[{"publication_status":"published","publisher":"Springer Nature","OA_type":"closed access","date_created":"2025-08-10T22:01:30Z","date_published":"2024-10-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Nature Mental Health","_id":"20157","day":"01","intvolume":"         2","month":"10","quality_controlled":"1","title":"Rethinking ethics in interdisciplinary and big data-driven neuroscience projects","type":"journal_article","status":"public","article_type":"comment","volume":2,"department":[{"_id":"GaNo"}],"issue":"10","article_processing_charge":"No","citation":{"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).","mla":"Stahl, Bernd, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” <i>Nature Mental Health</i>, vol. 2, no. 10, 1128–1130, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s44220-024-00320-3\">10.1038/s44220-024-00320-3</a>.","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.” <i>Nature Mental Health</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s44220-024-00320-3\">https://doi.org/10.1038/s44220-024-00320-3</a>.","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. <i>Nature Mental Health</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s44220-024-00320-3\">https://doi.org/10.1038/s44220-024-00320-3</a>","ama":"Stahl B, Ogoh G, Schumann G, et al. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. <i>Nature Mental Health</i>. 2024;2(10). doi:<a href=\"https://doi.org/10.1038/s44220-024-00320-3\">10.1038/s44220-024-00320-3</a>","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.","ieee":"B. Stahl <i>et al.</i>, “Rethinking ethics in interdisciplinary and big data-driven neuroscience projects,” <i>Nature Mental Health</i>, vol. 2, no. 10. Springer Nature, 2024."},"scopus_import":"1","year":"2024","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).","doi":"10.1038/s44220-024-00320-3","language":[{"iso":"eng"}],"author":[{"first_name":"Bernd","last_name":"Stahl","full_name":"Stahl, Bernd"},{"full_name":"Ogoh, George","first_name":"George","last_name":"Ogoh"},{"first_name":"Gunter","last_name":"Schumann","full_name":"Schumann, Gunter"},{"first_name":"Henrik","last_name":"Walter","full_name":"Walter, Henrik"},{"full_name":"Stahl, Bernd","last_name":"Stahl","first_name":"Bernd"},{"last_name":"Young","first_name":"Allan H.","full_name":"Young, Allan H."},{"last_name":"Desrivières","first_name":"Sylvane","full_name":"Desrivières, Sylvane"},{"first_name":"Nicholas","last_name":"Clinton","full_name":"Clinton, Nicholas"},{"first_name":"Paul","last_name":"Thompson","full_name":"Thompson, Paul"},{"full_name":"Schwalber, Ameli","first_name":"Ameli","last_name":"Schwalber"},{"last_name":"Liu","first_name":"Jingyu","full_name":"Liu, Jingyu"},{"first_name":"Vince","last_name":"Calhoun","full_name":"Calhoun, Vince"},{"full_name":"Chang, Xiao","first_name":"Xiao","last_name":"Chang"},{"first_name":"Yunman","last_name":"Xia","full_name":"Xia, Yunman"},{"full_name":"Gong, Yanting","last_name":"Gong","first_name":"Yanting"},{"full_name":"Jia, Tianye","first_name":"Tianye","last_name":"Jia"},{"full_name":"Renner, Paul","first_name":"Paul","last_name":"Renner"},{"full_name":"Hese, Sören","last_name":"Hese","first_name":"Sören"},{"first_name":"Arantxa","last_name":"Giner","full_name":"Giner, Arantxa"},{"full_name":"Sanchez, Mavi","last_name":"Sanchez","first_name":"Mavi"},{"full_name":"Alvarez, Elena","last_name":"Alvarez","first_name":"Elena"},{"last_name":"Spanlang","first_name":"Bernhard","full_name":"Spanlang, Bernhard"},{"last_name":"Pearmund","first_name":"Charlie","full_name":"Pearmund, Charlie"},{"last_name":"Athanasiadis","first_name":"Anastasios Polykarpos","full_name":"Athanasiadis, Anastasios Polykarpos"},{"first_name":"Lisa","last_name":"Otten","full_name":"Otten, Lisa"},{"first_name":"Séverine","last_name":"Pitel","full_name":"Pitel, Séverine"},{"full_name":"Petkoski, Spase","last_name":"Petkoski","first_name":"Spase"},{"first_name":"Viktor","last_name":"Jirsa","full_name":"Jirsa, Viktor"},{"full_name":"Schmitt, Karen","last_name":"Schmitt","first_name":"Karen"},{"full_name":"Wilbertz, Johannes","last_name":"Wilbertz","first_name":"Johannes"},{"full_name":"Patraskaki, Myrto","last_name":"Patraskaki","first_name":"Myrto"},{"first_name":"Peter","last_name":"Sommer","full_name":"Sommer, Peter"},{"full_name":"Heilmann-Heimbach, Stefanie","first_name":"Stefanie","last_name":"Heilmann-Heimbach"},{"full_name":"Mathey, Carina M.","first_name":"Carina M.","last_name":"Mathey"},{"last_name":"Miller","first_name":"Abigail","full_name":"Miller, Abigail"},{"full_name":"Claus, Isabelle","first_name":"Isabelle","last_name":"Claus"},{"full_name":"Nöthen, Markus M.","first_name":"Markus M.","last_name":"Nöthen"},{"last_name":"Hoffmann","first_name":"Per","full_name":"Hoffmann, Per"},{"first_name":"Andreas J.","last_name":"Forstner","full_name":"Forstner, Andreas J."},{"full_name":"Pastor, Alvaro","first_name":"Alvaro","last_name":"Pastor"},{"full_name":"Gallego, Jaime","first_name":"Jaime","last_name":"Gallego"},{"full_name":"Orosa, Francisco Eiroa","first_name":"Francisco Eiroa","last_name":"Orosa"},{"first_name":"Guillem Feixas","last_name":"Viapiana","full_name":"Viapiana, Guillem Feixas"},{"last_name":"Slater","first_name":"Mel","full_name":"Slater, Mel"},{"full_name":"Marr, Lena","first_name":"Lena","last_name":"Marr","id":"4406F586-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marquand","first_name":"Andre","full_name":"Marquand, Andre"},{"full_name":"Böttger, Sarah Jane","first_name":"Sarah Jane","last_name":"Böttger"},{"full_name":"Tschorn, Mira","first_name":"Mira","last_name":"Tschorn"},{"full_name":"Rapp, Michael","first_name":"Michael","last_name":"Rapp"},{"first_name":"Helga","last_name":"Ask","full_name":"Ask, Helga"},{"full_name":"Kjelkenes, Rikka","last_name":"Kjelkenes","first_name":"Rikka"},{"full_name":"Fernandez, Sara","last_name":"Fernandez","first_name":"Sara"},{"last_name":"Van Der Meer","first_name":"Dennis","full_name":"Van Der Meer, Dennis"},{"full_name":"Westlye, Lars T.","first_name":"Lars T.","last_name":"Westlye"},{"last_name":"Andreassen","first_name":"Ole A.","full_name":"Andreassen, Ole A."},{"first_name":"Rieke","last_name":"Aden","full_name":"Aden, Rieke"},{"full_name":"Seefried, Beke","last_name":"Seefried","first_name":"Beke"},{"full_name":"Siehl, Sebastian","last_name":"Siehl","first_name":"Sebastian"},{"full_name":"Nees, Frauke","last_name":"Nees","first_name":"Frauke"},{"full_name":"Neidhart, Maja","first_name":"Maja","last_name":"Neidhart"},{"first_name":"Argyris","last_name":"Stringaris","full_name":"Stringaris, Argyris"},{"first_name":"Emanuel","last_name":"Schwarz","full_name":"Schwarz, Emanuel"},{"first_name":"Nathalie","last_name":"Holz","full_name":"Holz, Nathalie"},{"last_name":"Tost","first_name":"Heike","full_name":"Tost, Heike"},{"full_name":"Meyer-Lindenberg, Andreas","first_name":"Andreas","last_name":"Meyer-Lindenberg"},{"full_name":"Christmann, Nina","last_name":"Christmann","first_name":"Nina"},{"full_name":"Jansone, Karina","first_name":"Karina","last_name":"Jansone"},{"full_name":"Banaschewski, Tobias","first_name":"Tobias","last_name":"Banaschewski"},{"first_name":"Jamie","last_name":"Banks","full_name":"Banks, Jamie"},{"first_name":"Kerstin","last_name":"Schepanski","full_name":"Schepanski, Kerstin"},{"last_name":"Schütz","first_name":"Tatjana","full_name":"Schütz, Tatjana"},{"full_name":"Taron, Ulrike Helene","last_name":"Taron","first_name":"Ulrike Helene"},{"full_name":"Eils, Roland","last_name":"Eils","first_name":"Roland"},{"full_name":"Roy, Jean Charles","last_name":"Roy","first_name":"Jean Charles"},{"last_name":"Lett","first_name":"Tristram A.","full_name":"Lett, Tristram A."},{"full_name":"Kebir, Hedi","first_name":"Hedi","last_name":"Kebir"},{"full_name":"Polemiti, Elli","first_name":"Elli","last_name":"Polemiti"},{"last_name":"Hitchen","first_name":"Esther","full_name":"Hitchen, Esther"},{"full_name":"Jentsch, Marcel","first_name":"Marcel","last_name":"Jentsch"},{"last_name":"Serin","first_name":"Emin","full_name":"Serin, Emin"},{"full_name":"Bernas, Antoine","last_name":"Bernas","first_name":"Antoine"},{"full_name":"Vaidya, Nilakshi","last_name":"Vaidya","first_name":"Nilakshi"},{"first_name":"Sven","last_name":"Twardziok","full_name":"Twardziok, Sven"},{"full_name":"Ralser, Markus","last_name":"Ralser","first_name":"Markus"},{"full_name":"Heinz, Andreas","first_name":"Andreas","last_name":"Heinz"},{"first_name":"Henrik","last_name":"Walter","full_name":"Walter, Henrik"}],"date_updated":"2025-08-11T06:53:55Z","fulldoi":"https://doi.org/10.1038/s44220-024-00320-3","oa_version":"None","article_number":"1128-1130","publication_identifier":{"eissn":["2731-6076"]}},{"citation":{"short":"L. Venkataraman, J. van Ruitenbeek, Nature Chemistry 16 (2024) 1767–1769.","mla":"Venkataraman, Latha, and Jan van Ruitenbeek. “Questioning Claims of Monitoring the Michael Addition Reaction at the Single-Molecule Level.” <i>Nature Chemistry</i>, vol. 16, no. 11, Springer Nature, 2024, pp. 1767–69, doi:<a href=\"https://doi.org/10.1038/s41557-024-01631-9\">10.1038/s41557-024-01631-9</a>.","chicago":"Venkataraman, Latha, and Jan van Ruitenbeek. “Questioning Claims of Monitoring the Michael Addition Reaction at the Single-Molecule Level.” <i>Nature Chemistry</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41557-024-01631-9\">https://doi.org/10.1038/s41557-024-01631-9</a>.","apa":"Venkataraman, L., &#38; van Ruitenbeek, J. (2024). Questioning claims of monitoring the Michael addition reaction at the single-molecule level. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-024-01631-9\">https://doi.org/10.1038/s41557-024-01631-9</a>","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.","ama":"Venkataraman L, van Ruitenbeek J. Questioning claims of monitoring the Michael addition reaction at the single-molecule level. <i>Nature Chemistry</i>. 2024;16(11):1767-1769. doi:<a href=\"https://doi.org/10.1038/s41557-024-01631-9\">10.1038/s41557-024-01631-9</a>","ieee":"L. Venkataraman and J. van Ruitenbeek, “Questioning claims of monitoring the Michael addition reaction at the single-molecule level,” <i>Nature Chemistry</i>, vol. 16, no. 11. Springer Nature, pp. 1767–1769, 2024."},"doi":"10.1038/s41557-024-01631-9","scopus_import":"1","year":"2024","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."}],"volume":16,"article_type":"letter_note","article_processing_charge":"No","issue":"11","extern":"1","fulldoi":"https://doi.org/10.1038/s41557-024-01631-9","oa_version":"None","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"pmid":1,"date_updated":"2025-10-23T12:58:52Z","author":[{"orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","first_name":"Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"},{"first_name":"Jan","last_name":"van Ruitenbeek","full_name":"van Ruitenbeek, Jan"}],"language":[{"iso":"eng"}],"publication":"Nature Chemistry","_id":"20527","page":"1767-1769","day":"01","publication_status":"published","publisher":"Springer Nature","date_created":"2025-10-23T12:16:57Z","date_published":"2024-11-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","month":"11","quality_controlled":"1","status":"public","title":"Questioning claims of monitoring the Michael addition reaction at the single-molecule level","type":"journal_article","intvolume":"        16","external_id":{"pmid":["39313629"]}},{"publisher":"American Chemical Society","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-12-04T00:00:00Z","date_created":"2025-10-23T12:20:19Z","OA_type":"closed access","_id":"20529","publication":"Journal of the American Chemical Society","page":"34394-34400","day":"04","intvolume":"       146","external_id":{"pmid":["39630979"]},"month":"12","quality_controlled":"1","status":"public","type":"journal_article","title":"Plasmon-exciton strong coupling in single-molecule junction electroluminescence","volume":146,"article_type":"original","article_processing_charge":"No","extern":"1","issue":"50","citation":{"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.","mla":"Paoletta, Angela L., et al. “Plasmon-Exciton Strong Coupling in Single-Molecule Junction Electroluminescence.” <i>Journal of the American Chemical Society</i>, vol. 146, no. 50, American Chemical Society, 2024, pp. 34394–400, doi:<a href=\"https://doi.org/10.1021/jacs.4c09782\">10.1021/jacs.4c09782</a>.","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.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/jacs.4c09782\">https://doi.org/10.1021/jacs.4c09782</a>.","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. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.4c09782\">https://doi.org/10.1021/jacs.4c09782</a>","ama":"Paoletta AL, Hoffmann NM, Cheng DW, et al. Plasmon-exciton strong coupling in single-molecule junction electroluminescence. <i>Journal of the American Chemical Society</i>. 2024;146(50):34394-34400. doi:<a href=\"https://doi.org/10.1021/jacs.4c09782\">10.1021/jacs.4c09782</a>","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.","ieee":"A. L. Paoletta <i>et al.</i>, “Plasmon-exciton strong coupling in single-molecule junction electroluminescence,” <i>Journal of the American Chemical Society</i>, vol. 146, no. 50. American Chemical Society, pp. 34394–34400, 2024."},"doi":"10.1021/jacs.4c09782","year":"2024","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","pmid":1,"author":[{"full_name":"Paoletta, Angela L.","last_name":"Paoletta","first_name":"Angela L."},{"full_name":"Hoffmann, Norah M.","last_name":"Hoffmann","first_name":"Norah M."},{"full_name":"Cheng, Daniel W.","first_name":"Daniel W.","last_name":"Cheng"},{"full_name":"York, Emma","last_name":"York","first_name":"Emma"},{"full_name":"Xu, Ding","first_name":"Ding","last_name":"Xu"},{"first_name":"Boyuan","last_name":"Zhang","full_name":"Zhang, Boyuan"},{"full_name":"Delor, Milan","last_name":"Delor","first_name":"Milan"},{"first_name":"Timothy C.","last_name":"Berkelbach","full_name":"Berkelbach, Timothy C."},{"full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","first_name":"Latha","last_name":"Venkataraman","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"date_updated":"2025-10-23T13:03:41Z","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1021/jacs.4c09782","oa_version":"None","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]}},{"date_updated":"2025-11-10T15:28:49Z","author":[{"first_name":"Xujia","last_name":"Chen","id":"968ad14a-fd86-11ee-a420-ea29715511a3","full_name":"Chen, Xujia"},{"last_name":"Zinger","first_name":"Aleksey","full_name":"Zinger, Aleksey"}],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9789811278556"],"isbn":["9789811278532"]},"status":"public","title":"Spin/Pin-structures and real enumerative geometry","type":"book","fulldoi":"https://doi.org/10.1142/13476","oa_version":"None","quality_controlled":"1","month":"01","date_created":"2025-11-10T08:40:10Z","article_processing_charge":"No","date_published":"2024-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"closed access","extern":"1","publication_status":"published","publisher":"World Scientific Publishing","day":"01","doi":"10.1142/13476","scopus_import":"1","year":"2024","abstract":[{"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.","lang":"eng"}],"_id":"20615","citation":{"ieee":"X. Chen and A. Zinger, <i>Spin/Pin-structures and real enumerative geometry</i>. World Scientific Publishing, 2024.","apa":"Chen, X., &#38; Zinger, A. (2024). <i>Spin/Pin-structures and real enumerative geometry</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/13476\">https://doi.org/10.1142/13476</a>","ama":"Chen X, Zinger A. <i>Spin/Pin-Structures and Real Enumerative Geometry</i>. World Scientific Publishing; 2024. doi:<a href=\"https://doi.org/10.1142/13476\">10.1142/13476</a>","ista":"Chen X, Zinger A. 2024. Spin/Pin-structures and real enumerative geometry, World Scientific Publishing,p.","chicago":"Chen, Xujia, and Aleksey Zinger. <i>Spin/Pin-Structures and Real Enumerative Geometry</i>. World Scientific Publishing, 2024. <a href=\"https://doi.org/10.1142/13476\">https://doi.org/10.1142/13476</a>.","short":"X. Chen, A. Zinger, Spin/Pin-Structures and Real Enumerative Geometry, World Scientific Publishing, 2024.","mla":"Chen, Xujia, and Aleksey Zinger. <i>Spin/Pin-Structures and Real Enumerative Geometry</i>. World Scientific Publishing, 2024, doi:<a href=\"https://doi.org/10.1142/13476\">10.1142/13476</a>."}},{"day":"01","OA_place":"repository","publication":"Current Opinion in Chemical Biology","_id":"20756","OA_type":"green","date_created":"2025-12-09T14:22:40Z","date_published":"2024-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Elsevier","title":"Catalyzing the future: Recent advances in chemical synthesis using enzymes","type":"journal_article","status":"public","quality_controlled":"1","month":"12","external_id":{"pmid":["39369557"]},"intvolume":"        83","scopus_import":"1","year":"2024","abstract":[{"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.","lang":"eng"}],"doi":"10.1016/j.cbpa.2024.102536","citation":{"mla":"Reisenbauer, Julia, et al. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” <i>Current Opinion in Chemical Biology</i>, vol. 83, 102536, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">10.1016/j.cbpa.2024.102536</a>.","short":"J. Reisenbauer, K.M. Sicinski, F.H. Arnold, Current Opinion in Chemical Biology 83 (2024).","chicago":"Reisenbauer, Julia, Kathleen M. Sicinski, and Frances H. Arnold. “Catalyzing the Future: Recent Advances in Chemical Synthesis Using Enzymes.” <i>Current Opinion in Chemical Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">https://doi.org/10.1016/j.cbpa.2024.102536</a>.","ama":"Reisenbauer J, Sicinski KM, Arnold FH. Catalyzing the future: Recent advances in chemical synthesis using enzymes. <i>Current Opinion in Chemical Biology</i>. 2024;83. doi:<a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">10.1016/j.cbpa.2024.102536</a>","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.","apa":"Reisenbauer, J., Sicinski, K. M., &#38; Arnold, F. H. (2024). Catalyzing the future: Recent advances in chemical synthesis using enzymes. <i>Current Opinion in Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cbpa.2024.102536\">https://doi.org/10.1016/j.cbpa.2024.102536</a>","ieee":"J. Reisenbauer, K. M. Sicinski, and F. H. Arnold, “Catalyzing the future: Recent advances in chemical synthesis using enzymes,” <i>Current Opinion in Chemical Biology</i>, vol. 83. Elsevier, 2024."},"extern":"1","article_processing_charge":"No","main_file_link":[{"url":"https://europepmc.org/article/med/39369557#free-full-text","open_access":"1"}],"volume":83,"article_type":"original","article_number":"102536","publication_identifier":{"eissn":["1879-0402"],"issn":["1367-5931"]},"oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1016/j.cbpa.2024.102536","language":[{"iso":"eng"}],"date_updated":"2025-12-16T13:03:48Z","author":[{"full_name":"Reisenbauer, Julia","id":"51d862e9-36ee-11f0-86d3-8534c85a5496","last_name":"Reisenbauer","first_name":"Julia"},{"last_name":"Sicinski","first_name":"Kathleen M.","full_name":"Sicinski, Kathleen M."},{"first_name":"Frances H.","last_name":"Arnold","full_name":"Arnold, Frances H."}],"pmid":1,"oa":1},{"citation":{"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.” <i>Chemical Communications</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d4cc02609h\">https://doi.org/10.1039/d4cc02609h</a>.","mla":"Botlik, Bence B., et al. “Versatile Dehydrogenation of Carbonyls Enabled by an Iodine(III) Reagent.” <i>Chemical Communications</i>, vol. 60, no. 69, Royal Society of Chemistry, 2024, pp. 9254–57, doi:<a href=\"https://doi.org/10.1039/d4cc02609h\">10.1039/d4cc02609h</a>.","short":"B.B. Botlik, P. Finkelstein, A.-S.K. Paschke, J. Reisenbauer, B. Morandi, Chemical Communications 60 (2024) 9254–9257.","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,” <i>Chemical Communications</i>, 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.","ama":"Botlik BB, Finkelstein P, Paschke A-SK, Reisenbauer J, Morandi B. Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. <i>Chemical Communications</i>. 2024;60(69):9254-9257. doi:<a href=\"https://doi.org/10.1039/d4cc02609h\">10.1039/d4cc02609h</a>","apa":"Botlik, B. B., Finkelstein, P., Paschke, A.-S. K., Reisenbauer, J., &#38; Morandi, B. (2024). Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent. <i>Chemical Communications</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4cc02609h\">https://doi.org/10.1039/d4cc02609h</a>"},"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"year":"2024","doi":"10.1039/d4cc02609h","article_type":"original","volume":60,"issue":"69","extern":"1","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/D4CC02609H"}],"fulldoi":"https://doi.org/10.1039/d4cc02609h","oa_version":"Published Version","publication_identifier":{"issn":["1359-7345"],"eissn":["1364-548X"]},"pmid":1,"oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-12-16T11:19:43Z","author":[{"first_name":"Bence B.","last_name":"Botlik","full_name":"Botlik, Bence B."},{"full_name":"Finkelstein, Patrick","first_name":"Patrick","last_name":"Finkelstein"},{"first_name":"Ann-Sophie K.","last_name":"Paschke","full_name":"Paschke, Ann-Sophie K."},{"full_name":"Reisenbauer, Julia","first_name":"Julia","id":"51d862e9-36ee-11f0-86d3-8534c85a5496","last_name":"Reisenbauer"},{"first_name":"Bill","last_name":"Morandi","full_name":"Morandi, Bill"}],"OA_place":"publisher","publication":"Chemical Communications","_id":"20757","day":"02","page":"9254-9257","publication_status":"published","publisher":"Royal Society of Chemistry","OA_type":"hybrid","date_created":"2025-12-09T14:23:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-08-02T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/3.0/","month":"08","quality_controlled":"1","title":"Versatile dehydrogenation of carbonyls enabled by an iodine(III) reagent","type":"journal_article","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"intvolume":"        60","has_accepted_license":"1","external_id":{"pmid":["39118590"]}},{"citation":{"ieee":"L. Panska <i>et al.</i>, “Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans,” <i>Bioscience Reports</i>, 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.","ama":"Panska L, Nedvedova S, Vacek V, et al. Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans. <i>Bioscience Reports</i>. 2024;44(1). doi:<a href=\"https://doi.org/10.1042/bsr20230502\">10.1042/bsr20230502</a>","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. <i>Bioscience Reports</i>. Portland Press. <a href=\"https://doi.org/10.1042/bsr20230502\">https://doi.org/10.1042/bsr20230502</a>","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.” <i>Bioscience Reports</i>. Portland Press, 2024. <a href=\"https://doi.org/10.1042/bsr20230502\">https://doi.org/10.1042/bsr20230502</a>.","mla":"Panska, Lucie, et al. “Uncovering the Essential Roles of Glutamate Carboxypeptidase 2 Orthologs in Caenorhabditis Elegans.” <i>Bioscience Reports</i>, vol. 44, no. 1, BSR20230502, Portland Press, 2024, doi:<a href=\"https://doi.org/10.1042/bsr20230502\">10.1042/bsr20230502</a>.","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)."},"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"year":"2024","doi":"10.1042/bsr20230502","ddc":["570"],"volume":44,"article_type":"original","issue":"1","extern":"1","article_processing_charge":"Yes (in subscription journal)","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1042/BSR20230502"}],"fulldoi":"https://doi.org/10.1042/bsr20230502","oa_version":"Published Version","publication_identifier":{"eissn":["1573-4935"],"issn":["0144-8463"]},"article_number":"BSR20230502","pmid":1,"oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-12-15T10:21:56Z","author":[{"last_name":"Panska","first_name":"Lucie","full_name":"Panska, Lucie"},{"last_name":"Nedvedova","first_name":"Stepanka","full_name":"Nedvedova, Stepanka"},{"first_name":"Vojtech","last_name":"Vacek","full_name":"Vacek, Vojtech"},{"first_name":"Daniela","last_name":"Krivska","full_name":"Krivska, Daniela"},{"full_name":"Konecny, Lukas","last_name":"Konecny","first_name":"Lukas"},{"orcid":"0000-0002-3845-3465","full_name":"Knop, Filip","last_name":"Knop","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","first_name":"Filip"},{"last_name":"Kutil","first_name":"Zsofia","full_name":"Kutil, Zsofia"},{"full_name":"Skultetyova, Lubica","last_name":"Skultetyova","first_name":"Lubica"},{"last_name":"Leontovyc","first_name":"Adrian","full_name":"Leontovyc, Adrian"},{"last_name":"Ulrychova","first_name":"Lenka","full_name":"Ulrychova, Lenka"},{"last_name":"Sakanari","first_name":"Judy","full_name":"Sakanari, Judy"},{"first_name":"Masako","last_name":"Asahina","full_name":"Asahina, Masako"},{"full_name":"Barinka, Cyril","first_name":"Cyril","last_name":"Barinka"},{"full_name":"Macurkova, Marie","last_name":"Macurkova","first_name":"Marie"},{"full_name":"Dvorak, Jan","last_name":"Dvorak","first_name":"Jan"}],"OA_place":"publisher","publication":"Bioscience Reports","_id":"20807","day":"12","publication_status":"published","publisher":"Portland Press","OA_type":"hybrid","date_created":"2025-12-12T09:03:54Z","date_published":"2024-01-12T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","quality_controlled":"1","title":"Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans","type":"journal_article","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        44","external_id":{"pmid":["38108122 "]},"has_accepted_license":"1"},{"day":"19","_id":"20808","publication":"eLife","OA_place":"publisher","date_published":"2024-07-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-12-12T09:06:31Z","OA_type":"gold","publisher":"eLife Sciences Publications","publication_status":"published","status":"public","type":"journal_article","title":"Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity","quality_controlled":"1","month":"07","external_id":{"pmid":["39028260"]},"intvolume":"        13","doi":"10.7554/elife.91054","year":"2024","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."}],"scopus_import":"1","citation":{"apa":"Knop, F., Zounarová, A., Šabata, V., Middelkoop, T. C., &#38; Macůrková, M. (2024). Caenorhabditis elegans SEL-5/AAK1 regulates cell migration and cell outgrowth independently of its kinase activity. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91054\">https://doi.org/10.7554/elife.91054</a>","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. <i>eLife</i>. 2024;13. doi:<a href=\"https://doi.org/10.7554/elife.91054\">10.7554/elife.91054</a>","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.","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,” <i>eLife</i>, vol. 13. eLife Sciences Publications, 2024.","short":"F. Knop, A. Zounarová, V. Šabata, T.C. Middelkoop, M. Macůrková, ELife 13 (2024).","mla":"Knop, Filip, et al. “Caenorhabditis Elegans SEL-5/AAK1 Regulates Cell Migration and Cell Outgrowth Independently of Its Kinase Activity.” <i>ELife</i>, vol. 13, e91054, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91054\">10.7554/elife.91054</a>.","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.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91054\">https://doi.org/10.7554/elife.91054</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/elife.91054"}],"article_processing_charge":"Yes","extern":"1","article_type":"original","volume":13,"publication_identifier":{"eissn":["2050-084X"]},"article_number":"e91054","fulldoi":"https://doi.org/10.7554/elife.91054","oa_version":"Published Version","date_updated":"2025-12-15T10:26:56Z","author":[{"first_name":"Filip","id":"25f3131f-6e7c-11ef-8296-b64ccd4a1b69","last_name":"Knop","full_name":"Knop, Filip","orcid":"0000-0002-3845-3465"},{"full_name":"Zounarová, Apolena","last_name":"Zounarová","first_name":"Apolena"},{"first_name":"Vojtěch","last_name":"Šabata","full_name":"Šabata, Vojtěch"},{"full_name":"Middelkoop, Teije Corneel","last_name":"Middelkoop","first_name":"Teije Corneel"},{"first_name":"Marie","last_name":"Macůrková","full_name":"Macůrková, Marie"}],"DOAJ_listed":"1","language":[{"iso":"eng"}],"oa":1,"pmid":1},{"language":[{"iso":"eng"}],"date_updated":"2025-04-23T07:37:26Z","author":[{"last_name":"Dymond","first_name":"Michael","full_name":"Dymond, Michael"},{"first_name":"Vojtech","last_name":"Kaluza","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","orcid":"0000-0002-2512-8698","full_name":"Kaluza, Vojtech"}],"pmid":1,"oa":1,"file":[{"content_type":"application/pdf","file_name":"2024_GeometriaeDedicata_Dymond.pdf","file_id":"17257","access_level":"open_access","creator":"dernst","checksum":"9418534ac2f3d6f1f091a8b8ccaed01e","date_updated":"2024-07-16T10:14:13Z","date_created":"2024-07-16T10:14:13Z","file_size":540981,"relation":"main_file","success":1}],"publication_identifier":{"eissn":["1572-9168"],"issn":["0046-5755"]},"isi":1,"article_number":"15","fulldoi":"https://doi.org/10.1007/s10711-023-00862-3","corr_author":"1","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","article_type":"original","volume":218,"department":[{"_id":"UlWa"}],"arxiv":1,"scopus_import":"1","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.","year":"2024","abstract":[{"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.","lang":"eng"}],"doi":"10.1007/s10711-023-00862-3","ddc":["510"],"citation":{"ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” <i>Geometriae Dedicata</i>, vol. 218. Springer Nature, 2024.","ista":"Dymond M, Kaluza V. 2024. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 218, 15.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. 2024;218. doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>","apa":"Dymond, M., &#38; Kaluza, V. (2024). Divergence of separated nets with respect to displacement equivalence. <i>Geometriae Dedicata</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s10711-023-00862-3\">https://doi.org/10.1007/s10711-023-00862-3</a>.","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” <i>Geometriae Dedicata</i>, vol. 218, 15, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s10711-023-00862-3\">10.1007/s10711-023-00862-3</a>.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata 218 (2024)."},"has_accepted_license":"1","external_id":{"pmid":["38021107"],"arxiv":["2102.13046"],"isi":["001105681500001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       218","title":"Divergence of separated nets with respect to displacement equivalence","type":"journal_article","file_date_updated":"2024-07-16T10:14:13Z","status":"public","quality_controlled":"1","month":"02","OA_type":"hybrid","date_created":"2021-07-14T07:01:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-02-01T00:00:00Z","publication_status":"published","publisher":"Springer Nature","day":"01","OA_place":"publisher","publication":"Geometriae Dedicata","_id":"9651"},{"quality_controlled":"1","month":"07","status":"public","file_date_updated":"2024-08-05T08:38:01Z","type":"journal_article","title":"A gate tunable transmon qubit in planar Ge","intvolume":"        15","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","external_id":{"pmid":["39080279"],"arxiv":["2403.16774"],"isi":["001281271000022"]},"_id":"17202","publication":"Nature Communications","OA_place":"publisher","related_material":{"record":[{"relation":"research_data","id":"17196","status":"public"},{"id":"18076","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://doi.org/10.1038/s41467-024-53910-1","relation":"erratum"}]},"day":"30","publisher":"Springer Nature","publication_status":"published","APC_amount":"6828 EUR","date_published":"2024-07-30T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-04T11:40:45Z","OA_type":"gold","fulldoi":"https://doi.org/10.1038/s41467-024-50763-6","oa_version":"Published Version","corr_author":"1","article_number":"6400","isi":1,"publication_identifier":{"eissn":["2041-1723"]},"file":[{"creator":"dernst","access_level":"open_access","checksum":"ddf5361dcb6c543e2cea818501c09910","date_updated":"2024-08-05T08:38:01Z","file_size":1928001,"date_created":"2024-08-05T08:38:01Z","file_id":"17388","file_name":"2024_NatureComm_Sagi.pdf","content_type":"application/pdf","success":1,"relation":"main_file"}],"oa":1,"pmid":1,"date_updated":"2026-04-07T13:01:55Z","author":[{"first_name":"Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver"},{"full_name":"Crippa, Alessandro","orcid":"0000-0002-2968-611X","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","last_name":"Crippa","first_name":"Alessandro"},{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","full_name":"Valentini, Marco"},{"first_name":"Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","orcid":"0009-0003-9037-8831","full_name":"Janik, Marian"},{"full_name":"Baghumyan, Levon","first_name":"Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","last_name":"Baghumyan"},{"full_name":"Fabris, Giorgio","first_name":"Giorgio","last_name":"Fabris","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352"},{"id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","first_name":"Lucky","orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky"},{"full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"},{"last_name":"Calcaterra","first_name":"Stefano","full_name":"Calcaterra, Stefano"},{"full_name":"Chrastina, Daniel","last_name":"Chrastina","first_name":"Daniel"},{"full_name":"Isella, Giovanni","last_name":"Isella","first_name":"Giovanni"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"DOAJ_listed":"1","language":[{"iso":"eng"}],"citation":{"ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>","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.","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>","ieee":"O. Sagi <i>et al.</i>, “A gate tunable transmon qubit in planar Ge,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” <i>Nature Communications</i>, vol. 15, 6400, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-50763-6\">10.1038/s41467-024-50763-6</a>.","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).","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.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-50763-6\">https://doi.org/10.1038/s41467-024-50763-6</a>."},"doi":"10.1038/s41467-024-50763-6","ddc":["530"],"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.","abstract":[{"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.","lang":"eng"}],"year":"2024","arxiv":1,"scopus_import":"1","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"article_type":"original","volume":15,"project":[{"name":"Merging spin and superconducting qubits in planar Ge","grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"},{"grant_number":"I05060","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","name":"High impedance circuit quantum electrodynamics with hole spins"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"article_processing_charge":"Yes"},{"keyword":["Topology Optimization","Mass Moments","Computational Geometry"],"day":"01","_id":"17203","publication":"Transactions on Graphics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-01T00:00:00Z","date_created":"2024-07-05T12:08:57Z","publisher":"Association for Computing Machinery","publication_status":"published","status":"public","type":"journal_article","file_date_updated":"2024-07-17T09:29:13Z","title":"Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments","month":"07","quality_controlled":"1","has_accepted_license":"1","external_id":{"isi":["001289270900045"]},"intvolume":"        43","doi":"10.1145/3658194","ddc":["516"],"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).","year":"2024","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","citation":{"apa":"Hafner, C., Ly, M., &#38; Wojtan, C. (2024). Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. <i>Transactions on Graphics</i>. Denver, Colorado: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658194\">https://doi.org/10.1145/3658194</a>","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.","ama":"Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. <i>Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658194\">10.1145/3658194</a>","ieee":"C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments,” <i>Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","short":"C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024).","mla":"Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” <i>Transactions on Graphics</i>, vol. 43, no. 4, 78, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658194\">10.1145/3658194</a>.","chicago":"Hafner, Christian, Mickaël Ly, and Chris Wojtan. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” <i>Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658194\">https://doi.org/10.1145/3658194</a>."},"article_processing_charge":"Yes (via OA deal)","issue":"4","department":[{"_id":"ChWo"}],"article_type":"original","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"volume":43,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"article_number":"78","isi":1,"file":[{"relation":"main_file","success":1,"content_type":"application/pdf","file_id":"17204","file_name":"sif-final.pdf","file_size":7225150,"date_updated":"2024-07-05T12:05:17Z","checksum":"0dc9f5a6422b8a49a79026900f349ee5","date_created":"2024-07-05T12:05:17Z","access_level":"open_access","creator":"chafner"},{"file_name":"sif-supp-final.pdf","file_id":"17205","content_type":"application/pdf","file_size":397262,"creator":"chafner","checksum":"cde433c6a40688d5f1187fb5721f6f94","access_level":"open_access","date_created":"2024-07-05T12:06:03Z","date_updated":"2024-07-05T12:06:03Z","relation":"supplementary_material"},{"content_type":"video/mp4","file_id":"17276","file_name":"sif-video-final.mp4","checksum":"c0457a09c2ab9a1c2935c995dcc84907","file_size":170001305,"access_level":"open_access","date_updated":"2024-07-17T09:29:13Z","date_created":"2024-07-17T09:29:13Z","creator":"chafner","relation":"supplementary_material","title":"Submission Video"}],"corr_author":"1","fulldoi":"https://doi.org/10.1145/3658194","oa_version":"Published Version","author":[{"full_name":"Hafner, Christian","first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mickaël","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","full_name":"Ly, Mickaël"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"date_updated":"2025-09-08T08:29:09Z","conference":{"location":"Denver, Colorado","start_date":"2024-07-28","end_date":"2024-08-01"},"language":[{"iso":"eng"}],"oa":1},{"external_id":{"isi":["001258359900001"],"pmid":["38941551"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        37","type":"journal_article","title":"Eco-evolutionary dynamics in changing environments: Integrating theory with data","status":"public","quality_controlled":"1","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-06-28T00:00:00Z","date_created":"2024-07-07T22:01:04Z","publisher":"Oxford University Press","publication_status":"published","day":"28","page":"579-587","_id":"17207","publication":"Journal of evolutionary biology","language":[{"iso":"eng"}],"date_updated":"2026-06-18T17:53:35Z","author":[{"full_name":"Fouqueau, Louise","orcid":"0000-0003-0371-9339","last_name":"Fouqueau","id":"1676e173-8143-11ed-8927-fe165216a93f","first_name":"Louise"},{"orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"oa":1,"publication_identifier":{"eissn":["1420-9101"]},"isi":1,"fulldoi":"https://doi.org/10.1093/jeb/voae067","oa_version":"Published Version","issue":"6","main_file_link":[{"url":"https://doi.org/10.1093/jeb/voae067","open_access":"1"}],"article_processing_charge":"No","article_type":"letter_note","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"volume":37,"department":[{"_id":"NiBa"}],"year":"2024","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.","scopus_import":"1","doi":"10.1093/jeb/voae067","ddc":["570"],"citation":{"ieee":"L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” <i>Journal of evolutionary biology</i>, 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.","ama":"Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of evolutionary biology</i>. 2024;37(6):579-587. doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>","apa":"Fouqueau, L., &#38; Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. <i>Journal of Evolutionary Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>","chicago":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/jeb/voae067\">https://doi.org/10.1093/jeb/voae067</a>.","mla":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” <i>Journal of Evolutionary Biology</i>, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:<a href=\"https://doi.org/10.1093/jeb/voae067\">10.1093/jeb/voae067</a>.","short":"L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587."}},{"month":"07","title":"Exploring the optimization landscape of variational quantum algorithms","file_date_updated":"2024-07-17T09:23:24Z","type":"dissertation","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","OA_place":"publisher","_id":"17208","page":"133","day":"09","keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10545"},{"status":"public","id":"10067","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17222","status":"public"},{"status":"public","id":"13125","relation":"part_of_dissertation"},{"status":"public","id":"11471","relation":"part_of_dissertation"}]},"supervisor":[{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","date_created":"2024-07-09T09:14:24Z","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2024-07-09T00:00:00Z","fulldoi":"https://doi.org/10.15479/at:ista:17208","oa_version":"Published Version","corr_author":"1","ec_funded":1,"file":[{"relation":"source_file","checksum":"6f45273d04f4418bc2adc018baed0525","access_level":"closed","date_updated":"2024-07-10T11:34:09Z","date_created":"2024-07-09T09:21:44Z","file_size":"14218691","creator":"rmedinar","content_type":"application/zip","file_id":"17212","file_name":"Raimel_Thesis-Final.zip"},{"relation":"main_file","success":1,"content_type":"application/pdf","file_id":"17275","file_name":"Raimel_Thesis-20_pdfa.pdf","file_size":11253627,"date_created":"2024-07-17T09:23:24Z","checksum":"6724a95bec772dbabc0111b9f08a805e","date_updated":"2024-07-17T09:23:24Z","access_level":"open_access","creator":"rmedinar"}],"publication_identifier":{"issn":["2663-337X"]},"oa":1,"language":[{"iso":"eng"}],"author":[{"id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","first_name":"Raimel A","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869"}],"date_updated":"2026-04-07T12:43:22Z","citation":{"short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","mla":"Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>.","apa":"Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational quantum algorithms</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17208\">https://doi.org/10.15479/at:ista:17208</a>","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17208\">10.15479/at:ista:17208</a>","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024."},"alternative_title":["ISTA Thesis"],"year":"2024","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."}],"ddc":["539"],"doi":"10.15479/at:ista:17208","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"article_processing_charge":"No"},{"month":"07","quality_controlled":"1","status":"public","title":"Primal-dual non-smooth friction for rigid body animation","type":"conference","file_date_updated":"2024-07-10T11:03:58Z","has_accepted_license":"1","external_id":{"isi":["001282218200091"]},"publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","_id":"17214","day":"01","keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"publication_status":"published","publisher":"Association for Computing Machinery","date_created":"2024-07-10T11:06:20Z","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","fulldoi":"https://doi.org/10.1145/3641519.3657485","oa_version":"Published Version","publication_identifier":{"isbn":["9798400705250"]},"isi":1,"file":[{"file_id":"17215","file_name":"sig24_friction_authors.pdf","content_type":"application/pdf","checksum":"b8b203ed09e3995ba0d7e6a76288663a","creator":"yichen","date_updated":"2024-07-10T11:03:14Z","access_level":"open_access","date_created":"2024-07-10T11:03:14Z","file_size":47309472,"relation":"main_file","success":1},{"relation":"main_file","success":1,"file_name":"sig24_friction_supplementary.pdf","file_id":"17216","content_type":"application/pdf","creator":"yichen","date_updated":"2024-07-10T11:03:12Z","date_created":"2024-07-10T11:03:12Z","checksum":"89d81b397b4b6469d828808a68b70820","access_level":"open_access","file_size":10518286},{"relation":"main_file","success":1,"file_id":"17217","file_name":"friction_paper_extra_video_finished.mp4","content_type":"video/mp4","access_level":"open_access","file_size":71789192,"checksum":"7123deed34a5456810e7b5336a31c657","date_created":"2024-07-10T11:03:51Z","date_updated":"2024-07-10T11:03:51Z","creator":"yichen"},{"success":1,"relation":"main_file","date_created":"2024-07-10T11:03:58Z","date_updated":"2024-07-10T11:03:58Z","access_level":"open_access","checksum":"e606fc1ae8f2610ce3b4421566800b45","creator":"yichen","file_size":280610763,"content_type":"video/mp4","file_name":"friction_paper_video_finished.mp4","file_id":"17218"}],"oa":1,"author":[{"full_name":"Chen, Yi-Lu","first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","last_name":"Chen"},{"last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"Mickaël","full_name":"Ly, Mickaël"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-09-08T08:54:38Z","language":[{"iso":"eng"}],"conference":{"location":"Denver, United States","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28","end_date":"2024-08-01"},"citation":{"apa":"Chen, Y.-L., Ly, M., &#38; Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Denver, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>","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.","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Denver, United States, 2024.","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.","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657485\">10.1145/3641519.3657485</a>.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In <i>Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3641519.3657485\">https://doi.org/10.1145/3641519.3657485</a>."},"ddc":["621","531","006"],"doi":"10.1145/3641519.3657485","scopus_import":"1","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).","year":"2024","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."}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"article_processing_charge":"Yes (via OA deal)"},{"OA_type":"hybrid","date_created":"2024-07-10T12:24:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-07-01T00:00:00Z","publication_status":"published","publisher":"Association for Computing Machinery","day":"01","keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19630"},{"status":"public","id":"18301","relation":"dissertation_contains"}]},"OA_place":"publisher","publication":"ACM Transactions on Graphics","_id":"17219","external_id":{"isi":["001289270900021"]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"intvolume":"        43","title":"Multi-material mesh-based surface tracking with implicit topology changes","type":"journal_article","file_date_updated":"2025-11-11T09:50:52Z","status":"public","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","quality_controlled":"1","month":"07","issue":"4","article_processing_charge":"Yes (via OA deal)","volume":43,"article_type":"original","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"scopus_import":"1","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).","abstract":[{"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.","lang":"eng"}],"year":"2024","doi":"10.1145/3658223","ddc":["004"],"citation":{"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.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2024. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>.","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024).","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>.","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,” <i>ACM Transactions on Graphics</i>, vol. 43, no. 4. Association for Computing Machinery, 2024.","apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., &#38; Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3658223\">https://doi.org/10.1145/3658223</a>","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.","ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. <i>ACM Transactions on Graphics</i>. 2024;43(4). doi:<a href=\"https://doi.org/10.1145/3658223\">10.1145/3658223</a>"},"language":[{"iso":"eng"}],"author":[{"first_name":"Peter","last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87","full_name":"Synak, Peter"},{"first_name":"Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","last_name":"Kalinov","orcid":"0000-0003-2189-3904","full_name":"Kalinov, Aleksei"},{"full_name":"Strugaru, Irina-Malina","id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","last_name":"Strugaru","first_name":"Irina-Malina"},{"id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","last_name":"Etemadihaghighi","first_name":"Arian","full_name":"Etemadihaghighi, Arian"},{"last_name":"Yang","first_name":"Huidong","full_name":"Yang, Huidong"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"date_updated":"2026-04-07T13:02:36Z","oa":1,"file":[{"content_type":"application/pdf","file_name":"2024_ACMToG_HeissSynak.pdf","file_id":"17317","file_size":48763368,"date_created":"2024-07-23T06:35:15Z","creator":"dernst","checksum":"1917067d4b52d7729019b03560004e43","access_level":"open_access","date_updated":"2024-07-23T06:35:15Z","relation":"main_file","success":1},{"checksum":"a4f0e293184bfa034c0c585848806b17","date_created":"2024-07-10T12:23:44Z","date_updated":"2024-07-10T12:23:44Z","file_size":48021463,"access_level":"open_access","creator":"akalinov","file_id":"17221","file_name":"sdtopofixer_final.mp4","content_type":"video/mp4","success":1,"relation":"main_file"},{"relation":"preprint","title":"Authors' version of the text","content_type":"application/pdf","file_id":"20633","file_name":"SuperDuperTopoFixer.pdf","file_size":48639581,"creator":"akalinov","date_updated":"2025-11-11T09:50:52Z","access_level":"open_access","checksum":"18fc310a78ec91651148c45a8b89fa44","date_created":"2025-11-11T09:50:52Z"}],"article_number":"54","isi":1,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"fulldoi":"https://doi.org/10.1145/3658223","corr_author":"1","oa_version":"Published Version"},{"oa":1,"author":[{"first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A"},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"date_updated":"2026-04-07T12:43:22Z","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.48550/arXiv.2405.10125","oa_version":"Preprint","corr_author":"1","article_number":"2405.10125","department":[{"_id":"MaSe"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.10125"}],"citation":{"ieee":"R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm,” <i>arXiv</i>. .","apa":"Medina Ramos, R. A., &#38; Serbyn, M. (n.d.). A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>","ama":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>","ista":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. 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.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2405.10125\">https://doi.org/10.48550/arXiv.2405.10125</a>.","short":"R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.).","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>, 2405.10125, doi:<a href=\"https://doi.org/10.48550/arXiv.2405.10125\">10.48550/arXiv.2405.10125</a>."},"doi":"10.48550/arXiv.2405.10125","arxiv":1,"year":"2024","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."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"arxiv":["2405.10125"]},"month":"05","status":"public","title":"A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm","type":"preprint","publication_status":"draft","date_created":"2024-07-10T13:12:09Z","date_published":"2024-05-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv","_id":"17222","OA_place":"repository","day":"16","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17208"}]}},{"external_id":{"pmid":["38968076"]},"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"         5","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"file_date_updated":"2025-01-09T12:16:53Z","type":"journal_article","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","status":"public","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"09","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-09-20T00:00:00Z","date_created":"2024-07-14T22:01:10Z","APC_amount":"804 EUR","publisher":"Elsevier","publication_status":"published","day":"20","OA_place":"publisher","_id":"17232","publication":"STAR Protocols","language":[{"iso":"eng"}],"date_updated":"2025-12-30T10:54:12Z","author":[{"orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"orcid":"0000-0002-3509-1948","full_name":"Koppensteiner, Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"oa":1,"file":[{"success":1,"relation":"main_file","date_updated":"2025-01-09T12:16:53Z","creator":"dernst","date_created":"2025-01-09T12:16:53Z","checksum":"464f52ecc6ec92f509552823bb82bf79","access_level":"open_access","file_size":6445556,"content_type":"application/pdf","file_name":"2024_STARProtoc_Cheung2.pdf","file_id":"18810"}],"article_number":"103168","publication_identifier":{"eissn":["2666-1667"]},"fulldoi":"https://doi.org/10.1016/j.xpro.2024.103168","corr_author":"1","oa_version":"Published Version","issue":"3","article_processing_charge":"Yes","article_type":"original","project":[{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"}],"volume":5,"department":[{"_id":"SiHi"},{"_id":"PreCl"}],"year":"2024","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"}],"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).","scopus_import":"1","doi":"10.1016/j.xpro.2024.103168","ddc":["570"],"citation":{"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.","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. <i>STAR Protocols</i>. 2024;5(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., &#38; Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>","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,” <i>STAR Protocols</i>, vol. 5, no. 3. Elsevier, 2024.","mla":"Cheung, Giselle T., et al. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” <i>STAR Protocols</i>, vol. 5, no. 3, 103168, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">10.1016/j.xpro.2024.103168</a>.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (2024).","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.” <i>STAR Protocols</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.xpro.2024.103168\">https://doi.org/10.1016/j.xpro.2024.103168</a>."}},{"article_type":"original","volume":14,"department":[{"_id":"MiSi"}],"issue":"13","article_processing_charge":"Yes","citation":{"short":"Z. LI, J. Huard, E.M. Bayer, V. Wattelet-Boyer, Bio-Protocol 14 (2024).","mla":"LI, ZIQIANG, et al. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>.","chicago":"LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” <i>Bio-Protocol</i>. Bio-Protocol, 2024. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>.","apa":"LI, Z., Huard, J., Bayer, E. M., &#38; Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-Protocol</i>. Bio-Protocol. <a href=\"https://doi.org/10.21769/BioProtoc.5029\">https://doi.org/10.21769/BioProtoc.5029</a>","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.","ama":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. <i>Bio-protocol</i>. 2024;14(13). doi:<a href=\"https://doi.org/10.21769/BioProtoc.5029\">10.21769/BioProtoc.5029</a>","ieee":"Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” <i>Bio-protocol</i>, vol. 14, no. 13. Bio-Protocol, 2024."},"scopus_import":"1","year":"2024","abstract":[{"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.","lang":"eng"}],"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.).","doi":"10.21769/BioProtoc.5029","ddc":["570"],"pmid":1,"oa":1,"language":[{"iso":"eng"}],"author":[{"last_name":"Li","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","first_name":"Ziqiang","full_name":"Li, Ziqiang"},{"full_name":"Huard, Jennifer","first_name":"Jennifer","last_name":"Huard"},{"first_name":"Emmanuelle M.","last_name":"Bayer","full_name":"Bayer, Emmanuelle M."},{"last_name":"Wattelet-Boyer","first_name":"Valérie","full_name":"Wattelet-Boyer, Valérie"}],"date_updated":"2025-03-06T10:28:18Z","oa_version":"Published Version","fulldoi":"https://doi.org/10.21769/BioProtoc.5029","file":[{"relation":"main_file","success":1,"file_id":"17242","file_name":"2024_BioProtocol_Li.pdf","content_type":"application/pdf","date_updated":"2024-07-16T06:16:11Z","file_size":2896048,"date_created":"2024-07-16T06:16:11Z","access_level":"open_access","creator":"dernst","checksum":"c8671c0ad483da6407cb16cc3fef1990"}],"article_number":"e5029","publication_identifier":{"eissn":["2331-8325"]},"publication_status":"published","publisher":"Bio-Protocol","date_created":"2024-07-14T22:01:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-07-05T00:00:00Z","publication":"Bio-protocol","_id":"17233","day":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        14","external_id":{"pmid":["39007160"]},"has_accepted_license":"1","quality_controlled":"1","month":"07","title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis","type":"journal_article","file_date_updated":"2024-07-16T06:16:11Z","status":"public"},{"doi":"10.3847/2041-8213/ad55f7","ddc":["520"],"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).","year":"2024","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."}],"scopus_import":"1","arxiv":1,"citation":{"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).","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.” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1, L13, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>.","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.” <i>Astrophysical Journal Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>.","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. <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">https://doi.org/10.3847/2041-8213/ad55f7</a>","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.","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. <i>Astrophysical Journal Letters</i>. 2024;969(1). doi:<a href=\"https://doi.org/10.3847/2041-8213/ad55f7\">10.3847/2041-8213/ad55f7</a>","ieee":"B. Wang <i>et al.</i>, “RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,” <i>Astrophysical Journal Letters</i>, vol. 969, no. 1. IOP Publishing, 2024."},"article_processing_charge":"Yes","issue":"1","department":[{"_id":"JoMa"}],"volume":969,"article_type":"original","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"article_number":"L13","isi":1,"file":[{"date_created":"2024-07-16T06:24:29Z","date_updated":"2024-07-16T06:24:29Z","access_level":"open_access","checksum":"bb1a6725586df12e745d091b5778bb2b","file_size":3273303,"creator":"dernst","file_name":"2024_AstrophysicalJourn_Wang.pdf","file_id":"17243","content_type":"application/pdf","success":1,"relation":"main_file"}],"fulldoi":"https://doi.org/10.3847/2041-8213/ad55f7","oa_version":"Published Version","date_updated":"2025-09-08T08:10:21Z","author":[{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"full_name":"De Graaff, Anna","first_name":"Anna","last_name":"De Graaff"},{"first_name":"Gabriel B.","last_name":"Brammer","full_name":"Brammer, Gabriel B."},{"full_name":"Weibel, Andrea","last_name":"Weibel","first_name":"Andrea"},{"first_name":"Pieter","last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter"},{"full_name":"Baggen, Josephine F.W.","first_name":"Josephine F.W.","last_name":"Baggen"},{"full_name":"Suess, Katherine A.","last_name":"Suess","first_name":"Katherine A."},{"full_name":"Greene, Jenny E.","first_name":"Jenny E.","last_name":"Greene"},{"last_name":"Bezanson","first_name":"Rachel","full_name":"Bezanson, Rachel"},{"first_name":"Nikko J.","last_name":"Cleri","full_name":"Cleri, Nikko J."},{"first_name":"Michaela","last_name":"Hirschmann","full_name":"Hirschmann, Michaela"},{"full_name":"Labbé, Ivo","first_name":"Ivo","last_name":"Labbé"},{"last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","first_name":"Jorryt J","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J"},{"full_name":"Mcconachie, Ian","last_name":"Mcconachie","first_name":"Ian"},{"last_name":"Naidu","first_name":"Rohan P.","full_name":"Naidu, Rohan P."},{"full_name":"Nelson, Erica","last_name":"Nelson","first_name":"Erica"},{"full_name":"Oesch, Pascal A.","last_name":"Oesch","first_name":"Pascal A."},{"first_name":"David J.","last_name":"Setton","full_name":"Setton, David J."},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."}],"DOAJ_listed":"1","language":[{"iso":"eng"}],"oa":1,"day":"01","_id":"17234","publication":"Astrophysical Journal Letters","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-14T22:01:11Z","publisher":"IOP Publishing","publication_status":"published","status":"public","file_date_updated":"2024-07-16T06:24:29Z","type":"journal_article","title":"RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec","quality_controlled":"1","month":"07","has_accepted_license":"1","external_id":{"isi":["001257903200001"],"arxiv":["2405.01473"]},"intvolume":"       969","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"day":"01","publication":"APL Materials","_id":"17235","date_created":"2024-07-14T22:01:11Z","date_published":"2024-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","publisher":"AIP Publishing","title":"Effect of ion irradiation on superconducting thin films","file_date_updated":"2024-07-16T06:30:30Z","type":"journal_article","status":"public","quality_controlled":"1","month":"07","has_accepted_license":"1","external_id":{"isi":["001260942200003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"        12","acknowledged_ssus":[{"_id":"EM-Fac"}],"scopus_import":"1","year":"2024","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."}],"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).","ddc":["530"],"doi":"10.1063/5.0202851","citation":{"mla":"Kohopää, Katja, et al. “Effect of Ion Irradiation on Superconducting Thin Films.” <i>APL Materials</i>, vol. 12, no. 7, 071101, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>.","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).","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.” <i>APL Materials</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>.","ama":"Kohopää K, Ronzani A, Jabdaraghi RN, et al. Effect of ion irradiation on superconducting thin films. <i>APL Materials</i>. 2024;12(7). doi:<a href=\"https://doi.org/10.1063/5.0202851\">10.1063/5.0202851</a>","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.","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. <i>APL Materials</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0202851\">https://doi.org/10.1063/5.0202851</a>","ieee":"K. Kohopää <i>et al.</i>, “Effect of ion irradiation on superconducting thin films,” <i>APL Materials</i>, vol. 12, no. 7. AIP Publishing, 2024."},"issue":"7","article_processing_charge":"Yes","volume":12,"article_type":"original","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"AnHi"}],"ec_funded":1,"file":[{"date_updated":"2024-07-16T06:30:30Z","checksum":"32a5cdf0ea9c937f806b6039f3219917","access_level":"open_access","date_created":"2024-07-16T06:30:30Z","creator":"dernst","file_size":9408198,"content_type":"application/pdf","file_id":"17244","file_name":"2024_APLMaterial_Kohopaa.pdf","success":1,"relation":"main_file"}],"publication_identifier":{"eissn":["2166-532X"]},"isi":1,"article_number":"071101","fulldoi":"https://doi.org/10.1063/5.0202851","oa_version":"Published Version","language":[{"iso":"eng"}],"date_updated":"2025-09-08T08:10:58Z","author":[{"last_name":"Kohopää","first_name":"Katja","full_name":"Kohopää, Katja"},{"full_name":"Ronzani, Alberto","last_name":"Ronzani","first_name":"Alberto"},{"full_name":"Jabdaraghi, Robab Najafi","last_name":"Jabdaraghi","first_name":"Robab Najafi"},{"full_name":"Bera, Arijit","last_name":"Bera","first_name":"Arijit"},{"full_name":"Ribeiro, Mário","first_name":"Mário","last_name":"Ribeiro"},{"full_name":"Hazra, Dibyendu","first_name":"Dibyendu","last_name":"Hazra"},{"orcid":"0000-0002-0672-9295","full_name":"Senior, Jorden L","id":"5479D234-2D30-11EA-89CC-40953DDC885E","last_name":"Senior","first_name":"Jorden L"},{"full_name":"Prunnila, Mika","first_name":"Mika","last_name":"Prunnila"},{"last_name":"Govenius","first_name":"Joonas","full_name":"Govenius, Joonas"},{"last_name":"Lehtinen","first_name":"Janne S.","full_name":"Lehtinen, Janne S."},{"full_name":"Kemppinen, Antti","first_name":"Antti","last_name":"Kemppinen"}],"oa":1}]