[{"title":"Mapping the attractor landscape of Boolean networks","_id":"19800","month":"09","oa_version":"Published Version","abstract":[{"text":"This archive contains all the code and data necessary to reproduce the results presented in the \r\n\"Mapping the attractor landscape of Boolean networks\" paper.","lang":"eng"}],"date_created":"2025-06-10T07:10:01Z","date_updated":"2025-09-30T12:46:33Z","doi":"10.5281/ZENODO.13854759","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.13854760"}],"type":"research_data_reference","OA_type":"green","article_processing_charge":"No","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"OA_place":"repository","oa":1,"author":[{"last_name":"trinh","full_name":"trinh, Van Giang","first_name":"Van Giang"},{"first_name":"Kyu Hyong","full_name":"Park, Kyu Hyong","last_name":"Park"},{"full_name":"Pastva, Samuel","first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","orcid":"0000-0003-1993-0331"},{"last_name":"Rozum","first_name":"Jordan","full_name":"Rozum, Jordan"}],"day":"28","ddc":["000"],"related_material":{"record":[{"status":"public","id":"19796","relation":"used_in_publication"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"trinh VG, Park KH, Pastva S, Rozum J. Mapping the attractor landscape of Boolean networks. 2024. doi:10.5281/ZENODO.13854759","ieee":"V. G. trinh, K. H. Park, S. Pastva, and J. Rozum, “Mapping the attractor landscape of Boolean networks.” Zenodo, 2024.","apa":"trinh, V. G., Park, K. H., Pastva, S., & Rozum, J. (2024). Mapping the attractor landscape of Boolean networks. Zenodo. https://doi.org/10.5281/ZENODO.13854759","ista":"trinh VG, Park KH, Pastva S, Rozum J. 2024. Mapping the attractor landscape of Boolean networks, Zenodo, 10.5281/ZENODO.13854759.","short":"V.G. trinh, K.H. Park, S. Pastva, J. Rozum, (2024).","chicago":"trinh, Van Giang, Kyu Hyong Park, Samuel Pastva, and Jordan Rozum. “Mapping the Attractor Landscape of Boolean Networks.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.13854759.","mla":"trinh, Van Giang, et al. Mapping the Attractor Landscape of Boolean Networks. Zenodo, 2024, doi:10.5281/ZENODO.13854759."},"date_published":"2024-09-28T00:00:00Z","year":"2024","status":"public","license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"ToHe"}],"publisher":"Zenodo"},{"date_created":"2025-06-24T06:09:18Z","date_updated":"2025-09-30T13:41:56Z","abstract":[{"text":"This is Marlin, a Mixed Auto-Regressive Linear kernel (and the name of one of the planet's fastest fish), an extremely optimized FP16xINT4 matmul kernel aimed at LLM inference that can deliver close to ideal (4x) speedups up to batchsizes of 16-32 tokens (in contrast to the 1-2 tokens of prior work with comparable speedup).\r\n\r\nAdditionally, it includes Sparse-Marlin, an extension of the MARLIN kernels adding support to 2:4 weight sparsity, achieving 5.3x speedups on NVIDIA GPUs (Ampere/Ada).","lang":"eng"}],"oa_version":"Published Version","_id":"19884","month":"11","title":"MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.14213091","open_access":"1"}],"doi":"10.5281/ZENODO.14213091","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"OA_place":"repository","article_processing_charge":"No","type":"research_data_reference","related_material":{"record":[{"relation":"used_for_analysis_in","id":"19877","status":"public"}]},"ddc":["000"],"day":"24","author":[{"first_name":"Elias","full_name":"Frantar, Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar"},{"last_name":"Castro","first_name":"Roberto","full_name":"Castro, Roberto"},{"first_name":"Jiale","full_name":"Chen, Jiale","last_name":"Chen","id":"4d0a9064-1ff6-11ee-9fa6-ec046c604785","orcid":"0000-0001-5337-5875"},{"first_name":"Torsten","full_name":"Hoefler, Torsten","last_name":"Hoefler"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"date_published":"2024-11-24T00:00:00Z","citation":{"ieee":"E. Frantar, R. Castro, J. Chen, T. Hoefler, and D.-A. Alistarh, “MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models.” Zenodo, 2024.","apa":"Frantar, E., Castro, R., Chen, J., Hoefler, T., & Alistarh, D.-A. (2024). MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. Zenodo. https://doi.org/10.5281/ZENODO.14213091","ama":"Frantar E, Castro R, Chen J, Hoefler T, Alistarh D-A. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models. 2024. doi:10.5281/ZENODO.14213091","short":"E. Frantar, R. Castro, J. Chen, T. Hoefler, D.-A. Alistarh, (2024).","chicago":"Frantar, Elias, Roberto Castro, Jiale Chen, Torsten Hoefler, and Dan-Adrian Alistarh. “MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.14213091.","mla":"Frantar, Elias, et al. MARLIN: Mixed-Precision Auto-Regressive Parallel Inference on Large Language Models. Zenodo, 2024, doi:10.5281/ZENODO.14213091.","ista":"Frantar E, Castro R, Chen J, Hoefler T, Alistarh D-A. 2024. MARLIN: Mixed-precision auto-regressive parallel inference on Large Language Models, Zenodo, 10.5281/ZENODO.14213091."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","status":"public","year":"2024","department":[{"_id":"DaAl"}],"publisher":"Zenodo"},{"article_processing_charge":"No","OA_type":"closed access","issue":"10","day":"01","author":[{"full_name":"Neidhart, Maja","first_name":"Maja","last_name":"Neidhart"},{"last_name":"Kjelkenes","first_name":"Rikka","full_name":"Kjelkenes, Rikka"},{"last_name":"Jansone","full_name":"Jansone, Karina","first_name":"Karina"},{"last_name":"Rehák Bučková","first_name":"Barbora","full_name":"Rehák Bučková, Barbora"},{"last_name":"Holz","full_name":"Holz, Nathalie","first_name":"Nathalie"},{"last_name":"Nees","full_name":"Nees, Frauke","first_name":"Frauke"},{"last_name":"Walter","first_name":"Henrik","full_name":"Walter, Henrik"},{"last_name":"Schumann","first_name":"Gunter","full_name":"Schumann, Gunter"},{"first_name":"Michael A.","full_name":"Rapp, Michael A.","last_name":"Rapp"},{"first_name":"Tobias","full_name":"Banaschewski, Tobias","last_name":"Banaschewski"},{"first_name":"Emanuel","full_name":"Schwarz, Emanuel","last_name":"Schwarz"},{"full_name":"Marquand, Andre","first_name":"Andre","last_name":"Marquand"},{"last_name":"Ogoh","full_name":"Ogoh, George","first_name":"George"},{"last_name":"Stahl","full_name":"Stahl, Bernd","first_name":"Bernd"},{"last_name":"Young","full_name":"Young, Allan H.","first_name":"Allan H."},{"full_name":"Desrivières, Sylvane","first_name":"Sylvane","last_name":"Desrivières"},{"full_name":"Clinton, Nicholas","first_name":"Nicholas","last_name":"Clinton"},{"last_name":"Thompson","first_name":"Paul","full_name":"Thompson, Paul"},{"last_name":"Schwalber","first_name":"Ameli","full_name":"Schwalber, Ameli"},{"full_name":"Liu, Jingyu","first_name":"Jingyu","last_name":"Liu"},{"last_name":"Calhoun","full_name":"Calhoun, Vince","first_name":"Vince"},{"last_name":"Chang","full_name":"Chang, Xiao","first_name":"Xiao"},{"last_name":"Xia","first_name":"Yunman","full_name":"Xia, Yunman"},{"first_name":"Yanting","full_name":"Gong, Yanting","last_name":"Gong"},{"full_name":"Jia, Tianye","first_name":"Tianye","last_name":"Jia"},{"last_name":"Renner","full_name":"Renner, Paul","first_name":"Paul"},{"first_name":"Sören","full_name":"Hese, Sören","last_name":"Hese"},{"full_name":"Giner, Arantxa","first_name":"Arantxa","last_name":"Giner"},{"full_name":"Sanchez, Mavi","first_name":"Mavi","last_name":"Sanchez"},{"first_name":"Elena","full_name":"Alvarez, Elena","last_name":"Alvarez"},{"first_name":"Bernhard","full_name":"Spanlang, Bernhard","last_name":"Spanlang"},{"last_name":"Pearmund","first_name":"Charlie","full_name":"Pearmund, Charlie"},{"last_name":"Athanasiadis","full_name":"Athanasiadis, Anastasios Polykarpos","first_name":"Anastasios Polykarpos"},{"full_name":"Otten, Lisa","first_name":"Lisa","last_name":"Otten"},{"last_name":"Pitel","full_name":"Pitel, Séverine","first_name":"Séverine"},{"full_name":"Petkoski, Spase","first_name":"Spase","last_name":"Petkoski"},{"last_name":"Jirsa","full_name":"Jirsa, Viktor","first_name":"Viktor"},{"full_name":"Schmitt, Karen","first_name":"Karen","last_name":"Schmitt"},{"last_name":"Wilbertz","full_name":"Wilbertz, Johannes","first_name":"Johannes"},{"last_name":"Patraskaki","full_name":"Patraskaki, Myrto","first_name":"Myrto"},{"full_name":"Sommer, Peter","first_name":"Peter","last_name":"Sommer"},{"last_name":"Heilmann-Heimbach","full_name":"Heilmann-Heimbach, Stefanie","first_name":"Stefanie"},{"last_name":"Mathey","first_name":"Carina M.","full_name":"Mathey, Carina M."},{"first_name":"Abigail","full_name":"Miller, Abigail","last_name":"Miller"},{"first_name":"Isabelle","full_name":"Claus, Isabelle","last_name":"Claus"},{"last_name":"Nöthen","full_name":"Nöthen, Markus M.","first_name":"Markus M."},{"full_name":"Hoffmann, Per","first_name":"Per","last_name":"Hoffmann"},{"last_name":"Forstner","full_name":"Forstner, Andreas J.","first_name":"Andreas J."},{"first_name":"Alvaro","full_name":"Pastor, Alvaro","last_name":"Pastor"},{"last_name":"Gallego","first_name":"Jaime","full_name":"Gallego, Jaime"},{"last_name":"Orosa","first_name":"Francisco Eiroa","full_name":"Orosa, Francisco Eiroa"},{"full_name":"Viapiana, Guillem Feixas","first_name":"Guillem Feixas","last_name":"Viapiana"},{"full_name":"Slater, Mel","first_name":"Mel","last_name":"Slater"},{"first_name":"Lena","full_name":"Marr, Lena","id":"4406F586-F248-11E8-B48F-1D18A9856A87","last_name":"Marr"},{"full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"full_name":"Böttger, Sarah Jane","first_name":"Sarah Jane","last_name":"Böttger"},{"full_name":"Tschorn, Mira","first_name":"Mira","last_name":"Tschorn"},{"last_name":"Rapp","first_name":"Michael","full_name":"Rapp, Michael"},{"last_name":"Ask","first_name":"Helga","full_name":"Ask, Helga"},{"last_name":"Fernandez","full_name":"Fernandez, Sara","first_name":"Sara"},{"last_name":"Van Der Meer","full_name":"Van Der Meer, Dennis","first_name":"Dennis"},{"full_name":"Westlye, Lars T.","first_name":"Lars T.","last_name":"Westlye"},{"full_name":"Andreassen, Ole A.","first_name":"Ole A.","last_name":"Andreassen"},{"last_name":"Aden","first_name":"Rieke","full_name":"Aden, Rieke"},{"last_name":"Seefried","full_name":"Seefried, Beke","first_name":"Beke"},{"last_name":"Siehl","first_name":"Sebastian","full_name":"Siehl, Sebastian"},{"last_name":"Nees","full_name":"Nees, Frauke","first_name":"Frauke"},{"last_name":"Stringaris","first_name":"Argyris","full_name":"Stringaris, Argyris"},{"last_name":"Tost","first_name":"Heike","full_name":"Tost, Heike"},{"full_name":"Meyer-Lindenberg, Andreas","first_name":"Andreas","last_name":"Meyer-Lindenberg"},{"last_name":"Christmann","full_name":"Christmann, Nina","first_name":"Nina"},{"full_name":"Banks, Jamie","first_name":"Jamie","last_name":"Banks"},{"last_name":"Schepanski","first_name":"Kerstin","full_name":"Schepanski, Kerstin"},{"last_name":"Schütz","full_name":"Schütz, Tatjana","first_name":"Tatjana"},{"last_name":"Taron","first_name":"Ulrike Helene","full_name":"Taron, Ulrike Helene"},{"last_name":"Eils","full_name":"Eils, Roland","first_name":"Roland"},{"first_name":"Jean Charles","full_name":"Roy, Jean Charles","last_name":"Roy"},{"last_name":"Lett","first_name":"Tristram A.","full_name":"Lett, Tristram A."},{"last_name":"Kebir","first_name":"Hedi","full_name":"Kebir, Hedi"},{"first_name":"Elli","full_name":"Polemiti, Elli","last_name":"Polemiti"},{"last_name":"Hitchen","full_name":"Hitchen, Esther","first_name":"Esther"},{"first_name":"Marcel","full_name":"Jentsch, Marcel","last_name":"Jentsch"},{"first_name":"Emin","full_name":"Serin, Emin","last_name":"Serin"},{"last_name":"Bernas","full_name":"Bernas, Antoine","first_name":"Antoine"},{"first_name":"Nilakshi","full_name":"Vaidya, Nilakshi","last_name":"Vaidya"},{"first_name":"Sven","full_name":"Twardziok, Sven","last_name":"Twardziok"},{"last_name":"Ralser","full_name":"Ralser, Markus","first_name":"Markus"},{"last_name":"Heinz","first_name":"Andreas","full_name":"Heinz, Andreas"}],"abstract":[{"text":"This Comment presents a high-level protocol for data harmonization within large cohorts, in which it postulates four main steps including (1) expert review, (2) pre-statistical harmonization, (3) statistical harmonization, and (4) validation.","lang":"eng"}],"title":"A protocol for data harmonization in large cohorts","page":"1134-1137","publication_status":"published","acknowledgement":"Funded by the European Union. Complementary funding was received by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee (10041392 and 10038599). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union, the European Health and Digital Executive Agency (HADEA) or UKRI. The European Union, HADEA or UKRI cannot be held responsible for them. This work received support from the Chinese Ministry for Science and Technology (MOST), the Horizon 2020-funded European Research Council advanced grant ‘STRATIFY’ (695313); the German Research Foundation (COPE; 675346; NE 1383/15-1 and BA 2088/7-1 (CoviDrug)), the National Natural Science Foundation of China grant 82150710554, the Hector II foundation and the German Center for Mental Health (DZPG) (01EE2301A, 01EE2304A, 01EE2301D).","publication":"Nature Mental Health","publication_identifier":{"eissn":["2731-6076"]},"language":[{"iso":"eng"}],"article_type":"comment","year":"2024","type":"journal_article","date_created":"2025-07-20T22:02:04Z","volume":2,"quality_controlled":"1","date_updated":"2025-07-22T08:59:10Z","month":"10","_id":"20039","oa_version":"None","scopus_import":"1","doi":"10.1038/s44220-024-00315-0","department":[{"_id":"GaNo"}],"publisher":"Springer Nature","date_published":"2024-10-01T00:00:00Z","citation":{"ama":"Neidhart M, Kjelkenes R, Jansone K, et al. A protocol for data harmonization in large cohorts. Nature Mental Health. 2024;2(10):1134-1137. doi:10.1038/s44220-024-00315-0","ieee":"M. Neidhart et al., “A protocol for data harmonization in large cohorts,” Nature Mental Health, vol. 2, no. 10. Springer Nature, pp. 1134–1137, 2024.","apa":"Neidhart, M., Kjelkenes, R., Jansone, K., Rehák Bučková, B., Holz, N., Nees, F., … Heinz, A. (2024). A protocol for data harmonization in large cohorts. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00315-0","ista":"Neidhart M, Kjelkenes R, Jansone K, Rehák Bučková B, Holz N, Nees F, Walter H, Schumann G, Rapp MA, Banaschewski T, Schwarz E, Marquand A, Ogoh G, 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, Böttger SJ, Tschorn M, Rapp M, Ask H, Fernandez S, Van Der Meer D, Westlye LT, Andreassen OA, Aden R, Seefried B, Siehl S, Nees F, Stringaris A, Tost H, Meyer-Lindenberg A, Christmann N, 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. 2024. A protocol for data harmonization in large cohorts. Nature Mental Health. 2(10), 1134–1137.","short":"M. Neidhart, R. Kjelkenes, K. Jansone, B. Rehák Bučková, N. Holz, F. Nees, H. Walter, G. Schumann, M.A. Rapp, T. Banaschewski, E. Schwarz, A. Marquand, G. Ogoh, 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, S.J. Böttger, M. Tschorn, M. Rapp, H. Ask, S. Fernandez, D. Van Der Meer, L.T. Westlye, O.A. Andreassen, R. Aden, B. Seefried, S. Siehl, F. Nees, A. Stringaris, H. Tost, A. Meyer-Lindenberg, N. Christmann, 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, Nature Mental Health 2 (2024) 1134–1137.","chicago":"Neidhart, Maja, Rikka Kjelkenes, Karina Jansone, Barbora Rehák Bučková, Nathalie Holz, Frauke Nees, Henrik Walter, et al. “A Protocol for Data Harmonization in Large Cohorts.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00315-0.","mla":"Neidhart, Maja, et al. “A Protocol for Data Harmonization in Large Cohorts.” Nature Mental Health, vol. 2, no. 10, Springer Nature, 2024, pp. 1134–37, doi:10.1038/s44220-024-00315-0."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2","status":"public"},{"title":"A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries","abstract":[{"lang":"eng","text":"In article number 2305128, Qing Sun, Shang Wang, Yanhong Tian, Andreu Cabot, and co-workers report an investigation of the energy-storage mechanism of a layered Bi2Te3-based cathode for aqueous zinc-ion batteries (ZIBs). They demonstrate that the zinc ion is not inserted into the cathode as previously assumed; in contrast, proton charge-storage dominates the process. They also demonstrate the great application prospects of aqueous ZIBs in flexible electronics via jet printing technology."}],"publication_status":"published","article_processing_charge":"No","OA_type":"free access","oa":1,"OA_place":"publisher","ddc":["530"],"day":"04","author":[{"last_name":"Zeng","full_name":"Zeng, Guifang","first_name":"Guifang"},{"last_name":"Sun","first_name":"Qing","full_name":"Sun, Qing"},{"full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"full_name":"Wang, Shang","first_name":"Shang","last_name":"Wang"},{"first_name":"Xuan","full_name":"Lu, Xuan","last_name":"Lu"},{"full_name":"Zhang, Chao Yue","first_name":"Chao Yue","last_name":"Zhang"},{"full_name":"Li, Jing","first_name":"Jing","last_name":"Li"},{"full_name":"Li, Junshan","first_name":"Junshan","last_name":"Li"},{"full_name":"Ci, Lijie","first_name":"Lijie","last_name":"Ci"},{"first_name":"Yanhong","full_name":"Tian, Yanhong","last_name":"Tian"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"issue":"1","language":[{"iso":"eng"}],"year":"2024","publication":"Advanced Materials","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"date_created":"2025-07-21T08:53:06Z","date_updated":"2026-06-18T18:19:28Z","quality_controlled":"1","volume":36,"_id":"20057","month":"01","oa_version":"Published Version","doi":"10.1002/adma.202470004","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/adma.202470004"}],"type":"other_academic_publication","intvolume":" 36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zeng, Guifang, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials, vol. 36, no. 1, 2470004, Wiley, 2024, doi:10.1002/adma.202470004.","chicago":"Zeng, Guifang, Qing Sun, Sharona Horta, Shang Wang, Xuan Lu, Chao Yue Zhang, Jing Li, et al. A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries. Advanced Materials. Vol. 36. Wiley, 2024. https://doi.org/10.1002/adma.202470004.","short":"G. Zeng, Q. Sun, S. Horta, S. Wang, X. Lu, C.Y. Zhang, J. Li, J. Li, L. Ci, Y. Tian, M. Ibáñez, A. Cabot, A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries, Wiley, 2024.","ista":"Zeng G, Sun Q, Horta S, Wang S, Lu X, Zhang CY, Li J, Li J, Ci L, Tian Y, Ibáñez M, Cabot A. 2024. A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries, Wiley,p.","apa":"Zeng, G., Sun, Q., Horta, S., Wang, S., Lu, X., Zhang, C. Y., … Cabot, A. (2024). A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials (Vol. 36). Wiley. https://doi.org/10.1002/adma.202470004","ieee":"G. Zeng et al., A layered Bi2Te3@PPy cathode for aqueous Zinc‐Ion batteries: Mechanism and application in printed flexible batteries, vol. 36, no. 1. Wiley, 2024.","ama":"Zeng G, Sun Q, Horta S, et al. A Layered Bi2Te3@PPy Cathode for Aqueous Zinc‐Ion Batteries: Mechanism and Application in Printed Flexible Batteries. Vol 36. Wiley; 2024. doi:10.1002/adma.202470004"},"date_published":"2024-01-04T00:00:00Z","article_number":"2470004","status":"public","department":[{"_id":"MaIb"}],"publisher":"Wiley"},{"publication":"arXiv","year":"2024","external_id":{"arxiv":["2409.08119"]},"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","last_name":"Dvorak","first_name":"Martin","full_name":"Dvorak, Martin"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"day":"12","OA_place":"repository","oa":1,"OA_type":"green","article_processing_charge":"No","publication_status":"draft","acknowledgement":"We would like to thank David Bartl and Jasmin Blanchette for frequent consultations. We would also like to express gratitude to Andrew Yang for the proof of Finset.univ sum of zero when not and to Henrik B¨oving for a help with generalization from extended rationals to extended linearly ordered fields. We would also like to acknowledge Antoine Chambert-Loir, Apurva Nakade, Ya¨el Dillies, Richard Copley, Edward van de Meent, Markus Himmel, Mario Carneiro, and Kevin Buzzard.","abstract":[{"lang":"eng","text":"Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take \"infinite values\"."}],"title":"Duality theory in linear optimization and its extensions -- formally verified","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"status":"public","corr_author":"1","article_number":"2409.08119","arxiv":1,"citation":{"ista":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. arXiv, 2409.08119.","short":"M. Dvorak, V. Kolmogorov, ArXiv (n.d.).","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.08119.","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” ArXiv, 2409.08119, doi:10.48550/arXiv.2409.08119.","ama":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. arXiv. doi:10.48550/arXiv.2409.08119","ieee":"M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally verified,” arXiv. .","apa":"Dvorak, M., & Kolmogorov, V. (n.d.). Duality theory in linear optimization and its extensions -- formally verified. arXiv. https://doi.org/10.48550/arXiv.2409.08119"},"date_published":"2024-09-12T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Farkas lemma","linear programming","extended reals","calculus of inductive constructions"],"related_material":{"record":[{"relation":"dissertation_contains","id":"21393","status":"public"}],"link":[{"url":"https://github.com/madvorak/duality/tree/v3.2","description":"full version of all definitions, statement, and proofs","relation":"software"}]},"type":"preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2409.08119","open_access":"1"}],"doi":"10.48550/arXiv.2409.08119","_id":"20071","oa_version":"Preprint","month":"09","date_created":"2025-07-23T11:21:52Z","date_updated":"2026-03-27T12:36:59Z"},{"_id":"20121","month":"09","oa_version":"Published Version","date_updated":"2025-09-30T14:14:42Z","date_created":"2025-08-05T06:49:59Z","abstract":[{"text":"PyDaddy is an open source package which is a key contribution of the manuscript Nabeel et al, arXiv:2205.02645. The basic scientific premise for this package is to discover the nature of stochasticity in ecological time series datasets. It is well known that the stochasticity can affect the dynamics of ecological systems in counter-intuitive ways. Without understanding the equations (typically, in the form of stochastic differential equations or SDEs, in short) that govern the dynamics of populations or ecosystems, it's challenging to determine the impact of randomness on real datasets. In this manuscript and accompanying package, we introduce a methodology for discovering equations (SDEs) that transforms time series data of state variables into stochastic differential equations. This approach merges traditional stochastic calculus with modern equation-discovery techniques. We showcase the generality of our method through various applications and discuss its limitations and potential pitfalls, offering diagnostic measures to address these challenges.","lang":"eng"}],"title":"PyDaddy: A Python Package for Discovering SDEs from Time Series Data","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7137151","open_access":"1"}],"doi":"10.5281/ZENODO.7137151","acknowledgement":"This study was partially funded by Science and Engineering Research Board, Department of Science and Technology, Government of India to Vishwesha Guttal.","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"has_accepted_license":"1","type":"research_data_reference","article_processing_charge":"No","author":[{"last_name":"Nabeel","first_name":"Arshed","full_name":"Nabeel, Arshed"},{"full_name":"Karichannavar, Ashwin","first_name":"Ashwin","last_name":"Karichannavar"},{"last_name":"Palathingal","first_name":"Shuaib","full_name":"Palathingal, Shuaib"},{"full_name":"Jhawar, Jitesh","first_name":"Jitesh","last_name":"Jhawar"},{"full_name":"Brückner, David","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner"},{"last_name":"Danny Raj","full_name":"Danny Raj, Masila","first_name":"Masila"},{"last_name":"Guttal","first_name":"Vishwesha","full_name":"Guttal, Vishwesha"}],"related_material":{"record":[{"status":"public","id":"20056","relation":"used_for_analysis_in"}]},"ddc":["570"],"day":"18","citation":{"ama":"Nabeel A, Karichannavar A, Palathingal S, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. 2024. doi:10.5281/ZENODO.7137151","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., & Guttal, V. (2024). PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo. https://doi.org/10.5281/ZENODO.7137151","ieee":"A. Nabeel et al., “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Danny Raj M, Guttal V. 2024. PyDaddy: A Python Package for Discovering SDEs from Time Series Data, Zenodo, 10.5281/ZENODO.7137151.","mla":"Nabeel, Arshed, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo, 2024, doi:10.5281/ZENODO.7137151.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024).","chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Masila Danny Raj, and Vishwesha Guttal. “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.7137151."},"date_published":"2024-09-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","year":"2024","department":[{"_id":"EdHa"}],"publisher":"Zenodo"},{"scopus_import":"1","_id":"20156","month":"10","oa_version":"None","quality_controlled":"1","date_created":"2025-08-10T22:01:30Z","volume":2,"date_updated":"2025-08-11T06:44:03Z","doi":"10.1038/s44220-024-00317-y","type":"journal_article","intvolume":" 2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-10-01T00:00:00Z","citation":{"apa":"Desrivières, S., Miller, A., Mathey, C. M., Yu, X., Chen, D., Agunbiade, K., … Walter, H. (2024). Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00317-y","ieee":"S. Desrivières et al., “Multi-omics analyses of the environMENTAL project provide insights into mental health and disease,” Nature Mental Health, vol. 2, no. 10. Springer Nature, pp. 1131–1133, 2024.","ama":"Desrivières S, Miller A, Mathey CM, et al. Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. Nature Mental Health. 2024;2(10):1131-1133. doi:10.1038/s44220-024-00317-y","mla":"Desrivières, Sylvane, et al. “Multi-Omics Analyses of the EnvironMENTAL Project Provide Insights into Mental Health and Disease.” Nature Mental Health, vol. 2, no. 10, Springer Nature, 2024, pp. 1131–33, doi:10.1038/s44220-024-00317-y.","short":"S. Desrivières, A. Miller, C.M. Mathey, X. Yu, D. Chen, K. Agunbiade, S. Heilmann-Heimbach, A.J. Forstner, G. Schumann, P. Hoffmann, M.M. Nöthen, G. Ogoh, B. Stahl, A.H. Young, 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, I. Claus, 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) 1131–1133.","chicago":"Desrivières, Sylvane, Abigail Miller, Carina M. Mathey, Xinyang Yu, Di Chen, Kofoworola Agunbiade, Stefanie Heilmann-Heimbach, et al. “Multi-Omics Analyses of the EnvironMENTAL Project Provide Insights into Mental Health and Disease.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00317-y.","ista":"Desrivières S, Miller A, Mathey CM, Yu X, Chen D, Agunbiade K, Heilmann-Heimbach S, Forstner AJ, Schumann G, Hoffmann P, Nöthen MM, Ogoh G, Stahl B, Young AH, 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, Claus I, 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. Multi-omics analyses of the environMENTAL project provide insights into mental health and disease. Nature Mental Health. 2(10), 1131–1133."},"status":"public","department":[{"_id":"GaNo"}],"publisher":"Springer Nature","title":"Multi-omics analyses of the environMENTAL project provide insights into mental health and disease","abstract":[{"lang":"eng","text":"Integrative analyses that incorporate different levels of ‘-omics’ data represent a powerful tool for deciphering the biological mechanisms that underlie environmental influences on mental health and disease. This Comment highlights various aspects of such multi-omics approaches, using the example of the EU-funded environMENTAL project."}],"acknowledgement":"This work was supported by the Horizon 2021 (grant 101057429) and UK Research and Innovation (grants 10038599 and 10041392)-funded project environMENTAL. Other funding included the Medical Research Council and Medical Research Foundation (MR/R00465X/, MRF-058-0004-RG-DESRI, ‘ESTRA’- Neurobiological underpinning of eating disorders: integrative biopsychosocial longitudinal analyses in adolescents; and MR/S020306/1, MRF-058-0009-RG-DESR-C0759 ‘ESTRA’-Establishing causal relationships between biopsychosocial predictors and correlates of eating disorders and their mediation by neural pathways), the EU-funded FP6 Integrated Project IMAGEN (reinforcement-related behavior in normal brain function and psychopathology; LSHM-CT- 2007-037286), the Horizon 2020-funded European Research Council advanced grant for STRATIFY (brain network-based stratification of reinforcement-related disorders; 695313) and the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. This paper represents independent research, partly funded by the NIHR Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. The views expressed are those of the authors and not necessarily those of the NIHR or the Department of Health and Social Care. The authors thank C. Schmäl for proofreading the manuscript.","publication_status":"published","page":"1131-1133","OA_type":"closed access","article_processing_charge":"No","author":[{"first_name":"Sylvane","full_name":"Desrivières, Sylvane","last_name":"Desrivières"},{"first_name":"Abigail","full_name":"Miller, Abigail","last_name":"Miller"},{"full_name":"Mathey, Carina M.","first_name":"Carina M.","last_name":"Mathey"},{"full_name":"Yu, Xinyang","first_name":"Xinyang","last_name":"Yu"},{"full_name":"Chen, Di","first_name":"Di","last_name":"Chen"},{"first_name":"Kofoworola","full_name":"Agunbiade, Kofoworola","last_name":"Agunbiade"},{"full_name":"Heilmann-Heimbach, Stefanie","first_name":"Stefanie","last_name":"Heilmann-Heimbach"},{"first_name":"Andreas J.","full_name":"Forstner, Andreas J.","last_name":"Forstner"},{"last_name":"Schumann","first_name":"Gunter","full_name":"Schumann, Gunter"},{"first_name":"Per","full_name":"Hoffmann, Per","last_name":"Hoffmann"},{"first_name":"Markus 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Andre","first_name":"Andre","last_name":"Marquand"},{"last_name":"Böttger","first_name":"Sarah Jane","full_name":"Böttger, Sarah Jane"},{"first_name":"Mira","full_name":"Tschorn, Mira","last_name":"Tschorn"},{"full_name":"Rapp, Michael","first_name":"Michael","last_name":"Rapp"},{"first_name":"Helga","full_name":"Ask, Helga","last_name":"Ask"},{"last_name":"Kjelkenes","first_name":"Rikka","full_name":"Kjelkenes, Rikka"},{"full_name":"Fernandez, Sara","first_name":"Sara","last_name":"Fernandez"},{"last_name":"Van Der Meer","full_name":"Van Der Meer, Dennis","first_name":"Dennis"},{"last_name":"Westlye","first_name":"Lars T.","full_name":"Westlye, Lars T."},{"full_name":"Andreassen, Ole A.","first_name":"Ole A.","last_name":"Andreassen"},{"full_name":"Aden, Rieke","first_name":"Rieke","last_name":"Aden"},{"last_name":"Seefried","first_name":"Beke","full_name":"Seefried, Beke"},{"full_name":"Siehl, Sebastian","first_name":"Sebastian","last_name":"Siehl"},{"full_name":"Nees, 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Tatjana"},{"full_name":"Taron, Ulrike Helene","first_name":"Ulrike Helene","last_name":"Taron"},{"last_name":"Eils","full_name":"Eils, Roland","first_name":"Roland"},{"full_name":"Roy, Jean Charles","first_name":"Jean Charles","last_name":"Roy"},{"last_name":"Lett","first_name":"Tristram A.","full_name":"Lett, Tristram A."},{"last_name":"Kebir","full_name":"Kebir, Hedi","first_name":"Hedi"},{"last_name":"Polemiti","first_name":"Elli","full_name":"Polemiti, Elli"},{"last_name":"Hitchen","first_name":"Esther","full_name":"Hitchen, Esther"},{"last_name":"Jentsch","first_name":"Marcel","full_name":"Jentsch, Marcel"},{"first_name":"Emin","full_name":"Serin, Emin","last_name":"Serin"},{"first_name":"Antoine","full_name":"Bernas, Antoine","last_name":"Bernas"},{"first_name":"Nilakshi","full_name":"Vaidya, Nilakshi","last_name":"Vaidya"},{"last_name":"Twardziok","first_name":"Sven","full_name":"Twardziok, Sven"},{"last_name":"Ralser","full_name":"Ralser, Markus","first_name":"Markus"},{"last_name":"Heinz","first_name":"Andreas","full_name":"Heinz, Andreas"},{"first_name":"Henrik","full_name":"Walter, Henrik","last_name":"Walter"}],"day":"01","issue":"10","language":[{"iso":"eng"}],"year":"2024","article_type":"comment","publication":"Nature Mental Health","publication_identifier":{"eissn":["2731-6076"]}},{"publication":"Nature Mental Health","publication_identifier":{"eissn":["2731-6076"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"comment","OA_type":"closed access","article_processing_charge":"No","author":[{"full_name":"Stahl, Bernd","first_name":"Bernd","last_name":"Stahl"},{"last_name":"Ogoh","full_name":"Ogoh, George","first_name":"George"},{"last_name":"Schumann","full_name":"Schumann, Gunter","first_name":"Gunter"},{"first_name":"Henrik","full_name":"Walter, Henrik","last_name":"Walter"},{"last_name":"Stahl","full_name":"Stahl, Bernd","first_name":"Bernd"},{"full_name":"Young, Allan H.","first_name":"Allan H.","last_name":"Young"},{"full_name":"Desrivières, Sylvane","first_name":"Sylvane","last_name":"Desrivières"},{"last_name":"Clinton","first_name":"Nicholas","full_name":"Clinton, Nicholas"},{"last_name":"Thompson","full_name":"Thompson, Paul","first_name":"Paul"},{"first_name":"Ameli","full_name":"Schwalber, Ameli","last_name":"Schwalber"},{"full_name":"Liu, Jingyu","first_name":"Jingyu","last_name":"Liu"},{"last_name":"Calhoun","first_name":"Vince","full_name":"Calhoun, Vince"},{"full_name":"Chang, Xiao","first_name":"Xiao","last_name":"Chang"},{"last_name":"Xia","full_name":"Xia, Yunman","first_name":"Yunman"},{"last_name":"Gong","full_name":"Gong, Yanting","first_name":"Yanting"},{"last_name":"Jia","full_name":"Jia, Tianye","first_name":"Tianye"},{"last_name":"Renner","full_name":"Renner, Paul","first_name":"Paul"},{"full_name":"Hese, Sören","first_name":"Sören","last_name":"Hese"},{"last_name":"Giner","first_name":"Arantxa","full_name":"Giner, Arantxa"},{"last_name":"Sanchez","full_name":"Sanchez, Mavi","first_name":"Mavi"},{"full_name":"Alvarez, Elena","first_name":"Elena","last_name":"Alvarez"},{"first_name":"Bernhard","full_name":"Spanlang, Bernhard","last_name":"Spanlang"},{"full_name":"Pearmund, Charlie","first_name":"Charlie","last_name":"Pearmund"},{"first_name":"Anastasios Polykarpos","full_name":"Athanasiadis, Anastasios Polykarpos","last_name":"Athanasiadis"},{"last_name":"Otten","first_name":"Lisa","full_name":"Otten, Lisa"},{"last_name":"Pitel","first_name":"Séverine","full_name":"Pitel, Séverine"},{"full_name":"Petkoski, Spase","first_name":"Spase","last_name":"Petkoski"},{"first_name":"Viktor","full_name":"Jirsa, Viktor","last_name":"Jirsa"},{"first_name":"Karen","full_name":"Schmitt, Karen","last_name":"Schmitt"},{"full_name":"Wilbertz, Johannes","first_name":"Johannes","last_name":"Wilbertz"},{"last_name":"Patraskaki","first_name":"Myrto","full_name":"Patraskaki, Myrto"},{"full_name":"Sommer, Peter","first_name":"Peter","last_name":"Sommer"},{"first_name":"Stefanie","full_name":"Heilmann-Heimbach, Stefanie","last_name":"Heilmann-Heimbach"},{"full_name":"Mathey, Carina M.","first_name":"Carina M.","last_name":"Mathey"},{"full_name":"Miller, Abigail","first_name":"Abigail","last_name":"Miller"},{"first_name":"Isabelle","full_name":"Claus, Isabelle","last_name":"Claus"},{"first_name":"Markus M.","full_name":"Nöthen, Markus M.","last_name":"Nöthen"},{"last_name":"Hoffmann","full_name":"Hoffmann, Per","first_name":"Per"},{"last_name":"Forstner","full_name":"Forstner, Andreas J.","first_name":"Andreas J."},{"last_name":"Pastor","full_name":"Pastor, Alvaro","first_name":"Alvaro"},{"full_name":"Gallego, Jaime","first_name":"Jaime","last_name":"Gallego"},{"full_name":"Orosa, Francisco Eiroa","first_name":"Francisco Eiroa","last_name":"Orosa"},{"full_name":"Viapiana, Guillem Feixas","first_name":"Guillem Feixas","last_name":"Viapiana"},{"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","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia"},{"last_name":"Marquand","full_name":"Marquand, Andre","first_name":"Andre"},{"first_name":"Sarah Jane","full_name":"Böttger, Sarah Jane","last_name":"Böttger"},{"first_name":"Mira","full_name":"Tschorn, Mira","last_name":"Tschorn"},{"first_name":"Michael","full_name":"Rapp, Michael","last_name":"Rapp"},{"full_name":"Ask, Helga","first_name":"Helga","last_name":"Ask"},{"last_name":"Kjelkenes","first_name":"Rikka","full_name":"Kjelkenes, Rikka"},{"first_name":"Sara","full_name":"Fernandez, Sara","last_name":"Fernandez"},{"first_name":"Dennis","full_name":"Van Der Meer, Dennis","last_name":"Van Der Meer"},{"last_name":"Westlye","full_name":"Westlye, Lars T.","first_name":"Lars T."},{"last_name":"Andreassen","full_name":"Andreassen, Ole A.","first_name":"Ole A."},{"first_name":"Rieke","full_name":"Aden, Rieke","last_name":"Aden"},{"full_name":"Seefried, Beke","first_name":"Beke","last_name":"Seefried"},{"full_name":"Siehl, Sebastian","first_name":"Sebastian","last_name":"Siehl"},{"full_name":"Nees, Frauke","first_name":"Frauke","last_name":"Nees"},{"last_name":"Neidhart","first_name":"Maja","full_name":"Neidhart, Maja"},{"full_name":"Stringaris, Argyris","first_name":"Argyris","last_name":"Stringaris"},{"last_name":"Schwarz","full_name":"Schwarz, Emanuel","first_name":"Emanuel"},{"last_name":"Holz","full_name":"Holz, Nathalie","first_name":"Nathalie"},{"last_name":"Tost","full_name":"Tost, Heike","first_name":"Heike"},{"full_name":"Meyer-Lindenberg, Andreas","first_name":"Andreas","last_name":"Meyer-Lindenberg"},{"last_name":"Christmann","first_name":"Nina","full_name":"Christmann, Nina"},{"last_name":"Jansone","first_name":"Karina","full_name":"Jansone, Karina"},{"last_name":"Banaschewski","full_name":"Banaschewski, Tobias","first_name":"Tobias"},{"full_name":"Banks, Jamie","first_name":"Jamie","last_name":"Banks"},{"last_name":"Schepanski","full_name":"Schepanski, Kerstin","first_name":"Kerstin"},{"full_name":"Schütz, Tatjana","first_name":"Tatjana","last_name":"Schütz"},{"full_name":"Taron, Ulrike Helene","first_name":"Ulrike Helene","last_name":"Taron"},{"last_name":"Eils","first_name":"Roland","full_name":"Eils, Roland"},{"last_name":"Roy","full_name":"Roy, Jean Charles","first_name":"Jean Charles"},{"last_name":"Lett","first_name":"Tristram A.","full_name":"Lett, Tristram A."},{"last_name":"Kebir","first_name":"Hedi","full_name":"Kebir, Hedi"},{"last_name":"Polemiti","full_name":"Polemiti, Elli","first_name":"Elli"},{"last_name":"Hitchen","first_name":"Esther","full_name":"Hitchen, Esther"},{"first_name":"Marcel","full_name":"Jentsch, Marcel","last_name":"Jentsch"},{"first_name":"Emin","full_name":"Serin, Emin","last_name":"Serin"},{"first_name":"Antoine","full_name":"Bernas, Antoine","last_name":"Bernas"},{"first_name":"Nilakshi","full_name":"Vaidya, Nilakshi","last_name":"Vaidya"},{"first_name":"Sven","full_name":"Twardziok, Sven","last_name":"Twardziok"},{"first_name":"Markus","full_name":"Ralser, Markus","last_name":"Ralser"},{"first_name":"Andreas","full_name":"Heinz, Andreas","last_name":"Heinz"},{"first_name":"Henrik","full_name":"Walter, Henrik","last_name":"Walter"}],"day":"01","issue":"10","title":"Rethinking ethics in interdisciplinary and big data-driven neuroscience projects","abstract":[{"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.","lang":"eng"}],"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).","publication_status":"published","department":[{"_id":"GaNo"}],"publisher":"Springer Nature","intvolume":" 2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Stahl, B., Ogoh, G., Schumann, G., Walter, H., Stahl, B., Young, A. H., … Walter, H. (2024). Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. Springer Nature. https://doi.org/10.1038/s44220-024-00320-3","ieee":"B. Stahl et al., “Rethinking ethics in interdisciplinary and big data-driven neuroscience projects,” Nature Mental Health, vol. 2, no. 10. Springer Nature, 2024.","ama":"Stahl B, Ogoh G, Schumann G, et al. Rethinking ethics in interdisciplinary and big data-driven neuroscience projects. Nature Mental Health. 2024;2(10). doi:10.1038/s44220-024-00320-3","mla":"Stahl, Bernd, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” Nature Mental Health, vol. 2, no. 10, 1128–1130, Springer Nature, 2024, doi:10.1038/s44220-024-00320-3.","chicago":"Stahl, Bernd, George Ogoh, Gunter Schumann, Henrik Walter, Bernd Stahl, Allan H. Young, Sylvane Desrivières, et al. “Rethinking Ethics in Interdisciplinary and Big Data-Driven Neuroscience Projects.” Nature Mental Health. Springer Nature, 2024. https://doi.org/10.1038/s44220-024-00320-3.","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).","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."},"date_published":"2024-10-01T00:00:00Z","article_number":"1128-1130","status":"public","type":"journal_article","scopus_import":"1","month":"10","_id":"20157","oa_version":"None","volume":2,"date_updated":"2025-08-11T06:53:55Z","quality_controlled":"1","date_created":"2025-08-10T22:01:30Z","doi":"10.1038/s44220-024-00320-3"},{"language":[{"iso":"eng"}],"external_id":{"arxiv":["2109.06778"],"isi":["000881319200001"]},"article_type":"original","year":"2024","publication":"Journal of the Institute of Mathematics of Jussieu","isi":1,"file":[{"success":1,"creator":"dernst","file_size":592305,"date_created":"2024-06-03T08:33:29Z","date_updated":"2024-06-03T08:33:29Z","content_type":"application/pdf","access_level":"open_access","file_name":"2024_JourMathJussieu_Derenthal.pdf","file_id":"17102","relation":"main_file","checksum":"c4698ea12cfe10ef2c6c79880290c7ac"}],"publication_identifier":{"eissn":["1475-3030 "],"issn":["1474-7480"]},"title":"Integral points on singular del Pezzo surfaces","abstract":[{"lang":"eng","text":"In order to study integral points of bounded log-anticanonical height on weak del Pezzo surfaces, we classify weak del Pezzo pairs. As a representative example, we consider a quartic del Pezzo surface of singularity type A1 + A3 and prove an analogue of Manin's conjecture for integral points with respect to its singularities and its lines."}],"acknowledgement":"The first author was partly supported by grant DE 1646/4-2 of the Deutsche Forschungsgemeinschaft. The second author was partly supported by FWF grant P 32428-N35 and conducted part of this work as a guest at the Institut de Mathématiques de Jussieu–Paris Rive Gauche invited by Antoine Chambert-Loir and funded by DAAD.","page":"1259-1294","publication_status":"published","article_processing_charge":"Yes (via OA deal)","oa":1,"day":"10","ddc":["510"],"author":[{"last_name":"Derenthal","full_name":"Derenthal, Ulrich","first_name":"Ulrich"},{"first_name":"Florian Alexander","full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","id":"560601DA-8D36-11E9-A136-7AC1E5697425","last_name":"Wilsch"}],"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 23","date_published":"2024-05-10T00:00:00Z","citation":{"apa":"Derenthal, U., & Wilsch, F. A. (2024). Integral points on singular del Pezzo surfaces. Journal of the Institute of Mathematics of Jussieu. Cambridge University Press. https://doi.org/10.1017/S1474748022000482","ieee":"U. Derenthal and F. A. Wilsch, “Integral points on singular del Pezzo surfaces,” Journal of the Institute of Mathematics of Jussieu, vol. 23, no. 3. Cambridge University Press, pp. 1259–1294, 2024.","ama":"Derenthal U, Wilsch FA. Integral points on singular del Pezzo surfaces. Journal of the Institute of Mathematics of Jussieu. 2024;23(3):1259-1294. doi:10.1017/S1474748022000482","mla":"Derenthal, Ulrich, and Florian Alexander Wilsch. “Integral Points on Singular Del Pezzo Surfaces.” Journal of the Institute of Mathematics of Jussieu, vol. 23, no. 3, Cambridge University Press, 2024, pp. 1259–94, doi:10.1017/S1474748022000482.","chicago":"Derenthal, Ulrich, and Florian Alexander Wilsch. “Integral Points on Singular Del Pezzo Surfaces.” Journal of the Institute of Mathematics of Jussieu. Cambridge University Press, 2024. https://doi.org/10.1017/S1474748022000482.","short":"U. Derenthal, F.A. Wilsch, Journal of the Institute of Mathematics of Jussieu 23 (2024) 1259–1294.","ista":"Derenthal U, Wilsch FA. 2024. Integral points on singular del Pezzo surfaces. Journal of the Institute of Mathematics of Jussieu. 23(3), 1259–1294."},"arxiv":1,"corr_author":"1","status":"public","department":[{"_id":"TiBr"}],"file_date_updated":"2024-06-03T08:33:29Z","publisher":"Cambridge University Press","project":[{"grant_number":"P32428","call_identifier":"FWF","name":"New frontiers of the Manin conjecture","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","date_updated":"2025-04-15T07:39:01Z","volume":23,"date_created":"2021-09-15T10:06:48Z","quality_controlled":"1","month":"05","_id":"10018","oa_version":"Published Version","doi":"10.1017/S1474748022000482","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","keyword":["Integral points","del Pezzo surface","universal torsor","Manin’s conjecture"]},{"OA_place":"publisher","oa":1,"OA_type":"gold","article_processing_charge":"Yes","author":[{"full_name":"Sagi, Oliver","first_name":"Oliver","last_name":"Sagi","id":"71616374-A8E9-11E9-A7CA-09ECE5697425"},{"last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","orcid":"0000-0002-2968-611X","first_name":"Alessandro","full_name":"Crippa, Alessandro"},{"full_name":"Valentini, Marco","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini"},{"orcid":"0009-0003-9037-8831","id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","first_name":"Marian","full_name":"Janik, Marian"},{"full_name":"Baghumyan, Levon","first_name":"Levon","last_name":"Baghumyan","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7"},{"full_name":"Fabris, Giorgio","first_name":"Giorgio","id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","last_name":"Fabris"},{"id":"84b9700b-15b2-11ec-abd3-831089e67615","last_name":"Kapoor","orcid":"0000-0001-8319-2148","full_name":"Kapoor, Lucky","first_name":"Lucky"},{"full_name":"Hassani, Farid","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani"},{"first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"},{"last_name":"Calcaterra","first_name":"Stefano","full_name":"Calcaterra, Stefano"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"full_name":"Katsaros, Georgios","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"day":"30","ddc":["530"],"APC_amount":"6828 EUR","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"}],"title":"A gate tunable transmon qubit in planar Ge","publication_status":"published","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.","publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"file":[{"file_size":1928001,"date_created":"2024-08-05T08:38:01Z","date_updated":"2024-08-05T08:38:01Z","creator":"dernst","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"17388","relation":"main_file","file_name":"2024_NatureComm_Sagi.pdf","checksum":"ddf5361dcb6c543e2cea818501c09910"}],"isi":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"external_id":{"pmid":["39080279"],"isi":["001281271000022"],"arxiv":["2403.16774"]},"pmid":1,"language":[{"iso":"eng"}],"year":"2024","article_type":"original","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-024-53910-1","relation":"erratum"}],"record":[{"id":"17196","relation":"research_data","status":"public"},{"status":"public","id":"18076","relation":"dissertation_contains"}]},"oa_version":"Published Version","_id":"17202","month":"07","date_created":"2024-07-04T11:40:45Z","volume":15,"date_updated":"2026-04-07T13:01:55Z","quality_controlled":"1","scopus_import":"1","project":[{"grant_number":"P36507","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","name":"Merging spin and superconducting qubits in planar Ge"},{"name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"doi":"10.1038/s41467-024-50763-6","file_date_updated":"2024-08-05T08:38:01Z","department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"publisher":"Springer Nature","date_published":"2024-07-30T00:00:00Z","citation":{"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.","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.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-50763-6.","mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature Communications, vol. 15, 6400, Springer Nature, 2024, doi:10.1038/s41467-024-50763-6.","ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. Nature Communications. 2024;15. doi:10.1038/s41467-024-50763-6","ieee":"O. Sagi et al., “A gate tunable transmon qubit in planar Ge,” Nature Communications, vol. 15. Springer Nature, 2024.","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-50763-6"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 15","DOAJ_listed":"1","status":"public","corr_author":"1","arxiv":1,"article_number":"6400"},{"publication_status":"published","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).","abstract":[{"lang":"eng","text":"The behavior of a rigid body primarily depends on its mass moments, which consist of the mass, center of mass, and moments of inertia. It is possible to manipulate these quantities without altering the geometric appearance of an object by introducing cavities in its interior. Algorithms that find cavities of suitable shapes and sizes have enabled the computational design of spinning tops, yo-yos, wheels, buoys, and statically balanced objects. Previous work is based, for example, on topology optimization on voxel grids, which introduces a large number of optimization variables and box constraints, or offset surface computation, which cannot guarantee that solutions to a feasible problem will always be found.\r\n\r\nIn this work, we provide a mathematical analysis of constrained topology optimization problems that depend only on mass moments. This class of problems covers, among others, all applications mentioned above. Our main result is to show that no matter the outer shape of the rigid body to be optimized or the optimization objective and constraints considered, the optimal solution always features a quadric-shaped interface between material and cavities. This proves that optimal interfaces are always ellipsoids, hyperboloids, paraboloids, or one of a few degenerate cases, such as planes.\r\n\r\nThis insight lets us replace a difficult topology optimization problem with a provably equivalent non-linear equation system in a small number (<10) of variables, which represent the coefficients of the quadric. This system can be solved in a few seconds for most examples, provides insights into the geometric structure of many specific applications, and lets us describe their solution properties. Finally, our method integrates seamlessly into modern fabrication workflows because our solutions are analytical surfaces that are native to the CAD domain."}],"title":"Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments","issue":"4","day":"01","ddc":["516"],"author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner","first_name":"Christian","full_name":"Hafner, Christian"},{"first_name":"Mickaël","full_name":"Ly, Mickaël","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"oa":1,"article_processing_charge":"Yes (via OA deal)","article_type":"original","year":"2024","language":[{"iso":"eng"}],"external_id":{"isi":["001289270900045"]},"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"isi":1,"file":[{"checksum":"0dc9f5a6422b8a49a79026900f349ee5","file_name":"sif-final.pdf","relation":"main_file","file_id":"17204","access_level":"open_access","content_type":"application/pdf","creator":"chafner","success":1,"file_size":7225150,"date_created":"2024-07-05T12:05:17Z","date_updated":"2024-07-05T12:05:17Z"},{"content_type":"application/pdf","access_level":"open_access","creator":"chafner","date_updated":"2024-07-05T12:06:03Z","date_created":"2024-07-05T12:06:03Z","file_size":397262,"checksum":"cde433c6a40688d5f1187fb5721f6f94","file_name":"sif-supp-final.pdf","file_id":"17205","relation":"supplementary_material"},{"checksum":"c0457a09c2ab9a1c2935c995dcc84907","file_name":"sif-video-final.mp4","file_id":"17276","relation":"supplementary_material","content_type":"video/mp4","access_level":"open_access","creator":"chafner","title":"Submission Video","file_size":170001305,"date_created":"2024-07-17T09:29:13Z","date_updated":"2024-07-17T09:29:13Z"}],"publication":"Transactions on Graphics","doi":"10.1145/3658194","date_created":"2024-07-05T12:08:57Z","volume":43,"date_updated":"2025-09-08T08:29:09Z","quality_controlled":"1","_id":"17203","oa_version":"Published Version","month":"07","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"scopus_import":"1","keyword":["Topology Optimization","Mass Moments","Computational Geometry"],"has_accepted_license":"1","conference":{"start_date":"2024-07-28","end_date":"2024-08-01","location":"Denver, Colorado"},"type":"journal_article","status":"public","corr_author":"1","article_number":"78","date_published":"2024-07-01T00:00:00Z","citation":{"mla":"Hafner, Christian, et al. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics, vol. 43, no. 4, 78, Association for Computing Machinery, 2024, doi:10.1145/3658194.","short":"C. Hafner, M. Ly, C. Wojtan, Transactions on Graphics 43 (2024).","chicago":"Hafner, Christian, Mickaël Ly, and Chris Wojtan. “Spin-It Faster: Quadrics Solve All Topology Optimization Problems That Depend Only on Mass Moments.” Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658194.","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.","apa":"Hafner, C., Ly, M., & Wojtan, C. (2024). Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. Denver, Colorado: Association for Computing Machinery. https://doi.org/10.1145/3658194","ieee":"C. Hafner, M. Ly, and C. Wojtan, “Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments,” Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024.","ama":"Hafner C, Ly M, Wojtan C. Spin-it faster: Quadrics solve all topology optimization problems that depend only on mass moments. Transactions on Graphics. 2024;43(4). doi:10.1145/3658194"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 43","publisher":"Association for Computing Machinery","department":[{"_id":"ChWo"}],"file_date_updated":"2024-07-17T09:29:13Z"},{"title":"Eco-evolutionary dynamics in changing environments: Integrating theory with data","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.","publication_status":"published","page":"579-587","article_processing_charge":"No","oa":1,"author":[{"first_name":"Louise","full_name":"Fouqueau, Louise","last_name":"Fouqueau","id":"1676e173-8143-11ed-8927-fe165216a93f","orcid":"0000-0003-0371-9339"},{"orcid":"0000-0003-0951-3112","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","full_name":"Polechova, Jitka"}],"day":"28","ddc":["570"],"issue":"6","pmid":1,"external_id":{"pmid":["38941551"],"isi":["001258359900001"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"letter_note","publication":"Journal of evolutionary biology","isi":1,"publication_identifier":{"eissn":["1420-9101"]},"scopus_import":"1","project":[{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","_id":"17207","month":"06","date_updated":"2026-06-18T17:53:35Z","date_created":"2024-07-07T22:01:04Z","volume":37,"quality_controlled":"1","doi":"10.1093/jeb/voae067","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/jeb/voae067"}],"type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 37","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Fouqueau L, Polechova J. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 2024;37(6):579-587. doi:10.1093/jeb/voae067","ieee":"L. Fouqueau and J. Polechova, “Eco-evolutionary dynamics in changing environments: Integrating theory with data,” Journal of evolutionary biology, vol. 37, no. 6. Oxford University Press, pp. 579–587, 2024.","apa":"Fouqueau, L., & Polechova, J. (2024). Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voae067","ista":"Fouqueau L, Polechova J. 2024. Eco-evolutionary dynamics in changing environments: Integrating theory with data. Journal of evolutionary biology. 37(6), 579–587.","short":"L. Fouqueau, J. Polechova, Journal of Evolutionary Biology 37 (2024) 579–587.","chicago":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology. Oxford University Press, 2024. https://doi.org/10.1093/jeb/voae067.","mla":"Fouqueau, Louise, and Jitka Polechova. “Eco-Evolutionary Dynamics in Changing Environments: Integrating Theory with Data.” Journal of Evolutionary Biology, vol. 37, no. 6, Oxford University Press, 2024, pp. 579–87, doi:10.1093/jeb/voae067."},"date_published":"2024-06-28T00:00:00Z","status":"public","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press"},{"ec_funded":1,"status":"public","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"apa":"Medina Ramos, R. A. (2024). Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17208","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:10.15479/at:ista:17208","mla":"Medina Ramos, Raimel A. Exploring the Optimization Landscape of Variational Quantum Algorithms. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17208.","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17208.","short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria."},"date_published":"2024-07-09T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"file_date_updated":"2024-07-17T09:23:24Z","doi":"10.15479/at:ista:17208","date_updated":"2026-04-07T12:43:22Z","date_created":"2024-07-09T09:14:24Z","month":"07","_id":"17208","oa_version":"Published Version","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"10545","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10067"},{"status":"public","relation":"part_of_dissertation","id":"17222"},{"id":"13125","relation":"part_of_dissertation","status":"public"},{"id":"11471","relation":"part_of_dissertation","status":"public"}]},"keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","type":"dissertation","year":"2024","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"file":[{"checksum":"6f45273d04f4418bc2adc018baed0525","relation":"source_file","file_id":"17212","file_name":"Raimel_Thesis-Final.zip","access_level":"closed","content_type":"application/zip","date_updated":"2024-07-10T11:34:09Z","date_created":"2024-07-09T09:21:44Z","file_size":"14218691","creator":"rmedinar"},{"date_created":"2024-07-17T09:23:24Z","date_updated":"2024-07-17T09:23:24Z","file_size":11253627,"creator":"rmedinar","success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"17275","file_name":"Raimel_Thesis-20_pdfa.pdf","checksum":"6724a95bec772dbabc0111b9f08a805e"}],"page":"133","publication_status":"published","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."}],"title":"Exploring the optimization landscape of variational quantum algorithms","supervisor":[{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"ddc":["539"],"day":"09","author":[{"first_name":"Raimel A","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos"}],"oa":1,"OA_place":"publisher","degree_awarded":"PhD","article_processing_charge":"No"},{"publisher":"Association for Computing Machinery","file_date_updated":"2024-07-10T11:03:58Z","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"status":"public","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Chen, Y.-L., Ly, M., & Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Denver, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657485","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Denver, United States, 2024.","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657485","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657485.","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657485.","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."},"date_published":"2024-07-01T00:00:00Z","keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"type":"conference","conference":{"start_date":"2024-07-28","end_date":"2024-08-01","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","location":"Denver, United States"},"has_accepted_license":"1","doi":"10.1145/3641519.3657485","scopus_import":"1","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"_id":"17214","month":"07","oa_version":"Published Version","date_updated":"2025-09-08T08:54:38Z","date_created":"2024-07-10T11:06:20Z","quality_controlled":"1","file":[{"checksum":"b8b203ed09e3995ba0d7e6a76288663a","file_name":"sig24_friction_authors.pdf","file_id":"17215","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"yichen","success":1,"date_created":"2024-07-10T11:03:14Z","file_size":47309472,"date_updated":"2024-07-10T11:03:14Z"},{"file_name":"sig24_friction_supplementary.pdf","file_id":"17216","relation":"main_file","checksum":"89d81b397b4b6469d828808a68b70820","creator":"yichen","success":1,"date_updated":"2024-07-10T11:03:12Z","file_size":10518286,"date_created":"2024-07-10T11:03:12Z","content_type":"application/pdf","access_level":"open_access"},{"file_name":"friction_paper_extra_video_finished.mp4","file_id":"17217","relation":"main_file","checksum":"7123deed34a5456810e7b5336a31c657","creator":"yichen","success":1,"date_created":"2024-07-10T11:03:51Z","file_size":71789192,"date_updated":"2024-07-10T11:03:51Z","content_type":"video/mp4","access_level":"open_access"},{"content_type":"video/mp4","access_level":"open_access","success":1,"creator":"yichen","date_updated":"2024-07-10T11:03:58Z","date_created":"2024-07-10T11:03:58Z","file_size":280610763,"checksum":"e606fc1ae8f2610ce3b4421566800b45","file_name":"friction_paper_video_finished.mp4","file_id":"17218","relation":"main_file"}],"isi":1,"publication_identifier":{"isbn":["9798400705250"]},"publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","year":"2024","external_id":{"isi":["001282218200091"]},"language":[{"iso":"eng"}],"author":[{"first_name":"Yi-Lu","full_name":"Chen, Yi-Lu","last_name":"Chen","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","last_name":"Ly","first_name":"Mickaël","full_name":"Ly, Mickaël"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"day":"01","ddc":["621","531","006"],"article_processing_charge":"Yes (via OA deal)","oa":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).","publication_status":"published","title":"Primal-dual non-smooth friction for rigid body animation","abstract":[{"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.","lang":"eng"}]},{"publisher":"Association for Computing Machinery","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"file_date_updated":"2025-11-11T09:50:52Z","article_number":"54","corr_author":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 43","citation":{"ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 2024;43(4). doi:10.1145/3658223","apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., & Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658223","ieee":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” ACM Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024.","ista":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54.","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:10.1145/3658223.","chicago":"Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658223.","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024)."},"date_published":"2024-07-01T00:00:00Z","related_material":{"record":[{"status":"public","id":"19630","relation":"dissertation_contains"},{"status":"public","id":"18301","relation":"dissertation_contains"}]},"keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"doi":"10.1145/3658223","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"scopus_import":"1","quality_controlled":"1","date_updated":"2026-04-07T13:02:36Z","date_created":"2024-07-10T12:24:00Z","volume":43,"_id":"17219","oa_version":"Published Version","month":"07","isi":1,"file":[{"content_type":"application/pdf","access_level":"open_access","file_size":48763368,"date_created":"2024-07-23T06:35:15Z","date_updated":"2024-07-23T06:35:15Z","success":1,"creator":"dernst","checksum":"1917067d4b52d7729019b03560004e43","file_id":"17317","relation":"main_file","file_name":"2024_ACMToG_HeissSynak.pdf"},{"file_size":48021463,"date_created":"2024-07-10T12:23:44Z","date_updated":"2024-07-10T12:23:44Z","creator":"akalinov","success":1,"content_type":"video/mp4","access_level":"open_access","file_id":"17221","relation":"main_file","file_name":"sdtopofixer_final.mp4","checksum":"a4f0e293184bfa034c0c585848806b17"},{"creator":"akalinov","title":"Authors' version of the text","date_created":"2025-11-11T09:50:52Z","date_updated":"2025-11-11T09:50:52Z","file_size":48639581,"content_type":"application/pdf","access_level":"open_access","file_name":"SuperDuperTopoFixer.pdf","file_id":"20633","relation":"preprint","checksum":"18fc310a78ec91651148c45a8b89fa44"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"publication":"ACM Transactions on Graphics","article_type":"original","year":"2024","language":[{"iso":"eng"}],"external_id":{"isi":["001289270900021"]},"day":"01","ddc":["004"],"author":[{"last_name":"Synak","id":"331776E2-F248-11E8-B48F-1D18A9856A87","full_name":"Synak, Peter","first_name":"Peter"},{"full_name":"Kalinov, Aleksei","first_name":"Aleksei","orcid":"0000-0003-2189-3904","last_name":"Kalinov","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02"},{"first_name":"Irina-Malina","full_name":"Strugaru, Irina-Malina","id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","last_name":"Strugaru"},{"first_name":"Arian","full_name":"Etemadihaghighi, Arian","id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","last_name":"Etemadihaghighi"},{"last_name":"Yang","full_name":"Yang, Huidong","first_name":"Huidong"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"issue":"4","article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","oa":1,"OA_place":"publisher","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).","publication_status":"published","title":"Multi-material mesh-based surface tracking with implicit topology changes","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"}]},{"author":[{"full_name":"Medina Ramos, Raimel A","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869"},{"first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17208"}]},"day":"16","type":"preprint","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"OA_place":"repository","doi":"10.48550/arXiv.2405.10125","publication_status":"draft","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.10125"}],"title":"A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm","_id":"17222","oa_version":"Preprint","month":"05","date_updated":"2026-04-07T12:43:22Z","abstract":[{"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.","lang":"eng"}],"date_created":"2024-07-10T13:12:09Z","publication":"arXiv","department":[{"_id":"MaSe"}],"arxiv":1,"article_number":"2405.10125","year":"2024","status":"public","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2405.10125"]},"language":[{"iso":"eng"}],"date_published":"2024-05-16T00:00:00Z","citation":{"ista":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv, 2405.10125.","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv, 2405.10125, doi:10.48550/arXiv.2405.10125.","short":"R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.).","chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on the Energy Improvement of the Quantum Approximate Optimization Algorithm.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2405.10125.","ama":"Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv. doi:10.48550/arXiv.2405.10125","apa":"Medina Ramos, R. A., & Serbyn, M. (n.d.). A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm. arXiv. https://doi.org/10.48550/arXiv.2405.10125","ieee":"R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement of the quantum approximate optimization algorithm,” arXiv. ."}},{"isi":1,"publication_identifier":{"eissn":["1553-5231"],"issn":["1078-0947"]},"publication":"Discrete and Continuous Dynamical Systems- Series A","year":"2024","article_type":"original","external_id":{"isi":["001230091000001"]},"language":[{"iso":"eng"}],"author":[{"first_name":"Corentin","full_name":"Fiorebe, Corentin","last_name":"Fiorebe","id":"06619f18-9070-11eb-847d-d1ee780bd88b"}],"day":"01","ddc":["500"],"issue":"11","OA_type":"free access","article_processing_charge":"No","oa":1,"publication_status":"published","page":"3287-3301","title":"Examples of projective billiards with open sets of periodic orbits","abstract":[{"text":"In the class of projective billiards, which contains the usual billiards, we exhibit counter-examples to Ivrii's conjecture, which states that in any planar billiard with smooth boundary the set of periodic orbits has zero measure. The counter-examples are polygons admitting a 2-parameters family of n-periodic orbits, with n being either 3 or any even integer greater than 4.","lang":"eng"}],"publisher":"American Institute of Mathematical Sciences","department":[{"_id":"VaKa"}],"corr_author":"1","status":"public","intvolume":" 44","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"C. Fiorebe, “Examples of projective billiards with open sets of periodic orbits,” Discrete and Continuous Dynamical Systems- Series A, vol. 44, no. 11. American Institute of Mathematical Sciences, pp. 3287–3301, 2024.","apa":"Fiorebe, C. (2024). Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. American Institute of Mathematical Sciences. https://doi.org/10.3934/dcds.2024059","ama":"Fiorebe C. Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. 2024;44(11):3287-3301. doi:10.3934/dcds.2024059","chicago":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” Discrete and Continuous Dynamical Systems- Series A. American Institute of Mathematical Sciences, 2024. https://doi.org/10.3934/dcds.2024059.","short":"C. Fiorebe, Discrete and Continuous Dynamical Systems- Series A 44 (2024) 3287–3301.","mla":"Fiorebe, Corentin. “Examples of Projective Billiards with Open Sets of Periodic Orbits.” Discrete and Continuous Dynamical Systems- Series A, vol. 44, no. 11, American Institute of Mathematical Sciences, 2024, pp. 3287–301, doi:10.3934/dcds.2024059.","ista":"Fiorebe C. 2024. Examples of projective billiards with open sets of periodic orbits. Discrete and Continuous Dynamical Systems- Series A. 44(11), 3287–3301."},"date_published":"2024-11-01T00:00:00Z","type":"journal_article","doi":"10.3934/dcds.2024059","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3934/dcds.2024059"}],"scopus_import":"1","oa_version":"Published Version","_id":"17231","month":"11","date_updated":"2026-06-18T17:54:16Z","quality_controlled":"1","date_created":"2024-07-14T22:01:10Z","volume":44},{"publication_identifier":{"eissn":["2666-1667"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"PreCl"}],"file":[{"success":1,"creator":"dernst","date_created":"2025-01-09T12:16:53Z","file_size":6445556,"date_updated":"2025-01-09T12:16:53Z","content_type":"application/pdf","access_level":"open_access","file_name":"2024_STARProtoc_Cheung2.pdf","file_id":"18810","relation":"main_file","checksum":"464f52ecc6ec92f509552823bb82bf79"}],"publication":"STAR Protocols","article_type":"original","year":"2024","language":[{"iso":"eng"}],"external_id":{"pmid":["38968076"]},"pmid":1,"issue":"3","day":"20","ddc":["570"],"author":[{"first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572"},{"full_name":"Pauler, Florian","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","orcid":"0000-0002-3509-1948","first_name":"Peter","full_name":"Koppensteiner, Peter"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"OA_place":"publisher","oa":1,"article_processing_charge":"Yes","OA_type":"gold","publication_status":"published","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).","abstract":[{"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","lang":"eng"}],"APC_amount":"804 EUR","title":"Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq","publisher":"Elsevier","department":[{"_id":"SiHi"},{"_id":"PreCl"}],"file_date_updated":"2025-01-09T12:16:53Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","status":"public","corr_author":"1","article_number":"103168","date_published":"2024-09-20T00:00:00Z","citation":{"ieee":"G. T. Cheung, F. Pauler, P. Koppensteiner, and S. Hippenmeyer, “Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., & Hippenmeyer, S. (2024). Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103168","ama":"Cheung GT, Pauler F, Koppensteiner P, Hippenmeyer S. Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103168","chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, and Simon Hippenmeyer. “Protocol for Mapping Cell Lineage and Cell-Type Identity of Clonally-Related Cells in Situ Using MADM-CloneSeq.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103168.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, S. Hippenmeyer, STAR Protocols 5 (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.” STAR Protocols, vol. 5, no. 3, 103168, Elsevier, 2024, doi:10.1016/j.xpro.2024.103168.","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."},"intvolume":" 5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","doi":"10.1016/j.xpro.2024.103168","quality_controlled":"1","date_created":"2024-07-14T22:01:10Z","date_updated":"2025-12-30T10:54:12Z","volume":5,"_id":"17232","oa_version":"Published Version","month":"09","project":[{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"scopus_import":"1"},{"title":"Versatile cloning strategy for efficient multigene editing in Arabidopsis","abstract":[{"lang":"eng","text":"CRISPR-Cas9 technology has become an essential tool for plant genome editing. Recent advancements have significantly improved the ability to target multiple genes simultaneously within the same genetic background through various strategies. Additionally, there has been significant progress in developing methods for inducible or tissue-specific editing. These advancements offer numerous possibilities for tailored genome modifications. Building upon existing research, we have developed an optimized and modular strategy allowing the targeting of several genes simultaneously in combination with the synchronized expression of the Cas9 endonuclease in the egg cell. This system allows significant editing efficiency while avoiding mosaicism. In addition, the versatile system we propose allows adaptation to inducible and/or tissue-specific edition according to the promoter chosen to drive the expression of the Cas9 gene. Here, we describe a step-by-step protocol for generating the binary vector necessary for establishing Arabidopsis edited lines using a versatile cloning strategy that combines Gateway® and Golden Gate technologies. We describe a versatile system that allows the cloning of as many guides as needed to target DNA, which can be multiplexed into a polycistronic gene and combined in the same construct with sequences for the expression of the Cas9 endonuclease. The expression of Cas9 is controlled by selecting from among a collection of promoters, including constitutive, inducible, ubiquitous, or tissue-specific promoters. Only one vector containing the polycistronic gene (tRNA-sgRNA) needs to be constructed. For that, sgRNA (composed of protospacers chosen to target the gene of interest and sgRNA scaffold) is cloned in tandem with the pre-tRNA sequence. Then, a single recombination reaction is required to assemble the promoter, the zCas9 coding sequence, and the tRNA-gRNA polycistronic gene. Each element is cloned in an entry vector and finally assembled according to the Multisite Gateway® Technology. Here, we detail the process to express zCas9 under the control of egg cell promoter fused to enhancer sequence (EC1.2en-EC1.1p) and to simultaneously target two multiple C2 domains and transmembrane region protein genes (MCTP3 and MCTP4, respectively at3g57880 and at1g51570), using one or two sgRNA per gene."}],"acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (project 772103-BRIDGING to E.M.B.).","publication_status":"published","article_processing_charge":"Yes","oa":1,"author":[{"last_name":"Li","id":"922e68bb-1727-11ee-857c-966e8cc1b6c3","first_name":"Ziqiang","full_name":"Li, Ziqiang"},{"first_name":"Jennifer","full_name":"Huard, Jennifer","last_name":"Huard"},{"last_name":"Bayer","full_name":"Bayer, Emmanuelle M.","first_name":"Emmanuelle M."},{"first_name":"Valérie","full_name":"Wattelet-Boyer, Valérie","last_name":"Wattelet-Boyer"}],"ddc":["570"],"day":"05","issue":"13","pmid":1,"external_id":{"pmid":["39007160"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"original","publication":"Bio-protocol","file":[{"date_created":"2024-07-16T06:16:11Z","file_size":2896048,"date_updated":"2024-07-16T06:16:11Z","success":1,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_id":"17242","relation":"main_file","file_name":"2024_BioProtocol_Li.pdf","checksum":"c8671c0ad483da6407cb16cc3fef1990"}],"publication_identifier":{"eissn":["2331-8325"]},"scopus_import":"1","_id":"17233","oa_version":"Published Version","month":"07","volume":14,"quality_controlled":"1","date_updated":"2025-03-06T10:28:18Z","date_created":"2024-07-14T22:01:11Z","doi":"10.21769/BioProtoc.5029","type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":" 14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"LI Z, Huard J, Bayer EM, Wattelet-Boyer V. Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-protocol. 2024;14(13). doi:10.21769/BioProtoc.5029","ieee":"Z. LI, J. Huard, E. M. Bayer, and V. Wattelet-Boyer, “Versatile cloning strategy for efficient multigene editing in Arabidopsis,” Bio-protocol, vol. 14, no. 13. Bio-Protocol, 2024.","apa":"LI, Z., Huard, J., Bayer, E. M., & Wattelet-Boyer, V. (2024). Versatile cloning strategy for efficient multigene editing in Arabidopsis. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/BioProtoc.5029","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.","chicago":"LI, ZIQIANG, Jennifer Huard, Emmanuelle M. Bayer, and Valérie Wattelet-Boyer. “Versatile Cloning Strategy for Efficient Multigene Editing in Arabidopsis.” Bio-Protocol. Bio-Protocol, 2024. https://doi.org/10.21769/BioProtoc.5029.","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.” Bio-Protocol, vol. 14, no. 13, e5029, Bio-Protocol, 2024, doi:10.21769/BioProtoc.5029."},"date_published":"2024-07-05T00:00:00Z","article_number":"e5029","status":"public","file_date_updated":"2024-07-16T06:16:11Z","department":[{"_id":"MiSi"}],"publisher":"Bio-Protocol"},{"ddc":["520"],"day":"01","author":[{"last_name":"Wang","first_name":"Bingjie","full_name":"Wang, Bingjie"},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"first_name":"Anna","full_name":"De Graaff, Anna","last_name":"De Graaff"},{"last_name":"Brammer","first_name":"Gabriel B.","full_name":"Brammer, Gabriel B."},{"first_name":"Andrea","full_name":"Weibel, Andrea","last_name":"Weibel"},{"last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter","first_name":"Pieter"},{"first_name":"Josephine F.W.","full_name":"Baggen, Josephine F.W.","last_name":"Baggen"},{"last_name":"Suess","first_name":"Katherine A.","full_name":"Suess, Katherine A."},{"first_name":"Jenny E.","full_name":"Greene, Jenny E.","last_name":"Greene"},{"last_name":"Bezanson","full_name":"Bezanson, Rachel","first_name":"Rachel"},{"first_name":"Nikko J.","full_name":"Cleri, Nikko J.","last_name":"Cleri"},{"last_name":"Hirschmann","full_name":"Hirschmann, Michaela","first_name":"Michaela"},{"last_name":"Labbé","first_name":"Ivo","full_name":"Labbé, Ivo"},{"last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","first_name":"Jorryt J"},{"full_name":"Mcconachie, Ian","first_name":"Ian","last_name":"Mcconachie"},{"full_name":"Naidu, Rohan P.","first_name":"Rohan P.","last_name":"Naidu"},{"first_name":"Erica","full_name":"Nelson, Erica","last_name":"Nelson"},{"full_name":"Oesch, Pascal A.","first_name":"Pascal A.","last_name":"Oesch"},{"first_name":"David J.","full_name":"Setton, David J.","last_name":"Setton"},{"last_name":"Williams","full_name":"Williams, Christina C.","first_name":"Christina C."}],"issue":"1","article_processing_charge":"Yes","oa":1,"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).","publication_status":"published","title":"RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec","abstract":[{"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.","lang":"eng"}],"isi":1,"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2024-07-16T06:24:29Z","file_size":3273303,"date_created":"2024-07-16T06:24:29Z","creator":"dernst","success":1,"checksum":"bb1a6725586df12e745d091b5778bb2b","relation":"main_file","file_id":"17243","file_name":"2024_AstrophysicalJourn_Wang.pdf"}],"publication_identifier":{"eissn":["2041-8213"],"issn":["2041-8205"]},"publication":"Astrophysical Journal Letters","article_type":"original","year":"2024","language":[{"iso":"eng"}],"external_id":{"arxiv":["2405.01473"],"isi":["001257903200001"]},"type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3847/2041-8213/ad55f7","scopus_import":"1","quality_controlled":"1","volume":969,"date_updated":"2025-09-08T08:10:21Z","date_created":"2024-07-14T22:01:11Z","oa_version":"Published Version","_id":"17234","month":"07","publisher":"IOP Publishing","department":[{"_id":"JoMa"}],"file_date_updated":"2024-07-16T06:24:29Z","arxiv":1,"article_number":"L13","status":"public","DOAJ_listed":"1","intvolume":" 969","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-01T00:00:00Z","citation":{"ieee":"B. Wang et al., “RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec,” Astrophysical Journal Letters, vol. 969, no. 1. IOP Publishing, 2024.","apa":"Wang, B., Leja, J., De Graaff, A., Brammer, G. B., Weibel, A., Van Dokkum, P., … Williams, C. C. (2024). RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. IOP Publishing. https://doi.org/10.3847/2041-8213/ad55f7","ama":"Wang B, Leja J, De Graaff A, et al. RUBIES: Evolved stellar populations with extended formation histories at z ∼ 7-8 in candidate massive galaxies identified with JWST/NIRSpec. Astrophysical Journal Letters. 2024;969(1). doi:10.3847/2041-8213/ad55f7","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).","chicago":"Wang, Bingjie, Joel Leja, Anna De Graaff, Gabriel B. Brammer, Andrea Weibel, Pieter Van Dokkum, Josephine F.W. Baggen, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” Astrophysical Journal Letters. IOP Publishing, 2024. https://doi.org/10.3847/2041-8213/ad55f7.","mla":"Wang, Bingjie, et al. “RUBIES: Evolved Stellar Populations with Extended Formation Histories at z ∼ 7-8 in Candidate Massive Galaxies Identified with JWST/NIRSpec.” Astrophysical Journal Letters, vol. 969, no. 1, L13, IOP Publishing, 2024, doi:10.3847/2041-8213/ad55f7.","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."}}]