[{"publisher":"IEEE","date_published":"2019-05-01T00:00:00Z","type":"conference","alternative_title":["ICRA"],"language":[{"iso":"eng"}],"ddc":["000"],"status":"public","month":"05","day":"01","quality_controlled":"1","project":[{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"last_name":"Zimmer","first_name":"Manuel","full_name":"Zimmer, Manuel"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"oa":1,"volume":"2019-May","publication":"Proceedings - IEEE International Conference on Robotics and Automation","date_updated":"2021-01-12T08:09:28Z","department":[{"_id":"ToHe"}],"publication_identifier":{"isbn":["9781538660270"]},"doi":"10.1109/icra.2019.8793840","scopus_import":"1","file_date_updated":"2020-10-08T17:30:38Z","oa_version":"Submitted Version","article_processing_charge":"No","title":"Designing worm-inspired neural networks for interpretable robotic control","publication_status":"published","abstract":[{"lang":"eng","text":"In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods."}],"article_number":"8793840","year":"2019","citation":{"ieee":"M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing worm-inspired neural networks for interpretable robotic control,” in <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, Montreal, QC, Canada, 2019, vol. 2019–May.","ista":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired neural networks for interpretable robotic control. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, vol. 2019–May, 8793840.","ama":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired neural networks for interpretable robotic control. In: <i>Proceedings - IEEE International Conference on Robotics and Automation</i>. Vol 2019-May. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/icra.2019.8793840\">10.1109/icra.2019.8793840</a>","apa":"Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., &#38; Grosu, R. (2019). Designing worm-inspired neural networks for interpretable robotic control. In <i>Proceedings - IEEE International Conference on Robotics and Automation</i> (Vol. 2019–May). Montreal, QC, Canada: IEEE. <a href=\"https://doi.org/10.1109/icra.2019.8793840\">https://doi.org/10.1109/icra.2019.8793840</a>","short":"M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2019.","chicago":"Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” In <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, Vol. 2019–May. IEEE, 2019. <a href=\"https://doi.org/10.1109/icra.2019.8793840\">https://doi.org/10.1109/icra.2019.8793840</a>.","mla":"Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, vol. 2019–May, 8793840, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/icra.2019.8793840\">10.1109/icra.2019.8793840</a>."},"_id":"6888","file":[{"checksum":"f5545a6b60c3ffd01feb3613f81d03b6","creator":"dernst","file_id":"8636","content_type":"application/pdf","date_updated":"2020-10-08T17:30:38Z","relation":"main_file","file_size":3265107,"date_created":"2020-10-08T17:30:38Z","file_name":"2019_ICRA_Lechner.pdf","access_level":"open_access","success":1}],"date_created":"2019-09-18T08:09:51Z","conference":{"location":"Montreal, QC, Canada","name":"ICRA: International Conference on Robotics and Automation","end_date":"2019-05-24","start_date":"2019-05-20"}},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"has_accepted_license":"1","quality_controlled":"1","day":"01","status":"public","month":"08","alternative_title":["LIPIcs"],"ddc":["000"],"language":[{"iso":"eng"}],"type":"conference","date_published":"2019-08-01T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"content_type":"application/pdf","file_id":"6923","creator":"kschuh","checksum":"7b2ecfd4d9d02360308c0ca986fc10a7","file_name":"2019_LIPIcs_Chatterjee.pdf","access_level":"open_access","relation":"main_file","file_size":509163,"date_created":"2019-10-01T08:49:45Z","date_updated":"2020-07-14T12:47:43Z"}],"date_created":"2019-09-18T08:11:43Z","_id":"6889","conference":{"start_date":"2019-08-27","end_date":"2019-08-30","name":"CONCUR: International Conference on Concurrency Theory","location":"Amsterdam, Netherlands"},"abstract":[{"text":"We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. ","lang":"eng"}],"citation":{"apa":"Chatterjee, K., &#38; Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">https://doi.org/10.4230/LIPICS.CONCUR.2019.6</a>","short":"K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">https://doi.org/10.4230/LIPICS.CONCUR.2019.6</a>.","mla":"Chatterjee, Krishnendu, and Nir Piterman. <i>Combinations of Qualitative Winning for Stochastic Parity Games</i>. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">10.4230/LIPICS.CONCUR.2019.6</a>.","ista":"Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 6.","ieee":"K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","ama":"Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">10.4230/LIPICS.CONCUR.2019.6</a>"},"year":"2019","article_number":"6","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:43Z","title":"Combinations of Qualitative Winning for Stochastic Parity Games","publication_status":"published","scopus_import":1,"doi":"10.4230/LIPICS.CONCUR.2019.6","date_updated":"2021-01-12T08:09:28Z","department":[{"_id":"KrCh"}],"intvolume":"       140","volume":140,"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Piterman, Nir","last_name":"Piterman","first_name":"Nir"}]},{"title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging","publication_status":"published","oa_version":"None","article_processing_charge":"No","doi":"10.1016/bs.aivir.2019.07.008","scopus_import":"1","publication_identifier":{"issn":["0065-3527"],"isbn":["9780128184561"]},"editor":[{"last_name":"Rey","first_name":"Félix A.","full_name":"Rey, Félix A."}],"_id":"6890","date_created":"2019-09-18T08:15:37Z","year":"2019","citation":{"ama":"Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. <i>Complementary Strategies to Study Virus Structure and Function</i>. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:<a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">10.1016/bs.aivir.2019.07.008</a>","ieee":"M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in <i>Complementary Strategies to Study Virus Structure and Function</i>, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159.","ista":"Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.","mla":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” <i>Complementary Strategies to Study Virus Structure and Function</i>, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:<a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">10.1016/bs.aivir.2019.07.008</a>.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159.","apa":"Obr, M., &#38; Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), <i>Complementary Strategies to Study Virus Structure and Function</i> (Vol. 105, pp. 117–159). Elsevier. <a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">https://doi.org/10.1016/bs.aivir.2019.07.008</a>","chicago":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In <i>Complementary Strategies to Study Virus Structure and Function</i>, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. <a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">https://doi.org/10.1016/bs.aivir.2019.07.008</a>."},"abstract":[{"lang":"eng","text":"Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods."}],"series_title":"Advances in Virus Research","volume":105,"author":[{"first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FlSc"}],"publication":"Complementary Strategies to Study Virus Structure and Function","date_updated":"2023-08-30T06:56:00Z","intvolume":"       105","quality_controlled":"1","page":"117-159","day":"27","date_published":"2019-08-27T00:00:00Z","external_id":{"pmid":["    31522703"],"isi":["000501594500006"]},"type":"book_chapter","publisher":"Elsevier","pmid":1,"month":"08","isi":1,"status":"public","language":[{"iso":"eng"}]},{"author":[{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/feeling-like-a-cell/","relation":"press_release"}],"record":[{"status":"public","relation":"part_of_dissertation","id":"6328"},{"status":"public","relation":"part_of_dissertation","id":"15"},{"relation":"part_of_dissertation","status":"public","id":"6877"}]},"oa":1,"degree_awarded":"PhD","department":[{"_id":"MiSi"}],"date_updated":"2023-10-18T08:49:17Z","doi":"10.15479/AT:ISTA:6891","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"title":"The implication of cytoskeletal dynamics on leukocyte migration","publication_status":"published","file_date_updated":"2020-10-17T22:30:03Z","article_processing_charge":"No","oa_version":"Published Version","year":"2019","citation":{"mla":"Kopf, Aglaja. <i>The Implication of Cytoskeletal Dynamics on Leukocyte Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","apa":"Kopf, A. (2019). <i>The implication of cytoskeletal dynamics on leukocyte migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>"},"abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt"}],"_id":"6891","file":[{"access_level":"closed","file_name":"Kopf_PhD_Thesis.docx","date_created":"2019-10-15T05:28:42Z","relation":"source_file","embargo_to":"open_access","file_size":74735267,"date_updated":"2020-10-17T22:30:03Z","creator":"akopf","file_id":"6950","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"00d100d6468e31e583051e0a006b640c"},{"file_size":52787224,"date_created":"2019-10-15T05:28:47Z","date_updated":"2020-10-17T22:30:03Z","relation":"main_file","embargo":"2020-10-16","access_level":"open_access","file_name":"Kopf_PhD_Thesis1.pdf","checksum":"5d1baa899993ae6ca81aebebe1797000","creator":"akopf","file_id":"6951","content_type":"application/pdf"}],"date_created":"2019-09-19T08:19:44Z","publisher":"Institute of Science and Technology Austria","date_published":"2019-07-24T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"ddc":["570"],"keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"alternative_title":["ISTA Thesis"],"month":"07","status":"public","page":"171","day":"24","project":[{"name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01250-B20"}],"has_accepted_license":"1"},{"status":"public","month":"09","alternative_title":["ISTA Thesis"],"ddc":["000"],"language":[{"iso":"eng"}],"type":"dissertation","date_published":"2019-09-30T00:00:00Z","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"day":"30","page":"132","date_updated":"2023-09-19T09:30:43Z","department":[{"_id":"ToHe"}],"degree_awarded":"PhD","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"631"},{"id":"647","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"140"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe"}],"file":[{"file_size":4100685,"date_created":"2019-09-27T14:15:05Z","date_updated":"2020-07-14T12:47:43Z","relation":"main_file","file_name":"giacobbe_thesis.pdf","access_level":"open_access","checksum":"773beaf4a85dc2acc2c12b578fbe1965","content_type":"application/pdf","file_id":"6916","creator":"mgiacobbe"},{"file_name":"giacobbe_thesis_src.tar.gz","access_level":"closed","relation":"source_file","file_size":7959732,"date_created":"2019-09-27T14:22:04Z","date_updated":"2020-07-14T12:47:43Z","content_type":"application/gzip","file_id":"6917","creator":"mgiacobbe","checksum":"97f1c3da71feefd27e6e625d32b4c75b"}],"date_created":"2019-09-22T14:08:44Z","_id":"6894","supervisor":[{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"citation":{"short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>.","apa":"Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>","mla":"Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>.","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria."},"year":"2019","oa_version":"Published Version","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:43Z","title":"Automatic time-unbounded reachability analysis of hybrid systems","publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6894"},{"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"12","pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2019-12-01T00:00:00Z","external_id":{"isi":["000491646600033"],"pmid":["31521639"]},"day":"01","quality_controlled":"1","intvolume":"      1724","date_updated":"2023-08-30T06:19:49Z","publication":"Brain Research","department":[{"_id":"GaNo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Oliveira","first_name":"Bárbara","full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yahya","first_name":"Aysan Çerağ","full_name":"Yahya, Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"volume":1724,"abstract":[{"text":"Until recently, a great amount of brain studies have been conducted in human post mortem tissues, cell lines and model organisms. These researches provided useful insights regarding cell-cell interactions occurring in the brain. However, such approaches suffer from technical limitations and inaccurate modeling of the tissue 3D cytoarchitecture. Importantly, they might lack a human genetic background essential for disease modeling. With the development of protocols to generate human cerebral organoids, we are now closer to reproducing the early stages of human brain development in vitro. As a result, more relevant cell-cell interaction studies can be conducted.\r\n\r\nIn this review, we discuss the advantages of 3D cultures over 2D in modulating brain cell-cell interactions during physiological and pathological development, as well as the progress made in developing organoids in which neurons, macroglia, microglia and vascularization are present. Finally, we debate the limitations of those models and possible future directions.","lang":"eng"}],"citation":{"ieee":"B. Oliveira, A. Ç. Yahya, and G. Novarino, “Modeling cell-cell interactions in the brain using cerebral organoids,” <i>Brain Research</i>, vol. 1724. Elsevier, 2019.","ista":"Oliveira B, Yahya AÇ, Novarino G. 2019. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. 1724, 146458.","ama":"Oliveira B, Yahya AÇ, Novarino G. Modeling cell-cell interactions in the brain using cerebral organoids. <i>Brain Research</i>. 2019;1724. doi:<a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">10.1016/j.brainres.2019.146458</a>","short":"B. Oliveira, A.Ç. Yahya, G. Novarino, Brain Research 1724 (2019).","chicago":"Oliveira, Bárbara, Aysan Çerağ Yahya, and Gaia Novarino. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” <i>Brain Research</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">https://doi.org/10.1016/j.brainres.2019.146458</a>.","apa":"Oliveira, B., Yahya, A. Ç., &#38; Novarino, G. (2019). Modeling cell-cell interactions in the brain using cerebral organoids. <i>Brain Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">https://doi.org/10.1016/j.brainres.2019.146458</a>","mla":"Oliveira, Bárbara, et al. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” <i>Brain Research</i>, vol. 1724, 146458, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">10.1016/j.brainres.2019.146458</a>."},"article_number":"146458","year":"2019","date_created":"2019-09-22T22:00:35Z","_id":"6896","publication_identifier":{"eissn":["18726240"],"issn":["00068993"]},"article_type":"original","scopus_import":"1","doi":"10.1016/j.brainres.2019.146458","article_processing_charge":"No","oa_version":"None","title":"Modeling cell-cell interactions in the brain using cerebral organoids","publication_status":"published"},{"abstract":[{"text":"The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins.","lang":"eng"}],"article_number":"dev175919","year":"2019","citation":{"mla":"Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>, vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>.","short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019).","apa":"Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., &#38; Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>","chicago":"Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>.","ama":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. 2019;146(17). doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>","ieee":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” <i>Development</i>, vol. 146, no. 17. The Company of Biologists, 2019.","ista":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919."},"_id":"6897","date_created":"2019-09-22T22:00:36Z","article_type":"original","publication_identifier":{"eissn":["14779129"]},"acknowledgement":"We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738).","doi":"10.1242/dev.175919","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.175919"}],"scopus_import":"1","article_processing_charge":"No","oa_version":"Published Version","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis","publication_status":"published","intvolume":"       146","publication":"Development","ec_funded":1,"date_updated":"2025-05-07T11:10:55Z","department":[{"_id":"EvBe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","last_name":"Zhu","first_name":"Qiang"},{"full_name":"Gallemi, Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","last_name":"Gallemi","first_name":"Marçal"},{"last_name":"Pospíšil","first_name":"Jiří","full_name":"Pospíšil, Jiří"},{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková"}],"oa":1,"volume":146,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","call_identifier":"FP7"}],"issue":"17","day":"12","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","month":"09","isi":1,"publisher":"The Company of Biologists","pmid":1,"external_id":{"isi":["000486297400011"],"pmid":["31391194"]},"date_published":"2019-09-12T00:00:00Z","type":"journal_article"},{"volume":20,"oa":1,"related_material":{"record":[{"id":"9731","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9783"},{"id":"9890","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9892"},{"status":"public","relation":"research_data","id":"9893"},{"id":"9894","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9895"},{"id":"9896","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9897"},{"id":"9898","status":"public","relation":"research_data"},{"id":"9899","relation":"research_data","status":"public"},{"id":"9900","status":"public","relation":"research_data"},{"id":"9901","relation":"research_data","status":"public"}]},"author":[{"full_name":"Sigalova, Olga M.","first_name":"Olga M.","last_name":"Sigalova"},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"full_name":"Burskaia, Valentina","last_name":"Burskaia","first_name":"Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"FyKo"}],"date_updated":"2023-08-30T06:20:22Z","publication":"BMC Genomics","intvolume":"        20","title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","publication_status":"published","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:44Z","scopus_import":"1","doi":"10.1186/s12864-019-6059-5","publication_identifier":{"eissn":["14712164"]},"date_created":"2019-09-22T22:00:36Z","file":[{"checksum":"b798773c5823012d31c812c9f7975da2","content_type":"application/pdf","creator":"kschuh","file_id":"6924","relation":"main_file","file_size":4157175,"date_created":"2019-10-01T10:33:17Z","date_updated":"2020-07-14T12:47:44Z","access_level":"open_access","file_name":"2019_BioMed_Sigalova.pdf"}],"_id":"6898","citation":{"mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>, vol. 20, no. 1, 710, BioMed Central, 2019, doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>. BioMed Central, 2019. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","ieee":"O. M. Sigalova <i>et al.</i>, “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” <i>BMC Genomics</i>, vol. 20, no. 1. BioMed Central, 2019.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. 2019;20(1). doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>"},"article_number":"710","year":"2019","abstract":[{"text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.","lang":"eng"}],"type":"journal_article","external_id":{"isi":["000485256100001"]},"date_published":"2019-09-12T00:00:00Z","publisher":"BioMed Central","isi":1,"month":"09","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"12","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1"},{"page":"4113","day":"11","quality_controlled":"1","issue":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"Nature Publishing Group","pmid":1,"date_published":"2019-09-11T00:00:00Z","external_id":{"isi":["000485216800009"],"pmid":["31511517"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["570"],"month":"09","isi":1,"status":"public","doi":"10.1038/s41467-019-12068-x","scopus_import":"1","publication_identifier":{"eissn":["20411723"]},"title":"Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions","publication_status":"published","file_date_updated":"2020-07-14T12:47:44Z","oa_version":"Published Version","article_processing_charge":"No","year":"2019","citation":{"ista":"Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature communications. 10(1), 4113.","ieee":"D. Bornhorst <i>et al.</i>, “Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions,” <i>Nature communications</i>, vol. 10, no. 1. Nature Publishing Group, p. 4113, 2019.","ama":"Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. <i>Nature communications</i>. 2019;10(1):4113. doi:<a href=\"https://doi.org/10.1038/s41467-019-12068-x\">10.1038/s41467-019-12068-x</a>","mla":"Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” <i>Nature Communications</i>, vol. 10, no. 1, Nature Publishing Group, 2019, p. 4113, doi:<a href=\"https://doi.org/10.1038/s41467-019-12068-x\">10.1038/s41467-019-12068-x</a>.","short":"D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N. Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications 10 (2019) 4113.","apa":"Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V., … Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-019-12068-x\">https://doi.org/10.1038/s41467-019-12068-x</a>","chicago":"Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.” <i>Nature Communications</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41467-019-12068-x\">https://doi.org/10.1038/s41467-019-12068-x</a>."},"abstract":[{"text":"Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed.","lang":"eng"}],"_id":"6899","file":[{"file_size":3905793,"date_created":"2019-10-01T11:18:50Z","date_updated":"2020-07-14T12:47:44Z","relation":"main_file","access_level":"open_access","file_name":"2019_Nature_Bornhorst.pdf","checksum":"62c2512712e16d27c1797d318d14ba9f","file_id":"6926","creator":"kschuh","content_type":"application/pdf"}],"date_created":"2019-09-22T22:00:37Z","author":[{"full_name":"Bornhorst, Dorothee","first_name":"Dorothee","last_name":"Bornhorst"},{"last_name":"Xia","first_name":"Peng","full_name":"Xia, Peng","orcid":"0000-0002-5419-7756","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nakajima","first_name":"Hiroyuki","full_name":"Nakajima, Hiroyuki"},{"first_name":"Chaitanya","last_name":"Dingare","full_name":"Dingare, Chaitanya"},{"first_name":"Wiebke","last_name":"Herzog","full_name":"Herzog, Wiebke"},{"first_name":"Virginie","last_name":"Lecaudey","full_name":"Lecaudey, Virginie"},{"last_name":"Mochizuki","first_name":"Naoki","full_name":"Mochizuki, Naoki"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Deborah","last_name":"Yelon","full_name":"Yelon, Deborah"},{"full_name":"Abdelilah-Seyfried, Salim","last_name":"Abdelilah-Seyfried","first_name":"Salim"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"volume":10,"intvolume":"        10","department":[{"_id":"CaHe"}],"publication":"Nature communications","date_updated":"2023-08-30T06:21:23Z"},{"type":"journal_article","external_id":{"pmid":["31479447"],"isi":["000489741800021"]},"date_published":"2019-09-03T00:00:00Z","pmid":1,"publisher":"Public Library of Science","status":"public","isi":1,"month":"09","ddc":["570"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"03","page":"e1007290","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","issue":"9","volume":15,"related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Cepeda Humerez","first_name":"Sarah A","full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:55:21Z","publication":"PLoS computational biology","department":[{"_id":"GaTk"}],"intvolume":"        15","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:44Z","title":"Estimating information in time-varying signals","publication_status":"published","publication_identifier":{"eissn":["15537358"]},"scopus_import":"1","doi":"10.1371/journal.pcbi.1007290","date_created":"2019-09-22T22:00:37Z","file":[{"access_level":"open_access","file_name":"2019_PLoS_Cepeda-Humerez.pdf","file_size":3081855,"date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T10:53:45Z","relation":"main_file","file_id":"6925","creator":"kschuh","content_type":"application/pdf","checksum":"81bdce1361c9aa8395d6fa635fb6ab47"}],"_id":"6900","abstract":[{"lang":"eng","text":"Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks."}],"citation":{"mla":"Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>.","apa":"Cepeda Humerez, S. A., Ruess, J., &#38; Tkačik, G. (2019). Estimating information in time-varying signals. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>","chicago":"Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>.","short":"S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.","ama":"Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. <i>PLoS computational biology</i>. 2019;15(9):e1007290. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>","ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.","ieee":"S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” <i>PLoS computational biology</i>, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019."},"year":"2019"},{"ec_funded":1,"date_updated":"2024-03-25T23:30:14Z","publication":"arXiv","department":[{"_id":"GeKa"}],"arxiv":1,"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10058"}]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hofmann","first_name":"Andrea C","full_name":"Hofmann, Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"full_name":"Borovkov, Maxim","first_name":"Maxim","last_name":"Borovkov"},{"first_name":"Ivan","last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"full_name":"Frigerio, Jacopo","last_name":"Frigerio","first_name":"Jacopo"},{"last_name":"Chrastina","first_name":"Daniel","full_name":"Chrastina, Daniel"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"date_created":"2021-10-01T12:14:51Z","_id":"10065","abstract":[{"lang":"eng","text":"We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit."}],"citation":{"ama":"Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>","ieee":"A. C. Hofmann <i>et al.</i>, “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” <i>arXiv</i>. .","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.","apa":"Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>","short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>.","mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, 1910.05841, doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>."},"article_number":"1910.05841","year":"2019","article_processing_charge":"No","oa_version":"Preprint","publication_status":"submitted","title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","doi":"10.48550/arXiv.1910.05841","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.05841"}],"status":"public","month":"10","language":[{"iso":"eng"}],"type":"preprint","external_id":{"arxiv":["1910.05841"]},"date_published":"2019-10-13T00:00:00Z","project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells"}],"day":"13"},{"publication_identifier":{"eissn":["2475-1421"]},"acknowledgement":"The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3360550"}],"doi":"10.1145/3360550","file_date_updated":"2021-11-12T11:41:56Z","oa_version":"Published Version","article_processing_charge":"No","title":"Value-centric dynamic partial order reduction","publication_status":"published","abstract":[{"lang":"eng","text":"The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning."}],"article_number":"124","year":"2019","citation":{"ama":"Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>","ista":"Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.","ieee":"K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Athens, Greece, 2019, vol. 3.","mla":"Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, vol. 3, 124, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360550\">10.1145/3360550</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Toman, V. (2019). Value-centric dynamic partial order reduction. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>","short":"K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications</i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360550\">https://doi.org/10.1145/3360550</a>."},"_id":"10190","file":[{"checksum":"2149979c46964c4d117af06ccb6c0834","content_type":"application/pdf","file_id":"10278","creator":"cchlebak","date_created":"2021-11-12T11:41:56Z","file_size":570829,"date_updated":"2021-11-12T11:41:56Z","relation":"main_file","access_level":"open_access","success":1,"file_name":"2019_ACM_Chatterjee.pdf"}],"date_created":"2021-10-27T14:57:06Z","conference":{"start_date":"2019-10-23","location":"Athens, Greece","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","end_date":"2019-10-25"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas"},{"full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","last_name":"Toman","first_name":"Viktor"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10199"}]},"oa":1,"volume":3,"intvolume":"         3","arxiv":1,"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","date_updated":"2025-07-14T09:10:15Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"day":"10","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"}],"has_accepted_license":"1","publisher":"ACM","external_id":{"arxiv":["1909.00989"]},"date_published":"2019-10-10T00:00:00Z","type":"conference","keyword":["safety","risk","reliability and quality","software"],"language":[{"iso":"eng"}],"ddc":["000"],"status":"public","month":"10"},{"pmid":1,"publisher":"Springer Nature","type":"journal_article","date_published":"2019-10-22T00:00:00Z","external_id":{"pmid":["31640700"]},"extern":"1","keyword":["cell biology"],"ddc":["570"],"language":[{"iso":"eng"}],"status":"public","month":"10","day":"22","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"issue":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Harker-Kirschneck, Lena","first_name":"Lena","last_name":"Harker-Kirschneck"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela"}],"volume":17,"oa":1,"intvolume":"        17","date_updated":"2021-11-26T11:54:29Z","publication":"BMC Biology","publication_identifier":{"issn":["1741-7007"]},"acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","article_type":"original","scopus_import":"1","doi":"10.1186/s12915-019-0700-2","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/559898","open_access":"1"}],"article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2021-11-26T11:37:54Z","title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","publication_status":"published","abstract":[{"text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems.","lang":"eng"}],"citation":{"ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. 2019;17(1). doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>","ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82.","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” <i>BMC Biology</i>, vol. 17, no. 1. Springer Nature, 2019.","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>, vol. 17, no. 1, 82, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s12915-019-0700-2\">10.1186/s12915-019-0700-2</a>.","short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” <i>BMC Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>.","apa":"Harker-Kirschneck, L., Baum, B., &#38; Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0700-2\">https://doi.org/10.1186/s12915-019-0700-2</a>"},"article_number":"82","year":"2019","file":[{"checksum":"31d8bae55a376d30925f53f7e1a02396","creator":"cchlebak","file_id":"10356","content_type":"application/pdf","date_updated":"2021-11-26T11:37:54Z","relation":"main_file","file_size":1648926,"date_created":"2021-11-26T11:37:54Z","access_level":"open_access","success":1,"file_name":"2019_BMCBio_Harker_Kirschneck.pdf"}],"date_created":"2021-11-26T11:25:03Z","_id":"10354"},{"page":"43-52","day":"18","quality_controlled":"1","pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2019-06-18T00:00:00Z","external_id":{"pmid":["31226513"]},"language":[{"iso":"eng"}],"extern":"1","keyword":["molecular biology","structural biology"],"month":"06","status":"public","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.09349"}],"doi":"10.1016/j.sbi.2019.05.018","publication_identifier":{"issn":["0959-440X"]},"acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","article_type":"original","title":"Minimal coarse-grained models for molecular self-organisation in biology","publication_status":"published","oa_version":"Preprint","article_processing_charge":"No","citation":{"mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” <i>Current Opinion in Structural Biology</i>, vol. 58, Elsevier, 2019, pp. 43–52, doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">10.1016/j.sbi.2019.05.018</a>.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">https://doi.org/10.1016/j.sbi.2019.05.018</a>.","apa":"Hafner, A. E., Krausser, J., &#38; Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">https://doi.org/10.1016/j.sbi.2019.05.018</a>","ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” <i>Current Opinion in Structural Biology</i>, vol. 58. Elsevier, pp. 43–52, 2019.","ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. <i>Current Opinion in Structural Biology</i>. 2019;58:43-52. doi:<a href=\"https://doi.org/10.1016/j.sbi.2019.05.018\">10.1016/j.sbi.2019.05.018</a>"},"year":"2019","abstract":[{"lang":"eng","text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments."}],"date_created":"2021-11-26T11:33:21Z","_id":"10355","author":[{"last_name":"Hafner","first_name":"Anne E","full_name":"Hafner, Anne E"},{"first_name":"Johannes","last_name":"Krausser","full_name":"Krausser, Johannes"},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":58,"oa":1,"intvolume":"        58","date_updated":"2021-11-26T11:54:25Z","publication":"Current Opinion in Structural Biology"},{"quality_controlled":"1","page":"161-166","day":"01","isi":1,"month":"01","publist_id":"7949","status":"public","language":[{"iso":"eng"}],"type":"journal_article","external_id":{"isi":["000454111500019"],"pmid":["30089829"]},"date_published":"2019-01-01T00:00:00Z","pmid":1,"publisher":"Springer Nature","date_created":"2018-12-11T11:44:39Z","_id":"105","citation":{"mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>, vol. 27, Springer Nature, 2019, pp. 161–66, doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>.","chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” <i>European Journal of Human Genetics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","apa":"Marsh, A., Novarino, G., Lockhart, P., &#38; Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-018-0231-2\">https://doi.org/10.1038/s41431-018-0231-2</a>","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. <i>European Journal of Human Genetics</i>. 2019;27:161-166. doi:<a href=\"https://doi.org/10.1038/s41431-018-0231-2\">10.1038/s41431-018-0231-2</a>","ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166.","ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” <i>European Journal of Human Genetics</i>, vol. 27. Springer Nature, pp. 161–166, 2019."},"year":"2019","abstract":[{"lang":"eng","text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771."}],"title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","publication_status":"published","oa_version":"Published Version","article_processing_charge":"No","scopus_import":"1","doi":"10.1038/s41431-018-0231-2","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41431-018-0231-2"}],"acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","article_type":"original","department":[{"_id":"GaNo"}],"date_updated":"2023-08-24T14:28:24Z","publication":"European Journal of Human Genetics","intvolume":"        27","volume":27,"oa":1,"author":[{"full_name":"Marsh, Ashley","first_name":"Ashley","last_name":"Marsh"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"full_name":"Lockhart, Paul","first_name":"Paul","last_name":"Lockhart"},{"full_name":"Leventer, Richard","last_name":"Leventer","first_name":"Richard"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publication_status":"published","title":"Intrinsic quantized anomalous Hall effect in a moiré heterostructure","article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.00261"}],"doi":"10.1126/science.aay5533","acknowledgement":"The authors acknowledge discussions with A. Macdonald, Y. Saito, and M. Zaletel.","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_type":"original","date_created":"2022-01-13T14:21:32Z","_id":"10619","citation":{"ama":"Serlin M, Tschirhart CL, Polshyn H, et al. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. <i>Science</i>. 2019;367(6480):900-903. doi:<a href=\"https://doi.org/10.1126/science.aay5533\">10.1126/science.aay5533</a>","ieee":"M. Serlin <i>et al.</i>, “Intrinsic quantized anomalous Hall effect in a moiré heterostructure,” <i>Science</i>, vol. 367, no. 6480. American Association for the Advancement of Science, pp. 900–903, 2019.","ista":"Serlin M, Tschirhart CL, Polshyn H, Zhang Y, Zhu J, Watanabe K, Taniguchi T, Balents L, Young AF. 2019. Intrinsic quantized anomalous Hall effect in a moiré heterostructure. Science. 367(6480), 900–903.","short":"M. Serlin, C.L. Tschirhart, H. Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, A.F. Young, Science 367 (2019) 900–903.","apa":"Serlin, M., Tschirhart, C. L., Polshyn, H., Zhang, Y., Zhu, J., Watanabe, K., … Young, A. F. (2019). Intrinsic quantized anomalous Hall effect in a moiré heterostructure. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aay5533\">https://doi.org/10.1126/science.aay5533</a>","chicago":"Serlin, M., C. L. Tschirhart, Hryhoriy Polshyn, Y. Zhang, J. Zhu, K. Watanabe, T. Taniguchi, L. Balents, and A. F. Young. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” <i>Science</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/science.aay5533\">https://doi.org/10.1126/science.aay5533</a>.","mla":"Serlin, M., et al. “Intrinsic Quantized Anomalous Hall Effect in a Moiré Heterostructure.” <i>Science</i>, vol. 367, no. 6480, American Association for the Advancement of Science, 2019, pp. 900–03, doi:<a href=\"https://doi.org/10.1126/science.aay5533\">10.1126/science.aay5533</a>."},"year":"2019","abstract":[{"text":"The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize the electrons into a single spin- and valley-resolved moiré miniband with Chern number C = 1. In contrast to magnetically doped systems, the measured transport energy gap is larger than the Curie temperature for magnetic ordering, and quantization to within 0.1% of the von Klitzing constant persists to temperatures of several kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably switch the magnetic order between states of opposite polarization, forming an electrically rewritable magnetic memory.","lang":"eng"}],"volume":367,"related_material":{"record":[{"relation":"other","status":"public","id":"10697"},{"id":"10698","status":"public","relation":"other"},{"relation":"other","status":"public","id":"10699"}]},"oa":1,"author":[{"last_name":"Serlin","first_name":"M.","full_name":"Serlin, M."},{"full_name":"Tschirhart, C. L.","last_name":"Tschirhart","first_name":"C. L."},{"first_name":"Hryhoriy","last_name":"Polshyn","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhang, Y.","first_name":"Y.","last_name":"Zhang"},{"full_name":"Zhu, J.","first_name":"J.","last_name":"Zhu"},{"full_name":"Watanabe, K.","last_name":"Watanabe","first_name":"K."},{"last_name":"Taniguchi","first_name":"T.","full_name":"Taniguchi, T."},{"full_name":"Balents, L.","last_name":"Balents","first_name":"L."},{"first_name":"A. F.","last_name":"Young","full_name":"Young, A. F."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-02-21T16:00:09Z","publication":"Science","arxiv":1,"intvolume":"       367","quality_controlled":"1","page":"900-903","day":"19","issue":"6480","type":"journal_article","date_published":"2019-12-19T00:00:00Z","external_id":{"arxiv":["1907.00261"],"pmid":["31857492"]},"pmid":1,"publisher":"American Association for the Advancement of Science","month":"12","status":"public","language":[{"iso":"eng"}],"extern":"1","keyword":["multidisciplinary"]},{"title":"Solids of quantum Hall skyrmions in graphene","publication_status":"published","article_processing_charge":"No","oa_version":"None","scopus_import":"1","doi":"10.1038/s41567-019-0729-8","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"acknowledgement":"We acknowledge discussions with B. Halperin, C. Huang, A. Macdonald and M. Zalatel. Experimental work at UCSB was supported by the Army Research Office under awards nos. MURI W911NF-16-1-0361 and W911NF-16-1-0482. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by MEXT (Japan) and CREST (JPMJCR15F3), JST. A.F.Y. acknowledges the support of the David and Lucile Packard Foundation and and Alfred. P. Sloan Foundation.","article_type":"original","date_created":"2022-01-13T14:45:16Z","_id":"10620","citation":{"mla":"Zhou, H., et al. “Solids of Quantum Hall Skyrmions in Graphene.” <i>Nature Physics</i>, vol. 16, no. 2, Springer Nature, 2019, pp. 154–58, doi:<a href=\"https://doi.org/10.1038/s41567-019-0729-8\">10.1038/s41567-019-0729-8</a>.","chicago":"Zhou, H., Hryhoriy Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young. “Solids of Quantum Hall Skyrmions in Graphene.” <i>Nature Physics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41567-019-0729-8\">https://doi.org/10.1038/s41567-019-0729-8</a>.","apa":"Zhou, H., Polshyn, H., Taniguchi, T., Watanabe, K., &#38; Young, A. F. (2019). Solids of quantum Hall skyrmions in graphene. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-019-0729-8\">https://doi.org/10.1038/s41567-019-0729-8</a>","short":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, A.F. Young, Nature Physics 16 (2019) 154–158.","ama":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. Solids of quantum Hall skyrmions in graphene. <i>Nature Physics</i>. 2019;16(2):154-158. doi:<a href=\"https://doi.org/10.1038/s41567-019-0729-8\">10.1038/s41567-019-0729-8</a>","ieee":"H. Zhou, H. Polshyn, T. Taniguchi, K. Watanabe, and A. F. Young, “Solids of quantum Hall skyrmions in graphene,” <i>Nature Physics</i>, vol. 16, no. 2. Springer Nature, pp. 154–158, 2019.","ista":"Zhou H, Polshyn H, Taniguchi T, Watanabe K, Young AF. 2019. Solids of quantum Hall skyrmions in graphene. Nature Physics. 16(2), 154–158."},"year":"2019","abstract":[{"text":"Partially filled Landau levels host competing electronic orders. For example, electron solids may prevail close to integer filling of the Landau levels before giving way to fractional quantum Hall liquids at higher carrier density1,2. Here, we report the observation of an electron solid with non-collinear spin texture in monolayer graphene, consistent with solidification of skyrmions3—topological spin textures characterized by quantized electrical charge4,5. We probe the spin texture of the solids using a modified Corbino geometry that allows ferromagnetic magnons to be launched and detected6,7. We find that magnon transport is highly efficient when one Landau level is filled (ν=1), consistent with quantum Hall ferromagnetic spin polarization. However, even minimal doping immediately quenches the magnon signal while leaving the vanishing low-temperature charge conductivity unchanged. Our results can be understood by the formation of a solid of charged skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay. Data near fractional fillings show evidence of several fractional skyrmion solids, suggesting that graphene hosts a highly tunable landscape of coupled spin and charge orders.","lang":"eng"}],"volume":16,"author":[{"first_name":"H.","last_name":"Zhou","full_name":"Zhou, H."},{"last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","date_updated":"2022-01-13T15:34:44Z","publication":"Nature Physics","intvolume":"        16","quality_controlled":"1","page":"154-158","day":"16","issue":"2","type":"journal_article","date_published":"2019-12-16T00:00:00Z","publisher":"Springer Nature","month":"12","status":"public","language":[{"iso":"eng"}],"extern":"1","keyword":["General Physics and Astronomy"]},{"external_id":{"arxiv":["1902.00763"]},"date_published":"2019-08-05T00:00:00Z","type":"journal_article","publisher":"Springer Nature","month":"08","status":"public","language":[{"iso":"eng"}],"keyword":["general physics and astronomy"],"extern":"1","quality_controlled":"1","page":"1011-1016","day":"05","issue":"10","oa":1,"volume":15,"author":[{"orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","last_name":"Polshyn"},{"full_name":"Yankowitz, Matthew","first_name":"Matthew","last_name":"Yankowitz"},{"full_name":"Chen, Shaowen","first_name":"Shaowen","last_name":"Chen"},{"first_name":"Yuxuan","last_name":"Zhang","full_name":"Zhang, Yuxuan"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"},{"first_name":"Andrea F.","last_name":"Young","full_name":"Young, Andrea F."}],"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication":"Nature Physics","date_updated":"2022-01-20T09:33:38Z","arxiv":1,"intvolume":"        15","title":"Large linear-in-temperature resistivity in twisted bilayer graphene","publication_status":"published","oa_version":"Preprint","article_processing_charge":"No","doi":"10.1038/s41567-019-0596-3","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.00763"}],"scopus_import":"1","article_type":"original","acknowledgement":"The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958.","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"_id":"10621","date_created":"2022-01-13T15:00:58Z","year":"2019","citation":{"ista":"Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016.","ieee":"H. Polshyn <i>et al.</i>, “Large linear-in-temperature resistivity in twisted bilayer graphene,” <i>Nature Physics</i>, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019.","ama":"Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. <i>Nature Physics</i>. 2019;15(10):1011-1016. doi:<a href=\"https://doi.org/10.1038/s41567-019-0596-3\">10.1038/s41567-019-0596-3</a>","short":"H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016.","chicago":"Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” <i>Nature Physics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41567-019-0596-3\">https://doi.org/10.1038/s41567-019-0596-3</a>.","apa":"Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-019-0596-3\">https://doi.org/10.1038/s41567-019-0596-3</a>","mla":"Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” <i>Nature Physics</i>, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:<a href=\"https://doi.org/10.1038/s41567-019-0596-3\">10.1038/s41567-019-0596-3</a>."},"abstract":[{"text":"Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity.","lang":"eng"}]},{"date_updated":"2022-01-13T15:41:24Z","publication":"Nano Letters","intvolume":"        19","arxiv":1,"volume":19,"oa":1,"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","author":[{"first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy"},{"last_name":"Naibert","first_name":"Tyler","full_name":"Naibert, Tyler"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"date_created":"2022-01-13T15:11:14Z","_id":"10622","abstract":[{"text":"We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing.","lang":"eng"}],"citation":{"mla":"Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” <i>Nano Letters</i>, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">10.1021/acs.nanolett.9b01983</a>.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” <i>Nano Letters</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">https://doi.org/10.1021/acs.nanolett.9b01983</a>.","short":"H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482.","apa":"Polshyn, H., Naibert, T., &#38; Budakian, R. (2019). Manipulating multivortex states in superconducting structures. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">https://doi.org/10.1021/acs.nanolett.9b01983</a>","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” <i>Nano Letters</i>, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019.","ista":"Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482.","ama":"Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. <i>Nano Letters</i>. 2019;19(8):5476-5482. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b01983\">10.1021/acs.nanolett.9b01983</a>"},"year":"2019","article_processing_charge":"No","oa_version":"Preprint","title":"Manipulating multivortex states in superconducting structures","publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"acknowledgement":"We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.","article_type":"original","scopus_import":"1","doi":"10.1021/acs.nanolett.9b01983","main_file_link":[{"url":"https://arxiv.org/abs/1905.06303","open_access":"1"}],"status":"public","month":"06","extern":"1","keyword":["mechanical engineering","condensed matter physics","general materials science","general chemistry","bioengineering"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2019-06-27T00:00:00Z","external_id":{"arxiv":["1905.06303"],"pmid":["31246034"]},"pmid":1,"publisher":"American Chemical Society","issue":"8","quality_controlled":"1","day":"27","page":"5476-5482"},{"arxiv":1,"intvolume":"       363","date_updated":"2022-01-14T13:48:32Z","publication":"Science","author":[{"last_name":"Yankowitz","first_name":"Matthew","full_name":"Yankowitz, Matthew"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"first_name":"Hryhoriy","last_name":"Polshyn","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhang, Yuxuan","first_name":"Yuxuan","last_name":"Zhang"},{"full_name":"Watanabe, K.","first_name":"K.","last_name":"Watanabe"},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"full_name":"Graf, David","last_name":"Graf","first_name":"David"},{"full_name":"Young, Andrea F.","first_name":"Andrea F.","last_name":"Young"},{"full_name":"Dean, Cory R.","first_name":"Cory R.","last_name":"Dean"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":363,"oa":1,"citation":{"chicago":"Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity in Twisted Bilayer Graphene.” <i>Science</i>. American Association for the Advancement of Science (AAAS), 2019. <a href=\"https://doi.org/10.1126/science.aav1910\">https://doi.org/10.1126/science.aav1910</a>.","short":"M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T., … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. <i>Science</i>. American Association for the Advancement of Science (AAAS). <a href=\"https://doi.org/10.1126/science.aav1910\">https://doi.org/10.1126/science.aav1910</a>","mla":"Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.” <i>Science</i>, vol. 363, no. 6431, American Association for the Advancement of Science (AAAS), 2019, pp. 1059–64, doi:<a href=\"https://doi.org/10.1126/science.aav1910\">10.1126/science.aav1910</a>.","ieee":"M. Yankowitz <i>et al.</i>, “Tuning superconductivity in twisted bilayer graphene,” <i>Science</i>, vol. 363, no. 6431. American Association for the Advancement of Science (AAAS), pp. 1059–1064, 2019.","ista":"Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene. Science. 363(6431), 1059–1064.","ama":"Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted bilayer graphene. <i>Science</i>. 2019;363(6431):1059-1064. doi:<a href=\"https://doi.org/10.1126/science.aav1910\">10.1126/science.aav1910</a>"},"year":"2019","abstract":[{"text":"The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures.","lang":"eng"}],"date_created":"2022-01-14T12:14:58Z","_id":"10625","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07865"}],"doi":"10.1126/science.aav1910","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"acknowledgement":"We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar, A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino, and P. Moon for helpful discussions.","article_type":"original","title":"Tuning superconductivity in twisted bilayer graphene","publication_status":"published","article_processing_charge":"No","oa_version":"Preprint","language":[{"iso":"eng"}],"extern":"1","keyword":["multidisciplinary"],"month":"01","status":"public","pmid":1,"publisher":"American Association for the Advancement of Science (AAAS)","type":"journal_article","date_published":"2019-01-24T00:00:00Z","external_id":{"pmid":["30679385 "],"arxiv":["1808.07865"]},"issue":"6431","page":"1059-1064","day":"24","quality_controlled":"1"}]