--- OA_type: closed access _id: '20157' abstract: - lang: eng text: The focus of much of contemporary research ethics is on compliance with established protocols. However, large data-driven neuroscience research raises new ethical concerns that have no agreed-upon solution. Here we reflect on these challenges and propose better integration of public and patient involvement in this evolving landscape. acknowledgement: Funded provided by the European Union. Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10131373and 10038599) and Ministry of Science and Technology of China (MOST) National Key Project of ‘Inter-governmental International Scientific and Technological Innovation Cooperation’ (2023YFE0199700). article_number: 1128-1130 article_processing_charge: No article_type: comment author: - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: George full_name: Ogoh, George last_name: Ogoh - first_name: Gunter full_name: Schumann, Gunter last_name: Schumann - first_name: Henrik full_name: Walter, Henrik last_name: Walter - first_name: Bernd full_name: Stahl, Bernd last_name: Stahl - first_name: Allan H. full_name: Young, Allan H. last_name: Young - first_name: Sylvane full_name: Desrivières, Sylvane last_name: Desrivières - first_name: Nicholas full_name: Clinton, Nicholas last_name: Clinton - first_name: Paul full_name: Thompson, Paul last_name: Thompson - first_name: Ameli full_name: Schwalber, Ameli last_name: Schwalber - first_name: Jingyu full_name: Liu, Jingyu last_name: Liu - first_name: Vince full_name: Calhoun, Vince last_name: Calhoun - first_name: Xiao full_name: Chang, Xiao last_name: Chang - first_name: Yunman full_name: Xia, Yunman last_name: Xia - first_name: Yanting full_name: Gong, Yanting last_name: Gong - first_name: Tianye full_name: Jia, Tianye last_name: Jia - first_name: Paul full_name: Renner, Paul last_name: Renner - first_name: Sören full_name: Hese, Sören last_name: Hese - first_name: Arantxa full_name: Giner, Arantxa last_name: Giner - first_name: Mavi full_name: Sanchez, Mavi last_name: Sanchez - first_name: Elena full_name: Alvarez, Elena last_name: Alvarez - first_name: Bernhard full_name: Spanlang, Bernhard last_name: Spanlang - first_name: Charlie full_name: Pearmund, Charlie last_name: Pearmund - first_name: Anastasios Polykarpos full_name: Athanasiadis, Anastasios Polykarpos last_name: Athanasiadis - first_name: Lisa full_name: Otten, Lisa last_name: Otten - first_name: Séverine full_name: Pitel, Séverine last_name: Pitel - first_name: Spase full_name: Petkoski, Spase last_name: Petkoski - first_name: Viktor full_name: Jirsa, Viktor last_name: Jirsa - first_name: Karen full_name: Schmitt, Karen last_name: Schmitt - first_name: Johannes full_name: Wilbertz, Johannes last_name: Wilbertz - first_name: Myrto full_name: Patraskaki, Myrto last_name: Patraskaki - first_name: Peter full_name: Sommer, Peter last_name: Sommer - first_name: Stefanie full_name: Heilmann-Heimbach, Stefanie last_name: Heilmann-Heimbach - first_name: Carina M. full_name: Mathey, Carina M. last_name: Mathey - first_name: Abigail full_name: Miller, Abigail last_name: Miller - first_name: Isabelle full_name: Claus, Isabelle last_name: Claus - first_name: Markus M. full_name: Nöthen, Markus M. last_name: Nöthen - first_name: Per full_name: Hoffmann, Per last_name: Hoffmann - first_name: Andreas J. full_name: Forstner, Andreas J. last_name: Forstner - first_name: Alvaro full_name: Pastor, Alvaro last_name: Pastor - first_name: Jaime full_name: Gallego, Jaime last_name: Gallego - first_name: Francisco Eiroa full_name: Orosa, Francisco Eiroa last_name: Orosa - first_name: Guillem Feixas full_name: Viapiana, Guillem Feixas last_name: Viapiana - first_name: Mel full_name: Slater, Mel last_name: Slater - first_name: Lena full_name: Marr, Lena id: 4406F586-F248-11E8-B48F-1D18A9856A87 last_name: Marr - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Andre full_name: Marquand, Andre last_name: Marquand - first_name: Sarah Jane full_name: Böttger, Sarah Jane last_name: Böttger - first_name: Mira full_name: Tschorn, Mira last_name: Tschorn - first_name: Michael full_name: Rapp, Michael last_name: Rapp - first_name: Helga full_name: Ask, Helga last_name: Ask - first_name: Rikka full_name: Kjelkenes, Rikka last_name: Kjelkenes - first_name: Sara full_name: Fernandez, Sara last_name: Fernandez - first_name: Dennis full_name: Van Der Meer, Dennis last_name: Van Der Meer - first_name: Lars T. full_name: Westlye, Lars T. last_name: Westlye - first_name: Ole A. full_name: Andreassen, Ole A. last_name: Andreassen - first_name: Rieke full_name: Aden, Rieke last_name: Aden - first_name: Beke full_name: Seefried, Beke last_name: Seefried - first_name: Sebastian full_name: Siehl, Sebastian last_name: Siehl - first_name: Frauke full_name: Nees, Frauke last_name: Nees - first_name: Maja full_name: Neidhart, Maja last_name: Neidhart - first_name: Argyris full_name: Stringaris, Argyris last_name: Stringaris - first_name: Emanuel full_name: Schwarz, Emanuel last_name: Schwarz - first_name: Nathalie full_name: Holz, Nathalie last_name: Holz - first_name: Heike full_name: Tost, Heike last_name: Tost - first_name: Andreas full_name: Meyer-Lindenberg, Andreas last_name: Meyer-Lindenberg - first_name: Nina full_name: Christmann, Nina last_name: Christmann - first_name: Karina full_name: Jansone, Karina last_name: Jansone - first_name: Tobias full_name: Banaschewski, Tobias last_name: Banaschewski - first_name: Jamie full_name: Banks, Jamie last_name: Banks - first_name: Kerstin full_name: Schepanski, Kerstin last_name: Schepanski - first_name: Tatjana full_name: Schütz, Tatjana last_name: Schütz - first_name: Ulrike Helene full_name: Taron, Ulrike Helene last_name: Taron - first_name: Roland full_name: Eils, Roland last_name: Eils - first_name: Jean Charles full_name: Roy, Jean Charles last_name: Roy - first_name: Tristram A. full_name: Lett, Tristram A. last_name: Lett - first_name: Hedi full_name: Kebir, Hedi last_name: Kebir - first_name: Elli full_name: Polemiti, Elli last_name: Polemiti - first_name: Esther full_name: Hitchen, Esther last_name: Hitchen - first_name: Marcel full_name: Jentsch, Marcel last_name: Jentsch - first_name: Emin full_name: Serin, Emin last_name: Serin - first_name: Antoine full_name: Bernas, Antoine last_name: Bernas - first_name: Nilakshi full_name: Vaidya, Nilakshi last_name: Vaidya - first_name: Sven full_name: Twardziok, Sven last_name: Twardziok - first_name: Markus full_name: Ralser, Markus last_name: Ralser - first_name: Andreas full_name: Heinz, Andreas last_name: Heinz - first_name: Henrik full_name: Walter, Henrik last_name: Walter citation: ama: Stahl B, Ogoh G, Schumann G, et al. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. 2024;2(10). doi:10.1038/s44220-024-00320-3 apa: Stahl, B., Ogoh, G., Schumann, G., Walter, H., Stahl, B., Young, A. H., … Walter, H. (2024). Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00320-3 chicago: Stahl, Bernd, George Ogoh, Gunter Schumann, Henrik Walter, Bernd Stahl, Allan H. Young, Sylvane Desrivières, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00320-3. ieee: B. Stahl et al., “Rethinking ethics in interdisciplinary and big data-driven neuroscience projects,” Nature Mental Health, vol. 2, no. 10. Springer Nature, 2024. ista: Stahl B, Ogoh G, Schumann G, Walter H, Stahl B, Young AH, Desrivières S, Clinton N, Thompson P, Schwalber A, Liu J, Calhoun V, Chang X, Xia Y, Gong Y, Jia T, Renner P, Hese S, Giner A, Sanchez M, Alvarez E, Spanlang B, Pearmund C, Athanasiadis AP, Otten L, Pitel S, Petkoski S, Jirsa V, Schmitt K, Wilbertz J, Patraskaki M, Sommer P, Heilmann-Heimbach S, Mathey CM, Miller A, Claus I, Nöthen MM, Hoffmann P, Forstner AJ, Pastor A, Gallego J, Orosa FE, Viapiana GF, Slater M, Marr L, Novarino G, Marquand A, Böttger SJ, Tschorn M, Rapp M, Ask H, Kjelkenes R, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Neidhart M, Stringaris A, Schwarz E, Holz N, Tost H, Meyer-Lindenberg A, Christmann N, Jansone K, Banaschewski T, Banks J, Schepanski K, Schütz T, Taron UH, Eils R, Roy JC, Lett TA, Kebir H, Polemiti E, Hitchen E, Jentsch M, Serin E, Bernas A, Vaidya N, Twardziok S, Ralser M, Heinz A, Walter H. 2024. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. 2(10), 1128–1130. mla: Stahl, Bernd, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” Nature Mental Health, vol. 2, no. 10, 1128–1130, Springer Nature, 2024, doi:10.1038/s44220-024-00320-3. short: B. Stahl, G. Ogoh, G. Schumann, H. Walter, B. Stahl, A.H. Young, S. Desrivières, N. Clinton, P. Thompson, A. Schwalber, J. Liu, V. Calhoun, X. Chang, Y. Xia, Y. Gong, T. Jia, P. Renner, S. Hese, A. Giner, M. Sanchez, E. Alvarez, B. Spanlang, C. Pearmund, A.P. Athanasiadis, L. Otten, S. Pitel, S. Petkoski, V. Jirsa, K. Schmitt, J. Wilbertz, M. Patraskaki, P. Sommer, S. Heilmann-Heimbach, C.M. Mathey, A. Miller, I. Claus, M.M. Nöthen, P. Hoffmann, A.J. Forstner, A. Pastor, J. Gallego, F.E. Orosa, G.F. Viapiana, M. Slater, L. Marr, G. Novarino, A. Marquand, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, R. Kjelkenes, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, M. Neidhart, A. Stringaris, E. Schwarz, N. Holz, H. Tost, A. Meyer-Lindenberg, N. Christmann, K. Jansone, T. Banaschewski, J. Banks, K. Schepanski, T. Schütz, U.H. Taron, R. Eils, J.C. Roy, T.A. Lett, H. Kebir, E. Polemiti, E. Hitchen, M. Jentsch, E. Serin, A. Bernas, N. Vaidya, S. Twardziok, M. Ralser, A. Heinz, H. Walter, Nature Mental Health 2 (2024). date_created: 2025-08-10T22:01:30Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-08-11T06:53:55Z day: '01' department: - _id: GaNo doi: 10.1038/s44220-024-00320-3 fulldoi: https://doi.org/10.1038/s44220-024-00320-3 intvolume: ' 2' issue: '10' language: - iso: eng month: '10' oa_version: None publication: Nature Mental Health publication_identifier: eissn: - 2731-6076 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Rethinking ethics in interdisciplinary and big data-driven neuroscience projects type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2024' ... --- OA_type: closed access _id: '20527' abstract: - lang: eng text: "Arising from C. Yang et al. Nature Chemistry https://doi.org/10.1038/s41557-023-01212-2 (2023)\r\n\r\nIn this work Yang et al.1 claim that an enantioselective Michael addition reaction with a barrier of 16 kcal mol−1 occurs at the single-molecule level in frozen solvent by measuring fluctuations in current flowing across graphene-based molecular devices. The article, however, contains major scientific errors that undermine their conclusions. We highlight issues with the fabrication of the devices, a lack of characterization, discrepancies between theory and experiment, unreliable inelastic electron tunnelling spectra (IETS) and a perceived misinterpretation of noise as evidence of reaction." article_processing_charge: No article_type: letter_note author: - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 - first_name: Jan full_name: van Ruitenbeek, Jan last_name: van Ruitenbeek citation: ama: Venkataraman L, van Ruitenbeek J. Questioning claims of monitoring the Michael addition reaction at the single-molecule level. Nature Chemistry. 2024;16(11):1767-1769. doi:10.1038/s41557-024-01631-9 apa: Venkataraman, L., & van Ruitenbeek, J. (2024). Questioning claims of monitoring the Michael addition reaction at the single-molecule level. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-024-01631-9 chicago: Venkataraman, Latha, and Jan van Ruitenbeek. “Questioning Claims of Monitoring the Michael Addition Reaction at the Single-Molecule Level.” Nature Chemistry. Springer Nature, 2024. https://doi.org/10.1038/s41557-024-01631-9. ieee: L. Venkataraman and J. van Ruitenbeek, “Questioning claims of monitoring the Michael addition reaction at the single-molecule level,” Nature Chemistry, vol. 16, no. 11. Springer Nature, pp. 1767–1769, 2024. ista: Venkataraman L, van Ruitenbeek J. 2024. Questioning claims of monitoring the Michael addition reaction at the single-molecule level. Nature Chemistry. 16(11), 1767–1769. mla: Venkataraman, Latha, and Jan van Ruitenbeek. “Questioning Claims of Monitoring the Michael Addition Reaction at the Single-Molecule Level.” Nature Chemistry, vol. 16, no. 11, Springer Nature, 2024, pp. 1767–69, doi:10.1038/s41557-024-01631-9. short: L. Venkataraman, J. van Ruitenbeek, Nature Chemistry 16 (2024) 1767–1769. date_created: 2025-10-23T12:16:57Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-10-23T12:58:52Z day: '01' doi: 10.1038/s41557-024-01631-9 extern: '1' external_id: pmid: - '39313629' fulldoi: https://doi.org/10.1038/s41557-024-01631-9 intvolume: ' 16' issue: '11' language: - iso: eng month: '11' oa_version: None page: 1767-1769 pmid: 1 publication: Nature Chemistry publication_identifier: eissn: - 1755-4349 issn: - 1755-4330 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Questioning claims of monitoring the Michael addition reaction at the single-molecule level type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2024' ... --- OA_type: closed access _id: '20529' abstract: - lang: eng text: Single molecules bridging two metallic electrodes can emit light through electroluminescence when subjected to a bias voltage. Typically, light emission in such devices results from transitions between molecular states, although in the presence of light-matter coupling, the emission can result from a transition between hybrid light-matter states. Here, we create single metal-molecule-metal junctions and simultaneously collect conductance and electroluminescence data using a scanning tunneling microscope (STM) equipped with a custom spectrometer. Through experimental analysis and electronic structure calculations, we provide evidence for a molecule-electrode interfacial exciton coupled to a junction cavity plasmon. Importantly, we find that close to resonant transport conditions, the molecular junction functions as a single emitter that is strongly coupled to the junction cavity mode, leading to characteristic Rabi splitting of the emission spectrum and providing the first example of an electroluminescence-driven single-molecule system in the regime of strong light-matter coupling. article_processing_charge: No article_type: original author: - first_name: Angela L. full_name: Paoletta, Angela L. last_name: Paoletta - first_name: Norah M. full_name: Hoffmann, Norah M. last_name: Hoffmann - first_name: Daniel W. full_name: Cheng, Daniel W. last_name: Cheng - first_name: Emma full_name: York, Emma last_name: York - first_name: Ding full_name: Xu, Ding last_name: Xu - first_name: Boyuan full_name: Zhang, Boyuan last_name: Zhang - first_name: Milan full_name: Delor, Milan last_name: Delor - first_name: Timothy C. full_name: Berkelbach, Timothy C. last_name: Berkelbach - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Paoletta AL, Hoffmann NM, Cheng DW, et al. Plasmon-exciton strong coupling in single-molecule junction electroluminescence. Journal of the American Chemical Society. 2024;146(50):34394-34400. doi:10.1021/jacs.4c09782 apa: Paoletta, A. L., Hoffmann, N. M., Cheng, D. W., York, E., Xu, D., Zhang, B., … Venkataraman, L. (2024). Plasmon-exciton strong coupling in single-molecule junction electroluminescence. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.4c09782 chicago: Paoletta, Angela L., Norah M. Hoffmann, Daniel W. Cheng, Emma York, Ding Xu, Boyuan Zhang, Milan Delor, Timothy C. Berkelbach, and Latha Venkataraman. “Plasmon-Exciton Strong Coupling in Single-Molecule Junction Electroluminescence.” Journal of the American Chemical Society. American Chemical Society, 2024. https://doi.org/10.1021/jacs.4c09782. ieee: A. L. Paoletta et al., “Plasmon-exciton strong coupling in single-molecule junction electroluminescence,” Journal of the American Chemical Society, vol. 146, no. 50. American Chemical Society, pp. 34394–34400, 2024. ista: Paoletta AL, Hoffmann NM, Cheng DW, York E, Xu D, Zhang B, Delor M, Berkelbach TC, Venkataraman L. 2024. Plasmon-exciton strong coupling in single-molecule junction electroluminescence. Journal of the American Chemical Society. 146(50), 34394–34400. mla: Paoletta, Angela L., et al. “Plasmon-Exciton Strong Coupling in Single-Molecule Junction Electroluminescence.” Journal of the American Chemical Society, vol. 146, no. 50, American Chemical Society, 2024, pp. 34394–400, doi:10.1021/jacs.4c09782. short: A.L. Paoletta, N.M. Hoffmann, D.W. Cheng, E. York, D. Xu, B. Zhang, M. Delor, T.C. Berkelbach, L. Venkataraman, Journal of the American Chemical Society 146 (2024) 34394–34400. date_created: 2025-10-23T12:20:19Z date_published: 2024-12-04T00:00:00Z date_updated: 2025-10-23T13:03:41Z day: '04' doi: 10.1021/jacs.4c09782 extern: '1' external_id: pmid: - '39630979' fulldoi: https://doi.org/10.1021/jacs.4c09782 intvolume: ' 146' issue: '50' language: - iso: eng month: '12' oa_version: None page: 34394-34400 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Plasmon-exciton strong coupling in single-molecule junction electroluminescence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 146 year: '2024' ... --- OA_type: closed access _id: '20615' abstract: - lang: eng text: "Spin/Pin-structures on vector bundles have long featured prominently in differential geometry, in particular providing part of the foundation for the original proof of the renowned Atiyah–Singer Index Theory. More recently, they have underpinned the symplectic topology foundations of the so-called real sector of the mirror symmetry of string theory.\r\n\r\nThis semi-expository three-part monograph provides an accessible introduction to Spin- and Pin-structures in general, demonstrates their role in the orientability considerations in symplectic topology, and presents their applications in enumerative geometry.\r\n\r\nPart I contains a systematic treatment of Spin/Pin-structures from different topological perspectives and may be suitable for an advanced undergraduate reading seminar. This leads to Part II, which systematically studies orientability problems for the determinants of real Cauchy–Riemann operators on vector bundles. Part III introduces enumerative geometry of curves in complex projective varieties and in symplectic manifolds, demonstrating some applications of the first two parts in the process. Two appendices review the Čech cohomology perspective on fiber bundles and Lie group covering spaces." article_processing_charge: No author: - first_name: Xujia full_name: Chen, Xujia id: 968ad14a-fd86-11ee-a420-ea29715511a3 last_name: Chen - first_name: Aleksey full_name: Zinger, Aleksey last_name: Zinger citation: ama: Chen X, Zinger A. Spin/Pin-Structures and Real Enumerative Geometry. World Scientific Publishing; 2024. doi:10.1142/13476 apa: Chen, X., & Zinger, A. (2024). Spin/Pin-structures and real enumerative geometry. World Scientific Publishing. https://doi.org/10.1142/13476 chicago: Chen, Xujia, and Aleksey Zinger. Spin/Pin-Structures and Real Enumerative Geometry. World Scientific Publishing, 2024. https://doi.org/10.1142/13476. ieee: X. Chen and A. Zinger, Spin/Pin-structures and real enumerative geometry. World Scientific Publishing, 2024. ista: Chen X, Zinger A. 2024. Spin/Pin-structures and real enumerative geometry, World Scientific Publishing,p. mla: Chen, Xujia, and Aleksey Zinger. Spin/Pin-Structures and Real Enumerative Geometry. World Scientific Publishing, 2024, doi:10.1142/13476. short: X. Chen, A. Zinger, Spin/Pin-Structures and Real Enumerative Geometry, World Scientific Publishing, 2024. date_created: 2025-11-10T08:40:10Z date_published: 2024-01-01T00:00:00Z date_updated: 2025-11-10T15:28:49Z day: '01' doi: 10.1142/13476 extern: '1' fulldoi: https://doi.org/10.1142/13476 language: - iso: eng month: '01' oa_version: None publication_identifier: eisbn: - '9789811278556' isbn: - '9789811278532' publication_status: published publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: Spin/Pin-structures and real enumerative geometry type: book user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '20756' abstract: - lang: eng text: Biocatalysis has the potential to address the need for more sustainable organic synthesis routes. Protein engineering can tune enzymes to perform in cascade reactions and for efficient synthesis of enantiomerically enriched compounds, using both natural and new-to-nature reaction pathways. This review highlights recent achievements in biocatalysis, especially the development of novel enzymatic syntheses to access versatile small molecule intermediates and complex biomolecules. Biocatalytic strategies for the degradation of persistent pollutants and approaches for biomass valorization are also discussed. The transition of chemical synthesis to a greener future will be accelerated by implementing enzymes and engineering them for high performance and new activities. article_number: '102536' article_processing_charge: No article_type: original author: - first_name: Julia full_name: Reisenbauer, Julia id: 51d862e9-36ee-11f0-86d3-8534c85a5496 last_name: Reisenbauer - first_name: Kathleen M. full_name: Sicinski, Kathleen M. last_name: Sicinski - first_name: Frances H. full_name: Arnold, Frances H. last_name: Arnold citation: ama: 'Reisenbauer J, Sicinski KM, Arnold FH. Catalyzing the future: Recent advances in chemical synthesis using enzymes. Current Opinion in Chemical Biology. 2024;83. doi:10.1016/j.cbpa.2024.102536' apa: 'Reisenbauer, J., Sicinski, K. M., & Arnold, F. H. (2024). Catalyzing the future: Recent advances in chemical synthesis using enzymes. Current Opinion in Chemical Biology. Elsevier. https://doi.org/10.1016/j.cbpa.2024.102536' chicago: 'Reisenbauer, Julia, Kathleen M. Sicinski, and Frances H. Arnold. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” Current Opinion in Chemical Biology. Elsevier, 2024. https://doi.org/10.1016/j.cbpa.2024.102536.' ieee: 'J. Reisenbauer, K. M. Sicinski, and F. H. Arnold, “Catalyzing the future: Recent advances in chemical synthesis using enzymes,” Current Opinion in Chemical Biology, vol. 83. Elsevier, 2024.' ista: 'Reisenbauer J, Sicinski KM, Arnold FH. 2024. Catalyzing the future: Recent advances in chemical synthesis using enzymes. Current Opinion in Chemical Biology. 83, 102536.' mla: 'Reisenbauer, Julia, et al. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” Current Opinion in Chemical Biology, vol. 83, 102536, Elsevier, 2024, doi:10.1016/j.cbpa.2024.102536.' short: J. Reisenbauer, K.M. Sicinski, F.H. Arnold, Current Opinion in Chemical Biology 83 (2024). date_created: 2025-12-09T14:22:40Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-12-16T13:03:48Z day: '01' doi: 10.1016/j.cbpa.2024.102536 extern: '1' external_id: pmid: - '39369557' fulldoi: https://doi.org/10.1016/j.cbpa.2024.102536 intvolume: ' 83' language: - iso: eng main_file_link: - open_access: '1' url: https://europepmc.org/article/med/39369557#free-full-text month: '12' oa: 1 oa_version: Submitted Version pmid: 1 publication: Current Opinion in Chemical Biology publication_identifier: eissn: - 1879-0402 issn: - 1367-5931 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Catalyzing the future: Recent advances in chemical synthesis using enzymes' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '20757' abstract: - lang: eng text: We report the utilisation of an iodine(III) reagent to access α,β-unsaturated carbonyls from the corresponding silyl enol ethers and enol phosphates. The transformation can also be carried out in one pot, directly dehydrogenating carbonyls. article_processing_charge: No article_type: original author: - first_name: Bence B. full_name: Botlik, Bence B. last_name: Botlik - first_name: Patrick full_name: Finkelstein, Patrick last_name: Finkelstein - first_name: Ann-Sophie K. full_name: Paschke, Ann-Sophie K. last_name: Paschke - first_name: Julia full_name: Reisenbauer, Julia id: 51d862e9-36ee-11f0-86d3-8534c85a5496 last_name: Reisenbauer - first_name: Bill full_name: Morandi, Bill last_name: Morandi citation: ama: Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. 2024;60(69):9254-9257. doi:10.1039/d4cc02609h apa: Botlik, B. B., Finkelstein, P., Paschke, A.-S. K., Reisenbauer, J., & Morandi, B. (2024). Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. Royal Society of Chemistry. https://doi.org/10.1039/d4cc02609h chicago: Botlik, Bence B., Patrick Finkelstein, Ann-Sophie K. Paschke, Julia Reisenbauer, and Bill Morandi. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” Chemical Communications. Royal Society of Chemistry, 2024. https://doi.org/10.1039/d4cc02609h. ieee: B. B. Botlik, P. Finkelstein, A.-S. K. Paschke, J. Reisenbauer, and B. Morandi, “Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent,” Chemical Communications, vol. 60, no. 69. Royal Society of Chemistry, pp. 9254–9257, 2024. ista: Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. 2024. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. Chemical Communications. 60(69), 9254–9257. mla: Botlik, Bence B., et al. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” Chemical Communications, vol. 60, no. 69, Royal Society of Chemistry, 2024, pp. 9254–57, doi:10.1039/d4cc02609h. short: B.B. Botlik, P. Finkelstein, A.-S.K. Paschke, J. Reisenbauer, B. Morandi, Chemical Communications 60 (2024) 9254–9257. date_created: 2025-12-09T14:23:00Z date_published: 2024-08-02T00:00:00Z date_updated: 2025-12-16T11:19:43Z day: '02' doi: 10.1039/d4cc02609h extern: '1' external_id: pmid: - '39118590' fulldoi: https://doi.org/10.1039/d4cc02609h has_accepted_license: '1' intvolume: ' 60' issue: '69' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ main_file_link: - open_access: '1' url: https://doi.org/10.1039/D4CC02609H month: '08' oa: 1 oa_version: Published Version page: 9254-9257 pmid: 1 publication: Chemical Communications publication_identifier: eissn: - 1364-548X issn: - 1359-7345 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '20807' abstract: - lang: eng text: Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organism Caenorhabditis elegans to genetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine, and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3 located in the excretory cell. The present study provides new insight into the unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to physiology of this protease group and in extension to human GCP2 involvement in pathophysiological processes. article_number: BSR20230502 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lucie full_name: Panska, Lucie last_name: Panska - first_name: Stepanka full_name: Nedvedova, Stepanka last_name: Nedvedova - first_name: Vojtech full_name: Vacek, Vojtech last_name: Vacek - first_name: Daniela full_name: Krivska, Daniela last_name: Krivska - first_name: Lukas full_name: Konecny, Lukas last_name: Konecny - first_name: Filip full_name: Knop, Filip id: 25f3131f-6e7c-11ef-8296-b64ccd4a1b69 last_name: Knop orcid: 0000-0002-3845-3465 - first_name: Zsofia full_name: Kutil, Zsofia last_name: Kutil - first_name: Lubica full_name: Skultetyova, Lubica last_name: Skultetyova - first_name: Adrian full_name: Leontovyc, Adrian last_name: Leontovyc - first_name: Lenka full_name: Ulrychova, Lenka last_name: Ulrychova - first_name: Judy full_name: Sakanari, Judy last_name: Sakanari - first_name: Masako full_name: Asahina, Masako last_name: Asahina - first_name: Cyril full_name: Barinka, Cyril last_name: Barinka - first_name: Marie full_name: Macurkova, Marie last_name: Macurkova - first_name: Jan full_name: Dvorak, Jan last_name: Dvorak citation: ama: Panska L, Nedvedova S, Vacek V, et al. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. 2024;44(1). doi:10.1042/bsr20230502 apa: Panska, L., Nedvedova, S., Vacek, V., Krivska, D., Konecny, L., Knop, F., … Dvorak, J. (2024). Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. Portland Press. https://doi.org/10.1042/bsr20230502 chicago: Panska, Lucie, Stepanka Nedvedova, Vojtech Vacek, Daniela Krivska, Lukas Konecny, Filip Knop, Zsofia Kutil, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” Bioscience Reports. Portland Press, 2024. https://doi.org/10.1042/bsr20230502. ieee: L. Panska et al., “Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans,” Bioscience Reports, vol. 44, no. 1. Portland Press, 2024. ista: Panska L, Nedvedova S, Vacek V, Krivska D, Konecny L, Knop F, Kutil Z, Skultetyova L, Leontovyc A, Ulrychova L, Sakanari J, Asahina M, Barinka C, Macurkova M, Dvorak J. 2024. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. Bioscience Reports. 44(1), BSR20230502. mla: Panska, Lucie, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” Bioscience Reports, vol. 44, no. 1, BSR20230502, Portland Press, 2024, doi:10.1042/bsr20230502. short: L. Panska, S. Nedvedova, V. Vacek, D. Krivska, L. Konecny, F. Knop, Z. Kutil, L. Skultetyova, A. Leontovyc, L. Ulrychova, J. Sakanari, M. Asahina, C. Barinka, M. Macurkova, J. Dvorak, Bioscience Reports 44 (2024). date_created: 2025-12-12T09:03:54Z date_published: 2024-01-12T00:00:00Z date_updated: 2025-12-15T10:21:56Z day: '12' ddc: - '570' doi: 10.1042/bsr20230502 extern: '1' external_id: pmid: - '38108122 ' fulldoi: https://doi.org/10.1042/bsr20230502 has_accepted_license: '1' intvolume: ' 44' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1042/BSR20230502 month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Bioscience Reports publication_identifier: eissn: - 1573-4935 issn: - 0144-8463 publication_status: published publisher: Portland Press quality_controlled: '1' scopus_import: '1' status: public title: Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '20808' abstract: - lang: eng text: During Caenorhabditis elegans development, multiple cells migrate long distances or extend processes to reach their final position and/or attain proper shape. The Wnt signalling pathway stands out as one of the major coordinators of cell migration or cell outgrowth along the anterior-posterior body axis. The outcome of Wnt signalling is fine-tuned by various mechanisms including endocytosis. In this study, we show that SEL-5, the C. elegans orthologue of mammalian AP2-associated kinase AAK1, acts together with the retromer complex as a positive regulator of EGL-20/Wnt signalling during the migration of QL neuroblast daughter cells. At the same time, SEL-5 in cooperation with the retromer complex is also required during excretory canal cell outgrowth. Importantly, SEL-5 kinase activity is not required for its role in neuronal migration or excretory cell outgrowth, and neither of these processes is dependent on DPY-23/AP2M1 phosphorylation. We further establish that the Wnt proteins CWN-1 and CWN-2, together with the Frizzled receptor CFZ-2, positively regulate excretory cell outgrowth, while LIN-44/Wnt and LIN-17/Frizzled together generate a stop signal inhibiting its extension. article_number: e91054 article_processing_charge: Yes article_type: original author: - first_name: Filip full_name: Knop, Filip id: 25f3131f-6e7c-11ef-8296-b64ccd4a1b69 last_name: Knop orcid: 0000-0002-3845-3465 - first_name: Apolena full_name: Zounarová, Apolena last_name: Zounarová - first_name: Vojtěch full_name: Šabata, Vojtěch last_name: Šabata - first_name: Teije Corneel full_name: Middelkoop, Teije Corneel last_name: Middelkoop - first_name: Marie full_name: Macůrková, Marie last_name: Macůrková citation: ama: Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. eLife. 2024;13. doi:10.7554/elife.91054 apa: Knop, F., Zounarová, A., Šabata, V., Middelkoop, T. C., & Macůrková, M. (2024). Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.91054 chicago: Knop, Filip, Apolena Zounarová, Vojtěch Šabata, Teije Corneel Middelkoop, and Marie Macůrková. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.91054. ieee: F. Knop, A. Zounarová, V. Šabata, T. C. Middelkoop, and M. Macůrková, “Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity,” eLife, vol. 13. eLife Sciences Publications, 2024. ista: Knop F, Zounarová A, Šabata V, Middelkoop TC, Macůrková M. 2024. Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. eLife. 13, e91054. mla: Knop, Filip, et al. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” ELife, vol. 13, e91054, eLife Sciences Publications, 2024, doi:10.7554/elife.91054. short: F. Knop, A. Zounarová, V. Šabata, T.C. Middelkoop, M. Macůrková, ELife 13 (2024). date_created: 2025-12-12T09:06:31Z date_published: 2024-07-19T00:00:00Z date_updated: 2025-12-15T10:26:56Z day: '19' doi: 10.7554/elife.91054 extern: '1' external_id: pmid: - '39028260' fulldoi: https://doi.org/10.7554/elife.91054 intvolume: ' 13' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7554/elife.91054 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '9651' abstract: - lang: eng text: We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence. acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.' article_number: '15' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Michael full_name: Dymond, Michael last_name: Dymond - first_name: Vojtech full_name: Kaluza, Vojtech id: 21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E last_name: Kaluza orcid: 0000-0002-2512-8698 citation: ama: Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2024;218. doi:10.1007/s10711-023-00862-3 apa: Dymond, M., & Kaluza, V. (2024). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3 chicago: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2024. https://doi.org/10.1007/s10711-023-00862-3. ieee: M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata, vol. 218. Springer Nature, 2024. ista: Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 218, 15. mla: Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, vol. 218, 15, Springer Nature, 2024, doi:10.1007/s10711-023-00862-3. short: M. Dymond, V. Kaluza, Geometriae Dedicata 218 (2024). corr_author: '1' date_created: 2021-07-14T07:01:27Z date_published: 2024-02-01T00:00:00Z date_updated: 2025-04-23T07:37:26Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.1007/s10711-023-00862-3 external_id: arxiv: - '2102.13046' isi: - '001105681500001' pmid: - '38021107' file: - access_level: open_access checksum: 9418534ac2f3d6f1f091a8b8ccaed01e content_type: application/pdf creator: dernst date_created: 2024-07-16T10:14:13Z date_updated: 2024-07-16T10:14:13Z file_id: '17257' file_name: 2024_GeometriaeDedicata_Dymond.pdf file_size: 540981 relation: main_file success: 1 file_date_updated: 2024-07-16T10:14:13Z fulldoi: https://doi.org/10.1007/s10711-023-00862-3 has_accepted_license: '1' intvolume: ' 218' isi: 1 language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Geometriae Dedicata publication_identifier: eissn: - 1572-9168 issn: - 0046-5755 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Divergence of separated nets with respect to displacement equivalence tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 218 year: '2024' ... --- APC_amount: 6828 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17202' abstract: - lang: eng text: Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material. acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: NanoFab acknowledgement: "We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support." article_number: '6400' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Oliver full_name: Sagi, Oliver id: 71616374-A8E9-11E9-A7CA-09ECE5697425 last_name: Sagi - first_name: Alessandro full_name: Crippa, Alessandro id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425 last_name: Crippa orcid: 0000-0002-2968-611X - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik orcid: 0009-0003-9037-8831 - first_name: Levon full_name: Baghumyan, Levon id: 7aa1f788-b527-11ee-aa9e-e6111a79e0c7 last_name: Baghumyan - first_name: Giorgio full_name: Fabris, Giorgio id: 298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352 last_name: Fabris - first_name: Lucky full_name: Kapoor, Lucky id: 84b9700b-15b2-11ec-abd3-831089e67615 last_name: Kapoor orcid: 0000-0001-8319-2148 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. Nature Communications. 2024;15. doi:10.1038/s41467-024-50763-6 apa: Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-50763-6 chicago: Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-50763-6. ieee: O. Sagi et al., “A gate tunable transmon qubit in planar Ge,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400. mla: Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature Communications, vol. 15, 6400, Springer Nature, 2024, doi:10.1038/s41467-024-50763-6. short: O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024). corr_author: '1' date_created: 2024-07-04T11:40:45Z date_published: 2024-07-30T00:00:00Z date_updated: 2026-04-07T13:01:55Z day: '30' ddc: - '530' department: - _id: GeKa - _id: JoFi - _id: GradSch doi: 10.1038/s41467-024-50763-6 external_id: arxiv: - '2403.16774' isi: - '001281271000022' pmid: - '39080279' file: - access_level: open_access checksum: ddf5361dcb6c543e2cea818501c09910 content_type: application/pdf creator: dernst date_created: 2024-08-05T08:38:01Z date_updated: 2024-08-05T08:38:01Z file_id: '17388' file_name: 2024_NatureComm_Sagi.pdf file_size: 1928001 relation: main_file success: 1 file_date_updated: 2024-08-05T08:38:01Z fulldoi: https://doi.org/10.1038/s41467-024-50763-6 has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins - _id: 262116AA-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-024-53910-1 record: - id: '17196' relation: research_data status: public - id: '18076' relation: dissertation_contains status: public scopus_import: '1' status: public title: A gate tunable transmon qubit in planar Ge tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- _id: '17203' abstract: - lang: eng text: "The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found.\r\n\r\nIn this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes.\r\n\r\nThis insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain." acknowledgement: We thank Gianmarco Cherchi for his help in tailoring the Mesh Booleans code for this project, Stefan Jeschke for his help with the photographs, Malina Strugaru and Aleksei Kalinov for their help with the samples, and the anonymous reviewers as well as the members of the ISTA Visual Computing Group for their feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA). article_number: '78' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Mickaël full_name: Ly, Mickaël id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1 last_name: Ly - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 2024;43(4). doi:10.1145/3658194' apa: 'Hafner, C., Ly, M., & Wojtan, C. (2024). Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. Denver, Colorado: Association for Computing Machinery. https://doi.org/10.1145/3658194' chicago: 'Hafner, Christian, Mickaël Ly, and Chris Wojtan. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658194.' ieee: 'C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments,” Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024.' ista: 'Hafner C, Ly M, Wojtan C. 2024. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 43(4), 78.' mla: 'Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics, vol. 43, no. 4, 78, Association for Computing Machinery, 2024, doi:10.1145/3658194.' short: C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024). conference: end_date: 2024-08-01 location: Denver, Colorado start_date: 2024-07-28 corr_author: '1' date_created: 2024-07-05T12:08:57Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-08T08:29:09Z day: '01' ddc: - '516' department: - _id: ChWo doi: 10.1145/3658194 external_id: isi: - '001289270900045' file: - access_level: open_access checksum: 0dc9f5a6422b8a49a79026900f349ee5 content_type: application/pdf creator: chafner date_created: 2024-07-05T12:05:17Z date_updated: 2024-07-05T12:05:17Z file_id: '17204' file_name: sif-final.pdf file_size: 7225150 relation: main_file success: 1 - access_level: open_access checksum: cde433c6a40688d5f1187fb5721f6f94 content_type: application/pdf creator: chafner date_created: 2024-07-05T12:06:03Z date_updated: 2024-07-05T12:06:03Z file_id: '17205' file_name: sif-supp-final.pdf file_size: 397262 relation: supplementary_material - access_level: open_access checksum: c0457a09c2ab9a1c2935c995dcc84907 content_type: video/mp4 creator: chafner date_created: 2024-07-17T09:29:13Z date_updated: 2024-07-17T09:29:13Z file_id: '17276' file_name: sif-video-final.mp4 file_size: 170001305 relation: supplementary_material title: Submission Video file_date_updated: 2024-07-17T09:29:13Z fulldoi: https://doi.org/10.1145/3658194 has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '4' keyword: - Topology Optimization - Mass Moments - Computational Geometry language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 43 year: '2024' ... --- _id: '17207' acknowledgement: "This research was funded by the Austrian Science Fund (FWF), project doi: 10.55776/P32896, Institutional Identifier: 501100002428, grant number: P32896 and L.F. acknowledges the support of the NOMIS-ISTA Fellowship Program.\r\nWe would like to thank Nick Barton, Roger Butlin, Stuart Baird, Patrik Nosil, and Jason Sexton for their insightful comments on the earlier drafts, and to John Carchrae for his valuable contribution in refining phrasing and enhancing clarity. For open access purposes, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission." article_processing_charge: No article_type: letter_note author: - first_name: Louise full_name: Fouqueau, Louise id: 1676e173-8143-11ed-8927-fe165216a93f last_name: Fouqueau orcid: 0000-0003-0371-9339 - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: 'Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 2024;37(6):579-587. doi:10.1093/jeb/voae067' apa: 'Fouqueau, L., & Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae067' chicago: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae067.' ieee: 'L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” Journal of evolutionary biology, vol. 37, no. 6. Oxford University Press, pp. 579–587, 2024.' ista: 'Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.' mla: 'Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:10.1093/jeb/voae067.' short: L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587. date_created: 2024-07-07T22:01:04Z date_published: 2024-06-28T00:00:00Z date_updated: 2026-06-18T17:53:35Z day: '28' ddc: - '570' department: - _id: NiBa doi: 10.1093/jeb/voae067 external_id: isi: - '001258359900001' pmid: - '38941551' fulldoi: https://doi.org/10.1093/jeb/voae067 intvolume: ' 37' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/jeb/voae067 month: '06' oa: 1 oa_version: Published Version page: 579-587 pmid: 1 project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Journal of evolutionary biology publication_identifier: eissn: - 1420-9101 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Eco-evolutionary dynamics in changing environments: Integrating theory with data' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2024' ... --- OA_place: publisher _id: '17208' abstract: - lang: eng text: "Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization. We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 citation: ama: Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:10.15479/at:ista:17208 apa: Medina Ramos, R. A. (2024). Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17208 chicago: Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17208. ieee: R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024. ista: Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria. mla: Medina Ramos, Raimel A. Exploring the Optimization Landscape of Variational Quantum Algorithms. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17208. short: R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-07-09T09:14:24Z date_published: 2024-07-09T00:00:00Z date_updated: 2026-04-07T12:43:22Z day: '09' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: MaSe doi: 10.15479/at:ista:17208 ec_funded: 1 file: - access_level: closed checksum: 6f45273d04f4418bc2adc018baed0525 content_type: application/zip creator: rmedinar date_created: 2024-07-09T09:21:44Z date_updated: 2024-07-10T11:34:09Z file_id: '17212' file_name: Raimel_Thesis-Final.zip file_size: '14218691' relation: source_file - access_level: open_access checksum: 6724a95bec772dbabc0111b9f08a805e content_type: application/pdf creator: rmedinar date_created: 2024-07-17T09:23:24Z date_updated: 2024-07-17T09:23:24Z file_id: '17275' file_name: Raimel_Thesis-20_pdfa.pdf file_size: 11253627 relation: main_file success: 1 file_date_updated: 2024-07-17T09:23:24Z fulldoi: https://doi.org/10.15479/at:ista:17208 has_accepted_license: '1' keyword: - Quantum computing - Variational Quantum Algorithms - Optimization language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '133' project: - _id: 23841C26-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '850899' name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10545' relation: part_of_dissertation status: public - id: '10067' relation: part_of_dissertation status: public - id: '17222' relation: part_of_dissertation status: public - id: '13125' relation: part_of_dissertation status: public - id: '11471' relation: part_of_dissertation status: public status: public supervisor: - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 title: Exploring the optimization landscape of variational quantum algorithms tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '17214' abstract: - lang: eng text: 'Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.' acknowledgement: We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). article_processing_charge: Yes (via OA deal) author: - first_name: Yi-Lu full_name: Chen, Yi-Lu id: 0b467602-dbcd-11ea-9d1d-ed480aa46b70 last_name: Chen - first_name: Mickaël full_name: Ly, Mickaël id: 6340d7f0-b48d-11eb-b10d-b7487e71d9f1 last_name: Ly - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657485' apa: 'Chen, Y.-L., Ly, M., & Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Denver, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657485' chicago: Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657485. ieee: Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Denver, United States, 2024. ista: 'Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.' mla: Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657485. short: Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024. conference: end_date: 2024-08-01 location: Denver, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2024-07-28 corr_author: '1' date_created: 2024-07-10T11:06:20Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-08T08:54:38Z day: '01' ddc: - '621' - '531' - '006' department: - _id: GradSch - _id: ChWo doi: 10.1145/3641519.3657485 external_id: isi: - '001282218200091' file: - access_level: open_access checksum: b8b203ed09e3995ba0d7e6a76288663a content_type: application/pdf creator: yichen date_created: 2024-07-10T11:03:14Z date_updated: 2024-07-10T11:03:14Z file_id: '17215' file_name: sig24_friction_authors.pdf file_size: 47309472 relation: main_file success: 1 - access_level: open_access checksum: 89d81b397b4b6469d828808a68b70820 content_type: application/pdf creator: yichen date_created: 2024-07-10T11:03:12Z date_updated: 2024-07-10T11:03:12Z file_id: '17216' file_name: sig24_friction_supplementary.pdf file_size: 10518286 relation: main_file success: 1 - access_level: open_access checksum: 7123deed34a5456810e7b5336a31c657 content_type: video/mp4 creator: yichen date_created: 2024-07-10T11:03:51Z date_updated: 2024-07-10T11:03:51Z file_id: '17217' file_name: friction_paper_extra_video_finished.mp4 file_size: 71789192 relation: main_file success: 1 - access_level: open_access checksum: e606fc1ae8f2610ce3b4421566800b45 content_type: video/mp4 creator: yichen date_created: 2024-07-10T11:03:58Z date_updated: 2024-07-10T11:03:58Z file_id: '17218' file_name: friction_paper_video_finished.mp4 file_size: 280610763 relation: main_file success: 1 file_date_updated: 2024-07-10T11:03:58Z fulldoi: https://doi.org/10.1145/3641519.3657485 has_accepted_license: '1' isi: 1 keyword: - physical simulation - frictional contact - rigid body mechanics - non-smooth dynamics language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24 publication_identifier: isbn: - '9798400705250' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Primal-dual non-smooth friction for rigid body animation type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17219' abstract: - lang: eng text: 'We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.' acknowledgement: Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA). article_number: '54' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Peter full_name: Synak, Peter id: 331776E2-F248-11E8-B48F-1D18A9856A87 last_name: Synak - first_name: Aleksei full_name: Kalinov, Aleksei id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02 last_name: Kalinov orcid: 0000-0003-2189-3904 - first_name: Irina-Malina full_name: Strugaru, Irina-Malina id: 2afc607f-f128-11eb-9611-8f2a0dfcf074 last_name: Strugaru - first_name: Arian full_name: Etemadihaghighi, Arian id: 36cea3aa-f38e-11ec-8ae0-c65ae6f6098f last_name: Etemadihaghighi - first_name: Huidong full_name: Yang, Huidong last_name: Yang - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 2024;43(4). doi:10.1145/3658223 apa: Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., & Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658223 chicago: Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658223. ieee: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” ACM Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024. ista: Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54. mla: Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:10.1145/3658223. short: P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024). corr_author: '1' date_created: 2024-07-10T12:24:00Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-04-07T13:02:36Z day: '01' ddc: - '004' department: - _id: GradSch - _id: ChWo doi: 10.1145/3658223 external_id: isi: - '001289270900021' file: - access_level: open_access checksum: 1917067d4b52d7729019b03560004e43 content_type: application/pdf creator: dernst date_created: 2024-07-23T06:35:15Z date_updated: 2024-07-23T06:35:15Z file_id: '17317' file_name: 2024_ACMToG_HeissSynak.pdf file_size: 48763368 relation: main_file success: 1 - access_level: open_access checksum: a4f0e293184bfa034c0c585848806b17 content_type: video/mp4 creator: akalinov date_created: 2024-07-10T12:23:44Z date_updated: 2024-07-10T12:23:44Z file_id: '17221' file_name: sdtopofixer_final.mp4 file_size: 48021463 relation: main_file success: 1 - access_level: open_access checksum: 18fc310a78ec91651148c45a8b89fa44 content_type: application/pdf creator: akalinov date_created: 2025-11-11T09:50:52Z date_updated: 2025-11-11T09:50:52Z file_id: '20633' file_name: SuperDuperTopoFixer.pdf file_size: 48639581 relation: preprint title: Authors' version of the text file_date_updated: 2025-11-11T09:50:52Z fulldoi: https://doi.org/10.1145/3658223 has_accepted_license: '1' intvolume: ' 43' isi: 1 issue: '4' keyword: - surface tracking - topology change - non- manifold meshes - multi-material flows - solid modeling language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: ACM Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '19630' relation: dissertation_contains status: public - id: '18301' relation: dissertation_contains status: public scopus_import: '1' status: public title: Multi-material mesh-based surface tracking with implicit topology changes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2024' ... --- OA_place: repository _id: '17222' abstract: - lang: eng text: "The quantum approximate optimization algorithm (QAOA) uses a quantum computer\r\nto implement a variational method with $2p$ layers of alternating unitary\r\noperators, optimized by a classical computer to minimize a cost function. While\r\nrigorous performance guarantees exist for the QAOA at small depths $p$, the\r\nbehavior at large depths remains less clear, though simulations suggest\r\nexponentially fast convergence for certain problems. In this work, we gain\r\ninsights into the deep QAOA using an analytic expansion of the cost function\r\naround transition states. Transition states are constructed in a recursive\r\nmanner: from the local minima of the QAOA with $p$ layers we obtain transition\r\nstates of the QAOA with $p+1$ layers, which are stationary points characterized\r\nby a unique direction of negative curvature. We construct an analytic estimate\r\nof the negative curvature and the corresponding direction in parameter space at\r\neach transition state. The expansion of the QAOA cost function along the\r\nnegative direction to the quartic order gives a lower bound of the QAOA cost\r\nfunction improvement. We provide physical intuition behind the analytic\r\nexpressions for the local curvature and quartic expansion coefficient. Our\r\nnumerical study confirms the accuracy of our approximations and reveals that\r\nthe obtained bound and the true value of the QAOA cost function gain have a\r\ncharacteristic exponential decrease with the number of layers $p$, with the\r\nbound decreasing more rapidly. Our study establishes an analytical method for\r\nrecursively studying the QAOA that is applicable in the regime of high circuit\r\ndepth." article_number: '2405.10125' article_processing_charge: No arxiv: 1 author: - first_name: Raimel A full_name: Medina Ramos, Raimel A id: CE680B90-D85A-11E9-B684-C920E6697425 last_name: Medina Ramos orcid: 0000-0002-5383-2869 - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv. doi:10.48550/arXiv.2405.10125 apa: Medina Ramos, R. A., & Serbyn, M. (n.d.). A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv. https://doi.org/10.48550/arXiv.2405.10125 chicago: Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.10125. ieee: R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm,” arXiv. . ista: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv, 2405.10125. mla: Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv, 2405.10125, doi:10.48550/arXiv.2405.10125. short: R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.). corr_author: '1' date_created: 2024-07-10T13:12:09Z date_published: 2024-05-16T00:00:00Z date_updated: 2026-04-07T12:43:22Z day: '16' department: - _id: MaSe doi: 10.48550/arXiv.2405.10125 external_id: arxiv: - '2405.10125' fulldoi: https://doi.org/10.48550/arXiv.2405.10125 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.10125 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '17208' relation: dissertation_contains status: public status: public title: A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- APC_amount: 804 EUR OA_place: publisher OA_type: gold _id: '17232' abstract: - lang: eng text: "The lineage relationship of clonally-related cells offers important insights into the ontogeny and cytoarchitecture of the brain in health and disease. Here, we provide a protocol to concurrently assess cell lineage relationship and cell-type identity among clonally-related cells in situ. We first describe the preparation and screening of acute brain slices containing clonally-related cells labeled using mosaic analysis with double markers (MADM). We then outline steps to collect RNA from individual cells for downstream applications and cell-type identification using RNA sequencing.\r\nFor complete details on the use and execution of this protocol, please refer to Cheung et al.\r\n1" acknowledged_ssus: - _id: Bio - _id: M-Shop - _id: PreCl acknowledgement: We thank R. Beattie and T. Asenov for designing and producing components of the multi-well slice recover chamber. We thank R. Shigemoto for providing equipment access. We thank C. Streicher and A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics, Miba Machine Shop, and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship) and S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation). article_number: '103168' article_processing_charge: Yes article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168 apa: Cheung, G. T., Pauler, F., Koppensteiner, P., & Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168 chicago: Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168. ieee: G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024. ista: Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. 2024. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 5(3), 103168. mla: Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols, vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168. short: G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-07-14T22:01:10Z date_published: 2024-09-20T00:00:00Z date_updated: 2025-12-30T10:54:12Z day: '20' ddc: - '570' department: - _id: SiHi - _id: PreCl doi: 10.1016/j.xpro.2024.103168 external_id: pmid: - '38968076' file: - access_level: open_access checksum: 464f52ecc6ec92f509552823bb82bf79 content_type: application/pdf creator: dernst date_created: 2025-01-09T12:16:53Z date_updated: 2025-01-09T12:16:53Z file_id: '18810' file_name: 2024_STARProtoc_Cheung2.pdf file_size: 6445556 relation: main_file success: 1 file_date_updated: 2025-01-09T12:16:53Z fulldoi: https://doi.org/10.1016/j.xpro.2024.103168 has_accepted_license: '1' intvolume: ' 5' issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F7805 name: Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- _id: '17233' abstract: - lang: eng text: CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene. acknowledgement: This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING to E.M.B.). article_number: e5029 article_processing_charge: Yes article_type: original author: - first_name: Ziqiang full_name: Li, Ziqiang id: 922e68bb-1727-11ee-857c-966e8cc1b6c3 last_name: Li - first_name: Jennifer full_name: Huard, Jennifer last_name: Huard - first_name: Emmanuelle M. full_name: Bayer, Emmanuelle M. last_name: Bayer - first_name: Valérie full_name: Wattelet-Boyer, Valérie last_name: Wattelet-Boyer citation: ama: LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 2024;14(13). doi:10.21769/BioProtoc.5029 apa: LI, Z., Huard, J., Bayer, E. M., & Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/BioProtoc.5029 chicago: LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” Bio-Protocol. Bio-Protocol, 2024. https://doi.org/10.21769/BioProtoc.5029. ieee: Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” Bio-protocol, vol. 14, no. 13. Bio-Protocol, 2024. ista: LI Z, Huard J, Bayer EM, Wattelet-Boyer V. 2024. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 14(13), e5029. mla: LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” Bio-Protocol, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:10.21769/BioProtoc.5029. short: Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024). date_created: 2024-07-14T22:01:11Z date_published: 2024-07-05T00:00:00Z date_updated: 2025-03-06T10:28:18Z day: '05' ddc: - '570' department: - _id: MiSi doi: 10.21769/BioProtoc.5029 external_id: pmid: - '39007160' file: - access_level: open_access checksum: c8671c0ad483da6407cb16cc3fef1990 content_type: application/pdf creator: dernst date_created: 2024-07-16T06:16:11Z date_updated: 2024-07-16T06:16:11Z file_id: '17242' file_name: 2024_BioProtocol_Li.pdf file_size: 2896048 relation: main_file success: 1 file_date_updated: 2024-07-16T06:16:11Z fulldoi: https://doi.org/10.21769/BioProtoc.5029 has_accepted_license: '1' intvolume: ' 14' issue: '13' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Bio-protocol publication_identifier: eissn: - 2331-8325 publication_status: published publisher: Bio-Protocol quality_controlled: '1' scopus_import: '1' status: public title: Versatile cloning strategy for efficient multigene editing in Arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2024' ... --- DOAJ_listed: '1' _id: '17234' abstract: - lang: eng text: The identification of red, apparently massive galaxies at z > 7 in early James Webb Space Telescope (JWST) photometry suggests a strongly accelerated time line compared to standard models of galaxy growth. A major uncertainty in the interpretation is whether the red colors are caused by evolved stellar populations, dust, or other effects such as emission lines or active galactic nuclei (AGNs). Here we show that three of the massive galaxy candidates at z = 6.7–8.4 have prominent Balmer breaks in JWST/NIRSpec spectroscopy from the RUBIES program. The Balmer breaks demonstrate unambiguously that stellar emission dominates at λrest = 0.4 μm and require formation histories extending hundreds of millions of years into the past in galaxies only 600–800 Myr after the big bang. Two of the three galaxies also show broad Balmer lines, with Hβ FWHM > 2500 km s−1, suggesting that dust-reddened AGNs contribute to, or even dominate, the spectral energy distributions of these galaxies at λrest ≳ 0.6 μm. All three galaxies have relatively narrow [O iii] lines, seemingly ruling out a high-mass interpretation if the lines arise in dynamically relaxed, inclined disks. Yet the inferred masses also remain highly uncertain. We model the high-quality spectra using Prospector to decompose the continuum into stellar and AGN components and explore limiting cases in stellar/AGN contribution. This produces a wide range of possible stellar masses, spanning M⋆ ∼ 109−1011M⊙. Nevertheless, all fits suggest a very early and rapid formation, most of which follow with a truncation in star formation. Potential origins and evolutionary tracks for these objects are discussed, from the cores of massive galaxies to low-mass galaxies with overmassive black holes. Intriguingly, we find all of these explanations to be incomplete; deeper and redder data are needed to understand the physics of these systems. acknowledgement: "We thank the anonymous referee for the helpful comments. B.W. and J.L. acknowledge support from JWST-GO04233.009-A. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team project No. 562 (First Light at Cosmic Dawn: Exploiting the James Webb Space Telescope Revolution). This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The JWST data presented in this Letter were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute. The specific observations analyzed can be accessed via doi:10.17909/3a4n-9p88. Computations for this research were performed on the Pennsylvania State University’s Institute for Computational and Data Sciences’ Roar supercomputer. This publication made use of the NASA Astrophysical Data System for bibliographic information. \r\nFacilities: HST (ACS, WFC3), JWST (NIRCam, NIRSpec). Software: Astropy (Astropy Collaboration et al. 2013, 2018, 2022), dynesty (Speagle 2020), EAzY (Brammer et al. 2008),\r\nemcee (Foreman-Mackey et al. 2013), Matplotlib (Hunter 2007), msaexp (Brammer 2023b), msafit (de Graaff et al. 2024a), NumPy (Harris et al. 2020), Prospector (Johnson et al. 2021), Python-FSPS (Johnson et al. 2023)." article_number: L13 article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Bingjie full_name: Wang, Bingjie last_name: Wang - first_name: Joel full_name: Leja, Joel last_name: Leja - first_name: Anna full_name: De Graaff, Anna last_name: De Graaff - first_name: Gabriel B. full_name: Brammer, Gabriel B. last_name: Brammer - first_name: Andrea full_name: Weibel, Andrea last_name: Weibel - first_name: Pieter full_name: Van Dokkum, Pieter last_name: Van Dokkum - first_name: Josephine F.W. full_name: Baggen, Josephine F.W. last_name: Baggen - first_name: Katherine A. full_name: Suess, Katherine A. last_name: Suess - first_name: Jenny E. full_name: Greene, Jenny E. last_name: Greene - first_name: Rachel full_name: Bezanson, Rachel last_name: Bezanson - first_name: Nikko J. full_name: Cleri, Nikko J. last_name: Cleri - first_name: Michaela full_name: Hirschmann, Michaela last_name: Hirschmann - first_name: Ivo full_name: Labbé, Ivo last_name: Labbé - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Ian full_name: Mcconachie, Ian last_name: Mcconachie - first_name: Rohan P. full_name: Naidu, Rohan P. last_name: Naidu - first_name: Erica full_name: Nelson, Erica last_name: Nelson - first_name: Pascal A. full_name: Oesch, Pascal A. last_name: Oesch - first_name: David J. full_name: Setton, David J. last_name: Setton - first_name: Christina C. full_name: Williams, Christina C. last_name: Williams citation: ama: 'Wang B, Leja J, De Graaff A, et al. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 2024;969(1). doi:10.3847/2041-8213/ad55f7' apa: 'Wang, B., Leja, J., De Graaff, A., Brammer, G. B., Weibel, A., Van Dokkum, P., … Williams, C. C. (2024). RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ad55f7' chicago: 'Wang, Bingjie, Joel Leja, Anna De Graaff, Gabriel B. Brammer, Andrea Weibel, Pieter Van Dokkum, Josephine F.W. Baggen, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” Astrophysical Journal Letters. IOP Publishing, 2024. https://doi.org/10.3847/2041-8213/ad55f7.' ieee: 'B. Wang et al., “RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,” Astrophysical Journal Letters, vol. 969, no. 1. IOP Publishing, 2024.' ista: 'Wang B, Leja J, De Graaff A, Brammer GB, Weibel A, Van Dokkum P, Baggen JFW, Suess KA, Greene JE, Bezanson R, Cleri NJ, Hirschmann M, Labbé I, Matthee JJ, Mcconachie I, Naidu RP, Nelson E, Oesch PA, Setton DJ, Williams CC. 2024. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 969(1), L13.' mla: 'Wang, Bingjie, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” Astrophysical Journal Letters, vol. 969, no. 1, L13, IOP Publishing, 2024, doi:10.3847/2041-8213/ad55f7.' short: B. Wang, J. Leja, A. De Graaff, G.B. Brammer, A. Weibel, P. Van Dokkum, J.F.W. Baggen, K.A. Suess, J.E. Greene, R. Bezanson, N.J. Cleri, M. Hirschmann, I. Labbé, J.J. Matthee, I. Mcconachie, R.P. Naidu, E. Nelson, P.A. Oesch, D.J. Setton, C.C. Williams, Astrophysical Journal Letters 969 (2024). date_created: 2024-07-14T22:01:11Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-08T08:10:21Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.3847/2041-8213/ad55f7 external_id: arxiv: - '2405.01473' isi: - '001257903200001' file: - access_level: open_access checksum: bb1a6725586df12e745d091b5778bb2b content_type: application/pdf creator: dernst date_created: 2024-07-16T06:24:29Z date_updated: 2024-07-16T06:24:29Z file_id: '17243' file_name: 2024_AstrophysicalJourn_Wang.pdf file_size: 3273303 relation: main_file success: 1 file_date_updated: 2024-07-16T06:24:29Z fulldoi: https://doi.org/10.3847/2041-8213/ad55f7 has_accepted_license: '1' intvolume: ' 969' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Astrophysical Journal Letters publication_identifier: eissn: - 2041-8213 issn: - 2041-8205 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 969 year: '2024' ... --- _id: '17235' abstract: - lang: eng text: We demonstrate ion irradiation by argon or gallium as a wafer-scale post-processing method to increase disorder in superconducting thin films. We study several widely used superconductors, both single-elements and compounds. We show that ion irradiation increases normal-state resistivity in all our films, which is expected to enable tuning their superconducting properties, for example, toward a higher kinetic inductance. We observe an increase in superconducting transition temperature for Al and MoSi and a decrease for Nb, NbN, and TiN. In MoSi, ion irradiation also improves the mixing of the two materials. We demonstrate the fabrication of an amorphous and homogeneous film of MoSi with uniform thickness, which is promising, for example, for superconducting nanowire single-photon detectors. acknowledged_ssus: - _id: EM-Fac acknowledgement: We thank J. A. Sauls for useful discussions. For funding of our research project, we acknowledge the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreement Nos. 862660/Quantum e-leaps, 899558/aCryComm, 766853/EFINED, and ECSEL programme 101007322/MatQu. This project has also received funding from Business Finland through Quantum Technologies Industrial (QuTI) Project No. 128291 and from Research Council of Finland through Grant Nos. 310909, 350220 and Finnish Quantum Flagship project 359284. This work was performed as part of the Research Council of Finland Centres of Excellence program (Project Nos. 336817, 336819, 352934, and 352935). We also acknowledge funding from an internal strategic innovation project of VTT related to the development of quantum computing technologies. This research was supported by the Scientific Service Units of IST Austria through resources provided by Electron Microscopy Facility. J. Senior acknowledges funding from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie Grant Agreement No. 754411. A. Ronzani acknowledges funding from Research Council of Finland (Research Fellowship Project No. 356542). article_number: '071101' article_processing_charge: Yes article_type: original author: - first_name: Katja full_name: Kohopää, Katja last_name: Kohopää - first_name: Alberto full_name: Ronzani, Alberto last_name: Ronzani - first_name: Robab Najafi full_name: Jabdaraghi, Robab Najafi last_name: Jabdaraghi - first_name: Arijit full_name: Bera, Arijit last_name: Bera - first_name: Mário full_name: Ribeiro, Mário last_name: Ribeiro - first_name: Dibyendu full_name: Hazra, Dibyendu last_name: Hazra - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Mika full_name: Prunnila, Mika last_name: Prunnila - first_name: Joonas full_name: Govenius, Joonas last_name: Govenius - first_name: Janne S. full_name: Lehtinen, Janne S. last_name: Lehtinen - first_name: Antti full_name: Kemppinen, Antti last_name: Kemppinen citation: ama: Kohopää K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting thin films. APL Materials. 2024;12(7). doi:10.1063/5.0202851 apa: Kohopää, K., Ronzani, A., Jabdaraghi, R. N., Bera, A., Ribeiro, M., Hazra, D., … Kemppinen, A. (2024). Effect of ion irradiation on superconducting thin films. APL Materials. AIP Publishing. https://doi.org/10.1063/5.0202851 chicago: Kohopää, Katja, Alberto Ronzani, Robab Najafi Jabdaraghi, Arijit Bera, Mário Ribeiro, Dibyendu Hazra, Jorden L Senior, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” APL Materials. AIP Publishing, 2024. https://doi.org/10.1063/5.0202851. ieee: K. Kohopää et al., “Effect of ion irradiation on superconducting thin films,” APL Materials, vol. 12, no. 7. AIP Publishing, 2024. ista: Kohopää K, Ronzani A, Jabdaraghi RN, Bera A, Ribeiro M, Hazra D, Senior JL, Prunnila M, Govenius J, Lehtinen JS, Kemppinen A. 2024. Effect of ion irradiation on superconducting thin films. APL Materials. 12(7), 071101. mla: Kohopää, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” APL Materials, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:10.1063/5.0202851. short: K. Kohopää, A. Ronzani, R.N. Jabdaraghi, A. Bera, M. Ribeiro, D. Hazra, J.L. Senior, M. Prunnila, J. Govenius, J.S. Lehtinen, A. Kemppinen, APL Materials 12 (2024). date_created: 2024-07-14T22:01:11Z date_published: 2024-07-01T00:00:00Z date_updated: 2025-09-08T08:10:58Z day: '01' ddc: - '530' department: - _id: AnHi doi: 10.1063/5.0202851 ec_funded: 1 external_id: isi: - '001260942200003' file: - access_level: open_access checksum: 32a5cdf0ea9c937f806b6039f3219917 content_type: application/pdf creator: dernst date_created: 2024-07-16T06:30:30Z date_updated: 2024-07-16T06:30:30Z file_id: '17244' file_name: 2024_APLMaterial_Kohopaa.pdf file_size: 9408198 relation: main_file success: 1 file_date_updated: 2024-07-16T06:30:30Z fulldoi: https://doi.org/10.1063/5.0202851 has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: APL Materials publication_identifier: eissn: - 2166-532X publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Effect of ion irradiation on superconducting thin films tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 12 year: '2024' ...