id":"42832B76-F248-11E8-B48F-1D18A9856A87","full_name":"De Nicola, Stefano"},{"full_name":"Wald, Sascha","first_name":"Sascha","last_name":"Wald"},{"full_name":"Gambassi, Andrea","first_name":"Andrea","last_name":"Gambassi"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"ec_funded":1,"language":[{"iso":"eng"}],"month":"04","publication_status":"published","intvolume":"         6","article_type":"original","ddc":["530"]},{"month":"01","article_type":"original","ddc":["530"],"publication_status":"published","intvolume":"        14","author":[{"full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller","first_name":"Lukas"},{"full_name":"Huber, David","first_name":"David","last_name":"Huber"},{"full_name":"Čufar, Matija","first_name":"Matija","last_name":"Čufar"},{"full_name":"Brand, Joachim","first_name":"Joachim","last_name":"Brand"},{"first_name":"Hans-Werner","last_name":"Hammer","full_name":"Hammer, Hans-Werner"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.21468/scipostphys.14.1.006","article_processing_charge":"No","arxiv":1,"publication_identifier":{"issn":["2542-4653"]},"oa":1,"doi":"10.21468/scipostphys.14.1.006","quality_controlled":"1","date_updated":"2023-12-13T11:39:32Z","oa_version":"Published Version","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"},"publisher":"SciPost Foundation","publication":"SciPost Physics","year":"2023","volume":14,"external_id":{"arxiv":["2204.01606"],"isi":["001000325800008"]},"file":[{"file_id":"13328","checksum":"ffdb70b9ae7aa45ea4ea6096ecbd6431","success":1,"file_size":1163444,"date_updated":"2023-07-31T08:44:38Z","date_created":"2023-07-31T08:44:38Z","file_name":"2023_SciPostPhysics_Rammelmueller.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf"}],"has_accepted_license":"1","file_date_updated":"2023-07-31T08:44:38Z","abstract":[{"lang":"eng","text":"We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity \"breaks\" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms."}],"_id":"13278","article_number":"006","status":"public","keyword":["General Physics and Astronomy"],"date_published":"2023-01-24T00:00:00Z","department":[{"_id":"MiLe"}],"issue":"1","scopus_import":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Magnetic impurity in a one-dimensional few-fermion system","day":"24","type":"journal_article","date_created":"2023-07-24T10:48:23Z","citation":{"short":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev, SciPost Physics 14 (2023).","ieee":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev, “Magnetic impurity in a one-dimensional few-fermion system,” <i>SciPost Physics</i>, vol. 14, no. 1. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., &#38; Volosniev, A. (2023). Magnetic impurity in a one-dimensional few-fermion system. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">https://doi.org/10.21468/scipostphys.14.1.006</a>","mla":"Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” <i>SciPost Physics</i>, vol. 14, no. 1, 006, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">10.21468/scipostphys.14.1.006</a>.","ista":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1), 006.","ama":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic impurity in a one-dimensional few-fermion system. <i>SciPost Physics</i>. 2023;14(1). doi:<a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">10.21468/scipostphys.14.1.006</a>","chicago":"Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">https://doi.org/10.21468/scipostphys.14.1.006</a>."}},{"file":[{"date_created":"2023-08-11T09:27:39Z","creator":"mvalenti","relation":"source_file","content_type":"application/x-zip-compressed","access_level":"closed","file_name":"PhD_thesis_Valentini_final.zip","file_size":56121429,"checksum":"666ee31c7eade89679806287c062fa14","file_id":"14033","date_updated":"2023-08-11T10:01:34Z"},{"file_name":"PhD_thesis_Valentini_final_validated.pdf","creator":"mvalenti","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_created":"2023-08-11T14:39:17Z","date_updated":"2023-08-11T14:39:17Z","checksum":"0992f2ebef152dee8e70055350ebbb55","file_id":"14035","file_size":38199711}],"page":"184","year":"2023","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"research_data","id":"12522","status":"public"},{"relation":"part_of_dissertation","id":"12118","status":"public"},{"relation":"part_of_dissertation","id":"8910","status":"public"},{"id":"13312","relation":"part_of_dissertation","status":"public"}]},"tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"date_updated":"2026-06-03T07:16:01Z","OA_place":"publisher","oa_version":"Published Version","doi":"10.15479/at:ista:13286","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"oa":1,"fulldoi":"https://doi.org/10.15479/at:ista:13286","degree_awarded":"PhD","corr_author":"1","article_processing_charge":"No","project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","grant_number":"F8606"}],"ec_funded":1,"language":[{"iso":"eng"}],"author":[{"id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini","full_name":"Valentini, Marco"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"month":"07","publication_status":"published","ddc":["530"],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"mla":"Valentini, Marco. <i>Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>.","apa":"Valentini, M. (2023). <i>Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>.","ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria."},"date_created":"2023-07-24T14:10:45Z","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"type":"dissertation","title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","day":"21","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"date_published":"2023-07-21T00:00:00Z","status":"public","_id":"13286","abstract":[{"lang":"eng","text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices."}],"file_date_updated":"2023-08-11T14:39:17Z","has_accepted_license":"1"},{"title":"Regular methods for operator precedence languages","day":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","citation":{"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.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Regular methods for operator precedence languages. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">https://doi.org/10.4230/LIPIcs.ICALP.2023.129</a>","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">10.4230/LIPIcs.ICALP.2023.129</a>.","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">10.4230/LIPIcs.ICALP.2023.129</a>","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">https://doi.org/10.4230/LIPIcs.ICALP.2023.129</a>.","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: Automata, Languages and Programming, LIPIcs, vol. 261, 129:1--129:20."},"date_created":"2023-07-24T15:11:41Z","type":"conference","_id":"13292","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"}],"file_date_updated":"2023-07-24T15:11:05Z","has_accepted_license":"1","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","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"date_published":"2023-07-05T00:00:00Z","status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"50th International Colloquium on Automata, Languages, and Programming","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"},"quality_controlled":"1","date_updated":"2025-07-10T11:50:41Z","oa_version":"Published Version","file":[{"date_updated":"2023-07-24T15:11:05Z","file_size":859379,"success":1,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2","file_id":"13293","creator":"esarac","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"icalp23.pdf","date_created":"2023-07-24T15:11:05Z"}],"page":"129:1--129:20","external_id":{"arxiv":["2305.03447"]},"volume":261,"year":"2023","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"language":[{"iso":"eng"}],"ec_funded":1,"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Pavol","last_name":"Kebis","full_name":"Kebis, Pavol"},{"full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"month":"07","publication_status":"published","ddc":["000"],"intvolume":"       261","conference":{"location":"Paderborn, Germany","name":"ICALP: Automata, Languages and Programming","start_date":"2023-07-10","end_date":"2023-07-14"},"doi":"10.4230/LIPIcs.ICALP.2023.129","alternative_title":["LIPIcs"],"oa":1,"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"fulldoi":"https://doi.org/10.4230/LIPIcs.ICALP.2023.129","corr_author":"1","arxiv":1,"article_processing_charge":"Yes"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Fundamental limits in structured principal component analysis and how to reach them","day":"25","issue":"30","scopus_import":"1","isi":1,"citation":{"short":"J. Barbier, F. Camilli, M. Mondelli, M. Sáenz, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ieee":"J. Barbier, F. Camilli, M. Mondelli, and M. Sáenz, “Fundamental limits in structured principal component analysis and how to reach them,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 30. National Academy of Sciences, 2023.","apa":"Barbier, J., Camilli, F., Mondelli, M., &#38; Sáenz, M. (2023). Fundamental limits in structured principal component analysis and how to reach them. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2302028120\">https://doi.org/10.1073/pnas.2302028120</a>","mla":"Barbier, Jean, et al. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 120, no. 30, e2302028120, National Academy of Sciences, 2023, doi:<a href=\"https://doi.org/10.1073/pnas.2302028120\">10.1073/pnas.2302028120</a>.","chicago":"Barbier, Jean, Francesco Camilli, Marco Mondelli, and Manuel Sáenz. “Fundamental Limits in Structured Principal Component Analysis and How to Reach Them.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2023. <a href=\"https://doi.org/10.1073/pnas.2302028120\">https://doi.org/10.1073/pnas.2302028120</a>.","ama":"Barbier J, Camilli F, Mondelli M, Sáenz M. Fundamental limits in structured principal component analysis and how to reach them. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2023;120(30). doi:<a href=\"https://doi.org/10.1073/pnas.2302028120\">10.1073/pnas.2302028120</a>","ista":"Barbier J, Camilli F, Mondelli M, Sáenz M. 2023. Fundamental limits in structured principal component analysis and how to reach them. Proceedings of the National Academy of Sciences of the United States of America. 120(30), e2302028120."},"date_created":"2023-07-30T22:01:02Z","type":"journal_article","abstract":[{"text":"How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties.","lang":"eng"}],"_id":"13315","acknowledgement":"J.B. was funded by the European Union (ERC, CHORAL, project number 101039794). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. M.M. was supported by the 2019 Lopez-Loreta Prize. We would like to thank the reviewers for the insightful comments and, in particular, for suggesting the BAMP-inspired denoisers leading to AMP-AP.","file_date_updated":"2023-07-31T07:30:48Z","has_accepted_license":"1","date_published":"2023-07-25T00:00:00Z","department":[{"_id":"MaMo"}],"article_number":"e2302028120","status":"public","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"},"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences of the United States of America","related_material":{"link":[{"relation":"software","url":"https://github.com/fcamilli95/Structured-PCA-"}]},"date_updated":"2025-09-09T12:41:50Z","quality_controlled":"1","oa_version":"Published Version","volume":120,"file":[{"relation":"main_file","content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_PNAS_Barbier.pdf","date_created":"2023-07-31T07:30:48Z","date_updated":"2023-07-31T07:30:48Z","file_size":995933,"success":1,"file_id":"13323","checksum":"1fc06228afdb3aa80cf8e7766bcf9dc5"}],"external_id":{"isi":["001121663500001"],"pmid":["37463204"]},"year":"2023","author":[{"first_name":"Jean","last_name":"Barbier","full_name":"Barbier, Jean"},{"last_name":"Camilli","first_name":"Francesco","full_name":"Camilli, Francesco"},{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"last_name":"Sáenz","first_name":"Manuel","full_name":"Sáenz, Manuel"}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"language":[{"iso":"eng"}],"intvolume":"       120","month":"07","article_type":"original","publication_status":"published","ddc":["000"],"doi":"10.1073/pnas.2302028120","fulldoi":"https://doi.org/10.1073/pnas.2302028120","article_processing_charge":"Yes (in subscription journal)","pmid":1,"publication_identifier":{"eissn":["1091-6490"]},"oa":1},{"doi":"10.7554/eLife.84850","fulldoi":"https://doi.org/10.7554/eLife.84850","article_processing_charge":"Yes","pmid":1,"oa":1,"publication_identifier":{"eissn":["2050-084X"]},"author":[{"first_name":"Junko Y.","last_name":"Toshima","full_name":"Toshima, Junko Y."},{"first_name":"Ayana","last_name":"Tsukahara","full_name":"Tsukahara, Ayana"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Tojima, Takuro","first_name":"Takuro","last_name":"Tojima"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"},{"full_name":"Nakano, Akihiko","first_name":"Akihiko","last_name":"Nakano"},{"first_name":"Jiro","last_name":"Toshima","full_name":"Toshima, Jiro"}],"language":[{"iso":"eng"}],"article_type":"original","intvolume":"        12","publication_status":"published","month":"07","ddc":["570"],"file":[{"date_updated":"2023-07-31T07:43:00Z","file_id":"13324","checksum":"2af111a00cf5e3a956f7f0fd13199b15","success":1,"file_size":11980913,"file_name":"2023_eLife_Toshima.pdf","access_level":"open_access","content_type":"application/pdf","creator":"dernst","relation":"main_file","date_created":"2023-07-31T07:43:00Z"}],"volume":12,"external_id":{"pmid":["37477116"],"isi":["001035372800001"]},"year":"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"},"publisher":"eLife Sciences Publications","publication":"eLife","quality_controlled":"1","date_updated":"2023-12-13T11:37:36Z","oa_version":"Published Version","date_published":"2023-07-21T00:00:00Z","department":[{"_id":"DaSi"}],"article_number":"e84850","status":"public","_id":"13316","abstract":[{"lang":"eng","text":"Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN."}],"acknowledgement":"This work was supported by JSPS KAKENHI grant #18K062291, and the Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the Takeda Science Foundation, and Life Science Foundation of Japan to JT.","file_date_updated":"2023-07-31T07:43:00Z","has_accepted_license":"1","citation":{"mla":"Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” <i>ELife</i>, vol. 12, e84850, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.84850\">10.7554/eLife.84850</a>.","short":"J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano, J. Toshima, ELife 12 (2023).","apa":"Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano, A., &#38; Toshima, J. (2023). The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.84850\">https://doi.org/10.7554/eLife.84850</a>","ieee":"J. Y. Toshima <i>et al.</i>, “The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","ista":"Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima J. 2023. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 12, e84850.","chicago":"Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.84850\">https://doi.org/10.7554/eLife.84850</a>.","ama":"Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.84850\">10.7554/eLife.84850</a>"},"date_created":"2023-07-30T22:01:02Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network","day":"21","scopus_import":"1","isi":1},{"abstract":[{"lang":"eng","text":"We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule."}],"_id":"13319","acknowledgement":"The authors are grateful to Martijn Caspers for helpful comments on a preliminary version of this manuscript. M. V. was supported by the NWO Vidi grant VI.Vidi.192.018 ‘Non-commutative harmonic analysis and rigidity of operator algebras’. M. W. was funded by the Austrian Science Fund (FWF) under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Open access funding provided by Austrian Science Fund (FWF).","has_accepted_license":"1","file_date_updated":"2024-01-30T12:15:11Z","date_published":"2023-10-01T00:00:00Z","department":[{"_id":"JaMa"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Derivations and KMS-symmetric quantum Markov semigroups","day":"01","scopus_import":"1","isi":1,"date_created":"2023-07-30T22:01:03Z","citation":{"ama":"Vernooij M, Wirth M. Derivations and KMS-symmetric quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. 2023;403:381-416. doi:<a href=\"https://doi.org/10.1007/s00220-023-04795-6\">10.1007/s00220-023-04795-6</a>","chicago":"Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00220-023-04795-6\">https://doi.org/10.1007/s00220-023-04795-6</a>.","ista":"Vernooij M, Wirth M. 2023. Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. 403, 381–416.","short":"M. Vernooij, M. Wirth, Communications in Mathematical Physics 403 (2023) 381–416.","apa":"Vernooij, M., &#38; Wirth, M. (2023). Derivations and KMS-symmetric quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-023-04795-6\">https://doi.org/10.1007/s00220-023-04795-6</a>","ieee":"M. Vernooij and M. Wirth, “Derivations and KMS-symmetric quantum Markov semigroups,” <i>Communications in Mathematical Physics</i>, vol. 403. Springer Nature, pp. 381–416, 2023.","mla":"Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>, vol. 403, Springer Nature, 2023, pp. 381–416, doi:<a href=\"https://doi.org/10.1007/s00220-023-04795-6\">10.1007/s00220-023-04795-6</a>."},"type":"journal_article","author":[{"full_name":"Vernooij, Matthijs","last_name":"Vernooij","first_name":"Matthijs"},{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"project":[{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"language":[{"iso":"eng"}],"ddc":["510"],"intvolume":"       403","publication_status":"published","article_type":"original","month":"10","doi":"10.1007/s00220-023-04795-6","corr_author":"1","fulldoi":"https://doi.org/10.1007/s00220-023-04795-6","article_processing_charge":"Yes (via OA deal)","arxiv":1,"pmid":1,"oa":1,"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"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"},"publisher":"Springer Nature","publication":"Communications in Mathematical Physics","quality_controlled":"1","date_updated":"2025-04-23T13:10:45Z","oa_version":"Published Version","page":"381-416","file":[{"date_created":"2024-01-30T12:15:11Z","file_name":"2023_CommMathPhysics_Vernooij.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"14905","checksum":"cca204e81891270216a0c84eb8bcd398","file_size":481209,"date_updated":"2024-01-30T12:15:11Z"}],"volume":403,"external_id":{"arxiv":["2303.15949"],"pmid":["37766789"],"isi":["001033655400002"]},"year":"2023"},{"title":"Exterior algebra and combinatorics","day":"31","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli"}],"type":"dissertation","citation":{"ama":"Köse S. Exterior algebra and combinatorics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>","chicago":"Köse, Seyda. “Exterior Algebra and Combinatorics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>.","ista":"Köse S. 2023. Exterior algebra and combinatorics. Institute of Science and Technology Austria.","short":"S. Köse, Exterior Algebra and Combinatorics, Institute of Science and Technology Austria, 2023.","ieee":"S. Köse, “Exterior algebra and combinatorics,” Institute of Science and Technology Austria, 2023.","apa":"Köse, S. (2023). <i>Exterior algebra and combinatorics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13331\">https://doi.org/10.15479/at:ista:13331</a>","mla":"Köse, Seyda. <i>Exterior Algebra and Combinatorics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13331\">10.15479/at:ista:13331</a>."},"date_created":"2023-07-31T10:20:55Z","has_accepted_license":"1","file_date_updated":"2023-08-03T15:28:55Z","abstract":[{"text":"The extension of extremal combinatorics to the setting of exterior algebra is a work\r\nin progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.\r\n","lang":"eng"}],"_id":"13331","status":"public","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"date_published":"2023-07-31T00:00:00Z","date_updated":"2026-04-07T13:29:29Z","OA_place":"publisher","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12680"}]},"publisher":"Institute of Science and Technology Austria","year":"2023","page":"26","file":[{"file_name":"Exterior Algebra and Combinatorics.zip","relation":"source_file","creator":"skoese","content_type":"application/x-zip-compressed","access_level":"closed","date_created":"2023-07-31T10:16:32Z","date_updated":"2023-07-31T10:16:32Z","checksum":"96ee518d796d02af71395622c45de03c","file_id":"13333","file_size":28684},{"date_updated":"2023-08-03T15:28:55Z","checksum":"f610f4713f88bc477de576aaa46b114e","file_id":"13480","success":1,"file_size":4953418,"file_name":"thesis-pdfa.pdf","access_level":"open_access","content_type":"application/pdf","creator":"skoese","relation":"main_file","date_created":"2023-08-03T15:28:55Z"}],"ddc":["510","516"],"publication_status":"published","month":"07","language":[{"iso":"eng"}],"author":[{"full_name":"Köse, Seyda","orcid":"0009-0008-0457-9730","first_name":"Seyda","last_name":"Köse","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"}],"oa":1,"alternative_title":["ISTA Master's Thesis"],"publication_identifier":{"issn":["2791-4585"]},"fulldoi":"https://doi.org/10.15479/at:ista:13331","degree_awarded":"MS","corr_author":"1","article_processing_charge":"No","doi":"10.15479/at:ista:13331"},{"ddc":["000"],"month":"06","author":[{"full_name":"Kleshnina, Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Kleshnina"}],"_id":"13336","corr_author":"1","fulldoi":"https://doi.org/10.5281/ZENODO.8059564","article_processing_charge":"No","status":"public","oa":1,"date_published":"2023-06-20T00:00:00Z","doi":"10.5281/ZENODO.8059564","department":[{"_id":"KrCh"}],"date_updated":"2025-04-15T06:54:58Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games","publisher":"Zenodo","day":"20","related_material":{"record":[{"id":"13258","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","year":"2023","date_created":"2023-07-31T11:30:46Z","citation":{"ista":"Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8059564\">10.5281/ZENODO.8059564</a>.","ama":"Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8059564\">10.5281/ZENODO.8059564</a>","chicago":"Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8059564\">https://doi.org/10.5281/ZENODO.8059564</a>.","apa":"Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8059564\">https://doi.org/10.5281/ZENODO.8059564</a>","short":"M. Kleshnina, (2023).","ieee":"M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.","mla":"Kleshnina, Maria. <i>Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8059564\">10.5281/ZENODO.8059564</a>."},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8059564","open_access":"1"}]},{"article_type":"original","publication_status":"published","ddc":["570"],"month":"11","language":[{"iso":"eng"}],"author":[{"full_name":"Kroll, Janina","first_name":"Janina","last_name":"Kroll"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kuznetcov, Arthur","first_name":"Arthur","last_name":"Kuznetcov"},{"last_name":"Stefanowski","first_name":"Kasia","full_name":"Stefanowski, Kasia"},{"full_name":"Hermann, Monika D.","last_name":"Hermann","first_name":"Monika D."},{"first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Shafeek, Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7180-6050","first_name":"Lubuna B","last_name":"Shafeek"},{"full_name":"Müller-Taubenberger, Annette","first_name":"Annette","last_name":"Müller-Taubenberger"},{"last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg"}],"oa":1,"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"pmid":1,"article_processing_charge":"Yes (via OA deal)","fulldoi":"https://doi.org/10.15252/embj.2023114557","doi":"10.15252/embj.2023114557","oa_version":"Published Version","date_updated":"2025-09-09T12:44:04Z","quality_controlled":"1","publication":"EMBO Journal","publisher":"Embo Press","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"year":"2023","file":[{"file_name":"2023_EmboJournal_Kroll.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_created":"2023-11-27T08:45:56Z","date_updated":"2023-11-27T08:45:56Z","success":1,"checksum":"6261d0041c7e8d284c39712c40079730","file_id":"14611","file_size":4862497}],"external_id":{"isi":["001120971800001"],"pmid":["37987147"]},"has_accepted_license":"1","file_date_updated":"2023-11-27T08:45:56Z","acknowledgement":"We thank Christoph Mayr and Bingzhi Wang for initial experiments on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry, EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support. This study was supported by the Peter Hans Hofschneider Professorship of the foundation “Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to JR), and the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled and organized by Projekt DEAL.","abstract":[{"text":"Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoeba<jats:italic>Dictyostelium discoideum</jats:italic>, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.","lang":"eng"}],"_id":"13342","status":"public","article_number":"e114557","department":[{"_id":"NanoFab"},{"_id":"Bio"}],"date_published":"2023-11-21T00:00:00Z","isi":1,"scopus_import":"1","day":"21","title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","citation":{"mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” <i>EMBO Journal</i>, e114557, Embo Press, 2023, doi:<a href=\"https://doi.org/10.15252/embj.2023114557\">10.15252/embj.2023114557</a>.","ieee":"J. Kroll <i>et al.</i>, “Adaptive pathfinding by nucleokinesis during amoeboid migration,” <i>EMBO Journal</i>. Embo Press, 2023.","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2023114557\">https://doi.org/10.15252/embj.2023114557</a>","short":"J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin, L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).","ista":"Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557.","chicago":"Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” <i>EMBO Journal</i>. Embo Press, 2023. <a href=\"https://doi.org/10.15252/embj.2023114557\">https://doi.org/10.15252/embj.2023114557</a>.","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. <i>EMBO Journal</i>. 2023. doi:<a href=\"https://doi.org/10.15252/embj.2023114557\">10.15252/embj.2023114557</a>"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_created":"2023-08-01T08:59:06Z"},{"date_published":"2023-01-10T00:00:00Z","keyword":["General Physics and Astronomy","General Engineering","General Materials Science"],"status":"public","_id":"13346","abstract":[{"lang":"eng","text":"The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the “band gap” requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice’s cavities."}],"date_created":"2023-08-01T09:30:29Z","citation":{"ama":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. <i>ACS Nano</i>. 2023;17(1):275-287. doi:<a href=\"https://doi.org/10.1021/acsnano.2c07558\">10.1021/acsnano.2c07558</a>","chicago":"Lionello, Chiara, Claudio Perego, Andrea Gardin, Rafal Klajn, and Giovanni M. Pavan. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” <i>ACS Nano</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsnano.2c07558\">https://doi.org/10.1021/acsnano.2c07558</a>.","ista":"Lionello C, Perego C, Gardin A, Klajn R, Pavan GM. 2023. Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. ACS Nano. 17(1), 275–287.","mla":"Lionello, Chiara, et al. “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices.” <i>ACS Nano</i>, vol. 17, no. 1, American Chemical Society, 2023, pp. 275–87, doi:<a href=\"https://doi.org/10.1021/acsnano.2c07558\">10.1021/acsnano.2c07558</a>.","short":"C. Lionello, C. Perego, A. Gardin, R. Klajn, G.M. Pavan, ACS Nano 17 (2023) 275–287.","apa":"Lionello, C., Perego, C., Gardin, A., Klajn, R., &#38; Pavan, G. M. (2023). Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.2c07558\">https://doi.org/10.1021/acsnano.2c07558</a>","ieee":"C. Lionello, C. Perego, A. Gardin, R. Klajn, and G. M. Pavan, “Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices,” <i>ACS Nano</i>, vol. 17, no. 1. American Chemical Society, pp. 275–287, 2023."},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","title":"Supramolecular semiconductivity through emerging ionic gates in ion–nanoparticle superlattices","issue":"1","scopus_import":"1","doi":"10.1021/acsnano.2c07558","article_processing_charge":"No","fulldoi":"https://doi.org/10.1021/acsnano.2c07558","oa":1,"publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"author":[{"last_name":"Lionello","first_name":"Chiara","full_name":"Lionello, Chiara"},{"first_name":"Claudio","last_name":"Perego","full_name":"Perego, Claudio"},{"last_name":"Gardin","first_name":"Andrea","full_name":"Gardin, Andrea"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"},{"full_name":"Pavan, Giovanni M.","last_name":"Pavan","first_name":"Giovanni M."}],"language":[{"iso":"eng"}],"month":"01","publication_status":"published","intvolume":"        17","article_type":"original","page":"275-287","volume":17,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsnano.2c07558"}],"year":"2023","publisher":"American Chemical Society","publication":"ACS Nano","oa_version":"Published Version","extern":"1","quality_controlled":"1","date_updated":"2023-08-02T06:51:15Z"},{"day":"09","title":"Photocleavable anionic glues for light-responsive nanoparticle aggregates","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","issue":"7","citation":{"ama":"Wang J, Peled TS, Klajn R. Photocleavable anionic glues for light-responsive nanoparticle aggregates. <i>Journal of the American Chemical Society</i>. 2023;145(7):4098-4108. doi:<a href=\"https://doi.org/10.1021/jacs.2c11973\">10.1021/jacs.2c11973</a>","chicago":"Wang, Jinhua, Tzuf Shay Peled, and Rafal Klajn. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.2c11973\">https://doi.org/10.1021/jacs.2c11973</a>.","ista":"Wang J, Peled TS, Klajn R. 2023. Photocleavable anionic glues for light-responsive nanoparticle aggregates. Journal of the American Chemical Society. 145(7), 4098–4108.","mla":"Wang, Jinhua, et al. “Photocleavable Anionic Glues for Light-Responsive Nanoparticle Aggregates.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 7, American Chemical Society, 2023, pp. 4098–108, doi:<a href=\"https://doi.org/10.1021/jacs.2c11973\">10.1021/jacs.2c11973</a>.","apa":"Wang, J., Peled, T. S., &#38; Klajn, R. (2023). Photocleavable anionic glues for light-responsive nanoparticle aggregates. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.2c11973\">https://doi.org/10.1021/jacs.2c11973</a>","short":"J. Wang, T.S. Peled, R. Klajn, Journal of the American Chemical Society 145 (2023) 4098–4108.","ieee":"J. Wang, T. S. Peled, and R. Klajn, “Photocleavable anionic glues for light-responsive nanoparticle aggregates,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 7. American Chemical Society, pp. 4098–4108, 2023."},"date_created":"2023-08-01T09:33:08Z","type":"journal_article","_id":"13354","abstract":[{"text":"Integrating light-sensitive molecules within nanoparticle (NP) assemblies is an attractive approach to fabricate new photoresponsive nanomaterials. Here, we describe the concept of photocleavable anionic glue (PAG): small trianions capable of mediating interactions between (and inducing the aggregation of) cationic NPs by means of electrostatic interactions. Exposure to light converts PAGs into dianionic products incapable of maintaining the NPs in an assembled state, resulting in light-triggered disassembly of NP aggregates. To demonstrate the proof-of-concept, we work with an organic PAG incorporating the UV-cleavable o-nitrobenzyl moiety and an inorganic PAG, the photosensitive trioxalatocobaltate(III) complex, which absorbs light across the entire visible spectrum. Both PAGs were used to prepare either amorphous NP assemblies or regular superlattices with a long-range NP order. These NP aggregates disassembled rapidly upon light exposure for a specific time, which could be tuned by the incident light wavelength or the amount of PAG used. Selective excitation of the inorganic PAG in a system combining the two PAGs results in a photodecomposition product that deactivates the organic PAG, enabling nontrivial disassembly profiles under a single type of external stimulus.","lang":"eng"}],"date_published":"2023-02-09T00:00:00Z","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","publisher":"American Chemical Society","publication":"Journal of the American Chemical Society","oa_version":"Published Version","extern":"1","quality_controlled":"1","date_updated":"2024-10-14T12:11:46Z","external_id":{"pmid":["36757850"]},"page":"4098-4108","volume":145,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.2c11973"}],"year":"2023","language":[{"iso":"eng"}],"author":[{"first_name":"Jinhua","last_name":"Wang","full_name":"Wang, Jinhua"},{"full_name":"Peled, Tzuf Shay","first_name":"Tzuf Shay","last_name":"Peled"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"month":"02","article_type":"original","publication_status":"published","intvolume":"       145","doi":"10.1021/jacs.2c11973","oa":1,"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"pmid":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.1021/jacs.2c11973"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"High‐affinity hybridization of complementary aromatic oligoamide strands in water","day":"27","issue":"48","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","citation":{"ama":"Koehler V, Bruschera G, Merlet E, et al. High‐affinity hybridization of complementary aromatic oligoamide strands in water. <i>Angewandte Chemie International Edition</i>. 2023;62(48). doi:<a href=\"https://doi.org/10.1002/anie.202311639\">10.1002/anie.202311639</a>","chicago":"Koehler, Victor, Gabrielle Bruschera, Eric Merlet, Pradeep K Mandal, Estelle Morvan, Frédéric Rosu, Céline Douat, Lucile Fischer, Ivan Huc, and Yann Ferrand. “High‐affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202311639\">https://doi.org/10.1002/anie.202311639</a>.","ista":"Koehler V, Bruschera G, Merlet E, Mandal PK, Morvan E, Rosu F, Douat C, Fischer L, Huc I, Ferrand Y. 2023. High‐affinity hybridization of complementary aromatic oligoamide strands in water. Angewandte Chemie International Edition. 62(48), e202311639.","apa":"Koehler, V., Bruschera, G., Merlet, E., Mandal, P. K., Morvan, E., Rosu, F., … Ferrand, Y. (2023). High‐affinity hybridization of complementary aromatic oligoamide strands in water. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202311639\">https://doi.org/10.1002/anie.202311639</a>","short":"V. Koehler, G. Bruschera, E. Merlet, P.K. Mandal, E. Morvan, F. Rosu, C. Douat, L. Fischer, I. Huc, Y. Ferrand, Angewandte Chemie International Edition 62 (2023).","ieee":"V. Koehler <i>et al.</i>, “High‐affinity hybridization of complementary aromatic oligoamide strands in water,” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 48. Wiley, 2023.","mla":"Koehler, Victor, et al. “High‐affinity Hybridization of Complementary Aromatic Oligoamide Strands in Water.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 48, e202311639, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202311639\">10.1002/anie.202311639</a>."},"date_created":"2026-01-11T14:22:21Z","type":"journal_article","_id":"20966","abstract":[{"text":"We prepared a series of water‐soluble aromatic oligoamide sequences all composed of a segment prone to form a single helix and a segment prone to dimerize into a double helix. These sequences exclusively assemble as antiparallel duplexes. The modification of the duplex inner rim by varying the nature of the substituents borne by the aromatic monomers allowed us to identify sequences that can hybridize by combining two chemically different strands, with high affinity and complete selectivity in water. X‐ray crystallography confirmed the expected antiparallel configuration of the duplexes whereas NMR spectroscopy and mass spectrometry allowed us to assess precisely the extent of the hybridization. The hybridization kinetics of the aromatic strands was shown to depend on both the nature of the substituents responsible for strand complementarity and the length of the aromatic strand. These results highlight the great potential of aromatic hetero‐duplex as a tool to construct non‐symmetrical dynamic supramolecular assemblies.","lang":"eng"}],"has_accepted_license":"1","date_published":"2023-11-27T00:00:00Z","article_number":"e202311639","status":"public","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","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"},"publication":"Angewandte Chemie International Edition","publisher":"Wiley","quality_controlled":"1","date_updated":"2026-01-19T11:58:27Z","OA_place":"publisher","extern":"1","oa_version":"Published Version","volume":62,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.202311639"}],"external_id":{"pmid":["37804233"]},"year":"2023","author":[{"full_name":"Koehler, Victor","last_name":"Koehler","first_name":"Victor"},{"first_name":"Gabrielle","last_name":"Bruschera","full_name":"Bruschera, Gabrielle"},{"full_name":"Merlet, Eric","last_name":"Merlet","first_name":"Eric"},{"full_name":"Mandal, Pradeep K","orcid":"0000-0001-5996-956X","first_name":"Pradeep K","last_name":"Mandal","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3"},{"last_name":"Morvan","first_name":"Estelle","full_name":"Morvan, Estelle"},{"first_name":"Frédéric","last_name":"Rosu","full_name":"Rosu, Frédéric"},{"full_name":"Douat, Céline","last_name":"Douat","first_name":"Céline"},{"first_name":"Lucile","last_name":"Fischer","full_name":"Fischer, Lucile"},{"last_name":"Huc","first_name":"Ivan","full_name":"Huc, Ivan"},{"first_name":"Yann","last_name":"Ferrand","full_name":"Ferrand, Yann"}],"language":[{"iso":"eng"}],"OA_type":"hybrid","month":"11","publication_status":"published","intvolume":"        62","ddc":["540"],"article_type":"original","doi":"10.1002/anie.202311639","fulldoi":"https://doi.org/10.1002/anie.202311639","article_processing_charge":"Yes (in subscription journal)","pmid":1,"oa":1,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]}},{"quality_controlled":"1","OA_place":"publisher","date_updated":"2026-01-20T07:00:50Z","oa_version":"Published Version","extern":"1","tmp":{"short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"publication":"Chemical Science","publisher":"Royal Society of Chemistry","year":"2023","page":"11251-11260","volume":14,"main_file_link":[{"url":"https://doi.org/10.1039/D3SC02020G","open_access":"1"}],"external_id":{"pmid":["37860656"]},"OA_type":"gold","month":"09","publication_status":"published","ddc":["540"],"intvolume":"        14","article_type":"original","author":[{"full_name":"Teng, Binhao","first_name":"Binhao","last_name":"Teng"},{"id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","last_name":"Mandal","first_name":"Pradeep K","orcid":"0000-0001-5996-956X","full_name":"Mandal, Pradeep K"},{"first_name":"Lars","last_name":"Allmendinger","full_name":"Allmendinger, Lars"},{"full_name":"Douat, Céline","first_name":"Céline","last_name":"Douat"},{"full_name":"Ferrand, Yann","first_name":"Yann","last_name":"Ferrand"},{"full_name":"Huc, Ivan","first_name":"Ivan","last_name":"Huc"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1039/d3sc02020g","article_processing_charge":"Yes","pmid":1,"PlanS_conform":"1","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"oa":1,"doi":"10.1039/d3sc02020g","issue":"40","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Controlling aromatic helix dimerization in water by tuning charge repulsions","day":"25","type":"journal_article","date_created":"2026-01-11T14:35:50Z","license":"https://creativecommons.org/licenses/by-nc/3.0/","citation":{"ista":"Teng B, Mandal PK, Allmendinger L, Douat C, Ferrand Y, Huc I. 2023. Controlling aromatic helix dimerization in water by tuning charge repulsions. Chemical Science. 14(40), 11251–11260.","ama":"Teng B, Mandal PK, Allmendinger L, Douat C, Ferrand Y, Huc I. Controlling aromatic helix dimerization in water by tuning charge repulsions. <i>Chemical Science</i>. 2023;14(40):11251-11260. doi:<a href=\"https://doi.org/10.1039/d3sc02020g\">10.1039/d3sc02020g</a>","chicago":"Teng, Binhao, Pradeep K Mandal, Lars Allmendinger, Céline Douat, Yann Ferrand, and Ivan Huc. “Controlling Aromatic Helix Dimerization in Water by Tuning Charge Repulsions.” <i>Chemical Science</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sc02020g\">https://doi.org/10.1039/d3sc02020g</a>.","mla":"Teng, Binhao, et al. “Controlling Aromatic Helix Dimerization in Water by Tuning Charge Repulsions.” <i>Chemical Science</i>, vol. 14, no. 40, Royal Society of Chemistry, 2023, pp. 11251–60, doi:<a href=\"https://doi.org/10.1039/d3sc02020g\">10.1039/d3sc02020g</a>.","short":"B. Teng, P.K. Mandal, L. Allmendinger, C. Douat, Y. Ferrand, I. Huc, Chemical Science 14 (2023) 11251–11260.","ieee":"B. Teng, P. K. Mandal, L. Allmendinger, C. Douat, Y. Ferrand, and I. Huc, “Controlling aromatic helix dimerization in water by tuning charge repulsions,” <i>Chemical Science</i>, vol. 14, no. 40. Royal Society of Chemistry, pp. 11251–11260, 2023.","apa":"Teng, B., Mandal, P. K., Allmendinger, L., Douat, C., Ferrand, Y., &#38; Huc, I. (2023). Controlling aromatic helix dimerization in water by tuning charge repulsions. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sc02020g\">https://doi.org/10.1039/d3sc02020g</a>"},"has_accepted_license":"1","DOAJ_listed":"1","abstract":[{"text":"Several helically folded aromatic oligoamides were designed and synthesized. The sequences were all water-soluble thanks to the charged side chains borne by the monomers. Replacing a few, sometimes only two, charged side chains by neutral methoxy groups was shown to trigger the formation of various aggregates which could be tentatively assigned to head-to-head stacked dimers of single helices, double helical duplexes and a quadruplex, none of which would form in organic solvent with organic-soluble analogues. The nature of the aggregates was supported by concentration and solvent dependent NMR studies, 1H DOSY experiments, mass spectrometry, and X-ray crystallography or energy-minimized models, as well as analogies with earlier studies. The hydrophobic effect appears to be the main driving force for aggregation but it can be finely modulated by the presence or absence of a small number of charges to an extent that had no precedent in aromatic foldamer architectures. These results will serve as a benchmark for future foldamer design in water.","lang":"eng"}],"_id":"20968","status":"public","date_published":"2023-09-25T00:00:00Z"}]