[{"date_created":"2021-09-12T22:01:25Z","abstract":[{"lang":"eng","text":"We study systems of nonlinear partial differential equations of parabolic type, in which the elliptic operator is replaced by the first-order divergence operator acting on a flux function, which is related to the spatial gradient of the unknown through an additional implicit equation. This setting, broad enough in terms of applications, significantly expands the paradigm of nonlinear parabolic problems. Formulating four conditions concerning the form of the implicit equation, we first show that these conditions describe a maximal monotone p-coercive graph. We then establish the global-in-time and large-data existence of a (weak) solution and its uniqueness. To this end, we adopt and significantly generalize Minty’s method of monotone mappings. A unified theory, containing several novel tools, is developed in a way to be tractable from the point of view of numerical approximations."}],"publisher":"World Scientific Publishing","language":[{"iso":"eng"}],"intvolume":"        31","issue":"09","publication":"Mathematical Models and Methods in Applied Sciences","month":"08","status":"public","type":"journal_article","isi":1,"oa":1,"article_processing_charge":"No","year":"2021","keyword":["Nonlinear parabolic systems","implicit constitutive theory","weak solutions","existence","uniqueness"],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-25T00:00:00Z","department":[{"_id":"JuFi"}],"scopus_import":"1","volume":31,"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"doi":"10.1142/S0218202521500457","citation":{"short":"M. Bulíček, E. Maringová, J. Málek, Mathematical Models and Methods in Applied Sciences 31 (2021).","chicago":"Bulíček, Miroslav, Erika Maringová, and Josef Málek. “On Nonlinear Problems of Parabolic Type with Implicit Constitutive Equations Involving Flux.” <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing, 2021. <a href=\"https://doi.org/10.1142/S0218202521500457\">https://doi.org/10.1142/S0218202521500457</a>.","apa":"Bulíček, M., Maringová, E., &#38; Málek, J. (2021). On nonlinear problems of parabolic type with implicit constitutive equations involving flux. <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0218202521500457\">https://doi.org/10.1142/S0218202521500457</a>","ista":"Bulíček M, Maringová E, Málek J. 2021. On nonlinear problems of parabolic type with implicit constitutive equations involving flux. Mathematical Models and Methods in Applied Sciences. 31(09).","ama":"Bulíček M, Maringová E, Málek J. On nonlinear problems of parabolic type with implicit constitutive equations involving flux. <i>Mathematical Models and Methods in Applied Sciences</i>. 2021;31(09). doi:<a href=\"https://doi.org/10.1142/S0218202521500457\">10.1142/S0218202521500457</a>","ieee":"M. Bulíček, E. Maringová, and J. Málek, “On nonlinear problems of parabolic type with implicit constitutive equations involving flux,” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 31, no. 09. World Scientific Publishing, 2021.","mla":"Bulíček, Miroslav, et al. “On Nonlinear Problems of Parabolic Type with Implicit Constitutive Equations Involving Flux.” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 31, no. 09, World Scientific Publishing, 2021, doi:<a href=\"https://doi.org/10.1142/S0218202521500457\">10.1142/S0218202521500457</a>."},"_id":"10005","main_file_link":[{"url":"https://arxiv.org/abs/2009.06917","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","publication_identifier":{"issn":["0218-2025"],"eissn":["1793-6314"]},"acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 18-12719S financed by the Czech\r\nScience foundation (GAČR). E. Maringová acknowledges support from Charles University Research program \r\nUNCE/SCI/023, the grant SVV-2020-260583 by the Ministry of Education, Youth and Sports, Czech Republic\r\nand from the Austrian Science Fund (FWF), grants P30000, W1245, and F65. M. Bulíček and J. Málek are\r\nmembers of the Nečas Center for Mathematical Modelling.\r\n","article_type":"original","day":"25","arxiv":1,"external_id":{"arxiv":["2009.06917"],"isi":["000722222900004"]},"author":[{"full_name":"Bulíček, Miroslav","last_name":"Bulíček","first_name":"Miroslav"},{"id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","full_name":"Maringová, Erika","last_name":"Maringová","first_name":"Erika"},{"first_name":"Josef","last_name":"Málek","full_name":"Málek, Josef"}],"date_updated":"2026-08-18T07:47:39Z","title":"On nonlinear problems of parabolic type with implicit constitutive equations involving flux"},{"main_file_link":[{"url":"https://ojs.aaai.org/index.php/AAAI/article/view/16496","open_access":"1"}],"oa_version":"Published Version","quality_controlled":"1","_id":"10665","volume":35,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"citation":{"short":"T.A. Henzinger, M. Lechner, D. Zikelic, in:, Proceedings of the AAAI Conference on Artificial Intelligence, AAAI Press, 2021, pp. 3787–3795.","chicago":"Henzinger, Thomas A, Mathias Lechner, and Dorde Zikelic. “Scalable Verification of Quantized Neural Networks.” In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 35:3787–95. AAAI Press, 2021. <a href=\"https://doi.org/10.1609/aaai.v35i5.16496\">https://doi.org/10.1609/aaai.v35i5.16496</a>.","apa":"Henzinger, T. A., Lechner, M., &#38; Zikelic, D. (2021). Scalable verification of quantized neural networks. In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i> (Vol. 35, pp. 3787–3795). Virtual: AAAI Press. <a href=\"https://doi.org/10.1609/aaai.v35i5.16496\">https://doi.org/10.1609/aaai.v35i5.16496</a>","ama":"Henzinger TA, Lechner M, Zikelic D. Scalable verification of quantized neural networks. In: <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>. Vol 35. AAAI Press; 2021:3787-3795. doi:<a href=\"https://doi.org/10.1609/aaai.v35i5.16496\">10.1609/aaai.v35i5.16496</a>","ista":"Henzinger TA, Lechner M, Zikelic D. 2021. Scalable verification of quantized neural networks. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence, Technical Tracks, vol. 35, 3787–3795.","mla":"Henzinger, Thomas A., et al. “Scalable Verification of Quantized Neural Networks.” <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, vol. 35, no. 5A, AAAI Press, 2021, pp. 3787–95, doi:<a href=\"https://doi.org/10.1609/aaai.v35i5.16496\">10.1609/aaai.v35i5.16496</a>.","ieee":"T. A. Henzinger, M. Lechner, and D. Zikelic, “Scalable verification of quantized neural networks,” in <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, Virtual, 2021, vol. 35, no. 5A, pp. 3787–3795."},"doi":"10.1609/aaai.v35i5.16496","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"author":[{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias"},{"first_name":"Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"date_updated":"2026-08-19T09:28:05Z","title":"Scalable verification of quantized neural networks","arxiv":1,"file_date_updated":"2022-01-26T07:41:16Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein\r\nAward), ERC CoG 863818 (FoRM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.\r\n","related_material":{"record":[{"relation":"dissertation_contains","id":"11362","status":"public"}]},"publication_identifier":{"eissn":["2374-3468"],"isbn":["978-1-57735-866-4"],"issn":["2159-5399"]},"day":"28","external_id":{"arxiv":["2012.08185"]},"conference":{"start_date":"2021-02-02","location":"Virtual","name":"AAAI: Association for the Advancement of Artificial Intelligence","end_date":"2021-02-09"},"issue":"5A","ddc":["000"],"corr_author":"1","publication":"Proceedings of the AAAI Conference on Artificial Intelligence","month":"05","status":"public","publisher":"AAAI Press","alternative_title":["Technical Tracks"],"has_accepted_license":"1","abstract":[{"text":"Formal verification of neural networks is an active topic of research, and recent advances have significantly increased the size of the networks that verification tools can handle. However, most methods are designed for verification of an idealized model of the actual network which works over real arithmetic and ignores rounding imprecisions. This idealization is in stark contrast to network quantization, which is a technique that trades numerical precision for computational efficiency and is, therefore, often applied in practice. Neglecting rounding errors of such low-bit quantized neural networks has been shown to lead to wrong conclusions about the network’s correctness. Thus, the desired approach for verifying quantized neural networks would be one that takes these rounding errors\r\ninto account. In this paper, we show that verifying the bitexact implementation of quantized neural networks with bitvector specifications is PSPACE-hard, even though verifying idealized real-valued networks and satisfiability of bit-vector specifications alone are each in NP. Furthermore, we explore several practical heuristics toward closing the complexity gap between idealized and bit-exact verification. In particular, we propose three techniques for making SMT-based verification of quantized neural networks more scalable. Our experiments demonstrate that our proposed methods allow a speedup of up to three orders of magnitude over existing approaches.","lang":"eng"}],"date_created":"2022-01-25T15:15:02Z","intvolume":"        35","language":[{"iso":"eng"}],"file":[{"date_created":"2022-01-26T07:41:16Z","relation":"main_file","file_name":"16496-Article Text-19990-1-2-20210518 (1).pdf","creator":"mlechner","checksum":"2bc8155b2526a70fba5b7301bc89dbd1","file_size":137235,"access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"10684","date_updated":"2022-01-26T07:41:16Z"}],"article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-05-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3787-3795","oa":1,"ec_funded":1,"type":"conference"},{"publication_status":"published","article_processing_charge":"No","year":"2021","file":[{"file_id":"10678","success":1,"date_updated":"2022-01-26T07:36:03Z","relation":"main_file","date_created":"2022-01-26T07:36:03Z","file_name":"16936-Article Text-20430-1-2-20210518 (1).pdf","creator":"mlechner","checksum":"0f06995fba06dbcfa7ed965fc66027ff","file_size":4302669,"content_type":"application/pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-05-28T00:00:00Z","page":"7657-7666","type":"conference","oa":1,"issue":"9","ddc":["000"],"publication":"Proceedings of the AAAI Conference on Artificial Intelligence","corr_author":"1","status":"public","month":"05","date_created":"2022-01-25T15:48:36Z","has_accepted_license":"1","abstract":[{"text":"We introduce a new class of time-continuous recurrent neural network models. Instead of declaring a learning system’s dynamics by implicit nonlinearities, we construct networks of linear first-order dynamical systems modulated via nonlinear interlinked gates. The resulting models represent dynamical systems with varying (i.e., liquid) time-constants coupled to their hidden state, with outputs being computed by numerical differential equation solvers. These neural networks exhibit stable and bounded behavior, yield superior expressivity within the family of neural ordinary differential equations, and give rise to improved performance on time-series prediction tasks. To demonstrate these properties, we first take a theoretical approach to find bounds over their dynamics, and compute their expressive power by the trajectory length measure in a latent trajectory space. We then conduct a series of time-series prediction experiments to manifest the approximation capability of Liquid Time-Constant Networks (LTCs) compared to classical and modern RNNs.","lang":"eng"}],"alternative_title":["Technical Tracks"],"publisher":"AAAI Press","language":[{"iso":"eng"}],"intvolume":"        35","author":[{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Amini","full_name":"Amini, Alexander"},{"first_name":"Daniela","last_name":"Rus","full_name":"Rus, Daniela"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"title":"Liquid time-constant networks","date_updated":"2026-08-19T09:24:30Z","day":"28","file_date_updated":"2022-01-26T07:36:03Z","publication_identifier":{"isbn":["978-1-57735-866-4"],"issn":["2159-5399"],"eissn":["2374-3468"]},"acknowledgement":"R.H. and D.R. are partially supported by Boeing. R.H. and R.G. were partially supported by the Horizon-2020 ECSEL\r\nProject grant No. 783163 (iDev40). M.L. was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). A.A. is supported by the National Science Foundation (NSF) Graduate Research Fellowship Program. This research work is partially drawn from the PhD dissertation of R.H.","arxiv":1,"conference":{"start_date":"2021-02-02","location":"Virtual","name":"AAAI: Association for the Advancement of Artificial Intelligence","end_date":"2021-02-09"},"external_id":{"arxiv":["2006.04439"]},"_id":"10671","quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"url":"https://ojs.aaai.org/index.php/AAAI/article/view/16936","open_access":"1"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"volume":35,"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"}],"doi":"10.1609/aaai.v35i9.16936","citation":{"short":"R. Hasani, M. Lechner, A. Amini, D. Rus, R. Grosu, in:, Proceedings of the AAAI Conference on Artificial Intelligence, AAAI Press, 2021, pp. 7657–7666.","chicago":"Hasani, Ramin, Mathias Lechner, Alexander Amini, Daniela Rus, and Radu Grosu. “Liquid Time-Constant Networks.” In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 35:7657–66. AAAI Press, 2021. <a href=\"https://doi.org/10.1609/aaai.v35i9.16936\">https://doi.org/10.1609/aaai.v35i9.16936</a>.","apa":"Hasani, R., Lechner, M., Amini, A., Rus, D., &#38; Grosu, R. (2021). Liquid time-constant networks. In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i> (Vol. 35, pp. 7657–7666). Virtual: AAAI Press. <a href=\"https://doi.org/10.1609/aaai.v35i9.16936\">https://doi.org/10.1609/aaai.v35i9.16936</a>","ista":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. 2021. Liquid time-constant networks. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence, Technical Tracks, vol. 35, 7657–7666.","ama":"Hasani R, Lechner M, Amini A, Rus D, Grosu R. Liquid time-constant networks. In: <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>. Vol 35. AAAI Press; 2021:7657-7666. doi:<a href=\"https://doi.org/10.1609/aaai.v35i9.16936\">10.1609/aaai.v35i9.16936</a>","mla":"Hasani, Ramin, et al. “Liquid Time-Constant Networks.” <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, vol. 35, no. 9, AAAI Press, 2021, pp. 7657–66, doi:<a href=\"https://doi.org/10.1609/aaai.v35i9.16936\">10.1609/aaai.v35i9.16936</a>.","ieee":"R. Hasani, M. Lechner, A. Amini, D. Rus, and R. Grosu, “Liquid time-constant networks,” in <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, Virtual, 2021, vol. 35, no. 9, pp. 7657–7666."}},{"arxiv":1,"acknowledgement":"Vyacheslav Kungurtsev was supported by the OP VVV project CZ.02.1.01/0.0/0.0/16 019/0000765 “Research Center for Informatics. Bapi Chatterjee was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754411 (ISTPlus). Dan Alistarh has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML).","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"],"isbn":["9781713835974"]},"day":"18","external_id":{"arxiv":["1905.11845"]},"conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"Virtual, Online","start_date":"2021-02-02","end_date":"2021-02-09"},"author":[{"first_name":"Vyacheslav","last_name":"Kungurtsev","full_name":"Kungurtsev, Vyacheslav"},{"last_name":"Egan","first_name":"Malcolm","full_name":"Egan, Malcolm"},{"full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi","last_name":"Chatterjee","orcid":"0000-0002-2742-4028"},{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"date_updated":"2026-08-19T09:25:06Z","title":"Asynchronous optimization methods for efficient training of deep neural networks with guarantees","volume":35,"department":[{"_id":"DaAl"}],"scopus_import":"1","doi":"10.1609/aaai.v35i9.16999","citation":{"ieee":"V. Kungurtsev, M. Egan, B. Chatterjee, and D.-A. Alistarh, “Asynchronous optimization methods for efficient training of deep neural networks with guarantees,” in <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>, Virtual, Online, 2021, vol. 35, no. 9B, pp. 8209–8216.","mla":"Kungurtsev, Vyacheslav, et al. “Asynchronous Optimization Methods for Efficient Training of Deep Neural Networks with Guarantees.” <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>, vol. 35, no. 9B, AAAI Press, 2021, pp. 8209–16, doi:<a href=\"https://doi.org/10.1609/aaai.v35i9.16999\">10.1609/aaai.v35i9.16999</a>.","ista":"Kungurtsev V, Egan M, Chatterjee B, Alistarh D-A. 2021. Asynchronous optimization methods for efficient training of deep neural networks with guarantees. 35th AAAI Conference on Artificial Intelligence, AAAI 2021. AAAI: Conference on Artificial Intelligence vol. 35, 8209–8216.","ama":"Kungurtsev V, Egan M, Chatterjee B, Alistarh D-A. Asynchronous optimization methods for efficient training of deep neural networks with guarantees. In: <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>. Vol 35. AAAI Press; 2021:8209-8216. doi:<a href=\"https://doi.org/10.1609/aaai.v35i9.16999\">10.1609/aaai.v35i9.16999</a>","apa":"Kungurtsev, V., Egan, M., Chatterjee, B., &#38; Alistarh, D.-A. (2021). Asynchronous optimization methods for efficient training of deep neural networks with guarantees. In <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i> (Vol. 35, pp. 8209–8216). Virtual, Online: AAAI Press. <a href=\"https://doi.org/10.1609/aaai.v35i9.16999\">https://doi.org/10.1609/aaai.v35i9.16999</a>","chicago":"Kungurtsev, Vyacheslav, Malcolm Egan, Bapi Chatterjee, and Dan-Adrian Alistarh. “Asynchronous Optimization Methods for Efficient Training of Deep Neural Networks with Guarantees.” In <i>35th AAAI Conference on Artificial Intelligence, AAAI 2021</i>, 35:8209–16. AAAI Press, 2021. <a href=\"https://doi.org/10.1609/aaai.v35i9.16999\">https://doi.org/10.1609/aaai.v35i9.16999</a>.","short":"V. Kungurtsev, M. Egan, B. Chatterjee, D.-A. Alistarh, in:, 35th AAAI Conference on Artificial Intelligence, AAAI 2021, AAAI Press, 2021, pp. 8209–8216."},"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1905.11845"}],"quality_controlled":"1","oa_version":"Preprint","_id":"11436","page":"8209-8216","oa":1,"type":"conference","ec_funded":1,"year":"2021","article_processing_charge":"No","publication_status":"published","date_published":"2021-05-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"AAAI Press","date_created":"2022-06-05T22:01:52Z","abstract":[{"lang":"eng","text":"Asynchronous distributed algorithms are a popular way to reduce synchronization costs in large-scale optimization, and in particular for neural network training. However, for nonsmooth and nonconvex objectives, few convergence guarantees exist beyond cases where closed-form proximal operator solutions are available. As training most popular deep neural networks corresponds to optimizing nonsmooth and nonconvex objectives, there is a pressing need for such convergence guarantees. In this paper, we analyze for the first time the convergence of stochastic asynchronous optimization for this general class of objectives. In particular, we focus on stochastic subgradient methods allowing for block variable partitioning, where the shared model is asynchronously updated by concurrent processes. To this end, we use a probabilistic model which captures key features of real asynchronous scheduling between concurrent processes. Under this model, we establish convergence with probability one to an invariant set for stochastic subgradient methods with momentum. From a practical perspective, one issue with the family of algorithms that we consider is that they are not efficiently supported by machine learning frameworks, which mostly focus on distributed data-parallel strategies. To address this, we propose a new implementation strategy for shared-memory based training of deep neural networks for a partitioned but shared model in single- and multi-GPU settings. Based on this implementation, we achieve on average1.2x speed-up in comparison to state-of-the-art training methods for popular image classification tasks, without compromising accuracy."}],"intvolume":"        35","language":[{"iso":"eng"}],"issue":"9B","status":"public","month":"05","publication":"35th AAAI Conference on Artificial Intelligence, AAAI 2021"},{"external_id":{"arxiv":["2012.08863"]},"conference":{"end_date":"2021-02-09","name":"AAAI: Association for the Advancement of Artificial Intelligence","location":"Virtual","start_date":"2021-02-02"},"arxiv":1,"acknowledgement":"The authors would like to thank the reviewers for their insightful comments. RH and RG were partially supported by\r\nHorizon-2020 ECSEL Project grant No. 783163 (iDev40). RH was partially supported by Boeing. ML was supported\r\nin part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). SG was funded by FWF\r\nproject W1255-N23. JC was partially supported by NAWA Polish Returns grant PPN/PPO/2018/1/00029. SS was supported by NSF awards DCL-2040599, CCF-1918225, and CPS-1446832.\r\n","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"],"isbn":["978-1-57735-866-4"]},"file_date_updated":"2022-01-26T07:38:08Z","day":"28","date_updated":"2026-08-19T09:29:48Z","title":"On the verification of neural ODEs with stochastic guarantees","author":[{"full_name":"Grunbacher, Sophie","last_name":"Grunbacher","first_name":"Sophie"},{"full_name":"Hasani, Ramin","first_name":"Ramin","last_name":"Hasani"},{"last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"first_name":"Jacek","last_name":"Cyranka","full_name":"Cyranka, Jacek"},{"first_name":"Scott A","last_name":"Smolka","full_name":"Smolka, Scott A"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"}],"citation":{"ama":"Grunbacher S, Hasani R, Lechner M, Cyranka J, Smolka SA, Grosu R. On the verification of neural ODEs with stochastic guarantees. In: <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>. Vol 35. AAAI Press; 2021:11525-11535. doi:<a href=\"https://doi.org/10.1609/aaai.v35i13.17372\">10.1609/aaai.v35i13.17372</a>","apa":"Grunbacher, S., Hasani, R., Lechner, M., Cyranka, J., Smolka, S. A., &#38; Grosu, R. (2021). On the verification of neural ODEs with stochastic guarantees. In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i> (Vol. 35, pp. 11525–11535). Virtual: AAAI Press. <a href=\"https://doi.org/10.1609/aaai.v35i13.17372\">https://doi.org/10.1609/aaai.v35i13.17372</a>","ista":"Grunbacher S, Hasani R, Lechner M, Cyranka J, Smolka SA, Grosu R. 2021. On the verification of neural ODEs with stochastic guarantees. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence, Technical Tracks, vol. 35, 11525–11535.","ieee":"S. Grunbacher, R. Hasani, M. Lechner, J. Cyranka, S. A. Smolka, and R. Grosu, “On the verification of neural ODEs with stochastic guarantees,” in <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, Virtual, 2021, vol. 35, no. 13, pp. 11525–11535.","mla":"Grunbacher, Sophie, et al. “On the Verification of Neural ODEs with Stochastic Guarantees.” <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, vol. 35, no. 13, AAAI Press, 2021, pp. 11525–35, doi:<a href=\"https://doi.org/10.1609/aaai.v35i13.17372\">10.1609/aaai.v35i13.17372</a>.","short":"S. Grunbacher, R. Hasani, M. Lechner, J. Cyranka, S.A. Smolka, R. Grosu, in:, Proceedings of the AAAI Conference on Artificial Intelligence, AAAI Press, 2021, pp. 11525–11535.","chicago":"Grunbacher, Sophie, Ramin Hasani, Mathias Lechner, Jacek Cyranka, Scott A Smolka, and Radu Grosu. “On the Verification of Neural ODEs with Stochastic Guarantees.” In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 35:11525–35. AAAI Press, 2021. <a href=\"https://doi.org/10.1609/aaai.v35i13.17372\">https://doi.org/10.1609/aaai.v35i13.17372</a>."},"doi":"10.1609/aaai.v35i13.17372","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"volume":35,"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"main_file_link":[{"url":"https://ojs.aaai.org/index.php/AAAI/article/view/17372","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","_id":"10669","oa":1,"type":"conference","page":"11525-11535","date_published":"2021-05-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"mlechner","checksum":"468d07041e282a1d46ffdae92f709630","file_name":"17372-Article Text-20866-1-2-20210518.pdf","relation":"main_file","date_created":"2022-01-26T07:38:08Z","content_type":"application/pdf","access_level":"open_access","file_size":286906,"success":1,"file_id":"10680","date_updated":"2022-01-26T07:38:08Z"}],"year":"2021","article_processing_charge":"No","publication_status":"published","intvolume":"        35","language":[{"iso":"eng"}],"publisher":"AAAI Press","alternative_title":["Technical Tracks"],"date_created":"2022-01-25T15:47:20Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We show that Neural ODEs, an emerging class of timecontinuous neural networks, can be verified by solving a set of global-optimization problems. For this purpose, we introduce Stochastic Lagrangian Reachability (SLR), an\r\nabstraction-based technique for constructing a tight Reachtube (an over-approximation of the set of reachable states\r\nover a given time-horizon), and provide stochastic guarantees in the form of confidence intervals for the Reachtube bounds. SLR inherently avoids the infamous wrapping effect (accumulation of over-approximation errors) by performing local optimization steps to expand safe regions instead of repeatedly forward-propagating them as is done by deterministic reachability methods. To enable fast local optimizations, we introduce a novel forward-mode adjoint sensitivity method to compute gradients without the need for backpropagation. Finally, we establish asymptotic and non-asymptotic convergence rates for SLR."}],"ddc":["000"],"corr_author":"1","publication":"Proceedings of the AAAI Conference on Artificial Intelligence","status":"public","month":"05","issue":"13"},{"has_accepted_license":"1","date_created":"2021-12-08T21:52:28Z","abstract":[{"lang":"eng","text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently  creates a race condition. This bottleneck  can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the  stochastic gradient descent (SGD) algorithm, which distribute computation  among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be  relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same."}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","ddc":["000"],"corr_author":"1","status":"public","month":"12","page":"132","ec_funded":1,"type":"dissertation","oa":1,"publication_status":"published","article_processing_charge":"No","year":"2021","file":[{"date_created":"2021-12-09T17:47:49Z","relation":"main_file","creator":"gnadirad","file_name":"Thesis_Final_09_12_2021.pdf","checksum":"6bf14e9a523387328f016c0689f5e10e","file_size":2370859,"access_level":"open_access","content_type":"application/pdf","file_id":"10436","success":1,"date_updated":"2021-12-09T17:47:49Z"},{"file_id":"10437","date_updated":"2022-03-28T12:55:12Z","creator":"gnadirad","file_name":"Thesis_Final_09_12_2021.zip","checksum":"914d6c5ca86bd0add471971a8f4c4341","date_created":"2021-12-09T17:47:49Z","relation":"source_file","access_level":"closed","content_type":"application/zip","file_size":2596924}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-12-09T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.15479/at:ista:10429","citation":{"chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10429\">https://doi.org/10.15479/at:ista:10429</a>.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","mla":"Nadiradze, Giorgi. <i>On Achieving Scalability through Relaxation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10429\">10.15479/at:ista:10429</a>.","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021.","apa":"Nadiradze, G. (2021). <i>On achieving scalability through relaxation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10429\">https://doi.org/10.15479/at:ista:10429</a>","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10429\">10.15479/at:ista:10429</a>","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria."},"_id":"10429","oa_version":"Published Version","day":"09","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6673"},{"status":"public","relation":"part_of_dissertation","id":"5965"},{"status":"public","relation":"part_of_dissertation","id":"10435"},{"status":"public","id":"10432","relation":"part_of_dissertation"}]},"file_date_updated":"2022-03-28T12:55:12Z","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","author":[{"first_name":"Giorgi","last_name":"Nadiradze","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"}],"title":"On achieving scalability through relaxation","date_updated":"2026-08-19T09:30:23Z"},{"title":"Elastic consistency: A practical consistency model for distributed stochastic gradient descent","date_updated":"2026-08-19T09:30:23Z","author":[{"full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","orcid":"0000-0001-5634-0731","first_name":"Giorgi"},{"id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia","last_name":"Markov","first_name":"Ilia"},{"full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-2742-4028","first_name":"Bapi"},{"full_name":"Kungurtsev, Vyacheslav ","first_name":"Vyacheslav ","last_name":"Kungurtsev"},{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"conference":{"start_date":"2021-02-02","location":"Virtual","name":"AAAI: Association for the Advancement of Artificial Intelligence","end_date":"2021-02-09"},"external_id":{"arxiv":["2001.05918"]},"day":"18","related_material":{"record":[{"id":"10429","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"We would like to thank Christopher De Sa for his feedback on an earlier draft of this paper, as well as the anonymous AAAI reviewers for their useful comments. This project has received\r\nfunding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Bapi\r\nChatterjee was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754411 (ISTPlus).","arxiv":1,"_id":"10432","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://ojs.aaai.org/index.php/AAAI/article/view/17092","open_access":"1"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}],"citation":{"ista":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. 2021. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. Proceedings of the AAAI Conference on Artificial Intelligence. AAAI: Association for the Advancement of Artificial Intelligence vol. 35, 9037–9045.","apa":"Nadiradze, G., Markov, I., Chatterjee, B., Kungurtsev, V., &#38; Alistarh, D.-A. (2021). Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i> (Vol. 35, pp. 9037–9045). Virtual. <a href=\"https://doi.org/10.1609/aaai.v35i10.17092\">https://doi.org/10.1609/aaai.v35i10.17092</a>","ama":"Nadiradze G, Markov I, Chatterjee B, Kungurtsev V, Alistarh D-A. Elastic consistency: A practical consistency model for distributed stochastic gradient descent. In: <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>. Vol 35. ; 2021:9037-9045. doi:<a href=\"https://doi.org/10.1609/aaai.v35i10.17092\">10.1609/aaai.v35i10.17092</a>","ieee":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh, “Elastic consistency: A practical consistency model for distributed stochastic gradient descent,” in <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, Virtual, 2021, vol. 35, no. 10, pp. 9037–9045.","mla":"Nadiradze, Giorgi, et al. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, vol. 35, no. 10, 2021, pp. 9037–45, doi:<a href=\"https://doi.org/10.1609/aaai.v35i10.17092\">10.1609/aaai.v35i10.17092</a>.","short":"G. Nadiradze, I. Markov, B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:, Proceedings of the AAAI Conference on Artificial Intelligence, 2021, pp. 9037–9045.","chicago":"Nadiradze, Giorgi, Ilia Markov, Bapi Chatterjee, Vyacheslav  Kungurtsev, and Dan-Adrian Alistarh. “Elastic Consistency: A Practical Consistency Model for Distributed Stochastic Gradient Descent.” In <i>Proceedings of the AAAI Conference on Artificial Intelligence</i>, 35:9037–45, 2021. <a href=\"https://doi.org/10.1609/aaai.v35i10.17092\">https://doi.org/10.1609/aaai.v35i10.17092</a>."},"doi":"10.1609/aaai.v35i10.17092","department":[{"_id":"DaAl"}],"volume":35,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-05-18T00:00:00Z","publication_status":"published","year":"2021","article_processing_charge":"No","type":"conference","ec_funded":1,"oa":1,"page":"9037-9045","ddc":["000"],"publication":"Proceedings of the AAAI Conference on Artificial Intelligence","month":"05","status":"public","issue":"10","language":[{"iso":"eng"}],"intvolume":"        35","abstract":[{"text":"One key element behind the recent progress of machine learning has been the ability to train machine learning models in large-scale distributed shared-memory and message-passing environments. Most of these models are trained employing variants of stochastic gradient descent (SGD) based optimization, but most methods involve some type of consistency relaxation relative to sequential SGD, to mitigate its large communication or synchronization costs at scale. In this paper, we introduce a general consistency condition covering communication-reduced and asynchronous distributed SGD implementations. Our framework, called elastic consistency, decouples the system-specific aspects of the implementation from the SGD convergence requirements, giving a general way to obtain convergence bounds for a wide variety of distributed SGD methods used in practice. Elastic consistency can be used to re-derive or improve several previous convergence bounds in message-passing and shared-memory settings, but also to analyze new models and distribution schemes. As a direct application, we propose and analyze a new synchronization-avoiding scheduling scheme for distributed SGD, and show that it can be used to efficiently train deep convolutional models for image classification.","lang":"eng"}],"date_created":"2021-12-09T09:21:35Z"},{"author":[{"full_name":"Shute, Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","last_name":"Shute","orcid":"0000-0002-1812-2810","first_name":"Alec L"}],"title":"On the leading constant in the Manin-type conjecture for Campana points","researchdata_availability":"no","date_updated":"2026-08-19T12:54:58Z","day":"30","acknowledgement":"The author would like to thank Damaris Schindler and Florian Wilsch for their helpful comments on the heights and Tamagawa measures used in Section 3, together with Marta Pieropan, Sho Tanimoto and Sam Streeter for providing valuable feedback on an earlier version of this paper, and Tim Browning for many useful comments and discussions during the development of this work. The author is also grateful to the anonymous referee for providing many valuable comments and suggestions that improved the quality of the paper.","related_material":{"record":[{"status":"public","id":"12072","relation":"dissertation_contains"},{"id":"17058","relation":"later_version","status":"public"}]},"arxiv":1,"external_id":{"arxiv":["2104.14946"]},"_id":"12077","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2104.14946","open_access":"1"}],"department":[{"_id":"TiBr"}],"doi":"10.48550/arXiv.2104.14946","citation":{"ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>","ista":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. arXiv, 2104.14946.","apa":"Shute, A. L. (n.d.). On the leading constant in the Manin-type conjecture for Campana points. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>","mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, 2104.14946, doi:<a href=\"https://doi.org/10.48550/arXiv.2104.14946\">10.48550/arXiv.2104.14946</a>.","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>arXiv</i>. .","short":"A.L. Shute, ArXiv (n.d.).","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2104.14946\">https://doi.org/10.48550/arXiv.2104.14946</a>."},"publication_status":"draft","article_processing_charge":"No","year":"2021","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"2104.14946","date_published":"2021-04-30T00:00:00Z","type":"preprint","oa":1,"das_tickbox":"0","publication":"arXiv","status":"public","corr_author":"1","month":"04","abstract":[{"lang":"eng","text":"We compare the Manin-type conjecture for Campana points recently formulated\r\nby Pieropan, Smeets, Tanimoto and V\\'{a}rilly-Alvarado with an alternative\r\nprediction of Browning and Van Valckenborgh in the special case of the orbifold\r\n$(\\mathbb{P}^1,D)$, where $D =\\frac{1}{2}[0]+\\frac{1}{2}[1]+\\frac{1}{2}[\\infty]$. We find that the two predicted leading constants do not agree, and we discuss whether thin sets\r\ncould explain this discrepancy. Motivated by this, we provide a counterexample\r\nto the Manin-type conjecture for Campana points, by considering orbifolds\r\ncorresponding to squareful values of binary quadratic forms."}],"date_created":"2022-09-09T10:43:17Z","supplementarymaterial":"no","language":[{"iso":"eng"}]},{"date_updated":"2026-09-02T08:16:31Z","title":"Coarse graining the state space of a turbulent flow using periodic orbits","author":[{"id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","first_name":"Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz"},{"first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","orcid":"0000-0003-0423-5010","first_name":"Nazmi B"}],"external_id":{"arxiv":["2007.02584"],"isi":["000663310100008"]},"arxiv":1,"acknowledgement":"We thank the referees for improving this Letter with their comments. We acknowledge stimulating discussions with\r\nH. Edelsbrunner. This work was supported by Grant No. 662960 from the Simons Foundation (B. H.). The numerical calculations were performed at TUBITAK ULAKBIM High Performance and Grid Computing Center (TRUBA resources) and IST Austria High Performance Computing cluster.","article_type":"letter_note","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"related_material":{"record":[{"status":"returned","relation":"popular_science","id":"19591"},{"status":"public","id":"19684","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/turbulent-flow-simplified/"}]},"day":"18","main_file_link":[{"url":"https://arxiv.org/abs/2007.02584","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","_id":"9558","doi":"10.1103/PhysRevLett.126.244502","citation":{"short":"G. Yalniz, B. Hof, N.B. Budanur, Physical Review Letters 126 (2021).","chicago":"Yalniz, Gökhan, Björn Hof, and Nazmi B Budanur. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>.","apa":"Yalniz, G., Hof, B., &#38; Budanur, N. B. (2021). Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">https://doi.org/10.1103/PhysRevLett.126.244502</a>","ista":"Yalniz G, Hof B, Budanur NB. 2021. Coarse graining the state space of a turbulent flow using periodic orbits. Physical Review Letters. 126(24), 244502.","ama":"Yalniz G, Hof B, Budanur NB. Coarse graining the state space of a turbulent flow using periodic orbits. <i>Physical Review Letters</i>. 2021;126(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>","mla":"Yalniz, Gökhan, et al. “Coarse Graining the State Space of a Turbulent Flow Using Periodic Orbits.” <i>Physical Review Letters</i>, vol. 126, no. 24, 244502, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.126.244502\">10.1103/PhysRevLett.126.244502</a>.","ieee":"G. Yalniz, B. Hof, and N. B. Budanur, “Coarse graining the state space of a turbulent flow using periodic orbits,” <i>Physical Review Letters</i>, vol. 126, no. 24. American Physical Society, 2021."},"project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics"}],"volume":126,"scopus_import":"1","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"article_number":"244502","date_published":"2021-06-18T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2021","article_processing_charge":"No","publication_status":"published","oa":1,"isi":1,"type":"journal_article","acknowledged_ssus":[{"_id":"ScienComp"}],"corr_author":"1","month":"06","status":"public","publication":"Physical Review Letters","issue":"24","intvolume":"       126","language":[{"iso":"eng"}],"publisher":"American Physical Society","abstract":[{"text":"We show that turbulent dynamics that arise in simulations of the three-dimensional Navier--Stokes equations in a triply-periodic domain under sinusoidal forcing can be described as transient visits to the neighborhoods of unstable time-periodic solutions. Based on this description, we reduce the original system with more than 10^5 degrees of freedom to a 17-node Markov chain where each node corresponds to the neighborhood of a periodic orbit. The model accurately reproduces long-term averages of the system's observables as weighted sums over the periodic orbits.\r\n","lang":"eng"}],"date_created":"2021-06-16T15:45:36Z"},{"year":"2021","article_processing_charge":"No","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-02-01T00:00:00Z","page":"267-274","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"month":"02","corr_author":"1","status":"public","publication":"Nature Physics","date_created":"2020-10-04T22:01:37Z","abstract":[{"lang":"eng","text":"Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration."}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"        17","author":[{"first_name":"Daniel R","orcid":"0000-0002-1585-2631","last_name":"Boocock","id":"453AF628-F248-11E8-B48F-1D18A9856A87","full_name":"Boocock, Daniel R"},{"full_name":"Hino, Naoya","last_name":"Hino","first_name":"Naoya"},{"last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"}],"date_updated":"2026-09-02T22:30:04Z","title":"Theory of mechanochemical patterning and optimal migration in cell monolayers","article_type":"original","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"related_material":{"record":[{"id":"12964","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/wound-healing-waves/","description":"News on IST Homepage"}]},"acknowledgement":"We would like to thank G. Tkacik and all of the members of the Hannezo and Hirashima groups for useful discussions, X. Trepat for help on traction force microscopy and M. Matsuda for use of the lab facility. E.H. acknowledges grants from the Austrian Science Fund (FWF) (P 31639) and the European Research Council (851288). T.H. acknowledges a grant from JST, PRESTO (JPMJPR1949). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 665385 (to D.B.), from JSPS KAKENHI grant no. 17J02107 (to N.H.) and from the SPIRITS 2018 of Kyoto University (to E.H. and T.H.).","day":"01","external_id":{"isi":["000573519500002"]},"_id":"8602","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.05.15.096479"}],"quality_controlled":"1","oa_version":"Preprint","department":[{"_id":"EdHa"}],"scopus_import":"1","volume":17,"project":[{"name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639","call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425"},{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41567-020-01037-7","citation":{"short":"D.R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, E.B. Hannezo, Nature Physics 17 (2021) 267–274.","chicago":"Boocock, Daniel R, Naoya Hino, Natalia Ruzickova, Tsuyoshi Hirashima, and Edouard B Hannezo. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>.","ama":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. 2021;17:267-274. doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>","ista":"Boocock DR, Hino N, Ruzickova N, Hirashima T, Hannezo EB. 2021. Theory of mechanochemical patterning and optimal migration in cell monolayers. Nature Physics. 17, 267–274.","apa":"Boocock, D. R., Hino, N., Ruzickova, N., Hirashima, T., &#38; Hannezo, E. B. (2021). Theory of mechanochemical patterning and optimal migration in cell monolayers. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-01037-7\">https://doi.org/10.1038/s41567-020-01037-7</a>","ieee":"D. R. Boocock, N. Hino, N. Ruzickova, T. Hirashima, and E. B. Hannezo, “Theory of mechanochemical patterning and optimal migration in cell monolayers,” <i>Nature Physics</i>, vol. 17. Springer Nature, pp. 267–274, 2021.","mla":"Boocock, Daniel R., et al. “Theory of Mechanochemical Patterning and Optimal Migration in Cell Monolayers.” <i>Nature Physics</i>, vol. 17, Springer Nature, 2021, pp. 267–74, doi:<a href=\"https://doi.org/10.1038/s41567-020-01037-7\">10.1038/s41567-020-01037-7</a>."}},{"publisher":"Association for Computing Machinery","date_created":"2021-08-08T22:01:26Z","has_accepted_license":"1","abstract":[{"text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements.","lang":"eng"}],"intvolume":"        40","language":[{"iso":"eng"}],"issue":"4","month":"07","status":"public","publication":"ACM Transactions on Graphics","ddc":["516"],"oa":1,"type":"journal_article","ec_funded":1,"isi":1,"file":[{"file_name":"elastic-curves-paper.pdf","checksum":"7e5d08ce46b0451b3102eacd3d00f85f","creator":"chafner","date_created":"2021-10-18T10:42:15Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":17064290,"file_id":"10150","success":1,"date_updated":"2021-10-18T10:42:15Z"},{"date_updated":"2021-10-18T10:42:22Z","file_id":"10151","access_level":"open_access","content_type":"application/pdf","file_size":547156,"checksum":"0088643478be7c01a703b5b10767348f","file_name":"elastic-curves-supp.pdf","creator":"chafner","date_created":"2021-10-18T10:42:22Z","relation":"supplementary_material"}],"publication_status":"published","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"article_processing_charge":"No","year":"2021","article_number":"126","date_published":"2021-07-19T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":40,"department":[{"_id":"BeBi"}],"scopus_import":"1","doi":"10.1145/3450626.3459800","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>.","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126.","ama":"Hafner C, Bickel B. The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>","apa":"Hafner, C., &#38; Bickel, B. (2021). The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021)."},"project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"quality_controlled":"1","oa_version":"Published Version","_id":"9817","day":"19","file_date_updated":"2021-10-18T10:42:22Z","acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","related_material":{"record":[{"status":"public","id":"12897","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","description":"News on IST Website"}]},"article_type":"original","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"external_id":{"isi":["000674930900091"]},"conference":{"end_date":"2021-08-13","start_date":"2021-08-09","location":"Virtual","name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques"},"license":"https://creativecommons.org/licenses/by/4.0/","author":[{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"}],"title":"The design space of plane elastic curves","date_updated":"2026-09-02T22:30:05Z"},{"author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Morandell"},{"full_name":"Schwarz, Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Lena A"},{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173","last_name":"Basilico","first_name":"Bernadette"},{"full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","last_name":"Tasciyan","orcid":"0000-0003-1671-393X"},{"orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","first_name":"Christoph"},{"first_name":"Lisa","last_name":"Knaus","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa"},{"full_name":"Dobler, Zoe","id":"D23090A2-9057-11EA-883A-A8396FC7A38F","first_name":"Zoe","last_name":"Dobler"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-09-02T22:30:09Z","title":"Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development","file_date_updated":"2021-05-28T12:39:43Z","publication_identifier":{"eissn":["2041-1723"]},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/"}],"record":[{"id":"19557","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"earlier_version","id":"7800"},{"id":"12401","relation":"dissertation_contains","status":"public"}]},"article_type":"original","acknowledgement":"We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A. Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the management of our animal colony, as well as M. Schunn and the Preclinical Facility team for technical assistance. We thank K. Heesom and her team at the University of Bristol Proteomics Facility for the proteomics sample preparation, data generation, and analysis support. We thank Y. B. Simon for kindly providing the plasmid for lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration and the fruitful discussions. This work was supported by the ISTPlus postdoctoral fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D (I3600-B27).","day":"24","external_id":{"isi":["000658769900010"]},"_id":"9429","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","department":[{"_id":"GaNo"},{"_id":"JoDa"},{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"LifeSc"},{"_id":"Bio"}],"volume":12,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232","name":"Molecular Drug Targets"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem cells in autism and epilepsy","grant_number":"F7807"},{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600"}],"citation":{"chicago":"Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan, Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>.","short":"J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas, C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur, J.G. Danzl, G. Novarino, Nature Communications 12 (2021).","ieee":"J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.” <i>Nature Communications</i>, vol. 12, no. 1, 3058, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>.","apa":"Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A., Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23123-x\">https://doi.org/10.1038/s41467-021-23123-x</a>","ista":"Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. Nature Communications. 12(1), 3058.","ama":"Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23123-x\">10.1038/s41467-021-23123-x</a>"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41467-021-23123-x","year":"2021","article_processing_charge":"No","keyword":["General Biochemistry","Genetics and Molecular Biology"],"publication_status":"published","file":[{"checksum":"337e0f7959c35ec959984cacdcb472ba","file_name":"2021_NatureCommunications_Morandell.pdf","creator":"kschuh","date_created":"2021-05-28T12:39:43Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":9358599,"success":1,"file_id":"9430","date_updated":"2021-05-28T12:39:43Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-05-24T00:00:00Z","article_number":"3058","isi":1,"ec_funded":1,"type":"journal_article","oa":1,"issue":"1","acknowledged_ssus":[{"_id":"PreCl"}],"status":"public","ddc":["572"],"publication":"Nature Communications","month":"05","corr_author":"1","date_created":"2021-05-28T11:49:46Z","has_accepted_license":"1","abstract":[{"text":"De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency leads to motor coordination deficits as well as ASD-relevant social and cognitive impairments. However, induction of Cul3 haploinsufficiency later in life does not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during a critical developmental window. Here we show that Cul3 is essential to regulate neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice display cortical lamination abnormalities. At the molecular level, we found that Cul3 controls neuronal migration by tightly regulating the amount of Plastin3 (Pls3), a previously unrecognized player of neural migration. Furthermore, we found that Pls3 cell-autonomously regulates cell migration by regulating actin cytoskeleton organization, and its levels are inversely proportional to neural migration speed. Finally, we provide evidence that cellular phenotypes associated with autism-linked gene haploinsufficiency can be rescued by transcriptional activation of the intact allele in vitro, offering a proof of concept for a potential therapeutic approach for ASDs.","lang":"eng"}],"publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"        12"},{"article_type":"original","acknowledgement":"We thank Nicoletta Petridou, Diana Pinheiro, Cornelia Schwayer and Stefania Tavano for feedback on the manuscript. Research in the Heisenberg lab is supported by an ERC Advanced Grant (MECSPEC 742573) to C.-P.H. A.S. is a recipient of a DOC Fellowship of the Austrian Academy of Science.","publication_identifier":{"issn":["0012-1606"]},"related_material":{"record":[{"status":"public","id":"12891","relation":"dissertation_contains"}]},"file_date_updated":"2021-08-11T10:28:06Z","day":"01","external_id":{"isi":["000639461800008"],"pmid":["33352181"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"first_name":"Alexandra","orcid":"0000-0001-7659-9142","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-09-02T22:30:13Z","title":"Reassembling gastrulation","volume":474,"scopus_import":"1","department":[{"_id":"CaHe"}],"doi":"10.1016/j.ydbio.2020.12.014","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"citation":{"mla":"Schauer, Alexandra, and Carl-Philipp J. Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>, vol. 474, Elsevier, 2021, pp. 71–81, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>.","ieee":"A. Schauer and C.-P. J. Heisenberg, “Reassembling gastrulation,” <i>Developmental Biology</i>, vol. 474. Elsevier, pp. 71–81, 2021.","ama":"Schauer A, Heisenberg C-PJ. Reassembling gastrulation. <i>Developmental Biology</i>. 2021;474:71-81. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">10.1016/j.ydbio.2020.12.014</a>","apa":"Schauer, A., &#38; Heisenberg, C.-P. J. (2021). Reassembling gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>","ista":"Schauer A, Heisenberg C-PJ. 2021. Reassembling gastrulation. Developmental Biology. 474, 71–81.","chicago":"Schauer, Alexandra, and Carl-Philipp J Heisenberg. “Reassembling Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.ydbio.2020.12.014\">https://doi.org/10.1016/j.ydbio.2020.12.014</a>.","short":"A. Schauer, C.-P.J. Heisenberg, Developmental Biology 474 (2021) 71–81."},"project":[{"call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Published Version","_id":"8966","page":"71-81","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"file":[{"date_updated":"2021-08-11T10:28:06Z","success":1,"file_id":"9880","access_level":"open_access","content_type":"application/pdf","file_size":1440321,"file_name":"2021_DevBiology_Schauer.pdf","checksum":"fa2a5731fd16ab171b029f32f031c440","creator":"kschuh","date_created":"2021-08-11T10:28:06Z","relation":"main_file"}],"keyword":["Developmental Biology","Cell Biology","Molecular Biology"],"year":"2021","article_processing_charge":"Yes (via OA deal)","publication_status":"published","date_published":"2021-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","date_created":"2020-12-22T09:53:34Z","abstract":[{"lang":"eng","text":"During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process."}],"has_accepted_license":"1","pmid":1,"intvolume":"       474","language":[{"iso":"eng"}],"status":"public","month":"06","ddc":["570"],"publication":"Developmental Biology"},{"issue":"4","month":"04","ddc":["570"],"status":"public","publication":"Physical biology","date_created":"2021-04-25T22:01:29Z","has_accepted_license":"1","pmid":1,"abstract":[{"text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.","lang":"eng"}],"publisher":"IOP Publishing","language":[{"iso":"eng"}],"intvolume":"        18","year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"date_created":"2021-04-27T08:38:35Z","relation":"main_file","file_name":"2021_PhysBio_Lenne.pdf","creator":"cziletti","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","file_size":6296324,"access_level":"open_access","content_type":"application/pdf","file_id":"9355","success":1,"date_updated":"2021-04-27T08:38:35Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-04-14T00:00:00Z","article_number":"041501","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"_id":"9349","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","department":[{"_id":"AnKi"},{"_id":"EdHa"}],"volume":18,"project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"},{"call_identifier":"FWF","_id":"268294B6-B435-11E9-9278-68D0E5697425","name":"Active mechano-chemical description of the cell cytoskeleton","grant_number":"P31639"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"doi":"10.1088/1478-3975/abd0db","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical biology</i>. 2021;18(4). doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>.","ieee":"P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” <i>Physical biology</i>, vol. 18, no. 4. IOP Publishing, 2021.","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>."},"author":[{"full_name":"Lenne, Pierre François","first_name":"Pierre François","last_name":"Lenne"},{"full_name":"Munro, Edwin","last_name":"Munro","first_name":"Edwin"},{"last_name":"Heemskerk","first_name":"Idse","full_name":"Heemskerk, Idse"},{"first_name":"Aryeh","last_name":"Warmflash","full_name":"Warmflash, Aryeh"},{"full_name":"Bocanegra, Laura","id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Bocanegra"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","full_name":"Kishi, Kasumi","first_name":"Kasumi","orcid":"0000-0001-6060-4795","last_name":"Kishi"},{"first_name":"Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Long, Yuchen","first_name":"Yuchen","last_name":"Long"},{"full_name":"Fruleux, Antoine","last_name":"Fruleux","first_name":"Antoine"},{"last_name":"Boudaoud","first_name":"Arezki","full_name":"Boudaoud, Arezki"},{"full_name":"Saunders, Timothy E.","first_name":"Timothy E.","last_name":"Saunders"},{"first_name":"Paolo","last_name":"Caldarelli","full_name":"Caldarelli, Paolo"},{"full_name":"Michaut, Arthur","first_name":"Arthur","last_name":"Michaut"},{"full_name":"Gros, Jerome","last_name":"Gros","first_name":"Jerome"},{"last_name":"Maroudas-Sacks","first_name":"Yonit","full_name":"Maroudas-Sacks, Yonit"},{"full_name":"Keren, Kinneret","first_name":"Kinneret","last_name":"Keren"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Gartner, Zev J.","first_name":"Zev J.","last_name":"Gartner"},{"full_name":"Stormo, Benjamin","last_name":"Stormo","first_name":"Benjamin"},{"full_name":"Gladfelter, Amy","first_name":"Amy","last_name":"Gladfelter"},{"first_name":"Alan","last_name":"Rodrigues","full_name":"Rodrigues, Alan"},{"first_name":"Amy","last_name":"Shyer","full_name":"Shyer, Amy"},{"first_name":"Nicolas","last_name":"Minc","full_name":"Minc, Nicolas"},{"last_name":"Maître","first_name":"Jean Léon","full_name":"Maître, Jean Léon"},{"full_name":"Di Talia, Stefano","first_name":"Stefano","last_name":"Di Talia"},{"full_name":"Khamaisi, Bassma","first_name":"Bassma","last_name":"Khamaisi"},{"full_name":"Sprinzak, David","last_name":"Sprinzak","first_name":"David"},{"full_name":"Tlili, Sham","last_name":"Tlili","first_name":"Sham"}],"date_updated":"2026-09-02T22:30:15Z","title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","article_type":"original","related_material":{"record":[{"status":"public","id":"13081","relation":"dissertation_contains"}]},"file_date_updated":"2021-04-27T08:38:35Z","acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","publication_identifier":{"eissn":["1478-3975"]},"day":"14","external_id":{"pmid":["33276350"],"isi":["000640396400001"]}},{"author":[{"last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","full_name":"Kuzmicz-Kowalska, Katarzyna"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna"}],"title":"Regulation of size and scale in vertebrate spinal cord development","date_updated":"2026-09-02T22:30:16Z","day":"15","article_type":"original","file_date_updated":"2020-11-24T13:11:39Z","acknowledgement":"Austrian Academy of Sciences, Grant/Award Number: DOC fellowship for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037","related_material":{"record":[{"id":"14323","relation":"dissertation_contains","status":"public"}]},"publication_identifier":{"issn":["1759-7684"],"eissn":["1759-7692"]},"external_id":{"pmid":["32391980"],"isi":["000531419400001"]},"OA_place":"publisher","quality_controlled":"1","oa_version":"Published Version","_id":"7883","department":[{"_id":"AnKi"}],"scopus_import":"1","doi":"10.1002/wdev.383","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>, e383, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>.","ieee":"K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate spinal cord development,” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021.","ama":"Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. 2021. doi:<a href=\"https://doi.org/10.1002/wdev.383\">10.1002/wdev.383</a>","ista":"Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology., e383.","apa":"Kuzmicz-Kowalska, K., &#38; Kicheva, A. (2021). Regulation of size and scale in vertebrate spinal cord development. <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>","chicago":"Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale in Vertebrate Spinal Cord Development.” <i>Wiley Interdisciplinary Reviews: Developmental Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/wdev.383\">https://doi.org/10.1002/wdev.383</a>.","short":"K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental Biology (2021)."},"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"},{"_id":"267AF0E4-B435-11E9-9278-68D0E5697425","name":"The role of morphogens in the regulation of neural tube growth"},{"grant_number":"F7802","name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E"}],"file":[{"relation":"main_file","date_created":"2020-11-24T13:11:39Z","checksum":"f0a7745d48afa09ea7025e876a0145a8","creator":"dernst","file_name":"2020_WIREs_DevBio_KuzmiczKowalska.pdf","file_size":2527276,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"8800","date_updated":"2020-11-24T13:11:39Z"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","year":"2021","article_number":"e383","date_published":"2021-04-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"ddc":["570"],"status":"public","corr_author":"1","month":"04","publication":"Wiley Interdisciplinary Reviews: Developmental Biology","publisher":"Wiley","has_accepted_license":"1","date_created":"2020-05-24T22:01:00Z","abstract":[{"lang":"eng","text":"All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern."}],"pmid":1,"OA_type":"hybrid","language":[{"iso":"eng"}]},{"acknowledged_ssus":[{"_id":"M-Shop"}],"status":"public","publication":"Nature Chemistry","ddc":["540"],"corr_author":"1","month":"03","issue":"5","intvolume":"        13","language":[{"iso":"eng"}],"publisher":"Springer Nature","has_accepted_license":"1","pmid":1,"date_created":"2021-03-16T11:12:20Z","abstract":[{"text":"Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides and parasitic reactions that are caused by the highly reactive singlet oxygen (1O2). Redox mediators are recognized to be key for improving rechargeability. However, it is unclear how they affect 1O2 formation, which hinders strategies for their improvement. Here we clarify the mechanism of mediated peroxide and superoxide oxidation and thus explain how redox mediators either enhance or suppress 1O2 formation. We show that charging commences with peroxide oxidation to a superoxide intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution from superoxide oxidation, while disproportionation always generates some 1O2. We find that 1O2 suppression requires oxidation to be faster than the generation of 1O2 from disproportionation. Oxidation rates decrease with growing driving force following Marcus inverted-region behaviour, establishing a region of maximum rate.","lang":"eng"}],"date_published":"2021-03-15T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":1811448,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-03-22T11:46:00Z","relation":"main_file","file_name":"2021_NatureChem_Petit_acceptedVersion.pdf","checksum":"3ee3f8dd79ed1b7bb0929fce184c8012","creator":"dernst","date_updated":"2021-09-16T22:30:03Z","embargo":"2021-09-15","file_id":"9276"}],"article_processing_charge":"No","year":"2021","keyword":["General Chemistry","General Chemical Engineering"],"publication_status":"published","oa":1,"type":"journal_article","isi":1,"page":"465-471","quality_controlled":"1","oa_version":"Submitted Version","_id":"9250","citation":{"short":"Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic, C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger, Nature Chemistry 13 (2021) 465–471.","chicago":"Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>.","ama":"Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. 2021;13(5):465-471. doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>","ista":"Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. Nature Chemistry. 13(5), 465–471.","apa":"Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic, D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-021-00643-z\">https://doi.org/10.1038/s41557-021-00643-z</a>","ieee":"Y. K. Petit <i>et al.</i>, “Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation,” <i>Nature Chemistry</i>, vol. 13, no. 5. Springer Nature, pp. 465–471, 2021.","mla":"Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” <i>Nature Chemistry</i>, vol. 13, no. 5, Springer Nature, 2021, pp. 465–71, doi:<a href=\"https://doi.org/10.1038/s41557-021-00643-z\">10.1038/s41557-021-00643-z</a>."},"doi":"10.1038/s41557-021-00643-z","volume":13,"department":[{"_id":"StFr"}],"scopus_import":"1","date_updated":"2024-10-09T21:00:28Z","title":"Mechanism of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation","author":[{"last_name":"Petit","first_name":"Yann K.","full_name":"Petit, Yann K."},{"full_name":"Mourad, Eléonore","first_name":"Eléonore","last_name":"Mourad"},{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"first_name":"Christian","last_name":"Leypold","full_name":"Leypold, Christian"},{"full_name":"Windischbacher, Andreas","last_name":"Windischbacher","first_name":"Andreas"},{"full_name":"Mijailovic, Daniel","last_name":"Mijailovic","first_name":"Daniel"},{"full_name":"Slugovc, Christian","first_name":"Christian","last_name":"Slugovc"},{"last_name":"Borisov","first_name":"Sergey M.","full_name":"Borisov, Sergey M."},{"full_name":"Zojer, Egbert","first_name":"Egbert","last_name":"Zojer"},{"full_name":"Brutti, Sergio","last_name":"Brutti","first_name":"Sergio"},{"first_name":"Olivier","last_name":"Fontaine","full_name":"Fontaine, Olivier"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander"}],"external_id":{"isi":["000629296400001"],"pmid":["33723377"]},"acknowledgement":"S.A.F. is indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 636069) as well as IST Austria. O.F thanks the French National Research Agency (STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany) for the pressure test cell. We thank R. Saf for help with the mass spectrometry, J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.","article_type":"original","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"file_date_updated":"2021-09-16T22:30:03Z","day":"15"},{"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"V00739","name":"Structural plasticity at mossy fiber-CA3 synapses","_id":"2696E7FE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"doi":"10.1038/s41596-021-00526-0","citation":{"short":"D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter, P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.","chicago":"Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>.","ista":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols. 16(6), 2947–2967.","apa":"Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter, B., &#38; Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41596-021-00526-0\">https://doi.org/10.1038/s41596-021-00526-0</a>","ama":"Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses. <i>Nature Protocols</i>. 2021;16(6):2947–2967. doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>","mla":"Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.” <i>Nature Protocols</i>, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967, doi:<a href=\"https://doi.org/10.1038/s41596-021-00526-0\">10.1038/s41596-021-00526-0</a>.","ieee":"D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter, and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses,” <i>Nature Protocols</i>, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021."},"department":[{"_id":"PeJo"}],"scopus_import":"1","volume":16,"_id":"9438","oa_version":"Submitted Version","quality_controlled":"1","external_id":{"pmid":["33990799"],"isi":["000650528700003"]},"day":"01","publication_identifier":{"eissn":["1750-2799"],"issn":["1754-2189"]},"article_type":"original","acknowledgement":"This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction, E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.","file_date_updated":"2021-12-02T23:30:05Z","title":"Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses","date_updated":"2025-04-22T22:30:43Z","author":[{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","orcid":"0000-0001-7577-1676","first_name":"David H"},{"first_name":"Yuji","last_name":"Okamoto","orcid":"0000-0003-0408-6094","full_name":"Okamoto, Yuji","id":"3337E116-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carolina","last_name":"Borges Merjane","orcid":"0000-0003-0005-401X","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vargas Barroso, Victor M","id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","first_name":"Victor M","last_name":"Vargas Barroso"},{"id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin","first_name":"Benjamin","orcid":"0000-0002-9885-6936","last_name":"Suter"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"intvolume":"        16","date_created":"2021-05-30T22:01:24Z","pmid":1,"abstract":[{"lang":"eng","text":"Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system."}],"has_accepted_license":"1","publisher":"Springer Nature","status":"public","month":"06","corr_author":"1","ddc":["570"],"publication":"Nature Protocols","acknowledged_ssus":[{"_id":"M-Shop"}],"issue":"6","isi":1,"type":"journal_article","ec_funded":1,"oa":1,"page":"2947–2967","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-06-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2021","file":[{"date_updated":"2021-12-02T23:30:05Z","embargo":"2021-12-01","file_id":"9639","file_size":38574802,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-07-08T12:27:55Z","relation":"main_file","checksum":"7eb580abd8893cdb0b410cf41bc8c263","creator":"cziletti","file_name":"VandaeletalAuthorVersion2021.pdf"}]},{"intvolume":"        17","language":[{"iso":"eng"}],"publisher":"Nature Research","abstract":[{"lang":"eng","text":"Thermalization is the inevitable fate of many complex quantum systems, whose dynamics allow them to fully explore the vast configuration space regardless of the initial state---the behaviour known as quantum ergodicity. In a quest for experimental realizations of coherent long-time dynamics, efforts have focused on ergodicity-breaking mechanisms, such as integrability and localization. The recent discovery of persistent revivals in quantum simulators based on Rydberg atoms have pointed to the existence of a new type of behaviour where the system rapidly relaxes for most initial conditions, while certain initial states give rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body scarring’by analogy with a related form of weak ergodicity breaking that occurs for a single particle inside a stadium billiard potential. In this Review, we provide a pedagogical introduction to quantum many-body scars and highlight the emerging connections with the semiclassical quantization of many-body systems. We discuss the relation between scars and more general routes towards weak violations of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight possible applications of scars in quantum technology."}],"date_created":"2021-05-28T09:03:50Z","has_accepted_license":"1","ddc":["539"],"publication":"Nature Physics","month":"06","status":"public","issue":"6","oa":1,"type":"journal_article","ec_funded":1,"isi":1,"page":"675–685","date_published":"2021-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":10028836,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-09-20T09:27:43Z","relation":"main_file","creator":"patrickd","checksum":"316ed42ea1b42b0f1a3025bb476266fc","file_name":"RevisedQMBSreview.pdf","date_updated":"2021-12-02T23:30:03Z","embargo":"2021-12-01","file_id":"10026"}],"publication_status":"published","year":"2021","article_processing_charge":"No","doi":"10.1038/s41567-021-01230-2","citation":{"ista":"Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking of ergodicity. Nature Physics. 17(6), 675–685.","ama":"Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. 2021;17(6):675–685. doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>","apa":"Serbyn, M., Abanin, D. A., &#38; Papić, Z. (2021). Quantum many-body scars and weak breaking of ergodicity. <i>Nature Physics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>","ieee":"M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking of ergodicity,” <i>Nature Physics</i>, vol. 17, no. 6. Nature Research, pp. 675–685, 2021.","mla":"Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:<a href=\"https://doi.org/10.1038/s41567-021-01230-2\">10.1038/s41567-021-01230-2</a>.","short":"M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.","chicago":"Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.” <i>Nature Physics</i>. Nature Research, 2021. <a href=\"https://doi.org/10.1038/s41567-021-01230-2\">https://doi.org/10.1038/s41567-021-01230-2</a>."},"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"volume":17,"scopus_import":"1","department":[{"_id":"MaSe"}],"oa_version":"Preprint","quality_controlled":"1","_id":"9428","external_id":{"arxiv":["2011.09486"],"isi":["000655563800002"]},"arxiv":1,"day":"01","file_date_updated":"2021-12-02T23:30:03Z","acknowledgement":"We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W. Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular A. Michailidis and C. Turner, without whom this work would not have been possible. We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran, P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850899). D.A.A. was supported by the Swiss National Science Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme Trust Research Leadership Award RL-2019-015.","article_type":"review","publication_identifier":{"eissn":["1745-2481"]},"title":"Quantum many-body scars and weak breaking of ergodicity","date_updated":"2025-04-14T07:52:09Z","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}]},{"oa_version":"Published Version","_id":"9397","citation":{"ista":"Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute of Science and Technology Austria.","ama":"Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>","apa":"Huljev, K. (2021). <i>Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>","ieee":"K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation,” Institute of Science and Technology Austria, 2021.","mla":"Huljev, Karla. <i>Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9397\">10.15479/at:ista:9397</a>.","short":"K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute of Science and Technology Austria, 2021.","chicago":"Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9397\">https://doi.org/10.15479/at:ista:9397</a>."},"doi":"10.15479/at:ista:9397","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"title":"Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation","date_updated":"2026-04-08T07:12:51Z","author":[{"last_name":"Huljev","first_name":"Karla","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","day":"18","publication_identifier":{"issn":["2663-337X"]},"file_date_updated":"2022-05-21T22:30:04Z","corr_author":"1","ddc":["571"],"month":"05","status":"public","degree_awarded":"PhD","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"publisher":"Institute of Science and Technology Austria","date_created":"2021-05-17T12:31:30Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation."}],"alternative_title":["ISTA Thesis"],"date_published":"2021-05-18T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":47799741,"checksum":"7f98532f5324a0b2f3fa8de2967baa19","creator":"khuljev","file_name":"KHuljev_Thesis_corrections.docx","relation":"source_file","date_created":"2021-05-17T12:29:12Z","date_updated":"2022-05-21T22:30:04Z","embargo_to":"open_access","file_id":"9398"},{"access_level":"open_access","content_type":"application/pdf","file_size":16542131,"file_name":"new_KHuljev_Thesis_corrections.pdf","checksum":"bf512f8a1e572a543778fc4b227c01ba","creator":"khuljev","date_created":"2021-05-18T14:50:28Z","relation":"main_file","date_updated":"2022-05-21T22:30:04Z","file_id":"9401","embargo":"2022-05-20"}],"publication_status":"published","year":"2021","article_processing_charge":"No","oa":1,"type":"dissertation","page":"101"},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","date_created":"2021-07-27T13:40:30Z","abstract":[{"text":"Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows.\r\n\r\nFor particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations.\r\n\r\nThe effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"}],"degree_awarded":"PhD","month":"07","ddc":["532"],"corr_author":"1","status":"public","acknowledged_ssus":[{"_id":"M-Shop"}],"page":"118","oa":1,"type":"dissertation","file":[{"date_updated":"2022-07-29T22:30:05Z","embargo_to":"open_access","file_id":"9744","content_type":"application/x-zip-compressed","access_level":"closed","file_size":22859658,"file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.zip","checksum":"77436be3563a90435024307b1b5ee7e8","creator":"nagrawal","relation":"source_file","date_created":"2021-07-28T13:32:02Z"},{"date_created":"2021-07-28T13:32:05Z","relation":"main_file","file_name":"Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.pdf","checksum":"72a891d7daba85445c29b868c22575ed","creator":"nagrawal","file_size":18658048,"access_level":"open_access","content_type":"application/pdf","embargo":"2022-07-28","file_id":"9745","date_updated":"2022-07-29T22:30:05Z"}],"publication_status":"published","year":"2021","keyword":["Drag Reduction","Transition to Turbulence","Multiphase Flows","particle Laden Flows","Complex Flows","Experiments","Fluid Dynamics"],"article_processing_charge":"No","date_published":"2021-07-29T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.15479/at:ista:9728","citation":{"chicago":"Agrawal, Nishchal. “Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>.","short":"N. Agrawal, Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows, Institute of Science and Technology Austria, 2021.","mla":"Agrawal, Nishchal. <i>Transition to Turbulence and Drag Reduction in Particle-Laden Pipe Flows</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>.","ieee":"N. Agrawal, “Transition to turbulence and drag reduction in particle-laden pipe flows,” Institute of Science and Technology Austria, 2021.","ama":"Agrawal N. Transition to turbulence and drag reduction in particle-laden pipe flows. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9728\">10.15479/at:ista:9728</a>","apa":"Agrawal, N. (2021). <i>Transition to turbulence and drag reduction in particle-laden pipe flows</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9728\">https://doi.org/10.15479/at:ista:9728</a>","ista":"Agrawal N. 2021. Transition to turbulence and drag reduction in particle-laden pipe flows. Institute of Science and Technology Austria."},"oa_version":"Published Version","_id":"9728","day":"29","file_date_updated":"2022-07-29T22:30:05Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6189"}]},"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","author":[{"full_name":"Agrawal, Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","last_name":"Agrawal","first_name":"Nishchal"}],"title":"Transition to turbulence and drag reduction in particle-laden pipe flows","date_updated":"2026-04-16T08:43:20Z"}]