[{"scopus_import":"1","volume":15,"related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"article_number":"evad113","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7","intvolume":"        15","oa":1,"file_date_updated":"2023-08-01T06:58:34Z","publication":"Genome biology and evolution","_id":"13260","date_created":"2023-07-23T22:01:11Z","external_id":{"isi":["001023444700003"],"pmid":["37341535"]},"title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","date_updated":"2023-08-02T06:42:35Z","month":"07","date_published":"2023-07-01T00:00:00Z","article_processing_charge":"Yes","file":[{"content_type":"application/pdf","date_updated":"2023-08-01T06:58:34Z","file_size":2382587,"relation":"main_file","checksum":"70de3c4878de6efe00dc56de2df8812f","success":1,"access_level":"open_access","file_name":"2023_GBE_Barata.pdf","file_id":"13339","creator":"dernst","date_created":"2023-08-01T06:58:34Z"}],"citation":{"ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol. 15, no. 7. Oxford Academic, 2023.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38; Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>.","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>"},"type":"journal_article","ddc":["570"],"article_type":"original","abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","pmid":1,"quality_controlled":"1","doi":"10.1093/gbe/evad113","oa_version":"Published Version","publisher":"Oxford Academic","day":"01","department":[{"_id":"BeVi"}],"publication_identifier":{"eissn":["1759-6653"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"author":[{"full_name":"De Castro Barbosa Rodrigues Barata, Carolina","last_name":"De Castro Barbosa Rodrigues Barata","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","first_name":"Carolina"},{"last_name":"Snook","full_name":"Snook, Rhonda R.","first_name":"Rhonda R."},{"first_name":"Michael G.","full_name":"Ritchie, Michael G.","last_name":"Ritchie"},{"first_name":"Carolin","full_name":"Kosiol, Carolin","last_name":"Kosiol"}],"year":"2023"},{"main_file_link":[{"url":"https://doi.org/10.1126/science.adf5568","open_access":"1"}],"volume":380,"intvolume":"       380","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","issue":"6652","scopus_import":"1","month":"06","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","date_updated":"2023-12-13T11:41:07Z","article_processing_charge":"No","date_published":"2023-06-29T00:00:00Z","page":"1357-1362","publication":"Science","external_id":{"isi":["001106405600028"]},"date_created":"2023-07-23T22:01:12Z","_id":"13261","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"343-2022"}],"status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.","lang":"eng"}],"quality_controlled":"1","citation":{"ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>.","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362.","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023."},"type":"journal_article","article_type":"original","department":[{"_id":"EdHa"}],"publication_identifier":{"eissn":["1095-9203"]},"year":"2023","author":[{"first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","last_name":"Brückner"},{"last_name":"Chen","full_name":"Chen, Hongtao","first_name":"Hongtao"},{"last_name":"Barinov","full_name":"Barinov, Lev","first_name":"Lev"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"}],"isi":1,"oa_version":"Preprint","doi":"10.1126/science.adf5568","day":"29","publisher":"American Association for the Advancement of Science"},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-06-17T00:00:00Z","month":"06","title":"Provably-efficient and internally-deterministic parallel Union-Find","date_updated":"2023-07-31T10:54:32Z","external_id":{"arxiv":["2304.09331"]},"date_created":"2023-07-23T22:01:12Z","_id":"13262","page":"261-271","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","file_date_updated":"2023-07-31T10:53:08Z","quality_controlled":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited."}],"publication_status":"published","ddc":["000"],"type":"conference","citation":{"short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., &#38; Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Orlando, FL, United States, 2023, pp. 261–271.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2023:261-271. doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 261–71. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2023, pp. 261–71, doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271."},"file":[{"file_id":"13334","date_created":"2023-07-31T10:53:08Z","creator":"dernst","content_type":"application/pdf","date_updated":"2023-07-31T10:53:08Z","file_size":2087937,"checksum":"72e312aabf0c5248c99b5cd3a88e4c88","relation":"main_file","success":1,"access_level":"open_access","file_name":"2023_SPAA_Fedorov.pdf"}],"year":"2023","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2023-06-19","location":"Orlando, FL, United States","start_date":"2023-06-17"},"author":[{"first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"full_name":"Hashemi, Diba","last_name":"Hashemi","first_name":"Diba","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_identifier":{"isbn":["9781450395458"]},"day":"17","publisher":"Association for Computing Machinery","oa_version":"Published Version","arxiv":1,"doi":"10.1145/3558481.3591082"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","issue":"Supplement_1","oa":1,"intvolume":"        39","volume":39,"related_material":{"link":[{"relation":"software","url":"https://github.com/giang-trinh/trap-mvn"}]},"scopus_import":"1","ec_funded":1,"date_published":"2023-06-30T00:00:00Z","article_processing_charge":"Yes","month":"06","title":"Trap spaces of multi-valued networks: Definition, computation, and applications","date_updated":"2023-12-13T11:41:52Z","date_created":"2023-07-23T22:01:12Z","external_id":{"pmid":["37387165"],"isi":["001027457000060"]},"project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020"}],"_id":"13263","page":"i513-i522","file_date_updated":"2023-07-31T11:09:05Z","publication":"Bioinformatics","quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models."}],"publication_status":"published","article_type":"original","ddc":["000"],"citation":{"ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” <i>Bioinformatics</i>, vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.","short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522.","apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., &#38; Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>, vol. 39, no. Supplement_1, Oxford Academic, 2023, pp. i513–22, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>.","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.","chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>.","ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. 2023;39(Supplement_1):i513-i522. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>"},"type":"journal_article","file":[{"file_id":"13335","creator":"dernst","date_created":"2023-07-31T11:09:05Z","relation":"main_file","checksum":"ba3abe1171df1958413b7c7f957f5486","content_type":"application/pdf","date_updated":"2023-07-31T11:09:05Z","file_size":641736,"file_name":"2023_Bioinformatics_Trinh.pdf","success":1,"access_level":"open_access"}],"isi":1,"author":[{"last_name":"Trinh","full_name":"Trinh, Van Giang","first_name":"Van Giang"},{"first_name":"Belaid","last_name":"Benhamou","full_name":"Benhamou, Belaid"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel"}],"year":"2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ToHe"}],"publication_identifier":{"eissn":["1367-4811"],"issn":["1367-4803"]},"day":"30","publisher":"Oxford Academic","oa_version":"Published Version","doi":"10.1093/bioinformatics/btad262"},{"day":"09","publisher":"American Physical Society","oa_version":"Preprint","arxiv":1,"doi":"10.1103/PhysRevApplied.19.064032","year":"2023","isi":1,"author":[{"last_name":"Phan","full_name":"Phan, Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","first_name":"Duc T"},{"last_name":"Falthansl-Scheinecker","full_name":"Falthansl-Scheinecker, Paul","first_name":"Paul","id":"85b43b21-15b2-11ec-abd3-e2c252cc2285"},{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","first_name":"Umang","last_name":"Mishra","full_name":"Mishra, Umang"},{"first_name":"W. M.","full_name":"Strickland, W. M.","last_name":"Strickland"},{"last_name":"Langone","full_name":"Langone, D.","first_name":"D."},{"first_name":"J.","last_name":"Shabani","full_name":"Shabani, J."},{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P"}],"department":[{"_id":"AnHi"},{"_id":"OnHo"}],"publication_identifier":{"eissn":["2331-7019"]},"article_type":"original","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"citation":{"ieee":"D. T. Phan <i>et al.</i>, “Gate-tunable superconductor-semiconductor parametric amplifier,” <i>Physical Review Applied</i>, vol. 19, no. 6. American Physical Society, 2023.","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., &#38; Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>.","ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” <i>Physical Review Applied</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">https://doi.org/10.1103/PhysRevApplied.19.064032</a>.","ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. <i>Physical Review Applied</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1103/PhysRevApplied.19.064032\">10.1103/PhysRevApplied.19.064032</a>"},"type":"journal_article","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n"}],"external_id":{"arxiv":["2206.05746"],"isi":["001012022600004"]},"date_created":"2023-07-23T22:01:12Z","_id":"13264","publication":"Physical Review Applied","article_processing_charge":"No","date_published":"2023-06-09T00:00:00Z","month":"06","title":"Gate-tunable superconductor-semiconductor parametric amplifier","date_updated":"2023-11-30T10:56:03Z","scopus_import":"1","oa":1,"intvolume":"        19","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","issue":"6","article_number":"064032","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2206.05746"}],"related_material":{"record":[{"id":"14547","status":"public","relation":"dissertation_contains"}]},"volume":19},{"date_published":"2023-03-17T00:00:00Z","article_processing_charge":"No","title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","date_updated":"2023-12-13T11:34:59Z","month":"03","_id":"13265","date_created":"2023-07-23T22:01:13Z","external_id":{"isi":["001018739600002"],"arxiv":["2201.02374"]},"publication":"ACM Transactions on Graphics","article_number":"26","issue":"3","acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        42","oa":1,"volume":42,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.02374"}],"scopus_import":"1","author":[{"first_name":"Fanchao","last_name":"Zhong","full_name":"Zhong, Fanchao"},{"first_name":"Yonglai","last_name":"Xu","full_name":"Xu, Yonglai"},{"id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","first_name":"Haisen","full_name":"Zhao, Haisen","orcid":"0000-0002-6389-1045","last_name":"Zhao"},{"full_name":"Lu, Lin","last_name":"Lu","first_name":"Lin"}],"isi":1,"year":"2023","department":[{"_id":"BeBi"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"publisher":"Association for Computing Machinery","day":"17","doi":"10.1145/3575859","oa_version":"Preprint","arxiv":1,"quality_controlled":"1","publication_status":"published","abstract":[{"text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality.","lang":"eng"}],"language":[{"iso":"eng"}],"status":"public","article_type":"original","type":"journal_article","citation":{"apa":"Zhong, F., Xu, Y., Zhao, H., &#38; Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>","short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).","ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3. Association for Computing Machinery, 2023.","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>.","ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>","mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>.","ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26."}},{"volume":240,"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.","oa":1,"intvolume":"       240","scopus_import":"1","date_updated":"2024-01-29T11:21:55Z","title":"Tale of cAMP as a second messenger in auxin signaling and beyond","month":"10","date_published":"2023-10-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-01-29T11:21:43Z","publication":"New Phytologist","page":"489-495","project":[{"name":"Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051","name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors"}],"_id":"13266","date_created":"2023-07-23T22:01:13Z","external_id":{"isi":["001026321500001"],"pmid":["37434303"]},"publication_status":"published","abstract":[{"lang":"eng","text":"The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general."}],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","pmid":1,"quality_controlled":"1","file":[{"date_created":"2024-01-29T11:21:43Z","creator":"dernst","file_id":"14898","access_level":"open_access","success":1,"file_name":"2023_NewPhytologist_Qi.pdf","file_size":974464,"date_updated":"2024-01-29T11:21:43Z","content_type":"application/pdf","checksum":"6d9bbd45b8e7bb3ceee2586d447bacb2","relation":"main_file"}],"citation":{"short":"L. Qi, J. Friml, New Phytologist 240 (2023) 489–495.","apa":"Qi, L., &#38; Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>","ieee":"L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” <i>New Phytologist</i>, vol. 240, no. 2. Wiley, pp. 489–495, 2023.","ama":"Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. 2023;240(2):489-495. doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>","chicago":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>.","mla":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>.","ista":"Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495."},"type":"journal_article","ddc":["580"],"article_type":"original","department":[{"_id":"JiFr"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"isi":1,"year":"2023","doi":"10.1111/nph.19123","oa_version":"Published Version","publisher":"Wiley","day":"01"},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"article_type":"original","citation":{"short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>."},"type":"journal_article","author":[{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp"},{"id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder","last_name":"Miguel Villalba","full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430"},{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","last_name":"Michalska"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","full_name":"Lyudchik, Julia","last_name":"Lyudchik"},{"first_name":"Donglai","full_name":"Wei, Donglai","last_name":"Wei"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson"},{"last_name":"Troidl","full_name":"Troidl, Jakob","first_name":"Jakob"},{"first_name":"Johanna","full_name":"Beyer, Johanna","last_name":"Beyer"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","full_name":"Ben Simon, Yoav","last_name":"Ben Simon"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"full_name":"Cenameri, Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban"},{"first_name":"Johannes","last_name":"Broichhagen","full_name":"Broichhagen, Johannes"},{"full_name":"Grant, Seth G.N.","last_name":"Grant","first_name":"Seth G.N."},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}],"isi":1,"year":"2023","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"publisher":"Springer Nature","day":"01","doi":"10.1038/s41592-023-01936-6","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","intvolume":"        20","oa":1,"volume":20,"related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}],"record":[{"id":"12817","status":"public","relation":"research_data"},{"id":"14770","relation":"shorter_version","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-023-01936-6"}],"scopus_import":"1","date_published":"2023-08-01T00:00:00Z","article_processing_charge":"Yes","ec_funded":1,"title":"Dense 4D nanoscale reconstruction of living brain tissue","date_updated":"2024-01-10T08:37:48Z","month":"08","project":[{"name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","call_identifier":"FWF"},{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057","_id":"2668BFA0-B435-11E9-9278-68D0E5697425"}],"_id":"13267","date_created":"2023-07-23T22:01:13Z","external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"publication":"Nature Methods","page":"1256-1265"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.01587","open_access":"1"}],"volume":30,"oa":1,"intvolume":"        30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The first author is supported by the ERC Synergy Grant HyperK. The second author is supported by the Max Planck Institute for Mathematics and the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","issue":"1","page":"125-141","publication":"Mathematical Research Letters","external_id":{"isi":["001027656000006"],"arxiv":["2108.01587"]},"date_created":"2023-07-23T22:01:14Z","project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"_id":"13268","month":"06","date_updated":"2024-01-16T12:00:47Z","title":"On type II degenerations of hyperkähler manifolds","ec_funded":1,"article_processing_charge":"No","date_published":"2023-06-21T00:00:00Z","type":"journal_article","citation":{"chicago":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>. International Press, 2023. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>.","ama":"Huybrechts D, Mauri M. On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. 2023;30(1):125-141. doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>","mla":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>, vol. 30, no. 1, International Press, 2023, pp. 125–41, doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>.","ista":"Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 30(1), 125–141.","apa":"Huybrechts, D., &#38; Mauri, M. (2023). On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. International Press. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>","short":"D. Huybrechts, M. Mauri, Mathematical Research Letters 30 (2023) 125–141.","ieee":"D. Huybrechts and M. Mauri, “On type II degenerations of hyperkähler manifolds,” <i>Mathematical Research Letters</i>, vol. 30, no. 1. International Press, pp. 125–141, 2023."},"article_type":"original","status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations."}],"quality_controlled":"1","arxiv":1,"oa_version":"Preprint","doi":"10.4310/mrl.2023.v30.n1.a6","day":"21","publisher":"International Press","department":[{"_id":"TaHa"}],"publication_identifier":{"issn":["1073-2780"],"eissn":["1945-001X"]},"year":"2023","author":[{"last_name":"Huybrechts","full_name":"Huybrechts, D.","first_name":"D."},{"first_name":"Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130","full_name":"Mauri, Mirko","last_name":"Mauri"}],"isi":1},{"department":[{"_id":"MaMo"}],"publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"isi":1,"author":[{"first_name":"Nikita","last_name":"Polyanskii","full_name":"Polyanskii, Nikita"},{"full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"}],"year":"2023","oa_version":"Preprint","arxiv":1,"doi":"10.1109/TIT.2023.3292219","day":"04","publisher":"Institute of Electrical and Electronics Engineers","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point."}],"quality_controlled":"1","citation":{"mla":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10, Institute of Electrical and Electronics Engineers, 2023, pp. 6340–57, doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>.","ista":"Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on Information Theory. 69(10), 6340–6357.","ama":"Polyanskii N, Zhang Y. Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. 2023;69(10):6340-6357. doi:<a href=\"https://doi.org/10.1109/TIT.2023.3292219\">10.1109/TIT.2023.3292219</a>","chicago":"Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>.","ieee":"N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” <i>IEEE Transactions on Information Theory</i>, vol. 69, no. 10. Institute of Electrical and Electronics Engineers, pp. 6340–6357, 2023.","short":"N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 6340–6357.","apa":"Polyanskii, N., &#38; Zhang, Y. (2023). Codes for the Z-channel. <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TIT.2023.3292219\">https://doi.org/10.1109/TIT.2023.3292219</a>"},"type":"journal_article","article_type":"original","month":"07","title":"Codes for the Z-channel","date_updated":"2024-01-29T11:10:54Z","date_published":"2023-07-04T00:00:00Z","article_processing_charge":"No","page":"6340-6357","publication":"IEEE Transactions on Information Theory","date_created":"2023-07-23T22:01:14Z","external_id":{"isi":["001069680100011"],"arxiv":["2105.01427"]},"_id":"13269","volume":69,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.01427","open_access":"1"}],"acknowledgement":"Nikita Polyanskii’s research was conducted in part during October 2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute of Science and Technology. His work was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang is supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","intvolume":"        69","oa":1,"scopus_import":"1"},{"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"department":[{"_id":"UlWa"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","isi":1,"author":[{"id":"6ab6e556-f394-11eb-9cf6-9dfb78f00d8d","first_name":"Florestan R","last_name":"Brunck","full_name":"Brunck, Florestan R"}],"doi":"10.1007/s00454-023-00500-5","arxiv":1,"oa_version":"Published Version","publisher":"Springer Nature","day":"05","abstract":[{"lang":"eng","text":"Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0\r\n such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses."}],"publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"file_size":1466020,"date_updated":"2024-01-29T11:15:22Z","content_type":"application/pdf","checksum":"865e68daafdd4edcfc280172ec50f5ea","relation":"main_file","access_level":"open_access","success":1,"file_name":"2023_DiscreteComputGeometry_Brunck.pdf","file_id":"14897","creator":"dernst","date_created":"2024-01-29T11:15:22Z"}],"type":"journal_article","citation":{"ista":"Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 70(3), 1059–1089.","mla":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3, Springer Nature, 2023, pp. 1059–89, doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>.","ama":"Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. 2023;70(3):1059-1089. doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>","chicago":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>.","ieee":"F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant curvature,” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3. Springer Nature, pp. 1059–1089, 2023.","short":"F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089.","apa":"Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>"},"ddc":["510"],"article_type":"original","title":"Iterated medial triangle subdivision in surfaces of constant curvature","date_updated":"2024-01-29T11:16:16Z","month":"07","article_processing_charge":"Yes (via OA deal)","date_published":"2023-07-05T00:00:00Z","publication":"Discrete and Computational Geometry","file_date_updated":"2024-01-29T11:15:22Z","page":"1059-1089","_id":"13270","external_id":{"arxiv":["2107.04112"],"isi":["001023742800003"]},"date_created":"2023-07-23T22:01:14Z","volume":70,"oa":1,"intvolume":"        70","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","scopus_import":"1"},{"day":"08","publisher":"Springer Nature","arxiv":1,"oa_version":"Preprint","doi":"10.1007/s00023-023-01345-7","isi":1,"author":[{"last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"year":"2023","publication_identifier":{"issn":["1424-0637"]},"department":[{"_id":"JaMa"}],"article_type":"original","type":"journal_article","citation":{"ama":"Zhang H. Some convexity and monotonicity results of trace functionals. <i>Annales Henri Poincare</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s00023-023-01345-7\">10.1007/s00023-023-01345-7</a>","chicago":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” <i>Annales Henri Poincare</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00023-023-01345-7\">https://doi.org/10.1007/s00023-023-01345-7</a>.","ista":"Zhang H. 2023. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare.","mla":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” <i>Annales Henri Poincare</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00023-023-01345-7\">10.1007/s00023-023-01345-7</a>.","apa":"Zhang, H. (2023). Some convexity and monotonicity results of trace functionals. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-023-01345-7\">https://doi.org/10.1007/s00023-023-01345-7</a>","short":"H. Zhang, Annales Henri Poincare (2023).","ieee":"H. Zhang, “Some convexity and monotonicity results of trace functionals,” <i>Annales Henri Poincare</i>. Springer Nature, 2023."},"quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"epub_ahead","abstract":[{"text":"In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,\r\nfor parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems.","lang":"eng"}],"date_created":"2023-07-23T22:01:15Z","external_id":{"isi":["001025709100001"],"arxiv":["2108.05785"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis"}],"_id":"13271","publication":"Annales Henri Poincare","ec_funded":1,"date_published":"2023-07-08T00:00:00Z","article_processing_charge":"No","month":"07","title":"Some convexity and monotonicity results of trace functionals","date_updated":"2023-12-13T11:33:46Z","scopus_import":"1","acknowledgement":"I am grateful to Boguslaw Zegarliński for asking me the questions in [3] and for helpful communication. I also want to thank Paata Ivanisvili for drawing [25] to my attention and for useful correspondence. Many thanks to the anonymous referee for the valuable comments and for pointing out some errors in an earlier version of the paper. This work is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.05785"}]},{"project":[{"name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","grant_number":"662960","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"_id":"13274","date_created":"2023-07-24T09:43:59Z","external_id":{"isi":["001052929900004"],"arxiv":["2306.05098"]},"publication":"Physical Review Letters","date_published":"2023-07-21T00:00:00Z","keyword":["General Physics and Astronomy"],"article_processing_charge":"No","title":"Direct path from turbulence to time-periodic solutions","date_updated":"2023-12-13T11:40:19Z","month":"07","article_number":"034002","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Baofang Song as well as the developers of Channelflow for sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful discussions. This work was supported by a grant from the Simons Foundation (662960, B. H.).","issue":"3","oa":1,"intvolume":"       131","volume":131,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.05098","open_access":"1"}],"publisher":"American Physical Society","day":"21","doi":"10.1103/physrevlett.131.034002","arxiv":1,"oa_version":"Preprint","isi":1,"author":[{"full_name":"Paranjape, Chaitanya S","last_name":"Paranjape","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","first_name":"Chaitanya S"},{"first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz"},{"first_name":"Yohann","last_name":"Duguet","full_name":"Duguet, Yohann"},{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"year":"2023","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"department":[{"_id":"GradSch"},{"_id":"BjHo"}],"article_type":"original","type":"journal_article","citation":{"mla":"Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” <i>Physical Review Letters</i>, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.131.034002\">10.1103/physrevlett.131.034002</a>.","ista":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.","ama":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. <i>Physical Review Letters</i>. 2023;131(3). doi:<a href=\"https://doi.org/10.1103/physrevlett.131.034002\">10.1103/physrevlett.131.034002</a>","chicago":"Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.131.034002\">https://doi.org/10.1103/physrevlett.131.034002</a>.","ieee":"C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” <i>Physical Review Letters</i>, vol. 131, no. 3. American Physical Society, 2023.","apa":"Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., &#38; Hof, B. (2023). Direct path from turbulence to time-periodic solutions. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.131.034002\">https://doi.org/10.1103/physrevlett.131.034002</a>","short":"C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023)."},"quality_controlled":"1","abstract":[{"text":"Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public"},{"citation":{"ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>.","mla":"Rammelmüller, Lukas, et al. <i>Codebase Release 1.0 for FermiFCI</i>. SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">https://doi.org/10.21468/scipostphyscodeb.12-r1.0</a>.","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12-r1.0\">10.21468/scipostphyscodeb.12-r1.0</a>"},"type":"research_data_reference","ddc":["530"],"abstract":[{"lang":"eng","text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"13276"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"doi":"10.21468/scipostphyscodeb.12-r1.0","oa_version":"Published Version","_id":"13275","publisher":"SciPost Foundation","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"date_created":"2023-07-24T10:46:23Z","day":"19","date_updated":"2023-07-31T09:16:02Z","title":"Codebase release 1.0 for FermiFCI","department":[{"_id":"MiLe"}],"month":"04","author":[{"first_name":"Lukas","full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"date_published":"2023-04-19T00:00:00Z","article_processing_charge":"No","year":"2023","ec_funded":1},{"title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","date_updated":"2023-07-31T09:16:02Z","month":"04","article_processing_charge":"No","date_published":"2023-04-19T00:00:00Z","ec_funded":1,"publication":"SciPost Physics Codebases","file_date_updated":"2023-07-31T09:09:23Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"_id":"13276","external_id":{"arxiv":["2202.04603"]},"date_created":"2023-07-24T10:47:15Z","related_material":{"record":[{"id":"13275","relation":"research_data","status":"public"}]},"article_number":"12","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","department":[{"_id":"MiLe"}],"publication_identifier":{"issn":["2949-804X"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","author":[{"first_name":"Lukas","last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"doi":"10.21468/scipostphyscodeb.12","arxiv":1,"oa_version":"Published Version","publisher":"SciPost Foundation","day":"19","publication_status":"published","abstract":[{"lang":"eng","text":"<jats:p>We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.</jats:p>"}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","file":[{"access_level":"open_access","success":1,"file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","file_size":551418,"date_updated":"2023-07-31T09:09:23Z","content_type":"application/pdf","checksum":"f583a70fe915d2208c803f5afb426daa","relation":"main_file","creator":"dernst","date_created":"2023-07-31T09:09:23Z","file_id":"13330"}],"citation":{"ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12.","mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” <i>SciPost Physics Codebases</i>, 12, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">10.21468/scipostphyscodeb.12</a>.","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. <i>SciPost Physics Codebases</i>. 2023. doi:<a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">10.21468/scipostphyscodeb.12</a>","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” <i>SciPost Physics Codebases</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">https://doi.org/10.21468/scipostphyscodeb.12</a>.","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” <i>SciPost Physics Codebases</i>. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., &#38; Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. <i>SciPost Physics Codebases</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscodeb.12\">https://doi.org/10.21468/scipostphyscodeb.12</a>","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023)."},"type":"journal_article","ddc":["530"],"article_type":"original"},{"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results."}],"quality_controlled":"1","citation":{"ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029.","mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” <i>SciPost Physics Core</i>, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">10.21468/scipostphyscore.6.2.029</a>.","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. <i>SciPost Physics Core</i>. 2023;6(2). doi:<a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">10.21468/scipostphyscore.6.2.029</a>","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” <i>SciPost Physics Core</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">https://doi.org/10.21468/scipostphyscore.6.2.029</a>.","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” <i>SciPost Physics Core</i>, vol. 6, no. 2. SciPost Foundation, 2023.","apa":"Tucci, G., De Nicola, S., Wald, S., &#38; Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. <i>SciPost Physics Core</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphyscore.6.2.029\">https://doi.org/10.21468/scipostphyscore.6.2.029</a>","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023)."},"type":"journal_article","file":[{"file_size":523236,"date_updated":"2023-07-31T09:02:27Z","content_type":"application/pdf","checksum":"b472bc82108747eda5d52adf9e2ac7f3","relation":"main_file","access_level":"open_access","success":1,"file_name":"2023_SciPostPhysCore_Tucci.pdf","file_id":"13329","creator":"dernst","date_created":"2023-07-31T09:02:27Z"}],"article_type":"original","ddc":["530"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["2666-9366"]},"department":[{"_id":"MaSe"}],"year":"2023","author":[{"full_name":"Tucci, Gennaro","last_name":"Tucci","first_name":"Gennaro"},{"id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","last_name":"De Nicola"},{"last_name":"Wald","full_name":"Wald, Sascha","first_name":"Sascha"},{"last_name":"Gambassi","full_name":"Gambassi, Andrea","first_name":"Andrea"}],"arxiv":1,"oa_version":"Published Version","doi":"10.21468/scipostphyscore.6.2.029","day":"14","publisher":"SciPost Foundation","volume":6,"oa":1,"intvolume":"         6","acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"029","month":"04","date_updated":"2023-07-31T09:03:28Z","title":"Stochastic representation of the quantum quartic oscillator","ec_funded":1,"article_processing_charge":"No","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"date_published":"2023-04-14T00:00:00Z","publication":"SciPost Physics Core","file_date_updated":"2023-07-31T09:02:27Z","external_id":{"arxiv":["2211.01923"]},"date_created":"2023-07-24T10:47:46Z","_id":"13277","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}]},{"publication_identifier":{"issn":["2542-4653"]},"department":[{"_id":"MiLe"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"author":[{"full_name":"Rammelmüller, Lukas","last_name":"Rammelmüller","first_name":"Lukas"},{"last_name":"Huber","full_name":"Huber, David","first_name":"David"},{"last_name":"Čufar","full_name":"Čufar, Matija","first_name":"Matija"},{"full_name":"Brand, Joachim","last_name":"Brand","first_name":"Joachim"},{"first_name":"Hans-Werner","full_name":"Hammer, Hans-Werner","last_name":"Hammer"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"year":"2023","doi":"10.21468/scipostphys.14.1.006","oa_version":"Published Version","arxiv":1,"publisher":"SciPost Foundation","day":"24","abstract":[{"lang":"eng","text":"We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity \"breaks\" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms."}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","quality_controlled":"1","file":[{"checksum":"ffdb70b9ae7aa45ea4ea6096ecbd6431","relation":"main_file","file_size":1163444,"date_updated":"2023-07-31T08:44:38Z","content_type":"application/pdf","file_name":"2023_SciPostPhysics_Rammelmueller.pdf","access_level":"open_access","success":1,"file_id":"13328","creator":"dernst","date_created":"2023-07-31T08:44:38Z"}],"citation":{"ieee":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev, “Magnetic impurity in a one-dimensional few-fermion system,” <i>SciPost Physics</i>, vol. 14, no. 1. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., &#38; Volosniev, A. (2023). Magnetic impurity in a one-dimensional few-fermion system. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">https://doi.org/10.21468/scipostphys.14.1.006</a>","short":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev, SciPost Physics 14 (2023).","mla":"Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” <i>SciPost Physics</i>, vol. 14, no. 1, 006, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">10.21468/scipostphys.14.1.006</a>.","ista":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1), 006.","chicago":"Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">https://doi.org/10.21468/scipostphys.14.1.006</a>.","ama":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic impurity in a one-dimensional few-fermion system. <i>SciPost Physics</i>. 2023;14(1). doi:<a href=\"https://doi.org/10.21468/scipostphys.14.1.006\">10.21468/scipostphys.14.1.006</a>"},"type":"journal_article","ddc":["530"],"article_type":"original","title":"Magnetic impurity in a one-dimensional few-fermion system","date_updated":"2023-12-13T11:39:32Z","month":"01","date_published":"2023-01-24T00:00:00Z","article_processing_charge":"No","keyword":["General Physics and Astronomy"],"file_date_updated":"2023-07-31T08:44:38Z","publication":"SciPost Physics","_id":"13278","date_created":"2023-07-24T10:48:23Z","external_id":{"isi":["001000325800008"],"arxiv":["2204.01606"]},"volume":14,"article_number":"006","issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        14","scopus_import":"1"},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"13312","status":"public","relation":"part_of_dissertation"},{"id":"12118","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8910"},{"status":"public","relation":"research_data","id":"12522"}]},"date_created":"2023-07-24T14:10:45Z","_id":"13286","project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"},{"name":"Conventional and unconventional topological superconductors","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606"}],"page":"184","file_date_updated":"2023-08-11T14:39:17Z","supervisor":[{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"ec_funded":1,"date_published":"2023-07-21T00:00:00Z","article_processing_charge":"No","month":"07","date_updated":"2024-02-21T12:35:34Z","title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"ddc":["530"],"citation":{"ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","mla":"Valentini, Marco. <i>Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>.","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13286\">10.15479/at:ista:13286</a>","chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>.","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","apa":"Valentini, M. (2023). <i>Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13286\">https://doi.org/10.15479/at:ista:13286</a>"},"type":"dissertation","file":[{"relation":"source_file","checksum":"666ee31c7eade89679806287c062fa14","file_size":56121429,"content_type":"application/x-zip-compressed","date_updated":"2023-08-11T10:01:34Z","file_name":"PhD_thesis_Valentini_final.zip","access_level":"closed","file_id":"14033","date_created":"2023-08-11T09:27:39Z","creator":"mvalenti"},{"file_id":"14035","creator":"mvalenti","date_created":"2023-08-11T14:39:17Z","checksum":"0992f2ebef152dee8e70055350ebbb55","relation":"main_file","content_type":"application/pdf","date_updated":"2023-08-11T14:39:17Z","file_size":38199711,"file_name":"PhD_thesis_Valentini_final_validated.pdf","access_level":"open_access"}],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices."}],"day":"21","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","doi":"10.15479/at:ista:13286","author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco","last_name":"Valentini"}],"year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"department":[{"_id":"GradSch"},{"_id":"GeKa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","oa":1,"intvolume":"       261","volume":261,"alternative_title":["LIPIcs"],"date_published":"2023-07-05T00:00:00Z","article_processing_charge":"Yes","ec_funded":1,"title":"Regular methods for operator precedence languages","date_updated":"2023-07-31T08:38:38Z","month":"07","_id":"13292","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"date_created":"2023-07-24T15:11:41Z","external_id":{"arxiv":["2305.03447"]},"file_date_updated":"2023-07-24T15:11:05Z","publication":"50th International Colloquium on Automata, Languages, and Programming","page":"129:1--129:20","quality_controlled":"1","publication_status":"published","abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","ddc":["000"],"file":[{"creator":"esarac","date_created":"2023-07-24T15:11:05Z","file_id":"13293","file_name":"icalp23.pdf","access_level":"open_access","success":1,"relation":"main_file","checksum":"5d4c8932ef3450615a53b9bb15d92eb2","file_size":859379,"date_updated":"2023-07-24T15:11:05Z","content_type":"application/pdf"}],"type":"conference","citation":{"ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">10.4230/LIPIcs.ICALP.2023.129</a>","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">https://doi.org/10.4230/LIPIcs.ICALP.2023.129</a>.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">10.4230/LIPIcs.ICALP.2023.129</a>.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Regular methods for operator precedence languages. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.129\">https://doi.org/10.4230/LIPIcs.ICALP.2023.129</a>","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20."},"author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kebis","full_name":"Kebis, Pavol","first_name":"Pavol"},{"full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien"},{"full_name":"Sarac, Naci E","last_name":"Sarac","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10"},"year":"2023","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"05","doi":"10.4230/LIPIcs.ICALP.2023.129","oa_version":"Published Version","arxiv":1},{"publication":"Computer Aided Verification","file_date_updated":"2023-07-31T08:11:20Z","page":"358–382","project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"_id":"13310","external_id":{"arxiv":["2305.15979"]},"date_created":"2023-07-25T18:32:40Z","title":"Monitoring algorithmic fairness","date_updated":"2023-09-05T15:14:00Z","month":"07","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-07-18T00:00:00Z","ec_funded":1,"volume":13965,"alternative_title":["LNCS"],"oa":1,"intvolume":"     13965","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1007/978-3-031-37703-7_17","arxiv":1,"oa_version":"Published Version","publisher":"Springer Nature","day":"18","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031377037"],"eissn":["1611-3349"],"isbn":["9783031377020"]},"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2023","conference":{"end_date":"2023-07-22","location":"Paris, France","start_date":"2023-07-17","name":"CAV: Computer Aided Verification"},"author":[{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mahyar","id":"f1dedef5-2f78-11ee-989a-c4c97bccf506","full_name":"Karimi, Mahyar","orcid":"0009-0005-0820-1696","last_name":"Karimi"},{"orcid":"0000-0001-8974-2542","full_name":"Kueffner, Konstantin","last_name":"Kueffner","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin"},{"id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","last_name":"Mallik"}],"file":[{"creator":"dernst","date_created":"2023-07-31T08:11:20Z","file_id":"13327","access_level":"open_access","success":1,"file_name":"2023_LNCS_CAV_HenzingerT.pdf","file_size":647760,"content_type":"application/pdf","date_updated":"2023-07-31T08:11:20Z","checksum":"ccaf94bf7d658ba012c016e11869b54c","relation":"main_file"}],"citation":{"ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” <i>Computer Aided Verification</i>, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:<a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">10.1007/978-3-031-37703-7_17</a>.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: <i>Computer Aided Verification</i>. Vol 13965. Springer Nature; 2023:358–382. doi:<a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">10.1007/978-3-031-37703-7_17</a>","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In <i>Computer Aided Verification</i>, 13965:358–382. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">https://doi.org/10.1007/978-3-031-37703-7_17</a>.","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13965, pp. 358–382.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382.","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., &#38; Mallik, K. (2023). Monitoring algorithmic fairness. In <i>Computer Aided Verification</i> (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37703-7_17\">https://doi.org/10.1007/978-3-031-37703-7_17</a>"},"type":"conference","ddc":["000"],"abstract":[{"lang":"eng","text":"Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation."}],"publication_status":"published","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1"}]