[{"department":[{"_id":"DaAl"}],"editor":[{"full_name":"Gibbons, P.","first_name":"P.","last_name":"Gibbons"},{"full_name":"Pekhimenko, G.","first_name":"G.","last_name":"Pekhimenko"},{"first_name":"C.","last_name":"De Sa","full_name":"De Sa, C."}],"day":"01","title":"L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publisher":"Association for Computing Machinery","conference":{"name":"MLSys: Machine Learning and Systems","location":"Athens, Greece","start_date":"2024-04-22","end_date":"2024-04-22"},"_id":"17456","date_published":"2024-04-01T00:00:00Z","quality_controlled":"1","month":"04","volume":6,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"17490"}]},"publication_status":"published","year":"2024","author":[{"full_name":"Markov, Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","first_name":"Ilia","last_name":"Markov"},{"last_name":"Alimohammadi","first_name":"Kaveh","full_name":"Alimohammadi, Kaveh"},{"first_name":"Elias","last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"arxiv":1,"date_updated":"2026-06-18T17:55:24Z","intvolume":"         6","language":[{"iso":"eng"}],"citation":{"ama":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In: Gibbons P, Pekhimenko G, De Sa C, eds. <i>Proceedings of Machine Learning and Systems </i>. Vol 6. Association for Computing Machinery; 2024.","ista":"Markov I, Alimohammadi K, Frantar E, Alistarh D-A. 2024. L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. Proceedings of Machine Learning and Systems . MLSys: Machine Learning and Systems vol. 6.","ieee":"I. Markov, K. Alimohammadi, E. Frantar, and D.-A. Alistarh, “L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning,” in <i>Proceedings of Machine Learning and Systems </i>, Athens, Greece, 2024, vol. 6.","apa":"Markov, I., Alimohammadi, K., Frantar, E., &#38; Alistarh, D.-A. (2024). L-GreCo: Layerwise-adaptive gradient compression for efficient data-parallel deep learning. In P. Gibbons, G. Pekhimenko, &#38; C. De Sa (Eds.), <i>Proceedings of Machine Learning and Systems </i> (Vol. 6). Athens, Greece: Association for Computing Machinery.","short":"I. Markov, K. Alimohammadi, E. Frantar, D.-A. Alistarh, in:, P. Gibbons, G. Pekhimenko, C. De Sa (Eds.), Proceedings of Machine Learning and Systems , Association for Computing Machinery, 2024.","mla":"Markov, Ilia, et al. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons et al., vol. 6, Association for Computing Machinery, 2024.","chicago":"Markov, Ilia, Kaveh Alimohammadi, Elias Frantar, and Dan-Adrian Alistarh. “L-GreCo: Layerwise-Adaptive Gradient Compression for Efficient Data-Parallel Deep Learning.” In <i>Proceedings of Machine Learning and Systems </i>, edited by P. Gibbons, G. Pekhimenko, and C. De Sa, Vol. 6. Association for Computing Machinery, 2024."},"external_id":{"arxiv":["2210.17357"]},"status":"public","abstract":[{"lang":"eng","text":"Data-parallel distributed training of deep neural networks (DNN) has gained very widespread adoption, but can still experience communication bottlenecks. To address this issue, entire families of compression mechanisms have been developed, including quantization, sparsification, and low-rank approximation, some of which are seeing significant practical adoption. Despite this progress, almost all known compression schemes apply compression uniformly across DNN layers, although layers are heterogeneous in terms of parameter count and their impact on model accuracy.In this work, we provide a general framework for adapting the degree of compression across the model's layers dynamically during training, improving the overall compression, while leading to substantial speedups, without sacrificing accuracy. Our framework, called L-GreCo, is based on an adaptive algorithm, which automatically picks the optimal compression parameters for model layers guaranteeing the best compression ratio while satisfying an error constraint. Extensive experiments over image classification and language modeling tasks shows that L-GreCo is effective across all existing families of compression methods, and achieves up to 2.5\r\n×\r\n training speedup and up to 5\r\n×\r\n compression improvement over efficient implementations of existing approaches, while recovering full accuracy. Moreover, L-GreCo is complementary to existing adaptive algorithms, improving their compression ratio by 50\\% and practical throughput by 66\\%. An anonymized implementation is available at https://github.com/LGrCo/L-GreCo."}],"corr_author":"1","main_file_link":[{"url":"https://proceedings.mlsys.org/paper_files/paper/2024/hash/9069a8976ff06f6443e7f4172990a580-Abstract-Conference.html","open_access":"1"}],"type":"conference","date_created":"2024-08-22T08:29:25Z","oa_version":"Published Version","publication":"Proceedings of Machine Learning and Systems "},{"ec_funded":1,"article_type":"original","citation":{"short":"C.E. Vanhille-Campos, K.D. Whitley, P. Radler, M. Loose, S. Holden, A. Šarić, Nature Physics 20 (2024) 1670–1678.","mla":"Vanhille-Campos, Christian Eduardo, et al. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1670–78, doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>.","ama":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. 2024;20:1670-1678. doi:<a href=\"https://doi.org/10.1038/s41567-024-02597-8\">10.1038/s41567-024-02597-8</a>","ista":"Vanhille-Campos CE, Whitley KD, Radler P, Loose M, Holden S, Šarić A. 2024. Self-organization of mortal filaments and its role in bacterial division ring formation. Nature Physics. 20, 1670–1678.","ieee":"C. E. Vanhille-Campos, K. D. Whitley, P. Radler, M. Loose, S. Holden, and A. Šarić, “Self-organization of mortal filaments and its role in bacterial division ring formation,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1670–1678, 2024.","apa":"Vanhille-Campos, C. E., Whitley, K. D., Radler, P., Loose, M., Holden, S., &#38; Šarić, A. (2024). Self-organization of mortal filaments and its role in bacterial division ring formation. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>","chicago":"Vanhille-Campos, Christian Eduardo, Kevin D. Whitley, Philipp Radler, Martin Loose, Séamus Holden, and Anđela Šarić. “Self-Organization of Mortal Filaments and Its Role in Bacterial Division Ring Formation.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02597-8\">https://doi.org/10.1038/s41567-024-02597-8</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Filaments in the cell commonly treadmill. Driven by energy consumption, they grow on one end while shrinking on the other, causing filaments to appear motile even though individual proteins remain static. This process is characteristic of cytoskeletal filaments and leads to collective filament self-organization. Here we show that treadmilling drives filament nematic ordering by dissolving misaligned filaments. Taking the bacterial FtsZ protein involved in cell division as an example, we show that this mechanism aligns FtsZ filaments in vitro and drives the organization of the division ring in living Bacillus subtilis cells. We find that ordering via local dissolution also allows the system to quickly respond to chemical and geometrical biases in the cell, enabling us to quantitatively explain the ring formation dynamics in vivo. Beyond FtsZ and other cytoskeletal filaments, our study identifies a mechanism for self-organization via constant birth and death of energy-consuming filaments."}],"has_accepted_license":"1","external_id":{"isi":["001289394500005"],"pmid":["39416851"]},"status":"public","date_created":"2024-08-25T22:01:08Z","oa_version":"Published Version","publication":"Nature Physics","scopus_import":"1","corr_author":"1","type":"journal_article","project":[{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"OA_type":"hybrid","date_updated":"2025-09-08T09:02:20Z","ddc":["570"],"OA_place":"publisher","intvolume":"        20","page":"1670-1678","pmid":1,"author":[{"full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo","last_name":"Vanhille-Campos"},{"last_name":"Whitley","first_name":"Kevin D.","full_name":"Whitley, Kevin D."},{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"last_name":"Holden","first_name":"Séamus","full_name":"Holden, Séamus"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"month":"10","volume":20,"file_date_updated":"2025-04-14T06:06:35Z","publication_status":"published","year":"2024","quality_controlled":"1","_id":"17460","date_published":"2024-10-01T00:00:00Z","publisher":"Springer Nature","doi":"10.1038/s41567-024-02597-8","acknowledgement":"We thank I. Palaia (ISTA) for useful discussions and K. Lim and R. W. Wong (WPI-Nano Life Science Institute, Kanazawa University) for providing access to HS-AFM. We would like to thank B. Prats Mateu (MSD Austria, Vienna) for providing the HS-AFM data. This work was supported by the Royal Society (grant no. UF160266; C.V.-C. and A.Š.), the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960; A.Š.), the Austrian Science Fund (FWF) Stand-Alone P34607 (M.L.) and a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (grant no. 206670/Z/17/Z; S.H. and K.D.W.).","isi":1,"file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","date_created":"2025-04-14T06:06:35Z","content_type":"application/pdf","file_size":8058249,"date_updated":"2025-04-14T06:06:35Z","file_id":"19556","file_name":"2024_NaturePhysics_VanhilleCampos.pdf","success":1,"checksum":"c4842152e2b90d67f48ea8c9ed7c473b"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","APC_amount":"12348 EUR","department":[{"_id":"AnSa"},{"_id":"MaLo"}],"day":"01","oa":1,"title":"Self-organization of mortal filaments and its role in bacterial division ring formation","license":"https://creativecommons.org/licenses/by/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Unconditional versus condition-dependent social immunity","day":"01","department":[{"_id":"SyCr"}],"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1471-5007"],"issn":["1471-4922"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1016/j.pt.2024.07.014","isi":1,"acknowledgement":"We thank Koos Boomsma and two anonymous reviewers for their constructive comments on the manuscript.","file":[{"date_created":"2025-01-09T13:46:05Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_name":"2024_TrendsParasitology_Cremer.pdf","file_id":"18816","date_updated":"2025-01-09T13:46:05Z","checksum":"362fc994e5df66caf3025b7dc437b647","success":1,"file_size":1068464}],"publisher":"Elsevier","_id":"17461","quality_controlled":"1","date_published":"2024-09-01T00:00:00Z","year":"2024","publication_status":"published","file_date_updated":"2025-01-09T13:46:05Z","issue":"9","volume":40,"month":"09","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"},{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","first_name":"Christopher","last_name":"Pull"}],"pmid":1,"page":"780-787","intvolume":"        40","OA_place":"publisher","date_updated":"2025-09-08T09:01:42Z","ddc":["570"],"OA_type":"hybrid","scopus_import":"1","date_created":"2024-08-25T22:01:08Z","publication":"Trends in Parasitology","oa_version":"Published Version","corr_author":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Socially living animals can counteract disease through cooperative defences, leading to social immunity that collectively exceeds the sum of individual defences. In superorganismal colonies of social insects with permanent caste separation between reproductive queen(s) and nonreproducing workers, workers are obligate altruists and thus engage in unconditional social immunity, including highly specialised and self-sacrificial hygiene behaviours. Contrastingly, cooperation is facultative in cooperatively breeding families, where all members are reproductively totipotent but offspring transiently forgo reproduction to help their parents rear more siblings. Here, helpers should either express condition-dependent social immunity or disperse to pursue independent reproduction. We advocate inclusive fitness theory as a framework to predict when and how indirect fitness gains may outweigh direct fitness costs, thus favouring conditional social immunity."}],"has_accepted_license":"1","status":"public","external_id":{"pmid":["39152078"],"isi":["001307815700001"]},"citation":{"chicago":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” <i>Trends in Parasitology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">https://doi.org/10.1016/j.pt.2024.07.014</a>.","ista":"Cremer S, Pull C. 2024. Unconditional versus condition-dependent social immunity. Trends in Parasitology. 40(9), 780–787.","ieee":"S. Cremer and C. Pull, “Unconditional versus condition-dependent social immunity,” <i>Trends in Parasitology</i>, vol. 40, no. 9. Elsevier, pp. 780–787, 2024.","ama":"Cremer S, Pull C. Unconditional versus condition-dependent social immunity. <i>Trends in Parasitology</i>. 2024;40(9):780-787. doi:<a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">10.1016/j.pt.2024.07.014</a>","apa":"Cremer, S., &#38; Pull, C. (2024). Unconditional versus condition-dependent social immunity. <i>Trends in Parasitology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">https://doi.org/10.1016/j.pt.2024.07.014</a>","short":"S. Cremer, C. Pull, Trends in Parasitology 40 (2024) 780–787.","mla":"Cremer, Sylvia, and Christopher Pull. “Unconditional versus Condition-Dependent Social Immunity.” <i>Trends in Parasitology</i>, vol. 40, no. 9, Elsevier, 2024, pp. 780–87, doi:<a href=\"https://doi.org/10.1016/j.pt.2024.07.014\">10.1016/j.pt.2024.07.014</a>."},"article_type":"original","language":[{"iso":"eng"}]},{"acknowledgement":"We would like to thank our affiliations, Institute of Science and Technology Austria and Max Planck Institute for Mathematics in the Sciences, for supporting the authors’ visits to each other, which greatly facilitated this work. We would like to thank Marc Josien and Quinn Winters for assistance in numerical implementation.","isi":1,"doi":"10.1137/23M1603819","publisher":"Society for Industrial and Applied Mathematics","date_published":"2024-09-01T00:00:00Z","_id":"17462","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Artificial boundary conditions for random elliptic systems with correlated coefficient field","day":"01","department":[{"_id":"JuFi"}],"article_processing_charge":"No","publication_identifier":{"issn":["1540-3459"],"eissn":["1540-3467"]},"intvolume":"        22","OA_place":"repository","date_updated":"2025-09-08T09:01:00Z","arxiv":1,"OA_type":"green","project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials","call_identifier":"H2020"}],"scopus_import":"1","publication":"Multiscale Modeling and Simulation","date_created":"2024-08-25T22:01:08Z","oa_version":"Preprint","corr_author":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2309.06798"}],"abstract":[{"text":"We are interested in numerical algorithms for computing the electrical field generated by a charge distribution localized on scale l in an infinite heterogeneous correlated random medium, in a situation where the medium is only known in a box of diameter L >>l around the support of the charge. We show that the algorithm in [J. Lu, F. Otto, and L. Wang, Optimal Artificial Boundary Conditions Based on Second-Order Correctors for Three Dimensional Random Ellilptic Media, preprint, arXiv:2109.01616, 2021], suggesting optimal Dirichlet boundary conditions motivated by the multipole expansion [P. Bella, A. Giunti, and F. Otto, Comm. Partial Differential Equations, 45 (2020), pp. 561–640], still performs well in correlated media. With overwhelming probability, we obtain a convergence rate in terms of l, L, and the size of the correlations for which optimality is supported with numerical simulations. These estimates are provided for ensembles which satisfy a multiscale logarithmic Sobolev inequality, where our main tool is an extension of the semigroup estimates in [N. Clozeau, Stoch. Partial Differ. Equ. Anal. Comput., 11 (2023), pp. 1254–1378]. As part of our strategy, we construct sublinear second-order correctors in this correlated setting, which is of independent interest.","lang":"eng"}],"status":"public","external_id":{"arxiv":["2309.06798"],"isi":["001285416500001"]},"citation":{"chicago":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” <i>Multiscale Modeling and Simulation</i>. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/23M1603819\">https://doi.org/10.1137/23M1603819</a>.","ieee":"N. Clozeau and L. Wang, “Artificial boundary conditions for random elliptic systems with correlated coefficient field,” <i>Multiscale Modeling and Simulation</i>, vol. 22, no. 3. Society for Industrial and Applied Mathematics, pp. 973–1029, 2024.","ama":"Clozeau N, Wang L. Artificial boundary conditions for random elliptic systems with correlated coefficient field. <i>Multiscale Modeling and Simulation</i>. 2024;22(3):973-1029. doi:<a href=\"https://doi.org/10.1137/23M1603819\">10.1137/23M1603819</a>","ista":"Clozeau N, Wang L. 2024. Artificial boundary conditions for random elliptic systems with correlated coefficient field. Multiscale Modeling and Simulation. 22(3), 973–1029.","apa":"Clozeau, N., &#38; Wang, L. (2024). Artificial boundary conditions for random elliptic systems with correlated coefficient field. <i>Multiscale Modeling and Simulation</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/23M1603819\">https://doi.org/10.1137/23M1603819</a>","short":"N. Clozeau, L. Wang, Multiscale Modeling and Simulation 22 (2024) 973–1029.","mla":"Clozeau, Nicolas, and Lihan Wang. “Artificial Boundary Conditions for Random Elliptic Systems with Correlated Coefficient Field.” <i>Multiscale Modeling and Simulation</i>, vol. 22, no. 3, Society for Industrial and Applied Mathematics, 2024, pp. 973–1029, doi:<a href=\"https://doi.org/10.1137/23M1603819\">10.1137/23M1603819</a>."},"ec_funded":1,"article_type":"original","language":[{"iso":"eng"}],"year":"2024","publication_status":"published","issue":"3","volume":22,"month":"09","author":[{"full_name":"Clozeau, Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","first_name":"Nicolas","last_name":"Clozeau"},{"full_name":"Wang, Lihan","last_name":"Wang","first_name":"Lihan"}],"page":"973-1029"},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"Yes (in subscription journal)","oa":1,"title":"De novo design of allosterically switchable protein assemblies","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"FlPr"}],"day":"22","date_published":"2024-08-22T00:00:00Z","_id":"17463","quality_controlled":"1","publisher":"Springer Nature","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2024-09-09T12:01:14Z","content_type":"application/pdf","file_size":16572040,"file_name":"2024_Nature_Pillai.pdf","file_id":"18005","date_updated":"2024-09-09T12:01:14Z","checksum":"39127601621a360ec0edc538627eb211","success":1}],"isi":1,"doi":"10.1038/s41586-024-07813-2","acknowledgement":"We thank D. D. Sahtoe, R. D. Kiber, Y. Hsia, N. Bethel and A. Favor for helpful discussions and K. VanWormer and L. Goldschmidt for technical support. We also thank X. Li and M. Lamb for mass spectrometry support. This work was supported by the Washington Research Foundation Postdoctoral Fellowship (grant no. GR027504, A. Pillai), a National Science Foundation Graduate Research Fellowship (grant no. DGE-2140004, A.I.), a Human Frontier Science Program Long Term Fellowship (grant no. LT000880/2019, F.P.), the Audacious Project at the Institute for Protein Design (A.B., A. Pillai, A. Philomin, A.I. and D.B.), a National Energy Research Scientific Computing Centre award (grant no. BER-ERCAP0022018), the Howard Hughes Medical Institute (D.B.), the Open Philanthropy Project Improving Protein Design Fund (P.J.Y.L., C.D. and D.B.) a gift from Microsoft (D.B.) and a grant from DARPA supporting the Harnessing Enzymatic Activity for Lifesaving Remedies programme (grant no. HR001120S0052, contract no. HR0011-21-2-0012, D.B.).","author":[{"first_name":"Arvind","last_name":"Pillai","full_name":"Pillai, Arvind"},{"first_name":"Abbas","last_name":"Idris","full_name":"Idris, Abbas"},{"first_name":"Annika","last_name":"Philomin","full_name":"Philomin, Annika"},{"full_name":"Weidle, Connor","first_name":"Connor","last_name":"Weidle"},{"full_name":"Skotheim, Rebecca","last_name":"Skotheim","first_name":"Rebecca"},{"last_name":"Leung","first_name":"Philip J.Y.","full_name":"Leung, Philip J.Y."},{"first_name":"Adam","last_name":"Broerman","full_name":"Broerman, Adam"},{"last_name":"Demakis","first_name":"Cullen","full_name":"Demakis, Cullen"},{"full_name":"Borst, Andrew J.","first_name":"Andrew J.","last_name":"Borst"},{"last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Baker","first_name":"David","full_name":"Baker, David"}],"page":"911–920 ","pmid":1,"file_date_updated":"2024-09-09T12:01:14Z","publication_status":"published","year":"2024","month":"08","volume":632,"abstract":[{"lang":"eng","text":"Allosteric modulation of protein function, wherein the binding of an effector to a protein triggers conformational changes at distant functional sites, plays a central part in the control of metabolism and cell signalling1,2,3. There has been considerable interest in designing allosteric systems, both to gain insight into the mechanisms underlying such ‘action at a distance’ modulation and to create synthetic proteins whose functions can be regulated by effectors4,5,6,7. However, emulating the subtle conformational changes distributed across many residues, characteristic of natural allosteric proteins, is a significant challenge8,9. Here, inspired by the classic Monod–Wyman–Changeux model of cooperativity10, we investigate the de novo design of allostery through rigid-body coupling of peptide-switchable hinge modules11 to protein interfaces12 that direct the formation of alternative oligomeric states. We find that this approach can be used to generate a wide variety of allosterically switchable systems, including cyclic rings that incorporate or eject subunits in response to peptide binding and dihedral cages that undergo effector-induced disassembly. Size-exclusion chromatography, mass photometry13 and electron microscopy reveal that these designed allosteric protein assemblies closely resemble the design models in both the presence and absence of peptide effectors and can have ligand-binding cooperativity comparable to classic natural systems such as haemoglobin14. Our results indicate that allostery can arise from global coupling of the energetics of protein substructures without optimized side-chain–side-chain allosteric communication pathways and provide a roadmap for generating allosterically triggerable delivery systems, protein nanomachines and cellular feedback control circuitry."}],"external_id":{"pmid":["39143214"],"isi":["001300534300019"]},"status":"public","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","date_created":"2024-08-25T22:01:08Z","publication":"Nature","corr_author":"1","type":"journal_article","citation":{"chicago":"Pillai, Arvind, Abbas Idris, Annika Philomin, Connor Weidle, Rebecca Skotheim, Philip J.Y. Leung, Adam Broerman, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>.","mla":"Pillai, Arvind, et al. “De Novo Design of Allosterically Switchable Protein Assemblies.” <i>Nature</i>, vol. 632, Springer Nature, 2024, pp. 911–920, doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>.","short":"A. Pillai, A. Idris, A. Philomin, C. Weidle, R. Skotheim, P.J.Y. Leung, A. Broerman, C. Demakis, A.J. Borst, F.M. Praetorius, D. Baker, Nature 632 (2024) 911–920.","apa":"Pillai, A., Idris, A., Philomin, A., Weidle, C., Skotheim, R., Leung, P. J. Y., … Baker, D. (2024). De novo design of allosterically switchable protein assemblies. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-024-07813-2\">https://doi.org/10.1038/s41586-024-07813-2</a>","ieee":"A. Pillai <i>et al.</i>, “De novo design of allosterically switchable protein assemblies,” <i>Nature</i>, vol. 632. Springer Nature, pp. 911–920, 2024.","ista":"Pillai A, Idris A, Philomin A, Weidle C, Skotheim R, Leung PJY, Broerman A, Demakis C, Borst AJ, Praetorius FM, Baker D. 2024. De novo design of allosterically switchable protein assemblies. Nature. 632, 911–920.","ama":"Pillai A, Idris A, Philomin A, et al. De novo design of allosterically switchable protein assemblies. <i>Nature</i>. 2024;632:911–920. doi:<a href=\"https://doi.org/10.1038/s41586-024-07813-2\">10.1038/s41586-024-07813-2</a>"},"article_type":"original","language":[{"iso":"eng"}],"date_updated":"2025-09-08T09:00:16Z","ddc":["570"],"intvolume":"       632"},{"author":[{"id":"6c292945-a610-11ed-9eec-c3be1ad62a80","full_name":"Desaules, Jean-Yves Marc","last_name":"Desaules","first_name":"Jean-Yves Marc","orcid":"0000-0002-3749-6375"}],"year":"2024","file_date_updated":"2024-08-30T13:19:57Z","contributor":[{"contributor_type":"researcher","last_name":"Shen","first_name":"Ruizhe"},{"first_name":"Fang","last_name":"Qin","contributor_type":"researcher"},{"last_name":"Desaules","orcid":"0000-0002-3749-6375","first_name":"Jean-Yves Marc","id":"6c292945-a610-11ed-9eec-c3be1ad62a80","contributor_type":"researcher"},{"first_name":"Zlatko","last_name":"Papić","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Ching Hua","last_name":"Lee"}],"related_material":{"record":[{"status":"public","id":"18627","relation":"used_in_publication"}]},"month":"08","oa_version":"Published Version","date_created":"2024-08-30T12:59:43Z","type":"research_data","abstract":[{"text":"Mechanisms for suppressing thermalization in disorder-free many-body systems, such as Hilbert space fragmentation and quantum many-body scars, have recently attracted much interest in foundations of quantum statistical physics and potential quantum information processing applications. However,  their sensitivity to realistic effects such as finite temperature remains largely unexplored. Here, we have utilized IBM's Kolkata quantum processor to demonstrate an unexpected robustness of quantum many-body scars at finite temperatures when the system is prepared in a thermal Gibbs ensemble. We identify such robustness in the PXP model, which describes quantum many-body scars in experimental systems of Rydberg atom arrays and ultracold atoms in tilted Bose--Hubbard optical lattices. By contrast, other theoretical models which host exact quantum many-body scars are found to lack such robustness, and their scarring properties quickly decay with temperature. Our study sheds light on the important differences between scarred models in terms of their algebraic structures, which impacts their resilience to finite temperature.","lang":"eng"}],"status":"public","has_accepted_license":"1","ec_funded":1,"citation":{"chicago":"Desaules, Jean-Yves Marc. “Data for ‘Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">https://doi.org/10.15479/AT:ISTA:17471</a>.","short":"J.-Y.M. Desaules, (2024).","mla":"Desaules, Jean-Yves Marc. <i>Data for “Enhanced Many-Body Quantum Scars from the Non-Hermitian Fock Skin Effect.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>.","ieee":"J.-Y. M. Desaules, “Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.’” Institute of Science and Technology Austria, 2024.","ama":"Desaules J-YM. Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>","ista":"Desaules J-YM. 2024. Data for ‘Enhanced many-body quantum scars from the non-Hermitian Fock skin effect’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">10.15479/AT:ISTA:17471</a>.","apa":"Desaules, J.-Y. M. (2024). Data for “Enhanced many-body quantum scars from the non-Hermitian Fock skin effect.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17471\">https://doi.org/10.15479/AT:ISTA:17471</a>"},"date_updated":"2026-06-10T07:52:53Z","ddc":["530"],"project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","oa":1,"title":"Data for \"Enhanced many-body quantum scars from the non-Hermitian Fock skin effect\"","day":"30","keyword":["quantum many-body scars","non-equilibrium physics","non-Hermitian physics"],"department":[{"_id":"MaSe"}],"_id":"17471","date_published":"2024-08-30T00:00:00Z","doi":"10.15479/AT:ISTA:17471","file":[{"creator":"jdesaule","relation":"main_file","access_level":"open_access","content_type":"application/zip","date_created":"2024-08-30T12:55:37Z","file_size":322400,"success":1,"checksum":"2bd49ce5a63f1951c1ed3d89cce4fe27","file_name":"FiguresData.zip","file_id":"17472","date_updated":"2024-08-30T12:55:37Z"},{"file_size":1368,"date_updated":"2024-08-30T13:19:57Z","file_name":"readme.txt","file_id":"17473","success":1,"checksum":"c2ba113a241e98c394cc3ca21f3fa126","access_level":"open_access","relation":"main_file","creator":"jdesaule","date_created":"2024-08-30T13:19:57Z","content_type":"text/plain"}],"publisher":"Institute of Science and Technology Austria"},{"article_number":"105214","quality_controlled":"1","_id":"17474","date_published":"2024-12-01T00:00:00Z","publisher":"Elsevier","acknowledgement":"Krishnendu Chatterjee reports financial support was provided by European Research Council.","isi":1,"doi":"10.1016/j.ic.2024.105214","file":[{"file_id":"18817","file_name":"2024_InformationComputation_Baier.pdf","date_updated":"2025-01-09T13:49:03Z","checksum":"f68e0c2f46f9b9c86815406bcf2ee2d4","success":1,"file_size":724703,"content_type":"application/pdf","date_created":"2025-01-09T13:49:03Z","access_level":"open_access","creator":"dernst","relation":"main_file"}],"publication_identifier":{"issn":["0890-5401"],"eissn":["1090-2651"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","oa":1,"title":"Entropic risk for turn-based stochastic games","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"KrCh"}],"day":"01","abstract":[{"text":"Entropic risk (ERisk) is an established risk measure in finance, quantifying risk by an exponential re-weighting of rewards. We study ERisk for the first time in the context of turn-based stochastic games with the total reward objective. This gives rise to an objective function that demands the control of systems in a risk-averse manner. We show that the resulting games are determined and, in particular, admit optimal memoryless deterministic strategies. This contrasts risk measures that previously have been considered in the special case of Markov decision processes and that require randomization and/or memory. We provide several results on the decidability and the computational complexity of the threshold problem, i.e. whether the optimal value of ERisk exceeds a given threshold. Furthermore, an approximation algorithm for the optimal value of ERisk is provided.","lang":"eng"}],"status":"public","has_accepted_license":"1","external_id":{"isi":["001301143400001"],"arxiv":["2307.06611"]},"scopus_import":"1","date_created":"2024-09-01T22:01:07Z","oa_version":"Published Version","publication":"Information and Computation","type":"journal_article","corr_author":"1","citation":{"chicago":"Baier, Christel, Krishnendu Chatterjee, Tobias Meggendorfer, and Jakob Piribauer. “Entropic Risk for Turn-Based Stochastic Games.” <i>Information and Computation</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.ic.2024.105214\">https://doi.org/10.1016/j.ic.2024.105214</a>.","mla":"Baier, Christel, et al. “Entropic Risk for Turn-Based Stochastic Games.” <i>Information and Computation</i>, vol. 301, 105214, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.ic.2024.105214\">10.1016/j.ic.2024.105214</a>.","short":"C. Baier, K. Chatterjee, T. Meggendorfer, J. Piribauer, Information and Computation 301 (2024).","apa":"Baier, C., Chatterjee, K., Meggendorfer, T., &#38; Piribauer, J. (2024). Entropic risk for turn-based stochastic games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2024.105214\">https://doi.org/10.1016/j.ic.2024.105214</a>","ista":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. 2024. Entropic risk for turn-based stochastic games. Information and Computation. 301, 105214.","ieee":"C. Baier, K. Chatterjee, T. Meggendorfer, and J. Piribauer, “Entropic risk for turn-based stochastic games,” <i>Information and Computation</i>, vol. 301. Elsevier, 2024.","ama":"Baier C, Chatterjee K, Meggendorfer T, Piribauer J. Entropic risk for turn-based stochastic games. <i>Information and Computation</i>. 2024;301. doi:<a href=\"https://doi.org/10.1016/j.ic.2024.105214\">10.1016/j.ic.2024.105214</a>"},"article_type":"original","language":[{"iso":"eng"}],"date_updated":"2025-09-08T09:10:06Z","arxiv":1,"ddc":["000"],"OA_place":"publisher","intvolume":"       301","OA_type":"hybrid","author":[{"first_name":"Christel","last_name":"Baier","full_name":"Baier, Christel"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165"},{"full_name":"Piribauer, Jakob","last_name":"Piribauer","first_name":"Jakob"}],"publication_status":"published","file_date_updated":"2025-01-09T13:49:03Z","year":"2024","month":"12","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"14417"}]},"volume":301},{"project":[{"grant_number":"101076777","name":"Randomness and structure in combinatorics","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"}],"intvolume":"        75","date_updated":"2025-09-08T09:09:41Z","arxiv":1,"ddc":["500"],"article_type":"original","citation":{"chicago":"Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” <i>Quarterly Journal of Mathematics</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/qmath/haae030\">https://doi.org/10.1093/qmath/haae030</a>.","apa":"Koval, I., &#38; Kwan, M. A. (2024). Exponentially many graphs are determined by their spectrum. <i>Quarterly Journal of Mathematics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/qmath/haae030\">https://doi.org/10.1093/qmath/haae030</a>","ista":"Koval I, Kwan MA. 2024. Exponentially many graphs are determined by their spectrum. Quarterly Journal of Mathematics. 75(3), 869–899.","ama":"Koval I, Kwan MA. Exponentially many graphs are determined by their spectrum. <i>Quarterly Journal of Mathematics</i>. 2024;75(3):869-899. doi:<a href=\"https://doi.org/10.1093/qmath/haae030\">10.1093/qmath/haae030</a>","ieee":"I. Koval and M. A. Kwan, “Exponentially many graphs are determined by their spectrum,” <i>Quarterly Journal of Mathematics</i>, vol. 75, no. 3. Oxford University Press, pp. 869–899, 2024.","mla":"Koval, Illya, and Matthew Alan Kwan. “Exponentially Many Graphs Are Determined by Their Spectrum.” <i>Quarterly Journal of Mathematics</i>, vol. 75, no. 3, Oxford University Press, 2024, pp. 869–99, doi:<a href=\"https://doi.org/10.1093/qmath/haae030\">10.1093/qmath/haae030</a>.","short":"I. Koval, M.A. Kwan, Quarterly Journal of Mathematics 75 (2024) 869–899."},"language":[{"iso":"eng"}],"publication":"Quarterly Journal of Mathematics","oa_version":"Published Version","date_created":"2024-09-01T22:01:07Z","scopus_import":"1","type":"journal_article","corr_author":"1","abstract":[{"lang":"eng","text":"As a discrete analogue of Kac’s celebrated question on ‘hearing the shape of a drum’ and towards a practical\r\ngraph isomorphism test, it is of interest to understand which graphs are determined up to isomorphism by\r\ntheir spectrum (of their adjacency matrix). A striking conjecture in this area, due to van Dam and Haemers,\r\nis that ‘almost all graphs are determined by their spectrum’, meaning that the fraction of unlabelled n-vertex\r\ngraphs which are determined by their spectrum converges to 1 as n → ∞.\r\nIn this paper, we make a step towards this conjecture, showing that there are exponentially many n-vertex\r\ngraphs which are determined by their spectrum. This improves on previous bounds (of shape e\r\nc\r\n√\r\nn\r\n). We also\r\npropose a number of further directions of research.\r\n"}],"external_id":{"arxiv":["2309.09788"],"isi":["001249741500001"]},"status":"public","has_accepted_license":"1","issue":"3","volume":75,"month":"06","year":"2024","publication_status":"published","file_date_updated":"2024-09-06T12:23:57Z","page":"869-899","author":[{"id":"2eed1f3b-896a-11ed-bdf8-93c7c4bf159e","full_name":"Koval, Illya","first_name":"Illya","last_name":"Koval"},{"first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"}],"doi":"10.1093/qmath/haae030","acknowledgement":"Matthew Kwan was supported by ERC Starting Grant ‘RANDSTRUCT’ No. 101076777.","isi":1,"file":[{"checksum":"abf200d37ad69e6f2c0750a30296ad97","success":1,"date_updated":"2024-09-06T12:23:57Z","file_name":"2024_QuJofMath_Koval.pdf","file_id":"17851","file_size":946411,"content_type":"application/pdf","date_created":"2024-09-06T12:23:57Z","relation":"main_file","creator":"cchlebak","access_level":"open_access"}],"publisher":"Oxford University Press","_id":"17475","date_published":"2024-06-19T00:00:00Z","quality_controlled":"1","day":"19","department":[{"_id":"MaKw"},{"_id":"VaKa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Exponentially many graphs are determined by their spectrum","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"issn":["0033-5606"],"eissn":["1464-3847"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"publisher":"American Physical Society","doi":"10.1103/PhysRevMaterials.8.085403","acknowledgement":"We gratefully acknowledge the assistance of Prof. John\r\nDudley.","isi":1,"article_number":"085403","quality_controlled":"1","_id":"17476","date_published":"2024-08-23T00:00:00Z","department":[{"_id":"ZhAl"}],"day":"23","title":"No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2475-9953"]},"article_processing_charge":"No","date_updated":"2025-09-08T09:06:34Z","intvolume":"         8","article_type":"original","citation":{"apa":"Lorenc, D., Zhumekenov, A., Bakr, O. M., &#38; Alpichshev, Z. (2024). No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">https://doi.org/10.1103/PhysRevMaterials.8.085403</a>","ieee":"D. Lorenc, A. Zhumekenov, O. M. Bakr, and Z. Alpichshev, “No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry,” <i>Physical Review Materials</i>, vol. 8, no. 8. American Physical Society, 2024.","ama":"Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. <i>Physical Review Materials</i>. 2024;8(8). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">10.1103/PhysRevMaterials.8.085403</a>","ista":"Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. 2024. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. 8(8), 085403.","mla":"Lorenc, Dusan, et al. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” <i>Physical Review Materials</i>, vol. 8, no. 8, 085403, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">10.1103/PhysRevMaterials.8.085403</a>.","short":"D. Lorenc, A. Zhumekenov, O.M. Bakr, Z. Alpichshev, Physical Review Materials 8 (2024).","chicago":"Lorenc, Dusan, Ayan Zhumekenov, Osman M. Bakr, and Zhanybek Alpichshev. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” <i>Physical Review Materials</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevMaterials.8.085403\">https://doi.org/10.1103/PhysRevMaterials.8.085403</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"Lead halide perovskites have recently been reported to demonstrate an exceptionally high nonlinear (Kerr) refractive index n2 of up to 10−8cm2/W in CH3⁢NH3⁢PbBr3. Other researchers, however, observe different, substantially more conservative numbers. In order to resolve this disagreement, the nonlinear Kerr index of a bulk sample of lead halide perovskite was measured directly by means of an interferometer. This approach has many advantages as compared to the more standard z-scan technique. In particular, this method allows studying the induced changes to the refractive index in a time-resolved manner, thus enabling to separate the different contributions to 𝑛2. The extracted 𝑛2 values for CsPbBr3 and MAPbBr3 at 𝜆≈1µ⁢m are 𝑛2=+2.1×10−14cm2/W and 𝑛2=+6×10−15cm2/W, respectively. Hence, these values are substantially lower than what has been indicated in most of the previous reports, implying the latter one should be regarded with great care.","lang":"eng"}],"external_id":{"isi":["001299497800001"]},"status":"public","publication":"Physical Review Materials","oa_version":"None","scopus_import":"1","date_created":"2024-09-01T22:01:08Z","type":"journal_article","corr_author":"1","month":"08","issue":"8","volume":8,"publication_status":"published","year":"2024","author":[{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"full_name":"Zhumekenov, Ayan","last_name":"Zhumekenov","first_name":"Ayan"},{"last_name":"Bakr","first_name":"Osman M.","full_name":"Bakr, Osman M."},{"full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","first_name":"Zhanybek"}]},{"intvolume":"        14","date_updated":"2025-09-08T09:07:29Z","arxiv":1,"ddc":["530"],"citation":{"ista":"Hawaldar S, Shahi P, Carter AL, Rey AM, Bollinger JJ, Shankar A. 2024. Bilayer crystals of trapped ions for quantum information processing. Physical Review X. 14(3), 031030.","ieee":"S. Hawaldar, P. Shahi, A. L. Carter, A. M. Rey, J. J. Bollinger, and A. Shankar, “Bilayer crystals of trapped ions for quantum information processing,” <i>Physical Review X</i>, vol. 14, no. 3. American Physical Society, 2024.","ama":"Hawaldar S, Shahi P, Carter AL, Rey AM, Bollinger JJ, Shankar A. Bilayer crystals of trapped ions for quantum information processing. <i>Physical Review X</i>. 2024;14(3). doi:<a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">10.1103/PhysRevX.14.031030</a>","apa":"Hawaldar, S., Shahi, P., Carter, A. L., Rey, A. M., Bollinger, J. J., &#38; Shankar, A. (2024). Bilayer crystals of trapped ions for quantum information processing. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">https://doi.org/10.1103/PhysRevX.14.031030</a>","short":"S. Hawaldar, P. Shahi, A.L. Carter, A.M. Rey, J.J. Bollinger, A. Shankar, Physical Review X 14 (2024).","mla":"Hawaldar, Samarth, et al. “Bilayer Crystals of Trapped Ions for Quantum Information Processing.” <i>Physical Review X</i>, vol. 14, no. 3, 031030, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">10.1103/PhysRevX.14.031030</a>.","chicago":"Hawaldar, Samarth, Prakriti Shahi, Allison L. Carter, Ana Maria Rey, John J. Bollinger, and Athreya Shankar. “Bilayer Crystals of Trapped Ions for Quantum Information Processing.” <i>Physical Review X</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevX.14.031030\">https://doi.org/10.1103/PhysRevX.14.031030</a>."},"DOAJ_listed":"1","article_type":"original","language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","publication":"Physical Review X","date_created":"2024-09-01T22:01:08Z","type":"journal_article","corr_author":"1","abstract":[{"lang":"eng","text":"Trapped-ion systems are a leading platform for quantum information processing, but they are currently limited to 1D and 2D arrays, which imposes restrictions on both their scalability and their range of applications. Here, we propose a path to overcome this limitation by demonstrating that Penning traps can be used to realize remarkably clean bilayer crystals, wherein hundreds of ions self-organize into two well-defined layers. These bilayer crystals are made possible by the inclusion of an anharmonic trapping potential, which is readily implementable with current technology. We study the normal modes of this system and discover salient differences compared to the modes of single-plane crystals. The bilayer geometry and the unique properties of the normal modes open new opportunities—in particular, in quantum sensing and quantum simulation—that are not straightforward in single-plane crystals. Furthermore, we illustrate that it may be possible to extend the ideas presented here to realize multilayer crystals with more than two layers. Our work increases the dimensionality of trapped-ion systems by efficiently utilizing all three spatial dimensions, and it lays the foundation for a new generation of quantum information processing experiments with multilayer 3D crystals of trapped ions."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["001293977800002"],"arxiv":["2312.10681"]},"issue":"3","volume":14,"month":"08","year":"2024","publication_status":"published","file_date_updated":"2024-09-06T09:43:53Z","author":[{"last_name":"Hawaldar","orcid":"0000-0002-1965-4309","first_name":"Samarth","full_name":"Hawaldar, Samarth","id":"221708e1-1ff6-11ee-9fa6-85146607433e"},{"last_name":"Shahi","first_name":"Prakriti","full_name":"Shahi, Prakriti"},{"last_name":"Carter","first_name":"Allison L.","full_name":"Carter, Allison L."},{"full_name":"Rey, Ana Maria","last_name":"Rey","first_name":"Ana Maria"},{"full_name":"Bollinger, John J.","first_name":"John J.","last_name":"Bollinger"},{"last_name":"Shankar","first_name":"Athreya","full_name":"Shankar, Athreya"}],"isi":1,"acknowledgement":"We thank M. Miskeen Khan, Jennifer Lilieholm, and Wes Johnson for a careful reading and feedback on the manuscript. We acknowledge discussions with Dan Dubin, John Zaris, and Scott Parker. S. H. acknowledges the support of Kishore Vaigyanik Protsahan Yojana, Department of Science and Technology, Government of India. A. S. acknowledges the support of a C. V. Raman post-doctoral fellowship. A. L. C., A. M. R., and J. J. B. acknowledge funding from the U.S. Department of Energy, Office of Science, NQI Science Research Centers, Quantum Systems Accelerator (QSA), a collaboration between the U.S. Department of Energy, Office of Science and other agencies. A. M. R. acknowledges additional support from VBFF, ARO Grant No. W911NF-24-1-0128, by the NSF Grants No. JILA-PFC PHY-2317149 and No. QLCI-OMA-2016244, and by NIST. J. J. B. acknowledges additional support from the DARPA ONISQ program and AFOSR Grant No. FA9550-201-0019.","doi":"10.1103/PhysRevX.14.031030","file":[{"access_level":"open_access","creator":"cchlebak","relation":"main_file","content_type":"application/pdf","date_created":"2024-09-06T09:43:53Z","file_size":3909653,"file_name":"2024_PhysRevX_Hawaldar.pdf","file_id":"17757","date_updated":"2024-09-06T09:43:53Z","success":1,"checksum":"5d39b7dda67fd7b9a960235f6f38e280"}],"publisher":"American Physical Society","_id":"17477","quality_controlled":"1","date_published":"2024-08-16T00:00:00Z","article_number":"031030","day":"16","department":[{"_id":"JoFi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Bilayer crystals of trapped ions for quantum information processing","article_processing_charge":"Yes","publication_identifier":{"eissn":["2160-3308"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"eissn":["1618-1913"],"issn":["0073-8301"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass","day":"01","department":[{"_id":"RoSe"}],"_id":"17478","date_published":"2024-12-01T00:00:00Z","quality_controlled":"1","file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_created":"2025-01-13T08:13:42Z","file_size":924342,"file_name":"2024_PublicMathIHES_Brooks.pdf","file_id":"18824","date_updated":"2025-01-13T08:13:42Z","checksum":"af3becc50f7534c9409d3ff8b5c47ed6","success":1}],"doi":"10.1007/s10240-024-00150-0","isi":1,"publisher":"Springer Nature","author":[{"last_name":"Brooks","orcid":"0000-0002-6249-0928","first_name":"Morris","full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"page":"271-309","year":"2024","publication_status":"published","file_date_updated":"2025-01-13T08:13:42Z","volume":140,"month":"12","publication":"Publications Mathematiques de l'Institut des Hautes Etudes Scientifiques","date_created":"2024-09-01T22:01:08Z","oa_version":"Published Version","scopus_import":"1","type":"journal_article","corr_author":"1","abstract":[{"lang":"eng","text":"We study the Fröhlich polaron model in R3, and prove a lower bound on its ground state energy as a function of the total momentum. The bound is asymptotically sharp at large coupling. In combination with a corresponding upper bound proved earlier (Mitrouskas et al. in Forum Math. Sigma 11:1–52, 2023), it shows that the energy is approximately parabolic below the continuum threshold, and that the polaron’s effective mass (defined as the semi-latus rectum of the\r\nparabola) is given by the celebrated Landau–Pekar formula. In particular, it diverges as α4 for large coupling constant α."}],"external_id":{"arxiv":["2211.03353"],"isi":["001297785000001"]},"status":"public","has_accepted_license":"1","citation":{"chicago":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part II — Energy-Momentum Relation and Effective Mass.” <i>Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s10240-024-00150-0\">https://doi.org/10.1007/s10240-024-00150-0</a>.","ieee":"M. Brooks and R. Seiringer, “The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass,” <i>Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques</i>, vol. 140. Springer Nature, pp. 271–309, 2024.","ama":"Brooks M, Seiringer R. The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. <i>Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques</i>. 2024;140:271-309. doi:<a href=\"https://doi.org/10.1007/s10240-024-00150-0\">10.1007/s10240-024-00150-0</a>","ista":"Brooks M, Seiringer R. 2024. The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. Publications Mathematiques de l’Institut des Hautes Etudes Scientifiques. 140, 271–309.","apa":"Brooks, M., &#38; Seiringer, R. (2024). The Fröhlich polaron at strong coupling: Part II — Energy-momentum relation and effective mass. <i>Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10240-024-00150-0\">https://doi.org/10.1007/s10240-024-00150-0</a>","short":"M. Brooks, R. Seiringer, Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques 140 (2024) 271–309.","mla":"Brooks, Morris, and Robert Seiringer. “The Fröhlich Polaron at Strong Coupling: Part II — Energy-Momentum Relation and Effective Mass.” <i>Publications Mathematiques de l’Institut Des Hautes Etudes Scientifiques</i>, vol. 140, Springer Nature, 2024, pp. 271–309, doi:<a href=\"https://doi.org/10.1007/s10240-024-00150-0\">10.1007/s10240-024-00150-0</a>."},"article_type":"original","language":[{"iso":"eng"}],"intvolume":"       140","OA_place":"publisher","date_updated":"2025-09-08T09:08:36Z","ddc":["510"],"arxiv":1,"OA_type":"hybrid"},{"_id":"17479","quality_controlled":"1","date_published":"2024-09-01T00:00:00Z","publisher":"American Chemical Society","file":[{"success":1,"checksum":"bd7e6a138c406e93eaf0a6268fc42bfe","date_updated":"2025-01-09T14:01:06Z","file_id":"18819","file_name":"2024_ACSPhotonics_TaboadaGutierrez_.pdf","file_size":2664512,"date_created":"2025-01-09T14:01:06Z","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access"}],"acknowledgement":"Funding Sources ─ A.I.F.T.-M. and G.Á.-P. acknowledge support through the Severo Ochoa program from the Government of the Principality of Asturias (references PA-21-PF-BP20-117 and PA20-PF-BP19-053, respectively). A.B.K. and J.T.-G. acknowledge support from the Swiss National Science Foundation (grant # 200020_201096). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I), the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00/AEI/10.13039/501100011033) and project PCI2022-132953 funded by MCIN/AEI/10.13039/501100011033 and the EU “NextGenerationEU”/PRTR”. P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). A.Y.N. acknowledges the Spanish Ministry of Science and Innovation (grant PID2020-115221GB-C42) and the Basque Department of Education (grant PIBA-2023-1-0007). M.V. and J.I.M. acknowledge support by Spanish MCIN/AEI/10.13039/501100011033/FEDER, UE under grant PID2022-136784NB and by Asturias FICYT under grant AYUD/2021/51185 with the support of FEDER funds. I.E. acknowledges funding from the Spanish Ministry of Science and Innovation (Grant No. PID2022-142861NA-I00) and the Department of Education, Universities, and Research of the Eusko Jaurlaritza and the University of the Basque Country UPV/EHU (Grant No. IT1527-22). J. Duan acknowledges the support from the Beijing Natural Science Foundation (Grant No. Z240005), and National Natural Science Foundation of China.","isi":1,"doi":"10.1021/acsphotonics.4c00485","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2330-4022"]},"article_processing_charge":"No","title":"Unveiling the mechanism of phonon-polariton damping in α‑MoO3","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NanoFab"}],"day":"01","has_accepted_license":"1","external_id":{"arxiv":["2408.09811"],"isi":["001298164600001"],"pmid":["39310295"]},"status":"public","abstract":[{"lang":"eng","text":"Phonon polaritons (PhPs), light coupled to lattice vibrations, in the highly anisotropic polar layered material molybdenum trioxide (α-MoO3) are currently the focus of intense research efforts due to their extreme subwavelength field confinement, directional propagation, and unprecedented low losses. Nevertheless, prior research has primarily concentrated on exploiting the squeezing and steering capabilities of α-MoO3 PhPs, without inquiring much into the dominant microscopic mechanism that determines their long lifetimes, which is key for their implementation in nanophotonic applications. This study delves into the fundamental processes that govern PhP damping in α-MoO3 by combining ab initio calculations with scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared (FTIR) spectroscopy measurements across a broad temperature range (8–300 K). The remarkable agreement between our theoretical predictions and experimental observations allows us to identify third-order anharmonic phonon–phonon scattering as the main damping mechanism of α-MoO3 PhPs. These findings shed light on the fundamental limits of low-loss PhPs, which is a crucial factor for assessing their implementation into nanophotonic devices."}],"type":"journal_article","publication":"ACS Photonics","date_created":"2024-09-01T22:01:09Z","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"article_type":"original","citation":{"chicago":"Taboada-Gutiérrez, Javier, Yixi Zhou, Ana I.F. Tresguerres-Mata, Christian Lanza, Abel Martínez-Suárez, Gonzalo Álvarez-Pérez, Jiahua Duan, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” <i>ACS Photonics</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">https://doi.org/10.1021/acsphotonics.4c00485</a>.","ama":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, et al. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. <i>ACS Photonics</i>. 2024;11(9):3570-3577. doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">10.1021/acsphotonics.4c00485</a>","ieee":"J. Taboada-Gutiérrez <i>et al.</i>, “Unveiling the mechanism of phonon-polariton damping in α‑MoO3,” <i>ACS Photonics</i>, vol. 11, no. 9. American Chemical Society, pp. 3570–3577, 2024.","ista":"Taboada-Gutiérrez J, Zhou Y, Tresguerres-Mata AIF, Lanza C, Martínez-Suárez A, Álvarez-Pérez G, Duan J, Martín JI, Vélez M, Prieto Gonzalez I, Bercher A, Teyssier J, Errea I, Nikitin AY, Martín-Sánchez J, Kuzmenko AB, Alonso-González P. 2024. Unveiling the mechanism of phonon-polariton damping in α‑MoO3. ACS Photonics. 11(9), 3570–3577.","apa":"Taboada-Gutiérrez, J., Zhou, Y., Tresguerres-Mata, A. I. F., Lanza, C., Martínez-Suárez, A., Álvarez-Pérez, G., … Alonso-González, P. (2024). Unveiling the mechanism of phonon-polariton damping in α‑MoO3. <i>ACS Photonics</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">https://doi.org/10.1021/acsphotonics.4c00485</a>","short":"J. Taboada-Gutiérrez, Y. Zhou, A.I.F. Tresguerres-Mata, C. Lanza, A. Martínez-Suárez, G. Álvarez-Pérez, J. Duan, J.I. Martín, M. Vélez, I. Prieto Gonzalez, A. Bercher, J. Teyssier, I. Errea, A.Y. Nikitin, J. Martín-Sánchez, A.B. Kuzmenko, P. Alonso-González, ACS Photonics 11 (2024) 3570–3577.","mla":"Taboada-Gutiérrez, Javier, et al. “Unveiling the Mechanism of Phonon-Polariton Damping in Α‑MoO3.” <i>ACS Photonics</i>, vol. 11, no. 9, American Chemical Society, 2024, pp. 3570–77, doi:<a href=\"https://doi.org/10.1021/acsphotonics.4c00485\">10.1021/acsphotonics.4c00485</a>."},"ddc":["530"],"arxiv":1,"date_updated":"2025-09-08T09:05:01Z","OA_place":"publisher","intvolume":"        11","OA_type":"hybrid","author":[{"first_name":"Javier","last_name":"Taboada-Gutiérrez","full_name":"Taboada-Gutiérrez, Javier"},{"full_name":"Zhou, Yixi","first_name":"Yixi","last_name":"Zhou"},{"full_name":"Tresguerres-Mata, Ana I.F.","first_name":"Ana I.F.","last_name":"Tresguerres-Mata"},{"full_name":"Lanza, Christian","first_name":"Christian","last_name":"Lanza"},{"first_name":"Abel","last_name":"Martínez-Suárez","full_name":"Martínez-Suárez, Abel"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"full_name":"Martín, José Ignacio","first_name":"José Ignacio","last_name":"Martín"},{"first_name":"María","last_name":"Vélez","full_name":"Vélez, María"},{"orcid":"0000-0002-7370-5357","first_name":"Ivan","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bercher, Adrien","last_name":"Bercher","first_name":"Adrien"},{"first_name":"Jérémie","last_name":"Teyssier","full_name":"Teyssier, Jérémie"},{"full_name":"Errea, Ion","first_name":"Ion","last_name":"Errea"},{"last_name":"Nikitin","first_name":"Alexey Y.","full_name":"Nikitin, Alexey Y."},{"full_name":"Martín-Sánchez, Javier","first_name":"Javier","last_name":"Martín-Sánchez"},{"full_name":"Kuzmenko, Alexey B.","last_name":"Kuzmenko","first_name":"Alexey B."},{"full_name":"Alonso-González, Pablo","last_name":"Alonso-González","first_name":"Pablo"}],"page":"3570-3577","pmid":1,"publication_status":"published","file_date_updated":"2025-01-09T14:01:06Z","year":"2024","month":"09","volume":11,"issue":"9"},{"day":"01","department":[{"_id":"AnHi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Bolometric detection of Josephson radiation","article_processing_charge":"No","publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"file":[{"file_size":3047567,"file_name":"2024_NatureNanotechnology_Karimi.pdf","file_id":"18818","date_updated":"2025-01-09T13:51:12Z","checksum":"8b067ef217ddef63c539ecdfe705ab95","success":1,"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2025-01-09T13:51:12Z","content_type":"application/pdf"}],"doi":"10.1038/s41565-024-01770-7","acknowledgement":"We thank M. Möttönen, D. Subero, V. Vadimov, A. Alizadeh, C. Strunk, N. Roch, S. Kafanov, S. Kubatkin, A. Kerman and J. Peltonen for scientific discussions and Z.-Y. Chen for technical assistance. B.K. and J.P.P. acknowledge funding from the Research Council of Finland Centre of Excellence programme grant 336810 and grant 349601 (THEPOW), G.O.S. and A.L.Y. financial support from the Spanish Ministry of Science through grant TED2021-130292B-C43 funded by MCIN/AEI/10.13039/501100011033, ‘ERDF A way of making Europe’ and the EU through FET-Open project AndQC, A.P.H. support from the NOMIS Foundation, and C.M.M. support from the Danish National Research Foundation and a research grant (Project 43951) from VILLUM FONDEN. We thank the facilities and technical support of Otaniemi Research Infrastructure for Micro and Nanotechnologies (OtaNano). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the paper.","publisher":"Springer Nature","_id":"17480","quality_controlled":"1","date_published":"2024-11-01T00:00:00Z","volume":19,"month":"11","year":"2024","file_date_updated":"2025-01-09T13:51:12Z","publication_status":"published","page":"1613-1618","author":[{"last_name":"Karimi","first_name":"Bayan","full_name":"Karimi, Bayan"},{"full_name":"Steffensen, Gorm Ole","first_name":"Gorm Ole","last_name":"Steffensen"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363"},{"full_name":"Marcus, Charles M.","last_name":"Marcus","first_name":"Charles M."},{"first_name":"Alfredo","last_name":"Levy Yeyati","full_name":"Levy Yeyati, Alfredo"},{"full_name":"Pekola, Jukka P.","first_name":"Jukka P.","last_name":"Pekola"}],"project":[{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"OA_type":"hybrid","intvolume":"        19","OA_place":"publisher","date_updated":"2026-06-03T07:16:01Z","arxiv":1,"ddc":["530"],"article_type":"original","citation":{"mla":"Karimi, Bayan, et al. “Bolometric Detection of Josephson Radiation.” <i>Nature Nanotechnology</i>, vol. 19, Springer Nature, 2024, pp. 1613–18, doi:<a href=\"https://doi.org/10.1038/s41565-024-01770-7\">10.1038/s41565-024-01770-7</a>.","short":"B. Karimi, G.O. Steffensen, A.P. Higginbotham, C.M. Marcus, A. Levy Yeyati, J.P. Pekola, Nature Nanotechnology 19 (2024) 1613–1618.","apa":"Karimi, B., Steffensen, G. O., Higginbotham, A. P., Marcus, C. M., Levy Yeyati, A., &#38; Pekola, J. P. (2024). Bolometric detection of Josephson radiation. <i>Nature Nanotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41565-024-01770-7\">https://doi.org/10.1038/s41565-024-01770-7</a>","ieee":"B. Karimi, G. O. Steffensen, A. P. Higginbotham, C. M. Marcus, A. Levy Yeyati, and J. P. Pekola, “Bolometric detection of Josephson radiation,” <i>Nature Nanotechnology</i>, vol. 19. Springer Nature, pp. 1613–1618, 2024.","ista":"Karimi B, Steffensen GO, Higginbotham AP, Marcus CM, Levy Yeyati A, Pekola JP. 2024. Bolometric detection of Josephson radiation. Nature Nanotechnology. 19, 1613–1618.","ama":"Karimi B, Steffensen GO, Higginbotham AP, Marcus CM, Levy Yeyati A, Pekola JP. Bolometric detection of Josephson radiation. <i>Nature Nanotechnology</i>. 2024;19:1613-1618. doi:<a href=\"https://doi.org/10.1038/s41565-024-01770-7\">10.1038/s41565-024-01770-7</a>","chicago":"Karimi, Bayan, Gorm Ole Steffensen, Andrew P Higginbotham, Charles M. Marcus, Alfredo Levy Yeyati, and Jukka P. Pekola. “Bolometric Detection of Josephson Radiation.” <i>Nature Nanotechnology</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41565-024-01770-7\">https://doi.org/10.1038/s41565-024-01770-7</a>."},"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Nature Nanotechnology","date_created":"2024-09-01T22:01:09Z","scopus_import":"1","type":"journal_article","abstract":[{"lang":"eng","text":"One of the most promising approaches towards large-scale quantum computation uses devices based on many Josephson junctions. Yet, even today, open questions regarding the single junction remain unsolved, such as the detailed understanding of the quantum phase transitions, the coupling of the Josephson junction to the environment or how to improve the coherence of a superconducting qubit. Here we design and build an engineered on-chip reservoir connected to a Josephson junction that acts as an efficient bolometer for detecting the Josephson radiation under non-equilibrium, that is, biased conditions. The bolometer converts the a.c. Josephson current at microwave frequencies up to about 100 GHz into a temperature rise measured by d.c. thermometry. A circuit model based on realistic parameter values captures both the current–voltage characteristics and the measured power quantitatively. The present experiment demonstrates an efficient, wide-band, thermal detection scheme of microwave photons and provides a sensitive detector of Josephson dynamics beyond the standard conductance measurements."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["001296522000002"],"arxiv":["2402.09314"]}},{"ddc":["570"],"date_updated":"2026-06-10T07:58:35Z","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:17488","file":[{"access_level":"open_access","creator":"rsatapat","relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2024-09-03T17:39:32Z","file_size":965778072,"file_name":"BehaviouralData.zip","file_id":"17489","date_updated":"2024-09-03T17:39:32Z","checksum":"df9d6c8ddffa046c3b1639281f83cfcf","success":1}],"project":[{"name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716"}],"status":"public","has_accepted_license":"1","abstract":[{"text":"Behavioural data for Pokusaeva, Satapathy et al. Relevant information can be found in the 'README.txt' file.","lang":"eng"}],"type":"research_data","corr_author":"1","oa_version":"Published Version","date_created":"2024-09-03T17:42:46Z","citation":{"chicago":"Satapathy, Roshan K, Maximilian A Jösch, Olga Symonova, and Victoria Pokusaeva. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>.","ieee":"R. K. Satapathy, M. A. Jösch, O. Symonova, and V. Pokusaeva, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies.” Institute of Science and Technology Austria, 2024.","ama":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>","ista":"Satapathy RK, Jösch MA, Symonova O, Pokusaeva V. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>.","apa":"Satapathy, R. K., Jösch, M. A., Symonova, O., &#38; Pokusaeva, V. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17488\">https://doi.org/10.15479/AT:ISTA:17488</a>","short":"R.K. Satapathy, M.A. Jösch, O. Symonova, V. Pokusaeva, (2024).","mla":"Satapathy, Roshan K., et al. <i>Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17488\">10.15479/AT:ISTA:17488</a>."},"_id":"17488","date_published":"2024-09-01T00:00:00Z","title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","oa":1,"file_date_updated":"2024-09-03T17:39:32Z","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","year":"2024","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"month":"09","keyword":["drosophila","behaviour","locomotion","gap junctions"],"related_material":{"record":[{"status":"public","id":"18444","relation":"used_in_publication"}]},"author":[{"last_name":"Satapathy","first_name":"Roshan K","orcid":"0009-0006-2974-5075","id":"46046B7A-F248-11E8-B48F-1D18A9856A87","full_name":"Satapathy, Roshan K"},{"last_name":"Jösch","first_name":"Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A"},{"full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","orcid":"0000-0003-2012-9947","first_name":"Olga"},{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","first_name":"Victoria","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"M-Shop"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No"},{"year":"2024","publication_status":"published","file_date_updated":"2024-09-04T08:36:06Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14461"},{"id":"12780","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"17456"}]},"month":"09","alternative_title":["ISTA Thesis"],"author":[{"last_name":"Markov","first_name":"Ilia","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"page":"102","OA_place":"publisher","ddc":["000"],"date_updated":"2026-06-18T17:55:23Z","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"type":"dissertation","corr_author":"1","oa_version":"Published Version","date_created":"2024-09-04T08:51:11Z","status":"public","has_accepted_license":"1","abstract":[{"text":"Deep learning is essential in numerous applications nowadays, with many recent advancements made possible by training very large models. Despite their broad applicability, training neural networks is often time-intensive, and it is usually impractical to manage large models and datasets on a single machine. To address these issues, distributed deep learning training has become increasingly important. However, distributed training requires synchronization among nodes, and the mini-batch stochastic gradient descent algorithm places a significant load on network connections. A possible solution to tackle the synchronization bottleneck is to reduce a message size by lossy compression.\r\n\r\nIn this thesis, we investigate systems and algorithmic approaches to communication compression during training. From the systems perspective, we demonstrate that a common approach of expensive hardware overprovisioning can be replaced through a thorough system design. We introduce a framework that introduces efficient software support for compressed communication in machine learning applications, applicable to both multi-GPU single-node training and larger-scale multi-node training. Our framework integrates with popular ML frameworks, providing up to 3x speedups for multi-GPU nodes based on commodity hardware and order-of-magnitude improvements in the multi-node setting, with negligible impact on accuracy.\r\n\r\nAlso, we consider an application of our framework to different communication schemes, such as Fully Sharded Data Parallel. We provide strong convergence guarantees for the compression in such a setup. Empirical validation shows that our method preserves model accuracy for GPT-family models with up to 1.3 billion parameters, while completely removing the communication bottlenecks of non-compressed alternatives, providing up to 2.2x speedups end-to-end.\r\n\r\nFrom the algorithmic side, we propose a general framework that dynamically adjusts the degree of compression across a model's layers during training. This approach enhances overall compression and results in significant speedups without compromising accuracy. Our algorithm utilizes an adaptive algorithm that automatically selects the optimal compression parameters for model layers, ensuring the best compression ratio while adhering to an error constraint. Our method is effective across all existing families of compression methods. It achieves up to 2.5x faster training and up to a 5x improvement in compression compared to efficient implementations of current approaches. Additionally, LGreCo can complement existing adaptive algorithms.\r\n","lang":"eng"}],"language":[{"iso":"eng"}],"citation":{"chicago":"Markov, Ilia. “Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17490\">https://doi.org/10.15479/at:ista:17490</a>.","short":"I. Markov, Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective, Institute of Science and Technology Austria, 2024.","mla":"Markov, Ilia. <i>Communication-Efficient Distributed Training of Deep Neural Networks : An Algorithms and Systems Perspective</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17490\">10.15479/at:ista:17490</a>.","ista":"Markov I. 2024. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. Institute of Science and Technology Austria.","ama":"Markov I. Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17490\">10.15479/at:ista:17490</a>","ieee":"I. Markov, “Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective,” Institute of Science and Technology Austria, 2024.","apa":"Markov, I. (2024). <i>Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17490\">https://doi.org/10.15479/at:ista:17490</a>"},"ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","title":"Communication-efficient distributed training of deep neural networks : An algorithms and systems perspective","oa":1,"day":"04","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"article_processing_charge":"No","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:17490","file":[{"file_size":43327753,"file_name":"Thesis.zip","file_id":"17491","date_updated":"2024-09-04T08:35:35Z","checksum":"77609f4835d2730e46fa0d42d9134ed9","access_level":"closed","creator":"imarkov","relation":"source_file","content_type":"application/x-zip-compressed","date_created":"2024-09-04T08:35:35Z"},{"access_level":"open_access","creator":"imarkov","relation":"main_file","content_type":"application/pdf","date_created":"2024-09-04T08:36:06Z","file_size":2756082,"file_name":"Thesis_final_version_pdfa2.pdf","file_id":"17492","date_updated":"2024-09-04T08:36:06Z","success":1,"checksum":"9e68f7217570f756ceb8f70b980938cd"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","supervisor":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"_id":"17490","date_published":"2024-09-04T00:00:00Z"},{"author":[{"first_name":"Benoît","last_name":"Vermersch","full_name":"Vermersch, Benoît"},{"orcid":"0000-0003-0038-7068","first_name":"Marko","last_name":"Ljubotina","full_name":"Ljubotina, Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"first_name":"J. Ignacio","last_name":"Cirac","full_name":"Cirac, J. Ignacio"},{"full_name":"Zoller, Peter","last_name":"Zoller","first_name":"Peter"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"first_name":"Lorenzo","last_name":"Piroli","full_name":"Piroli, Lorenzo"}],"file_date_updated":"2024-09-05T09:39:00Z","publication_status":"published","year":"2024","month":"08","volume":14,"issue":"3","has_accepted_license":"1","external_id":{"isi":["001299667100002"],"arxiv":["2311.08108"]},"status":"public","abstract":[{"text":"Estimating global properties of many-body quantum systems such as entropy or bipartite entanglement is a notoriously difficult task, typically requiring a number of measurements or classical postprocessing resources growing exponentially in the system size. In this work, we address the problem of estimating global entropies and mixed-state entanglement via partial-transposed (PT) moments and show that efficient estimation strategies exist under the assumption that all the spatial correlation lengths are finite. Focusing on one-dimensional systems, we identify a set of approximate factorization conditions (AFCs) on the system density matrix, which allow us to reconstruct entropies and PT moments from information on local subsystems. This identification yields a simple and efficient strategy for entropy and entanglement estimation. Our method could be implemented in different ways, depending on how information on local subsystems is extracted. Focusing on randomized measurements providing a practical and common measurement scheme, we prove that our protocol requires only polynomially many measurements and postprocessing operations, assuming that the state to be measured satisfies the AFCs. We prove that the AFCs hold for finite-depth quantum-circuit states and translation-invariant matrix-product density operators and provide numerical evidence that they are satisfied in more general, physically interesting cases, including thermal states of local Hamiltonians. We argue that our method could be practically useful to detect bipartite mixed-state entanglement for large numbers of qubits available in today’s quantum platforms.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","scopus_import":"1","date_created":"2024-09-04T18:57:11Z","publication":"Physical Review X","language":[{"iso":"eng"}],"article_type":"original","DOAJ_listed":"1","citation":{"apa":"Vermersch, B., Ljubotina, M., Cirac, J. I., Zoller, P., Serbyn, M., &#38; Piroli, L. (2024). Many-body entropies and entanglement from polynomially many local measurements. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.14.031035\">https://doi.org/10.1103/physrevx.14.031035</a>","ama":"Vermersch B, Ljubotina M, Cirac JI, Zoller P, Serbyn M, Piroli L. Many-body entropies and entanglement from polynomially many local measurements. <i>Physical Review X</i>. 2024;14(3). doi:<a href=\"https://doi.org/10.1103/physrevx.14.031035\">10.1103/physrevx.14.031035</a>","ista":"Vermersch B, Ljubotina M, Cirac JI, Zoller P, Serbyn M, Piroli L. 2024. Many-body entropies and entanglement from polynomially many local measurements. Physical Review X. 14(3), 031035.","ieee":"B. Vermersch, M. Ljubotina, J. I. Cirac, P. Zoller, M. Serbyn, and L. Piroli, “Many-body entropies and entanglement from polynomially many local measurements,” <i>Physical Review X</i>, vol. 14, no. 3. American Physical Society, 2024.","mla":"Vermersch, Benoît, et al. “Many-Body Entropies and Entanglement from Polynomially Many Local Measurements.” <i>Physical Review X</i>, vol. 14, no. 3, 031035, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/physrevx.14.031035\">10.1103/physrevx.14.031035</a>.","short":"B. Vermersch, M. Ljubotina, J.I. Cirac, P. Zoller, M. Serbyn, L. Piroli, Physical Review X 14 (2024).","chicago":"Vermersch, Benoît, Marko Ljubotina, J. Ignacio Cirac, Peter Zoller, Maksym Serbyn, and Lorenzo Piroli. “Many-Body Entropies and Entanglement from Polynomially Many Local Measurements.” <i>Physical Review X</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/physrevx.14.031035\">https://doi.org/10.1103/physrevx.14.031035</a>."},"ec_funded":1,"arxiv":1,"ddc":["530"],"date_updated":"2025-09-08T09:04:14Z","intvolume":"        14","OA_place":"publisher","OA_type":"gold","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2160-3308"]},"APC_amount":"4863,6 EUR","article_processing_charge":"Yes","title":"Many-body entropies and entanglement from polynomially many local measurements","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MaSe"}],"day":"26","article_number":"031035","date_published":"2024-08-26T00:00:00Z","_id":"17493","quality_controlled":"1","publisher":"American Physical Society","isi":1,"file":[{"date_created":"2024-09-05T09:39:00Z","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","relation":"main_file","file_name":"2024_PhysRevX_Vermersch.pdf","file_id":"17532","date_updated":"2024-09-05T09:39:00Z","checksum":"1b114acc89025120727200681e4e9074","success":1,"file_size":1408836}],"doi":"10.1103/physrevx.14.031035","acknowledgement":"B. V. acknowledges funding from the Austrian Science Foundation (Grant No. FWF, P 32597 N), from the French National Research Agency via the JCJC project QRand (Grant No. ANR-20-CE47-0005), and via the research programs Plan France 2030 EPIQ (Grant No. ANR-22-PETQ-0007), QUBITAF (Grant No. ANR-22-PETQ-0004), and HQI (Grant No. ANR-22-PNCQ-0002). M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). M. S. acknowledges the hospitality of KITP supported in part by the National Science Foundation under Grants No. NSF PHY-1748958 and No. NSF PHY-2309135. J. I. C. is supported by the Hightech Agenda Bayern Plus through the Munich Quantum Valley and the German Federal Ministry of Education and Research through EQUAHUMO (Grant No. 13N16066). P. Z. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 101113690 (PASQuanS2.1)."},{"quality_controlled":"1","_id":"17494","date_published":"2024-10-01T00:00:00Z","publisher":"Taylor & Francis","acknowledgement":"I would like to thank K Kiernan for insightful comments and feedback. J P K Bravo is supported by IST Austria.","doi":"10.1080/17460913.2024.2389720","isi":1,"publication_identifier":{"issn":["1746-0913"],"eissn":["1746-0921"]},"article_processing_charge":"No","department":[{"_id":"JaBr"}],"day":"01","oa":1,"title":"Anti-plasmid immunity: A key to pathogen success?","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Bravo JPK. Anti-plasmid immunity: A key to pathogen success? <i>Future Microbiology</i>. 2024;19(15):1269-1272. doi:<a href=\"https://doi.org/10.1080/17460913.2024.2389720\">10.1080/17460913.2024.2389720</a>","ieee":"J. P. K. Bravo, “Anti-plasmid immunity: A key to pathogen success?,” <i>Future Microbiology</i>, vol. 19, no. 15. Taylor &#38; Francis, pp. 1269–1272, 2024.","ista":"Bravo JPK. 2024. Anti-plasmid immunity: A key to pathogen success? Future Microbiology. 19(15), 1269–1272.","apa":"Bravo, J. P. K. (2024). Anti-plasmid immunity: A key to pathogen success? <i>Future Microbiology</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/17460913.2024.2389720\">https://doi.org/10.1080/17460913.2024.2389720</a>","short":"J.P.K. Bravo, Future Microbiology 19 (2024) 1269–1272.","mla":"Bravo, Jack Peter Kelly. “Anti-Plasmid Immunity: A Key to Pathogen Success?” <i>Future Microbiology</i>, vol. 19, no. 15, Taylor &#38; Francis, 2024, pp. 1269–72, doi:<a href=\"https://doi.org/10.1080/17460913.2024.2389720\">10.1080/17460913.2024.2389720</a>.","chicago":"Bravo, Jack Peter Kelly. “Anti-Plasmid Immunity: A Key to Pathogen Success?” <i>Future Microbiology</i>. Taylor &#38; Francis, 2024. <a href=\"https://doi.org/10.1080/17460913.2024.2389720\">https://doi.org/10.1080/17460913.2024.2389720</a>."},"article_type":"letter_note","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","external_id":{"pmid":["39230568"],"isi":["001306115400001"]},"date_created":"2024-09-05T07:32:00Z","publication":"Future Microbiology","oa_version":"Published Version","scopus_import":"1","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1080/17460913.2024.2389720","open_access":"1"}],"corr_author":"1","OA_type":"free access","date_updated":"2026-06-18T17:56:59Z","ddc":["570"],"intvolume":"        19","OA_place":"publisher","page":"1269-1272","pmid":1,"author":[{"full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","last_name":"Bravo"}],"month":"10","issue":"15","volume":19,"publication_status":"published","year":"2024"},{"ddc":["570"],"date_updated":"2026-04-07T13:25:01Z","OA_place":"publisher","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"}],"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design."}],"corr_author":"1","type":"dissertation","oa_version":"Published Version","date_created":"2024-09-06T12:57:44Z","language":[{"iso":"eng"}],"citation":{"chicago":"Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>.","apa":"Gonzalez Somermeyer, L. (2024). <i>Fitness landscapes of orthologous green fluorescent proteins</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17850\">https://doi.org/10.15479/at:ista:17850</a>","ieee":"L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024.","ama":"Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>","ista":"Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria.","mla":"Gonzalez Somermeyer, Louisa. <i>Fitness Landscapes of Orthologous Green Fluorescent Proteins</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17850\">10.15479/at:ista:17850</a>.","short":"L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024."},"ec_funded":1,"publication_status":"published","file_date_updated":"2024-09-27T10:34:34Z","year":"2024","month":"09","related_material":{"link":[{"relation":"software","url":"https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks"}],"record":[{"relation":"part_of_dissertation","status":"public","id":"11448"}]},"author":[{"last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"alternative_title":["ISTA Thesis"],"page":"89","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","file":[{"content_type":"application/pdf","date_created":"2024-09-27T10:32:33Z","access_level":"open_access","relation":"main_file","creator":"lgonzale","date_updated":"2024-09-27T10:32:33Z","file_name":"louisa_thesis_draft__240904b.pdf","file_id":"18151","checksum":"d3303724e8d3c91321d71bbad4062048","file_size":11219837},{"date_created":"2024-09-27T10:34:34Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","creator":"lgonzale","relation":"source_file","file_name":"louisa_thesis_draft__240904b.docx","file_id":"18152","date_updated":"2024-09-27T10:34:34Z","checksum":"22e63f7f9014dffde2af7a47e7d1d014","file_size":43338677}],"doi":"10.15479/at:ista:17850","supervisor":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694"}],"_id":"17850","date_published":"2024-09-06T00:00:00Z","title":"Fitness landscapes of orthologous green fluorescent proteins","oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"day":"06","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No"},{"department":[{"_id":"EM-Fac"}],"day":"29","oa":1,"title":"The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["2041-1723"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","publisher":"Springer Nature","acknowledgement":"We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit, Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae, Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus de la Cruz for sharing strains or providing antibodies. We thank the members of the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. This research was funded in whole, or in part, by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451] and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","doi":"10.1038/s41467-024-51754-3","file":[{"content_type":"application/pdf","date_created":"2024-09-09T08:56:12Z","relation":"main_file","creator":"dernst","access_level":"open_access","success":1,"checksum":"7c044538a47182c826d1b526c52958a2","date_updated":"2024-09-09T08:56:12Z","file_id":"17946","file_name":"2024_NatureComm_Kofler.pdf","file_size":3735024}],"isi":1,"article_number":"7511","_id":"17885","date_published":"2024-08-29T00:00:00Z","quality_controlled":"1","month":"08","volume":15,"publication_status":"published","file_date_updated":"2024-09-09T08:56:12Z","year":"2024","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"author":[{"first_name":"Lisa","last_name":"Kofler","full_name":"Kofler, Lisa"},{"first_name":"Lorenz","last_name":"Grundmann","full_name":"Grundmann, Lorenz"},{"full_name":"Gerhalter, Magdalena","last_name":"Gerhalter","first_name":"Magdalena"},{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"full_name":"Merl-Pham, Juliane","first_name":"Juliane","last_name":"Merl-Pham"},{"last_name":"Zisser","first_name":"Gertrude","full_name":"Zisser, Gertrude"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3904-947X","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Vareka, Martin","last_name":"Vareka","first_name":"Martin"},{"full_name":"Breinbauer, Rolf","last_name":"Breinbauer","first_name":"Rolf"},{"last_name":"Hauck","first_name":"Stefanie M.","full_name":"Hauck, Stefanie M."},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"first_name":"Helmut","last_name":"Bergler","full_name":"Bergler, Helmut"}],"OA_type":"gold","date_updated":"2025-09-08T09:13:01Z","ddc":["570"],"intvolume":"        15","OA_place":"publisher","article_type":"original","citation":{"short":"L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser, I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach, H. Bergler, Nature Communications 15 (2024).","mla":"Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” <i>Nature Communications</i>, vol. 15, 7511, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-51754-3\">10.1038/s41467-024-51754-3</a>.","ista":"Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 15, 7511.","ama":"Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-51754-3\">10.1038/s41467-024-51754-3</a>","ieee":"L. Kofler <i>et al.</i>, “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-51754-3\">https://doi.org/10.1038/s41467-024-51754-3</a>","chicago":"Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-51754-3\">https://doi.org/10.1038/s41467-024-51754-3</a>."},"DOAJ_listed":"1","language":[{"iso":"eng"}],"abstract":[{"text":"The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.","lang":"eng"}],"external_id":{"pmid":["39209816"],"isi":["001457895200001"]},"status":"public","has_accepted_license":"1","date_created":"2024-09-08T22:01:10Z","publication":"Nature Communications","oa_version":"Published Version","scopus_import":"1","type":"journal_article"},{"pmid":1,"author":[{"last_name":"Zendrikov","first_name":"Dmitrii","full_name":"Zendrikov, Dmitrii"},{"last_name":"Paraskevov","first_name":"Alexander","id":"d05e3c56-9262-11ed-9231-be692464e5ac","full_name":"Paraskevov, Alexander"}],"month":"12","volume":180,"file_date_updated":"2025-01-13T08:26:08Z","publication_status":"published","year":"2024","language":[{"iso":"eng"}],"citation":{"chicago":"Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” <i>Neural Networks</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neunet.2024.106589\">https://doi.org/10.1016/j.neunet.2024.106589</a>.","mla":"Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” <i>Neural Networks</i>, vol. 180, 106589, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.neunet.2024.106589\">10.1016/j.neunet.2024.106589</a>.","short":"D. Zendrikov, A. Paraskevov, Neural Networks 180 (2024).","apa":"Zendrikov, D., &#38; Paraskevov, A. (2024). The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. <i>Neural Networks</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neunet.2024.106589\">https://doi.org/10.1016/j.neunet.2024.106589</a>","ama":"Zendrikov D, Paraskevov A. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. <i>Neural Networks</i>. 2024;180. doi:<a href=\"https://doi.org/10.1016/j.neunet.2024.106589\">10.1016/j.neunet.2024.106589</a>","ista":"Zendrikov D, Paraskevov A. 2024. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. 180, 106589.","ieee":"D. Zendrikov and A. Paraskevov, “The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks,” <i>Neural Networks</i>, vol. 180. Elsevier, 2024."},"article_type":"original","ec_funded":1,"has_accepted_license":"1","external_id":{"pmid":["39217864"],"isi":["001316474600001"]},"status":"public","abstract":[{"lang":"eng","text":"Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatially-embedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: (1) the network distribution of neuronal excitability, (2) the distribution of connections between neurons of the network, and (3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models."}],"type":"journal_article","corr_author":"1","oa_version":"Published Version","date_created":"2024-09-08T22:01:10Z","scopus_import":"1","publication":"Neural Networks","project":[{"grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"}],"OA_type":"hybrid","ddc":["570"],"date_updated":"2025-09-08T09:12:20Z","OA_place":"publisher","intvolume":"       180","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["0893-6080"],"eissn":["1879-2782"]},"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"TiVo"}],"day":"01","title":"The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"106589","date_published":"2024-12-01T00:00:00Z","_id":"17886","quality_controlled":"1","publisher":"Elsevier","file":[{"file_size":6162281,"date_updated":"2025-01-13T08:26:08Z","file_name":"2024_NeuralNetworks_Zendrikov.pdf","file_id":"18825","success":1,"checksum":"6a194323234e01d4ae725f674529cdb1","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_created":"2025-01-13T08:26:08Z"}],"acknowledgement":"A.P. is grateful to Chaitanya Chintaluri, Douglas Feitosa Tomé, and Tim P. Vogels for useful discussions. This work was supported by a European Research Council Consolidator Grant (SYNAPSEEK, 819603, to Tim P. Vogels).","doi":"10.1016/j.neunet.2024.106589","isi":1}]