[{"conference":{"end_date":"2022-06-17","name":"PLDI: Programming Language Design and Implementation","start_date":"2022-06-13","location":"San Diego, CA, United States"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","month":"06","oa_version":"Published Version","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"citation":{"ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>","ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>.","ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457."},"type":"conference","author":[{"first_name":"Dorde","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic"},{"first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan","last_name":"Chang"},{"full_name":"Bolignano, Pauline","first_name":"Pauline","last_name":"Bolignano"},{"last_name":"Raimondi","first_name":"Franco","full_name":"Raimondi, Franco"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2022-06-27T07:38:21Z","status":"public","has_accepted_license":"1","isi":1,"language":[{"iso":"eng"}],"ddc":["000"],"file":[{"file_size":318697,"access_level":"open_access","file_id":"11466","content_type":"application/pdf","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","file_name":"2022_PLDI_Zikelic.pdf","creator":"dernst","success":1,"date_created":"2022-06-27T07:38:21Z","relation":"main_file","date_updated":"2022-06-27T07:38:21Z"}],"date_updated":"2025-04-14T07:52:47Z","date_created":"2022-06-21T09:26:15Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"oa":1,"publication_identifier":{"isbn":["9781450392655"]},"corr_author":"1","_id":"11459","title":"Differential cost analysis with simultaneous potentials and anti-potentials","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2022-06-09T00:00:00Z","year":"2022","doi":"10.1145/3519939.3523435","day":"09","acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt).","fulldoi":"https://doi.org/10.1145/3519939.3523435","ec_funded":1,"abstract":[{"text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples.","lang":"eng"}],"project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"arxiv":1,"publisher":"Association for Computing Machinery","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","page":"442-457","external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]}},{"isi":1,"language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"ddc":["570"],"status":"public","has_accepted_license":"1","date_updated":"2025-06-11T13:34:57Z","date_created":"2022-06-23T14:28:55Z","file":[{"file_size":7552298,"access_level":"open_access","file_id":"11461","content_type":"application/pdf","checksum":"525d2618e855139089bbfc3e3d49d1b2","creator":"dernst","file_name":"2022_MolecularAutism_Schaaf.pdf","success":1,"date_created":"2022-06-24T08:22:59Z","date_updated":"2022-06-24T08:22:59Z","relation":"main_file"}],"month":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","citation":{"ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022.","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","quality_controlled":"1","file_date_updated":"2022-06-24T08:22:59Z","type":"journal_article","author":[{"full_name":"Schaaf, Zachary A.","first_name":"Zachary A.","last_name":"Schaaf"},{"last_name":"Tat","full_name":"Tat, Lyvin","first_name":"Lyvin"},{"first_name":"Noemi","full_name":"Cannizzaro, Noemi","last_name":"Cannizzaro"},{"last_name":"Green","full_name":"Green, Ralph","first_name":"Ralph"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Zarbalis, Konstantinos S.","first_name":"Konstantinos S.","last_name":"Zarbalis"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life."}],"volume":13,"doi":"10.1186/s13229-022-00508-3","year":"2022","day":"22","acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","fulldoi":"https://doi.org/10.1186/s13229-022-00508-3","keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"pmid":1,"publisher":"Springer Nature","publication":"Molecular Autism","external_id":{"pmid":["35733184"],"isi":["000814641400001"]},"_id":"11460","department":[{"_id":"SiHi"}],"oa":1,"publication_identifier":{"issn":["2040-2392"]},"article_type":"original","date_published":"2022-06-22T00:00:00Z","article_number":"27","intvolume":"        13","scopus_import":"1","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","license":"https://creativecommons.org/licenses/by/4.0/"},{"volume":106,"abstract":[{"text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens.","lang":"eng"}],"fulldoi":"https://doi.org/10.1007/s00253-022-12022-w","acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","day":"01","year":"2022","doi":"10.1007/s00253-022-12022-w","page":"5093-5103","external_id":{"isi":["000813677500001"],"pmid":["35723693"]},"publication":"Applied Microbiology and Biotechnology","publisher":"Springer Nature","pmid":1,"_id":"11462","publication_identifier":{"issn":["0175-7598"],"eissn":["1432-0614"]},"department":[{"_id":"GradSch"},{"_id":"LeSa"}],"date_published":"2022-08-01T00:00:00Z","article_type":"original","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","scopus_import":"1","intvolume":"       106","language":[{"iso":"eng"}],"isi":1,"status":"public","date_created":"2022-06-26T22:01:34Z","date_updated":"2023-10-10T07:15:02Z","citation":{"ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>","ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022.","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103."},"oa_version":"None","month":"08","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Dormeshkin","first_name":"Dmitri","full_name":"Dormeshkin, Dmitri"},{"last_name":"Shapira","first_name":"Michail","full_name":"Shapira, Michail"},{"first_name":"Alena","full_name":"Karputs, Alena","last_name":"Karputs"},{"id":"62304f89-eb97-11eb-a6c2-8903dd183976","last_name":"Kavaleuski","orcid":"0000-0003-2091-526X","first_name":"Anton","full_name":"Kavaleuski, Anton"},{"full_name":"Kuzminski, Ivan","first_name":"Ivan","last_name":"Kuzminski"},{"first_name":"Elena","full_name":"Stepanova, Elena","last_name":"Stepanova"},{"full_name":"Gilep, Andrei","first_name":"Andrei","last_name":"Gilep"}],"type":"journal_article"},{"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"issue":"22","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"12732","relation":"dissertation_contains"}]},"date_updated":"2026-04-07T13:26:31Z","date_created":"2022-06-29T20:19:51Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","oa_version":"Preprint","citation":{"ista":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. 2022. Localization of a mobile impurity interacting with an Anderson insulator. Physical Review B. 105(22), 224208.","short":"P. Brighi, A. Michailidis, K. Kirova, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","mla":"Brighi, Pietro, et al. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, 224208, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>.","chicago":"Brighi, Pietro, Alexios Michailidis, Kristina Kirova, Dmitry A. Abanin, and Maksym Serbyn. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>.","ama":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>","ieee":"P. Brighi, A. Michailidis, K. Kirova, D. A. Abanin, and M. Serbyn, “Localization of a mobile impurity interacting with an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","apa":"Brighi, P., Michailidis, A., Kirova, K., Abanin, D. A., &#38; Serbyn, M. (2022). Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>"},"author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","orcid":"0000-0002-7969-2729","first_name":"Pietro","full_name":"Brighi, Pietro"},{"full_name":"Michailidis, Alexios","first_name":"Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kirova","id":"4aeda2ae-f847-11ec-98e0-c4a66fe174d4","full_name":"Kirova, Kristina","first_name":"Kristina"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A.","first_name":"Dmitry A."},{"full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","year":"2022","doi":"10.1103/physrevb.105.224208","fulldoi":"https://doi.org/10.1103/physrevb.105.224208","day":"27","acknowledgement":"We thank M. Ljubotina for insightful discussions. P. B., A. M. and M. S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D. A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","ec_funded":1,"abstract":[{"text":"Thermalizing and localized many-body quantum systems present two distinct dynamical phases of matter. Recently the fate of a localized system coupled to a thermalizing system viewed as a quantum bath received significant theoretical and experimental attention. In this work, we study a mobile impurity, representing a small quantum bath, that interacts locally with an Anderson insulator with a finite density of localized particles. Using static Hartree approximation to obtain an effective disorder strength, we formulate an analytic criterion for the perturbative stability of the localization. Next, we use an approximate dynamical Hartree method and the quasi-exact time-evolved block decimation (TEBD) algorithm to study the dynamics of the system. We find that the dynamical Hartree approach which completely ignores entanglement between the impurity and localized particles predicts the delocalization of the system. In contrast, the full numerical simulation of the unitary dynamics with TEBD suggests the stability of localization on numerically accessible timescales. Finally, using an extension of the density matrix renormalization group algorithm to excited states (DMRG-X), we approximate the highly excited eigenstates of the system. We find that the impurity remains localized in the eigenstates and entanglement is enhanced in a finite region around the position of the impurity, confirming the dynamical predictions. Dynamics and the DMRG-X results provide compelling evidence for the stability of localization.","lang":"eng"}],"volume":105,"project":[{"grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.08603"}],"publication":"Physical Review B","external_id":{"isi":["000823050000001"],"arxiv":["2111.08603"]},"arxiv":1,"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"oa":1,"corr_author":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"_id":"11469","scopus_import":"1","title":"Localization of a mobile impurity interacting with an Anderson insulator","intvolume":"       105","article_number":"224208","date_published":"2022-06-27T00:00:00Z","article_type":"original"},{"_id":"11470","oa":1,"department":[{"_id":"MaSe"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"corr_author":"1","article_type":"original","date_published":"2022-06-27T00:00:00Z","intvolume":"       105","article_number":"L220203","scopus_import":"1","title":"Propagation of many-body localization in an Anderson insulator","ec_funded":1,"abstract":[{"text":"Many-body localization (MBL) is an example of a dynamical phase of matter that avoids thermalization. While the MBL phase is robust to weak local perturbations, the fate of an MBL system coupled to a thermalizing quantum system that represents a “heat bath” is an open question that is actively investigated theoretically and experimentally. In this work, we consider the stability of an Anderson insulator with a finite density of particles interacting with a single mobile impurity—a small quantum bath. We give perturbative arguments that support the stability of localization in the strong interaction regime. Large-scale tensor network simulations of dynamics are employed to corroborate the presence of the localized phase and give quantitative predictions in the thermodynamic limit. We develop a phenomenological description of the dynamics in the strong interaction regime, and we demonstrate that the impurity effectively turns the Anderson insulator into an MBL phase, giving rise to nontrivial entanglement dynamics well captured by our phenomenology.","lang":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"volume":105,"year":"2022","doi":"10.1103/physrevb.105.l220203","acknowledgement":"We acknowledge useful discussions with M. Ljubotina. P. B., A. M., and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","day":"27","fulldoi":"https://doi.org/10.1103/physrevb.105.l220203","publisher":"American Physical Society","arxiv":1,"publication":"Physical Review B","external_id":{"isi":["000823050000012"],"arxiv":["2109.07332"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.07332"}],"month":"06","oa_version":"Preprint","citation":{"ama":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>","ieee":"P. Brighi, A. A. Michailidis, D. A. Abanin, and M. Serbyn, “Propagation of many-body localization in an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","apa":"Brighi, P., Michailidis, A. A., Abanin, D. A., &#38; Serbyn, M. (2022). Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>","chicago":"Brighi, Pietro, Alexios A. Michailidis, Dmitry A. Abanin, and Maksym Serbyn. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>.","mla":"Brighi, Pietro, et al. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, L220203, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>.","ista":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. 2022. Propagation of many-body localization in an Anderson insulator. Physical Review B. 105(22), L220203.","short":"P. Brighi, A.A. Michailidis, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","quality_controlled":"1","type":"journal_article","author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","orcid":"0000-0002-7969-2729","first_name":"Pietro","full_name":"Brighi, Pietro"},{"full_name":"Michailidis, Alexios A.","first_name":"Alexios A.","last_name":"Michailidis"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"publication_status":"published","issue":"22","isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12732"}]},"language":[{"iso":"eng"}],"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2026-04-07T13:26:31Z","date_created":"2022-06-29T20:20:47Z"},{"file_date_updated":"2022-07-05T08:17:12Z","author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"publication_status":"published","month":"07","citation":{"ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>","apa":"Mysliwy, K. (2022). <i>Polarons in Bose gases and polar crystals: Some rigorous energy estimates</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>.","mla":"Mysliwy, Krzysztof. <i>Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>.","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria."},"oa_version":"Published Version","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2022-06-30T12:15:03Z","date_updated":"2026-04-07T14:14:52Z","file":[{"content_type":"application/pdf","checksum":"7970714a20a6052f75fb27a6c3e9976e","success":1,"file_name":"thes1_no_isbn_2_1b.pdf","creator":"kmysliwy","relation":"main_file","date_updated":"2022-07-05T08:12:56Z","date_created":"2022-07-05T08:12:56Z","access_level":"open_access","file_size":1830973,"file_id":"11486"},{"file_id":"11487","access_level":"closed","file_size":5831060,"creator":"kmysliwy","file_name":"thes_source.zip","date_created":"2022-07-05T08:15:52Z","date_updated":"2022-07-05T08:17:12Z","relation":"source_file","content_type":"application/zip","checksum":"647a2011fdf56277096c9350fefe1097"}],"degree_awarded":"PhD","ddc":["515","539"],"language":[{"iso":"eng"}],"OA_place":"publisher","related_material":{"record":[{"id":"10564","relation":"part_of_dissertation","status":"public"},{"id":"8705","relation":"part_of_dissertation","status":"public"}]},"has_accepted_license":"1","status":"public","acknowledged_ssus":[{"_id":"SSU"}],"date_published":"2022-07-01T00:00:00Z","title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","_id":"11473","oa":1,"department":[{"_id":"GradSch"},{"_id":"RoSe"}],"corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"page":"138","publisher":"Institute of Science and Technology Austria","ec_funded":1,"abstract":[{"lang":"eng","text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n"}],"project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2022","doi":"10.15479/at:ista:11473","fulldoi":"https://doi.org/10.15479/at:ista:11473","day":"01"},{"page":"6352","publication":"International Journal of Molecular Sciences","external_id":{"isi":["000808733300001"],"pmid":["35683031"]},"publisher":"MDPI","pmid":1,"volume":23,"project":[{"call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.","lang":"eng"}],"fulldoi":"https://doi.org/10.3390/ijms23116352","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","day":"06","year":"2022","doi":"10.3390/ijms23116352","date_published":"2022-06-06T00:00:00Z","article_type":"original","scopus_import":"1","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","intvolume":"        23","_id":"11489","corr_author":"1","publication_identifier":{"issn":["1422-0067"]},"oa":1,"department":[{"_id":"JiFr"}],"date_created":"2022-07-05T15:14:34Z","date_updated":"2025-04-15T08:12:07Z","file":[{"success":1,"creator":"cchlebak","file_name":"2022_IntJMolSci_Bilanovicova.pdf","date_updated":"2022-07-06T07:36:59Z","date_created":"2022-07-06T07:36:59Z","relation":"main_file","content_type":"application/pdf","checksum":"e997a57a928ec9d51fad8ce824a05935","file_id":"11492","access_level":"open_access","file_size":2324542}],"language":[{"iso":"eng"}],"ddc":["570"],"isi":1,"issue":"11","has_accepted_license":"1","status":"public","file_date_updated":"2022-07-06T07:36:59Z","quality_controlled":"1","publication_status":"published","author":[{"first_name":"V","full_name":"Bilanovičová, V","last_name":"Bilanovičová"},{"last_name":"Rýdza","full_name":"Rýdza, N","first_name":"N"},{"last_name":"Koczka","full_name":"Koczka, L","first_name":"L"},{"full_name":"Hess, M","first_name":"M","last_name":"Hess"},{"last_name":"Feraru","first_name":"E","full_name":"Feraru, E"},{"first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"T","full_name":"Nodzyński, T","last_name":"Nodzyński"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>."},"oa_version":"Published Version","month":"06","article_processing_charge":"Yes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"citation":{"apa":"Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>","ieee":"R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022.","ama":"Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>","chicago":"Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">https://doi.org/10.15479/AT:ISTA:11542</a>.","mla":"Schulz, Rouven. <i>Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses)</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","ista":"Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11542\">10.15479/AT:ISTA:11542</a>.","short":"R. Schulz, (2022)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"None","_id":"11542","corr_author":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"oa":1,"date_published":"2022-01-01T00:00:00Z","file_date_updated":"2022-07-08T10:56:52Z","contributor":[{"contributor_type":"contact_person","first_name":"Sandra","orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert"}],"title":"Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)","author":[{"first_name":"Rouven","full_name":"Schulz, Rouven","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","orcid":"0000-0001-5297-733X"}],"type":"research_data","related_material":{"link":[{"relation":"contains","url":"https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1"}],"record":[{"id":"11995","relation":"used_in_publication","status":"public"}]},"fulldoi":"https://doi.org/10.15479/AT:ISTA:11542","doi":"10.15479/AT:ISTA:11542","has_accepted_license":"1","year":"2022","status":"public","date_created":"2022-07-08T11:03:02Z","date_updated":"2025-04-15T07:27:21Z","publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","checksum":"71e8186583f3adbb6c69a88ac9e6e49b","creator":"rschulz","file_name":"Source Data.xlsx","success":1,"date_created":"2022-07-08T10:56:52Z","date_updated":"2022-07-08T10:56:52Z","relation":"main_file","file_size":135784571,"access_level":"open_access","file_id":"11543"}]},{"page":"145-179","external_id":{"isi":["000861841100004"]},"publication":"Journal of Algebra","publisher":"Elsevier","year":"2022","doi":"10.1016/j.jalgebra.2022.06.017","fulldoi":"https://doi.org/10.1016/j.jalgebra.2022.06.017","keyword":["Algebra and Number Theory"],"acknowledgement":"We thank Catharina Stroppel and Jens Niklas Eberhardt for interesting discussions. The first author acknowledges the support of the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. The second author is supported by the National Science Foundation Award No. 1803059 and the Australian Research Council grant DP170101579.","day":"01","ec_funded":1,"abstract":[{"text":"We classify contravariant pairings between standard Whittaker modules and Verma modules over a complex semisimple Lie algebra. These contravariant pairings are useful in extending several classical techniques for category O to the Miličić–Soergel category N . We introduce a class of costandard modules which generalize dual Verma modules, and describe canonical maps from standard to costandard modules in terms of contravariant pairings.\r\nWe show that costandard modules have unique irreducible submodules and share the same composition factors as the corresponding standard Whittaker modules. We show that costandard modules give an algebraic characterization of the global sections of costandard twisted Harish-Chandra sheaves on the associated flag variety, which are defined using holonomic duality of D-modules. We prove that with these costandard modules, blocks of category\r\nN have the structure of highest weight categories and we establish a BGG reciprocity theorem for N .","lang":"eng"}],"volume":609,"project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","title":"Contravariant pairings between standard Whittaker modules and Verma modules","intvolume":"       609","date_published":"2022-11-01T00:00:00Z","article_type":"original","department":[{"_id":"HeEd"}],"oa":1,"corr_author":"1","publication_identifier":{"issn":["0021-8693"]},"_id":"11545","file":[{"access_level":"open_access","file_size":582962,"file_id":"12473","checksum":"82abaee3d7837f703e499a9ecbb25b7c","content_type":"application/pdf","date_updated":"2023-02-02T07:32:48Z","relation":"main_file","date_created":"2023-02-02T07:32:48Z","success":1,"creator":"dernst","file_name":"2022_JournalAlgebra_Brown.pdf"}],"date_created":"2022-07-08T11:40:07Z","date_updated":"2025-04-14T07:43:58Z","has_accepted_license":"1","status":"public","isi":1,"issue":"11","language":[{"iso":"eng"}],"ddc":["510"],"author":[{"first_name":"Adam","full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","last_name":"Brown"},{"last_name":"Romanov","full_name":"Romanov, Anna","first_name":"Anna"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","file_date_updated":"2023-02-02T07:32:48Z","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","citation":{"ama":"Brown A, Romanov A. Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. 2022;609(11):145-179. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>","apa":"Brown, A., &#38; Romanov, A. (2022). Contravariant pairings between standard Whittaker modules and Verma modules. <i>Journal of Algebra</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>","ieee":"A. Brown and A. Romanov, “Contravariant pairings between standard Whittaker modules and Verma modules,” <i>Journal of Algebra</i>, vol. 609, no. 11. Elsevier, pp. 145–179, 2022.","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">https://doi.org/10.1016/j.jalgebra.2022.06.017</a>.","mla":"Brown, Adam, and Anna Romanov. “Contravariant Pairings between Standard Whittaker Modules and Verma Modules.” <i>Journal of Algebra</i>, vol. 609, no. 11, Elsevier, 2022, pp. 145–79, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2022.06.017\">10.1016/j.jalgebra.2022.06.017</a>.","short":"A. Brown, A. Romanov, Journal of Algebra 609 (2022) 145–179.","ista":"Brown A, Romanov A. 2022. Contravariant pairings between standard Whittaker modules and Verma modules. Journal of Algebra. 609(11), 145–179."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","citation":{"mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"08","publication_status":"published","type":"journal_article","author":[{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"file_date_updated":"2023-02-02T08:20:29Z","quality_controlled":"1","status":"public","has_accepted_license":"1","ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"issue":"1856","file":[{"date_created":"2023-02-02T08:20:29Z","date_updated":"2023-02-02T08:20:29Z","relation":"main_file","success":1,"creator":"dernst","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","content_type":"application/pdf","file_id":"12479","access_level":"open_access","file_size":920304}],"date_created":"2022-07-08T11:41:56Z","date_updated":"2025-06-12T06:10:18Z","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"corr_author":"1","oa":1,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"_id":"11546","intvolume":"       377","article_number":"20210203","scopus_import":"1","title":"Inversions and parallel evolution","article_type":"original","date_published":"2022-08-01T00:00:00Z","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","day":"01","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"fulldoi":"https://doi.org/10.1098/rstb.2021.0203","doi":"10.1098/rstb.2021.0203","year":"2022","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation","grant_number":"P32166"}],"volume":377,"abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"publisher":"Royal Society of London","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","external_id":{"isi":["000812317300005"],"pmid":["35694747"]},"pmid":1},{"pmid":1,"publisher":"Springer Nature","external_id":{"isi":["000815098500002"],"pmid":[" 35739187"]},"publication":"Communications Biology","doi":"10.1038/s42003-022-03568-6","year":"2022","day":"23","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","fulldoi":"https://doi.org/10.1038/s42003-022-03568-6","abstract":[{"text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.","lang":"eng"}],"volume":5,"intvolume":"         5","article_number":"620","scopus_import":"1","title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","date_published":"2022-06-23T00:00:00Z","department":[{"_id":"LeSa"}],"oa":1,"publication_identifier":{"eissn":["2399-3642"]},"_id":"11551","file":[{"content_type":"application/pdf","checksum":"965f88bbcef3fd0c3e121340555c4467","creator":"kschuh","file_name":"2022_communicationsbiology_Molina-Granada.pdf","success":1,"date_updated":"2022-07-13T07:44:58Z","relation":"main_file","date_created":"2022-07-13T07:44:58Z","file_size":2335369,"access_level":"open_access","file_id":"11571"}],"date_updated":"2026-04-02T13:22:53Z","date_created":"2022-07-10T22:01:52Z","status":"public","has_accepted_license":"1","issue":"1","isi":1,"ddc":["570"],"language":[{"iso":"eng"}],"type":"journal_article","author":[{"last_name":"Molina-Granada","full_name":"Molina-Granada, David","first_name":"David"},{"last_name":"González-Vioque","full_name":"González-Vioque, Emiliano","first_name":"Emiliano"},{"first_name":"Marris G.","full_name":"Dibley, Marris G.","last_name":"Dibley"},{"full_name":"Cabrera-Pérez, Raquel","first_name":"Raquel","last_name":"Cabrera-Pérez"},{"last_name":"Vallbona-Garcia","first_name":"Antoni","full_name":"Vallbona-Garcia, Antoni"},{"full_name":"Torres-Torronteras, Javier","first_name":"Javier","last_name":"Torres-Torronteras"},{"first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","orcid":"0000-0002-0977-7989"},{"first_name":"Michael T.","full_name":"Ryan, Michael T.","last_name":"Ryan"},{"first_name":"Yolanda","full_name":"Cámara, Yolanda","last_name":"Cámara"},{"last_name":"Martí","first_name":"Ramon","full_name":"Martí, Ramon"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2022-07-13T07:44:58Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","month":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","citation":{"apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>","ieee":"D. Molina-Granada <i>et al.</i>, “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” <i>Communications Biology</i>, vol. 5, no. 1. Springer Nature, 2022.","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. 2022;5(1). doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>","chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>.","mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>, vol. 5, no. 1, 620, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>.","short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022).","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620."}},{"project":[{"name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"volume":128,"abstract":[{"lang":"eng","text":"Rotational dynamics of D2 molecules inside helium nanodroplets is induced by a moderately intense femtosecond pump pulse and measured as a function of time by recording the yield of HeD+ ions, created through strong-field dissociative ionization with a delayed femtosecond probe pulse. The yield oscillates with a period of 185 fs, reflecting field-free rotational wave packet dynamics, and the oscillation persists for more than 500 periods. Within the experimental uncertainty, the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier analysis, is the same as Bgas for an isolated D2 molecule. Our observations show that the D2 molecules inside helium nanodroplets essentially rotate as free D2 molecules."}],"ec_funded":1,"OA_type":"green","day":"16","fulldoi":"https://doi.org/10.1103/PhysRevLett.128.243201","doi":"10.1103/PhysRevLett.128.243201","year":"2022","publisher":"American Physical Society","arxiv":1,"external_id":{"isi":["000820659700002"],"pmid":["35776471"],"arxiv":["2201.09281"]},"publication":"Physical Review Letters","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.09281"}],"_id":"11552","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"oa":1,"department":[{"_id":"MiLe"}],"article_type":"original","date_published":"2022-06-16T00:00:00Z","intvolume":"       128","article_number":"243201","title":"Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets","scopus_import":"1","language":[{"iso":"eng"}],"OA_place":"repository","issue":"24","isi":1,"status":"public","date_updated":"2026-04-16T08:18:26Z","date_created":"2022-07-10T22:01:52Z","citation":{"ieee":"J. Qiang <i>et al.</i>, “Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets,” <i>Physical Review Letters</i>, vol. 128, no. 24. American Physical Society, 2022.","apa":"Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>","ama":"Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. 2022;128(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>","chicago":"Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>.","mla":"Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>, vol. 128, no. 24, 243201, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>.","ista":"Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W, Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I, Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201.","short":"J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun, W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt, I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022)."},"oa_version":"Preprint","month":"06","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"last_name":"Qiang","full_name":"Qiang, Junjie","first_name":"Junjie"},{"last_name":"Zhou","first_name":"Lianrong","full_name":"Zhou, Lianrong"},{"last_name":"Lu","first_name":"Peifen","full_name":"Lu, Peifen"},{"first_name":"Kang","full_name":"Lin, Kang","last_name":"Lin"},{"last_name":"Ma","full_name":"Ma, Yongzhe","first_name":"Yongzhe"},{"last_name":"Pan","full_name":"Pan, Shengzhe","first_name":"Shengzhe"},{"first_name":"Chenxu","full_name":"Lu, Chenxu","last_name":"Lu"},{"full_name":"Jiang, Wenyu","first_name":"Wenyu","last_name":"Jiang"},{"last_name":"Sun","full_name":"Sun, Fenghao","first_name":"Fenghao"},{"first_name":"Wenbin","full_name":"Zhang, Wenbin","last_name":"Zhang"},{"last_name":"Li","full_name":"Li, Hui","first_name":"Hui"},{"last_name":"Gong","first_name":"Xiaochun","full_name":"Gong, Xiaochun"},{"last_name":"Averbukh","full_name":"Averbukh, Ilya Sh","first_name":"Ilya Sh"},{"first_name":"Yehiam","full_name":"Prior, Yehiam","last_name":"Prior"},{"full_name":"Schouder, Constant A.","first_name":"Constant A.","last_name":"Schouder"},{"full_name":"Stapelfeldt, Henrik","first_name":"Henrik","last_name":"Stapelfeldt"},{"first_name":"Igor","full_name":"Cherepanov, Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov"},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"},{"last_name":"Jäger","full_name":"Jäger, Wolfgang","first_name":"Wolfgang"},{"last_name":"Wu","first_name":"Jian","full_name":"Wu, Jian"}]},{"date_updated":"2025-07-10T11:50:12Z","date_created":"2022-07-10T22:01:53Z","file":[{"success":1,"creator":"kschuh","file_name":"2022_ArnoldMathematicalJournal_Clark.pdf","relation":"main_file","date_created":"2022-07-12T10:04:55Z","date_updated":"2022-07-12T10:04:55Z","content_type":"application/pdf","checksum":"16e7c659dee9073c6c8aeb87316ef201","file_id":"11559","access_level":"open_access","file_size":2509915}],"issue":"2","language":[{"iso":"eng"}],"OA_place":"publisher","related_material":{"link":[{"url":"https://doi.org/10.1007/s40598-022-00209-y","relation":"erratum"},{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00218-x"}]},"ddc":["500"],"status":"public","has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2022-07-12T10:04:55Z","type":"journal_article","author":[{"last_name":"Clark","first_name":"Trevor","full_name":"Clark, Trevor"},{"id":"fe8209e2-906f-11eb-847d-950f8fc09115","last_name":"Drach","orcid":"0000-0002-9156-8616","first_name":"Kostiantyn","full_name":"Drach, Kostiantyn"},{"first_name":"Oleg","full_name":"Kozlovski, Oleg","last_name":"Kozlovski"},{"last_name":"Strien","first_name":"Sebastian Van","full_name":"Strien, Sebastian Van"}],"publication_status":"published","month":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ieee":"T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex box mappings,” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2. Springer Nature, pp. 319–410, 2022.","apa":"Clark, T., Drach, K., Kozlovski, O., &#38; Strien, S. V. (2022). The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>","ama":"Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. 2022;8(2):319-410. doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>","chicago":"Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>.","mla":"Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>.","ista":"Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box mappings. Arnold Mathematical Journal. 8(2), 319–410.","short":"T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal 8 (2022) 319–410."},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publisher":"Springer Nature","page":"319-410","publication":"Arnold Mathematical Journal","abstract":[{"text":"In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:\r\n• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.\r\n• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:\r\n  • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;\r\n  • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n   • the QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.\r\n• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:\r\n   • puzzle pieces shrink to points,\r\n   • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings\r\nare the analogues of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.","lang":"eng"}],"ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"volume":8,"doi":"10.1007/s40598-022-00200-7","year":"2022","day":"01","acknowledgement":"We would also like to thank Dzmitry Dudko and Dierk Schleicher for many stimulating discussions and encouragement during our work on this project, and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are grateful to Leon Staresinic who carefully read the revised version of the manuscript and provided many helpful suggestions.","OA_type":"hybrid","fulldoi":"https://doi.org/10.1007/s40598-022-00200-7","article_type":"original","date_published":"2022-06-01T00:00:00Z","intvolume":"         8","scopus_import":"1","title":"The dynamics of complex box mappings","_id":"11553","oa":1,"department":[{"_id":"VaKa"}],"publication_identifier":{"issn":["2199-6792"],"eissn":["2199-6806"]}},{"language":[{"iso":"eng"}],"ddc":["518"],"isi":1,"status":"public","date_created":"2022-07-11T12:19:59Z","date_updated":"2024-10-21T06:01:47Z","oa_version":"Preprint","citation":{"chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022.","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>."},"month":"10","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"full_name":"Kalinov, Aleksei","first_name":"Aleksei","orcid":"0000-0003-2189-3904","last_name":"Kalinov","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02"},{"full_name":"Osinskiy, A.I.","first_name":"A.I.","last_name":"Osinskiy"},{"first_name":"S.A.","full_name":"Matveev, S.A.","last_name":"Matveev"},{"last_name":"Otieno","full_name":"Otieno, W.","first_name":"W."},{"full_name":"Brilliantov, N.V.","first_name":"N.V.","last_name":"Brilliantov"}],"volume":467,"abstract":[{"text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise.","lang":"eng"}],"acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","day":"15","fulldoi":"https://doi.org/10.1016/j.jcp.2022.111439","keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"year":"2022","doi":"10.1016/j.jcp.2022.111439","arxiv":1,"publisher":"Elsevier","publication":"Journal of Computational Physics","external_id":{"arxiv":["2103.09481"],"isi":["000917225500013"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"_id":"11556","publication_identifier":{"issn":["0021-9991"]},"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"oa":1,"article_type":"original","date_published":"2022-10-15T00:00:00Z","intvolume":"       467","article_number":"111439","scopus_import":"1","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics"},{"citation":{"chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>.","ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>","ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022.","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file_date_updated":"2022-07-18T08:15:24Z","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"last_name":"Zhang","first_name":"Runxuan","full_name":"Zhang, Runxuan"},{"last_name":"Kuo","full_name":"Kuo, Richard","first_name":"Richard"},{"full_name":"Coulter, Max","first_name":"Max","last_name":"Coulter"},{"first_name":"Cristiane P.G.","full_name":"Calixto, Cristiane P.G.","last_name":"Calixto"},{"last_name":"Entizne","full_name":"Entizne, Juan Carlos","first_name":"Juan Carlos"},{"last_name":"Guo","first_name":"Wenbin","full_name":"Guo, Wenbin"},{"last_name":"Marquez","first_name":"Yamile","full_name":"Marquez, Yamile"},{"last_name":"Milne","full_name":"Milne, Linda","first_name":"Linda"},{"first_name":"Stefan","full_name":"Riegler, Stefan","orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler"},{"last_name":"Matsui","full_name":"Matsui, Akihiro","first_name":"Akihiro"},{"full_name":"Tanaka, Maho","first_name":"Maho","last_name":"Tanaka"},{"first_name":"Sarah","full_name":"Harvey, Sarah","last_name":"Harvey"},{"last_name":"Gao","first_name":"Yubang","full_name":"Gao, Yubang"},{"first_name":"Theresa","full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh"},{"last_name":"Paniagua","first_name":"Alejandro","full_name":"Paniagua, Alejandro"},{"full_name":"Crespi, Martin","first_name":"Martin","last_name":"Crespi"},{"first_name":"Katherine","full_name":"Denby, Katherine","last_name":"Denby"},{"first_name":"Asa Ben","full_name":"Hur, Asa Ben","last_name":"Hur"},{"full_name":"Huq, Enamul","first_name":"Enamul","last_name":"Huq"},{"full_name":"Jantsch, Michael","first_name":"Michael","last_name":"Jantsch"},{"full_name":"Jarmolowski, Artur","first_name":"Artur","last_name":"Jarmolowski"},{"full_name":"Koester, Tino","first_name":"Tino","last_name":"Koester"},{"last_name":"Laubinger","full_name":"Laubinger, Sascha","first_name":"Sascha"},{"full_name":"Li, Qingshun Quinn","first_name":"Qingshun Quinn","last_name":"Li"},{"full_name":"Gu, Lianfeng","first_name":"Lianfeng","last_name":"Gu"},{"first_name":"Motoaki","full_name":"Seki, Motoaki","last_name":"Seki"},{"full_name":"Staiger, Dorothee","first_name":"Dorothee","last_name":"Staiger"},{"last_name":"Sunkar","full_name":"Sunkar, Ramanjulu","first_name":"Ramanjulu"},{"first_name":"Zofia","full_name":"Szweykowska-Kulinska, Zofia","last_name":"Szweykowska-Kulinska"},{"full_name":"Tu, Shih Long","first_name":"Shih Long","last_name":"Tu"},{"first_name":"Andreas","full_name":"Wachter, Andreas","last_name":"Wachter"},{"first_name":"Robbie","full_name":"Waugh, Robbie","last_name":"Waugh"},{"last_name":"Xiong","first_name":"Liming","full_name":"Xiong, Liming"},{"last_name":"Zhang","first_name":"Xiao Ning","full_name":"Zhang, Xiao Ning"},{"last_name":"Conesa","first_name":"Ana","full_name":"Conesa, Ana"},{"last_name":"Reddy","first_name":"Anireddy S.N.","full_name":"Reddy, Anireddy S.N."},{"first_name":"Andrea","full_name":"Barta, Andrea","last_name":"Barta"},{"last_name":"Kalyna","first_name":"Maria","full_name":"Kalyna, Maria"},{"first_name":"John W.S.","full_name":"Brown, John W.S.","last_name":"Brown"}],"ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"status":"public","has_accepted_license":"1","date_created":"2022-07-17T22:01:53Z","date_updated":"2025-06-11T13:37:00Z","file":[{"access_level":"open_access","file_size":3146207,"file_id":"11597","content_type":"application/pdf","checksum":"2c30ef84151d257a6b835b4e069b70ac","success":1,"creator":"dernst","file_name":"2022_GenomeBiology_Zhang.pdf","date_created":"2022-07-18T08:15:24Z","relation":"main_file","date_updated":"2022-07-18T08:15:24Z"}],"_id":"11587","publication_identifier":{"eissn":["1474-760X"]},"oa":1,"department":[{"_id":"FyKo"}],"article_type":"original","date_published":"2022-07-07T00:00:00Z","article_number":"149","intvolume":"        23","scopus_import":"1","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","volume":23,"abstract":[{"text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.","lang":"eng"}],"day":"07","acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","fulldoi":"https://doi.org/10.1186/s13059-022-02711-0","year":"2022","doi":"10.1186/s13059-022-02711-0","publisher":"BioMed Central","external_id":{"pmid":["35799267"],"isi":["000821915500002"]},"publication":"Genome Biology","pmid":1},{"status":"public","has_accepted_license":"1","issue":"7","isi":1,"ddc":["570"],"language":[{"iso":"eng"}],"file":[{"file_id":"11595","access_level":"open_access","file_size":1722094,"date_updated":"2022-07-18T07:51:55Z","relation":"main_file","date_created":"2022-07-18T07:51:55Z","success":1,"file_name":"2022_Haematologica_Nicolai.pdf","creator":"dernst","checksum":"9b47830945f3c30428fe9cfee2dc4a8a","content_type":"application/pdf"}],"date_updated":"2025-04-14T07:43:16Z","date_created":"2022-07-17T22:01:54Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","month":"07","citation":{"ista":"Nicolai L, Kaiser R, Escaig R, Hoffknecht ML, Anjum A, Leunig A, Pircher J, Ehrlich A, Lorenz M, Ishikawa-Ankerhold H, Aird WC, Massberg S, Gärtner FR. 2022. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica. 107(7), 1669–1680.","short":"L. Nicolai, R. Kaiser, R. Escaig, M.L. Hoffknecht, A. Anjum, A. Leunig, J. Pircher, A. Ehrlich, M. Lorenz, H. Ishikawa-Ankerhold, W.C. Aird, S. Massberg, F.R. Gärtner, Haematologica 107 (2022) 1669–1680.","mla":"Nicolai, Leo, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>, vol. 107, no. 7, Ferrata Storti Foundation, 2022, pp. 1669–80, doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>.","chicago":"Nicolai, Leo, Rainer Kaiser, Raphael Escaig, Marie Louise Hoffknecht, Afra Anjum, Alexander Leunig, Joachim Pircher, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>. Ferrata Storti Foundation, 2022. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>.","ieee":"L. Nicolai <i>et al.</i>, “Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo,” <i>Haematologica</i>, vol. 107, no. 7. Ferrata Storti Foundation, pp. 1669–1680, 2022.","apa":"Nicolai, L., Kaiser, R., Escaig, R., Hoffknecht, M. L., Anjum, A., Leunig, A., … Gärtner, F. R. (2022). Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. Ferrata Storti Foundation. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>","ama":"Nicolai L, Kaiser R, Escaig R, et al. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. 2022;107(7):1669-1680. doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>"},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"oa_version":"Published Version","type":"journal_article","author":[{"last_name":"Nicolai","full_name":"Nicolai, Leo","first_name":"Leo"},{"first_name":"Rainer","full_name":"Kaiser, Rainer","last_name":"Kaiser"},{"first_name":"Raphael","full_name":"Escaig, Raphael","last_name":"Escaig"},{"last_name":"Hoffknecht","full_name":"Hoffknecht, Marie Louise","first_name":"Marie Louise"},{"last_name":"Anjum","first_name":"Afra","full_name":"Anjum, Afra"},{"first_name":"Alexander","full_name":"Leunig, Alexander","last_name":"Leunig"},{"last_name":"Pircher","first_name":"Joachim","full_name":"Pircher, Joachim"},{"last_name":"Ehrlich","first_name":"Andreas","full_name":"Ehrlich, Andreas"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"full_name":"Ishikawa-Ankerhold, Hellen","first_name":"Hellen","last_name":"Ishikawa-Ankerhold"},{"last_name":"Aird","full_name":"Aird, William C.","first_name":"William C."},{"full_name":"Massberg, Steffen","first_name":"Steffen","last_name":"Massberg"},{"full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2022-07-18T07:51:55Z","year":"2022","doi":"10.3324/haematol.2021.278896","acknowledgement":"This study was supported by the Deutsche Forschungsgemeinschaft (DFG) SFB 914 ( to SM [B02 and Z01]), the DFG SFB 1123 (to SM [B06]), the DFG FOR 2033 (to SM), the German\r\nCenter for Cardiovascular Research (DZHK) (Clinician Scientist Programme), MHA 1.4VD (to SM), Postdoc Start-up Grant, 81X3600213 (to FG), 81X3600222 (to LN), the FP7 program\r\n(project 260309, PRESTIGE [to SM]). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 83344, ERC-2018-ADG “IMMUNOTHROMBOSIS” [to SM] and the Marie Skłodowska Curie Individual Fellowship (EU project 747687, LamelliActin [to FG]). ","day":"01","fulldoi":"https://doi.org/10.3324/haematol.2021.278896","abstract":[{"lang":"eng","text":"Visualizing cell behavior and effector function on a single cell level has been crucial for understanding key aspects of mammalian biology. Due to their small size, large number and rapid recruitment into thrombi, there is a lack of data on fate and behavior of individual platelets in thrombosis and hemostasis. Here we report the use of platelet lineage restricted multi-color reporter mouse strains to delineate platelet function on a single cell level. We show that genetic labeling allows for single platelet and megakaryocyte (MK) tracking and morphological analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven Confetti expression, we provide insights into temporal gene expression patterns as well as spatial clustering of MK in the bone marrow. In the vasculature, shape analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia formation with no evidence of lamellipodia formation. Single cell tracking in complex thrombi reveals prominent myosin-dependent motility of platelets and highlights thrombus formation as a highly dynamic process amenable to modification and intervention of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry, as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions of multicolor reporter mice compared to wild-type controls. In conclusion, platelet lineage multicolor reporter mice prove useful in furthering our understanding of platelet and MK biology on a single cell level."}],"ec_funded":1,"project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","call_identifier":"H2020"}],"volume":107,"publisher":"Ferrata Storti Foundation","publication":"Haematologica","page":"1669-1680","external_id":{"isi":["000823746100018"]},"oa":1,"department":[{"_id":"MiSi"}],"publication_identifier":{"issn":["0390-6078"],"eissn":["1592-8721"]},"corr_author":"1","_id":"11588","intvolume":"       107","scopus_import":"1","title":"Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_type":"original","date_published":"2022-07-01T00:00:00Z"},{"publisher":"Frontiers","publication":"Frontiers in Plant Science","external_id":{"isi":["000819250500001"],"pmid":["35783951"]},"pmid":1,"acknowledgement":"RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript.","day":"16","fulldoi":"https://doi.org/10.3389/fpls.2022.862398","doi":"10.3389/fpls.2022.862398","year":"2022","volume":13,"abstract":[{"lang":"eng","text":"Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana."}],"intvolume":"        13","article_number":"862398","scopus_import":"1","title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","article_type":"original","date_published":"2022-06-16T00:00:00Z","publication_identifier":{"eissn":["1664-462X"]},"department":[{"_id":"JiFr"}],"oa":1,"_id":"11589","file":[{"file_id":"11596","access_level":"open_access","file_size":5040638,"date_created":"2022-07-18T08:05:15Z","relation":"main_file","date_updated":"2022-07-18T08:05:15Z","success":1,"file_name":"2022_FrontiersPlantScience_Wang.pdf","creator":"dernst","checksum":"95313515637c0f84de591d204375d764","content_type":"application/pdf"}],"date_updated":"2023-08-03T12:01:47Z","date_created":"2022-07-17T22:01:54Z","status":"public","has_accepted_license":"1","ddc":["580"],"related_material":{"link":[{"url":"https://doi.org/10.3389/fpls.2022.1100792","relation":"erratum"}]},"language":[{"iso":"eng"}],"isi":1,"publication_status":"published","type":"journal_article","author":[{"first_name":"Ren","full_name":"Wang, Ren","last_name":"Wang"},{"last_name":"Himschoot","full_name":"Himschoot, Ellie","first_name":"Ellie"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"last_name":"Boudsocq","full_name":"Boudsocq, Marie","first_name":"Marie"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"}],"file_date_updated":"2022-07-18T08:05:15Z","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","citation":{"mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>, vol. 13, 862398, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>.","ista":"Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>","apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>","ieee":"R. Wang <i>et al.</i>, “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” <i>Frontiers in Plant Science</i>, vol. 13. Frontiers, 2022.","chicago":"Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"06"},{"language":[{"iso":"eng"}],"ddc":["530"],"isi":1,"issue":"6","status":"public","has_accepted_license":"1","date_created":"2022-07-17T22:01:55Z","date_updated":"2025-04-14T07:43:58Z","file":[{"file_id":"11594","file_size":3415721,"access_level":"open_access","file_name":"2022_NewJournalPhysics_Brauneis.pdf","creator":"dernst","success":1,"relation":"main_file","date_created":"2022-07-18T06:33:13Z","date_updated":"2022-07-18T06:33:13Z","content_type":"application/pdf","checksum":"dc67b60f2e50e9ef2bd820ca0d7333d2"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Brauneis, Fabian, Timothy G. Backert, Simeon I. Mistakidis, Mikhail Lemeshko, Hans Werner Hammer, and Artem Volosniev. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>.","apa":"Brauneis, F., Backert, T. G., Mistakidis, S. I., Lemeshko, M., Hammer, H. W., &#38; Volosniev, A. (2022). Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>","ieee":"F. Brauneis, T. G. Backert, S. I. Mistakidis, M. Lemeshko, H. W. Hammer, and A. Volosniev, “Artificial atoms from cold bosons in one dimension,” <i>New Journal of Physics</i>, vol. 24, no. 6. IOP Publishing, 2022.","ama":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. 2022;24(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>","ista":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. 2022. Artificial atoms from cold bosons in one dimension. New Journal of Physics. 24(6), 063036.","short":"F. Brauneis, T.G. Backert, S.I. Mistakidis, M. Lemeshko, H.W. Hammer, A. Volosniev, New Journal of Physics 24 (2022).","mla":"Brauneis, Fabian, et al. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>, vol. 24, no. 6, 063036, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>."},"oa_version":"Published Version","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","file_date_updated":"2022-07-18T06:33:13Z","quality_controlled":"1","publication_status":"published","type":"journal_article","author":[{"full_name":"Brauneis, Fabian","first_name":"Fabian","last_name":"Brauneis"},{"first_name":"Timothy G.","full_name":"Backert, Timothy G.","last_name":"Backert"},{"last_name":"Mistakidis","full_name":"Mistakidis, Simeon I.","first_name":"Simeon I."},{"first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"},{"last_name":"Hammer","first_name":"Hans Werner","full_name":"Hammer, Hans Werner"},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"volume":24,"ec_funded":1,"abstract":[{"lang":"eng","text":"We investigate the ground-state properties of weakly repulsive one-dimensional bosons in the presence of an attractive zero-range impurity potential. First, we derive mean-field solutions to the problem on a finite ring for the two asymptotic cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering state. Moreover, we derive the critical line that separates these regimes in the parameter space. In the thermodynamic limit, this critical line determines the maximum number of bosons that can be bound by the impurity potential, forming an artificial atom. Second, we validate the mean-field results using the flow equation approach and the multi-layer multi-configuration time-dependent Hartree method for atomic mixtures. While beyond-mean-field effects destroy long-range order in the Bose gas, the critical boson number is unaffected. Our findings are important for understanding such artificial atoms in low-density Bose gases with static and mobile impurities."}],"day":"01","acknowledgement":"This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (FB, H-WH, AGV) and European Union's Horizon 2020 research and innovation programme under the Marie Skĺodowska-Curie Grant Agreement No. 754411 (AGV). ML acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). SIM acknowledges support from the NSF through a grant for ITAMP at Harvard University.","fulldoi":"https://doi.org/10.1088/1367-2630/ac78d8","doi":"10.1088/1367-2630/ac78d8","year":"2022","publisher":"IOP Publishing","external_id":{"isi":["000818530000001"]},"publication":"New Journal of Physics","_id":"11590","publication_identifier":{"issn":["1367-2630"]},"oa":1,"department":[{"_id":"MiLe"}],"article_type":"original","date_published":"2022-06-01T00:00:00Z","intvolume":"        24","article_number":"063036","scopus_import":"1","title":"Artificial atoms from cold bosons in one dimension"},{"month":"06","citation":{"chicago":"Agustí, J., Y. Minoguchi, Johannes M Fink, and P. Rabl. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>.","ieee":"J. Agustí, Y. Minoguchi, J. M. Fink, and P. Rabl, “Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","apa":"Agustí, J., Minoguchi, Y., Fink, J. M., &#38; Rabl, P. (2022). Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>","ama":"Agustí J, Minoguchi Y, Fink JM, Rabl P. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>","short":"J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).","ista":"Agustí J, Minoguchi Y, Fink JM, Rabl P. 2022. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. Physical Review A. 105(6), 062454.","mla":"Agustí, J., et al. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>, vol. 105, no. 6, 062454, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>."},"oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","quality_controlled":"1","type":"journal_article","author":[{"last_name":"Agustí","first_name":"J.","full_name":"Agustí, J."},{"full_name":"Minoguchi, Y.","first_name":"Y.","last_name":"Minoguchi"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"last_name":"Rabl","full_name":"Rabl, P.","first_name":"P."}],"publication_status":"published","issue":"6","isi":1,"language":[{"iso":"eng"}],"status":"public","date_updated":"2025-04-14T07:53:28Z","date_created":"2022-07-17T22:01:55Z","_id":"11591","department":[{"_id":"JoFi"}],"oa":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"article_type":"original","date_published":"2022-06-29T00:00:00Z","intvolume":"       105","article_number":"062454","title":"Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams","scopus_import":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We investigate the deterministic generation and distribution of entanglement in large quantum networks by driving distant qubits with the output fields of a nondegenerate parametric amplifier. In this setting, the amplifier produces a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated reservoir for the qubits and relaxes them into a highly entangled steady state. Here we are interested in the maximal amount of entanglement and the optimal entanglement generation rates that can be achieved with this scheme under realistic conditions taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation delays into account. By combining exact numerical simulations of the full network with approximate analytic results, we predict the optimal working point for the amplifier and the corresponding qubit-qubit entanglement under various conditions. Our findings show that this passive conversion of Gaussian into discrete-variable entanglement offers a robust and experimentally very attractive approach for operating large optical, microwave, or hybrid quantum networks, for which efficient parametric amplifiers are currently developed."}],"project":[{"_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","grant_number":"899354","call_identifier":"H2020"}],"volume":105,"year":"2022","doi":"10.1103/PhysRevA.105.062454","day":"29","acknowledgement":"We thank T. Mavrogordatos and D. Zhu for initial contribution on the presented topic and K. Fedorov for stimulating discussions on entangled microwave beams. This work was supported by the Austrian Science Fund (FWF) through Grant No. P32299 (PHONED) and the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 899354 (SuperQuLAN). Most of the computational results presented were obtained using the CLIP cluster [65].","fulldoi":"https://doi.org/10.1103/PhysRevA.105.062454","publisher":"American Physical Society","arxiv":1,"external_id":{"isi":["000824330200003"],"arxiv":["2204.02993"]},"publication":"Physical Review A","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2204.02993"}]},{"status":"public","issue":"6","isi":1,"language":[{"iso":"eng"}],"date_updated":"2023-08-03T12:00:11Z","date_created":"2022-07-17T22:01:55Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","month":"06","citation":{"apa":"Bighin, G., Cappellaro, A., &#38; Salasnich, L. (2022). Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>","ieee":"G. Bighin, A. Cappellaro, and L. Salasnich, “Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","ama":"Bighin G, Cappellaro A, Salasnich L. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>","chicago":"Bighin, Giacomo, Alberto Cappellaro, and L. Salasnich. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>.","mla":"Bighin, Giacomo, et al. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>, vol. 105, no. 6, 063329, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>.","short":"G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022).","ista":"Bighin G, Cappellaro A, Salasnich L. 2022. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. Physical Review A. 105(6), 063329."},"oa_version":"Preprint","type":"journal_article","author":[{"full_name":"Bighin, Giacomo","first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777"},{"last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","first_name":"Alberto"},{"first_name":"L.","full_name":"Salasnich, L.","last_name":"Salasnich"}],"publication_status":"published","quality_controlled":"1","doi":"10.1103/PhysRevA.105.063329","year":"2022","day":"30","acknowledgement":"The authors gratefully acknowledge stimulating discussions with T. Enss, and thank an anonymous referee for suggestions and remarks that allowed us to improve the original manuscript. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster).","fulldoi":"https://doi.org/10.1103/PhysRevA.105.063329","abstract":[{"text":"We compare recent experimental results [Science 375, 528 (2022)] of the superfluid unitary Fermi gas near the critical temperature with a thermodynamic model based on the elementary excitations of the system. We find good agreement between experimental data and our theory for several quantities such as first sound, second sound, and superfluid fraction. We also show that mode mixing between first and second sound occurs. Finally, we characterize the response amplitude to a density perturbation: Close to the critical temperature both first and second sound can be excited through a density perturbation, whereas at lower temperatures only the first sound mode exhibits a significant response.","lang":"eng"}],"volume":105,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2206.03924","open_access":"1"}],"publisher":"American Physical Society","arxiv":1,"external_id":{"isi":["000829758500010"],"arxiv":["2206.03924"]},"publication":"Physical Review A","department":[{"_id":"MiLe"}],"oa":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"_id":"11592","article_number":"063329","intvolume":"       105","scopus_import":"1","title":"Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations","article_type":"original","date_published":"2022-06-30T00:00:00Z"}]