[{"citation":{"mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>.","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>.","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., &#38; Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” <i>Bioinformatics</i>, vol. 39, no. 4. Oxford Academic, 2023.","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. 2023;39(4). doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158."},"day":"03","pmid":1,"month":"04","file_date_updated":"2023-05-02T07:39:04Z","ddc":["000"],"license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","checksum":"2cb90ddf781baefddf47eac4b54e2a03","content_type":"application/pdf","success":1,"date_updated":"2023-05-02T07:39:04Z","file_name":"2023_Bioinformatics_Benes.pdf","file_size":478740,"relation":"main_file","creator":"dernst","file_id":"12886","date_created":"2023-05-02T07:39:04Z"}],"has_accepted_license":"1","article_processing_charge":"No","volume":39,"title":"Boolean network sketches: A unifying framework for logical model inference","author":[{"first_name":"Nikola","full_name":"Beneš, Nikola","last_name":"Beneš"},{"last_name":"Brim","full_name":"Brim, Luboš","first_name":"Luboš"},{"full_name":"Huvar, Ondřej","last_name":"Huvar","first_name":"Ondřej"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","full_name":"Pastva, Samuel","last_name":"Pastva"},{"full_name":"Šafránek, David","last_name":"Šafránek","first_name":"David"}],"_id":"12876","abstract":[{"lang":"eng","text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data."}],"issue":"4","doi":"10.1093/bioinformatics/btad158","publication_identifier":{"eissn":["1367-4811"]},"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"publication_status":"published","status":"public","acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","ec_funded":1,"department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000976610800001"],"pmid":["37004199"]},"date_published":"2023-04-03T00:00:00Z","date_created":"2023-04-30T22:01:05Z","scopus_import":"1","publisher":"Oxford Academic","intvolume":"        39","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","oa":1,"year":"2023","publication":"Bioinformatics","date_updated":"2023-08-01T14:27:28Z","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"article_number":"btad158","article_type":"original"},{"article_type":"original","page":"829-901","date_updated":"2023-10-04T11:25:37Z","publication":"Inventiones Mathematicae","year":"2023","oa":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.00890","open_access":"1"}],"intvolume":"       233","publisher":"Springer Nature","scopus_import":"1","date_created":"2023-04-30T22:01:05Z","external_id":{"isi":["000978887600001"],"arxiv":["1905.00890"]},"date_published":"2023-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"VaKa"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"J.D.S. and M.L. have been partially supported by the NSERC Discovery grant, reference number 502617-2017. M.L. was also supported by the ERC project 692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012). V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","grant_number":"885707","call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows"}],"publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"doi":"10.1007/s00222-023-01191-8","abstract":[{"lang":"eng","text":"We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table."}],"_id":"12877","author":[{"first_name":"Jacopo","full_name":"De Simoi, Jacopo","last_name":"De Simoi"},{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","orcid":"0000-0002-6051-2628"},{"first_name":"Martin","full_name":"Leguil, Martin","last_name":"Leguil"}],"title":"Marked Length Spectral determination of analytic chaotic billiards with axial symmetries","volume":233,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","month":"08","day":"01","citation":{"chicago":"De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>.","mla":"De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>, vol. 233, Springer Nature, 2023, pp. 829–901, doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>.","ieee":"J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination of analytic chaotic billiards with axial symmetries,” <i>Inventiones Mathematicae</i>, vol. 233. Springer Nature, pp. 829–901, 2023.","apa":"De Simoi, J., Kaloshin, V., &#38; Leguil, M. (2023). Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>","short":"J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023) 829–901.","ama":"De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. 2023;233:829-901. doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>","ista":"De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae. 233, 829–901."}},{"publication_identifier":{"eissn":["1365-313X"],"issn":["0960-7412"]},"publication_status":"published","acknowledgement":"The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).","status":"public","_id":"12878","title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","author":[{"last_name":"Jiang","full_name":"Jiang, Lihui","first_name":"Lihui"},{"full_name":"Yao, Baolin","last_name":"Yao","first_name":"Baolin"},{"full_name":"Zhang, Xiaoyan","last_name":"Zhang","first_name":"Xiaoyan"},{"first_name":"Lixia","full_name":"Wu, Lixia","last_name":"Wu"},{"first_name":"Qijing","full_name":"Fu, Qijing","last_name":"Fu"},{"full_name":"Zhao, Yiting","last_name":"Zhao","first_name":"Yiting"},{"full_name":"Cao, Yuxin","last_name":"Cao","first_name":"Yuxin"},{"last_name":"Zhu","full_name":"Zhu, Ruomeng","first_name":"Ruomeng"},{"first_name":"Xinqi","last_name":"Lu","full_name":"Lu, Xinqi"},{"full_name":"Huang, Wuying","last_name":"Huang","first_name":"Wuying"},{"last_name":"Zhao","full_name":"Zhao, Jianping","first_name":"Jianping"},{"last_name":"Li","full_name":"Li, Kuixiu","first_name":"Kuixiu"},{"first_name":"Shuanglu","full_name":"Zhao, Shuanglu","last_name":"Zhao"},{"first_name":"Li","last_name":"Han","full_name":"Han, Li"},{"first_name":"Xuan","full_name":"Zhou, Xuan","last_name":"Zhou"},{"first_name":"Chongyu","full_name":"Luo, Chongyu","last_name":"Luo"},{"first_name":"Haiyan","full_name":"Zhu, Haiyan","last_name":"Zhu"},{"first_name":"Jing","last_name":"Yang","full_name":"Yang, Jing"},{"last_name":"Huang","full_name":"Huang, Huichuan","first_name":"Huichuan"},{"first_name":"Zhengge","full_name":"Zhu, Zhengge","last_name":"Zhu"},{"first_name":"Xiahong","last_name":"He","full_name":"He, Xiahong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Zhongkai","last_name":"Zhang","full_name":"Zhang, Zhongkai"},{"first_name":"Changning","full_name":"Liu, Changning","last_name":"Liu"},{"first_name":"Yunlong","last_name":"Du","full_name":"Du, Yunlong"}],"doi":"10.1111/tpj.16218","abstract":[{"lang":"eng","text":"Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components."}],"issue":"1","article_processing_charge":"No","volume":115,"month":"07","pmid":1,"citation":{"ieee":"L. Jiang <i>et al.</i>, “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” <i>Plant Journal</i>, vol. 115, no. 1. Wiley, pp. 155–174, 2023.","apa":"Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>","ama":"Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. 2023;115(1):155-174. doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>","short":"L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174.","ista":"Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174.","mla":"Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>.","chicago":"Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>."},"day":"01","oa_version":"None","date_updated":"2023-08-01T14:16:33Z","publication":"Plant Journal","page":"155-174","article_type":"original","year":"2023","publisher":"Wiley","intvolume":"       115","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JiFr"}],"date_created":"2023-04-30T22:01:06Z","scopus_import":"1","external_id":{"isi":["000971861400001"],"pmid":["37025008 "]},"date_published":"2023-07-01T00:00:00Z"},{"publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","publication_status":"published","status":"public","author":[{"id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","first_name":"Ke","full_name":"Chen, Ke","last_name":"Chen"},{"last_name":"Kunkel","full_name":"Kunkel, Christian","first_name":"Christian"},{"last_name":"Cheng","full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"full_name":"Reuter, Karsten","last_name":"Reuter","first_name":"Karsten"},{"last_name":"Margraf","full_name":"Margraf, Johannes T.","first_name":"Johannes T."}],"title":"Physics-inspired machine learning of localized intensive properties","_id":"12879","abstract":[{"text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations.","lang":"eng"}],"doi":"10.1039/d3sc00841j","file":[{"date_created":"2023-05-02T07:17:05Z","file_id":"12883","relation":"main_file","creator":"dernst","file_size":1515446,"file_name":"2023_ChemialScience_Chen.pdf","checksum":"5eeec69a51e192dcd94b955d84423836","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-05-02T07:17:05Z","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","article_processing_charge":"No","day":"10","citation":{"apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., &#38; Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” <i>Chemical Science</i>. Royal Society of Chemistry, 2023.","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science.","ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. 2023. doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).","chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>.","mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>, Royal Society of Chemistry, 2023, doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>."},"file_date_updated":"2023-05-02T07:17:05Z","ddc":["000","540"],"month":"04","license":"https://creativecommons.org/licenses/by/3.0/","oa_version":"Published Version","publication":"Chemical Science","date_updated":"2023-08-01T14:18:10Z","article_type":"original","oa":1,"year":"2023","publisher":"Royal Society of Chemistry","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"BiCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2023-04-10T00:00:00Z","external_id":{"isi":["000971508100001"]},"scopus_import":"1","date_created":"2023-04-30T22:01:06Z"},{"acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","status":"public","publication_status":"published","publication_identifier":{"eissn":["1949-1042"],"issn":["1949-1034"]},"issue":"1","abstract":[{"lang":"eng","text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1."}],"doi":"10.1080/19491034.2023.2202548","author":[{"full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro","first_name":"Jeanae M."},{"last_name":"Capitanio","full_name":"Capitanio, Juliana S.","first_name":"Juliana S."},{"orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"Hetzer","full_name":"Hetzer, Martin W"}],"title":"Lamin B1 overexpression alters chromatin organization and gene expression","_id":"12880","has_accepted_license":"1","volume":14,"article_processing_charge":"No","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"creator":"dernst","relation":"main_file","file_size":3811113,"file_name":"2023_Nucleus_Kaneshiro.pdf","date_updated":"2023-05-02T07:24:55Z","success":1,"content_type":"application/pdf","checksum":"8e707eda84f64dbad7f03545ae0a83ef","access_level":"open_access","date_created":"2023-05-02T07:24:55Z","file_id":"12884"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Published Version","day":"18","citation":{"mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>, vol. 14, no. 1, 2202548, Taylor &#38; Francis, 2023, doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>.","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>. Taylor &#38; Francis, 2023. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>.","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” <i>Nucleus</i>, vol. 14, no. 1. Taylor &#38; Francis, 2023.","apa":"Kaneshiro, J. M., Capitanio, J. S., &#38; Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. 2023;14(1). doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548."},"month":"04","pmid":1,"file_date_updated":"2023-05-02T07:24:55Z","ddc":["570"],"article_type":"original","article_number":"2202548","publication":"Nucleus","date_updated":"2023-08-01T14:18:46Z","year":"2023","oa":1,"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":"        14","publisher":"Taylor & Francis","external_id":{"pmid":["37071033"],"isi":["000971629400001"]},"date_published":"2023-04-18T00:00:00Z","scopus_import":"1","date_created":"2023-04-30T22:01:06Z","department":[{"_id":"MaHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"_id":"12885","title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","supervisor":[{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0001-5013-2843"}],"author":[{"first_name":"Mariano","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","last_name":"Calcabrini","full_name":"Calcabrini, Mariano","orcid":"0000-0003-4566-5877"}],"doi":"10.15479/at:ista:12885","abstract":[{"lang":"eng","text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"ec_funded":1,"status":"public","publication_status":"published","month":"04","ddc":["546","541"],"file_date_updated":"2023-05-02T07:43:18Z","citation":{"mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023."},"day":"28","oa_version":"Published Version","file":[{"file_id":"12887","date_created":"2023-05-02T07:43:18Z","access_level":"closed","checksum":"9347b0e09425f56fdcede5d3528404dc","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-05-02T07:43:18Z","file_name":"Thesis_Calcabrini.docx","creator":"mcalcabr","relation":"source_file","file_size":99627036},{"file_name":"Thesis_Calcabrini_pdfa.pdf","file_size":8742220,"relation":"main_file","creator":"mcalcabr","success":1,"date_updated":"2023-05-02T07:42:45Z","access_level":"open_access","checksum":"2d188b76621086cd384f0b9264b0a576","content_type":"application/pdf","file_id":"12888","date_created":"2023-05-02T07:42:45Z"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","oa":1,"alternative_title":["ISTA Thesis"],"year":"2023","date_updated":"2023-08-14T07:25:26Z","page":"82","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10806"},{"status":"public","relation":"part_of_dissertation","id":"10042"},{"id":"12237","status":"public","relation":"part_of_dissertation"},{"id":"9118","status":"public","relation":"part_of_dissertation"},{"id":"10123","relation":"part_of_dissertation","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"date_created":"2023-05-02T07:58:57Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"date_published":"2023-04-28T00:00:00Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}]},{"status":"public","acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","publication_status":"published","publication_identifier":{"issn":["2470-0045"],"eissn":["2470-0053"]},"abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders."}],"issue":"5","doi":"10.1103/PhysRevE.108.054307","title":"Stochastic cellular automaton model of culture formation","author":[{"first_name":"Frederik Ravn","last_name":"Klausen","full_name":"Klausen, Frederik Ravn"},{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"_id":"12890","volume":108,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","citation":{"chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>.","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” <i>Physical Review E</i>, vol. 108, no. 5. American Physical Society, 2023.","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. 2023;108(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307."},"day":"08","month":"11","related_material":{"link":[{"url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation","relation":"software"}],"record":[{"id":"12869","relation":"research_data","status":"public"}]},"article_number":"054307","article_type":"original","publication":"Physical Review E","date_updated":"2023-11-13T07:47:30Z","year":"2023","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"American Physical Society","intvolume":"       108","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.02153","open_access":"1"}],"external_id":{"arxiv":["2305.02153"]},"date_published":"2023-11-08T00:00:00Z","date_created":"2023-05-04T08:35:01Z","scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"alternative_title":["ISTA Thesis"],"year":"2023","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8966"},{"status":"public","relation":"part_of_dissertation","id":"7888"}]},"page":"190","date_updated":"2023-08-21T06:25:48Z","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-05T08:48:20Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context."}],"doi":"10.15479/at:ista:12891","title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"author":[{"full_name":"Schauer, Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra","orcid":"0000-0001-7659-9142"}],"_id":"12891","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"issn":["2663 - 337X"]},"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","grant_number":"25239"}],"oa_version":"Published Version","citation":{"apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>."},"day":"05","file_date_updated":"2023-05-05T13:04:15Z","month":"05","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"embargo_to":"open_access","date_created":"2023-05-05T13:01:14Z","file_id":"12907","content_type":"application/pdf","checksum":"59b0303dc483f40a96a610a90aab7ee9","access_level":"closed","date_updated":"2023-05-05T13:01:14Z","creator":"aschauer","file_size":31434230,"relation":"main_file","file_name":"Thesis_Schauer_final.pdf","embargo":"2024-05-05"},{"file_name":"Thesis_Schauer_final.docx","creator":"aschauer","relation":"source_file","file_size":43809109,"date_updated":"2023-05-05T13:04:15Z","access_level":"closed","checksum":"25f54e12479b6adaabd129a20568e6c1","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12908","date_created":"2023-05-05T13:04:15Z"}]},{"publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"BeBi"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"date_created":"2023-05-05T10:40:14Z","date_published":"2023-05-05T00:00:00Z","date_updated":"2024-01-29T10:47:51Z","page":"180","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9817"},{"status":"public","relation":"part_of_dissertation","id":"7117"},{"id":"13188","relation":"dissertation_contains","status":"public"}]},"oa":1,"year":"2023","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2023-12-08T23:30:04Z","access_level":"open_access","content_type":"application/pdf","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","embargo":"2023-12-07","file_name":"thesis-hafner-2023may11-a2b.pdf","relation":"main_file","creator":"chafner","file_size":50714445,"file_id":"12942","date_created":"2023-05-11T10:43:20Z"},{"embargo_to":"open_access","file_id":"12943","date_created":"2023-05-11T10:43:44Z","access_level":"closed","content_type":"application/pdf","checksum":"a6b51334be2b81672357b1549afab40c","date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-release-form.pdf","file_size":265319,"creator":"chafner","relation":"source_file"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","ddc":["516","004","518","531"],"month":"05","file_date_updated":"2023-12-08T23:30:04Z","day":"05","citation":{"mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>"},"oa_version":"Published Version","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"12897","author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hafner, Christian","last_name":"Hafner"}],"supervisor":[{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"}],"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","doi":"10.15479/at:ista:12897","abstract":[{"text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.","lang":"eng"}]},{"year":"2023","alternative_title":["ISTA Thesis"],"keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"9114"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"id":"13175","status":"public","relation":"new_edition"}]},"page":"190","date_updated":"2024-10-29T09:11:05Z","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-05T11:08:50Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"doi":"10.15479/at:ista:12900","supervisor":[{"last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"title":"Cavity quantum electrooptics","author":[{"orcid":"0000-0001-6264-2162","first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","full_name":"Sahu, Rishabh"}],"_id":"12900","status":"public","publication_status":"published","ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-030-5"],"issn":["2663 - 337X"]},"project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","grant_number":"899354"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","citation":{"ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>."},"day":"05","ddc":["537","535","539"],"file_date_updated":"2023-07-06T11:37:40Z","month":"05","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"file":[{"date_updated":"2023-06-06T22:30:03Z","content_type":"application/x-zip-compressed","checksum":"8cbdab9c37ee55e591092a6f66b272c4","access_level":"closed","creator":"rsahu","relation":"source_file","file_size":36767177,"file_name":"thesis.zip","date_created":"2023-05-09T08:45:14Z","file_id":"12928","embargo_to":"open_access"},{"date_created":"2023-05-09T08:51:17Z","file_id":"12929","date_updated":"2023-07-06T11:37:40Z","checksum":"439659ead46618147309be39d9dd5a8c","content_type":"application/pdf","access_level":"closed","file_size":17501990,"relation":"main_file","creator":"rsahu","file_name":"thesis_pdfa_final.pdf"}]},{"oa_version":"Preprint","citation":{"ista":"Feliciangeli D, Gerolin A, Portinale L. 2023. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. Journal of Functional Analysis. 285(4), 109963.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, Journal of Functional Analysis 285 (2023).","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>Journal of Functional Analysis</i>. 2023;285(4). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">10.1016/j.jfa.2023.109963</a>","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” <i>Journal of Functional Analysis</i>, vol. 285, no. 4. Elsevier, 2023.","apa":"Feliciangeli, D., Gerolin, A., &#38; Portinale, L. (2023). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">https://doi.org/10.1016/j.jfa.2023.109963</a>","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>Journal of Functional Analysis</i>, vol. 285, no. 4, 109963, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">10.1016/j.jfa.2023.109963</a>.","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.109963\">https://doi.org/10.1016/j.jfa.2023.109963</a>."},"day":"15","month":"08","article_processing_charge":"No","volume":285,"arxiv":1,"abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"issue":"4","doi":"10.1016/j.jfa.2023.109963","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","author":[{"last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530"},{"first_name":"Augusto","full_name":"Gerolin, Augusto","last_name":"Gerolin"},{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","full_name":"Portinale, Lorenzo","last_name":"Portinale"}],"_id":"12911","status":"public","publication_status":"published","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thank the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. The authors also thank J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. Finally, we acknowledge the high quality review done by the anonymous referee of our paper, who we would like to thank for the excellent work and constructive feedback.\r\nD.F acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the HORIZON EUROPE European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942] as well as partial support of his research by the Canada Research Chairs Program (ID 2021-00234) and Natural Sciences and Engineering Research Council of Canada, RGPIN-2022-05207. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and No F65, and by the Deutsche Forschungsgemeinschaft (DFG) - Project number 390685813.","ec_funded":1,"publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504"}],"date_published":"2023-08-15T00:00:00Z","external_id":{"arxiv":["2106.11217"],"isi":["000990804300001"]},"date_created":"2023-05-07T22:01:02Z","scopus_import":"1","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Elsevier","intvolume":"       285","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.11217"}],"year":"2023","oa":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9792"}]},"article_number":"109963","article_type":"original","publication":"Journal of Functional Analysis","date_updated":"2023-11-14T13:21:01Z"},{"doi":"10.1063/5.0146711","abstract":[{"text":"The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.","lang":"eng"}],"issue":"16","_id":"12912","title":"Computing chemical potentials of adsorbed or confined fluids","author":[{"full_name":"Schmid, Rochus","last_name":"Schmid","first_name":"Rochus"},{"full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","orcid":"0000-0002-3584-9632"}],"acknowledgement":"We thank Aleks Reinhardt and Daan Frenkel for their insightful comments and suggestions on the article. B.C. acknowledges the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1.","publication_status":"published","status":"public","publication_identifier":{"eissn":["1089-7690"]},"oa_version":"Published Version","pmid":1,"ddc":["540"],"month":"04","file_date_updated":"2023-05-08T07:44:49Z","citation":{"ama":"Schmid R, Cheng B. Computing chemical potentials of adsorbed or confined fluids. <i>The Journal of Chemical Physics</i>. 2023;158(16). doi:<a href=\"https://doi.org/10.1063/5.0146711\">10.1063/5.0146711</a>","short":"R. Schmid, B. Cheng, The Journal of Chemical Physics 158 (2023).","ista":"Schmid R, Cheng B. 2023. Computing chemical potentials of adsorbed or confined fluids. The Journal of Chemical Physics. 158(16), 161101.","ieee":"R. Schmid and B. Cheng, “Computing chemical potentials of adsorbed or confined fluids,” <i>The Journal of Chemical Physics</i>, vol. 158, no. 16. AIP Publishing, 2023.","apa":"Schmid, R., &#38; Cheng, B. (2023). Computing chemical potentials of adsorbed or confined fluids. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0146711\">https://doi.org/10.1063/5.0146711</a>","mla":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” <i>The Journal of Chemical Physics</i>, vol. 158, no. 16, 161101, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0146711\">10.1063/5.0146711</a>.","chicago":"Schmid, Rochus, and Bingqing Cheng. “Computing Chemical Potentials of Adsorbed or Confined Fluids.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0146711\">https://doi.org/10.1063/5.0146711</a>."},"day":"24","volume":158,"article_processing_charge":"No","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","creator":"dernst","file_size":6499468,"file_name":"2023_JourChemicalPhysics_Schmid.pdf","date_updated":"2023-05-08T07:44:49Z","success":1,"content_type":"application/pdf","checksum":"4ab8c965f2fa4e17920bfa846847f137","access_level":"open_access","date_created":"2023-05-08T07:44:49Z","file_id":"12918"}],"arxiv":1,"year":"2023","oa":1,"article_number":"161101 ","article_type":"original","related_material":{"link":[{"url":"https://github.com/BingqingCheng/mu-adsorption","relation":"software"},{"url":"https://github.com/BingqingCheng/S0","relation":"software"}]},"date_updated":"2023-08-01T14:34:49Z","publication":"The Journal of Chemical Physics","date_created":"2023-05-07T22:01:03Z","scopus_import":"1","external_id":{"arxiv":["2302.01297"],"pmid":["37093149"],"isi":["001010676000010"]},"date_published":"2023-04-24T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BiCh"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"AIP Publishing","intvolume":"       158"},{"_id":"12913","title":"Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene","author":[{"first_name":"J.","full_name":"Díez-Mérida, J.","last_name":"Díez-Mérida"},{"last_name":"Díez-Carlón","full_name":"Díez-Carlón, A.","first_name":"A."},{"first_name":"S. Y.","last_name":"Yang","full_name":"Yang, S. Y."},{"first_name":"Y. M.","full_name":"Xie, Y. M.","last_name":"Xie"},{"first_name":"X. J.","last_name":"Gao","full_name":"Gao, X. J."},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","first_name":"Jorden L","full_name":"Senior, Jorden L","last_name":"Senior"},{"last_name":"Watanabe","full_name":"Watanabe, K.","first_name":"K."},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"first_name":"X.","last_name":"Lu","full_name":"Lu, X."},{"orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"},{"full_name":"Law, K. T.","last_name":"Law","first_name":"K. T."},{"last_name":"Efetov","full_name":"Efetov, Dmitri K.","first_name":"Dmitri K."}],"doi":"10.1038/s41467-023-38005-7","abstract":[{"text":"The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices.","lang":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","acknowledgement":"We are grateful for the fruitful discussions with Allan MacDonald and Andrei Bernevig. D.K.E. acknowledges support from the Ministry of Economy and Competitiveness of Spain through the “Severo Ochoa” program for Centers of Excellence in R&D (SE5-0522), Fundació Privada Cellex, Fundació Privada Mir-Puig, the Generalitat de Catalunya through the CERCA program, funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 852927)” and the La Caixa Foundation. K.T.L. acknowledges the support of the Ministry of Science and Technology of China and the HKRGC through grants MOST20SC04, C6025-19G, 16310219, 16309718, and 16310520. J.D.M. acknowledges support from the INPhINIT ‘la Caixa’ Foundation (ID 100010434) fellowship program (LCF/BQ/DI19/11730021). Y.M.X. acknowledges the support of HKRGC through Grant No. PDFS2223-6S01.","status":"public","file_date_updated":"2023-05-08T07:26:40Z","month":"04","ddc":["530"],"pmid":1,"citation":{"mla":"Díez-Mérida, J., et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” <i>Nature Communications</i>, vol. 14, 2396, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38005-7\">10.1038/s41467-023-38005-7</a>.","chicago":"Díez-Mérida, J., A. Díez-Carlón, S. Y. Yang, Y. M. Xie, X. J. Gao, Jorden L Senior, K. Watanabe, et al. “Symmetry-Broken Josephson Junctions and Superconducting Diodes in Magic-Angle Twisted Bilayer Graphene.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38005-7\">https://doi.org/10.1038/s41467-023-38005-7</a>.","ieee":"J. Díez-Mérida <i>et al.</i>, “Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Díez-Mérida, J., Díez-Carlón, A., Yang, S. Y., Xie, Y. M., Gao, X. J., Senior, J. L., … Efetov, D. K. (2023). Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38005-7\">https://doi.org/10.1038/s41467-023-38005-7</a>","short":"J. Díez-Mérida, A. Díez-Carlón, S.Y. Yang, Y.M. Xie, X.J. Gao, J.L. Senior, K. Watanabe, T. Taniguchi, X. Lu, A.P. Higginbotham, K.T. Law, D.K. Efetov, Nature Communications 14 (2023).","ista":"Díez-Mérida J, Díez-Carlón A, Yang SY, Xie YM, Gao XJ, Senior JL, Watanabe K, Taniguchi T, Lu X, Higginbotham AP, Law KT, Efetov DK. 2023. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. Nature Communications. 14, 2396.","ama":"Díez-Mérida J, Díez-Carlón A, Yang SY, et al. Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38005-7\">10.1038/s41467-023-38005-7</a>"},"day":"26","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-05-08T07:26:40Z","file_id":"12917","date_updated":"2023-05-08T07:26:40Z","success":1,"checksum":"a778105665c10beb2354c92d2b295115","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":1405588,"file_name":"2023_NatureComm_DiezMerida.pdf"}],"volume":14,"article_processing_charge":"No","has_accepted_license":"1","oa":1,"year":"2023","date_updated":"2023-08-01T14:34:00Z","publication":"Nature Communications","article_number":"2396","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"AnHi"}],"date_created":"2023-05-07T22:01:03Z","scopus_import":"1","date_published":"2023-04-26T00:00:00Z","external_id":{"isi":["000979744000004"],"pmid":["37100775"]},"publisher":"Springer Nature","intvolume":"        14","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1},{"date_created":"2023-05-07T22:01:03Z","scopus_import":"1","date_published":"2023-04-20T00:00:00Z","external_id":{"arxiv":["2207.13130"],"isi":["000975799300006"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MiLe"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"American Physical Society","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2207.13130","open_access":"1"}],"intvolume":"       107","year":"2023","oa":1,"article_number":"042216","article_type":"original","date_updated":"2023-08-01T14:33:21Z","publication":"Physical Review A","oa_version":"Preprint","month":"04","citation":{"apa":"Suzuki, F., &#38; Unruh, W. G. (2023). Numerical quantum clock simulations for measuring tunneling times. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">https://doi.org/10.1103/PhysRevA.107.042216</a>","ieee":"F. Suzuki and W. G. Unruh, “Numerical quantum clock simulations for measuring tunneling times,” <i>Physical Review A</i>, vol. 107, no. 4. American Physical Society, 2023.","short":"F. Suzuki, W.G. Unruh, Physical Review A 107 (2023).","ama":"Suzuki F, Unruh WG. Numerical quantum clock simulations for measuring tunneling times. <i>Physical Review A</i>. 2023;107(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">10.1103/PhysRevA.107.042216</a>","ista":"Suzuki F, Unruh WG. 2023. Numerical quantum clock simulations for measuring tunneling times. Physical Review A. 107(4), 042216.","chicago":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” <i>Physical Review A</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">https://doi.org/10.1103/PhysRevA.107.042216</a>.","mla":"Suzuki, Fumika, and William G. Unruh. “Numerical Quantum Clock Simulations for Measuring Tunneling Times.” <i>Physical Review A</i>, vol. 107, no. 4, 042216, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevA.107.042216\">10.1103/PhysRevA.107.042216</a>."},"day":"20","article_processing_charge":"No","volume":107,"arxiv":1,"doi":"10.1103/PhysRevA.107.042216","abstract":[{"lang":"eng","text":"We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier."}],"issue":"4","_id":"12914","title":"Numerical quantum clock simulations for measuring tunneling times","author":[{"last_name":"Suzuki","full_name":"Suzuki, Fumika","first_name":"Fumika","id":"650C99FC-1079-11EA-A3C0-73AE3DDC885E","orcid":"0000-0003-4982-5970"},{"full_name":"Unruh, William G.","last_name":"Unruh","first_name":"William G."}],"ec_funded":1,"status":"public","acknowledgement":"We thank W. H. Zurek, N. Sinitsyn, M. O. Scully, M. Arndt, and C. H. Marrows for helpful discussions. F.S. acknowledges support from the Los Alamos National Laboratory LDRD program under Project No. 20230049DR and the Center for Nonlinear Studies. F.S. also thanks the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411 for support. W.G.U. thanks the Natural Science and Engineering Research Council of Canada, the Hagler Institute of Texas A&M University, the Helmholz Inst HZDR, Germany for support while this work was being done.","publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]}},{"_id":"12915","title":"Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites","author":[{"last_name":"Xing","full_name":"Xing, Congcong","first_name":"Congcong"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"first_name":"Xu","last_name":"Han","full_name":"Han, Xu"},{"orcid":"0000-0001-7313-6740","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu","full_name":"Liu, Yu","last_name":"Liu"},{"first_name":"Bingfei","last_name":"Nan","full_name":"Nan, Bingfei"},{"last_name":"Ramon","full_name":"Ramon, Maria Garcia","first_name":"Maria Garcia","id":"1ffff7cd-ed76-11ed-8d5f-be5e7c364eb9"},{"last_name":"Lim","full_name":"Lim, Khak Ho","first_name":"Khak Ho"},{"last_name":"Li","full_name":"Li, Junshan","first_name":"Junshan"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"first_name":"Bed","full_name":"Poudel, Bed","last_name":"Poudel"},{"full_name":"Nozariasbmarz, Amin","last_name":"Nozariasbmarz","first_name":"Amin"},{"last_name":"Li","full_name":"Li, Wenjie","first_name":"Wenjie"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"doi":"10.1021/acsnano.3c00495","abstract":[{"lang":"eng","text":"Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric (TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another member of the copper chalcogenide family, typically exhibits low Seebeck coefficients that limit its potential to achieve a superior thermoelectric figure of merit, zT, particularly in the low-temperature range where this material could be effective. To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering strategy allows for precise adjustment of Cu/Te ratios and results in a reversible phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically confirmed by in situ high-temperature X-ray diffraction combined with differential scanning calorimetry analysis. The phase transition leads to a conversion from metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain growth, minimizing thermal conductivity and decreasing hole concentration. These properties indicate that copper telluride based compounds have a promising thermoelectric potential, translated into a high dimensionless zT of 1.3 at 560 K."}],"issue":"9","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"status":"public","acknowledgement":"The authors acknowledge support from the projects ENE2016-77798-C4-3-R and NANOGEN (PID2020-116093RB-C43) funded by MCIN/AEI/10.13039/501100011033/and by “ERDF A way of making Europe”, and by the “European Union”. K.X. and B.N. thank the China Scholarship Council (CSC) for scholarship support. The authors acknowledge funding from Generalitat de Catalunya 2017 SGR 327 and 2017 SGR 1246. ICN2 is supported by the Severo Ochoa program from the Spanish MCIN/AEI (Grant No.: CEX2021-001214-S). IREC and ICN2 are funded by the CERCA Programme/Generalitat de Catalunya. J.L. acknowledges support from the Natural Science Foundation of Sichuan province (2022NSFSC1229). Part of the present work was performed in the frameworks of Universitat de Barcelona Nanoscience Ph.D. program and Universitat Autònoma de Barcelona Materials Science Ph.D. program. Y.L. acknowledges funding from the National Natural Science Foundation of China (Grant No. 22209034) and the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grants No. 2022LCX002). K.H.L. acknowledges the financial support of the National Natural Science Foundation of China (Grant No. 22208293).","publication_status":"published","pmid":1,"month":"05","citation":{"chicago":"Xing, Congcong, Yu Zhang, Ke Xiao, Xu Han, Yu Liu, Bingfei Nan, Maria Garcia Ramon, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se Nanocomposites.” <i>ACS Nano</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsnano.3c00495\">https://doi.org/10.1021/acsnano.3c00495</a>.","mla":"Xing, Congcong, et al. “Thermoelectric Performance of Surface-Engineered Cu1.5–XTe–Cu2Se Nanocomposites.” <i>ACS Nano</i>, vol. 17, no. 9, American Chemical Society, 2023, pp. 8442–52, doi:<a href=\"https://doi.org/10.1021/acsnano.3c00495\">10.1021/acsnano.3c00495</a>.","ama":"Xing C, Zhang Y, Xiao K, et al. Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. <i>ACS Nano</i>. 2023;17(9):8442-8452. doi:<a href=\"https://doi.org/10.1021/acsnano.3c00495\">10.1021/acsnano.3c00495</a>","ista":"Xing C, Zhang Y, Xiao K, Han X, Liu Y, Nan B, Ramon MG, Lim KH, Li J, Arbiol J, Poudel B, Nozariasbmarz A, Li W, Ibáñez M, Cabot A. 2023. Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. ACS Nano. 17(9), 8442–8452.","short":"C. Xing, Y. Zhang, K. Xiao, X. Han, Y. Liu, B. Nan, M.G. Ramon, K.H. Lim, J. Li, J. Arbiol, B. Poudel, A. Nozariasbmarz, W. Li, M. Ibáñez, A. Cabot, ACS Nano 17 (2023) 8442–8452.","apa":"Xing, C., Zhang, Y., Xiao, K., Han, X., Liu, Y., Nan, B., … Cabot, A. (2023). Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c00495\">https://doi.org/10.1021/acsnano.3c00495</a>","ieee":"C. Xing <i>et al.</i>, “Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites,” <i>ACS Nano</i>, vol. 17, no. 9. American Chemical Society, pp. 8442–8452, 2023."},"day":"09","oa_version":"None","article_processing_charge":"No","volume":17,"year":"2023","date_updated":"2023-10-04T11:29:22Z","publication":"ACS Nano","page":"8442-8452","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"}],"date_created":"2023-05-07T22:01:04Z","scopus_import":"1","external_id":{"isi":["000976063200001"],"pmid":["37071412"]},"date_published":"2023-05-09T00:00:00Z","publisher":"American Chemical Society","intvolume":"        17","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1},{"date_published":"2023-02-16T00:00:00Z","external_id":{"arxiv":["2007.14182"]},"date_created":"2023-05-07T22:01:04Z","scopus_import":"1","department":[{"_id":"TiBr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Scuola Normale Superiore - Edizioni della Normale","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2007.14182"}],"intvolume":"        24","year":"2023","oa":1,"page":"173-204","article_type":"original","publication":"Annali della Scuola Normale Superiore di Pisa - Classe di Scienze","date_updated":"2023-10-18T06:54:30Z","oa_version":"Preprint","citation":{"chicago":"Bonolis, Dante, and Timothy D Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” <i>Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale, 2023. <a href=\"https://doi.org/10.2422/2036-2145.202010_018\">https://doi.org/10.2422/2036-2145.202010_018</a>.","mla":"Bonolis, Dante, and Timothy D. Browning. “Uniform Bounds for Rational Points on Hyperelliptic Fibrations.” <i>Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze</i>, vol. 24, no. 1, Scuola Normale Superiore - Edizioni della Normale, 2023, pp. 173–204, doi:<a href=\"https://doi.org/10.2422/2036-2145.202010_018\">10.2422/2036-2145.202010_018</a>.","ieee":"D. Bonolis and T. D. Browning, “Uniform bounds for rational points on hyperelliptic fibrations,” <i>Annali della Scuola Normale Superiore di Pisa - Classe di Scienze</i>, vol. 24, no. 1. Scuola Normale Superiore - Edizioni della Normale, pp. 173–204, 2023.","apa":"Bonolis, D., &#38; Browning, T. D. (2023). Uniform bounds for rational points on hyperelliptic fibrations. <i>Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze</i>. Scuola Normale Superiore - Edizioni della Normale. <a href=\"https://doi.org/10.2422/2036-2145.202010_018\">https://doi.org/10.2422/2036-2145.202010_018</a>","short":"D. Bonolis, T.D. Browning, Annali Della Scuola Normale Superiore Di Pisa - Classe Di Scienze 24 (2023) 173–204.","ista":"Bonolis D, Browning TD. 2023. Uniform bounds for rational points on hyperelliptic fibrations. Annali della Scuola Normale Superiore di Pisa - Classe di Scienze. 24(1), 173–204.","ama":"Bonolis D, Browning TD. Uniform bounds for rational points on hyperelliptic fibrations. <i>Annali della Scuola Normale Superiore di Pisa - Classe di Scienze</i>. 2023;24(1):173-204. doi:<a href=\"https://doi.org/10.2422/2036-2145.202010_018\">10.2422/2036-2145.202010_018</a>"},"day":"16","month":"02","article_processing_charge":"No","volume":24,"arxiv":1,"abstract":[{"text":"We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface.\r\n","lang":"eng"}],"issue":"1","doi":"10.2422/2036-2145.202010_018","title":"Uniform bounds for rational points on hyperelliptic fibrations","author":[{"full_name":"Bonolis, Dante","last_name":"Bonolis","id":"6A459894-5FDD-11E9-AF35-BB24E6697425","first_name":"Dante"},{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","full_name":"Browning, Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177"}],"_id":"12916","publication_status":"published","status":"public","publication_identifier":{"issn":["0391-173X"],"eissn":["2036-2145"]}},{"day":"15","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"citation":{"chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">https://doi.org/10.15479/AT:ISTA:12933</a>.","mla":"Puixeu Sala, Gemma. <i>Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","short":"G. Puixeu Sala, (2023).","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>","ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 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(2023). Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12945\">https://doi.org/10.15479/AT:ISTA:12945</a>","ieee":"S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.","short":"S. Cremer, (2023).","ama":"Cremer S. Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12945\">10.15479/AT:ISTA:12945</a>","ista":"Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12945\">10.15479/AT:ISTA:12945</a>.","mla":"Cremer, Sylvia. <i>Data from: “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants” </i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12945\">10.15479/AT:ISTA:12945</a>.","chicago":"Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12945\">https://doi.org/10.15479/AT:ISTA:12945</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","file_date_updated":"2023-05-12T08:04:08Z","ddc":["570"],"date_published":"2023-05-12T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"}],"date_created":"2023-05-11T21:35:17Z","oa_version":"None","date_updated":"2023-08-07T13:09:09Z","status":"public","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","related_material":{"record":[{"id":"13127","relation":"used_in_publication","status":"public"}]},"author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"oa":1,"title":"Data from: \"Dynamic pathogen detection and social feedback shape collective hygiene in ants\" ","_id":"12945","year":"2023","abstract":[{"text":"basic data for use in code for experimental data analysis for manuscript under revision: \r\nDynamic pathogen detection and social feedback shape collective hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S","lang":"eng"}],"keyword":["collective behavior","host-pathogen interactions","social immunity","epidemiology","social insects","probabilistic modeling"],"doi":"10.15479/AT:ISTA:12945"},{"publisher":"Institute of Science and Technology 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Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12949\">https://doi.org/10.15479/AT:ISTA:12949</a>.","mla":"Barton, Nicholas H. <i>The Infinitesimal Model with Dominance</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12949\">10.15479/AT:ISTA:12949</a>.","short":"N.H. Barton, (2023).","ista":"Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12949\">10.15479/AT:ISTA:12949</a>.","ama":"Barton NH. The infinitesimal model with dominance. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12949\">10.15479/AT:ISTA:12949</a>","apa":"Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12949\">https://doi.org/10.15479/AT:ISTA:12949</a>","ieee":"N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023."},"department":[{"_id":"NiBa"}],"day":"13","oa_version":"Published Version","date_created":"2023-05-13T09:49:09Z","date_published":"2023-05-13T00:00:00Z","date_updated":"2025-05-28T11:57:00Z","project":[{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14452"}]},"status":"public","_id":"12949","title":"The infinitesimal model with dominance","oa":1,"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"doi":"10.15479/AT:ISTA:12949","keyword":["Quantitative genetics","infinitesimal model"],"abstract":[{"lang":"eng","text":"The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in  the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each  of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed."}],"year":"2023"},{"article_processing_charge":"Yes (via OA deal)","volume":62,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2023-10-04T11:34:10Z","success":1,"content_type":"application/pdf","checksum":"359bee38d94b7e0aa73925063cb8884d","access_level":"open_access","file_size":1240995,"relation":"main_file","creator":"dernst","file_name":"2023_CalculusEquations_Gladbach.pdf","date_created":"2023-10-04T11:34:10Z","file_id":"14393"}],"arxiv":1,"oa_version":"Published Version","file_date_updated":"2023-10-04T11:34:10Z","ddc":["510"],"month":"04","day":"28","citation":{"ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of dynamical optimal transport on periodic graphs. <i>Calculus of Variations and Partial Differential Equations</i>. 2023;62(5). doi:<a href=\"https://doi.org/10.1007/s00526-023-02472-z\">10.1007/s00526-023-02472-z</a>","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Calculus of Variations and Partial Differential Equations 62 (2023).","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2023. Homogenisation of dynamical optimal transport on periodic graphs. Calculus of Variations and Partial Differential Equations. 62(5), 143.","apa":"Gladbach, P., Kopfer, E., Maas, J., &#38; Portinale, L. (2023). Homogenisation of dynamical optimal transport on periodic graphs. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-023-02472-z\">https://doi.org/10.1007/s00526-023-02472-z</a>","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of dynamical optimal transport on periodic graphs,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 62, no. 5. Springer Nature, 2023.","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of Dynamical Optimal Transport on Periodic Graphs.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00526-023-02472-z\">https://doi.org/10.1007/s00526-023-02472-z</a>.","mla":"Gladbach, Peter, et al. “Homogenisation of Dynamical Optimal Transport on Periodic Graphs.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 62, no. 5, 143, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00526-023-02472-z\">10.1007/s00526-023-02472-z</a>."},"ec_funded":1,"publication_status":"published","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117). J.M and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—350398276. We thank the anonymous reviewer for the careful reading and for useful suggestions. Open access funding provided by Austrian Science Fund (FWF).","status":"public","project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"call_identifier":"FWF","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["1432-0835"],"issn":["0944-2669"]},"doi":"10.1007/s00526-023-02472-z","issue":"5","abstract":[{"text":"This paper deals with the large-scale behaviour of dynamical optimal transport on Zd\r\n-periodic graphs with general lower semicontinuous and convex energy densities. Our main contribution is a homogenisation result that describes the effective behaviour of the discrete problems in terms of a continuous optimal transport problem. The effective energy density can be explicitly expressed in terms of a cell formula, which is a finite-dimensional convex programming problem that depends non-trivially on the local geometry of the discrete graph and the discrete energy density. Our homogenisation result is derived from a Γ\r\n-convergence result for action functionals on curves of measures, which we prove under very mild growth conditions on the energy density. We investigate the cell formula in several cases of interest, including finite-volume discretisations of the Wasserstein distance, where non-trivial limiting behaviour occurs.","lang":"eng"}],"_id":"12959","author":[{"first_name":"Peter","last_name":"Gladbach","full_name":"Gladbach, Peter"},{"first_name":"Eva","last_name":"Kopfer","full_name":"Kopfer, Eva"},{"orcid":"0000-0002-0845-1338","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan"},{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","full_name":"Portinale, Lorenzo"}],"title":"Homogenisation of dynamical optimal transport on periodic graphs","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":"        62","publisher":"Springer Nature","scopus_import":"1","date_created":"2023-05-14T22:01:00Z","external_id":{"isi":["000980588900001"],"arxiv":["2110.15321"]},"date_published":"2023-04-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"article_type":"original","article_number":"143","date_updated":"2023-10-04T11:34:49Z","publication":"Calculus of Variations and Partial Differential Equations","year":"2023","oa":1}]