[{"quality_controlled":"1","external_id":{"isi":["000967601700001"]},"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"day":"01","oa_version":"Submitted Version","volume":58,"OA_type":"green","abstract":[{"lang":"eng","text":"The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2."}],"main_file_link":[{"url":"http://hdl.handle.net/2117/389931","open_access":"1"}],"article_type":"original","publication_status":"published","publication_identifier":{"eissn":["2405-8297"]},"publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.ensm.2023.03.022","date_published":"2023-04-01T00:00:00Z","year":"2023","citation":{"ista":"He R, Yang L, Zhang Y, Wang X, Lee S, Zhang T, Li L, Liang Z, Chen J, Li J, Ostovari Moghaddam A, Llorca J, Ibáñez M, Arbiol J, Xu Y, Cabot A. 2023. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. Energy Storage Materials. 58(4), 287–298.","ieee":"R. He <i>et al.</i>, “A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance,” <i>Energy Storage Materials</i>, vol. 58, no. 4. Elsevier, pp. 287–298, 2023.","mla":"He, Ren, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” <i>Energy Storage Materials</i>, vol. 58, no. 4, Elsevier, 2023, pp. 287–98, doi:<a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">10.1016/j.ensm.2023.03.022</a>.","short":"R. He, L. Yang, Y. Zhang, X. Wang, S. Lee, T. Zhang, L. Li, Z. Liang, J. Chen, J. Li, A. Ostovari Moghaddam, J. Llorca, M. Ibáñez, J. Arbiol, Y. Xu, A. Cabot, Energy Storage Materials 58 (2023) 287–298.","apa":"He, R., Yang, L., Zhang, Y., Wang, X., Lee, S., Zhang, T., … Cabot, A. (2023). A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. <i>Energy Storage Materials</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">https://doi.org/10.1016/j.ensm.2023.03.022</a>","ama":"He R, Yang L, Zhang Y, et al. A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance. <i>Energy Storage Materials</i>. 2023;58(4):287-298. doi:<a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">10.1016/j.ensm.2023.03.022</a>","chicago":"He, Ren, Linlin Yang, Yu Zhang, Xiang Wang, Seungho Lee, Ting Zhang, Lingxiao Li, et al. “A CrMnFeCoNi High Entropy Alloy Boosting Oxygen Evolution/Reduction Reactions and Zinc-Air Battery Performance.” <i>Energy Storage Materials</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ensm.2023.03.022\">https://doi.org/10.1016/j.ensm.2023.03.022</a>."},"title":"A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance","isi":1,"date_updated":"2025-06-25T06:12:51Z","department":[{"_id":"MaIb"}],"month":"04","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication":"Energy Storage Materials","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2023-04-16T22:01:07Z","status":"public","page":"287-298","intvolume":"        58","_id":"12832","OA_place":"repository","oa":1,"acknowledgement":"The authors thank the support from the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación. The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581 and 2021 SGR 00457. ICN2 acknowledges the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706). IREC and ICN2 are funded by the CERCA Programme from the Generalitat de Catalunya. ICN2 is supported by the Severo Ochoa program from Spanish MCIN / AEI (Grant No.: CEX2021-001214-S). ICN2 acknowledges funding from Generalitat de Catalunya 2017 SGR 327. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya. The authors thank the support from the project NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”. Part of the present work has been performed in the frameworks of Universitat de Barcelona Nanoscience PhD program. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF). S. Lee. and M. Ibáñez acknowledge funding by IST Austria and the Werner Siemens Foundation. J. Llorca is a Serra Húnter Fellow and is grateful to ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2017 SGR 128. L. L.Yang thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). Z. F. Liang acknowledges funding from MINECO SO-FPT PhD grant (SEV-2013-0295-17-1). J. W. Chen and Y. Xu thank the support from The Key Research and Development Program of Hebei Province (No. 20314305D) and the cooperative scientific research project of the “Chunhui Program” of the Ministry of Education (2018-7). This work was supported by the Natural Science Foundation of Sichuan province (NSFSC) and funded by the Science and Technology Department of Sichuan Province (2022NSFSC1229).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ren","full_name":"He, Ren","last_name":"He"},{"first_name":"Linlin","last_name":"Yang","full_name":"Yang, Linlin"},{"last_name":"Zhang","full_name":"Zhang, Yu","first_name":"Yu"},{"first_name":"Xiang","full_name":"Wang, Xiang","last_name":"Wang"},{"last_name":"Lee","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","orcid":"0000-0002-6962-8598"},{"first_name":"Ting","full_name":"Zhang, Ting","last_name":"Zhang"},{"first_name":"Lingxiao","full_name":"Li, Lingxiao","last_name":"Li"},{"last_name":"Liang","full_name":"Liang, Zhifu","first_name":"Zhifu"},{"last_name":"Chen","full_name":"Chen, Jingwei","first_name":"Jingwei"},{"first_name":"Junshan","full_name":"Li, Junshan","last_name":"Li"},{"first_name":"Ahmad","last_name":"Ostovari Moghaddam","full_name":"Ostovari Moghaddam, Ahmad"},{"first_name":"Jordi","full_name":"Llorca, Jordi","last_name":"Llorca"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"last_name":"Xu","full_name":"Xu, Ying","first_name":"Ying"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"type":"journal_article","issue":"4"},{"quality_controlled":"1","external_id":{"arxiv":["1903.06981"]},"oa_version":"Published Version","day":"18","volume":24,"abstract":[{"lang":"eng","text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved."}],"article_type":"original","publication_status":"published","doi":"10.46298/DMTCS.8383","publisher":"EPI Sciences","publication_identifier":{"issn":["1462-7264"],"eissn":["1365-8050"]},"article_processing_charge":"No","citation":{"mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” <i>Discrete Mathematics and Theoretical Computer Science</i>, vol. 24, no. 2, 9, EPI Sciences, 2023, doi:<a href=\"https://doi.org/10.46298/DMTCS.8383\">10.46298/DMTCS.8383</a>.","ieee":"A. Biniaz <i>et al.</i>, “Token swapping on trees,” <i>Discrete Mathematics and Theoretical Computer Science</i>, vol. 24, no. 2. EPI Sciences, 2023.","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. 2023. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 24(2), 9.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” <i>Discrete Mathematics and Theoretical Computer Science</i>. EPI Sciences, 2023. <a href=\"https://doi.org/10.46298/DMTCS.8383\">https://doi.org/10.46298/DMTCS.8383</a>.","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. <i>Discrete Mathematics and Theoretical Computer Science</i>. 2023;24(2). doi:<a href=\"https://doi.org/10.46298/DMTCS.8383\">10.46298/DMTCS.8383</a>","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (2023). Token swapping on trees. <i>Discrete Mathematics and Theoretical Computer Science</i>. EPI Sciences. <a href=\"https://doi.org/10.46298/DMTCS.8383\">https://doi.org/10.46298/DMTCS.8383</a>","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, Discrete Mathematics and Theoretical Computer Science 24 (2023)."},"date_published":"2023-01-18T00:00:00Z","year":"2023","title":"Token swapping on trees","article_number":"9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"KrCh"},{"_id":"HeEd"},{"_id":"UlWa"}],"month":"01","date_updated":"2025-01-20T14:05:09Z","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Discrete Mathematics and Theoretical Computer Science","date_created":"2023-04-16T22:01:08Z","scopus_import":"1","status":"public","intvolume":"        24","file":[{"file_id":"12844","creator":"dernst","file_name":"2022_DMTCS_Biniaz.pdf","date_updated":"2023-04-17T08:10:28Z","content_type":"application/pdf","access_level":"open_access","success":1,"file_size":2072197,"relation":"main_file","date_created":"2023-04-17T08:10:28Z","checksum":"439102ea4f6e2aeefd7107dfb9ccf532"}],"ddc":["000"],"_id":"12833","arxiv":1,"oa":1,"related_material":{"record":[{"relation":"earlier_version","id":"7950","status":"public"}]},"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"full_name":"Jain, Kshitij","last_name":"Jain","first_name":"Kshitij"},{"first_name":"Anna","full_name":"Lubiw, Anna","last_name":"Lubiw"},{"first_name":"Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová","full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tillmann","full_name":"Miltzow, Tillmann","last_name":"Miltzow"},{"first_name":"Debajyoti","last_name":"Mondal","full_name":"Mondal, Debajyoti"},{"last_name":"Naredla","full_name":"Naredla, Anurag Murty","first_name":"Anurag Murty"},{"orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexi","last_name":"Turcotte","full_name":"Turcotte, Alexi"}],"acknowledgement":"This work was begun at the University of Waterloo and was partially supported by the Natural Sciences and Engineering Council of Canada (NSERC).\r\n","file_date_updated":"2023-04-17T08:10:28Z","issue":"2"},{"date_updated":"2023-10-04T11:15:17Z","department":[{"_id":"MiLe"}],"month":"07","title":"Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities","isi":1,"article_number":"2202631","year":"2023","date_published":"2023-07-04T00:00:00Z","citation":{"chicago":"Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, Kausik Majumdar, and Vinod Menon. “Optical Manipulation of Layer–Valley Coherence via Strong Exciton–Photon Coupling in Microcavities.” <i>Advanced Optical Materials</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/adom.202202631\">https://doi.org/10.1002/adom.202202631</a>.","ama":"Khatoniar M, Yama N, Ghazaryan A, et al. Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. <i>Advanced Optical Materials</i>. 2023;11(13). doi:<a href=\"https://doi.org/10.1002/adom.202202631\">10.1002/adom.202202631</a>","apa":"Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., Majumdar, K., &#38; Menon, V. (2023). Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. <i>Advanced Optical Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adom.202202631\">https://doi.org/10.1002/adom.202202631</a>","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, K. Majumdar, V. Menon, Advanced Optical Materials 11 (2023).","mla":"Khatoniar, Mandeep, et al. “Optical Manipulation of Layer–Valley Coherence via Strong Exciton–Photon Coupling in Microcavities.” <i>Advanced Optical Materials</i>, vol. 11, no. 13, 2202631, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/adom.202202631\">10.1002/adom.202202631</a>.","ieee":"M. Khatoniar <i>et al.</i>, “Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities,” <i>Advanced Optical Materials</i>, vol. 11, no. 13. Wiley, 2023.","ista":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Majumdar K, Menon V. 2023. Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities. Advanced Optical Materials. 11(13), 2202631."},"publication_status":"published","publisher":"Wiley","article_processing_charge":"No","publication_identifier":{"eissn":["2195-1071"]},"doi":"10.1002/adom.202202631","abstract":[{"text":"Coherent control and manipulation of quantum degrees of freedom such as spins forms the basis of emerging quantum technologies. In this context, the robust valley degree of freedom and the associated valley pseudospin found in two-dimensional transition metal dichalcogenides is a highly attractive platform. Valley polarization and coherent superposition of valley states have been observed in these systems even up to room temperature. Control of valley coherence is an important building block for the implementation of valley qubit. Large magnetic fields or high-power lasers have been used in the past to demonstrate the control (initialization and rotation) of the valley coherent states. Here, the control of layer–valley coherence via strong coupling of valley excitons in bilayer WS2 to microcavity photons is demonstrated by exploiting the pseudomagnetic field arising in optical cavities owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The use of photonic structures to generate pseudomagnetic fields which can be used to manipulate exciton-polaritons presents an attractive approach to control optical responses without the need for large magnets or high-intensity optical pump powers.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.08755","open_access":"1"}],"article_type":"original","volume":11,"oa_version":"Preprint","day":"04","external_id":{"isi":["000963866700001"],"arxiv":["2211.08755"]},"quality_controlled":"1","issue":"13","author":[{"first_name":"Mandeep","full_name":"Khatoniar, Mandeep","last_name":"Khatoniar"},{"first_name":"Nicholas","full_name":"Yama, Nicholas","last_name":"Yama"},{"last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg"},{"first_name":"Sriram","last_name":"Guddala","full_name":"Guddala, Sriram"},{"full_name":"Ghaemi, Pouyan","last_name":"Ghaemi","first_name":"Pouyan"},{"full_name":"Majumdar, Kausik","last_name":"Majumdar","first_name":"Kausik"},{"last_name":"Menon","full_name":"Menon, Vinod","first_name":"Vinod"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors acknowledge insightful discussions with Prof. Wang Yao and graphics by Rezlind Bushati. M.K. and N.Y. acknowledge support from NSF grants NSF DMR-1709996 and NSF OMA 1936276. S.G. was supported by the Army Research Office Multidisciplinary University Research Initiative program (W911NF-17-1-0312) and V.M.M. by the Army Research Office grant (W911NF-22-1-0091). K.M acknowledges the SPARC program that supported his collaboration with the CUNY team. The authors acknowledge the Nanofabrication facility at the CUNY Advanced Science Research Center where the cavity devices were fabricated.","type":"journal_article","oa":1,"_id":"12836","arxiv":1,"intvolume":"        11","date_created":"2023-04-16T22:01:09Z","status":"public","scopus_import":"1","publication":"Advanced Optical Materials","language":[{"iso":"eng"}]},{"title":"Multiple packing: Lower bounds via infinite constellations","isi":1,"date_updated":"2023-12-13T11:16:46Z","department":[{"_id":"MaMo"}],"month":"07","publication_status":"published","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"publisher":"IEEE","article_processing_charge":"No","doi":"10.1109/TIT.2023.3260950","year":"2023","date_published":"2023-07-01T00:00:00Z","citation":{"ama":"Zhang Y, Vatedka S. Multiple packing: Lower bounds via infinite constellations. <i>IEEE Transactions on Information Theory</i>. 2023;69(7):4513-4527. doi:<a href=\"https://doi.org/10.1109/TIT.2023.3260950\">10.1109/TIT.2023.3260950</a>","chicago":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2023. <a href=\"https://doi.org/10.1109/TIT.2023.3260950\">https://doi.org/10.1109/TIT.2023.3260950</a>.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 69 (2023) 4513–4527.","apa":"Zhang, Y., &#38; Vatedka, S. (2023). Multiple packing: Lower bounds via infinite constellations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2023.3260950\">https://doi.org/10.1109/TIT.2023.3260950</a>","ieee":"Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via infinite constellations,” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 7. IEEE, pp. 4513–4527, 2023.","mla":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 7, IEEE, 2023, pp. 4513–27, doi:<a href=\"https://doi.org/10.1109/TIT.2023.3260950\">10.1109/TIT.2023.3260950</a>.","ista":"Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. 69(7), 4513–4527."},"abstract":[{"text":"We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L – 1 balls of radius √ nN around points in C . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04407","open_access":"1"}],"article_type":"original","quality_controlled":"1","external_id":{"isi":["001017307000023"],"arxiv":["2211.04407"]},"volume":69,"oa_version":"Preprint","day":"01","author":[{"first_name":"Yihan","orcid":"0000-0002-6465-6258","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan"},{"last_name":"Vatedka","full_name":"Vatedka, Shashank","first_name":"Shashank"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"YZ thanks Jiajin Li for making the observation given by Equation (23). He also would like to thank Nir Ailon and Ely Porat for several helpful conversations throughout this project, and Alexander Barg for insightful comments on the manuscript.\r\nYZ has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]. The work of SV was supported by a seed grant from IIT Hyderabad and the start-up research grant from the Science and Engineering Research Board, India (SRG/2020/000910).","type":"journal_article","issue":"7","_id":"12838","arxiv":1,"oa":1,"intvolume":"        69","page":"4513-4527","publication":"IEEE Transactions on Information Theory","language":[{"iso":"eng"}],"date_created":"2023-04-16T22:01:09Z","scopus_import":"1","status":"public"},{"abstract":[{"text":"Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport.","lang":"eng"}],"article_type":"original","external_id":{"isi":["000957625700001"]},"quality_controlled":"1","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"}],"oa_version":"Published Version","day":"07","volume":13,"ec_funded":1,"title":"Superdiffusive energy transport in kinetically constrained models","isi":1,"article_number":"011033","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:52:07Z","month":"03","department":[{"_id":"MaSe"}],"publication_status":"published","publisher":"American Physical Society","article_processing_charge":"No","publication_identifier":{"eissn":["2160-3308"]},"doi":"10.1103/PhysRevX.13.011033","year":"2023","date_published":"2023-03-07T00:00:00Z","citation":{"ama":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. <i>Physical Review X</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">10.1103/PhysRevX.13.011033</a>","chicago":"Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” <i>Physical Review X</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">https://doi.org/10.1103/PhysRevX.13.011033</a>.","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023).","apa":"Ljubotina, M., Desaules, J. Y., Serbyn, M., &#38; Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">https://doi.org/10.1103/PhysRevX.13.011033</a>","ieee":"M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” <i>Physical Review X</i>, vol. 13, no. 1. American Physical Society, 2023.","mla":"Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” <i>Physical Review X</i>, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">10.1103/PhysRevX.13.011033</a>.","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033."},"intvolume":"        13","file":[{"date_updated":"2023-04-17T08:36:53Z","file_name":"2023_PhysReviewX_Ljubotina.pdf","content_type":"application/pdf","creator":"dernst","file_id":"12845","date_created":"2023-04-17T08:36:53Z","checksum":"ee060cea609af79bba7af74b1ce28078","access_level":"open_access","success":1,"file_size":1958523,"relation":"main_file"}],"ddc":["530"],"has_accepted_license":"1","publication":"Physical Review X","language":[{"iso":"eng"}],"date_created":"2023-04-16T22:01:09Z","status":"public","scopus_import":"1","acknowledgement":"We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54].","author":[{"full_name":"Ljubotina, Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","first_name":"Marko","orcid":"0000-0003-0038-7068"},{"full_name":"Desaules, Jean Yves","last_name":"Desaules","first_name":"Jean Yves"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","file_date_updated":"2023-04-17T08:36:53Z","corr_author":"1","issue":"1","_id":"12839","oa":1},{"intvolume":"     13994","page":"535-540","ddc":["000"],"file":[{"success":1,"access_level":"open_access","relation":"main_file","file_size":16096413,"date_created":"2023-04-25T06:58:36Z","checksum":"120d2c2a38384058ad0630fdf8288312","file_id":"12864","creator":"dernst","date_updated":"2023-04-25T06:58:36Z","file_name":"2023_LNCS_Chalupa.pdf","content_type":"application/pdf"}],"publication":"Tools and Algorithms for the Construction and Analysis of Systems","language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2023-04-20T08:22:53Z","scopus_import":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"type":"conference","corr_author":"1","file_date_updated":"2023-04-25T06:58:36Z","_id":"12854","oa":1,"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"abstract":[{"text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP  2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.","lang":"eng"}],"alternative_title":["LNCS"],"quality_controlled":"1","external_id":{"isi":["001288698100041"]},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093"}],"ec_funded":1,"oa_version":"Published Version","day":"20","volume":13994,"isi":1,"title":"Bubaak: Runtime monitoring of program verifiers","date_updated":"2025-09-09T12:24:56Z","month":"04","department":[{"_id":"ToHe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031308208"],"eissn":["1611-3349"],"isbn":["9783031308192"]},"publisher":"Springer Nature","doi":"10.1007/978-3-031-30820-8_32","publication_status":"published","date_published":"2023-04-20T00:00:00Z","year":"2023","citation":{"ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Paris, France, 2023, vol. 13994, pp. 535–540.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">10.1007/978-3-031-30820-8_32</a>.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","apa":"Chalupa, M., &#38; Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">https://doi.org/10.1007/978-3-031-30820-8_32</a>","ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 13994. Springer Nature; 2023:535-540. doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">10.1007/978-3-031-30820-8_32</a>","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 13994:535–40. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">https://doi.org/10.1007/978-3-031-30820-8_32</a>."}},{"related_material":{"record":[{"relation":"later_version","status":"public","id":"18169"},{"relation":"earlier_version","id":"12407","status":"public"}]},"oa":1,"_id":"12856","corr_author":"1","file_date_updated":"2023-04-25T07:16:36Z","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Marek","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa"},{"first_name":"Fabian","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck"},{"first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724"}],"type":"conference","date_created":"2023-04-20T08:29:42Z","scopus_import":"1","status":"public","publication":"Fundamental Approaches to Software Engineering","language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["000"],"file":[{"file_id":"12865","creator":"dernst","file_name":"2023_LNCS_ChalupaM.pdf","date_updated":"2023-04-25T07:16:36Z","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":580828,"relation":"main_file","date_created":"2023-04-25T07:16:36Z","checksum":"17a7c8e08be609cf2408d37ea55e322c"}],"page":"260-281","intvolume":"     13991","year":"2023","date_published":"2023-04-20T00:00:00Z","citation":{"ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in <i>Fundamental Approaches to Software Engineering</i>, Paris, France, 2023, vol. 13991, pp. 260–281.","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” <i>Fundamental Approaches to Software Engineering</i>, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:<a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">10.1007/978-3-031-30826-0_15</a>.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., &#38; Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In <i>Fundamental Approaches to Software Engineering</i> (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">https://doi.org/10.1007/978-3-031-30826-0_15</a>","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: <i>Fundamental Approaches to Software Engineering</i>. Vol 13991. Springer Nature; 2023:260-281. doi:<a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">10.1007/978-3-031-30826-0_15</a>","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In <i>Fundamental Approaches to Software Engineering</i>, 13991:260–81. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">https://doi.org/10.1007/978-3-031-30826-0_15</a>."},"article_processing_charge":"No","publisher":"Springer Nature","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031308260"],"eissn":["1611-3349"],"isbn":["9783031308253"]},"doi":"10.1007/978-3-031-30826-0_15","publication_status":"published","date_updated":"2025-09-09T12:25:29Z","month":"04","department":[{"_id":"ToHe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"title":"Vamos: Middleware for best-effort third-party monitoring","ec_funded":1,"volume":13991,"day":"20","oa_version":"Published Version","alternative_title":["LNCS"],"quality_controlled":"1","external_id":{"isi":["001284136600015"]},"project":[{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"conference":{"name":"FASE: Fundamental Approaches to Software Engineering","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"}},{"corr_author":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n","author":[{"first_name":"Simone","full_name":"Bombari, Simone","id":"ca726dda-de17-11ea-bc14-f9da834f63aa","last_name":"Bombari"},{"first_name":"Shayan","last_name":"Kiyani","id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","full_name":"Kiyani, Shayan"},{"first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/simone-bombari/beyond-universal-robustness"}]},"oa":1,"_id":"12859","arxiv":1,"intvolume":"       202","page":"2738-2776","date_created":"2023-04-23T16:11:03Z","status":"public","language":[{"iso":"eng"}],"publication":"Proceedings of the 40th International Conference on Machine Learning","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"month":"10","date_updated":"2025-04-15T07:50:16Z","title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","citation":{"ista":"Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.","ieee":"S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.","mla":"Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 2738–76.","short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.","apa":"Bombari, S., Kiyani, S., &#38; Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.","ama":"Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:2738-2776.","chicago":"Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:2738–76. ML Research Press, 2023."},"year":"2023","date_published":"2023-10-27T00:00:00Z","publication_status":"published","publisher":"ML Research Press","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/2302.01629","open_access":"1"}],"abstract":[{"lang":"eng","text":"Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this \"universal\" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an \"interaction matrix\", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10)."}],"conference":{"start_date":"2023-07-23","location":"Honolulu, HI, United States","name":"ICML: International Conference on Machine Learning","end_date":"2023-07-29"},"oa_version":"Preprint","day":"27","volume":202,"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"external_id":{"arxiv":["2302.01629"]},"quality_controlled":"1","alternative_title":["PMLR"]},{"article_type":"original","abstract":[{"text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations.","lang":"eng"}],"ec_funded":1,"volume":14,"oa_version":"Published Version","day":"12","external_id":{"pmid":["37045828"],"isi":["001003644100020"]},"quality_controlled":"1","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"date_updated":"2025-04-15T06:26:15Z","month":"04","department":[{"_id":"KrCh"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"2086","isi":1,"title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","year":"2023","date_published":"2023-04-12T00:00:00Z","citation":{"apa":"Schmid, L., Ekbatani, F., Hilbe, C., &#38; Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023).","chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>.","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086.","mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>, vol. 14, 2086, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>.","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"publisher":"Springer Nature","publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"No","doi":"10.1038/s41467-023-37817-x","publication_status":"published","ddc":["000"],"file":[{"date_created":"2023-04-25T09:13:53Z","checksum":"a4b3b7b36fbef068cabf4fb99501fef6","success":1,"access_level":"open_access","file_size":1786475,"relation":"main_file","date_updated":"2023-04-25T09:13:53Z","file_name":"2023_NatureComm_Schmid.pdf","content_type":"application/pdf","file_id":"12868","creator":"dernst"}],"pmid":1,"intvolume":"        14","date_created":"2023-04-23T22:01:03Z","status":"public","scopus_import":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2023-04-25T09:13:53Z","author":[{"first_name":"Laura","orcid":"0000-0002-6978-7329","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","last_name":"Schmid"},{"first_name":"Farbod","last_name":"Ekbatani","full_name":"Ekbatani, Farbod"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","type":"journal_article","oa":1,"_id":"12861"},{"date_published":"2023-04-01T00:00:00Z","year":"2023","citation":{"ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” <i>PLoS Computational Biology</i>, vol. 19, no. 4. Public Library of Science, 2023.","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>.","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., &#38; Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>","ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. 2023;19(4). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>","chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>."},"publication_status":"published","article_processing_charge":"No","publication_identifier":{"eissn":["1553-7358"]},"publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1010983","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-04-23T08:54:49Z","department":[{"_id":"JoCs"}],"month":"04","title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","isi":1,"article_number":"e1010983","oa_version":"Published Version","day":"01","volume":19,"quality_controlled":"1","external_id":{"pmid":["37011110"],"isi":["000962668700002"]},"abstract":[{"lang":"eng","text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings."}],"article_type":"original","related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"oa":1,"_id":"12862","file_date_updated":"2023-04-25T08:59:18Z","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Safavi","full_name":"Safavi, Shervin","first_name":"Shervin"},{"full_name":"Panagiotaropoulos, Theofanis I.","last_name":"Panagiotaropoulos","first_name":"Theofanis I."},{"first_name":"Vishal","last_name":"Kapoor","full_name":"Kapoor, Vishal"},{"full_name":"Ramirez Villegas, Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","last_name":"Ramirez Villegas","first_name":"Juan F"},{"last_name":"Logothetis","full_name":"Logothetis, Nikos K.","first_name":"Nikos K."},{"full_name":"Besserve, Michel","last_name":"Besserve","first_name":"Michel"}],"acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","type":"journal_article","scopus_import":"1","date_created":"2023-04-23T22:01:03Z","status":"public","has_accepted_license":"1","publication":"PLoS Computational Biology","language":[{"iso":"eng"}],"file":[{"success":1,"access_level":"open_access","relation":"main_file","file_size":4737671,"date_created":"2023-04-25T08:59:18Z","checksum":"edeb9d09f3e41ba7c0251308b9e372e7","file_id":"12867","creator":"dernst","file_name":"2023_PLoSCompBio_Safavi.pdf","date_updated":"2023-04-25T08:59:18Z","content_type":"application/pdf"}],"ddc":["570"],"pmid":1,"intvolume":"        19"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","author":[{"last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka","first_name":"Vlatka"},{"id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","full_name":"Krasnici, Nesrete","last_name":"Krasnici","first_name":"Nesrete"},{"first_name":"Damir","last_name":"Valić","full_name":"Valić, Damir"},{"first_name":"Damir","full_name":"Kapetanović, Damir","last_name":"Kapetanović"},{"full_name":"Vardić Smrzlić, Irena","last_name":"Vardić Smrzlić","first_name":"Irena"},{"last_name":"Jordanova","full_name":"Jordanova, Maja","first_name":"Maja"},{"full_name":"Rebok, Katerina","last_name":"Rebok","first_name":"Katerina"},{"last_name":"Ramani","full_name":"Ramani, Sheriban","first_name":"Sheriban"},{"first_name":"Vasil","full_name":"Kostov, Vasil","last_name":"Kostov"},{"full_name":"Nastova, Rodne","last_name":"Nastova","first_name":"Rodne"},{"full_name":"Dragun, Zrinka","last_name":"Dragun","first_name":"Zrinka"}],"type":"journal_article","_id":"12863","page":"63510-63521","intvolume":"        30","pmid":1,"date_created":"2023-04-23T22:01:03Z","status":"public","scopus_import":"1","publication":"Environmental Science and Pollution Research","language":[{"iso":"eng"}],"date_updated":"2023-10-04T11:23:10Z","month":"05","department":[{"_id":"LifeSc"}],"isi":1,"title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","year":"2023","date_published":"2023-05-01T00:00:00Z","citation":{"ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. 2023;30:63510-63521. doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>","chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>.","short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521.","apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>","ieee":"V. Filipović Marijić <i>et al.</i>, “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” <i>Environmental Science and Pollution Research</i>, vol. 30. Springer Nature, pp. 63510–63521, 2023.","mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>.","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521."},"publisher":"Springer Nature","publication_identifier":{"issn":["0944-1344"],"eissn":["1614-7499"]},"article_processing_charge":"No","doi":"10.1007/s11356-023-26844-2","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems."}],"volume":30,"oa_version":"None","day":"01","external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"quality_controlled":"1"},{"title":"Altered childhood brain development in autism and epilepsy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4809-5059","first_name":"Christopher","last_name":"Currin","full_name":"Currin, Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9"},{"last_name":"Beyer","full_name":"Beyer, Chad","first_name":"Chad"}],"type":"book_chapter","corr_author":"1","date_updated":"2024-10-21T06:01:23Z","department":[{"_id":"TiVo"}],"month":"02","_id":"12866","publication_status":"published","article_processing_charge":"No","publisher":"Elsevier","publication_identifier":{"isbn":["9780128188736"]},"doi":"10.1016/b978-0-12-818872-9.00129-1","editor":[{"first_name":"Bonnie","last_name":"Halpern-Felsher","full_name":"Halpern-Felsher, Bonnie"}],"year":"2023","date_published":"2023-02-01T00:00:00Z","citation":{"ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98.","mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” <i>Encyclopedia of Child and Adolescent Health</i>, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:<a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">10.1016/b978-0-12-818872-9.00129-1</a>.","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in <i>Encyclopedia of Child and Adolescent Health</i>, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","apa":"Currin, C., &#38; Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), <i>Encyclopedia of Child and Adolescent Health</i> (1st ed., pp. 86–98). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">https://doi.org/10.1016/b978-0-12-818872-9.00129-1</a>","short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In <i>Encyclopedia of Child and Adolescent Health</i>, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. <a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">https://doi.org/10.1016/b978-0-12-818872-9.00129-1</a>.","ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. <i>Encyclopedia of Child and Adolescent Health</i>. 1st ed. Elsevier; 2023:86-98. doi:<a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">10.1016/b978-0-12-818872-9.00129-1</a>"},"page":"86-98","abstract":[{"text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain.","lang":"eng"}],"quality_controlled":"1","publication":"Encyclopedia of Child and Adolescent Health","alternative_title":["Vol. 1: Biological Development and Physical Health"],"language":[{"iso":"eng"}],"oa_version":"None","day":"01","date_created":"2023-04-25T07:52:43Z","scopus_import":"1","edition":"1","status":"public"},{"has_accepted_license":"1","day":"26","oa_version":"Published Version","date_created":"2023-04-26T12:34:49Z","status":"public","file":[{"checksum":"85ede12d38bb8d944022a8cba4d719f5","date_created":"2023-04-26T12:30:06Z","file_size":4567,"relation":"main_file","access_level":"open_access","success":1,"content_type":"application/octet-stream","file_name":"README.md","date_updated":"2023-04-26T12:30:06Z","creator":"alaurits","file_id":"12870"},{"success":1,"access_level":"open_access","file_size":732586731,"relation":"main_file","date_created":"2023-04-26T12:27:34Z","checksum":"25bf79452ae895f9c8a20571a096b4c3","file_id":"12871","creator":"alaurits","date_updated":"2023-04-26T12:27:34Z","file_name":"simulations_era=10_flux_varied_europe.zip","content_type":"application/x-zip-compressed"},{"content_type":"application/x-zip-compressed","file_name":"simulations_era=10_flux_varied_torus.zip","date_updated":"2023-04-26T12:29:53Z","creator":"alaurits","file_id":"12872","checksum":"bca48d80ece73eb169aee7211a4a751a","date_created":"2023-04-26T12:29:53Z","file_size":1743893150,"relation":"main_file","access_level":"open_access","success":1},{"checksum":"e77a655db15486a387a36362fbf0b665","date_created":"2023-04-26T12:29:19Z","file_size":878391851,"relation":"main_file","success":1,"access_level":"open_access","content_type":"application/x-zip-compressed","file_name":"simulations_era=10_R_varied_torus.zip","date_updated":"2023-04-26T12:29:19Z","creator":"alaurits","file_id":"12873"},{"file_id":"12874","creator":"alaurits","date_updated":"2023-04-26T12:30:05Z","file_name":"simulations_era=100.zip","content_type":"application/x-zip-compressed","success":1,"access_level":"open_access","relation":"main_file","file_size":201652478,"date_created":"2023-04-26T12:30:05Z","checksum":"8556406513adc4aa2e0417f46680f627"}],"abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage.  We first analyse the model  with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. "}],"ddc":["000"],"_id":"12869","doi":"10.15479/AT:ISTA:12869","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>.","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>","short":"F.R. Klausen, A.B. Lauritsen, (2023).","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. <i>Research Data for: A Stochastic Cellular Automaton Model of Culture Formation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>."},"year":"2023","related_material":{"record":[{"status":"deleted","id":"14505","relation":"used_in_publication"},{"relation":"used_in_publication","id":"12890","status":"public"}]},"oa":1,"date_published":"2023-04-26T00:00:00Z","title":"Research data for: A stochastic cellular automaton model of culture formation","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Frederik Ravn","full_name":"Klausen, Frederik Ravn","last_name":"Klausen"},{"full_name":"Lauritsen, Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard"}],"acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","file_date_updated":"2023-04-26T12:30:06Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"04","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"date_updated":"2025-09-09T12:26:01Z","corr_author":"1"},{"ddc":["000"],"file":[{"success":1,"access_level":"open_access","relation":"main_file","file_size":478740,"date_created":"2023-05-02T07:39:04Z","checksum":"2cb90ddf781baefddf47eac4b54e2a03","creator":"dernst","file_id":"12886","date_updated":"2023-05-02T07:39:04Z","file_name":"2023_Bioinformatics_Benes.pdf","content_type":"application/pdf"}],"pmid":1,"intvolume":"        39","date_created":"2023-04-30T22:01:05Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Bioinformatics","has_accepted_license":"1","issue":"4","file_date_updated":"2023-05-02T07:39:04Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"first_name":"Luboš","last_name":"Brim","full_name":"Brim, Luboš"},{"first_name":"Ondřej","last_name":"Huvar","full_name":"Huvar, Ondřej"},{"first_name":"Samuel","orcid":"0000-0003-1993-0331","last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","full_name":"Pastva, Samuel"},{"first_name":"David","last_name":"Šafránek","full_name":"Šafránek, David"}],"related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"oa":1,"_id":"12876","article_type":"original","abstract":[{"lang":"eng","text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data."}],"ec_funded":1,"oa_version":"Published Version","volume":39,"day":"03","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"external_id":{"pmid":["37004199"],"isi":["000976610800001"]},"quality_controlled":"1","month":"04","department":[{"_id":"ToHe"}],"date_updated":"2025-05-14T11:06:50Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"btad158","title":"Boolean network sketches: A unifying framework for logical model inference","citation":{"mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>, vol. 39, no. 4, btad158, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>.","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” <i>Bioinformatics</i>, vol. 39, no. 4. Oxford University Press, 2023.","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>.","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. 2023;39(4). doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., &#38; Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023)."},"date_published":"2023-04-03T00:00:00Z","year":"2023","doi":"10.1093/bioinformatics/btad158","publication_identifier":{"eissn":["1367-4811"]},"publisher":"Oxford University Press","article_processing_charge":"No","publication_status":"published"},{"intvolume":"       233","page":"829-901","scopus_import":"1","date_created":"2023-04-30T22:01:05Z","status":"public","publication":"Inventiones Mathematicae","language":[{"iso":"eng"}],"author":[{"first_name":"Jacopo","last_name":"De Simoi","full_name":"De Simoi, Jacopo"},{"full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","first_name":"Vadim"},{"first_name":"Martin","full_name":"Leguil, Martin","last_name":"Leguil"}],"acknowledgement":"J.D.S. and M.L. have been partially supported by the NSERC Discovery grant, reference number 502617-2017. M.L. was also supported by the ERC project 692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012). V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa":1,"_id":"12877","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.00890","open_access":"1"}],"abstract":[{"text":"We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table.","lang":"eng"}],"article_type":"original","volume":233,"oa_version":"Preprint","day":"01","ec_funded":1,"quality_controlled":"1","external_id":{"isi":["000978887600001"],"arxiv":["1905.00890"]},"project":[{"call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707"}],"date_updated":"2025-04-14T07:53:46Z","department":[{"_id":"VaKa"}],"month":"08","title":"Marked Length Spectral determination of analytic chaotic billiards with axial symmetries","isi":1,"year":"2023","date_published":"2023-08-01T00:00:00Z","citation":{"ista":"De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae. 233, 829–901.","mla":"De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>, vol. 233, Springer Nature, 2023, pp. 829–901, doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>.","ieee":"J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination of analytic chaotic billiards with axial symmetries,” <i>Inventiones Mathematicae</i>, vol. 233. Springer Nature, pp. 829–901, 2023.","apa":"De Simoi, J., Kaloshin, V., &#38; Leguil, M. (2023). Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>","short":"J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023) 829–901.","chicago":"De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>.","ama":"De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. 2023;233:829-901. doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>"},"publication_status":"published","publisher":"Springer Nature","publication_identifier":{"eissn":["1432-1297"],"issn":["0020-9910"]},"article_processing_charge":"No","doi":"10.1007/s00222-023-01191-8"},{"oa_version":"Published Version","day":"01","volume":115,"external_id":{"isi":["000971861400001"],"pmid":["37025008 "]},"quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components."}],"main_file_link":[{"url":"https://doi.org/10.1111/tpj.16218","open_access":"1"}],"OA_type":"free access","year":"2023","date_published":"2023-07-01T00:00:00Z","citation":{"ista":"Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174.","ieee":"L. Jiang <i>et al.</i>, “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” <i>Plant Journal</i>, vol. 115, no. 1. Wiley, pp. 155–174, 2023.","mla":"Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>.","short":"L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174.","apa":"Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>","ama":"Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. 2023;115(1):155-174. doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>","chicago":"Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>."},"publisher":"Wiley","publication_identifier":{"eissn":["1365-313X"],"issn":["0960-7412"]},"article_processing_charge":"No","doi":"10.1111/tpj.16218","publication_status":"published","date_updated":"2025-06-25T08:50:43Z","department":[{"_id":"JiFr"}],"month":"07","isi":1,"title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","status":"public","date_created":"2023-04-30T22:01:06Z","scopus_import":"1","publication":"Plant Journal","language":[{"iso":"eng"}],"pmid":1,"intvolume":"       115","page":"155-174","oa":1,"_id":"12878","OA_place":"publisher","issue":"1","acknowledgement":"The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).","author":[{"last_name":"Jiang","full_name":"Jiang, Lihui","first_name":"Lihui"},{"first_name":"Baolin","last_name":"Yao","full_name":"Yao, Baolin"},{"full_name":"Zhang, Xiaoyan","last_name":"Zhang","first_name":"Xiaoyan"},{"first_name":"Lixia","last_name":"Wu","full_name":"Wu, Lixia"},{"full_name":"Fu, Qijing","last_name":"Fu","first_name":"Qijing"},{"full_name":"Zhao, Yiting","last_name":"Zhao","first_name":"Yiting"},{"full_name":"Cao, Yuxin","last_name":"Cao","first_name":"Yuxin"},{"last_name":"Zhu","full_name":"Zhu, Ruomeng","first_name":"Ruomeng"},{"last_name":"Lu","full_name":"Lu, Xinqi","first_name":"Xinqi"},{"first_name":"Wuying","last_name":"Huang","full_name":"Huang, Wuying"},{"first_name":"Jianping","full_name":"Zhao, Jianping","last_name":"Zhao"},{"first_name":"Kuixiu","last_name":"Li","full_name":"Li, Kuixiu"},{"full_name":"Zhao, Shuanglu","last_name":"Zhao","first_name":"Shuanglu"},{"first_name":"Li","last_name":"Han","full_name":"Han, Li"},{"first_name":"Xuan","full_name":"Zhou, Xuan","last_name":"Zhou"},{"first_name":"Chongyu","full_name":"Luo, Chongyu","last_name":"Luo"},{"last_name":"Zhu","full_name":"Zhu, Haiyan","first_name":"Haiyan"},{"last_name":"Yang","full_name":"Yang, Jing","first_name":"Jing"},{"first_name":"Huichuan","last_name":"Huang","full_name":"Huang, Huichuan"},{"first_name":"Zhengge","full_name":"Zhu, Zhengge","last_name":"Zhu"},{"last_name":"He","full_name":"He, Xiahong","first_name":"Xiahong"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Zhongkai","full_name":"Zhang, Zhongkai","last_name":"Zhang"},{"first_name":"Changning","full_name":"Liu, Changning","last_name":"Liu"},{"full_name":"Du, Yunlong","last_name":"Du","first_name":"Yunlong"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"file_date_updated":"2023-05-02T07:17:05Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ke","full_name":"Chen, Ke","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","last_name":"Chen"},{"first_name":"Christian","last_name":"Kunkel","full_name":"Kunkel, Christian"},{"last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","first_name":"Bingqing"},{"full_name":"Reuter, Karsten","last_name":"Reuter","first_name":"Karsten"},{"full_name":"Margraf, Johannes T.","last_name":"Margraf","first_name":"Johannes T."}],"acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","oa":1,"_id":"12879","ddc":["000","540"],"file":[{"file_id":"12883","creator":"dernst","content_type":"application/pdf","date_updated":"2023-05-02T07:17:05Z","file_name":"2023_ChemialScience_Chen.pdf","file_size":1515446,"relation":"main_file","access_level":"open_access","success":1,"checksum":"5eeec69a51e192dcd94b955d84423836","date_created":"2023-05-02T07:17:05Z"}],"scopus_import":"1","date_created":"2023-04-30T22:01:06Z","status":"public","language":[{"iso":"eng"}],"publication":"Chemical Science","has_accepted_license":"1","month":"04","department":[{"_id":"BiCh"}],"date_updated":"2023-08-01T14:18:10Z","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"isi":1,"title":"Physics-inspired machine learning of localized intensive properties","citation":{"apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., &#38; Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).","chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>.","ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. 2023. doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science.","mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>, Royal Society of Chemistry, 2023, doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>.","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” <i>Chemical Science</i>. Royal Society of Chemistry, 2023."},"year":"2023","date_published":"2023-04-10T00:00:00Z","doi":"10.1039/d3sc00841j","article_processing_charge":"No","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"publisher":"Royal Society of Chemistry","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations."}],"oa_version":"Published Version","day":"10","quality_controlled":"1","external_id":{"isi":["000971508100001"]}},{"tmp":{"image":"/images/cc_by_nc.png","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)","short":"CC BY-NC (4.0)"},"date_updated":"2024-10-09T21:05:01Z","month":"04","department":[{"_id":"MaHe"}],"title":"Lamin B1 overexpression alters chromatin organization and gene expression","isi":1,"article_number":"2202548","date_published":"2023-04-18T00:00:00Z","year":"2023","citation":{"apa":"Kaneshiro, J. M., Capitanio, J. S., &#38; Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>. Taylor &#38; Francis, 2023. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>.","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. 2023;14(1). doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>, vol. 14, no. 1, 2202548, Taylor &#38; Francis, 2023, doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>.","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” <i>Nucleus</i>, vol. 14, no. 1. Taylor &#38; Francis, 2023."},"publication_status":"published","publisher":"Taylor & Francis","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"article_processing_charge":"No","doi":"10.1080/19491034.2023.2202548","abstract":[{"text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.","lang":"eng"}],"article_type":"original","oa_version":"Published Version","volume":14,"day":"18","quality_controlled":"1","external_id":{"pmid":["37071033"],"isi":["000971629400001"]},"file_date_updated":"2023-05-02T07:24:55Z","corr_author":"1","issue":"1","author":[{"first_name":"Jeanae M.","full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro"},{"first_name":"Juliana S.","full_name":"Capitanio, Juliana S.","last_name":"Capitanio"},{"full_name":"Hetzer, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"Hetzer","first_name":"Martin W","orcid":"0000-0002-2111-992X"}],"acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa":1,"_id":"12880","file":[{"content_type":"application/pdf","file_name":"2023_Nucleus_Kaneshiro.pdf","date_updated":"2023-05-02T07:24:55Z","file_id":"12884","creator":"dernst","checksum":"8e707eda84f64dbad7f03545ae0a83ef","date_created":"2023-05-02T07:24:55Z","file_size":3811113,"relation":"main_file","success":1,"access_level":"open_access"}],"ddc":["570"],"intvolume":"        14","pmid":1,"scopus_import":"1","status":"public","date_created":"2023-04-30T22:01:06Z","has_accepted_license":"1","publication":"Nucleus","language":[{"iso":"eng"}]},{"publication":"Physical Review E","language":[{"iso":"eng"}],"date_created":"2023-05-04T08:35:01Z","scopus_import":"1","status":"public","pmid":1,"intvolume":"       108","_id":"12890","arxiv":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}],"record":[{"relation":"research_data","id":"12869","status":"public"}]},"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Klausen, Frederik Ravn","last_name":"Klausen","first_name":"Frederik Ravn"},{"orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"}],"acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","type":"journal_article","corr_author":"1","issue":"5","external_id":{"isi":["001106396300005"],"arxiv":["2305.02153"],"pmid":["38115445"]},"quality_controlled":"1","day":"08","volume":108,"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"1"}],"abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.","lang":"eng"}],"article_type":"original","publication_status":"published","publisher":"American Physical Society","article_processing_charge":"No","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"doi":"10.1103/PhysRevE.108.054307","year":"2023","date_published":"2023-11-08T00:00:00Z","citation":{"ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” <i>Physical Review E</i>, vol. 108, no. 5. American Physical Society, 2023.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>.","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. 2023;108(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>.","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>"},"title":"Stochastic cellular automaton model of culture formation","article_number":"054307","isi":1,"date_updated":"2025-09-09T12:26:01Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"month":"11"},{"article_number":"109963","isi":1,"title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"month":"08","date_updated":"2025-04-15T08:31:52Z","doi":"10.1016/j.jfa.2023.109963","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"publisher":"Elsevier","article_processing_charge":"No","publication_status":"published","citation":{"apa":"Feliciangeli, D., Gerolin, A., &#38; Portinale, L. (2023). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">https://doi.org/10.1016/j.jfa.2023.109963</a>","short":"D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis 285 (2023).","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">https://doi.org/10.1016/j.jfa.2023.109963</a>.","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>Journal of Functional Analysis</i>. 2023;285(4). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">10.1016/j.jfa.2023.109963</a>","ista":"Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 285(4), 109963.","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>Journal of Functional Analysis</i>, vol. 285, no. 4, 109963, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">10.1016/j.jfa.2023.109963</a>.","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” <i>Journal of Functional Analysis</i>, vol. 285, no. 4. Elsevier, 2023."},"date_published":"2023-08-15T00:00:00Z","year":"2023","article_type":"original","abstract":[{"lang":"eng","text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.11217"}],"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"},{"call_identifier":"FWF","name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":"F06504"}],"quality_controlled":"1","external_id":{"arxiv":["2106.11217"],"isi":["000990804300001"]},"ec_funded":1,"day":"15","oa_version":"Preprint","volume":285,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. The authors also thank J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. Finally, we acknowledge the high quality review done by the anonymous referee of our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813.","author":[{"first_name":"Dario","orcid":"0000-0003-0754-8530","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario"},{"first_name":"Augusto","last_name":"Gerolin","full_name":"Gerolin, Augusto"},{"last_name":"Portinale","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo"}],"issue":"4","arxiv":1,"_id":"12911","oa":1,"related_material":{"record":[{"relation":"earlier_version","id":"9792","status":"public"}]},"intvolume":"       285","language":[{"iso":"eng"}],"publication":"Journal of Functional Analysis","status":"public","date_created":"2023-05-07T22:01:02Z","scopus_import":"1"}]