[{"ec_funded":1,"day":"13","publication_status":"published","acknowledgement":"We would like to thank Raimel A. Medina, Hansveer Singh, and Dmitry Abanin for useful\r\ndiscussions.The authors acknowledge support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). We acknowledge support by the Erwin Schrödinger International\r\nInstitute for Mathematics and Physics (ESI).","month":"09","related_material":{"record":[{"relation":"earlier_version","id":"12750","status":"public"}]},"abstract":[{"text":"Quantum kinetically constrained models have recently attracted significant attention due to their anomalous dynamics and thermalization. In this work, we introduce a hitherto unexplored family of kinetically constrained models featuring conserved particle number and strong inversion-symmetry breaking due to facilitated hopping. We demonstrate that these models provide a generic example of so-called quantum Hilbert space fragmentation, that is manifested in disconnected sectors in the Hilbert space that are not apparent in the computational basis. Quantum Hilbert space fragmentation leads to an exponential in system size number of eigenstates with exactly zero entanglement entropy across several bipartite cuts. These eigenstates can be probed dynamically using quenches from simple initial product states. In addition, we study the particle spreading under unitary dynamics launched from the domain wall state, and find faster than diffusive dynamics at high particle densities, that crosses over into logarithmically slow relaxation at smaller densities. Using a classically simulable cellular automaton, we reproduce the logarithmic dynamics observed in the quantum case. Our work suggests that particle conserving constrained models with inversion symmetry breaking realize so far unexplored dynamical behavior and invite their further theoretical and experimental studies.","lang":"eng"}],"doi":"10.21468/scipostphys.15.3.093","issue":"3","publication_identifier":{"issn":["2542-4653"]},"status":"public","arxiv":1,"language":[{"iso":"eng"}],"article_type":"original","intvolume":"        15","article_number":"093","publisher":"SciPost Foundation","author":[{"full_name":"Brighi, Pietro","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","last_name":"Brighi"},{"last_name":"Ljubotina","orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","first_name":"Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"ama":"Brighi P, Ljubotina M, Serbyn M. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. 2023;15(3). doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>","short":"P. Brighi, M. Ljubotina, M. Serbyn, SciPost Physics 15 (2023).","chicago":"Brighi, Pietro, Marko Ljubotina, and Maksym Serbyn. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>. SciPost Foundation, 2023. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>.","ieee":"P. Brighi, M. Ljubotina, and M. Serbyn, “Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models,” <i>SciPost Physics</i>, vol. 15, no. 3. SciPost Foundation, 2023.","ista":"Brighi P, Ljubotina M, Serbyn M. 2023. Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. SciPost Physics. 15(3), 093.","apa":"Brighi, P., Ljubotina, M., &#38; Serbyn, M. (2023). Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">https://doi.org/10.21468/scipostphys.15.3.093</a>","mla":"Brighi, Pietro, et al. “Hilbert Space Fragmentation and Slow Dynamics in Particle-Conserving Quantum East Models.” <i>SciPost Physics</i>, vol. 15, no. 3, 093, SciPost Foundation, 2023, doi:<a href=\"https://doi.org/10.21468/scipostphys.15.3.093\">10.21468/scipostphys.15.3.093</a>."},"department":[{"_id":"MaSe"}],"file":[{"date_updated":"2023-09-20T10:46:10Z","content_type":"application/pdf","file_size":4866506,"file_name":"2023_SciPostPhysics_Brighi.pdf","file_id":"14350","success":1,"date_created":"2023-09-20T10:46:10Z","access_level":"open_access","creator":"dernst","checksum":"4cef6a8021f6b6c47ab2f2f2b1387ac2","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2023-09-20T10:46:29Z","type":"journal_article","file_date_updated":"2023-09-20T10:46:10Z","external_id":{"arxiv":["2210.15607"]},"_id":"14334","article_processing_charge":"No","volume":15,"publication":"SciPost Physics","year":"2023","date_created":"2023-09-14T13:08:23Z","ddc":["530"],"quality_controlled":"1","date_published":"2023-09-13T00:00:00Z","title":"Hilbert space fragmentation and slow dynamics in particle-conserving quantum East models","keyword":["General Physics and Astronomy"],"project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"doi":"10.1038/s41477-023-01478-x","abstract":[{"text":"Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.","lang":"eng"}],"publication_identifier":{"issn":["2055-0278"]},"pmid":1,"status":"public","day":"01","acknowledgement":"We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.).","publication_status":"published","month":"09","isi":1,"publisher":"Springer Nature","language":[{"iso":"eng"}],"page":"1500-1513","article_type":"original","intvolume":"         9","file_date_updated":"2023-09-20T10:51:31Z","external_id":{"isi":["001069238800014"],"pmid":["37666965"]},"_id":"14339","oa":1,"author":[{"last_name":"Roychoudhry","first_name":"S","full_name":"Roychoudhry, S"},{"last_name":"Sageman-Furnas","first_name":"K","full_name":"Sageman-Furnas, K"},{"first_name":"C","full_name":"Wolverton, C","last_name":"Wolverton"},{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","last_name":"Grones"},{"orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","last_name":"Tan"},{"last_name":"Molnar","first_name":"Gergely","full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Angelis","first_name":"M","full_name":"De Angelis, M"},{"full_name":"Goodman, HL","first_name":"HL","last_name":"Goodman"},{"last_name":"Capstaff","full_name":"Capstaff, N","first_name":"N"},{"last_name":"JPB","first_name":"Lloyd","full_name":"JPB, Lloyd"},{"last_name":"Mullen","first_name":"J","full_name":"Mullen, J"},{"full_name":"Hangarter, R","first_name":"R","last_name":"Hangarter"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"S","full_name":"Kepinski, S","last_name":"Kepinski"}],"citation":{"mla":"Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>.","apa":"Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>","ista":"Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513.","ieee":"S. Roychoudhry <i>et al.</i>, “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” <i>Nature Plants</i>, vol. 9. Springer Nature, pp. 1500–1513, 2023.","chicago":"Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” <i>Nature Plants</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41477-023-01478-x\">https://doi.org/10.1038/s41477-023-01478-x</a>.","short":"S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513.","ama":"Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. <i>Nature Plants</i>. 2023;9:1500-1513. doi:<a href=\"https://doi.org/10.1038/s41477-023-01478-x\">10.1038/s41477-023-01478-x</a>"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-09-20T10:51:31Z","content_type":"application/pdf","file_size":9647103,"file_name":"2023_NaturePlants_Roychoudhry.pdf","file_id":"14351","success":1,"date_created":"2023-09-20T10:51:31Z","access_level":"open_access","creator":"dernst","checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","relation":"main_file"}],"department":[{"_id":"JiFr"}],"oa_version":"Published Version","date_updated":"2023-12-13T12:23:49Z","type":"journal_article","quality_controlled":"1","title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","date_published":"2023-09-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":9,"article_processing_charge":"Yes (in subscription journal)","publication":"Nature Plants","year":"2023","date_created":"2023-09-15T09:56:01Z","ddc":["580"]},{"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"},{"_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF","grant_number":"I04188","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids"}],"date_published":"2023-09-07T00:00:00Z","title":"Turbulence suppression by cardiac-cycle-inspired driving of pipe flow","quality_controlled":"1","date_created":"2023-09-17T22:01:09Z","year":"2023","publication":"Nature","volume":621,"article_processing_charge":"No","_id":"14341","external_id":{"pmid":["37673988"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-09-20T12:10:22Z","oa_version":"None","department":[{"_id":"BjHo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"D. Scarselli, J. M. Lopez Alonso, A. Varshney, and B. Hof, “Turbulence suppression by cardiac-cycle-inspired driving of pipe flow,” <i>Nature</i>, vol. 621, no. 7977. Springer Nature, pp. 71–74, 2023.","chicago":"Scarselli, Davide, Jose M Lopez Alonso, Atul Varshney, and Björn Hof. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>.","ama":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. 2023;621(7977):71-74. doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>","short":"D. Scarselli, J.M. Lopez Alonso, A. Varshney, B. Hof, Nature 621 (2023) 71–74.","apa":"Scarselli, D., Lopez Alonso, J. M., Varshney, A., &#38; Hof, B. (2023). Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06399-5\">https://doi.org/10.1038/s41586-023-06399-5</a>","mla":"Scarselli, Davide, et al. “Turbulence Suppression by Cardiac-Cycle-Inspired Driving of Pipe Flow.” <i>Nature</i>, vol. 621, no. 7977, Springer Nature, 2023, pp. 71–74, doi:<a href=\"https://doi.org/10.1038/s41586-023-06399-5\">10.1038/s41586-023-06399-5</a>.","ista":"Scarselli D, Lopez Alonso JM, Varshney A, Hof B. 2023. Turbulence suppression by cardiac-cycle-inspired driving of pipe flow. Nature. 621(7977), 71–74."},"author":[{"last_name":"Scarselli","orcid":"0000-0001-5227-4271","full_name":"Scarselli, Davide","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"publisher":"Springer Nature","intvolume":"       621","article_type":"original","page":"71-74","language":[{"iso":"eng"}],"status":"public","pmid":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"issue":"7977","abstract":[{"lang":"eng","text":"Flows through pipes and channels are, in practice, almost always turbulent, and the multiscale eddying motion is responsible for a major part of the encountered friction losses and pumping costs1. Conversely, for pulsatile flows, in particular for aortic blood flow, turbulence levels remain low despite relatively large peak velocities. For aortic blood flow, high turbulence levels are intolerable as they would damage the shear-sensitive endothelial cell layer2,3,4,5. Here we show that turbulence in ordinary pipe flow is diminished if the flow is driven in a pulsatile mode that incorporates all the key features of the cardiac waveform. At Reynolds numbers comparable to those of aortic blood flow, turbulence is largely inhibited, whereas at much higher speeds, the turbulent drag is reduced by more than 25%. This specific operation mode is more efficient when compared with steady driving, which is the present situation for virtually all fluid transport processes ranging from heating circuits to water, gas and oil pipelines."}],"doi":"10.1038/s41586-023-06399-5","related_material":{"link":[{"url":"https://www.ista.ac.at/en/news/pumping-like-the-heart/","relation":"press_release","description":"News on ISTA website"}]},"month":"09","publication_status":"published","acknowledgement":"We acknowledge the assistance of the Miba machine shop and the team of the ISTA-HPC cluster. We thank M. Quadrio for the discussions. The work was supported by the Simons Foundation (grant no. 662960) and by the Austrian Science Fund (grant no. I4188-N30), within Deutsche Forschungsgemeinschaft research unit FOR 2688.","day":"07"},{"publisher":"AIP Publishing","article_type":"original","intvolume":"       123","article_number":"091104","language":[{"iso":"eng"}],"arxiv":1,"publication_identifier":{"issn":["0003-6951"]},"status":"public","doi":"10.1063/5.0161713","abstract":[{"text":"We propose a simple method to measure nonlinear Kerr refractive index in mid-infrared frequency range that avoids using sophisticated infrared detectors. Our approach is based on using a near-infrared probe beam which interacts with a mid-IR beam via wavelength-non-degenerate cross-phase modulation (XPM). By carefully measuring XPM-induced spectral modifications in the probe beam and comparing the experimental data with simulation results, we extract the value for the non-degenerate Kerr index. Finally, in order to obtain the value of degenerate mid-IR Kerr index, we use the well-established two-band formalism of Sheik-Bahae et al., which is shown to become particularly simple in the limit of low frequencies. The proposed technique is complementary to the conventional techniques, such as z-scan, and has the advantage of not requiring any mid-infrared detectors.","lang":"eng"}],"issue":"9","month":"08","day":"28","publication_status":"published","acknowledgement":"The work was supported by IST Austria. The authors would like to gratefully acknowledge the help and assistance of Professor John M. Dudley.","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","title":"Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam","date_published":"2023-08-28T00:00:00Z","date_created":"2023-09-17T22:01:09Z","ddc":["530"],"article_processing_charge":"Yes (in subscription journal)","volume":123,"publication":"Applied Physics Letters","year":"2023","_id":"14342","scopus_import":"1","file_date_updated":"2023-09-20T11:36:16Z","external_id":{"arxiv":["2306.09043"]},"type":"journal_article","author":[{"last_name":"Lorenc","first_name":"Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan"},{"orcid":"0000-0002-7183-5203","first_name":"Zhanybek","full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>, vol. 123, no. 9, 091104, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>.","apa":"Lorenc, D., &#38; Alpichshev, Z. (2023). Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>","ista":"Lorenc D, Alpichshev Z. 2023. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. Applied Physics Letters. 123(9), 091104.","chicago":"Lorenc, Dusan, and Zhanybek Alpichshev. “Mid-Infrared Kerr Index Evaluation via Cross-Phase Modulation with a near-Infrared Probe Beam.” <i>Applied Physics Letters</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0161713\">https://doi.org/10.1063/5.0161713</a>.","ama":"Lorenc D, Alpichshev Z. Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam. <i>Applied Physics Letters</i>. 2023;123(9). doi:<a href=\"https://doi.org/10.1063/5.0161713\">10.1063/5.0161713</a>","short":"D. Lorenc, Z. Alpichshev, Applied Physics Letters 123 (2023).","ieee":"D. Lorenc and Z. Alpichshev, “Mid-infrared Kerr index evaluation via cross-phase modulation with a near-infrared probe beam,” <i>Applied Physics Letters</i>, vol. 123, no. 9. AIP Publishing, 2023."},"has_accepted_license":"1","department":[{"_id":"ZhAl"}],"file":[{"file_name":"2023_ApplPhysLetter_Lorenc.pdf","date_updated":"2023-09-20T11:36:16Z","content_type":"application/pdf","file_size":1486715,"access_level":"open_access","file_id":"14353","success":1,"date_created":"2023-09-20T11:36:16Z","checksum":"89a1b604d58b209fec66c6b6f919ac98","relation":"main_file","creator":"dernst"}],"date_updated":"2023-09-20T11:50:06Z","oa_version":"Published Version"},{"publisher":"Cambridge University Press","language":[{"iso":"eng"}],"arxiv":1,"article_type":"original","intvolume":"        11","article_number":"e74","doi":"10.1017/fms.2023.70","abstract":[{"text":"The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation.","lang":"eng"}],"publication_identifier":{"eissn":["2050-5094"]},"status":"public","ec_funded":1,"day":"23","publication_status":"published","acknowledgement":"G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.","month":"08","isi":1,"quality_controlled":"1","title":"Gaussian fluctuations in the equipartition principle for Wigner matrices","date_published":"2023-08-23T00:00:00Z","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","volume":11,"publication":"Forum of Mathematics, Sigma","year":"2023","date_created":"2023-09-17T22:01:09Z","ddc":["510"],"scopus_import":"1","file_date_updated":"2023-09-20T11:09:35Z","external_id":{"arxiv":["2301.05181"],"isi":["001051980200001"]},"_id":"14343","author":[{"last_name":"Cipolloni","orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","last_name":"Erdös"},{"last_name":"Henheik","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X"},{"last_name":"Kolupaiev","first_name":"Oleksii","full_name":"Kolupaiev, Oleksii","id":"149b70d4-896a-11ed-bdf8-8c63fd44ca61"}],"oa":1,"citation":{"ista":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74.","mla":"Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>, vol. 11, e74, Cambridge University Press, 2023, doi:<a href=\"https://doi.org/10.1017/fms.2023.70\">10.1017/fms.2023.70</a>.","apa":"Cipolloni, G., Erdös, L., Henheik, S. J., &#38; Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2023.70\">https://doi.org/10.1017/fms.2023.70</a>","ieee":"G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” <i>Forum of Mathematics, Sigma</i>, vol. 11. Cambridge University Press, 2023.","short":"G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023).","ama":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. <i>Forum of Mathematics, Sigma</i>. 2023;11. doi:<a href=\"https://doi.org/10.1017/fms.2023.70\">10.1017/fms.2023.70</a>","chicago":"Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.1017/fms.2023.70\">https://doi.org/10.1017/fms.2023.70</a>."},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2023_ForumMathematics_Cipolloni.pdf","file_size":852652,"content_type":"application/pdf","date_updated":"2023-09-20T11:09:35Z","access_level":"open_access","success":1,"date_created":"2023-09-20T11:09:35Z","file_id":"14352","relation":"main_file","checksum":"eb747420e6a88a7796fa934151957676","creator":"dernst"}],"department":[{"_id":"LaEr"},{"_id":"GradSch"}],"date_updated":"2023-12-13T12:24:23Z","oa_version":"Published Version","type":"journal_article"},{"conference":{"end_date":"2023-01-25","start_date":"2023-01-22","location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms"},"quality_controlled":"1","title":"Fast algorithms for solving the Hamilton cycle problem with high probability","date_published":"2023-01-01T00:00:00Z","date_created":"2023-09-17T22:01:10Z","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","article_processing_charge":"No","volume":2023,"year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2111.14759"}],"_id":"14344","scopus_import":"1","external_id":{"arxiv":["2111.14759"]},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Anastos M. 2023. Fast algorithms for solving the Hamilton cycle problem with high probability. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2023, 2286–2323.","apa":"Anastos, M. (2023). Fast algorithms for solving the Hamilton cycle problem with high probability. In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2023, pp. 2286–2323). Florence, Italy: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>","mla":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2023, Society for Industrial and Applied Mathematics, 2023, pp. 2286–323, doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>.","ama":"Anastos M. Fast algorithms for solving the Hamilton cycle problem with high probability. In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2023. Society for Industrial and Applied Mathematics; 2023:2286-2323. doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">10.1137/1.9781611977554.ch88</a>","short":"M. Anastos, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 2286–2323.","chicago":"Anastos, Michael. “Fast Algorithms for Solving the Hamilton Cycle Problem with High Probability.” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2023:2286–2323. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/1.9781611977554.ch88\">https://doi.org/10.1137/1.9781611977554.ch88</a>.","ieee":"M. Anastos, “Fast algorithms for solving the Hamilton cycle problem with high probability,” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Florence, Italy, 2023, vol. 2023, pp. 2286–2323."},"author":[{"first_name":"Michael","full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","last_name":"Anastos"}],"oa":1,"oa_version":"Preprint","date_updated":"2023-09-25T09:13:41Z","department":[{"_id":"MaKw"}],"publisher":"Society for Industrial and Applied Mathematics","page":"2286-2323","intvolume":"      2023","arxiv":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781611977554"]},"status":"public","abstract":[{"text":"We study the Hamilton cycle problem with input a random graph G ~ G(n,p) in two different settings. In the first one, G is given to us in the form of randomly ordered adjacency lists while in the second one, we are given the adjacency matrix of G. In each of the two settings we derive a deterministic algorithm that w.h.p. either finds a Hamilton cycle or returns a certificate that such a cycle does not exist for p = p(n) ≥ 0. The running times of our algorithms are O(n) and  respectively, each being best possible in its own setting.","lang":"eng"}],"doi":"10.1137/1.9781611977554.ch88","month":"01","day":"01","publication_status":"published"},{"author":[{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Garber","full_name":"Garber, Alexey","first_name":"Alexey"},{"last_name":"Ghafari","full_name":"Ghafari, Mohadese","first_name":"Mohadese"},{"orcid":"0000-0002-1780-2689","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","full_name":"Heiss, Teresa","first_name":"Teresa","last_name":"Heiss"},{"id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza","first_name":"Morteza","last_name":"Saghafian"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. 2023. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry.","mla":"Edelsbrunner, Herbert, et al. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” <i>Discrete and Computational Geometry</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00454-023-00566-1\">10.1007/s00454-023-00566-1</a>.","apa":"Edelsbrunner, H., Garber, A., Ghafari, M., Heiss, T., &#38; Saghafian, M. (2023). On angles in higher order Brillouin tessellations and related tilings in the plane. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00566-1\">https://doi.org/10.1007/s00454-023-00566-1</a>","ieee":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, and M. Saghafian, “On angles in higher order Brillouin tessellations and related tilings in the plane,” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023.","short":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, M. Saghafian, Discrete and Computational Geometry (2023).","ama":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. On angles in higher order Brillouin tessellations and related tilings in the plane. <i>Discrete and Computational Geometry</i>. 2023. doi:<a href=\"https://doi.org/10.1007/s00454-023-00566-1\">10.1007/s00454-023-00566-1</a>","chicago":"Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafari, Teresa Heiss, and Morteza Saghafian. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00566-1\">https://doi.org/10.1007/s00454-023-00566-1</a>."},"department":[{"_id":"HeEd"}],"date_updated":"2023-12-13T12:25:06Z","oa_version":"Published Version","type":"journal_article","scopus_import":"1","external_id":{"isi":["001060727600004"],"arxiv":["2204.01076"]},"_id":"14345","article_processing_charge":"Yes (via OA deal)","publication":"Discrete and Computational Geometry","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-023-00566-1"}],"year":"2023","date_created":"2023-09-17T22:01:10Z","quality_controlled":"1","date_published":"2023-09-07T00:00:00Z","title":"On angles in higher order Brillouin tessellations and related tilings in the plane","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"ec_funded":1,"day":"07","publication_status":"epub_ahead","acknowledgement":"Work by all authors but A. Garber is supported by the European Research Council (ERC), Grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), Grant No. I 02979-N35. Work by A. Garber is partially supported by the Alexander von Humboldt Foundation.","month":"09","isi":1,"doi":"10.1007/s00454-023-00566-1","abstract":[{"text":"For a locally finite set in R2, the order-k Brillouin tessellations form an infinite sequence of convex face-to-face tilings of the plane. If the set is coarsely dense and generic, then the corresponding infinite sequences of minimum and maximum angles are both monotonic in k. As an example, a stationary Poisson point process in R2  is locally finite, coarsely dense, and generic with probability one. For such a set, the distributions of angles in the Voronoi tessellations, Delaunay mosaics, and Brillouin tessellations are independent of the order and can be derived from the formula for angles in order-1 Delaunay mosaics given by Miles (Math. Biosci. 6, 85–127 (1970)).","lang":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"status":"public","arxiv":1,"language":[{"iso":"eng"}],"article_type":"original","publisher":"Springer Nature"},{"_id":"14360","external_id":{"pmid":["37704612"],"isi":["001087583700008"]},"scopus_import":"1","file_date_updated":"2023-09-25T08:22:58Z","type":"journal_article","file":[{"file_id":"14365","success":1,"date_created":"2023-09-25T08:22:58Z","access_level":"open_access","date_updated":"2023-09-25T08:22:58Z","content_type":"application/pdf","file_size":2725421,"file_name":"2023_NatureComm_Sitarska.pdf","creator":"dernst","checksum":"ad670e3b3c64fc585675948370f6b149","relation":"main_file"}],"department":[{"_id":"MiSi"}],"date_updated":"2023-12-21T14:30:01Z","oa_version":"Published Version","oa":1,"author":[{"last_name":"Sitarska","first_name":"Ewa","full_name":"Sitarska, Ewa"},{"first_name":"Silvia Dias","full_name":"Almeida, Silvia Dias","last_name":"Almeida"},{"last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold","first_name":"Marianne Sandvold"},{"last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","first_name":"Julian A"},{"full_name":"Czuchnowski, Jakub","first_name":"Jakub","last_name":"Czuchnowski"},{"last_name":"Siggel","full_name":"Siggel, Marc","first_name":"Marc"},{"last_name":"Roessner","full_name":"Roessner, Rita","first_name":"Rita"},{"last_name":"Tschanz","first_name":"Aline","full_name":"Tschanz, Aline"},{"full_name":"Ejsing, Christer","first_name":"Christer","last_name":"Ejsing"},{"full_name":"Schwab, Yannick","first_name":"Yannick","last_name":"Schwab"},{"full_name":"Kosinski, Jan","first_name":"Jan","last_name":"Kosinski"},{"full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"last_name":"Erzberger","first_name":"Anna","full_name":"Erzberger, Anna"},{"full_name":"Diz-Muñoz, Alba","first_name":"Alba","last_name":"Diz-Muñoz"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>.","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>","ieee":"E. Sitarska <i>et al.</i>, “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” <i>Nature Communications</i>, vol. 14, 5644, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41173-1\">10.1038/s41467-023-41173-1</a>.","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41173-1\">https://doi.org/10.1038/s41467-023-41173-1</a>","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","date_published":"2023-09-13T00:00:00Z","quality_controlled":"1","date_created":"2023-09-24T22:01:10Z","ddc":["570"],"year":"2023","article_processing_charge":"Yes (via OA deal)","volume":14,"publication":"Nature Communications","status":"public","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"doi":"10.1038/s41467-023-41173-1","month":"09","related_material":{"record":[{"id":"14697","relation":"dissertation_contains","status":"public"}]},"isi":1,"acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL.","publication_status":"published","day":"13","publisher":"Springer Nature","intvolume":"        14","article_number":"5644","article_type":"original","language":[{"iso":"eng"}]},{"month":"09","isi":1,"publication_status":"published","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","ec_funded":1,"day":"13","pmid":1,"status":"public","publication_identifier":{"eissn":["2041-1723"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"doi":"10.1038/s41467-023-41432-1","abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"intvolume":"        14","article_number":"5633","article_type":"original","language":[{"iso":"eng"}],"publisher":"Springer Nature","type":"journal_article","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"file":[{"relation":"main_file","checksum":"82d2d4ad736cc8493db8ce45cd313f7b","creator":"dernst","file_name":"2023_NatureComm_Riedl.pdf","file_size":2317272,"date_updated":"2023-09-25T08:32:37Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-09-25T08:32:37Z","success":1,"file_id":"14366"}],"oa_version":"Published Version","date_updated":"2023-12-13T12:29:41Z","oa":1,"author":[{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl"},{"last_name":"Mayer","first_name":"Isabelle D","full_name":"Mayer, Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>.","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., &#38; Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41432-1\">https://doi.org/10.1038/s41467-023-41432-1</a>","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” <i>Nature Communications</i>, vol. 14, 5633, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41432-1\">10.1038/s41467-023-41432-1</a>.","ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633."},"_id":"14361","external_id":{"isi":["001087583700030"],"pmid":["37704595"]},"scopus_import":"1","file_date_updated":"2023-09-25T08:32:37Z","date_created":"2023-09-24T22:01:10Z","ddc":["530","570"],"year":"2023","article_processing_charge":"Yes","volume":14,"publication":"Nature Communications","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-09-13T00:00:00Z","title":"Synchronization in collectively moving inanimate and living active matter","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"}],"quality_controlled":"1"},{"publication":"Theoretical Computer Science","article_processing_charge":"No","volume":977,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.08424 ","open_access":"1"}],"year":"2023","date_created":"2023-09-24T22:01:11Z","quality_controlled":"1","title":"Weakly weighted generalised quasi-metric spaces and semilattices","date_published":"2023-10-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Castellano, Ilaria, Anna Giordano Bruno, and Nicolò Zava. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>.","ama":"Castellano I, Giordano Bruno A, Zava N. Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. 2023;977. doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>","short":"I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977 (2023).","ieee":"I. Castellano, A. Giordano Bruno, and N. Zava, “Weakly weighted generalised quasi-metric spaces and semilattices,” <i>Theoretical Computer Science</i>, vol. 977. Elsevier, 2023.","apa":"Castellano, I., Giordano Bruno, A., &#38; Zava, N. (2023). Weakly weighted generalised quasi-metric spaces and semilattices. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">https://doi.org/10.1016/j.tcs.2023.114129</a>","mla":"Castellano, Ilaria, et al. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” <i>Theoretical Computer Science</i>, vol. 977, 114129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.tcs.2023.114129\">10.1016/j.tcs.2023.114129</a>.","ista":"Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129."},"oa":1,"author":[{"full_name":"Castellano, Ilaria","first_name":"Ilaria","last_name":"Castellano"},{"first_name":"Anna","full_name":"Giordano Bruno, Anna","last_name":"Giordano Bruno"},{"first_name":"Nicolò","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","full_name":"Zava, Nicolò","orcid":"0000-0001-8686-1888","last_name":"Zava"}],"oa_version":"Preprint","date_updated":"2024-01-30T13:22:04Z","department":[{"_id":"HeEd"}],"type":"journal_article","scopus_import":"1","external_id":{"arxiv":["2212.08424"],"isi":["001076934000001"]},"_id":"14362","language":[{"iso":"eng"}],"arxiv":1,"article_type":"original","article_number":"114129","intvolume":"       977","publisher":"Elsevier","day":"25","publication_status":"published","isi":1,"month":"10","abstract":[{"text":"Motivated by recent applications to entropy theory in dynamical systems, we generalise notions introduced by Matthews and define weakly weighted and componentwise weakly weighted (generalised) quasi-metrics. We then systematise and extend to full generality the correspondences between these objects and other structures arising in theoretical computer science and dynamics. In particular, we study the correspondences with weak partial metrics and, if the underlying space is a semilattice, with invariant (generalised) quasi-metrics satisfying the descending path condition, and with strictly monotone semi(-co-)valuations.\r\nWe conclude discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation of both the known intrinsic semilattice entropy and the semigroup entropy.","lang":"eng"}],"doi":"10.1016/j.tcs.2023.114129","publication_identifier":{"issn":["0304-3975"]},"status":"public"},{"external_id":{"pmid":["37731609"],"isi":["001080403500001"]},"file_date_updated":"2023-11-07T08:53:21Z","scopus_import":"1","_id":"14363","date_updated":"2023-12-13T12:27:30Z","oa_version":"Published Version","department":[{"_id":"SaSi"}],"file":[{"file_id":"14497","success":1,"date_created":"2023-11-07T08:53:21Z","access_level":"open_access","date_updated":"2023-11-07T08:53:21Z","content_type":"application/pdf","file_size":8197935,"file_name":"2023_iScience_Maes.pdf","creator":"dernst","checksum":"be1a560efdd96d20712311f4fc54aac2","relation":"main_file"}],"citation":{"apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., &#38; Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>","mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>, vol. 26, no. 10, 107780, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>.","ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780.","chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107780\">https://doi.org/10.1016/j.isci.2023.107780</a>.","ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. <i>iScience</i>. 2023;26(10). doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107780\">10.1016/j.isci.2023.107780</a>","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023).","ieee":"M. E. Maes <i>et al.</i>, “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” <i>iScience</i>, vol. 26, no. 10. Elsevier, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","oa":1,"author":[{"orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes"},{"last_name":"Colombo","full_name":"Colombo, Gloria","first_name":"Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902"},{"full_name":"Schoot Uiterkamp, Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","first_name":"Florianne E","last_name":"Schoot Uiterkamp"},{"last_name":"Sternberg","first_name":"Felix","full_name":"Sternberg, Felix"},{"last_name":"Venturino","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403"},{"first_name":"Elena E.","full_name":"Pohl, Elena E.","last_name":"Pohl"},{"last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"}],"type":"journal_article","date_published":"2023-10-20T00:00:00Z","title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2023","publication":"iScience","article_processing_charge":"Yes","volume":26,"ddc":["570"],"date_created":"2023-09-24T22:01:11Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"issue":"10","abstract":[{"text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies.","lang":"eng"}],"doi":"10.1016/j.isci.2023.107780","status":"public","pmid":1,"publication_identifier":{"eissn":["2589-0042"]},"acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","publication_status":"published","day":"20","isi":1,"month":"10","publisher":"Elsevier","language":[{"iso":"eng"}],"article_number":"107780","intvolume":"        26","article_type":"original"},{"external_id":{"arxiv":["1811.01421"],"isi":["001082972300004"]},"scopus_import":"1","_id":"14364","department":[{"_id":"DaAl"}],"date_updated":"2023-12-13T12:28:29Z","oa_version":"Preprint","oa":1,"author":[{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"last_name":"Zhu","id":"a2117c59-cee4-11ed-b9d0-874ecf0f8ac5","first_name":"Leqi","full_name":"Zhu, Leqi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. 2023;52(4):913-944. doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” <i>SIAM Journal on Computing</i>, vol. 52, no. 4. Society for Industrial and Applied Mathematics, pp. 913–944, 2023.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based proofs fail. SIAM Journal on Computing. 52(4), 913–944.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., &#38; Zhu, L. (2023). Why extension-based proofs fail. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1375851\">https://doi.org/10.1137/20M1375851</a>","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” <i>SIAM Journal on Computing</i>, vol. 52, no. 4, Society for Industrial and Applied Mathematics, 2023, pp. 913–44, doi:<a href=\"https://doi.org/10.1137/20M1375851\">10.1137/20M1375851</a>."},"type":"journal_article","title":"Why extension-based proofs fail","date_published":"2023-07-25T00:00:00Z","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","year":"2023","main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"volume":52,"article_processing_charge":"No","publication":"SIAM Journal on Computing","date_created":"2023-09-24T22:01:11Z","issue":"4","abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve -set agreement among  processes or approximate agreement on a cycle of length 4 among  processes in a wait-free manner in asynchronous models where processes communicate using objects that can be constructed from shared registers. However, it was unknown whether proofs based on simpler techniques were possible. We show that these impossibility results cannot be obtained by extension-based proofs in the iterated snapshot model and, hence, extension-based proofs are limited in power.","lang":"eng"}],"doi":"10.1137/20M1375851","status":"public","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"acknowledgement":"We would like to thank Valerie King, Toniann Pitassi, and Michael Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research was supported by the Natural Science and Engineering Research Council of Canada under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship, and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship; the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385, CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel corporations. Some of the work on this paper was done while Faith Ellen was visiting IST Austria.","publication_status":"published","ec_funded":1,"day":"25","month":"07","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6676"}]},"isi":1,"publisher":"Society for Industrial and Applied Mathematics","arxiv":1,"language":[{"iso":"eng"}],"intvolume":"        52","page":"913-944","article_type":"original"},{"citation":{"ista":"Roos B. 2023. Boundary superconductivity in BCS theory. Institute of Science and Technology Austria.","apa":"Roos, B. (2023). <i>Boundary superconductivity in BCS theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>","mla":"Roos, Barbara. <i>Boundary Superconductivity in BCS Theory</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>.","short":"B. Roos, Boundary Superconductivity in BCS Theory, Institute of Science and Technology Austria, 2023.","ama":"Roos B. Boundary superconductivity in BCS theory. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14374\">10.15479/at:ista:14374</a>","chicago":"Roos, Barbara. “Boundary Superconductivity in BCS Theory.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14374\">https://doi.org/10.15479/at:ista:14374</a>.","ieee":"B. Roos, “Boundary superconductivity in BCS theory,” Institute of Science and Technology Austria, 2023."},"has_accepted_license":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"author":[{"full_name":"Roos, Barbara","first_name":"Barbara","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","orcid":"0000-0002-9071-5880","last_name":"Roos"}],"date_updated":"2023-10-27T10:37:30Z","oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"file":[{"checksum":"ef039ffc3de2cb8dee5b14110938e9b6","relation":"main_file","creator":"broos","file_name":"phd-thesis-draft_pdfa_acrobat.pdf","date_updated":"2023-10-06T11:35:56Z","content_type":"application/pdf","file_size":2365702,"access_level":"open_access","file_id":"14398","date_created":"2023-10-06T11:35:56Z"},{"checksum":"81dcac33daeefaf0111db52f41bb1fd0","relation":"source_file","creator":"broos","file_name":"Version5.zip","date_updated":"2023-10-06T11:38:01Z","content_type":"application/x-zip-compressed","file_size":4691734,"access_level":"closed","file_id":"14399","date_created":"2023-10-06T11:38:01Z"}],"type":"dissertation","file_date_updated":"2023-10-06T11:38:01Z","_id":"14374","article_processing_charge":"No","year":"2023","ddc":["515","539"],"date_created":"2023-09-28T14:23:04Z","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"date_published":"2023-09-30T00:00:00Z","title":"Boundary superconductivity in BCS theory","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"day":"30","ec_funded":1,"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"13207","status":"public"},{"relation":"part_of_dissertation","id":"10850","status":"public"}]},"month":"09","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:14374","abstract":[{"text":"Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.\r\n\r\nBCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.\r\nFor Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.\r\n\r\nSecond, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap  in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.\r\n\r\nIn the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.","lang":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","status":"public","language":[{"iso":"eng"}],"page":"206","supervisor":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"publisher":"Institute of Science and Technology Austria"},{"department":[{"_id":"EdHa"}],"file":[{"creator":"dernst","checksum":"4fe5423403f2531753bcd9e0fea48e05","relation":"main_file","file_id":"14384","success":1,"date_created":"2023-10-03T07:46:36Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-10-03T07:46:36Z","file_size":8143264,"file_name":"2023_NatureComm_Ucar.pdf"}],"date_updated":"2023-12-13T12:31:05Z","oa_version":"Published Version","author":[{"last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","orcid":"0000-0003-0506-4217"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"full_name":"Tiilikainen, Emmi","first_name":"Emmi","last_name":"Tiilikainen"},{"full_name":"Liaqat, Inam","first_name":"Inam","last_name":"Liaqat"},{"last_name":"Jakobsson","full_name":"Jakobsson, Emma","first_name":"Emma"},{"last_name":"Nurmi","full_name":"Nurmi, Harri","first_name":"Harri"},{"last_name":"Vaahtomeri","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>, vol. 14, 5878, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>.","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., &#38; Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>","ista":"Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. 2023. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 14, 5878.","ieee":"M. C. Ucar <i>et al.</i>, “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-41456-7\">https://doi.org/10.1038/s41467-023-41456-7</a>.","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-41456-7\">10.1038/s41467-023-41456-7</a>","short":"M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023)."},"has_accepted_license":"1","type":"journal_article","external_id":{"pmid":["37735168"],"isi":["001075884500007"]},"scopus_import":"1","file_date_updated":"2023-10-03T07:46:36Z","_id":"14378","year":"2023","article_processing_charge":"Yes","volume":14,"publication":"Nature Communications","date_created":"2023-10-01T22:01:13Z","ddc":["570"],"date_published":"2023-09-21T00:00:00Z","title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","acknowledgement":"We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions. We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.), University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the support of Biocenter Finland. The AAVpreparations were produced at the Helsinki Virus (HelVi) Core.","ec_funded":1,"day":"21","month":"09","isi":1,"doi":"10.1038/s41467-023-41456-7","abstract":[{"lang":"eng","text":"Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization."}],"status":"public","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"intvolume":"        14","article_number":"5878","article_type":"original","publisher":"Springer Nature"},{"_id":"14379","scopus_import":"1","external_id":{"isi":["001083568900001"]},"type":"journal_article","author":[{"last_name":"Mahato","first_name":"Neelima","full_name":"Mahato, Neelima"},{"full_name":"Singh, Saurabh","first_name":"Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","last_name":"Singh"},{"last_name":"Faisal","full_name":"Faisal, Mohammad","first_name":"Mohammad"},{"first_name":"T. V.M.","full_name":"Sreekanth, T. V.M.","last_name":"Sreekanth"},{"full_name":"Majumder, Sutripto","first_name":"Sutripto","last_name":"Majumder"},{"first_name":"Kisoo","full_name":"Yoo, Kisoo","last_name":"Yoo"},{"last_name":"Kim","full_name":"Kim, Jonghoon","first_name":"Jonghoon"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mahato, Neelima, et al. “Polycrystalline Phases Grown In-Situ Engendering Unique Mechanism of Charge Storage in Polyaniline-Graphite Composite.” <i>Synthetic Metals</i>, vol. 299, 117463, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">10.1016/j.synthmet.2023.117463</a>.","apa":"Mahato, N., Singh, S., Faisal, M., Sreekanth, T. V. M., Majumder, S., Yoo, K., &#38; Kim, J. (2023). Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. <i>Synthetic Metals</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">https://doi.org/10.1016/j.synthmet.2023.117463</a>","ista":"Mahato N, Singh S, Faisal M, Sreekanth TVM, Majumder S, Yoo K, Kim J. 2023. Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. Synthetic Metals. 299, 117463.","ieee":"N. Mahato <i>et al.</i>, “Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite,” <i>Synthetic Metals</i>, vol. 299. Elsevier, 2023.","chicago":"Mahato, Neelima, Saurabh Singh, Mohammad Faisal, T. V.M. Sreekanth, Sutripto Majumder, Kisoo Yoo, and Jonghoon Kim. “Polycrystalline Phases Grown In-Situ Engendering Unique Mechanism of Charge Storage in Polyaniline-Graphite Composite.” <i>Synthetic Metals</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">https://doi.org/10.1016/j.synthmet.2023.117463</a>.","short":"N. Mahato, S. Singh, M. Faisal, T.V.M. Sreekanth, S. Majumder, K. Yoo, J. Kim, Synthetic Metals 299 (2023).","ama":"Mahato N, Singh S, Faisal M, et al. Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite. <i>Synthetic Metals</i>. 2023;299. doi:<a href=\"https://doi.org/10.1016/j.synthmet.2023.117463\">10.1016/j.synthmet.2023.117463</a>"},"department":[{"_id":"MaIb"}],"oa_version":"None","date_updated":"2024-01-30T13:55:50Z","quality_controlled":"1","date_published":"2023-11-01T00:00:00Z","title":"Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite","date_created":"2023-10-01T22:01:13Z","article_processing_charge":"No","volume":299,"publication":"Synthetic Metals","year":"2023","publication_identifier":{"issn":["0379-6779"]},"status":"public","abstract":[{"text":"We report on a simple surfactant/template free chemical route for the synthesis of semi-polycrystalline polyaniline-graphite (SPani-graphite) composite and its application as an electroactive material in electrochemical charge storage. The synthesized material exhibits well-defined poly-crystallographic lattices in high resolution transmission electron micrographs and sharp peaks in x-ray diffraction spectra suggesting crystalline nature of the material. The specific capacitance computed from the galvanostatic charge-discharge (GCD) data obtained from 3-electrode cell configuration using 1 M aq. Na2SO4 as an electrolyte was 111.4 F g−1 at a current density of 0.1 A g−1 which rises to 269 F g−1 at an elevated current density of 1.0 A g−1. A similar pattern of increase in the specific capacitance values with an increase in the current density was observed in the results obtained from 2-electrode symmetric device configuration using polymer gel electrolyte (xanthan gum in 1 M aq. Na2SO4). The specific capacitance computed from the GCD data obtained from the device configuration was 20 F g−1 at the current density of 1.0 A g−1. The device delivers an energy density of 1.7 Wh kg−1 and a power density of 2.48 kWh kg−1 at an applied current density of 0.5 A g−1 suggesting an excellent rate capability and power management. In addition, the device exhibits ⁓92 % specific capacitance retention up to 8000 continuous GCD cycles and ⁓80 % coulombic efficiency up to 10,000 continuous GCD cycles indicating excellent cycling stability. The unique feature of increasing specific capacitance with respect to applied current density is attributed to the presence of semi-polycrystalline phases in the SPani-graphite matrix. The material behaves as a surface redox supercapacitor and its unique mechanism of charge storage is discussed in detail in the article.","lang":"eng"}],"doi":"10.1016/j.synthmet.2023.117463","month":"11","isi":1,"day":"01","acknowledgement":"This work was supported by 2023 Yeungnam University Research Grant.","publication_status":"published","publisher":"Elsevier","article_type":"original","intvolume":"       299","article_number":"117463","language":[{"iso":"eng"}]},{"_id":"14400","external_id":{"arxiv":["2101.00834"],"isi":["001093188100001"]},"scopus_import":"1","type":"journal_article","department":[{"_id":"ToHe"}],"oa_version":"Published Version","date_updated":"2023-12-13T12:58:56Z","oa":1,"author":[{"first_name":"Rupak","full_name":"Majumdar, Rupak","last_name":"Majumdar"},{"last_name":"Mallik","orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik","full_name":"Mallik, Kaushik"},{"last_name":"Schmuck","first_name":"Anne Kathrin","full_name":"Schmuck, Anne Kathrin"},{"first_name":"Sadegh","full_name":"Soudjani, Sadegh","last_name":"Soudjani"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Majumdar, K. Mallik, A.K. Schmuck, S. Soudjani, Nonlinear Analysis: Hybrid Systems 51 (2023).","ama":"Majumdar R, Mallik K, Schmuck AK, Soudjani S. Symbolic control for stochastic systems via finite parity games. <i>Nonlinear Analysis: Hybrid Systems</i>. 2023;51. doi:<a href=\"https://doi.org/10.1016/j.nahs.2023.101430\">10.1016/j.nahs.2023.101430</a>","chicago":"Majumdar, Rupak, Kaushik Mallik, Anne Kathrin Schmuck, and Sadegh Soudjani. “Symbolic Control for Stochastic Systems via Finite Parity Games.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.nahs.2023.101430\">https://doi.org/10.1016/j.nahs.2023.101430</a>.","ieee":"R. Majumdar, K. Mallik, A. K. Schmuck, and S. Soudjani, “Symbolic control for stochastic systems via finite parity games,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 51. Elsevier, 2023.","ista":"Majumdar R, Mallik K, Schmuck AK, Soudjani S. 2023. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 51, 101430.","mla":"Majumdar, Rupak, et al. “Symbolic Control for Stochastic Systems via Finite Parity Games.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 51, 101430, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.nahs.2023.101430\">10.1016/j.nahs.2023.101430</a>.","apa":"Majumdar, R., Mallik, K., Schmuck, A. K., &#38; Soudjani, S. (2023). Symbolic control for stochastic systems via finite parity games. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2023.101430\">https://doi.org/10.1016/j.nahs.2023.101430</a>"},"date_published":"2023-09-27T00:00:00Z","title":"Symbolic control for stochastic systems via finite parity games","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"quality_controlled":"1","date_created":"2023-10-08T22:01:15Z","year":"2023","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.nahs.2023.101430"}],"article_processing_charge":"No","volume":51,"publication":"Nonlinear Analysis: Hybrid Systems","status":"public","publication_identifier":{"issn":["1751-570X"]},"abstract":[{"text":"We consider the problem of computing the maximal probability of satisfying an \r\n-regular specification for stochastic, continuous-state, nonlinear systems evolving in discrete time. The problem reduces, after automata-theoretic constructions, to finding the maximal probability of satisfying a parity condition on a (possibly hybrid) state space. While characterizing the exact satisfaction probability is open, we show that a lower bound on this probability can be obtained by (I) computing an under-approximation of the qualitative winning region, i.e., states from which the parity condition can be enforced almost surely, and (II) computing the maximal probability of reaching this qualitative winning region.\r\nThe heart of our approach is a technique to symbolically compute the under-approximation of the qualitative winning region in step (I) via a finite-state abstraction of the original system as a \r\n-player parity game. Our abstraction procedure uses only the support of the probabilistic evolution; it does not use precise numerical transition probabilities. We prove that the winning set in the abstract -player game induces an under-approximation of the qualitative winning region in the original synthesis problem, along with a policy to solve it. By combining these contributions with (a) a symbolic fixpoint algorithm to solve \r\n-player games and (b) existing techniques for reachability policy synthesis in stochastic nonlinear systems, we get an abstraction-based algorithm for finding a lower bound on the maximal satisfaction probability.\r\nWe have implemented the abstraction-based algorithm in Mascot-SDS, where we combined the outlined abstraction step with our tool Genie (Majumdar et al., 2023) that solves \r\n-player parity games (through a reduction to Rabin games) more efficiently than existing algorithms. We evaluated our implementation on the nonlinear model of a perturbed bistable switch from the literature. We show empirically that the lower bound on the winning region computed by our approach is precise, by comparing against an over-approximation of the qualitative winning region. Moreover, our implementation outperforms a recently proposed tool for solving this problem by a large margin.","lang":"eng"}],"doi":"10.1016/j.nahs.2023.101430","month":"09","isi":1,"publication_status":"epub_ahead","acknowledgement":"We thank Daniel Hausmann and Nir Piterman for their valuable comments on an earlier version of the manuscript of our other paper [22] where we present, among other things, the parity fixpoint for 2 1/2-player games (for a slightly more general class of games) with a different and indirect proof of correctness. Based on their comments we observed that, unlike the other fixpoints that we present in [22], the parity fixpoint does not follow the exact same structure as its counterpart for 2-player games, which we also use int his paper.\r\nWe also thank Thejaswini Raghavan for observing that our symbolic parity fixpoint algorithm can be solved in quasi-polynomial time using recent improved algorithms for solving \r\n-calculus expressions. This significantly improved the complexity bounds of our algorithm in this paper.\r\nThe work of R. Majumdar and A.-K. Schmuck are partially supported by DFG, Germany project 389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG, Germany project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802, and ERC 101089047.","ec_funded":1,"day":"27","publisher":"Elsevier","intvolume":"        51","article_number":"101430","article_type":"original","language":[{"iso":"eng"}],"arxiv":1},{"_id":"14401","file_date_updated":"2024-01-30T14:33:31Z","scopus_import":"1","external_id":{"pmid":["37292963"],"isi":["001071403800001"]},"type":"journal_article","has_accepted_license":"1","citation":{"ista":"Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. 2023. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. Molecular Neurodegeneration. 18, 67.","mla":"Maes, Margaret E., et al. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” <i>Molecular Neurodegeneration</i>, vol. 18, 67, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1186/s13024-023-00659-8\">10.1186/s13024-023-00659-8</a>.","apa":"Maes, M. E., Donahue, R. J., Schlamp, C. L., Marola, O. J., Libby, R. T., &#38; Nickells, R. W. (2023). BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. <i>Molecular Neurodegeneration</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13024-023-00659-8\">https://doi.org/10.1186/s13024-023-00659-8</a>","ieee":"M. E. Maes, R. J. Donahue, C. L. Schlamp, O. J. Marola, R. T. Libby, and R. W. Nickells, “BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps,” <i>Molecular Neurodegeneration</i>, vol. 18. Springer Nature, 2023.","ama":"Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. <i>Molecular Neurodegeneration</i>. 2023;18. doi:<a href=\"https://doi.org/10.1186/s13024-023-00659-8\">10.1186/s13024-023-00659-8</a>","short":"M.E. Maes, R.J. Donahue, C.L. Schlamp, O.J. Marola, R.T. Libby, R.W. Nickells, Molecular Neurodegeneration 18 (2023).","chicago":"Maes, Margaret E, Ryan J. Donahue, Cassandra L. Schlamp, Olivia J. Marola, Richard T. Libby, and Robert W. Nickells. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” <i>Molecular Neurodegeneration</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1186/s13024-023-00659-8\">https://doi.org/10.1186/s13024-023-00659-8</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"orcid":"0000-0001-9642-1085","first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","last_name":"Maes"},{"last_name":"Donahue","full_name":"Donahue, Ryan J.","first_name":"Ryan J."},{"last_name":"Schlamp","first_name":"Cassandra L.","full_name":"Schlamp, Cassandra L."},{"full_name":"Marola, Olivia J.","first_name":"Olivia J.","last_name":"Marola"},{"last_name":"Libby","first_name":"Richard T.","full_name":"Libby, Richard T."},{"first_name":"Robert W.","full_name":"Nickells, Robert W.","last_name":"Nickells"}],"oa_version":"Published Version","date_updated":"2024-01-30T14:34:21Z","department":[{"_id":"SaSi"}],"file":[{"content_type":"application/pdf","date_updated":"2024-01-30T14:33:31Z","file_size":11568350,"file_name":"2023_MolecularNeurodegeneration_Maes.pdf","file_id":"14917","success":1,"date_created":"2024-01-30T14:33:31Z","access_level":"open_access","creator":"dernst","checksum":"3aa218ddea4a082d8fd5e196ae55ca06","relation":"main_file"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":"1","date_published":"2023-09-26T00:00:00Z","title":"BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps","ddc":["570"],"date_created":"2023-10-08T22:01:15Z","publication":"Molecular Neurodegeneration","volume":18,"article_processing_charge":"Yes","year":"2023","publication_identifier":{"eissn":["1750-1326"]},"status":"public","pmid":1,"abstract":[{"text":"Background: \r\nPro-apoptotic BAX is a central mediator of retinal ganglion cell (RGC) death after optic nerve damage. BAX activation occurs in two stages including translocation of latent BAX to the mitochondrial outer membrane (MOM) and then permeabilization of the MOM to facilitate the release of apoptotic signaling molecules. As a critical component of RGC death, BAX is an attractive target for neuroprotective therapies and an understanding of the kinetics of BAX activation and the mechanisms controlling the two stages of this process in RGCs is potentially valuable in informing the development of a neuroprotective strategy.\r\nMethods:\r\nThe kinetics of BAX translocation were assessed by both static and live-cell imaging of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC) protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX was assessed by staining with the 6A7 monoclonal antibody, which recognizes a conformational change in this protein after MOM insertion. Assessment of individual kinases associated with both stages of activation was made using small molecule inhibitors injected into the vitreous either independently or in concert with ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase cascade was evaluated using mice with a double conditional knock-out of both Mkk4 and Mkk7.\r\nResults:\r\nONC induces the translocation of GFP-BAX in RGCs at a slower rate and with less intracellular synchronicity than 661W cells, but exhibits less variability among mitochondrial foci within a single cell. GFP-BAX was also found to translocate in all compartments of an RGC including the dendritic arbor and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation of BAX immediately following translocation. Unlike tissue culture cells, which exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant delay between these two stages, similar to detached cells undergoing anoikis. Translocation, with minimal permeabilization could be induced in a subset of RGCs using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor (sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.\r\nConclusions:\r\nA comparison between BAX activation kinetics in tissue culture cells and in cells of a complex tissue environment shows distinct differences indicating that caution should be used when translating findings from one condition to the other. RGCs exhibit both a delay between translocation and permeabilization and the ability for translocated BAX to be retrotranslocated, suggesting several stages at which intervention of the activation process could be exploited in the design of a therapeutic strategy.","lang":"eng"}],"doi":"10.1186/s13024-023-00659-8","isi":1,"month":"09","day":"26","publication_status":"published","acknowledgement":"The authors would like to thank Mr. Joel Dietz for management of the mouse colony and helpful advice for conducting quantitative PCR studies and Mr. Santoshi Kinoshita at the Translational Research Initiative in Pathology laboratory at the University of Wisconsin-Madison for cutting sections analyzed in this study.\r\nThis work was supported by National Eye Institute grants R01 EY030123 (RWN), R01 EY018606 (RTL), P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), T32 EY027721 (RJD) and F31 EY030739 (OJM). Additional funding was provided by the BrightFocus Foundation (RWN) and unrestricted grants from Research to Prevent Blindness, Inc to the Department of Ophthalmology and Visual Sciences (University of Wisconsin-Madison) and to the Department of Ophthalmology (University of Rochester).","publisher":"Springer Nature","article_type":"original","article_number":"67","intvolume":"        18","language":[{"iso":"eng"}]},{"project":[{"name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state","date_published":"2023-10-31T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2023","publication":"Cell Reports","article_processing_charge":"Yes","volume":42,"ddc":["570"],"date_created":"2023-10-08T22:01:15Z","external_id":{"pmid":["37777965"],"isi":["001086695500001"]},"file_date_updated":"2024-01-30T14:07:08Z","scopus_import":"1","_id":"14402","oa_version":"Published Version","date_updated":"2024-01-30T14:07:40Z","department":[{"_id":"GaTk"}],"file":[{"checksum":"9c71eb2a03aa160415f01ad95f49ceb5","relation":"main_file","creator":"dernst","file_name":"2023_CellReports_Lombardi.pdf","date_updated":"2024-01-30T14:07:08Z","content_type":"application/pdf","file_size":5599007,"access_level":"open_access","file_id":"14914","date_created":"2024-01-30T14:07:08Z","success":1}],"citation":{"mla":"Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” <i>Cell Reports</i>, vol. 42, no. 10, 113162, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 42(10), 113162.","ieee":"F. Lombardi <i>et al.</i>, “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” <i>Cell Reports</i>, vol. 42, no. 10. Elsevier, 2023.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>.","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. <i>Cell Reports</i>. 2023;42(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","oa":1,"author":[{"last_name":"Lombardi","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249"},{"full_name":"Herrmann, Hans J.","first_name":"Hans J.","last_name":"Herrmann"},{"last_name":"Parrino","full_name":"Parrino, Liborio","first_name":"Liborio"},{"last_name":"Plenz","full_name":"Plenz, Dietmar","first_name":"Dietmar"},{"last_name":"Scarpetta","first_name":"Silvia","full_name":"Scarpetta, Silvia"},{"last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta","first_name":"Anna Elisabetta"},{"last_name":"De Arcangelis","first_name":"Lucilla","full_name":"De Arcangelis, Lucilla"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"}],"type":"journal_article","publisher":"Elsevier","language":[{"iso":"eng"}],"article_number":"113162","intvolume":"        42","article_type":"original","issue":"10","abstract":[{"text":"Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition).","lang":"eng"}],"doi":"10.1016/j.celrep.2023.113162","pmid":1,"status":"public","publication_identifier":{"eissn":["2211-1247"]},"publication_status":"published","acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP [brain criticality and information processing]). L.d.A. acknowledges support from the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU (NGEU) funded by the Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022). O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The work was supported in part by DIRP ZIAMH02797 (to D.P.).","day":"31","ec_funded":1,"isi":1,"month":"10"},{"quality_controlled":"1","title":"Widening the use of 3D printing","date_published":"2023-09-29T00:00:00Z","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"date_created":"2023-10-08T22:01:16Z","volume":381,"article_processing_charge":"No","publication":"Science","year":"2023","_id":"14404","scopus_import":"1","external_id":{"pmid":["37769110"]},"type":"journal_article","author":[{"last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","full_name":"Balazs, Daniel","first_name":"Daniel","orcid":"0000-0001-7597-043X"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez"}],"citation":{"ieee":"D. Balazs and M. Ibáñez, “Widening the use of 3D printing,” <i>Science</i>, vol. 381, no. 6665. AAAS, pp. 1413–1414, 2023.","short":"D. Balazs, M. Ibáñez, Science 381 (2023) 1413–1414.","ama":"Balazs D, Ibáñez M. Widening the use of 3D printing. <i>Science</i>. 2023;381(6665):1413-1414. doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>","chicago":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>. AAAS, 2023. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>.","ista":"Balazs D, Ibáñez M. 2023. Widening the use of 3D printing. Science. 381(6665), 1413–1414.","mla":"Balazs, Daniel, and Maria Ibáñez. “Widening the Use of 3D Printing.” <i>Science</i>, vol. 381, no. 6665, AAAS, 2023, pp. 1413–14, doi:<a href=\"https://doi.org/10.1126/science.adk3070\">10.1126/science.adk3070</a>.","apa":"Balazs, D., &#38; Ibáñez, M. (2023). Widening the use of 3D printing. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adk3070\">https://doi.org/10.1126/science.adk3070</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"date_updated":"2023-10-09T07:32:58Z","oa_version":"None","publisher":"AAAS","article_type":"letter_note","page":"1413-1414","intvolume":"       381","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"]},"status":"public","pmid":1,"abstract":[{"lang":"eng","text":"A light-triggered fabrication method extends the functionality of printable nanomaterials"}],"doi":"10.1126/science.adk3070","issue":"6665","month":"09","day":"29","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support.","publication_status":"published"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_number":"21","intvolume":"       279","language":[{"iso":"eng"}],"arxiv":1,"status":"public","publication_identifier":{"isbn":["9783959772990"],"issn":["18688969"]},"abstract":[{"text":"We introduce hypernode automata as a new specification formalism for hyperproperties of concurrent systems. They are finite automata with nodes labeled with hypernode logic formulas and transitions labeled with actions. A hypernode logic formula specifies relations between sequences of variable values in different system executions. Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces by constraining the values and the order of value changes of each variable without correlating the timing of the changes. Different execution traces are synchronized solely through the transitions of hypernode automata. Hypernode automata naturally combine asynchronicity at the node level with synchronicity at the transition level. We show that the model-checking problem for hypernode automata is decidable over action-labeled Kripke structures, whose actions induce transitions of the specification automata. For this reason, hypernode automaton is a suitable formalism for specifying and verifying asynchronous hyperproperties, such as declassifying observational determinism in multi-threaded programs.","lang":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2023.21","alternative_title":["LIPIcs"],"month":"09","acknowledgement":"This work was supported in part by the Austrian Science Fund (FWF) SFB project\r\nSpyCoDe F8502, by the FWF projects ZK-35 and W1255-N23, and by the ERC Advanced Grant\r\nVAMOS 101020093.","publication_status":"published","day":"01","ec_funded":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"name":"CONCUR: Conference on Concurrency Theory","end_date":"2023-09-22","location":"Antwerp, Belgium","start_date":"2023-09-19"},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"date_published":"2023-09-01T00:00:00Z","title":"Hypernode automata","quality_controlled":"1","ddc":["000"],"date_created":"2023-10-08T22:01:16Z","year":"2023","publication":"34th International Conference on Concurrency Theory","volume":279,"article_processing_charge":"Yes","_id":"14405","external_id":{"arxiv":["2305.02836"]},"file_date_updated":"2023-10-09T07:42:45Z","scopus_import":"1","type":"conference","date_updated":"2023-10-09T07:43:44Z","oa_version":"Published Version","department":[{"_id":"ToHe"}],"file":[{"file_id":"14413","success":1,"date_created":"2023-10-09T07:42:45Z","access_level":"open_access","date_updated":"2023-10-09T07:42:45Z","content_type":"application/pdf","file_size":795790,"file_name":"2023_LIPcs_Bartocci.pdf","creator":"dernst","checksum":"215765e40454d806174ac0a223e8d6fa","relation":"main_file"}],"citation":{"ieee":"E. Bartocci, T. A. Henzinger, D. Nickovic, and A. Oliveira da Costa, “Hypernode automata,” in <i>34th International Conference on Concurrency Theory</i>, Antwerp, Belgium, 2023, vol. 279.","chicago":"Bartocci, Ezio, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira da Costa. “Hypernode Automata.” In <i>34th International Conference on Concurrency Theory</i>, Vol. 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.21</a>.","short":"E. Bartocci, T.A. Henzinger, D. Nickovic, A. Oliveira da Costa, in:, 34th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ama":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. Hypernode automata. In: <i>34th International Conference on Concurrency Theory</i>. Vol 279. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">10.4230/LIPIcs.CONCUR.2023.21</a>","mla":"Bartocci, Ezio, et al. “Hypernode Automata.” <i>34th International Conference on Concurrency Theory</i>, vol. 279, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">10.4230/LIPIcs.CONCUR.2023.21</a>.","apa":"Bartocci, E., Henzinger, T. A., Nickovic, D., &#38; Oliveira da Costa, A. (2023). Hypernode automata. In <i>34th International Conference on Concurrency Theory</i> (Vol. 279). Antwerp, Belgium: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2023.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2023.21</a>","ista":"Bartocci E, Henzinger TA, Nickovic D, Oliveira da Costa A. 2023. Hypernode automata. 34th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 279, 21."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","author":[{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724"},{"last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","full_name":"Nickovic, Dejan"},{"last_name":"Oliveira da Costa","orcid":"0000-0002-8741-5799","id":"f347ec37-6676-11ee-b395-a888cb7b4fb4","first_name":"Ana","full_name":"Oliveira da Costa, Ana"}],"oa":1}]