[{"file":[{"file_size":2114557,"file_name":"2021_RSCAdvances_Dar.pdf","relation":"main_file","creator":"asandaue","access_level":"open_access","content_type":"application/pdf","date_created":"2021-06-23T13:09:34Z","checksum":"cd582d67ace7151078e46b3a896871a9","file_id":"9596","success":1,"date_updated":"2021-06-23T13:09:34Z"}],"issue":"35","file_date_updated":"2021-06-23T13:09:34Z","department":[{"_id":"KiMo"}],"external_id":{"isi":["000665644000048"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"has_accepted_license":"1","publication_identifier":{"eissn":["2046-2069"]},"article_processing_charge":"No","citation":{"ama":"Dar MS, Akram KB, Sohail A, et al. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. <i>RSC Advances</i>. 2021;11(35):21702-21715. doi:<a href=\"https://doi.org/10.1039/d1ra03428f\">10.1039/d1ra03428f</a>","chicago":"Dar, M. S., Khush Bakhat Akram, Ayesha Sohail, Fatima Arif, Fatemeh Zabihi, Shengyuan Yang, Shamsa Munir, Meifang Zhu, M. Abid, and Muhammad Nauman. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” <i>RSC Advances</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d1ra03428f\">https://doi.org/10.1039/d1ra03428f</a>.","apa":"Dar, M. S., Akram, K. B., Sohail, A., Arif, F., Zabihi, F., Yang, S., … Nauman, M. (2021). Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. <i>RSC Advances</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d1ra03428f\">https://doi.org/10.1039/d1ra03428f</a>","ista":"Dar MS, Akram KB, Sohail A, Arif F, Zabihi F, Yang S, Munir S, Zhu M, Abid M, Nauman M. 2021. Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling. RSC Advances. 11(35), 21702–21715.","mla":"Dar, M. S., et al. “Heat Induction in Two-Dimensional Graphene–Fe3O4 Nanohybrids for Magnetic Hyperthermia Applications with Artificial Neural Network Modeling.” <i>RSC Advances</i>, vol. 11, no. 35, Royal Society of Chemistry, 2021, pp. 21702–15, doi:<a href=\"https://doi.org/10.1039/d1ra03428f\">10.1039/d1ra03428f</a>.","short":"M.S. Dar, K.B. Akram, A. Sohail, F. Arif, F. Zabihi, S. Yang, S. Munir, M. Zhu, M. Abid, M. Nauman, RSC Advances 11 (2021) 21702–21715.","ieee":"M. S. Dar <i>et al.</i>, “Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling,” <i>RSC Advances</i>, vol. 11, no. 35. Royal Society of Chemistry, pp. 21702–21715, 2021."},"language":[{"iso":"eng"}],"publication_status":"published","date_published":"2021-06-18T00:00:00Z","year":"2021","date_created":"2021-06-19T07:27:45Z","date_updated":"2024-10-21T06:02:02Z","intvolume":"        11","type":"journal_article","acknowledgement":"The research is funded by Higher Education Commission (HEC) Pakistan under start-up research grant program (SRGP) Project no. 2454.","isi":1,"_id":"9569","page":"21702-21715","publication":"RSC Advances","oa":1,"day":"18","publisher":"Royal Society of Chemistry","oa_version":"Published Version","volume":11,"article_type":"original","scopus_import":"1","month":"06","doi":"10.1039/d1ra03428f","author":[{"first_name":"M. S.","last_name":"Dar","full_name":"Dar, M. S."},{"last_name":"Akram","first_name":"Khush Bakhat","full_name":"Akram, Khush Bakhat"},{"last_name":"Sohail","first_name":"Ayesha","full_name":"Sohail, Ayesha"},{"last_name":"Arif","first_name":"Fatima","full_name":"Arif, Fatima"},{"full_name":"Zabihi, Fatemeh","first_name":"Fatemeh","last_name":"Zabihi"},{"full_name":"Yang, Shengyuan","first_name":"Shengyuan","last_name":"Yang"},{"full_name":"Munir, Shamsa","first_name":"Shamsa","last_name":"Munir"},{"last_name":"Zhu","first_name":"Meifang","full_name":"Zhu, Meifang"},{"full_name":"Abid, M.","first_name":"M.","last_name":"Abid"},{"orcid":"0000-0002-2111-4846","full_name":"Nauman, Muhammad","last_name":"Nauman","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad"}],"quality_controlled":"1","ddc":["540"],"status":"public","abstract":[{"text":"We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values.","lang":"eng"}]},{"author":[{"orcid":"0000-0003-1144-2763","full_name":"Puglia, Denise","last_name":"Puglia","id":"4D495994-AE37-11E9-AC72-31CAE5697425","first_name":"Denise"},{"full_name":"Martinez, E. A.","last_name":"Martinez","first_name":"E. A."},{"full_name":"Ménard, G. C.","first_name":"G. C.","last_name":"Ménard"},{"first_name":"A.","last_name":"Pöschl","full_name":"Pöschl, A."},{"full_name":"Gronin, S.","last_name":"Gronin","first_name":"S."},{"first_name":"G. C.","last_name":"Gardner","full_name":"Gardner, G. C."},{"full_name":"Kallaher, R.","first_name":"R.","last_name":"Kallaher"},{"last_name":"Manfra","first_name":"M. J.","full_name":"Manfra, M. J."},{"last_name":"Marcus","first_name":"C. M.","full_name":"Marcus, C. M."},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"},{"first_name":"L.","last_name":"Casparis","full_name":"Casparis, L."}],"doi":"10.1103/PhysRevB.103.235201","month":"06","scopus_import":"1","volume":103,"article_type":"original","oa_version":"Preprint","publisher":"American Physical Society","publication":"Physical Review B","oa":1,"day":"15","arxiv":1,"abstract":[{"lang":"eng","text":"We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity."}],"main_file_link":[{"url":"https://arxiv.org/abs/2006.01275","open_access":"1"}],"article_number":"235201","status":"public","quality_controlled":"1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"title":"Closing of the induced gap in a hybrid superconductor-semiconductor nanowire","external_id":{"arxiv":["2006.01275"],"isi":["000661512500002"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"AnHi"}],"issue":"23","_id":"9570","related_material":{"record":[{"relation":"research_data","status":"public","id":"13080"}]},"acknowledgement":"We acknowledge insightful discussions with K. Flensberg, E. B. Hansen, T. Karzig, R. Lutchyn, D. Pikulin, E. Prada, and R. Aguado. This work was supported by Microsoft Project Q and the Danmarks Grundforskningsfond. C.M.M. acknowledges support from the Villum Fonden. A.P.H. and L.C. contributed equally to this work.","isi":1,"intvolume":"       103","date_updated":"2025-07-10T12:01:53Z","type":"journal_article","date_published":"2021-06-15T00:00:00Z","year":"2021","date_created":"2021-06-20T22:01:33Z","citation":{"short":"D. Puglia, E.A. Martinez, G.C. Ménard, A. Pöschl, S. Gronin, G.C. Gardner, R. Kallaher, M.J. Manfra, C.M. Marcus, A.P. Higginbotham, L. Casparis, Physical Review B 103 (2021).","ieee":"D. Puglia <i>et al.</i>, “Closing of the induced gap in a hybrid superconductor-semiconductor nanowire,” <i>Physical Review B</i>, vol. 103, no. 23. American Physical Society, 2021.","apa":"Puglia, D., Martinez, E. A., Ménard, G. C., Pöschl, A., Gronin, S., Gardner, G. C., … Casparis, L. (2021). Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">https://doi.org/10.1103/PhysRevB.103.235201</a>","chicago":"Puglia, Denise, E. A. Martinez, G. C. Ménard, A. Pöschl, S. Gronin, G. C. Gardner, R. Kallaher, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” <i>Physical Review B</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">https://doi.org/10.1103/PhysRevB.103.235201</a>.","ama":"Puglia D, Martinez EA, Ménard GC, et al. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. <i>Physical Review B</i>. 2021;103(23). doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">10.1103/PhysRevB.103.235201</a>","mla":"Puglia, Denise, et al. “Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” <i>Physical Review B</i>, vol. 103, no. 23, 235201, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevB.103.235201\">10.1103/PhysRevB.103.235201</a>.","ista":"Puglia D, Martinez EA, Ménard GC, Pöschl A, Gronin S, Gardner GC, Kallaher R, Manfra MJ, Marcus CM, Higginbotham AP, Casparis L. 2021. Closing of the induced gap in a hybrid superconductor-semiconductor nanowire. Physical Review B. 103(23), 235201."},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_status":"published"},{"title":"NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["1533-7928"],"issn":["1532-4435"]},"file":[{"date_updated":"2021-06-23T07:09:41Z","success":1,"file_id":"9595","checksum":"6428aa8bcb67768b6949c99b55d5281d","date_created":"2021-06-23T07:09:41Z","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","relation":"main_file","file_name":"2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf","file_size":11237154}],"issue":"114","department":[{"_id":"DaAl"}],"file_date_updated":"2021-06-23T07:09:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1908.06077"]},"_id":"9571","page":"1−43","publication_status":"published","article_processing_charge":"No","citation":{"ieee":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization,” <i>Journal of Machine Learning Research</i>, vol. 22, no. 114. Journal of Machine Learning Research, p. 1−43, 2021.","short":"A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M. Roy, Journal of Machine Learning Research 22 (2021) 1−43.","mla":"Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” <i>Journal of Machine Learning Research</i>, vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43.","ista":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. Journal of Machine Learning Research. 22(114), 1−43.","apa":"Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A., &#38; Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","chicago":"Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel SGD via Nonuniform Quantization.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2021.","ama":"Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization. <i>Journal of Machine Learning Research</i>. 2021;22(114):1−43."},"language":[{"iso":"eng"}],"date_created":"2021-06-20T22:01:33Z","year":"2021","date_published":"2021-04-01T00:00:00Z","type":"journal_article","date_updated":"2025-07-10T12:01:54Z","intvolume":"        22","oa_version":"Published Version","corr_author":"1","volume":22,"article_type":"original","scopus_import":"1","month":"04","author":[{"first_name":"Ali","last_name":"Ramezani-Kebrya","full_name":"Ramezani-Kebrya, Ali"},{"full_name":"Faghri, Fartash","first_name":"Fartash","last_name":"Faghri"},{"full_name":"Markov, Ilya","last_name":"Markov","first_name":"Ilya"},{"full_name":"Aksenov, Vitalii","first_name":"Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","last_name":"Aksenov"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"},{"full_name":"Roy, Daniel M.","first_name":"Daniel M.","last_name":"Roy"}],"arxiv":1,"oa":1,"day":"01","publication":"Journal of Machine Learning Research","publisher":"Journal of Machine Learning Research","status":"public","main_file_link":[{"url":"https://www.jmlr.org/papers/v22/20-255.html","open_access":"1"}],"abstract":[{"lang":"eng","text":"As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods."}],"quality_controlled":"1","ddc":["000"]},{"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"title":"Massively winning configurations in the convex grabbing game on the plane","file":[{"relation":"main_file","file_name":"Convex-Grabbing-Game_CCCG_proc_version.pdf","file_size":381306,"content_type":"application/pdf","access_level":"open_access","creator":"mdvorak","file_id":"9616","success":1,"date_created":"2021-06-28T20:23:13Z","checksum":"45accb1de9b7e0e4bb2fbfe5fd3e6239","date_updated":"2021-06-28T20:23:13Z"},{"date_updated":"2021-08-12T10:57:21Z","file_id":"9902","success":1,"checksum":"9199cf18c65658553487458cc24d0ab2","date_created":"2021-08-12T10:57:21Z","content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"Convex-Grabbing-Game_FULL-VERSION.pdf","relation":"main_file","file_size":403645}],"external_id":{"arxiv":["2106.11247"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-08-12T10:57:21Z","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"_id":"9592","date_published":"2021-06-29T00:00:00Z","date_created":"2021-06-22T15:57:11Z","year":"2021","article_processing_charge":"No","citation":{"ieee":"M. Dvorak and S. Nicholson, “Massively winning configurations in the convex grabbing game on the plane,” in <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, Halifax, NS, Canada; Virtual, 2021.","short":"M. Dvorak, S. Nicholson, in:, Proceedings of the 33rd Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2021.","ama":"Dvorak M, Nicholson S. Massively winning configurations in the convex grabbing game on the plane. In: <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Canadian Conference on Computational Geometry; 2021.","chicago":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Canadian Conference on Computational Geometry, 2021.","apa":"Dvorak, M., &#38; Nicholson, S. (2021). Massively winning configurations in the convex grabbing game on the plane. In <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>. Halifax, NS, Canada; Virtual: Canadian Conference on Computational Geometry.","ista":"Dvorak M, Nicholson S. 2021. Massively winning configurations in the convex grabbing game on the plane. Proceedings of the 33rd Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry.","mla":"Dvorak, Martin, and Sara Nicholson. “Massively Winning Configurations in the Convex Grabbing Game on the Plane.” <i>Proceedings of the 33rd Canadian Conference on Computational Geometry</i>, Canadian Conference on Computational Geometry, 2021."},"language":[{"iso":"eng"}],"publication_status":"published","date_updated":"2025-05-14T11:23:45Z","type":"conference","oa_version":"Published Version","author":[{"id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin","last_name":"Dvorak","full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X"},{"last_name":"Nicholson","first_name":"Sara","full_name":"Nicholson, Sara"}],"month":"06","publication":"Proceedings of the 33rd Canadian Conference on Computational Geometry","day":"29","oa":1,"arxiv":1,"publisher":"Canadian Conference on Computational Geometry","conference":{"end_date":"2021-08-12","location":"Halifax, NS, Canada; Virtual","name":"CCCG: Canadian Conference on Computational Geometry","start_date":"2021-08-10"},"status":"public","keyword":["convex grabbing game","graph grabbing game","combinatorial game","convex geometry"],"abstract":[{"lang":"eng","text":"The convex grabbing game is a game where two players, Alice and Bob, alternate taking extremal points from the convex hull of a point set on the plane. Rational weights are given to the points. The goal of each player is to maximize the total weight over all points that they obtain. We restrict the setting to the case of binary weights. We show a construction of an arbitrarily large odd-sized point set that allows Bob to obtain almost 3/4 of the total weight. This construction answers a question asked by Matsumoto, Nakamigawa, and Sakuma in [Graphs and Combinatorics, 36/1 (2020)]. We also present an arbitrarily large even-sized point set where Bob can obtain the entirety of the total weight. Finally, we discuss conjectures about optimum moves in the convex grabbing game for both players in general."}],"ddc":["516"],"quality_controlled":"1"},{"oa_version":"Published Version","corr_author":"1","article_type":"original","volume":151,"scopus_import":"1","project":[{"grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science"}],"month":"06","author":[{"last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János","full_name":"Pach, János"},{"full_name":"Tomon, István","last_name":"Tomon","first_name":"István"}],"doi":"10.1016/j.jctb.2021.05.004","oa":1,"day":"09","publication":"Journal of Combinatorial Theory. Series B","publisher":"Elsevier","status":"public","abstract":[{"lang":"eng","text":"An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.\r\nA key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees."}],"quality_controlled":"1","ddc":["510"],"title":"Erdős-Hajnal-type results for monotone paths","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","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","publication_identifier":{"issn":["0095-8956"]},"file":[{"file_id":"9612","success":1,"date_created":"2021-06-28T13:33:23Z","checksum":"15fbc9064cd9d1c777ac0043b78c8f12","date_updated":"2021-06-28T13:33:23Z","file_name":"2021_JournalOfCombinatorialTheory_Pach.pdf","relation":"main_file","file_size":418168,"content_type":"application/pdf","creator":"asandaue","access_level":"open_access"}],"department":[{"_id":"HeEd"}],"file_date_updated":"2021-06-28T13:33:23Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000702280800002"]},"_id":"9602","page":"21-37","publication_status":"published","language":[{"iso":"eng"}],"citation":{"mla":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” <i>Journal of Combinatorial Theory. Series B</i>, vol. 151, Elsevier, 2021, pp. 21–37, doi:<a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">10.1016/j.jctb.2021.05.004</a>.","ista":"Pach J, Tomon I. 2021. Erdős-Hajnal-type results for monotone paths. Journal of Combinatorial Theory. Series B. 151, 21–37.","apa":"Pach, J., &#38; Tomon, I. (2021). Erdős-Hajnal-type results for monotone paths. <i>Journal of Combinatorial Theory. Series B</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">https://doi.org/10.1016/j.jctb.2021.05.004</a>","ama":"Pach J, Tomon I. Erdős-Hajnal-type results for monotone paths. <i>Journal of Combinatorial Theory Series B</i>. 2021;151:21-37. doi:<a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">10.1016/j.jctb.2021.05.004</a>","chicago":"Pach, János, and István Tomon. “Erdős-Hajnal-Type Results for Monotone Paths.” <i>Journal of Combinatorial Theory. Series B</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jctb.2021.05.004\">https://doi.org/10.1016/j.jctb.2021.05.004</a>.","ieee":"J. Pach and I. Tomon, “Erdős-Hajnal-type results for monotone paths,” <i>Journal of Combinatorial Theory. Series B</i>, vol. 151. Elsevier, pp. 21–37, 2021.","short":"J. Pach, I. Tomon, Journal of Combinatorial Theory. Series B 151 (2021) 21–37."},"article_processing_charge":"No","year":"2021","date_created":"2021-06-27T22:01:47Z","date_published":"2021-06-09T00:00:00Z","type":"journal_article","intvolume":"       151","date_updated":"2025-04-15T07:16:52Z","acknowledgement":"We would like to thank the anonymous referees for their useful comments and suggestions. János Pach is partially supported by Austrian Science Fund (FWF) grant Z 342-N31 and by ERC Advanced grant “GeoScape.” István Tomon is partially supported by Swiss National Science Foundation grant no. 200021_196965, and thanks the support of MIPT Moscow. Both authors are partially supported by The Russian Government in the framework of MegaGrant no. 075-15-2019-1926.","isi":1},{"article_number":"16","abstract":[{"text":"Generalizing Lee’s inductive argument for counting the cells of higher order Voronoi tessellations in ℝ² to ℝ³, we get precise relations in terms of Morse theoretic quantities for piecewise constant functions on planar arrangements. Specifically, we prove that for a generic set of n ≥ 5 points in ℝ³, the number of regions in the order-k Voronoi tessellation is N_{k-1} - binom(k,2)n + n, for 1 ≤ k ≤ n-1, in which N_{k-1} is the sum of Euler characteristics of these function’s first k-1 sublevel sets. We get similar expressions for the vertices, edges, and polygons of the order-k Voronoi tessellation.","lang":"eng"}],"status":"public","conference":{"start_date":"2021-06-07","name":"SoCG: International Symposium on Computational Geometry","location":"Online","end_date":"2021-06-11"},"ddc":["516"],"quality_controlled":"1","ec_funded":1,"doi":"10.4230/LIPIcs.SoCG.2021.16","author":[{"last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890"},{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832"},{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"last_name":"Saghafian","first_name":"Morteza","full_name":"Saghafian, Morteza"}],"month":"06","scopus_import":"1","volume":189,"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I4887","name":"Persistent Homology, Algorithms and Stochastic Geometry","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"}],"oa_version":"Published Version","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"oa":1,"day":"02","publication":"Leibniz International Proceedings in Informatics","_id":"9604","type":"conference","date_updated":"2025-07-10T12:01:56Z","intvolume":"       189","date_created":"2021-06-27T22:01:48Z","year":"2021","date_published":"2021-06-02T00:00:00Z","publication_status":"published","citation":{"ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory,” in <i>Leibniz International Proceedings in Informatics</i>, Online, 2021, vol. 189.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","mla":"Biswas, Ranita, et al. “Counting Cells of Order-k Voronoi Tessellations in ℝ<sup>3</sup> with Morse Theory.” <i>Leibniz International Proceedings in Informatics</i>, vol. 189, 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">10.4230/LIPIcs.SoCG.2021.16</a>.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2021. Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory. Leibniz International Proceedings in Informatics. SoCG: International Symposium on Computational Geometry, LIPIcs, vol. 189, 16.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2021). Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">https://doi.org/10.4230/LIPIcs.SoCG.2021.16</a>","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Counting Cells of Order-k Voronoi Tessellations in ℝ<sup>3</sup> with Morse Theory.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">https://doi.org/10.4230/LIPIcs.SoCG.2021.16</a>.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.16\">10.4230/LIPIcs.SoCG.2021.16</a>"},"language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771849"]},"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Counting cells of order-k voronoi tessellations in ℝ<sup>3</sup> with morse theory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-06-28T13:11:39Z","department":[{"_id":"HeEd"}],"file":[{"date_updated":"2021-06-28T13:11:39Z","success":1,"file_id":"9611","checksum":"22b11a719018b22ecba2471b51f2eb40","date_created":"2021-06-28T13:11:39Z","content_type":"application/pdf","creator":"asandaue","access_level":"open_access","file_name":"2021_LIPIcs_Biswas.pdf","relation":"main_file","file_size":727817}]},{"volume":189,"scopus_import":"1","oa_version":"Published Version","author":[{"last_name":"Corbet","first_name":"René","full_name":"Corbet, René"},{"full_name":"Kerber, Michael","first_name":"Michael","last_name":"Kerber"},{"first_name":"Michael","last_name":"Lesnick","full_name":"Lesnick, Michael"},{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.4230/LIPIcs.SoCG.2021.27","month":"06","oa":1,"day":"02","publication":"Leibniz International Proceedings in Informatics","arxiv":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"status":"public","conference":{"start_date":"2021-06-07","name":"SoCG: International Symposium on Computational Geometry","location":"Online","end_date":"2021-06-11"},"abstract":[{"text":"Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness. ","lang":"eng"}],"article_number":"27","ddc":["516"],"quality_controlled":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","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","title":"Computing the multicover bifiltration","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771849"]},"file":[{"date_updated":"2021-06-28T12:40:47Z","success":1,"file_id":"9610","checksum":"0de217501e7ba8b267d58deed0d51761","date_created":"2021-06-28T12:40:47Z","content_type":"application/pdf","creator":"cziletti","access_level":"open_access","file_name":"2021_LIPIcs_Corbet.pdf","relation":"main_file","file_size":"1367983"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2103.07823"]},"department":[{"_id":"HeEd"}],"file_date_updated":"2021-06-28T12:40:47Z","_id":"9605","date_created":"2021-06-27T22:01:49Z","year":"2021","date_published":"2021-06-02T00:00:00Z","publication_status":"published","article_processing_charge":"No","citation":{"mla":"Corbet, René, et al. “Computing the Multicover Bifiltration.” <i>Leibniz International Proceedings in Informatics</i>, vol. 189, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">10.4230/LIPIcs.SoCG.2021.27</a>.","ista":"Corbet R, Kerber M, Lesnick M, Osang GF. 2021. Computing the multicover bifiltration. Leibniz International Proceedings in Informatics. SoCG: International Symposium on Computational Geometry, LIPIcs, vol. 189, 27.","apa":"Corbet, R., Kerber, M., Lesnick, M., &#38; Osang, G. F. (2021). Computing the multicover bifiltration. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 189). Online: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">https://doi.org/10.4230/LIPIcs.SoCG.2021.27</a>","chicago":"Corbet, René, Michael Kerber, Michael Lesnick, and Georg F Osang. “Computing the Multicover Bifiltration.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">https://doi.org/10.4230/LIPIcs.SoCG.2021.27</a>.","ama":"Corbet R, Kerber M, Lesnick M, Osang GF. Computing the multicover bifiltration. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.27\">10.4230/LIPIcs.SoCG.2021.27</a>","ieee":"R. Corbet, M. Kerber, M. Lesnick, and G. F. Osang, “Computing the multicover bifiltration,” in <i>Leibniz International Proceedings in Informatics</i>, Online, 2021, vol. 189.","short":"R. Corbet, M. Kerber, M. Lesnick, G.F. Osang, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021."},"language":[{"iso":"eng"}],"acknowledgement":"The authors want to thank the reviewers for many helpful comments and suggestions.","related_material":{"record":[{"id":"12709","status":"public","relation":"later_version"}],"link":[{"url":"https://arxiv.org/abs/2103.07823","relation":"extended_version"}]},"type":"conference","date_updated":"2025-07-10T12:01:57Z","intvolume":"       189"},{"quality_controlled":"1","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06491"}],"abstract":[{"text":"Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results.","lang":"eng"}],"article_number":"L061303","oa":1,"day":"01","publication":"Physical Review A","arxiv":1,"publisher":"American Physical Society","volume":103,"article_type":"letter_note","scopus_import":"1","oa_version":"Preprint","doi":"10.1103/PhysRevA.103.L061303","author":[{"last_name":"Tononi","first_name":"A.","full_name":"Tononi, A."},{"orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","last_name":"Cappellaro"},{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"full_name":"Salasnich, L.","last_name":"Salasnich","first_name":"L."}],"month":"06","date_created":"2021-06-27T22:01:49Z","year":"2021","date_published":"2021-06-01T00:00:00Z","publication_status":"published","citation":{"short":"A. Tononi, A. Cappellaro, G. Bighin, L. Salasnich, Physical Review A 103 (2021).","ieee":"A. Tononi, A. Cappellaro, G. Bighin, and L. Salasnich, “Propagation of first and second sound in a two-dimensional Fermi superfluid,” <i>Physical Review A</i>, vol. 103, no. 6. American Physical Society, 2021.","ista":"Tononi A, Cappellaro A, Bighin G, Salasnich L. 2021. Propagation of first and second sound in a two-dimensional Fermi superfluid. Physical Review A. 103(6), L061303.","mla":"Tononi, A., et al. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” <i>Physical Review A</i>, vol. 103, no. 6, L061303, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">10.1103/PhysRevA.103.L061303</a>.","ama":"Tononi A, Cappellaro A, Bighin G, Salasnich L. Propagation of first and second sound in a two-dimensional Fermi superfluid. <i>Physical Review A</i>. 2021;103(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">10.1103/PhysRevA.103.L061303</a>","chicago":"Tononi, A., Alberto Cappellaro, Giacomo Bighin, and L. Salasnich. “Propagation of First and Second Sound in a Two-Dimensional Fermi Superfluid.” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">https://doi.org/10.1103/PhysRevA.103.L061303</a>.","apa":"Tononi, A., Cappellaro, A., Bighin, G., &#38; Salasnich, L. (2021). Propagation of first and second sound in a two-dimensional Fermi superfluid. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.103.L061303\">https://doi.org/10.1103/PhysRevA.103.L061303</a>"},"language":[{"iso":"eng"}],"article_processing_charge":"No","isi":1,"acknowledgement":"G.B. acknowledges support from the Austrian Science Fund (FWF), under Project No. M2641-N27. This work was\r\npartially supported by the University of Padua, BIRD project “Superfluid properties of Fermi gases in optical potentials.”\r\nThe authors thank Miki Ota, Tomoki Ozawa, Sandro Stringari, Tilman Enss, Hauke Biss, Henning Moritz, and Nicolò Defenu for fruitful discussions. The authors thank Henning Moritz and Markus Bohlen for providing their experimental\r\ndata.","type":"journal_article","intvolume":"       103","date_updated":"2025-07-10T12:01:58Z","_id":"9606","issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2009.06491"],"isi":["000662296700014"]},"department":[{"_id":"MiLe"}],"title":"Propagation of first and second sound in a two-dimensional Fermi superfluid","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]}},{"_id":"9618","page":"1355-1359","publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"ista":"Bluvstein D, Omran A, Levine H, Keesling A, Semeghini G, Ebadi S, Wang TT, Michailidis A, Maskara N, Ho WW, Choi S, Serbyn M, Greiner M, Vuletić V, Lukin MD. 2021. Controlling quantum many-body dynamics in driven Rydberg atom arrays. Science. 371(6536), 1355–1359.","mla":"Bluvstein, D., et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” <i>Science</i>, vol. 371, no. 6536, AAAS, 2021, pp. 1355–59, doi:<a href=\"https://doi.org/10.1126/science.abg2530\">10.1126/science.abg2530</a>.","ama":"Bluvstein D, Omran A, Levine H, et al. Controlling quantum many-body dynamics in driven Rydberg atom arrays. <i>Science</i>. 2021;371(6536):1355-1359. doi:<a href=\"https://doi.org/10.1126/science.abg2530\">10.1126/science.abg2530</a>","chicago":"Bluvstein, D., A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T. T. Wang, et al. “Controlling Quantum Many-Body Dynamics in Driven Rydberg Atom Arrays.” <i>Science</i>. AAAS, 2021. <a href=\"https://doi.org/10.1126/science.abg2530\">https://doi.org/10.1126/science.abg2530</a>.","apa":"Bluvstein, D., Omran, A., Levine, H., Keesling, A., Semeghini, G., Ebadi, S., … Lukin, M. D. (2021). Controlling quantum many-body dynamics in driven Rydberg atom arrays. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.abg2530\">https://doi.org/10.1126/science.abg2530</a>","ieee":"D. Bluvstein <i>et al.</i>, “Controlling quantum many-body dynamics in driven Rydberg atom arrays,” <i>Science</i>, vol. 371, no. 6536. AAAS, pp. 1355–1359, 2021.","short":"D. Bluvstein, A. Omran, H. Levine, A. Keesling, G. Semeghini, S. Ebadi, T.T. Wang, A. Michailidis, N. Maskara, W.W. Ho, S. Choi, M. Serbyn, M. Greiner, V. Vuletić, M.D. Lukin, Science 371 (2021) 1355–1359."},"date_created":"2021-06-29T12:04:05Z","year":"2021","date_published":"2021-03-26T00:00:00Z","type":"journal_article","intvolume":"       371","date_updated":"2025-04-14T07:52:05Z","isi":1,"acknowledgement":"We thank many members of the Harvard AMO community, particularly E. Urbach, S. Dakoulas, and J. Doyle for their efforts enabling safe and productive operation of our laboratories during 2020. We thank D. Abanin, I. Cong, F. Machado, H. Pichler, N. Yao, B. Ye, and H. Zhou for stimulating discussions. Funding: We acknowledge financial support from the Center for Ultracold Atoms, the National Science Foundation, the Vannevar Bush Faculty Fellowship, the U.S. Department of Energy (LBNL QSA Center and grant no. DE-SC0021013), the Office of Naval Research, the Army Research Office MURI, the DARPA DRINQS program (grant no. D18AC00033), and the DARPA ONISQ program (grant no. W911NF2010021). The authors acknowledge support from the NSF Graduate Research Fellowship Program (grant DGE1745303) and The Fannie and John Hertz Foundation (D.B.); a National Defense Science and Engineering Graduate (NDSEG) fellowship (H.L.); a fellowship from the Max Planck/Harvard Research Center for Quantum Optics (G.S.); Gordon College (T.T.W.); the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 850899) (A.A.M. and M.S.); a Department of Energy Computational Science Graduate Fellowship under award number DE-SC0021110 (N.M.); the Moore Foundation’s EPiQS Initiative grant no. GBMF4306, the NUS Development grant AY2019/2020, and the Stanford Institute of Theoretical Physics (W.W.H.); and the Miller Institute for Basic Research in Science (S.C.). Author contributions: D.B., A.O., H.L., A.K., G.S., S.E., and T.T.W. contributed to the building of the experimental setup, performed the measurements, and analyzed the data. A.A.M., N.M., W.W.H., S.C., and M.S. performed theoretical analysis. All work was supervised by M.G., V.V., and M.D.L. All authors discussed the results and contributed to the manuscript. Competing interests: M.G., V.V., and M.D.L. are co-founders and shareholders of QuEra Computing. A.O. is a shareholder of QuEra Computing. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and the supplementary materials.","title":"Controlling quantum many-body dynamics in driven Rydberg atom arrays","has_accepted_license":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"issue":"6536","file":[{"date_updated":"2021-09-23T14:00:05Z","date_created":"2021-09-23T14:00:05Z","checksum":"0b356fd10ab9bb95177d4c047d4e9c1a","file_id":"10040","success":1,"access_level":"open_access","creator":"patrickd","content_type":"application/pdf","file_size":3671159,"relation":"main_file","file_name":"scars_subharmonic_combined_manuscript_2_11_2021 (2)-1.pdf"}],"department":[{"_id":"MaSe"}],"file_date_updated":"2021-09-23T14:00:05Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["33632894"],"arxiv":["2012.12276"],"isi":["000636043400048"]},"keyword":["Multidisciplinary"],"status":"public","abstract":[{"text":"The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science.","lang":"eng"}],"ec_funded":1,"quality_controlled":"1","ddc":["539"],"oa_version":"Preprint","volume":371,"article_type":"original","scopus_import":"1","pmid":1,"project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"month":"03","author":[{"first_name":"D.","last_name":"Bluvstein","full_name":"Bluvstein, D."},{"last_name":"Omran","first_name":"A.","full_name":"Omran, A."},{"first_name":"H.","last_name":"Levine","full_name":"Levine, H."},{"last_name":"Keesling","first_name":"A.","full_name":"Keesling, A."},{"last_name":"Semeghini","first_name":"G.","full_name":"Semeghini, G."},{"full_name":"Ebadi, S.","last_name":"Ebadi","first_name":"S."},{"full_name":"Wang, T. T.","last_name":"Wang","first_name":"T. T."},{"full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"N.","last_name":"Maskara","full_name":"Maskara, N."},{"last_name":"Ho","first_name":"W. W.","full_name":"Ho, W. W."},{"full_name":"Choi, S.","first_name":"S.","last_name":"Choi"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"full_name":"Greiner, M.","last_name":"Greiner","first_name":"M."},{"full_name":"Vuletić, V.","first_name":"V.","last_name":"Vuletić"},{"full_name":"Lukin, M. D.","last_name":"Lukin","first_name":"M. D."}],"doi":"10.1126/science.abg2530","arxiv":1,"day":"26","oa":1,"publication":"Science","publisher":"AAAS"},{"type":"conference","intvolume":"     12810","date_updated":"2025-09-10T10:04:46Z","acknowledgement":"Peter Davies is supported by the European Union’s Horizon2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","isi":1,"publication_status":"published","article_processing_charge":"No","citation":{"short":"D.-A. Alistarh, P. Davies, in:, Structural Information and Communication Complexity, Springer Nature, 2021, pp. 3–12.","ieee":"D.-A. Alistarh and P. Davies, “Collecting coupons is faster with friends,” in <i>Structural Information and Communication Complexity</i>, Wrocław, Poland, 2021, vol. 12810, pp. 3–12.","chicago":"Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with Friends.” In <i>Structural Information and Communication Complexity</i>, 12810:3–12. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">https://doi.org/10.1007/978-3-030-79527-6_1</a>.","ama":"Alistarh D-A, Davies P. Collecting coupons is faster with friends. In: <i>Structural Information and Communication Complexity</i>. Vol 12810. Springer Nature; 2021:3-12. doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">10.1007/978-3-030-79527-6_1</a>","apa":"Alistarh, D.-A., &#38; Davies, P. (2021). Collecting coupons is faster with friends. In <i>Structural Information and Communication Complexity</i> (Vol. 12810, pp. 3–12). Wrocław, Poland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">https://doi.org/10.1007/978-3-030-79527-6_1</a>","ista":"Alistarh D-A, Davies P. 2021. Collecting coupons is faster with friends. Structural Information and Communication Complexity. SIROCCO: International Colloquium on Structural Information and Communication Complexity, LNCS, vol. 12810, 3–12.","mla":"Alistarh, Dan-Adrian, and Peter Davies. “Collecting Coupons Is Faster with Friends.” <i>Structural Information and Communication Complexity</i>, vol. 12810, Springer Nature, 2021, pp. 3–12, doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_1\">10.1007/978-3-030-79527-6_1</a>."},"language":[{"iso":"eng"}],"date_created":"2021-07-01T11:04:43Z","year":"2021","date_published":"2021-06-20T00:00:00Z","_id":"9620","page":"3-12","department":[{"_id":"DaAl"}],"file_date_updated":"2021-07-01T11:21:40Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001292788400001"]},"file":[{"access_level":"open_access","creator":"pdavies","content_type":"application/pdf","file_size":319728,"relation":"main_file","file_name":"Population_Coupon_Collector.pdf","date_updated":"2021-07-01T11:21:40Z","checksum":"fe37fb9af3f5016c1084af9d6e7109bd","date_created":"2021-07-01T11:21:40Z","file_id":"9621"}],"publication_identifier":{"isbn":["9783030795269"],"eisbn":["9783030795276"],"eissn":["1611-3349"],"issn":["0302-9743"]},"title":"Collecting coupons is faster with friends","has_accepted_license":"1","quality_controlled":"1","ddc":["000"],"ec_funded":1,"abstract":[{"text":"In this note, we introduce a distributed twist on the classic coupon collector problem: a set of m collectors wish to each obtain a set of n coupons; for this, they can each sample coupons uniformly at random, but can also meet in pairwise interactions, during which they can exchange coupons. By doing so, they hope to reduce the number of coupons that must be sampled by each collector in order to obtain a full set. This extension is natural when considering real-world manifestations of the coupon collector phenomenon, and has been remarked upon and studied empirically (Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019).\r\n\r\nWe provide the first theoretical analysis for such a scenario. We find that “coupon collecting with friends” can indeed significantly reduce the number of coupons each collector must sample, and raises interesting connections to the more traditional variants of the problem. While our analysis is in most cases asymptotically tight, there are several open questions raised, regarding finer-grained analysis of both “coupon collecting with friends,” and of a long-studied variant of the original problem in which a collector requires multiple full sets of coupons.","lang":"eng"}],"status":"public","conference":{"end_date":"2021-07-01","location":"Wrocław, Poland","start_date":"2021-06-28","name":"SIROCCO: International Colloquium on Structural Information and Communication Complexity"},"alternative_title":["LNCS"],"publisher":"Springer Nature","oa":1,"day":"20","publication":"Structural Information and Communication Complexity","month":"06","doi":"10.1007/978-3-030-79527-6_1","author":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Peter","id":"11396234-BB50-11E9-B24C-90FCE5697425","last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter"}],"oa_version":"Preprint","volume":12810,"scopus_import":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}]},{"corr_author":"1","oa_version":"None","volume":20,"article_type":"original","scopus_import":"1","month":"06","doi":"10.1016/j.mtphys.2021.100452","author":[{"full_name":"Su, Lizhong","first_name":"Lizhong","last_name":"Su"},{"last_name":"Hong","first_name":"Tao","full_name":"Hong, Tao"},{"full_name":"Wang, Dongyang","last_name":"Wang","first_name":"Dongyang"},{"last_name":"Wang","first_name":"Sining","full_name":"Wang, Sining"},{"first_name":"Bingchao","last_name":"Qin","full_name":"Qin, Bingchao"},{"full_name":"Zhang, Mengmeng","first_name":"Mengmeng","last_name":"Zhang"},{"full_name":"Gao, Xiang","last_name":"Gao","first_name":"Xiang"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"}],"day":"03","publication":"Materials Today Physics","publisher":"Elsevier","status":"public","abstract":[{"text":"SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors.","lang":"eng"}],"article_number":"100452","quality_controlled":"1","title":"Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation","publication_identifier":{"eissn":["2542-5293"]},"department":[{"_id":"MaIb"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000703159600010"]},"_id":"9626","publication_status":"published","citation":{"short":"L. Su, T. Hong, D. Wang, S. Wang, B. Qin, M. Zhang, X. Gao, C. Chang, L.D. Zhao, Materials Today Physics 20 (2021).","ieee":"L. Su <i>et al.</i>, “Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation,” <i>Materials Today Physics</i>, vol. 20. Elsevier, 2021.","mla":"Su, Lizhong, et al. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” <i>Materials Today Physics</i>, vol. 20, 100452, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">10.1016/j.mtphys.2021.100452</a>.","ista":"Su L, Hong T, Wang D, Wang S, Qin B, Zhang M, Gao X, Chang C, Zhao LD. 2021. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. Materials Today Physics. 20, 100452.","apa":"Su, L., Hong, T., Wang, D., Wang, S., Qin, B., Zhang, M., … Zhao, L. D. (2021). Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. <i>Materials Today Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">https://doi.org/10.1016/j.mtphys.2021.100452</a>","ama":"Su L, Hong T, Wang D, et al. Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation. <i>Materials Today Physics</i>. 2021;20. doi:<a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">10.1016/j.mtphys.2021.100452</a>","chicago":"Su, Lizhong, Tao Hong, Dongyang Wang, Sining Wang, Bingchao Qin, Mengmeng Zhang, Xiang Gao, Cheng Chang, and Li Dong Zhao. “Realizing High Doping Efficiency and Thermoelectric Performance in N-Type SnSe Polycrystals via Bandgap Engineering and Vacancy Compensation.” <i>Materials Today Physics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.mtphys.2021.100452\">https://doi.org/10.1016/j.mtphys.2021.100452</a>."},"article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2021","date_created":"2021-07-04T22:01:24Z","date_published":"2021-06-03T00:00:00Z","type":"journal_article","date_updated":"2024-10-09T21:00:40Z","intvolume":"        20","acknowledgement":"This work was supported by National Natural Science Foundation of China (51772012), National Key Research and Development Program of China (2018YFA0702100 and 2018YFB0703600), the Beijing Natural Science Foundation (JQ18004). This work was also supported by Lise Meitner Project (M2889-N) and the National Postdoctoral Program for Innovative Talents (BX20200028). L.D.Z. appreciates the support of the High Performance Computing (HPC) resources at Beihang University, the National Science Fund for Distinguished Young Scholars (51925101), and center for High Pressure Science and Technology Advanced Research (HPSTAR) for SEM measurements.","isi":1},{"isi":1,"acknowledgement":"M. W. gratefully acknowledges financial support by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes). T.W. thanks PAO Gazprom Neft, the Euler International Mathematical Institute in Saint Petersburg and ORISA GmbH for their financial support in the form of scholarships during his Master's and Bachelor's studies respectively. The authors want to thank Mark Malamud for pointing out the reference [1] to them. This work was supported by the Ministry of Science and Higher Education of the Russian Federation, agreement No 075-15-2019-1619.","type":"journal_article","intvolume":"        64","date_updated":"2024-10-09T21:05:06Z","date_created":"2021-07-04T22:01:24Z","year":"2021","date_published":"2021-08-01T00:00:00Z","publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"chicago":"Lenz, Daniel, Timon Weinmann, and Melchior Wirth. “Self-Adjoint Extensions of Bipartite Hamiltonians.” <i>Proceedings of the Edinburgh Mathematical Society</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/S0013091521000080\">https://doi.org/10.1017/S0013091521000080</a>.","ama":"Lenz D, Weinmann T, Wirth M. Self-adjoint extensions of bipartite Hamiltonians. <i>Proceedings of the Edinburgh Mathematical Society</i>. 2021;64(3):443-447. doi:<a href=\"https://doi.org/10.1017/S0013091521000080\">10.1017/S0013091521000080</a>","apa":"Lenz, D., Weinmann, T., &#38; Wirth, M. (2021). Self-adjoint extensions of bipartite Hamiltonians. <i>Proceedings of the Edinburgh Mathematical Society</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0013091521000080\">https://doi.org/10.1017/S0013091521000080</a>","ista":"Lenz D, Weinmann T, Wirth M. 2021. Self-adjoint extensions of bipartite Hamiltonians. Proceedings of the Edinburgh Mathematical Society. 64(3), 443–447.","mla":"Lenz, Daniel, et al. “Self-Adjoint Extensions of Bipartite Hamiltonians.” <i>Proceedings of the Edinburgh Mathematical Society</i>, vol. 64, no. 3, Cambridge University Press, 2021, pp. 443–47, doi:<a href=\"https://doi.org/10.1017/S0013091521000080\">10.1017/S0013091521000080</a>.","short":"D. Lenz, T. Weinmann, M. Wirth, Proceedings of the Edinburgh Mathematical Society 64 (2021) 443–447.","ieee":"D. Lenz, T. Weinmann, and M. Wirth, “Self-adjoint extensions of bipartite Hamiltonians,” <i>Proceedings of the Edinburgh Mathematical Society</i>, vol. 64, no. 3. Cambridge University Press, pp. 443–447, 2021."},"page":"443-447","_id":"9627","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000721363700003"],"arxiv":["1912.03670"]},"department":[{"_id":"JaMa"}],"issue":"3","publication_identifier":{"eissn":["1464-3839"],"issn":["0013-0915"]},"title":"Self-adjoint extensions of bipartite Hamiltonians","quality_controlled":"1","abstract":[{"text":"We compute the deficiency spaces of operators of the form 𝐻𝐴⊗̂ 𝐼+𝐼⊗̂ 𝐻𝐵, for symmetric 𝐻𝐴 and self-adjoint 𝐻𝐵. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of 𝐻𝐵 having discrete, non-degenerate spectrum.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1017/S0013091521000080","open_access":"1"}],"status":"public","publisher":"Cambridge University Press","day":"01","oa":1,"publication":"Proceedings of the Edinburgh Mathematical Society","arxiv":1,"doi":"10.1017/S0013091521000080","author":[{"first_name":"Daniel","last_name":"Lenz","full_name":"Lenz, Daniel"},{"full_name":"Weinmann, Timon","first_name":"Timon","last_name":"Weinmann"},{"full_name":"Wirth, Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","last_name":"Wirth"}],"month":"08","article_type":"original","volume":64,"scopus_import":"1","oa_version":"Published Version","corr_author":"1"},{"type":"journal_article","date_updated":"2025-04-14T07:52:26Z","intvolume":"        23","acknowledgement":"We acknowledge the members of the Lennon-Duménil laboratory for sharing the mouse line of Myh9-GFP. We are grateful to the members of the Liberali laboratory and the FMI facilities for their support. We thank E. Tagliavini for IT support; L. Gelman for assistance and training; S. Bichet and A. Bogucki for helping with histology of mouse tissues; H. Kohler for fluorescence-activated cell sorting; G. Q. G. de Medeiros for maintenance of light-sheet microscopy; M. G. Stadler for scRNA-seq analysis; G. Gay for discussions on the 3D vertex model; the members of the Liberali laboratory, C. P. Heisenberg and C. Tsiairis for reading and providing feedback on the manuscript. Funding: Q.Y. is supported by a Postdoc fellowship from Peter und Taul Engelhorn Stiftung (PTES). This work received funding from the European Research Council (ERC) under the EU Horizon 2020 research and Innovation Programme Grant Agreement no. 758617 (to P.L.), the Swiss National Foundation (SNF) (POOP3_157531, to P.L.) and from the ERC under the EU Horizon 2020 Research and Innovation Program Grant Agreements 851288 (to E.H.) and the Austrian Science Fund (FWF) (P31639, to E.H.).","isi":1,"publication_status":"published","citation":{"ieee":"Q. Yang <i>et al.</i>, “Cell fate coordinates mechano-osmotic forces in intestinal crypt formation,” <i>Nature Cell Biology</i>, vol. 23. Springer Nature, pp. 733–744, 2021.","short":"Q. Yang, S. Xue, C.J. Chan, M. Rempfler, D. Vischi, F. Maurer-Gutierrez, T. Hiiragi, E.B. Hannezo, P. Liberali, Nature Cell Biology 23 (2021) 733–744.","ama":"Yang Q, Xue S, Chan CJ, et al. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. <i>Nature Cell Biology</i>. 2021;23:733–744. doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>","chicago":"Yang, Qiutan, Shi-lei Xue, Chii Jou Chan, Markus Rempfler, Dario Vischi, Francisca Maurer-Gutierrez, Takashi Hiiragi, Edouard B Hannezo, and Prisca Liberali. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” <i>Nature Cell Biology</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>.","apa":"Yang, Q., Xue, S., Chan, C. J., Rempfler, M., Vischi, D., Maurer-Gutierrez, F., … Liberali, P. (2021). Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-021-00700-2\">https://doi.org/10.1038/s41556-021-00700-2</a>","ista":"Yang Q, Xue S, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo EB, Liberali P. 2021. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nature Cell Biology. 23, 733–744.","mla":"Yang, Qiutan, et al. “Cell Fate Coordinates Mechano-Osmotic Forces in Intestinal Crypt Formation.” <i>Nature Cell Biology</i>, vol. 23, Springer Nature, 2021, pp. 733–744, doi:<a href=\"https://doi.org/10.1038/s41556-021-00700-2\">10.1038/s41556-021-00700-2</a>."},"article_processing_charge":"No","language":[{"iso":"eng"}],"date_created":"2021-07-04T22:01:25Z","year":"2021","date_published":"2021-06-21T00:00:00Z","_id":"9629","page":"733–744","department":[{"_id":"EdHa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000664016300003"],"pmid":["34155381"]},"publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","quality_controlled":"1","ec_funded":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.13.094359","open_access":"1"}],"abstract":[{"lang":"eng","text":"Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis."}],"status":"public","publisher":"Springer Nature","day":"21","oa":1,"publication":"Nature Cell Biology","month":"06","author":[{"full_name":"Yang, Qiutan","first_name":"Qiutan","last_name":"Yang"},{"first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","last_name":"Xue","full_name":"Xue, Shi-lei"},{"first_name":"Chii Jou","last_name":"Chan","full_name":"Chan, Chii Jou"},{"full_name":"Rempfler, Markus","last_name":"Rempfler","first_name":"Markus"},{"full_name":"Vischi, Dario","last_name":"Vischi","first_name":"Dario"},{"first_name":"Francisca","last_name":"Maurer-Gutierrez","full_name":"Maurer-Gutierrez, Francisca"},{"full_name":"Hiiragi, Takashi","first_name":"Takashi","last_name":"Hiiragi"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Liberali","first_name":"Prisca","full_name":"Liberali, Prisca"}],"doi":"10.1038/s41556-021-00700-2","corr_author":"1","oa_version":"Preprint","scopus_import":"1","article_type":"original","volume":23,"project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"P31639","name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"pmid":1},{"related_material":{"record":[{"id":"10029","relation":"used_in_publication","status":"public"}]},"date_updated":"2025-04-15T06:54:43Z","type":"research_data","date_published":"2021-01-01T00:00:00Z","date_created":"2021-07-07T20:43:10Z","year":"2021","citation":{"mla":"Higginbotham, Andrew P. <i>Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.”</i> Institute of Science and Technology Austria, 2021.","ista":"Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.","apa":"Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.","ama":"Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021.","chicago":"Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021.","short":"A.P. Higginbotham, (2021).","ieee":"A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","status":"public","_id":"9636","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2021-07-07T20:37:28Z","department":[{"_id":"AnHi"}],"file":[{"success":1,"file_id":"9637","checksum":"18e90687ec7bbd75f8bfea4d8293fb30","date_created":"2021-07-07T20:37:28Z","date_updated":"2021-07-07T20:37:28Z","file_name":"figures_data.zip","relation":"main_file","file_size":3345244,"content_type":"application/zip","creator":"ahigginb","access_level":"open_access"}],"oa":1,"author":[{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","last_name":"Higginbotham"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"has_accepted_license":"1","oa_version":"Submitted Version","title":"Data for \"Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid\""},{"file":[{"access_level":"open_access","creator":"cziletti","content_type":"application/pdf","file_size":1994793,"relation":"main_file","file_name":"2021_NeurobLearnMemory_Fredes.pdf","date_updated":"2021-07-19T13:46:06Z","date_created":"2021-07-19T13:46:06Z","checksum":"8e8298a9e8c7df146ad23f32c2a63929","file_id":"9694","success":1}],"external_id":{"pmid":["34214666"],"isi":["000677694900004"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RySh"}],"file_date_updated":"2021-07-19T13:46:06Z","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"},"title":"The role of hippocampal mossy cells in novelty detection","publication_identifier":{"issn":["1074-7427"],"eissn":["1095-9564"]},"date_published":"2021-06-30T00:00:00Z","year":"2021","date_created":"2021-07-11T22:01:16Z","language":[{"iso":"eng"}],"citation":{"mla":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>, vol. 183, 107486, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>.","ista":"Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486.","apa":"Fredes, F., &#38; Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>","ama":"Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. <i>Neurobiology of Learning and Memory</i>. 2021;183. doi:<a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">10.1016/j.nlm.2021.107486</a>","chicago":"Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” <i>Neurobiology of Learning and Memory</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.nlm.2021.107486\">https://doi.org/10.1016/j.nlm.2021.107486</a>.","short":"F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021).","ieee":"F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” <i>Neurobiology of Learning and Memory</i>, vol. 183. Elsevier, 2021."},"article_processing_charge":"No","publication_status":"published","acknowledgement":"This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto.","isi":1,"intvolume":"       183","date_updated":"2025-07-10T12:02:00Z","type":"journal_article","_id":"9641","publication":"Neurobiology of Learning and Memory","day":"30","oa":1,"publisher":"Elsevier","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"}],"pmid":1,"article_type":"original","volume":183,"scopus_import":"1","oa_version":"Published Version","author":[{"first_name":"Felipe","last_name":"Fredes","full_name":"Fredes, Felipe"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"}],"doi":"10.1016/j.nlm.2021.107486","month":"06","ec_funded":1,"ddc":["610"],"quality_controlled":"1","status":"public","article_number":"107486","abstract":[{"lang":"eng","text":"At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000723661700050"]},"department":[{"_id":"KrCh"}],"title":"Polynomial reachability witnesses via Stellensätze","publication_identifier":{"isbn":["9781450383912"]},"date_created":"2021-07-11T22:01:17Z","year":"2021","date_published":"2021-06-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","citation":{"ama":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:772-787. doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>","chicago":"Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 772–87. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>.","apa":"Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., &#38; Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 772–787). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454076\">https://doi.org/10.1145/3453483.3454076</a>","ista":"Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.","mla":"Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 772–87, doi:<a href=\"https://doi.org/10.1145/3453483.3454076\">10.1145/3453483.3454076</a>.","ieee":"A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 772–787.","short":"A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787."},"language":[{"iso":"eng"}],"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW).","isi":1,"type":"conference","date_updated":"2025-07-10T12:02:00Z","page":"772-787","_id":"9645","oa":1,"day":"01","publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","publisher":"Association for Computing Machinery","scopus_import":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"oa_version":"Submitted Version","doi":"10.1145/3453483.3454076","author":[{"first_name":"Ali","last_name":"Asadi","full_name":"Asadi, Ali"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"},{"full_name":"Mahdavi, Mohammad","last_name":"Mahdavi","first_name":"Mohammad"}],"month":"06","ec_funded":1,"quality_controlled":"1","status":"public","conference":{"start_date":"2021-06-20","name":"PLDI: Programming Language Design and Implementation","location":"Online","end_date":"2021-06-26"},"abstract":[{"text":"We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03183862/"}]},{"year":"2021","date_created":"2021-07-11T22:01:18Z","date_published":"2021-06-01T00:00:00Z","publication_status":"published","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"ieee":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Online, 2021, pp. 1171–1186.","short":"J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186.","ista":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.","mla":"Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2021, pp. 1171–86, doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>.","ama":"Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2021:1171-1186. doi:<a href=\"https://doi.org/10.1145/3453483.3454102\">10.1145/3453483.3454102</a>","chicago":"Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 1171–86. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>.","apa":"Wang, J., Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In <i>Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 1171–1186). Online: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453483.3454102\">https://doi.org/10.1145/3453483.3454102</a>"},"acknowledgement":"We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).","isi":1,"type":"conference","date_updated":"2025-04-15T07:55:05Z","page":"1171-1186","_id":"9646","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000723661700076"],"arxiv":["2011.14617"]},"department":[{"_id":"KrCh"}],"title":"Quantitative analysis of assertion violations in probabilistic programs","publication_identifier":{"isbn":["9781450383912"]},"ec_funded":1,"quality_controlled":"1","status":"public","conference":{"end_date":"2021-06-26","location":"Online","name":"PLDI: Programming Language Design and Implementation","start_date":"2021-06-20"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.14617"}],"abstract":[{"lang":"eng","text":"We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude."}],"day":"01","oa":1,"publication":"Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation","arxiv":1,"publisher":"Association for Computing Machinery","scopus_import":"1","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","doi":"10.1145/3453483.3454102","author":[{"last_name":"Wang","first_name":"Jinyi","full_name":"Wang, Jinyi"},{"last_name":"Sun","first_name":"Yican","full_name":"Sun, Yican"},{"last_name":"Fu","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady"}],"month":"06"},{"project":[{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"scopus_import":"1","article_type":"original","volume":893,"corr_author":"1","oa_version":"Published Version","author":[{"full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana"},{"full_name":"Igler, Claudia","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"doi":"10.1016/j.tcs.2021.05.023","month":"06","publication":"Theoretical Computer Science","day":"04","oa":1,"publisher":"Elsevier","status":"public","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"ddc":["004"],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"has_accepted_license":"1","title":"Long lived transients in gene regulation","publication_identifier":{"issn":["0304-3975"]},"file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2021_TheoreticalComputerScience_Petrov.pdf","file_size":2566504,"date_updated":"2022-05-12T12:13:27Z","file_id":"11364","success":1,"checksum":"d3aef34cfb13e53bba4cf44d01680793","date_created":"2022-05-12T12:13:27Z"}],"external_id":{"isi":["000710180500002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"file_date_updated":"2022-05-12T12:13:27Z","page":"1-16","_id":"9647","date_published":"2021-06-04T00:00:00Z","date_created":"2021-07-11T22:01:18Z","year":"2021","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” <i>Theoretical Computer Science</i>, vol. 893. Elsevier, pp. 1–16, 2021.","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. 2021;893:1-16. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., &#38; Guet, C. C. (2021). Long lived transients in gene regulation. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">https://doi.org/10.1016/j.tcs.2021.05.023</a>","ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” <i>Theoretical Computer Science</i>, vol. 893, Elsevier, 2021, pp. 1–16, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.05.023\">10.1016/j.tcs.2021.05.023</a>."},"publication_status":"published","isi":1,"acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","date_updated":"2025-04-15T06:25:56Z","intvolume":"       893","type":"journal_article"},{"ec_funded":1,"ddc":["580"],"quality_controlled":"1","status":"public","abstract":[{"text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.","lang":"eng"}],"publication":"New Phytologist","oa":1,"day":"01","publisher":"Wiley","pmid":1,"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"volume":232,"scopus_import":"1","article_type":"original","oa_version":"Published Version","corr_author":"1","author":[{"last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin"},{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257"},{"orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","last_name":"Qi","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"full_name":"Alotaibi, SS","first_name":"SS","last_name":"Alotaibi"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"doi":"10.1111/nph.17617","month":"10","date_published":"2021-10-01T00:00:00Z","date_created":"2021-07-14T15:29:14Z","year":"2021","article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"citation":{"mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>.","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., &#38; Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. 2021;232(2):510-522. doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” <i>New Phytologist</i>, vol. 232, no. 2. Wiley, pp. 510–522, 2021."},"publication_status":"published","isi":1,"acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","intvolume":"       232","date_updated":"2025-04-14T07:45:00Z","type":"journal_article","page":"510-522","_id":"9656","issue":"2","file":[{"file_size":1939800,"file_name":"2021_NewPhytologist_Han.pdf","relation":"main_file","creator":"kschuh","access_level":"open_access","content_type":"application/pdf","checksum":"6422a6eb329b52d96279daaee0fcf189","date_created":"2021-10-07T13:42:47Z","file_id":"10105","success":1,"date_updated":"2021-10-07T13:42:47Z"}],"external_id":{"isi":["000680587100001"],"pmid":["34254313"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"file_date_updated":"2021-10-07T13:42:47Z","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"PIN-mediated polar auxin transport regulations in plant tropic responses","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]}},{"year":"2021","date_created":"2021-07-14T15:32:43Z","date_published":"2021-07-07T00:00:00Z","publication_status":"published","article_processing_charge":"No","language":[{"iso":"eng"}],"citation":{"ieee":"Z. Gao <i>et al.</i>, “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” <i>Plant Cell</i>, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. 2021;33(9):2981–3003. doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>.","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>.","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003."},"isi":1,"type":"journal_article","date_updated":"2024-10-21T06:02:03Z","intvolume":"        33","page":"2981–3003","_id":"9657","file":[{"content_type":"application/pdf","access_level":"open_access","creator":"cziletti","relation":"main_file","file_name":"2021_PlantCell_Gao.pdf","file_size":10566921,"date_updated":"2021-07-19T12:13:34Z","file_id":"9691","success":1,"checksum":"6715712ec306c321f0204c817b7f8ae7","date_created":"2021-07-19T12:13:34Z"}],"issue":"9","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"file_date_updated":"2021-07-19T12:13:34Z","department":[{"_id":"JiFr"}],"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"},"title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"ddc":["580"],"quality_controlled":"1","status":"public","abstract":[{"text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.","lang":"eng"}],"oa":1,"day":"07","publication":"Plant Cell","publisher":"American Society of Plant Biologists","volume":33,"article_type":"original","scopus_import":"1","pmid":1,"oa_version":"Published Version","doi":"10.1093/plcell/koab183","author":[{"full_name":"Gao, Z","first_name":"Z","last_name":"Gao"},{"full_name":"Chen, Z","first_name":"Z","last_name":"Chen"},{"full_name":"Cui, Y","first_name":"Y","last_name":"Cui"},{"last_name":"Ke","first_name":"M","full_name":"Ke, M"},{"last_name":"Xu","first_name":"H","full_name":"Xu, H"},{"first_name":"Q","last_name":"Xu","full_name":"Xu, Q"},{"full_name":"Chen, J","first_name":"J","last_name":"Chen"},{"full_name":"Li, Y","last_name":"Li","first_name":"Y"},{"full_name":"Huang, L","last_name":"Huang","first_name":"L"},{"last_name":"Zhao","first_name":"H","full_name":"Zhao, H"},{"last_name":"Huang","first_name":"D","full_name":"Huang, D"},{"first_name":"S","last_name":"Mai","full_name":"Mai, S"},{"last_name":"Xu","first_name":"T","full_name":"Xu, T"},{"full_name":"Liu, X","last_name":"Liu","first_name":"X"},{"full_name":"Li, S","first_name":"S","last_name":"Li"},{"full_name":"Guan, Y","last_name":"Guan","first_name":"Y"},{"full_name":"Yang, W","last_name":"Yang","first_name":"W"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Petrášek","first_name":"J","full_name":"Petrášek, J"},{"last_name":"Zhang","first_name":"J","full_name":"Zhang, J"},{"last_name":"Chen","first_name":"X","full_name":"Chen, X"}],"month":"07"}]