[{"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"isi":1,"pmid":1,"ec_funded":1,"_id":"11400","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"AnSa"}],"title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","date_updated":"2025-06-11T14:00:32Z","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"article_type":"original","month":"05","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"},{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"}],"oa_version":"Published Version","publication_status":"published","publisher":"AIP Publishing","type":"journal_article","day":"16","corr_author":"1","scopus_import":"1","citation":{"ista":"Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 156(19), 194902.","apa":"Palaia, I., &#38; Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>.","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>.","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19. AIP Publishing, 2022.","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. 2022;156(19). doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>"},"date_created":"2022-05-22T17:04:48Z","quality_controlled":"1","doi":"10.1063/5.0087769","intvolume":"       156","file_date_updated":"2022-05-23T07:45:33Z","oa":1,"abstract":[{"text":"By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.","lang":"eng"}],"ddc":["540"],"has_accepted_license":"1","article_processing_charge":"No","article_number":"194902","acknowledgement":"The authors thank Longhui Zeng and Xiaolei Su (Yale University) for bringing the topic to their attention and for useful comments. This work has received funding from the European Research Council under the European Union’s Horizon\r\n2020 research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie Grant No. 101034413). The authors are grateful to the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by EPSRC (Grant Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and from the Royal Society (Grant No. UF160266).","status":"public","external_id":{"isi":["000797236000004"],"pmid":["35597653"]},"author":[{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan"},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"volume":156,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-05-16T00:00:00Z","file":[{"checksum":"7fada58059676a4bb0944b82247af740","content_type":"application/pdf","access_level":"open_access","date_created":"2022-05-23T07:45:33Z","success":1,"file_name":"2022_JourChemPhysics_Palaia.pdf","file_size":6387208,"creator":"dernst","file_id":"11405","relation":"main_file","date_updated":"2022-05-23T07:45:33Z"}],"issue":"19","language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","year":"2022"},{"article_processing_charge":"No","article_number":"42","has_accepted_license":"1","abstract":[{"text":"Tin selenide (SnSe) is considered a robust candidate for thermoelectric applications due to its very high thermoelectric figure of merit, ZT, with values of 2.6 in p-type and 2.8 in n-type single crystals. Sn has been replaced with various lower group dopants to achieve successful p-type doping in SnSe with high ZT values. A known, facile, and powerful alternative way to introduce a hole carrier is to use a natural single Sn vacancy, VSn. Through transport and scanning tunneling microscopy studies, we discovered that VSn are dominant in high-quality (slow cooling rate) SnSe single crystals, while multiple vacancies, Vmulti, are dominant in low-quality (high cooling rate) single crystals. Surprisingly, both VSn and Vmulti help to increase the power factors of SnSe, whereas samples with dominant VSn have superior thermoelectric properties in SnSe single crystals. Additionally, the observation that Vmulti are good p-type sources observed in relatively low-quality single crystals is useful in thermoelectric applications because polycrystalline SnSe can be used due to its mechanical strength; this substance is usually fabricated at very high cooling speeds.","lang":"eng"}],"ddc":["540"],"file_date_updated":"2022-05-23T06:47:57Z","oa":1,"intvolume":"        14","doi":"10.1038/s41427-022-00393-5","scopus_import":"1","date_created":"2022-05-22T22:01:40Z","citation":{"ama":"Nguyen VQ, Trinh TL, Chang C, et al. Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. 2022;14. doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>","short":"V.Q. Nguyen, T.L. Trinh, C. Chang, L.D. Zhao, T.H. Nguyen, V.T. Duong, A.T. Duong, J.H. Park, S. Park, J. Kim, S. Cho, NPG Asia Materials 14 (2022).","ieee":"V. Q. Nguyen <i>et al.</i>, “Unidentified major p-type source in SnSe: Multivacancies,” <i>NPG Asia Materials</i>, vol. 14. Springer Nature, 2022.","ista":"Nguyen VQ, Trinh TL, Chang C, Zhao LD, Nguyen TH, Duong VT, Duong AT, Park JH, Park S, Kim J, Cho S. 2022. Unidentified major p-type source in SnSe: Multivacancies. NPG Asia Materials. 14, 42.","chicago":"Nguyen, Van Quang, Thi Ly Trinh, Cheng Chang, Li Dong Zhao, Thi Huong Nguyen, Van Thiet Duong, Anh Tuan Duong, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>.","apa":"Nguyen, V. Q., Trinh, T. L., Chang, C., Zhao, L. D., Nguyen, T. H., Duong, V. T., … Cho, S. (2022). Unidentified major p-type source in SnSe: Multivacancies. <i>NPG Asia Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41427-022-00393-5\">https://doi.org/10.1038/s41427-022-00393-5</a>","mla":"Nguyen, Van Quang, et al. “Unidentified Major P-Type Source in SnSe: Multivacancies.” <i>NPG Asia Materials</i>, vol. 14, 42, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41427-022-00393-5\">10.1038/s41427-022-00393-5</a>."},"quality_controlled":"1","day":"13","year":"2022","language":[{"iso":"eng"}],"publication":"NPG Asia Materials","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-05-13T00:00:00Z","file":[{"relation":"main_file","file_id":"11404","creator":"dernst","date_updated":"2022-05-23T06:47:57Z","date_created":"2022-05-23T06:47:57Z","access_level":"open_access","content_type":"application/pdf","checksum":"0579997cc1d28bf66e29357e08e3e39d","file_size":6202545,"success":1,"file_name":"2022_NPGAsiaMaterials_Nguyen.pdf"}],"author":[{"last_name":"Nguyen","full_name":"Nguyen, Van Quang","first_name":"Van Quang"},{"last_name":"Trinh","full_name":"Trinh, Thi Ly","first_name":"Thi Ly"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","last_name":"Chang","full_name":"Chang, Cheng","orcid":"0000-0002-9515-4277","first_name":"Cheng"},{"full_name":"Zhao, Li Dong","last_name":"Zhao","first_name":"Li Dong"},{"first_name":"Thi Huong","last_name":"Nguyen","full_name":"Nguyen, Thi Huong"},{"first_name":"Van Thiet","full_name":"Duong, Van Thiet","last_name":"Duong"},{"full_name":"Duong, Anh Tuan","last_name":"Duong","first_name":"Anh Tuan"},{"full_name":"Park, Jong Ho","last_name":"Park","first_name":"Jong Ho"},{"full_name":"Park, Sudong","last_name":"Park","first_name":"Sudong"},{"last_name":"Kim","full_name":"Kim, Jungdae","first_name":"Jungdae"},{"last_name":"Cho","full_name":"Cho, Sunglae","first_name":"Sunglae"}],"external_id":{"isi":["000794880200001"]},"volume":14,"status":"public","acknowledgement":"This work was supported by the National Research Foundation of Korea [NRF-2019R1F1A1058473, NRF-2019R1A6A1A11053838, and NRF-2020K1A4A7A02095438].","date_updated":"2023-08-03T07:13:58Z","department":[{"_id":"MaIb"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Unidentified major p-type source in SnSe: Multivacancies","_id":"11401","isi":1,"publication_identifier":{"eissn":["1884-4057"],"issn":["1884-4049"]},"publication_status":"published","publisher":"Springer Nature","type":"journal_article","oa_version":"Published Version","month":"05","article_type":"original"},{"isi":1,"publication_identifier":{"eissn":["1090-2724"],"issn":["0022-0000"]},"_id":"11402","ec_funded":1,"title":"Graph planning with expected finite horizon","department":[{"_id":"KrCh"}],"date_updated":"2025-07-10T11:54:34Z","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1802.03642","open_access":"1"}],"month":"11","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"article_type":"original","arxiv":1,"publisher":"Elsevier","publication_status":"published","type":"journal_article","oa_version":"Preprint","quality_controlled":"1","date_created":"2022-05-22T22:01:40Z","citation":{"ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. 2022;129:1-21. doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>","short":"K. Chatterjee, L. Doyen, Journal of Computer and System Sciences 129 (2022) 1–21.","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” <i>Journal of Computer and System Sciences</i>, vol. 129. Elsevier, pp. 1–21, 2022.","apa":"Chatterjee, K., &#38; Doyen, L. (2022). Graph planning with expected finite horizon. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">https://doi.org/10.1016/j.jcss.2022.04.003</a>.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” <i>Journal of Computer and System Sciences</i>, vol. 129, Elsevier, 2022, pp. 1–21, doi:<a href=\"https://doi.org/10.1016/j.jcss.2022.04.003\">10.1016/j.jcss.2022.04.003</a>.","ista":"Chatterjee K, Doyen L. 2022. Graph planning with expected finite horizon. Journal of Computer and System Sciences. 129, 1–21."},"scopus_import":"1","day":"01","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"7402"}]},"intvolume":"       129","doi":"10.1016/j.jcss.2022.04.003","abstract":[{"text":"Fixed-horizon planning considers a weighted graph and asks to construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping-time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary as the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping-time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time.","lang":"eng"}],"oa":1,"article_processing_charge":"No","acknowledgement":"This work was partially supported by Austrian Science Fund (FWF) NFN Grant No RiSE/SHiNE S11407 and by the grant ERC CoG 863818 (ForM-SMArt).","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-11-01T00:00:00Z","volume":129,"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"publication":"Journal of Computer and System Sciences","language":[{"iso":"eng"}],"page":"1-21","year":"2022"},{"article_processing_charge":"No","scopus_import":"1","citation":{"ista":"Stöllner A. 2022. Measuring airborne nanoplastics using aerosol physics. Nature Reviews Earth and Environment. 3(6), 360.","chicago":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” <i>Nature Reviews Earth and Environment</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s43017-022-00302-y\">https://doi.org/10.1038/s43017-022-00302-y</a>.","apa":"Stöllner, A. (2022). Measuring airborne nanoplastics using aerosol physics. <i>Nature Reviews Earth and Environment</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43017-022-00302-y\">https://doi.org/10.1038/s43017-022-00302-y</a>","mla":"Stöllner, Andrea. “Measuring Airborne Nanoplastics Using Aerosol Physics.” <i>Nature Reviews Earth and Environment</i>, vol. 3, no. 6, Springer Nature, 2022, p. 360, doi:<a href=\"https://doi.org/10.1038/s43017-022-00302-y\">10.1038/s43017-022-00302-y</a>.","ama":"Stöllner A. Measuring airborne nanoplastics using aerosol physics. <i>Nature Reviews Earth and Environment</i>. 2022;3(6):360. doi:<a href=\"https://doi.org/10.1038/s43017-022-00302-y\">10.1038/s43017-022-00302-y</a>","short":"A. Stöllner, Nature Reviews Earth and Environment 3 (2022) 360.","ieee":"A. Stöllner, “Measuring airborne nanoplastics using aerosol physics,” <i>Nature Reviews Earth and Environment</i>, vol. 3, no. 6. Springer Nature, p. 360, 2022."},"date_created":"2022-05-22T22:01:41Z","quality_controlled":"1","day":"01","corr_author":"1","intvolume":"         3","doi":"10.1038/s43017-022-00302-y","publication":"Nature Reviews Earth and Environment","language":[{"iso":"eng"}],"page":"360","issue":"6","year":"2022","status":"public","date_published":"2022-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000791125600002"]},"author":[{"first_name":"Andrea","id":"4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed","last_name":"Stöllner","orcid":"0000-0002-0464-8440","full_name":"Stöllner, Andrea"}],"volume":3,"title":"Measuring airborne nanoplastics using aerosol physics","department":[{"_id":"GradSch"}],"date_updated":"2024-10-09T21:02:28Z","isi":1,"publication_identifier":{"eissn":["2662-138X"]},"_id":"11403","type":"journal_article","publisher":"Springer Nature","publication_status":"published","oa_version":"None","month":"06","article_type":"original"},{"arxiv":1,"publisher":"Institute of Mathematical Statistics","publication_status":"published","type":"journal_article","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2103.06730","open_access":"1"}],"month":"05","article_type":"original","department":[{"_id":"LaEr"}],"title":"Normal fluctuation in quantum ergodicity for Wigner matrices","date_updated":"2023-08-03T07:16:53Z","isi":1,"publication_identifier":{"issn":["0091-1798"],"eissn":["2168-894X"]},"_id":"11418","publication":"Annals of Probability","language":[{"iso":"eng"}],"page":"984-1012","issue":"3","year":"2022","status":"public","acknowledgement":"L.E. would like to thank Zhigang Bao for many illuminating discussions in an early stage of this research. The authors are also grateful to Paul Bourgade for his comments on the manuscript and the anonymous referee for several useful suggestions.","date_published":"2022-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000793963400005"],"arxiv":["2103.06730"]},"author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","last_name":"Cipolloni","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Dominik J","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder"}],"volume":50,"abstract":[{"text":"We consider the quadratic form of a general high-rank deterministic matrix on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian fluctuation for each bulk eigenvector in the large N limit. The proof is a combination of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau (2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"oa":1,"article_processing_charge":"No","scopus_import":"1","date_created":"2022-05-29T22:01:53Z","quality_controlled":"1","citation":{"ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum ergodicity for Wigner matrices,” <i>Annals of Probability</i>, vol. 50, no. 3. Institute of Mathematical Statistics, pp. 984–1012, 2022.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.","ama":"Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. 2022;50(3):984-1012. doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 984–1012.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>","mla":"Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>, vol. 50, no. 3, Institute of Mathematical Statistics, 2022, pp. 984–1012, doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>."},"day":"01","intvolume":"        50","doi":"10.1214/21-AOP1552"},{"day":"05","date_created":"2022-05-29T22:01:54Z","citation":{"short":"T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra, H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).","ieee":"T. Hori <i>et al.</i>, “Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>","mla":"Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>, vol. 11, e73542, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>.","apa":"Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z., … Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>","chicago":"Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>.","ista":"Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. eLife. 11, e73542."},"quality_controlled":"1","scopus_import":"1","doi":"10.7554/eLife.73542","intvolume":"        11","oa":1,"file_date_updated":"2022-05-30T08:09:16Z","abstract":[{"lang":"eng","text":"Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission."}],"ddc":["616"],"has_accepted_license":"1","article_number":"e73542","article_processing_charge":"No","status":"public","acknowledgement":"We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda for technical assistant with in vitro analysis of tau. This research was supported by funding from Okinawa Institute of Science and Technology and from Technology (OIST) and Core Research for the Evolutional Science and Technology of Japan Science and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas to TM (Brain Protein Aging and Dementia Control 26117004).","volume":11,"external_id":{"pmid":["35471147 "],"isi":["000876231600001"]},"author":[{"full_name":"Hori, Tetsuya","last_name":"Hori","first_name":"Tetsuya"},{"first_name":"Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku"},{"full_name":"Wang, Han Ying","last_name":"Wang","first_name":"Han Ying"},{"last_name":"Miyasaka","full_name":"Miyasaka, Tomohiro","first_name":"Tomohiro"},{"last_name":"Guillaud","full_name":"Guillaud, Laurent","first_name":"Laurent"},{"full_name":"Taoufiq, Zacharie","last_name":"Taoufiq","first_name":"Zacharie"},{"first_name":"Satyajit","last_name":"Mahapatra","full_name":"Mahapatra, Satyajit"},{"last_name":"Yamada","full_name":"Yamada, Hiroshi","first_name":"Hiroshi"},{"first_name":"Kohji","last_name":"Takei","full_name":"Takei, Kohji"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"date_published":"2022-05-05T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2022-05-30T08:09:16Z","creator":"cchlebak","file_id":"11421","relation":"main_file","file_name":"elife-73542-v2.pdf","success":1,"file_size":2466296,"checksum":"ccddbd167e00ff8375f12998af497152","access_level":"open_access","content_type":"application/pdf","date_created":"2022-05-30T08:09:16Z"}],"publication":"eLife","language":[{"iso":"eng"}],"year":"2022","publication_identifier":{"eissn":["2050-084X"]},"isi":1,"pmid":1,"_id":"11419","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"RySh"}],"title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","date_updated":"2023-08-03T07:15:49Z","article_type":"original","month":"05","oa_version":"Published Version","type":"journal_article","publisher":"eLife Sciences Publications","publication_status":"published"},{"status":"public","acknowledgement":"Partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics” and the European Research Council (ERC), grant no. 788183, “Alpha Shape Theory Extended”. Erin Chambers: Supported in part by the National Science Foundation through grants DBI-1759807, CCF-1907612, and CCF-2106672. Mathijs Wintraecken: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073 Acknowledgements We thank André Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early discussions on this work. We also thank Lu Liu, Yajie Yan and Tao Ju for sharing code to generate the examples.","file":[{"content_type":"application/pdf","access_level":"open_access","date_created":"2022-06-07T07:58:30Z","checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","file_size":17580705,"success":1,"file_name":"2022_LIPICs_Chambers.pdf","relation":"main_file","creator":"dernst","file_id":"11437","date_updated":"2022-06-07T07:58:30Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-01T00:00:00Z","volume":224,"author":[{"full_name":"Chambers, Erin","last_name":"Chambers","first_name":"Erin"},{"first_name":"Christopher D","last_name":"Fillmore","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","full_name":"Fillmore, Christopher D"},{"first_name":"Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","full_name":"Stephenson, Elizabeth R"},{"last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","first_name":"Mathijs"}],"publication":"38th International Symposium on Computational Geometry","page":"66:1-66:9","language":[{"iso":"eng"}],"year":"2022","quality_controlled":"1","date_created":"2022-06-01T14:18:04Z","citation":{"chicago":"Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” In <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, 224:66:1-66:9. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>.","apa":"Chambers, E., Fillmore, C. D., Stephenson, E. R., &#38; Wintraecken, M. (2022). A cautionary tale: Burning the medial axis is unstable. In X. Goaoc &#38; M. Kerber (Eds.), <i>38th International Symposium on Computational Geometry</i> (Vol. 224, p. 66:1-66:9). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>","mla":"Chambers, Erin, et al. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, vol. 224, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>.","ista":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. 2022. A cautionary tale: Burning the medial axis is unstable. 38th International Symposium on Computational Geometry. SoCG: Symposium on Computational GeometryLIPIcs vol. 224, 66:1-66:9.","ieee":"E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “A cautionary tale: Burning the medial axis is unstable,” in <i>38th International Symposium on Computational Geometry</i>, Berlin, Germany, 2022, vol. 224, p. 66:1-66:9.","short":"E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, X. Goaoc, M. Kerber (Eds.), 38th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9.","ama":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. A cautionary tale: Burning the medial axis is unstable. In: Goaoc X, Kerber M, eds. <i>38th International Symposium on Computational Geometry</i>. Vol 224. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022:66:1-66:9. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>"},"scopus_import":"1","day":"01","corr_author":"1","intvolume":"       224","doi":"10.4230/LIPIcs.SoCG.2022.66","ddc":["510"],"abstract":[{"text":"The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible.","lang":"eng"}],"oa":1,"editor":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael"}],"file_date_updated":"2022-06-07T07:58:30Z","conference":{"start_date":"2022-06-07","end_date":"2022-06-10","location":"Berlin, Germany","name":"SoCG: Symposium on Computational Geometry"},"article_processing_charge":"No","has_accepted_license":"1","project":[{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"},{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"month":"06","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"conference","publication_status":"published","oa_version":"Published Version","series_title":"LIPIcs","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-227-3"]},"_id":"11428","ec_funded":1,"title":"A cautionary tale: Burning the medial axis is unstable","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"HeEd"}],"date_updated":"2025-04-14T07:43:57Z"},{"date_updated":"2024-10-09T21:02:30Z","article_processing_charge":"No","abstract":[{"text":"This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022.\r\nThe 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions.  The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks.","lang":"eng"}],"department":[{"_id":"HeEd"}],"title":"Web and Wireless Geographical Information Systems","editor":[{"first_name":"Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","last_name":"Karimipour","orcid":"0000-0001-6746-4174","full_name":"Karimipour, Farid"},{"last_name":"Storandt","full_name":"Storandt, Sabine","first_name":"Sabine"}],"_id":"11429","intvolume":"     13238","doi":"10.1007/978-3-031-06245-2","quality_controlled":"1","date_created":"2022-06-02T05:40:53Z","citation":{"ama":"Karimipour F, Storandt S, eds. <i>Web and Wireless Geographical Information Systems</i>. Vol 13238. 1st ed. Cham: Springer Nature; 2022. doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>","ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","short":"F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information Systems, 1st ed., Springer Nature, Cham, 2022.","chicago":"Karimipour, Farid, and Sabine Storandt, eds. <i>Web and Wireless Geographical Information Systems</i>. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>.","apa":"Karimipour, F., &#38; Storandt, S. (Eds.). (2022). <i>Web and Wireless Geographical Information Systems</i> (1st ed., Vol. 13238). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>","mla":"Karimipour, Farid, and Sabine Storandt, editors. <i>Web and Wireless Geographical Information Systems</i>. 1st ed., vol. 13238, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>.","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p."},"day":"01","corr_author":"1","alternative_title":["LNCS"],"publication_identifier":{"isbn":["9783031062445"],"eissn":["1611-3349"],"eisbn":["9783031062452"],"issn":["0302-9743"]},"publisher":"Springer Nature","publication_status":"published","type":"book_editor","year":"2022","oa_version":"None","language":[{"iso":"eng"}],"page":"153","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-05-01T00:00:00Z","edition":"1","month":"05","volume":13238,"status":"public","place":"Cham"},{"doi":"10.1111/cgf.14478","intvolume":"        41","corr_author":"1","day":"01","quality_controlled":"1","date_created":"2022-06-05T22:01:49Z","citation":{"ista":"Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. Computer Graphics Forum. 41(2), 343–353.","mla":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 343–53, doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>.","chicago":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>.","apa":"Schreck, C., &#38; Wojtan, C. (2022). Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353.","ieee":"C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 343–353, 2022.","ama":"Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. 2022;41(2):343-353. doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>"},"scopus_import":"1","article_processing_charge":"No","oa":1,"abstract":[{"text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics.","lang":"eng"}],"volume":41,"author":[{"last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille","first_name":"Camille"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"external_id":{"isi":["000802723900027"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-05-01T00:00:00Z","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria and MFX Team at INRIA for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","status":"public","year":"2022","issue":"2","page":"343-353","publication":"Computer Graphics Forum","language":[{"iso":"eng"}],"_id":"11432","ec_funded":1,"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"date_updated":"2024-10-22T09:58:19Z","department":[{"_id":"ChWo"}],"title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","article_type":"original","project":[{"grant_number":"638176","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"month":"05","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03641349/"}],"oa_version":"Submitted Version","publication_status":"published","publisher":"Wiley","type":"journal_article"},{"day":"11","scopus_import":"1","citation":{"ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","chicago":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>.","mla":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2, Society for Industrial and Applied Mathematics, 2022, pp. 951–57, doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>.","apa":"Ivanov, G., &#38; Naszodi, M. (2022). A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>","ieee":"G. Ivanov and M. Naszodi, “A quantitative Helly-type theorem: Containment in a homothet,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2. Society for Industrial and Applied Mathematics, pp. 951–957, 2022.","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957.","ama":"Ivanov G, Naszodi M. A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. 2022;36(2):951-957. doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>"},"quality_controlled":"1","date_created":"2022-06-05T22:01:50Z","doi":"10.1137/21M1403308","intvolume":"        36","oa":1,"abstract":[{"text":"We introduce a new variant of quantitative Helly-type theorems: the minimal homothetic distance of the intersection of a family of convex sets to the intersection of a subfamily of a fixed size. As an application, we establish the following quantitative Helly-type result for the diameter. If $K$ is the intersection of finitely many convex bodies in $\\mathbb{R}^d$, then one can select $2d$ of these bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25], is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$ conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982), pp. 109--114] cannot be improved. The bounds above follow from our key result that concerns sparse approximation of a convex polytope by the convex hull of a well-chosen subset of its vertices: Assume that $Q \\subset {\\mathbb R}^d$ is a polytope whose centroid is the origin. Then there exist at most 2d vertices of $Q$ whose convex hull $Q^{\\prime \\prime}$ satisfies $Q \\subset - 8d^3 Q^{\\prime \\prime}.$","lang":"eng"}],"article_processing_charge":"No","acknowledgement":"G.I. acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and\r\nKKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI.","status":"public","author":[{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","full_name":"Ivanov, Grigory","first_name":"Grigory"},{"last_name":"Naszodi","full_name":"Naszodi, Marton","first_name":"Marton"}],"external_id":{"isi":["000793158200002"],"arxiv":["2103.04122"]},"volume":36,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-04-11T00:00:00Z","issue":"2","language":[{"iso":"eng"}],"page":"951-957","publication":"SIAM Journal on Discrete Mathematics","year":"2022","publication_identifier":{"issn":["0895-4801"]},"isi":1,"_id":"11435","title":"A quantitative Helly-type theorem: Containment in a homothet","department":[{"_id":"UlWa"}],"date_updated":"2023-10-18T06:58:03Z","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2103.04122","open_access":"1"}],"article_type":"original","month":"04","arxiv":1,"oa_version":"Preprint","publication_status":"published","type":"journal_article","publisher":"Society for Industrial and Applied Mathematics"},{"department":[{"_id":"LeSa"}],"title":"The assembly, regulation and function of the mitochondrial respiratory chain","date_updated":"2024-10-09T21:01:03Z","publication_identifier":{"issn":["1471-0072"],"eissn":["1471-0080"]},"isi":1,"pmid":1,"_id":"10182","oa_version":"None","publisher":"Springer Nature","publication_status":"published","type":"journal_article","article_type":"original","month":"02","abstract":[{"lang":"eng","text":"The mitochondrial oxidative phosphorylation system is central to cellular metabolism. It comprises five enzymatic complexes and two mobile electron carriers that work in a mitochondrial respiratory chain. By coupling the oxidation of reducing equivalents coming into mitochondria to the generation and subsequent dissipation of a proton gradient across the inner mitochondrial membrane, this electron transport chain drives the production of ATP, which is then used as a primary energy carrier in virtually all cellular processes. Minimal perturbations of the respiratory chain activity are linked to diseases; therefore, it is necessary to understand how these complexes are assembled and regulated and how they function. In this Review, we outline the latest assembly models for each individual complex, and we also highlight the recent discoveries indicating that the formation of larger assemblies, known as respiratory supercomplexes, originates from the association of the intermediates of individual complexes. We then discuss how recent cryo-electron microscopy structures have been key to answering open questions on the function of the electron transport chain in mitochondrial respiration and how supercomplexes and other factors, including metabolites, can regulate the activity of the single complexes. When relevant, we discuss how these mechanisms contribute to physiology and outline their deregulation in human diseases."}],"article_processing_charge":"No","day":"01","corr_author":"1","scopus_import":"1","date_created":"2021-10-24T22:01:35Z","citation":{"short":"I. Vercellino, L.A. Sazanov, Nature Reviews Molecular Cell Biology 23 (2022) 141–161.","ieee":"I. Vercellino and L. A. Sazanov, “The assembly, regulation and function of the mitochondrial respiratory chain,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 23. Springer Nature, pp. 141–161, 2022.","ama":"Vercellino I, Sazanov LA. The assembly, regulation and function of the mitochondrial respiratory chain. <i>Nature Reviews Molecular Cell Biology</i>. 2022;23:141–161. doi:<a href=\"https://doi.org/10.1038/s41580-021-00415-0\">10.1038/s41580-021-00415-0</a>","ista":"Vercellino I, Sazanov LA. 2022. The assembly, regulation and function of the mitochondrial respiratory chain. Nature Reviews Molecular Cell Biology. 23, 141–161.","mla":"Vercellino, Irene, and Leonid A. Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 23, Springer Nature, 2022, pp. 141–161, doi:<a href=\"https://doi.org/10.1038/s41580-021-00415-0\">10.1038/s41580-021-00415-0</a>.","chicago":"Vercellino, Irene, and Leonid A Sazanov. “The Assembly, Regulation and Function of the Mitochondrial Respiratory Chain.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41580-021-00415-0\">https://doi.org/10.1038/s41580-021-00415-0</a>.","apa":"Vercellino, I., &#38; Sazanov, L. A. (2022). The assembly, regulation and function of the mitochondrial respiratory chain. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41580-021-00415-0\">https://doi.org/10.1038/s41580-021-00415-0</a>"},"quality_controlled":"1","doi":"10.1038/s41580-021-00415-0","intvolume":"        23","page":"141–161","language":[{"iso":"eng"}],"publication":"Nature Reviews Molecular Cell Biology","year":"2022","status":"public","external_id":{"isi":["000705697100001"],"pmid":["34621061"]},"author":[{"first_name":"Irene","full_name":"Vercellino, Irene","orcid":" 0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","first_name":"Leonid A"}],"volume":23,"date_published":"2022-02-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"isi":1,"publication_identifier":{"issn":["1615-3375"],"eissn":["1615-3383"]},"_id":"10211","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"MaMo"}],"title":"Optimal combination of linear and spectral estimators for generalized linear models","date_updated":"2025-04-15T06:53:08Z","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computational Mathematics","Analysis"],"month":"10","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_type":"original","arxiv":1,"publication_status":"published","publisher":"Springer","type":"journal_article","oa_version":"Published Version","scopus_import":"1","date_created":"2021-11-03T10:59:08Z","quality_controlled":"1","citation":{"apa":"Mondelli, M., Thrampoulidis, C., &#38; Venkataramanan, R. (2022). Optimal combination of linear and spectral estimators for generalized linear models. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-021-09531-x\">https://doi.org/10.1007/s10208-021-09531-x</a>","mla":"Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” <i>Foundations of Computational Mathematics</i>, vol. 22, no. 5, Springer, 2022, pp. 1513–66, doi:<a href=\"https://doi.org/10.1007/s10208-021-09531-x\">10.1007/s10208-021-09531-x</a>.","chicago":"Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” <i>Foundations of Computational Mathematics</i>. Springer, 2022. <a href=\"https://doi.org/10.1007/s10208-021-09531-x\">https://doi.org/10.1007/s10208-021-09531-x</a>.","ista":"Mondelli M, Thrampoulidis C, Venkataramanan R. 2022. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics. 22(5), 1513–1566.","ama":"Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear and spectral estimators for generalized linear models. <i>Foundations of Computational Mathematics</i>. 2022;22(5):1513-1566. doi:<a href=\"https://doi.org/10.1007/s10208-021-09531-x\">10.1007/s10208-021-09531-x</a>","short":"M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics 22 (2022) 1513–1566.","ieee":"M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination of linear and spectral estimators for generalized linear models,” <i>Foundations of Computational Mathematics</i>, vol. 22, no. 5. Springer, pp. 1513–1566, 2022."},"day":"01","intvolume":"        22","doi":"10.1007/s10208-021-09531-x","ddc":["510"],"abstract":[{"text":"We study the problem of recovering an unknown signal 𝑥𝑥 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator 𝑥𝑥^L and a spectral estimator 𝑥𝑥^s. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine 𝑥𝑥^L and 𝑥𝑥^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of 𝑥𝑥^L and 𝑥𝑥^s, given the limiting distribution of the signal 𝑥𝑥. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form 𝜃𝑥𝑥^L+𝑥𝑥^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s), we design and analyze an approximate message passing algorithm whose iterates give 𝑥𝑥^L and approach 𝑥𝑥^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately.","lang":"eng"}],"file_date_updated":"2021-12-13T15:47:54Z","oa":1,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","acknowledgement":"M. Mondelli would like to thank Andrea Montanari for helpful discussions. All the authors would like to thank the anonymous reviewers for their helpful comments.","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":2305731,"success":1,"file_name":"2021_Springer_Mondelli.pdf","date_created":"2021-12-13T15:47:54Z","content_type":"application/pdf","access_level":"open_access","checksum":"9ea12dd8045a0678000a3a59295221cb","date_updated":"2021-12-13T15:47:54Z","relation":"main_file","file_id":"10542","creator":"alisjak"}],"date_published":"2022-10-01T00:00:00Z","author":[{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"full_name":"Thrampoulidis, Christos","last_name":"Thrampoulidis","first_name":"Christos"},{"first_name":"Ramji","last_name":"Venkataramanan","full_name":"Venkataramanan, Ramji"}],"external_id":{"isi":["000685721000001"],"arxiv":["2008.03326"]},"volume":22,"language":[{"iso":"eng"}],"publication":"Foundations of Computational Mathematics","page":"1513-1566","issue":"5","year":"2022"},{"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development."}],"oa":1,"intvolume":"       233","doi":"10.1111/nph.17792","scopus_import":"1","date_created":"2021-11-14T23:01:24Z","quality_controlled":"1","citation":{"ieee":"I. Kashkan <i>et al.</i>, “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 233, no. 1. Wiley, pp. 329–343, 2022.","short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2022) 329–343.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. 2022;233(1):329-343. doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2022. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233(1), 329–343.","chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 233, no. 1, Wiley, 2022, pp. 329–43, doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>.","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2022). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>"},"day":"01","year":"2022","page":"329-343","publication":"New Phytologist","language":[{"iso":"eng"}],"issue":"1","date_published":"2022-01-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000714678100001"],"pmid":["34637542"]},"author":[{"first_name":"Ivan","last_name":"Kashkan","full_name":"Kashkan, Ivan"},{"first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"first_name":"Katarzyna","last_name":"Retzer","full_name":"Retzer, Katarzyna"},{"first_name":"Jana","last_name":"Humpolíčková","full_name":"Humpolíčková, Jana"},{"first_name":"Aswathy","last_name":"Jayasree","full_name":"Jayasree, Aswathy"},{"last_name":"Filepová","full_name":"Filepová, Roberta","first_name":"Roberta"},{"full_name":"Vondráková, Zuzana","last_name":"Vondráková","first_name":"Zuzana"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","first_name":"Sibu"},{"first_name":"Debbie","last_name":"Rombaut","full_name":"Rombaut, Debbie"},{"last_name":"Jacobs","full_name":"Jacobs, Thomas B.","first_name":"Thomas B."},{"first_name":"Mikko J.","last_name":"Frilander","full_name":"Frilander, Mikko J."},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"full_name":"Růžička, Kamil","last_name":"Růžička","first_name":"Kamil"}],"volume":233,"status":"public","acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","date_updated":"2024-05-22T11:33:15Z","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","department":[{"_id":"JiFr"}],"_id":"10282","pmid":1,"isi":1,"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"publication_status":"published","type":"journal_article","publisher":"Wiley","oa_version":"Preprint","month":"01","article_type":"original","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2"}]},{"doi":"10.1111/ele.13907","related_material":{"record":[{"relation":"research_data","status":"public","id":"13061"}]},"intvolume":"        25","corr_author":"1","day":"01","citation":{"short":"B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, Ecology Letters 25 (2022) 89–100.","ieee":"B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies,” <i>Ecology Letters</i>, vol. 25, no. 1. Wiley, pp. 89–100, 2022.","ama":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. 2022;25(1):89-100. doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>","ista":"Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2022. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Ecology Letters. 25(1), 89–100.","mla":"Casillas Perez, Barbara E., et al. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>, vol. 25, no. 1, Wiley, 2022, pp. 89–100, doi:<a href=\"https://doi.org/10.1111/ele.13907\">10.1111/ele.13907</a>.","apa":"Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., &#38; Cremer, S. (2022). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>","chicago":"Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” <i>Ecology Letters</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/ele.13907\">https://doi.org/10.1111/ele.13907</a>."},"date_created":"2021-11-14T23:01:25Z","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","oa":1,"file_date_updated":"2022-02-03T13:37:11Z","ddc":["573"],"abstract":[{"text":"Infections early in life can have enduring effects on an organism's development and immunity. In this study, we show that this equally applies to developing ‘superorganisms’––incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen's immune system to suppress pathogen proliferation. Early-life queen pathogen exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen's pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.","lang":"eng"}],"volume":25,"external_id":{"isi":["000713396100001"],"pmid":["34725912"]},"author":[{"full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E"},{"first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982"},{"full_name":"Naiser, Filip","last_name":"Naiser","first_name":"Filip"},{"last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","full_name":"Naderlinger, Elisabeth","first_name":"Elisabeth"},{"first_name":"Jiri","last_name":"Matas","full_name":"Matas, Jiri"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia"}],"date_published":"2022-01-01T00:00:00Z","file":[{"file_name":"2021_EcologyLetters_CasillasPerez.pdf","success":1,"file_size":700087,"checksum":"0bd4210400e9876609b7c538ab4f9a3c","access_level":"open_access","content_type":"application/pdf","date_created":"2022-02-03T13:37:11Z","date_updated":"2022-02-03T13:37:11Z","creator":"cchlebak","file_id":"10721","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","acknowledgement":"The authors are grateful to G. Tkačik and V. Mireles for advice on data analyses and to A. Schloegl for help using the IST Austria HPC cluster for data processing. The authors thank J. Eilenberg for providing the fungal strain and A.V. Grasse for support with the molecular analysis. The authors also thank the Social Immunity group at IST Austria, in particular B. Milutinović, for discussions throughout and comments on the manuscript.","year":"2022","issue":"1","publication":"Ecology Letters","page":"89-100","language":[{"iso":"eng"}],"pmid":1,"_id":"10284","ec_funded":1,"publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"date_updated":"2025-04-14T13:55:31Z","title":"Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"SyCr"}],"article_type":"original","month":"01","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","publication_status":"published","type":"journal_article","publisher":"Wiley"},{"acknowledgement":"V. K. gratefully acknowledges the support of Austrian Science Fund (FWF): P 30902-N35. This work was done mostly while he was employed at the University of Innsbruck. During the early stage of this research, V. K. was partially supported by Charles University project GAUK 926416. M. T. is supported by the grant no. 19-04113Y of the Czech Science Foundation(GA ˇCR) and partially supported by Charles University project UNCE/SCI/004.","status":"public","external_id":{"isi":["000798210100003"],"arxiv":["1907.05055"]},"author":[{"first_name":"Vojtech","full_name":"Kaluza, Vojtech","orcid":"0000-0002-2512-8698","last_name":"Kaluza","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E"},{"first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714"}],"volume":42,"date_published":"2022-12-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Combinatorica","page":"1317-1345","language":[{"iso":"eng"}],"year":"2022","day":"01","corr_author":"1","scopus_import":"1","quality_controlled":"1","date_created":"2021-11-25T13:49:16Z","citation":{"ama":"Kaluza V, Tancer M. Even maps, the Colin de Verdière number and representations of graphs. <i>Combinatorica</i>. 2022;42:1317-1345. doi:<a href=\"https://doi.org/10.1007/s00493-021-4443-7\">10.1007/s00493-021-4443-7</a>","ieee":"V. Kaluza and M. Tancer, “Even maps, the Colin de Verdière number and representations of graphs,” <i>Combinatorica</i>, vol. 42. Springer Nature, pp. 1317–1345, 2022.","short":"V. Kaluza, M. Tancer, Combinatorica 42 (2022) 1317–1345.","ista":"Kaluza V, Tancer M. 2022. Even maps, the Colin de Verdière number and representations of graphs. Combinatorica. 42, 1317–1345.","chicago":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” <i>Combinatorica</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00493-021-4443-7\">https://doi.org/10.1007/s00493-021-4443-7</a>.","apa":"Kaluza, V., &#38; Tancer, M. (2022). Even maps, the Colin de Verdière number and representations of graphs. <i>Combinatorica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00493-021-4443-7\">https://doi.org/10.1007/s00493-021-4443-7</a>","mla":"Kaluza, Vojtech, and Martin Tancer. “Even Maps, the Colin de Verdière Number and Representations of Graphs.” <i>Combinatorica</i>, vol. 42, Springer Nature, 2022, pp. 1317–45, doi:<a href=\"https://doi.org/10.1007/s00493-021-4443-7\">10.1007/s00493-021-4443-7</a>."},"doi":"10.1007/s00493-021-4443-7","intvolume":"        42","oa":1,"abstract":[{"text":"Van der Holst and Pendavingh introduced a graph parameter σ, which coincides with the more famous Colin de Verdière graph parameter μ for small values. However, the definition of a is much more geometric/topological directly reflecting embeddability properties of the graph. They proved μ(G) ≤ σ(G) + 2 and conjectured σ(G) ≤ σ(G) for any graph G. We confirm this conjecture. As far as we know, this is the first topological upper bound on σ(G) which is, in general, tight.\r\nEquality between μ and σ does not hold in general as van der Holst and Pendavingh showed that there is a graph G with μ(G) ≤ 18 and σ(G) ≥ 20. We show that the gap appears at much smaller values, namely, we exhibit a graph H for which μ(H) ≥ 7 and σ(H) ≥ 8. We also prove that, in general, the gap can be large: The incidence graphs Hq of finite projective planes of order q satisfy μ(Hq) ∈ O(q3/2) and σ(Hq) ≥ q2.","lang":"eng"}],"ddc":["514","516"],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1907.05055"}],"article_type":"original","month":"12","arxiv":1,"oa_version":"Preprint","publisher":"Springer Nature","publication_status":"published","type":"journal_article","publication_identifier":{"issn":["0209-9683"]},"isi":1,"_id":"10335","title":"Even maps, the Colin de Verdière number and representations of graphs","department":[{"_id":"UlWa"}],"date_updated":"2024-10-09T20:53:51Z"},{"department":[{"_id":"MaMo"}],"title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","date_updated":"2025-04-15T07:50:11Z","isi":1,"publication_identifier":{"issn":["1536-1276"],"eissn":["1558-2248"]},"_id":"10364","arxiv":1,"publisher":"Institute of Electrical and Electronics Engineers","type":"journal_article","publication_status":"published","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2012.13378","open_access":"1"}],"month":"06","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"article_type":"original","abstract":[{"lang":"eng","text":"This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1-1/μ + N/P log2 log2 N/P), where N is the block length of the code and μ is the scaling exponent of the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P = N/2, the latency of SSC decoding is O(N1-1/μ), which is sublinear in the block length. This recovers a result from our earlier work. Second, in a fully-serial implementation where P = 1, the latency of SSC decoding scales as O(N log2 log2 N). The multiplicative constant is also calculated: we show that the latency of SSC decoding when P = 1 is given by (2 + o(1))N log2 log2 N. Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P = N1/μ. The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations."}],"oa":1,"article_processing_charge":"No","quality_controlled":"1","date_created":"2021-11-28T23:01:29Z","citation":{"chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>.","apa":"Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., &#38; Goldsmith, A. (2022). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>","mla":"Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6, Institute of Electrical and Electronics Engineers, 2022, pp. 3909–20, doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>.","ista":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2022. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 21(6), 3909–3920.","ama":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2022;21(6):3909-3920. doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>","short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 21 (2022) 3909–3920.","ieee":"S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6. Institute of Electrical and Electronics Engineers, pp. 3909–3920, 2022."},"scopus_import":"1","day":"01","related_material":{"record":[{"id":"10053","status":"public","relation":"earlier_version"}]},"intvolume":"        21","doi":"10.1109/TWC.2021.3125626","page":"3909-3920","publication":"IEEE Transactions on Wireless Communications","language":[{"iso":"eng"}],"issue":"6","year":"2022","status":"public","acknowledgement":"S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC) and by Huawei. M. Mondelli is partially\r\nsupported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by\r\nthe National Science Foundation under Grant CCF-1764104.","date_published":"2022-06-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":21,"external_id":{"arxiv":["2012.13378"],"isi":["000809406400028"]},"author":[{"last_name":"Hashemi","full_name":"Hashemi, Seyyed Ali","first_name":"Seyyed Ali"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"},{"first_name":"Arman","full_name":"Fazeli, Arman","last_name":"Fazeli"},{"full_name":"Vardy, Alexander","last_name":"Vardy","first_name":"Alexander"},{"full_name":"Cioffi, John","last_name":"Cioffi","first_name":"John"},{"first_name":"Andrea","last_name":"Goldsmith","full_name":"Goldsmith, Andrea"}]},{"language":[{"iso":"eng"}],"publication":"Topology and its Applications","year":"2022","status":"public","acknowledgement":"Dedicated to the memory of Hans-Peter Künzi.","date_published":"2022-03-15T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000791838800012"]},"author":[{"first_name":"Dikran","full_name":"Dikranjan, Dikran","last_name":"Dikranjan"},{"first_name":"Anna","full_name":"Giordano Bruno, Anna","last_name":"Giordano Bruno"},{"first_name":"Hans Peter","last_name":"Künzi","full_name":"Künzi, Hans Peter"},{"last_name":"Zava","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","orcid":"0000-0001-8686-1888","full_name":"Zava, Nicolò","first_name":"Nicolò"},{"full_name":"Toller, Daniele","last_name":"Toller","first_name":"Daniele"}],"volume":309,"abstract":[{"lang":"eng","text":"Motivated by the recent introduction of the intrinsic semilattice entropy, we study generalized quasi-metric semilattices and their categories. We investigate the relationship between these objects and generalized semivaluations, extending Nakamura and Schellekens' approach. Finally, we use this correspondence to compare the intrinsic semilattice entropy and the semigroup entropy induced in particular situations, like sets, torsion abelian groups and vector spaces."}],"article_processing_charge":"No","article_number":"107916","scopus_import":"1","date_created":"2021-12-05T23:01:44Z","quality_controlled":"1","citation":{"ista":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. 2022. Generalized quasi-metric semilattices. Topology and its Applications. 309, 107916.","mla":"Dikranjan, Dikran, et al. “Generalized Quasi-Metric Semilattices.” <i>Topology and Its Applications</i>, vol. 309, 107916, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.topol.2021.107916\">10.1016/j.topol.2021.107916</a>.","apa":"Dikranjan, D., Giordano Bruno, A., Künzi, H. P., Zava, N., &#38; Toller, D. (2022). Generalized quasi-metric semilattices. <i>Topology and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.topol.2021.107916\">https://doi.org/10.1016/j.topol.2021.107916</a>","chicago":"Dikranjan, Dikran, Anna Giordano Bruno, Hans Peter Künzi, Nicolò Zava, and Daniele Toller. “Generalized Quasi-Metric Semilattices.” <i>Topology and Its Applications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.topol.2021.107916\">https://doi.org/10.1016/j.topol.2021.107916</a>.","short":"D. Dikranjan, A. Giordano Bruno, H.P. Künzi, N. Zava, D. Toller, Topology and Its Applications 309 (2022).","ieee":"D. Dikranjan, A. Giordano Bruno, H. P. Künzi, N. Zava, and D. Toller, “Generalized quasi-metric semilattices,” <i>Topology and its Applications</i>, vol. 309. Elsevier, 2022.","ama":"Dikranjan D, Giordano Bruno A, Künzi HP, Zava N, Toller D. Generalized quasi-metric semilattices. <i>Topology and its Applications</i>. 2022;309. doi:<a href=\"https://doi.org/10.1016/j.topol.2021.107916\">10.1016/j.topol.2021.107916</a>"},"day":"15","corr_author":"1","intvolume":"       309","doi":"10.1016/j.topol.2021.107916","publisher":"Elsevier","publication_status":"published","type":"journal_article","oa_version":"None","month":"03","article_type":"original","title":"Generalized quasi-metric semilattices","department":[{"_id":"HeEd"}],"date_updated":"2024-10-09T21:01:16Z","isi":1,"publication_identifier":{"issn":["0166-8641"]},"_id":"10413"},{"publication_identifier":{"issn":["0006-3495"]},"isi":1,"pmid":1,"_id":"10530","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"date_updated":"2025-06-11T13:59:29Z","keyword":["Biophysics"],"article_type":"original","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"month":"01","oa_version":"Published Version","type":"journal_article","publication_status":"published","publisher":"Elsevier","day":"04","scopus_import":"1","date_created":"2021-12-10T09:48:19Z","quality_controlled":"1","citation":{"ieee":"T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. 2022;121(1):P44-60. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>.","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>.","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60."},"doi":"10.1016/j.bpj.2021.12.006","intvolume":"       121","file_date_updated":"2022-07-29T10:17:10Z","oa":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["570"],"abstract":[{"lang":"eng","text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n"}],"has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","status":"public","author":[{"first_name":"Themistoklis","full_name":"Zisis, Themistoklis","last_name":"Zisis"},{"first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"first_name":"Tom","last_name":"Brandstätter","full_name":"Brandstätter, Tom"},{"first_name":"Wei Xiong","last_name":"Siow","full_name":"Siow, Wei Xiong"},{"full_name":"d’Alessandro, Joseph","last_name":"d’Alessandro","first_name":"Joseph"},{"full_name":"Vollmar, Angelika M.","last_name":"Vollmar","first_name":"Angelika M."},{"first_name":"Chase P.","full_name":"Broedersz, Chase P.","last_name":"Broedersz"},{"last_name":"Zahler","full_name":"Zahler, Stefan","first_name":"Stefan"}],"external_id":{"isi":["000740815400007"],"pmid":["34890578"]},"volume":121,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-01-04T00:00:00Z","file":[{"file_size":4475504,"success":1,"file_name":"2022_BiophysicalJour_Zisis.pdf","date_created":"2022-07-29T10:17:10Z","access_level":"open_access","content_type":"application/pdf","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","date_updated":"2022-07-29T10:17:10Z","relation":"main_file","file_id":"11697","creator":"dernst"}],"issue":"1","page":"P44-60","language":[{"iso":"eng"}],"publication":"Biophysical Journal","year":"2022"},{"article_type":"original","month":"05","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/2103.08224","open_access":"1"}],"oa_version":"Preprint","publisher":"Springer Nature","type":"journal_article","publication_status":"published","arxiv":1,"_id":"10537","ec_funded":1,"publication_identifier":{"issn":["1424-0637"]},"isi":1,"date_updated":"2025-04-14T07:26:53Z","department":[{"_id":"RoSe"}],"title":"Bosonization of fermionic many-body dynamics","volume":23,"external_id":{"arxiv":["2103.08224"],"isi":["000725405700001"]},"author":[{"last_name":"Benedikter","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091","full_name":"Benedikter, Niels P","first_name":"Niels P"},{"last_name":"Nam","full_name":"Nam, Phan Thành","first_name":"Phan Thành"},{"first_name":"Marcello","last_name":"Porta","full_name":"Porta, Marcello"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2022-05-01T00:00:00Z","acknowledgement":"NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782).","status":"public","year":"2022","issue":"5","publication":"Annales Henri Poincaré","page":"1725-1764","language":[{"iso":"eng"}],"doi":"10.1007/s00023-021-01136-y","intvolume":"        23","day":"01","date_created":"2021-12-12T23:01:28Z","quality_controlled":"1","citation":{"ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2022. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 23(5), 1725–1764.","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” <i>Annales Henri Poincaré</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00023-021-01136-y\">https://doi.org/10.1007/s00023-021-01136-y</a>.","mla":"Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” <i>Annales Henri Poincaré</i>, vol. 23, no. 5, Springer Nature, 2022, pp. 1725–64, doi:<a href=\"https://doi.org/10.1007/s00023-021-01136-y\">10.1007/s00023-021-01136-y</a>.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R. (2022). Bosonization of fermionic many-body dynamics. <i>Annales Henri Poincaré</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01136-y\">https://doi.org/10.1007/s00023-021-01136-y</a>","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. <i>Annales Henri Poincaré</i>. 2022;23(5):1725-1764. doi:<a href=\"https://doi.org/10.1007/s00023-021-01136-y\">10.1007/s00023-021-01136-y</a>","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” <i>Annales Henri Poincaré</i>, vol. 23, no. 5. Springer Nature, pp. 1725–1764, 2022.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré 23 (2022) 1725–1764."},"scopus_import":"1","article_processing_charge":"No","oa":1,"abstract":[{"lang":"eng","text":"We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations."}]},{"oa":1,"abstract":[{"lang":"eng","text":"We establish global-in-time existence results for thermodynamically consistent reaction-(cross-)diffusion systems coupled to an equation describing heat transfer. Our main interest is to model species-dependent diffusivities,\r\nwhile at the same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal case lies in the intrinsic presence of cross-diffusion type phenomena like the Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic equilibria, a nonvanishing temperature gradient may drive a concentration flux even in a situation with constant concentrations; likewise, a nonvanishing concentration gradient may drive a heat flux even in a case of spatially constant temperature. We use time discretisation and regularisation techniques and derive a priori estimates based on a suitable entropy and the associated entropy production. Renormalised solutions are used in cases where non-integrable diffusion fluxes or reaction terms appear."}],"article_processing_charge":"No","day":"04","quality_controlled":"1","date_created":"2021-12-16T12:08:56Z","citation":{"ista":"Fischer JL, Hopf K, Kniely M, Mielke A. 2022. Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 54(1), 220–267.","mla":"Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>.","apa":"Fischer, J. L., Hopf, K., Kniely, M., &#38; Mielke, A. (2022). Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>","chicago":"Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>.","ieee":"J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis of energy-reaction-diffusion systems,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022.","short":"J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical Analysis 54 (2022) 220–267.","ama":"Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(1):220-267. doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>"},"scopus_import":"1","doi":"10.1137/20M1387237","intvolume":"        54","issue":"1","language":[{"iso":"eng"}],"publication":"SIAM Journal on Mathematical Analysis","page":"220-267","year":"2022","acknowledgement":"M.K. gratefully acknowledges the hospitality of WIAS Berlin, where a major part of the project was carried out. The research stay of M.K. at WIAS Berlin was funded by the Austrian Federal Ministry of Education, Science and Research through a research fellowship for graduates of a promotio sub auspiciis. The research of A.M. has been partially supported by Deutsche Forschungsgemeinschaft (DFG) through the Collaborative Research Center SFB 1114 “Scaling Cascades in Complex Systems” (Project no. 235221301), Subproject C05 “Effective models for materials and interfaces with multiple scales”. J.F. and A.M. are grateful for the hospitality of the Erwin Schrödinger Institute in Vienna, where some ideas for this work have been developed. The authors are grateful to two anonymous referees for several helpful comments, in particular for the short proof of estimate (2.7).","status":"public","volume":54,"author":[{"first_name":"Julian L","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katharina","last_name":"Hopf","full_name":"Hopf, Katharina"},{"last_name":"Kniely","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5645-4333","full_name":"Kniely, Michael","first_name":"Michael"},{"last_name":"Mielke","full_name":"Mielke, Alexander","first_name":"Alexander"}],"external_id":{"isi":["000762768000006"],"arxiv":["2012.03792 "]},"date_published":"2022-01-04T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Global existence analysis of energy-reaction-diffusion systems","department":[{"_id":"JuFi"}],"date_updated":"2023-08-02T13:37:03Z","publication_identifier":{"issn":["0036-1410"]},"isi":1,"_id":"10547","arxiv":1,"oa_version":"Preprint","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.03792"}],"keyword":["Energy-Reaction-Diffusion Systems","Cross Diffusion","Global-In-Time Existence of Weak/Renormalised Solutions","Entropy Method","Onsager System","Soret/Dufour Effect"],"article_type":"original","month":"01"}]