[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1103/PhysRevB.102.180508","publication_status":"published","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Physical Review B","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"fulldoi":"https://doi.org/10.1103/PhysRevB.102.180508","abstract":[{"text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field đ”đ‘2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At đ”đ‘2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above đ”đ‘2.","lang":"eng"}],"day":"01","date_published":"2020-11-01T00:00:00Z","issue":"18","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/2011.04329","open_access":"1"}],"month":"11","department":[{"_id":"JoFi"}],"article_number":"180508","date_updated":"2025-07-10T12:01:27Z","oa_version":"Preprint","year":"2020","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel KoĆĄice. ","author":[{"first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","full_name":"Zemlicka, Martin"},{"first_name":"M.","last_name":"Kopčík","full_name":"Kopčík, M."},{"last_name":"SzabĂł","full_name":"SzabĂł, P.","first_name":"P."},{"last_name":"Samuely","full_name":"Samuely, T.","first_name":"T."},{"first_name":"J.","full_name":"Kačmarčík, J.","last_name":"Kačmarčík"},{"first_name":"P.","full_name":"Neilinger, P.","last_name":"Neilinger"},{"last_name":"Grajcar","full_name":"Grajcar, M.","first_name":"M."},{"first_name":"P.","full_name":"Samuely, P.","last_name":"Samuely"}],"oa":1,"title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","intvolume":" 102","arxiv":1,"status":"public","date_created":"2020-12-13T23:01:21Z","citation":{"apa":"Zemlicka, M., Kopčík, M., SzabĂł, P., Samuely, T., Kačmarčík, J., Neilinger, P., 
 Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.102.180508","short":"M. Zemlicka, M. Kopčík, P. SzabĂł, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","ista":"Zemlicka M, Kopčík M, SzabĂł P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:10.1103/PhysRevB.102.180508.","ama":"Zemlicka M, Kopčík M, SzabĂł P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 2020;102(18). doi:10.1103/PhysRevB.102.180508","chicago":"Zemlicka, Martin, M. Kopčík, P. SzabĂł, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.102.180508.","ieee":"M. Zemlicka et al., “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” Physical Review B, vol. 102, no. 18. American Physical Society, 2020."},"volume":102,"article_processing_charge":"No","publisher":"American Physical Society","_id":"8944","article_type":"original","external_id":{"isi":["000591509900003"],"arxiv":["2011.04329"]}},{"publisher":"MDPI","volume":9,"article_processing_charge":"No","date_created":"2020-12-14T08:04:03Z","citation":{"ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” Cells, vol. 9, no. 12, 2662, MDPI, 2020, doi:10.3390/cells9122662.","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 2020;9(12). doi:10.3390/cells9122662","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., & Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. MDPI. https://doi.org/10.3390/cells9122662","ieee":"X. Zhang et al., “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” Cells, vol. 9, no. 12. MDPI, 2020.","chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” Cells. MDPI, 2020. https://doi.org/10.3390/cells9122662."},"external_id":{"pmid":["33322301"],"isi":["000601787300001"]},"article_type":"original","_id":"8949","intvolume":" 9","title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","oa":1,"status":"public","pmid":1,"file_date_updated":"2020-12-14T08:09:43Z","ddc":["570"],"date_updated":"2025-06-12T07:02:43Z","article_number":"2662","acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","author":[{"first_name":"Xuying","last_name":"Zhang","full_name":"Zhang, Xuying"},{"last_name":"Mennicke","full_name":"Mennicke, Christine V.","first_name":"Christine V."},{"last_name":"Xiao","full_name":"Xiao, Guanxi","first_name":"Guanxi"},{"first_name":"Robert J","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie"},{"first_name":"Mansoor","last_name":"Haider","full_name":"Haider, Mansoor"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"first_name":"H. Troy","last_name":"Ghashghaei","full_name":"Ghashghaei, H. Troy"}],"year":"2020","oa_version":"Published Version","issue":"12","has_accepted_license":"1","department":[{"_id":"SiHi"}],"month":"12","isi":1,"day":"11","abstract":[{"lang":"eng","text":"Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis."}],"file":[{"date_updated":"2020-12-14T08:09:43Z","date_created":"2020-12-14T08:09:43Z","checksum":"5095cbdc728c9a510c5761cf60a8861c","access_level":"open_access","file_id":"8950","relation":"main_file","file_name":"2020_Cells_Zhang.pdf","file_size":3504525,"content_type":"application/pdf","success":1,"creator":"dernst"}],"date_published":"2020-12-11T00:00:00Z","publication_identifier":{"issn":["2073-4409"]},"project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"}],"ec_funded":1,"fulldoi":"https://doi.org/10.3390/cells9122662","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"Cells","doi":"10.3390/cells9122662","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","publication_status":"published"},{"date_published":"2020-12-21T00:00:00Z","file":[{"date_created":"2020-12-20T09:52:52Z","date_updated":"2020-12-20T09:52:52Z","checksum":"f57862aeee1690c7effd2b1117d40ed1","file_id":"8952","access_level":"open_access","relation":"main_file","file_name":"readme.txt","content_type":"text/plain","file_size":523,"success":1,"creator":"bkavcic"},{"date_created":"2020-12-20T22:01:44Z","date_updated":"2020-12-20T22:01:44Z","checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_id":"8954","access_level":"open_access","file_name":"GRNs Research depository.gb","relation":"main_file","content_type":"application/octet-stream","file_size":379228,"success":1,"creator":"bkavcic"}],"_id":"8951","day":"21","publisher":"Institute of Science and Technology Austria","date_created":"2020-12-20T10:00:26Z","article_processing_charge":"No","citation":{"ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","short":"A.A. Nagy-Staron, (2020)."},"abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"corr_author":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:8951","status":"public","file_date_updated":"2020-12-20T22:01:44Z","oa":1,"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"author":[{"first_name":"Anna A","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron"}],"oa_version":"Published Version","year":"2020","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["570"],"related_material":{"record":[{"id":"9283","relation":"used_in_publication","status":"public"}]},"date_updated":"2025-06-12T06:36:16Z","department":[{"_id":"CaGu"}],"month":"12","type":"research_data","doi":"10.15479/AT:ISTA:8951","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","contributor_type":"project_member","first_name":"Anna A"},{"first_name":"Kathrin","contributor_type":"project_member","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek"},{"first_name":"Caroline","contributor_type":"project_member","last_name":"Caruso Carter"},{"first_name":"Elisabeth","contributor_type":"project_member","last_name":"Sonnleitner"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","orcid":"0000-0001-6041-254X","contributor_type":"project_member","first_name":"Bor"},{"last_name":"PaixĂŁo","contributor_type":"project_member","first_name":"Tiago"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","contributor_type":"project_manager"}]},{"has_accepted_license":"1","department":[{"_id":"GaTk"}],"isi":1,"month":"11","ddc":["570"],"article_number":"558070","date_updated":"2025-04-14T07:43:50Z","acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","author":[{"first_name":"Rossella","full_name":"Rizzo, Rossella","last_name":"Rizzo"},{"last_name":"Zhang","full_name":"Zhang, Xiyun","first_name":"Xiyun"},{"full_name":"Wang, Jilin W.J.L.","last_name":"Wang","first_name":"Jilin W.J.L."},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","first_name":"Fabrizio"},{"full_name":"Ivanov, Plamen Ch","last_name":"Ivanov","first_name":"Plamen Ch"}],"year":"2020","oa_version":"Published Version","oa":1,"title":"Network physiology of cortico–muscular interactions","intvolume":" 11","status":"public","pmid":1,"file_date_updated":"2020-12-21T10:37:50Z","publisher":"Frontiers","citation":{"chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070.","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” Frontiers in Physiology, vol. 11. Frontiers, 2020.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology. Frontiers. https://doi.org/10.3389/fphys.2020.558070","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070"},"date_created":"2020-12-20T23:01:18Z","volume":11,"article_processing_charge":"No","external_id":{"isi":["000596849400001"],"pmid":["33324233"]},"_id":"8955","article_type":"original","scopus_import":"1","doi":"10.3389/fphys.2020.558070","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","quality_controlled":"1","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication":"Frontiers in Physiology","publication_identifier":{"eissn":["1664042X"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ec_funded":1,"fulldoi":"https://doi.org/10.3389/fphys.2020.558070","day":"26","abstract":[{"text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies.","lang":"eng"}],"file":[{"checksum":"ef9515b28c5619b7126c0f347958bcb3","access_level":"open_access","file_id":"8961","date_updated":"2020-12-21T10:37:50Z","date_created":"2020-12-21T10:37:50Z","success":1,"creator":"dernst","relation":"main_file","file_name":"2020_Frontiers_Rizzo.pdf","file_size":13380030,"content_type":"application/pdf"}],"date_published":"2020-11-26T00:00:00Z"},{"department":[{"_id":"CaHe"}],"isi":1,"month":"12","issue":"6","acknowledgement":"We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas LeclĂšre and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8).","author":[{"last_name":"Godard","id":"33280250-F248-11E8-B48F-1D18A9856A87","full_name":"Godard, Benoit G","first_name":"Benoit G"},{"full_name":"Dumollard, RĂ©mi","last_name":"Dumollard","first_name":"RĂ©mi"},{"last_name":"Munro","full_name":"Munro, Edwin","first_name":"Edwin"},{"first_name":"Janet","last_name":"Chenevert","full_name":"Chenevert, Janet"},{"last_name":"Hebras","full_name":"Hebras, CĂ©line","first_name":"CĂ©line"},{"first_name":"Alex","last_name":"Mcdougall","full_name":"Mcdougall, Alex"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"year":"2020","oa_version":"None","date_updated":"2025-07-10T12:01:28Z","status":"public","pmid":1,"title":"Apical relaxation during mitotic rounding promotes tension-oriented cell division","intvolume":" 55","external_id":{"isi":["000600665700008"],"pmid":["33207225"]},"_id":"8957","article_type":"original","publisher":"Elsevier","date_created":"2020-12-20T23:01:19Z","article_processing_charge":"No","volume":55,"citation":{"short":"B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706.","apa":"Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., & Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.10.016","ama":"Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 2020;55(6):695-706. doi:10.1016/j.devcel.2020.10.016","mla":"Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:10.1016/j.devcel.2020.10.016.","ista":"Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706.","chicago":"Godard, Benoit G, RĂ©mi Dumollard, Edwin Munro, Janet Chenevert, CĂ©line Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.10.016.","ieee":"B. G. Godard et al., “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” Developmental Cell, vol. 55, no. 6. Elsevier, pp. 695–706, 2020."},"publication_status":"published","type":"journal_article","quality_controlled":"1","scopus_import":"1","doi":"10.1016/j.devcel.2020.10.016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Developmental Cell","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/relaxing-cell-divisions/"}]},"language":[{"iso":"eng"}],"corr_author":"1","fulldoi":"https://doi.org/10.1016/j.devcel.2020.10.016","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"date_published":"2020-12-21T00:00:00Z","page":"695-706","day":"21","abstract":[{"text":"Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"}]},{"article_number":"6437","date_updated":"2025-04-15T07:52:12Z","ddc":["570"],"oa_version":"Published Version","year":"2020","author":[{"last_name":"FĂ€ĂŸler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"FĂ€ĂŸler, Florian","orcid":"0000-0001-7149-769X","first_name":"Florian"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A","first_name":"Georgi A","orcid":"0000-0001-8370-6161"},{"first_name":"Victor-Valentin","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William","full_name":"Wan, William","last_name":"Wan"},{"orcid":"0000-0003-4790-8078","first_name":"Florian KM","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","has_accepted_license":"1","isi":1,"month":"12","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"article_processing_charge":"No","citation":{"ama":"FĂ€ĂŸler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x","ista":"FĂ€ĂŸler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","mla":"FĂ€ĂŸler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications, vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x.","short":"F. FĂ€ĂŸler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","apa":"FĂ€ĂŸler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x","ieee":"F. FĂ€ĂŸler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” Nature Communications, vol. 11. Springer Nature, 2020.","chicago":"FĂ€ĂŸler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x."},"date_created":"2020-12-23T08:25:45Z","volume":11,"publisher":"Springer Nature","_id":"8971","article_type":"original","external_id":{"isi":["000603078000003"]},"oa":1,"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","intvolume":" 11","file_date_updated":"2020-12-28T08:16:10Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/"}]},"publication":"Nature Communications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","doi":"10.1038/s41467-020-20286-x","publication_status":"published","quality_controlled":"1","type":"journal_article","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.","lang":"eng"}],"day":"22","file":[{"access_level":"open_access","file_id":"8975","checksum":"55d43ea0061cc4027ba45e966e1db8cc","date_updated":"2020-12-28T08:16:10Z","date_created":"2020-12-28T08:16:10Z","creator":"dernst","success":1,"file_size":3958727,"content_type":"application/pdf","file_name":"2020_NatureComm_Faessler.pdf","relation":"main_file"}],"date_published":"2020-12-22T00:00:00Z","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"name":"Protein structure and function in filopodia across scales","grant_number":"M02495","call_identifier":"FWF","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"publication_identifier":{"issn":["2041-1723"]},"fulldoi":"https://doi.org/10.1038/s41467-020-20286-x","corr_author":"1"},{"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication":"STAR Protocols","scopus_import":"1","doi":"10.1016/j.xpro.2020.100215","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","quality_controlled":"1","type":"journal_article","day":"18","abstract":[{"text":"Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b).","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_published":"2020-12-18T00:00:00Z","file":[{"date_updated":"2021-01-07T15:57:27Z","date_created":"2021-01-07T15:57:27Z","checksum":"f1e9a433e9cb0f41f7b6df6b76db1f6e","access_level":"open_access","file_id":"8996","relation":"main_file","file_name":"2020_STARProtocols_Laukoter.pdf","file_size":4031449,"content_type":"application/pdf","success":1,"creator":"dernst"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["2666-1667"]},"project":[{"call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"},{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1016/j.xpro.2020.100215","ec_funded":1,"corr_author":"1","ddc":["570"],"article_number":"100215","date_updated":"2025-04-15T08:23:06Z","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). N.A received support from the FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","author":[{"first_name":"Susanne","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter"},{"orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pauler, Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"oa_version":"Published Version","year":"2020","issue":"3","has_accepted_license":"1","department":[{"_id":"SiHi"}],"month":"12","publisher":"Elsevier","date_created":"2020-12-30T10:17:07Z","volume":1,"citation":{"ama":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 2020;1(3). doi:10.1016/j.xpro.2020.100215","ista":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. 2020. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 1(3), 100215.","mla":"Laukoter, Susanne, et al. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” STAR Protocols, vol. 1, no. 3, 100215, Elsevier, 2020, doi:10.1016/j.xpro.2020.100215.","short":"S. Laukoter, N. Amberg, F. Pauler, S. Hippenmeyer, STAR Protocols 1 (2020).","apa":"Laukoter, S., Amberg, N., Pauler, F., & Hippenmeyer, S. (2020). Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2020.100215","ieee":"S. Laukoter, N. Amberg, F. Pauler, and S. Hippenmeyer, “Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy,” STAR Protocols, vol. 1, no. 3. Elsevier, 2020.","chicago":"Laukoter, Susanne, Nicole Amberg, Florian Pauler, and Simon Hippenmeyer. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” STAR Protocols. Elsevier, 2020. https://doi.org/10.1016/j.xpro.2020.100215."},"article_processing_charge":"No","external_id":{"pmid":["33377108"]},"_id":"8978","article_type":"original","oa":1,"intvolume":" 1","title":"Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy","status":"public","pmid":1,"file_date_updated":"2021-01-07T15:57:27Z"},{"type":"conference","quality_controlled":"1","publication_status":"published","doi":"10.1007/978-3-030-65277-7_1","scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"Progress in Cryptology","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1007/978-3-030-65277-7_1","ec_funded":1,"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030652760"]},"series_title":"LNCS","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020"}],"date_published":"2020-12-08T00:00:00Z","page":"3-15","day":"08","conference":{"location":"Bangalore, India","name":"INDOCRYPT: International Conference on Cryptology in India","end_date":"2020-12-16","start_date":"2020-12-13"},"abstract":[{"lang":"eng","text":"Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message."}],"department":[{"_id":"KrPi"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/418"}],"month":"12","isi":1,"author":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"}],"oa_version":"Preprint","year":"2020","date_updated":"2026-04-16T09:33:26Z","status":"public","intvolume":" 12578","title":"Delayed authentication: Preventing replay and relay attacks in private contact tracing","oa":1,"external_id":{"isi":["000927592800001"]},"_id":"8987","publisher":"Springer Nature","article_processing_charge":"No","citation":{"ama":"Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: Progress in Cryptology. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:10.1007/978-3-030-65277-7_1","mla":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” Progress in Cryptology, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:10.1007/978-3-030-65277-7_1.","ista":"Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15.","apa":"Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In Progress in Cryptology (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. https://doi.org/10.1007/978-3-030-65277-7_1","short":"K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15.","ieee":"K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in Progress in Cryptology, Bangalore, India, 2020, vol. 12578, pp. 3–15.","chicago":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In Progress in Cryptology, 12578:3–15. LNCS. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-65277-7_1."},"date_created":"2021-01-03T23:01:23Z","volume":12578},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/"}]},"type":"journal_article","quality_controlled":"1","publication_status":"published","doi":"10.1073/pnas.2006731117","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-12-15T00:00:00Z","file":[{"file_name":"2020_PNAS_Grah.pdf","relation":"main_file","content_type":"application/pdf","file_size":1199247,"success":1,"creator":"dernst","date_created":"2021-01-11T08:37:31Z","date_updated":"2021-01-11T08:37:31Z","checksum":"69039cd402a571983aa6cb4815ffa863","file_id":"9004","access_level":"open_access"}],"page":"31614-31622","day":"15","abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future."}],"fulldoi":"https://doi.org/10.1073/pnas.2006731117","corr_author":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","author":[{"orcid":"0000-0003-2539-3560","first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"orcid":"0000-0002-6699-1455","first_name":"GaĆĄper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, GaĆĄper"}],"year":"2020","oa_version":"Published Version","ddc":["570"],"date_updated":"2025-05-14T10:57:50Z","department":[{"_id":"GaTk"}],"month":"12","isi":1,"issue":"50","has_accepted_license":"1","external_id":{"isi":["000600608300015"],"pmid":["33268497"]},"article_type":"original","_id":"9000","publisher":"National Academy of Sciences","volume":117,"citation":{"chicago":"Grah, Rok, Benjamin Zoller, and GaĆĄper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020.","short":"R. Grah, B. Zoller, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 31614–31622.","apa":"Grah, R., Zoller, B., & Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2006731117","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. Proceedings of the National Academy of Sciences of the United States of America. 117(50), 31614–31622.","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117."},"article_processing_charge":"No","date_created":"2021-01-10T23:01:17Z","status":"public","file_date_updated":"2021-01-11T08:37:31Z","pmid":1,"intvolume":" 117","title":"Nonequilibrium models of optimal enhancer function","oa":1},{"month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1908.03058","open_access":"1"}],"isi":1,"department":[{"_id":"JoFi"}],"issue":"9","oa_version":"Preprint","year":"2020","acknowledgement":"This work was supported by the Institute of Science and Technology Austria (IST Austria), the European Research Council under grant agreement number 758053 (ERC StG QUNNECT) and the EU’s Horizon 2020 research and innovation programme under grant agreement number 862644 (FET Open QUARTET). S.B. acknowledges support from the Marie SkƂodowska Curie\r\nfellowship number 707438 (MSC-IF SUPEREOM), DV acknowledge support from EU’s Horizon 2020 research and innovation programme under grant agreement number 732894 (FET Proactive HOT) and the Project QuaSeRT funded by the QuantERA ERANET Cofund in Quantum Technologies, and J.M.F from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and\r\ninnovation programme under grant agreement number 732894 (FET Proactive\r\nHOT).","author":[{"last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","first_name":"Shabir"},{"first_name":"Stefano","last_name":"Pirandola","full_name":"Pirandola, Stefano"},{"first_name":"David","full_name":"Vitali, David","last_name":"Vitali"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M"}],"date_updated":"2026-04-15T06:42:36Z","article_number":"9266397","status":"public","arxiv":1,"intvolume":" 2020","title":"Microwave quantum illumination with a digital phase-conjugated receiver","oa":1,"_id":"9001","external_id":{"arxiv":["1908.03058"],"isi":["000612224900089"]},"volume":2020,"article_processing_charge":"No","date_created":"2021-01-10T23:01:17Z","citation":{"short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, in:, IEEE National Radar Conference - Proceedings, IEEE, 2020.","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., & Fink, J. M. (2020). Microwave quantum illumination with a digital phase-conjugated receiver. In IEEE National Radar Conference - Proceedings (Vol. 2020). Florence, Italy: IEEE. https://doi.org/10.1109/RadarConf2043947.2020.9266397","ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination with a digital phase-conjugated receiver. IEEE National Radar Conference - Proceedings. RadarConf: National Conference on Radar vol. 2020, 9266397.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination with a digital phase-conjugated receiver. In: IEEE National Radar Conference - Proceedings. Vol 2020. IEEE; 2020. doi:10.1109/RadarConf2043947.2020.9266397","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” IEEE National Radar Conference - Proceedings, vol. 2020, no. 9, 9266397, IEEE, 2020, doi:10.1109/RadarConf2043947.2020.9266397.","chicago":"Barzanjeh, Shabir, Stefano Pirandola, David Vitali, and Johannes M Fink. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” In IEEE National Radar Conference - Proceedings, Vol. 2020. IEEE, 2020. https://doi.org/10.1109/RadarConf2043947.2020.9266397.","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination with a digital phase-conjugated receiver,” in IEEE National Radar Conference - Proceedings, Florence, Italy, 2020, vol. 2020, no. 9."},"publisher":"IEEE","type":"conference","quality_controlled":"1","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1109/RadarConf2043947.2020.9266397","scopus_import":"1","publication":"IEEE National Radar Conference - Proceedings","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"7910","relation":"earlier_version"}]},"ec_funded":1,"fulldoi":"https://doi.org/10.1109/RadarConf2043947.2020.9266397","project":[{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644","call_identifier":"H2020"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","call_identifier":"H2020"},{"grant_number":"732894","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["1097-5659"],"isbn":["9781728189420"]},"date_published":"2020-09-21T00:00:00Z","abstract":[{"text":"Quantum illumination is a sensing technique that employs entangled signal-idler beams to improve the detection efficiency of low-reflectivity objects in environments with large thermal noise. The advantage over classical strategies is evident at low signal brightness, a feature which could make the protocol an ideal prototype for non-invasive scanning or low-power short-range radar. Here we experimentally investigate the concept of quantum illumination at microwave frequencies, by generating entangled fields using a Josephson parametric converter which are then amplified to illuminate a room-temperature object at a distance of 1 meter. Starting from experimental data, we simulate the case of perfect idler photon number detection, which results in a quantum advantage compared to the relative classical benchmark. Our results highlight the opportunities and challenges on the way towards a first room-temperature application of microwave quantum circuits.","lang":"eng"}],"day":"21","conference":{"start_date":"2020-09-21","end_date":"2020-09-25","name":"RadarConf: National Conference on Radar","location":"Florence, Italy"}},{"date_created":"2021-01-17T23:01:13Z","article_processing_charge":"No","volume":14,"citation":{"short":"E. Kokoris Kogias, E.C. Alp, L. Gasser, P. Jovanovic, E. Syta, B. Ford, Proceedings of the VLDB Endowment 14 (2020) 586–599.","apa":"Kokoris Kogias, E., Alp, E. C., Gasser, L., Jovanovic, P., Syta, E., & Ford, B. (2020). CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. Association for Computing Machinery. https://doi.org/10.14778/3436905.3436917","ama":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 2020;14(4):586-599. doi:10.14778/3436905.3436917","ista":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. 2020. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 14(4), 586–599.","mla":"Kokoris Kogias, Eleftherios, et al. “CALYPSO: Private Data Management for Decentralized Ledgers.” Proceedings of the VLDB Endowment, vol. 14, no. 4, Association for Computing Machinery, 2020, pp. 586–99, doi:10.14778/3436905.3436917.","chicago":"Kokoris Kogias, Eleftherios, Enis Ceyhun Alp, Linus Gasser, Philipp Jovanovic, Ewa Syta, and Bryan Ford. “CALYPSO: Private Data Management for Decentralized Ledgers.” Proceedings of the VLDB Endowment. Association for Computing Machinery, 2020. https://doi.org/10.14778/3436905.3436917.","ieee":"E. Kokoris Kogias, E. C. Alp, L. Gasser, P. Jovanovic, E. Syta, and B. Ford, “CALYPSO: Private data management for decentralized ledgers,” Proceedings of the VLDB Endowment, vol. 14, no. 4. Association for Computing Machinery, pp. 586–599, 2020."},"publisher":"Association for Computing Machinery","article_type":"original","_id":"9011","external_id":{"isi":["000658495400012"]},"title":"CALYPSO: Private data management for decentralized ledgers","intvolume":" 14","oa":1,"status":"public","date_updated":"2026-06-18T19:40:17Z","ddc":["000"],"oa_version":"Published Version","year":"2020","author":[{"first_name":"Eleftherios","orcid":"0000-0002-8827-3382","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Alp, Enis Ceyhun","last_name":"Alp","first_name":"Enis Ceyhun"},{"last_name":"Gasser","full_name":"Gasser, Linus","first_name":"Linus"},{"first_name":"Philipp","last_name":"Jovanovic","full_name":"Jovanovic, Philipp"},{"full_name":"Syta, Ewa","last_name":"Syta","first_name":"Ewa"},{"last_name":"Ford","full_name":"Ford, Bryan","first_name":"Bryan"}],"acknowledgement":"We thank Nicolas Gailly, Vincent Graf, Jean-Pierre Hubaux, Wouter Lueks, Massimo Marelli, Carmela Troncoso, Juan-RamĂłn Troncoso Pastoriza, FrĂ©dĂ©ric Pont, and Sandra Siby for their valuable feedback. This project was supported in part by the ETH domain under PHRT grant #2017−201, and by the AXA Research Fund, Byzgen, DFINITY, and the Swiss Data Science Center (SDSC).","issue":"4","main_file_link":[{"url":"https://dl.acm.org/doi/10.14778/3436905.3436917","open_access":"1"}],"month":"12","isi":1,"department":[{"_id":"ElKo"}],"abstract":[{"lang":"eng","text":"Distributed ledgers provide high availability and integrity, making them a key enabler for practical and secure computation of distributed workloads among mutually distrustful parties. Many practical applications also require strong confidentiality, however. This work enhances permissioned and permissionless blockchains with the ability to manage confidential data without forfeiting availability or decentralization. The proposed Calypso architecture addresses two orthogonal challenges confronting modern distributed ledgers: (a) enabling the auditable management of secrets and (b) protecting distributed computations against arbitrage attacks when their results depend on the ordering and secrecy of inputs.\r\n\r\nCalypso introduces on-chain secrets, a novel abstraction that enforces atomic deposition of an auditable trace whenever users access confidential data. Calypso provides user-controlled consent management that ensures revocation atomicity and accountable anonymity. To enable permissionless deployment, we introduce an incentive scheme and provide users with the option to select their preferred trustees. We evaluated our Calypso prototype with a confidential document-sharing application and a decentralized lottery. Our benchmarks show that transaction-processing latency increases linearly in terms of security (number of trustees) and is in the range of 0.2 to 8 seconds for 16 to 128 trustees."}],"day":"01","page":"586-599","date_published":"2020-12-01T00:00:00Z","publication_identifier":{"eissn":["2150-8097"]},"corr_author":"1","fulldoi":"https://doi.org/10.14778/3436905.3436917","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"publication":"Proceedings of the VLDB Endowment","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.14778/3436905.3436917","scopus_import":"1","type":"journal_article","quality_controlled":"1","publication_status":"published"},{"volume":52,"article_processing_charge":"No","date_created":"2021-01-24T23:01:09Z","citation":{"chicago":"Fischer, Julian L, Tim Laux, and Theresa M. Simon. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/20M1322182.","ieee":"J. L. Fischer, T. Laux, and T. M. Simon, “Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies,” SIAM Journal on Mathematical Analysis, vol. 52, no. 6. Society for Industrial and Applied Mathematics, pp. 6222–6233, 2020.","short":"J.L. Fischer, T. Laux, T.M. Simon, SIAM Journal on Mathematical Analysis 52 (2020) 6222–6233.","apa":"Fischer, J. L., Laux, T., & Simon, T. M. (2020). Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1322182","ista":"Fischer JL, Laux T, Simon TM. 2020. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 52(6), 6222–6233.","mla":"Fischer, Julian L., et al. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” SIAM Journal on Mathematical Analysis, vol. 52, no. 6, Society for Industrial and Applied Mathematics, 2020, pp. 6222–33, doi:10.1137/20M1322182.","ama":"Fischer JL, Laux T, Simon TM. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 2020;52(6):6222-6233. doi:10.1137/20M1322182"},"publisher":"Society for Industrial and Applied Mathematics","_id":"9039","article_type":"original","external_id":{"isi":["000600695200027"]},"oa":1,"intvolume":" 52","title":"Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies","file_date_updated":"2021-01-25T07:48:39Z","status":"public","date_updated":"2025-07-10T12:01:32Z","ddc":["510"],"oa_version":"Published Version","year":"2020","acknowledgement":"This work was supported by the European Union's Horizon 2020 Research and Innovation\r\nProgramme under Marie Sklodowska-Curie grant agreement 665385 and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy, EXC-2047/1--390685813.","author":[{"full_name":"Fischer, Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","orcid":"0000-0002-0479-558X","first_name":"Julian L"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"},{"last_name":"Simon","full_name":"Simon, Theresa M.","first_name":"Theresa M."}],"has_accepted_license":"1","issue":"6","isi":1,"month":"12","department":[{"_id":"JuFi"}],"abstract":[{"text":"We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems.","lang":"eng"}],"day":"15","page":"6222-6233","file":[{"access_level":"open_access","file_id":"9041","checksum":"21aa1cf4c30a86a00cae15a984819b5d","date_updated":"2021-01-25T07:48:39Z","date_created":"2021-01-25T07:48:39Z","creator":"dernst","success":1,"file_size":310655,"content_type":"application/pdf","file_name":"2020_SIAM_Fischer.pdf","relation":"main_file"}],"date_published":"2020-12-15T00:00:00Z","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"fulldoi":"https://doi.org/10.1137/20M1322182","ec_funded":1,"corr_author":"1","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication":"SIAM Journal on Mathematical Analysis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1137/20M1322182","publication_status":"published","quality_controlled":"1","type":"journal_article"},{"publication":"Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","type":"conference","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.34727/2020/isbn.978-3-85448-042-6_21","scopus_import":"1","page":"138-147","date_published":"2020-09-21T00:00:00Z","file":[{"success":1,"creator":"dernst","relation":"main_file","file_name":"2020_FMCAD_Alamdari.pdf","content_type":"application/pdf","file_size":990999,"checksum":"d616d549a0ade78606b16f8a9540820f","file_id":"9109","access_level":"open_access","date_created":"2021-02-09T09:39:02Z","date_updated":"2021-02-09T09:39:02Z"}],"abstract":[{"text":"Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training.","lang":"eng"}],"day":"21","conference":{"start_date":"2020-09-21","end_date":"2020-09-24","name":"FMCAD: Formal Methods in Computer-Aided Design","location":"Online Conference"},"fulldoi":"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21","project":[{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"eissn":["2708-7824"],"isbn":["9783854480426"]},"year":"2020","oa_version":"Published Version","author":[{"full_name":"Alamdari, Par Alizadeh","last_name":"Alamdari","first_name":"Par Alizadeh"},{"first_name":"Guy","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Anna","full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","last_name":"Lukina"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","date_updated":"2025-07-10T12:01:32Z","ddc":["000"],"month":"09","department":[{"_id":"ToHe"}],"has_accepted_license":"1","_id":"9040","article_processing_charge":"No","date_created":"2021-01-24T23:01:10Z","citation":{"ieee":"P. A. Alamdari, G. Avni, T. A. Henzinger, and A. Lukina, “Formal methods with a touch of magic,” in Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, Online Conference, 2020, pp. 138–147.","chicago":"Alamdari, Par Alizadeh, Guy Avni, Thomas A Henzinger, and Anna Lukina. “Formal Methods with a Touch of Magic.” In Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, 138–47. TU Wien Academic Press, 2020. https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21.","ista":"Alamdari PA, Avni G, Henzinger TA, Lukina A. 2020. Formal methods with a touch of magic. Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 138–147.","mla":"Alamdari, Par Alizadeh, et al. “Formal Methods with a Touch of Magic.” Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2020, pp. 138–47, doi:10.34727/2020/isbn.978-3-85448-042-6_21.","ama":"Alamdari PA, Avni G, Henzinger TA, Lukina A. Formal methods with a touch of magic. In: Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design. TU Wien Academic Press; 2020:138-147. doi:10.34727/2020/isbn.978-3-85448-042-6_21","apa":"Alamdari, P. A., Avni, G., Henzinger, T. A., & Lukina, A. (2020). Formal methods with a touch of magic. In Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design (pp. 138–147). Online Conference: TU Wien Academic Press. https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21","short":"P.A. Alamdari, G. Avni, T.A. Henzinger, A. Lukina, in:, Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2020, pp. 138–147."},"publisher":"TU Wien Academic Press","file_date_updated":"2021-02-09T09:39:02Z","status":"public","title":"Formal methods with a touch of magic","oa":1},{"author":[{"full_name":"Schmid-Hempel, Paul","last_name":"Schmid-Hempel","first_name":"Paul"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia M","first_name":"Sylvia M","orcid":"0000-0002-2193-3868"}],"publication":"Encyclopedia of Social Insects","place":"Cham","year":"2020","oa_version":"None","editor":[{"first_name":"C","full_name":"Starr, C","last_name":"Starr"}],"language":[{"iso":"eng"}],"date_updated":"2021-02-05T12:19:21Z","department":[{"_id":"SyCr"}],"publication_status":"published","type":"book_chapter","month":"02","quality_controlled":"1","doi":"10.1007/978-3-319-90306-4_94-1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-02-22T00:00:00Z","_id":"9096","day":"22","publisher":"Springer Nature","citation":{"short":"P. Schmid-Hempel, S. Cremer, in:, C. Starr (Ed.), Encyclopedia of Social Insects, Springer Nature, Cham, 2020.","apa":"Schmid-Hempel, P., & Cremer, S. (2020). Parasites and Pathogens. In C. Starr (Ed.), Encyclopedia of Social Insects. Cham: Springer Nature. https://doi.org/10.1007/978-3-319-90306-4_94-1","mla":"Schmid-Hempel, Paul, and Sylvia Cremer. “Parasites and Pathogens.” Encyclopedia of Social Insects, edited by C Starr, Springer Nature, 2020, doi:10.1007/978-3-319-90306-4_94-1.","ista":"Schmid-Hempel P, Cremer S. 2020.Parasites and Pathogens. In: Encyclopedia of Social Insects. .","ama":"Schmid-Hempel P, Cremer S. Parasites and Pathogens. In: Starr C, ed. Encyclopedia of Social Insects. Cham: Springer Nature; 2020. doi:10.1007/978-3-319-90306-4_94-1","chicago":"Schmid-Hempel, Paul, and Sylvia Cremer. “Parasites and Pathogens.” In Encyclopedia of Social Insects, edited by C Starr. Cham: Springer Nature, 2020. https://doi.org/10.1007/978-3-319-90306-4_94-1.","ieee":"P. Schmid-Hempel and S. Cremer, “Parasites and Pathogens,” in Encyclopedia of Social Insects, C. Starr, Ed. Cham: Springer Nature, 2020."},"date_created":"2021-02-05T12:15:18Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1007/978-3-319-90306-4_94-1","status":"public","publication_identifier":{"isbn":["9783319903064"]},"title":"Parasites and Pathogens"},{"citation":{"short":"S. Gruenbacher, J. Cyranka, M. Lechner, M.A. Islam, S.A. Smolka, R. Grosu, in:, Proceedings of the 59th IEEE Conference on Decision and Control, IEEE, 2020, pp. 1556–1563.","apa":"Gruenbacher, S., Cyranka, J., Lechner, M., Islam, M. A., Smolka, S. A., & Grosu, R. (2020). Lagrangian reachtubes: The next generation. In Proceedings of the 59th IEEE Conference on Decision and Control (Vol. 2020, pp. 1556–1563). Jeju Islang, Korea (South): IEEE. https://doi.org/10.1109/CDC42340.2020.9304042","ista":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. 2020. Lagrangian reachtubes: The next generation. Proceedings of the 59th IEEE Conference on Decision and Control. CDC: Conference on Decision and Control vol. 2020, 1556–1563.","ama":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. Lagrangian reachtubes: The next generation. In: Proceedings of the 59th IEEE Conference on Decision and Control. Vol 2020. IEEE; 2020:1556-1563. doi:10.1109/CDC42340.2020.9304042","mla":"Gruenbacher, Sophie, et al. “Lagrangian Reachtubes: The next Generation.” Proceedings of the 59th IEEE Conference on Decision and Control, vol. 2020, IEEE, 2020, pp. 1556–63, doi:10.1109/CDC42340.2020.9304042.","chicago":"Gruenbacher, Sophie, Jacek Cyranka, Mathias Lechner, Md Ariful Islam, Scott A. Smolka, and Radu Grosu. “Lagrangian Reachtubes: The next Generation.” In Proceedings of the 59th IEEE Conference on Decision and Control, 2020:1556–63. IEEE, 2020. https://doi.org/10.1109/CDC42340.2020.9304042.","ieee":"S. Gruenbacher, J. Cyranka, M. Lechner, M. A. Islam, S. A. Smolka, and R. Grosu, “Lagrangian reachtubes: The next generation,” in Proceedings of the 59th IEEE Conference on Decision and Control, Jeju Islang, Korea (South), 2020, vol. 2020, pp. 1556–1563."},"volume":2020,"article_processing_charge":"No","date_created":"2021-02-07T23:01:14Z","publisher":"IEEE","_id":"9103","external_id":{"arxiv":["2012.07458"]},"title":"Lagrangian reachtubes: The next generation","intvolume":" 2020","oa":1,"status":"public","arxiv":1,"date_updated":"2026-04-16T09:34:59Z","oa_version":"Preprint","year":"2020","acknowledgement":"The authors would like to thank Ramin Hasani and Guillaume Berger for intellectual discussions about the research which lead to the generation of new ideas. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Smolka’s research was supported by NSF grants CPS-1446832 and CCF-1918225. Gruenbacher is funded by FWF project W1255-N23. JC was partially supported by NAWA Polish Returns grant\r\nPPN/PPO/2018/1/00029.\r\n","author":[{"first_name":"Sophie","full_name":"Gruenbacher, Sophie","last_name":"Gruenbacher"},{"first_name":"Jacek","last_name":"Cyranka","full_name":"Cyranka, Jacek"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias"},{"full_name":"Islam, Md Ariful","last_name":"Islam","first_name":"Md Ariful"},{"full_name":"Smolka, Scott A.","last_name":"Smolka","first_name":"Scott A."},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"}],"month":"12","main_file_link":[{"url":"https://arxiv.org/abs/2012.07458","open_access":"1"}],"department":[{"_id":"ToHe"}],"abstract":[{"text":"We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball’s volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the \"wrapping effect\" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG’s superior performance compared to LRT, CAPD, and Flow*.","lang":"eng"}],"day":"14","conference":{"location":"Jeju Islang, Korea (South)","start_date":"2020-12-14","end_date":"2020-12-18","name":"CDC: Conference on Decision and Control"},"page":"1556-1563","date_published":"2020-12-14T00:00:00Z","project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["9781728174471"],"issn":["0743-1546"]},"fulldoi":"https://doi.org/10.1109/CDC42340.2020.9304042","language":[{"iso":"eng"}],"publication":"Proceedings of the 59th IEEE Conference on Decision and Control","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1109/CDC42340.2020.9304042","scopus_import":"1","type":"conference","quality_controlled":"1","publication_status":"published"},{"status":"public","arxiv":1,"title":"On the support of the free additive convolution","intvolume":" 142","oa":1,"article_type":"original","_id":"9104","external_id":{"arxiv":["1804.11199"],"isi":["000611879400008"]},"article_processing_charge":"No","date_created":"2021-02-07T23:01:15Z","volume":142,"citation":{"chicago":"Bao, Zhigang, LĂĄszlĂł Erdös, and Kevin Schnelli. “On the Support of the Free Additive Convolution.” Journal d’Analyse Mathematique. Springer Nature, 2020. https://doi.org/10.1007/s11854-020-0135-2.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “On the support of the free additive convolution,” Journal d’Analyse Mathematique, vol. 142. Springer Nature, pp. 323–348, 2020.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2020). On the support of the free additive convolution. Journal d’Analyse Mathematique. Springer Nature. https://doi.org/10.1007/s11854-020-0135-2","short":"Z. Bao, L. Erdös, K. Schnelli, Journal d’Analyse Mathematique 142 (2020) 323–348.","ista":"Bao Z, Erdös L, Schnelli K. 2020. On the support of the free additive convolution. Journal d’Analyse Mathematique. 142, 323–348.","ama":"Bao Z, Erdös L, Schnelli K. On the support of the free additive convolution. Journal d’Analyse Mathematique. 2020;142:323-348. doi:10.1007/s11854-020-0135-2","mla":"Bao, Zhigang, et al. “On the Support of the Free Additive Convolution.” Journal d’Analyse Mathematique, vol. 142, Springer Nature, 2020, pp. 323–48, doi:10.1007/s11854-020-0135-2."},"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11199"}],"month":"11","isi":1,"department":[{"_id":"LaEr"}],"oa_version":"Preprint","year":"2020","author":[{"full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, LĂĄszlĂł","first_name":"LĂĄszlĂł","orcid":"0000-0001-5366-9603"},{"full_name":"Schnelli, Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin","orcid":"0000-0003-0954-3231"}],"acknowledgement":"Supported in part by Hong Kong RGC Grant ECS 26301517.\r\nSupported in part by ERC Advanced Grant RANMAT No. 338804.\r\nSupported in part by the Knut and Alice Wallenberg Foundation and the Swedish Research Council Grant VR-2017-05195.","date_updated":"2025-07-10T12:01:37Z","fulldoi":"https://doi.org/10.1007/s11854-020-0135-2","ec_funded":1,"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["0021-7670"],"eissn":["1565-8538"]},"page":"323-348","date_published":"2020-11-01T00:00:00Z","abstract":[{"lang":"eng","text":"We consider the free additive convolution of two probability measures ÎŒ and Îœ on the real line and show that ÎŒ ⊞ v is supported on a single interval if ÎŒ and Îœ each has single interval support. Moreover, the density of ÎŒ ⊞ Îœ is proven to vanish as a square root near the edges of its support if both ÎŒ and Îœ have power law behavior with exponents between −1 and 1 near their edges. In particular, these results show the ubiquity of the conditions in our recent work on optimal local law at the spectral edges for addition of random matrices [5]."}],"day":"01","type":"journal_article","quality_controlled":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s11854-020-0135-2","scopus_import":"1","publication":"Journal d'Analyse Mathematique","language":[{"iso":"eng"}]},{"_id":"9123","date_published":"2020-05-16T00:00:00Z","date_created":"2021-02-15T12:39:04Z","article_processing_charge":"No","citation":{"ieee":"A. M. Westram, R. Faria, R. Butlin, and K. Johannesson, “Inversions and Evolution,” in eLS, Wiley, 2020.","chicago":"Westram, Anja M, Rui Faria, Roger Butlin, and Kerstin Johannesson. “Inversions and Evolution.” In ELS. Wiley, 2020. https://doi.org/10.1002/9780470015902.a0029007.","mla":"Westram, Anja M., et al. “Inversions and Evolution.” ELS, Wiley, 2020, doi:10.1002/9780470015902.a0029007.","ista":"Westram AM, Faria R, Butlin R, Johannesson K. 2020.Inversions and Evolution. In: eLS. .","ama":"Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: ELS. Wiley; 2020. doi:10.1002/9780470015902.a0029007","apa":"Westram, A. M., Faria, R., Butlin, R., & Johannesson, K. (2020). Inversions and Evolution. In eLS. Wiley. https://doi.org/10.1002/9780470015902.a0029007","short":"A.M. Westram, R. Faria, R. Butlin, K. Johannesson, in:, ELS, Wiley, 2020."},"abstract":[{"lang":"eng","text":"Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution."}],"day":"16","publisher":"Wiley","fulldoi":"https://doi.org/10.1002/9780470015902.a0029007","status":"public","publication_identifier":{"eissn":["9780470015902"],"isbn":["9780470016176"]},"title":"Inversions and Evolution","oa_version":"None","year":"2020","author":[{"first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"}],"publication":"eLS","date_updated":"2026-04-16T10:25:26Z","language":[{"iso":"eng"}],"publication_status":"published","type":"book_chapter","month":"05","quality_controlled":"1","department":[{"_id":"NiBa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1002/9780470015902.a0029007"},{"publication":"Computational and Mathematical Biophysics","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication_status":"published","type":"journal_article","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","doi":"10.1515/cmb-2020-0101","page":"74-88","date_published":"2020-07-21T00:00:00Z","file":[{"date_created":"2021-02-19T13:33:19Z","date_updated":"2021-02-19T13:33:19Z","file_id":"9170","access_level":"open_access","checksum":"ca43a7440834eab6bbea29c59b56ef3a","content_type":"application/pdf","file_size":707452,"relation":"main_file","file_name":"2020_CompMathBiophysics_Akopyan.pdf","creator":"dernst","success":1}],"abstract":[{"text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.","lang":"eng"}],"day":"21","corr_author":"1","fulldoi":"https://doi.org/10.1515/cmb-2020-0101","ec_funded":1,"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2544-7297"]},"oa_version":"Published Version","year":"2020","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert"}],"date_updated":"2025-04-14T07:48:34Z","ddc":["510"],"month":"07","department":[{"_id":"HeEd"}],"has_accepted_license":"1","issue":"1","_id":"9156","article_type":"original","external_id":{"arxiv":["1908.06777"]},"article_processing_charge":"No","citation":{"ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88.","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88."},"volume":8,"date_created":"2021-02-17T15:12:44Z","publisher":"De Gruyter","file_date_updated":"2021-02-19T13:33:19Z","arxiv":1,"status":"public","oa":1,"title":"The weighted Gaussian curvature derivative of a space-filling diagram","intvolume":" 8"},{"article_type":"original","_id":"9157","publisher":"De Gruyter","volume":8,"article_processing_charge":"No","date_created":"2021-02-17T15:13:01Z","citation":{"short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020."},"status":"public","file_date_updated":"2021-02-19T13:56:24Z","intvolume":" 8","title":"The weighted mean curvature derivative of a space-filling diagram","oa":1,"acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","author":[{"orcid":"0000-0002-2548-617X","first_name":"Arseniy","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan"},{"first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"oa_version":"Published Version","year":"2020","ddc":["510"],"date_updated":"2025-04-14T07:48:35Z","department":[{"_id":"HeEd"}],"month":"06","issue":"1","has_accepted_license":"1","date_published":"2020-06-20T00:00:00Z","file":[{"file_size":562359,"content_type":"application/pdf","file_name":"2020_CompMathBiophysics_Akopyan2.pdf","relation":"main_file","creator":"dernst","success":1,"date_updated":"2021-02-19T13:56:24Z","date_created":"2021-02-19T13:56:24Z","access_level":"open_access","file_id":"9171","checksum":"cea41de9937d07a3b927d71ee8b4e432"}],"page":"51-67","day":"20","abstract":[{"lang":"eng","text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy."}],"ec_funded":1,"fulldoi":"https://doi.org/10.1515/cmb-2020-0100","corr_author":"1","publication_identifier":{"issn":["2544-7297"]},"project":[{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"publication":"Computational and Mathematical Biophysics","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"journal_article","quality_controlled":"1","publication_status":"published","doi":"10.1515/cmb-2020-0100","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"has_accepted_license":"1","issue":"2","month":"03","isi":1,"department":[{"_id":"JoFi"}],"date_updated":"2024-10-22T09:36:25Z","article_number":"020501","ddc":["530"],"oa_version":"Published Version","year":"2020","acknowledgement":"During the writing of this article we became aware of another review of quantum transduction with somewhat different emphasis [99].\r\nWe would like to thank the participants of the transduction workshop at Caltech in September 2018 for helpful and stimulating discussions. We particularly thank John Bartholomew, Andrei Faraon, Johannes Fink, Jeff Holzgrafe, Linbo Shao, Marko Lončar, Daniel Oblak, and Oskar Painter.\r\nN L and N S acknowledge support from the Alliance for Quantum Technologies' (AQT) Intelligent Quantum Networks and Technologies (INQNET) research program and by DOE/HEP QuantISED program grant, QCCFP (Quantum Communication Channels for Fundamental Physics), award number DE-SC0019219. NS further acknowledges support by the Natural Sciences and Engineering Research Council of Canada (NSERC). SB acknowledges support from the Marie SkƂodowska Curie fellowship number 707 438 (MSC-IF SUPEREOM). JPC acknowledges support from the Caltech PMA prize postdoctoral fellowship. MS acknowledges support from the ARL-CDQI and the National Science Foundation. CS acknowledges NSERC, Quantum Alberta, and the Alberta Major Innovation Fund.","author":[{"last_name":"Lauk","full_name":"Lauk, Nikolai","first_name":"Nikolai"},{"first_name":"Neil","last_name":"Sinclair","full_name":"Sinclair, Neil"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","first_name":"Shabir"},{"full_name":"Covey, Jacob P","last_name":"Covey","first_name":"Jacob P"},{"first_name":"Mark","last_name":"Saffman","full_name":"Saffman, Mark"},{"first_name":"Maria","full_name":"Spiropulu, Maria","last_name":"Spiropulu"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"intvolume":" 5","title":"Perspectives on quantum transduction","oa":1,"file_date_updated":"2021-03-02T09:47:13Z","status":"public","date_created":"2021-02-25T08:32:29Z","citation":{"short":"N. Lauk, N. Sinclair, S. Barzanjeh, J.P. Covey, M. Saffman, M. Spiropulu, C. Simon, Quantum Science and Technology 5 (2020).","apa":"Lauk, N., Sinclair, N., Barzanjeh, S., Covey, J. P., Saffman, M., Spiropulu, M., & Simon, C. (2020). Perspectives on quantum transduction. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ab788a","ista":"Lauk N, Sinclair N, Barzanjeh S, Covey JP, Saffman M, Spiropulu M, Simon C. 2020. Perspectives on quantum transduction. Quantum Science and Technology. 5(2), 020501.","ama":"Lauk N, Sinclair N, Barzanjeh S, et al. Perspectives on quantum transduction. Quantum Science and Technology. 2020;5(2). doi:10.1088/2058-9565/ab788a","mla":"Lauk, Nikolai, et al. “Perspectives on Quantum Transduction.” Quantum Science and Technology, vol. 5, no. 2, 020501, IOP Publishing, 2020, doi:10.1088/2058-9565/ab788a.","chicago":"Lauk, Nikolai, Neil Sinclair, Shabir Barzanjeh, Jacob P Covey, Mark Saffman, Maria Spiropulu, and Christoph Simon. “Perspectives on Quantum Transduction.” Quantum Science and Technology. IOP Publishing, 2020. https://doi.org/10.1088/2058-9565/ab788a.","ieee":"N. Lauk et al., “Perspectives on quantum transduction,” Quantum Science and Technology, vol. 5, no. 2. IOP Publishing, 2020."},"volume":5,"article_processing_charge":"No","publisher":"IOP Publishing","article_type":"review","_id":"9194","external_id":{"isi":["000521449500001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1088/2058-9565/ab788a","scopus_import":"1","type":"journal_article","quality_controlled":"1","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"publication":"Quantum Science and Technology","project":[{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2058-9565"]},"ec_funded":1,"fulldoi":"https://doi.org/10.1088/2058-9565/ab788a","abstract":[{"lang":"eng","text":"Quantum transduction, the process of converting quantum signals from one form of energy to another, is an important area of quantum science and technology. The present perspective article reviews quantum transduction between microwave and optical photons, an area that has recently seen a lot of activity and progress because of its relevance for connecting superconducting quantum processors over long distances, among other applications. Our review covers the leading approaches to achieving such transduction, with an emphasis on those based on atomic ensembles, opto-electro-mechanics, and electro-optics. We briefly discuss relevant metrics from the point of view of different applications, as well as challenges for the future."}],"day":"01","file":[{"success":1,"creator":"dernst","relation":"main_file","file_name":"2020_QuantumScience_Lauk.pdf","content_type":"application/pdf","file_size":974399,"checksum":"a8562c42124a66b86836fe2489eb5f4f","file_id":"9215","access_level":"open_access","date_created":"2021-03-02T09:47:13Z","date_updated":"2021-03-02T09:47:13Z"}],"date_published":"2020-03-01T00:00:00Z"}]