[{"department":[{"_id":"BjHo"}],"publist_id":"6862","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at   Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics."}],"scopus_import":"1","publication":"Journal of Fluid Mechanics","publisher":"Cambridge University Press","quality_controlled":"1","citation":{"ieee":"N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative periodic orbits form the backbone of turbulent pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 833. Cambridge University Press, pp. 274–301, 2017.","ista":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833, 274–301.","mla":"Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 833, Cambridge University Press, 2017, pp. 274–301, doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>.","short":"N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of Fluid Mechanics 833 (2017) 274–301.","ama":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;833:274-301. doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>","apa":"Budanur, N. B., Short, K., Farazmand, M., Willis, A., &#38; Cvitanović, P. (2017). Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>","chicago":"Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>."},"publication_status":"published","isi":1,"month":"12","intvolume":"       833","page":"274 - 301","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.03720"}],"type":"journal_article","external_id":{"isi":["000414641700001"]},"date_published":"2017-12-25T00:00:00Z","day":"25","author":[{"orcid":"0000-0003-0423-5010","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kimberly","full_name":"Short, Kimberly","last_name":"Short"},{"first_name":"Mohammad","full_name":"Farazmand, Mohammad","last_name":"Farazmand"},{"last_name":"Willis","full_name":"Willis, Ashley","first_name":"Ashley"},{"first_name":"Predrag","full_name":"Cvitanović, Predrag","last_name":"Cvitanović"}],"status":"public","oa_version":"Submitted Version","date_created":"2018-12-11T11:48:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":833,"doi":"10.1017/jfm.2017.699","project":[{"name":"ROOTS Genome-wide Analysis of Root Traits","_id":"25636330-B435-11E9-9278-68D0E5697425","grant_number":"11-NSF-1070"}],"year":"2017","publication_identifier":{"issn":["00221120"]},"oa":1,"title":"Relative periodic orbits form the backbone of turbulent pipe flow","article_processing_charge":"No","date_updated":"2023-09-27T12:17:35Z","_id":"792"},{"doi":"10.1016/j.comgeo.2017.07.002","volume":66,"date_created":"2018-12-11T11:48:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mojarrad","full_name":"Mojarrad, Hossein","first_name":"Hossein"},{"last_name":"Naszódi","first_name":"Márton","full_name":"Naszódi, Márton"},{"last_name":"Solymosi","full_name":"Solymosi, József","first_name":"József"},{"last_name":"Stich","first_name":"Sebastian","full_name":"Stich, Sebastian"},{"last_name":"Szedlák","first_name":"May","full_name":"Szedlák, May"}],"status":"public","day":"01","date_published":"2017-01-01T00:00:00Z","external_id":{"isi":["000412039700003"]},"_id":"793","date_updated":"2023-09-27T12:15:16Z","article_processing_charge":"No","title":"On the existence of ordinary triangles","oa":1,"publication_identifier":{"issn":["09257721"]},"project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2017","publication_status":"published","citation":{"ista":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.","ieee":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 28–31, 2017.","short":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31.","mla":"Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 28–31, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>.","ama":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. 2017;66:28-31. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>","chicago":"Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>.","apa":"Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., &#38; Szedlák, M. (2017). On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>"},"quality_controlled":"1","publisher":"Elsevier","publication":"Computational Geometry: Theory and Applications","abstract":[{"text":"Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c &gt; 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). ","lang":"eng"}],"language":[{"iso":"eng"}],"publist_id":"6861","department":[{"_id":"UlWa"}],"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1701.08183"}],"ec_funded":1,"page":"28 - 31","intvolume":"        66","isi":1,"month":"01"},{"oa":1,"year":"2017","acknowledgement":"I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous referees for many comments and suggestions that helped to improve the presentation of the result.","related_material":{"record":[{"status":"public","id":"1165","relation":"earlier_version"}]},"_id":"794","date_updated":"2023-09-27T12:14:49Z","title":"C-planarity of embedded cyclic c-graphs","article_processing_charge":"No","date_published":"2017-12-01T00:00:00Z","day":"01","external_id":{"isi":["000412039700001"]},"volume":66,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:32Z","doi":"10.1016/j.comgeo.2017.06.016","status":"public","author":[{"last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","full_name":"Fulek, Radoslav"}],"oa_version":"Preprint","page":"1 - 13","isi":1,"month":"12","intvolume":"        66","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1602.01346","open_access":"1"}],"publication":"Computational Geometry: Theory and Applications","scopus_import":"1","publisher":"Elsevier","publist_id":"6860","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"abstract":[{"text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Fulek R. C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. 2017;66:1-13. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>","apa":"Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>.","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 1–13, 2017.","ista":"Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 66, 1–13.","short":"R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13.","mla":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 1–13, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>."},"quality_controlled":"1"},{"ec_funded":1,"issue":"3","intvolume":"        24","article_number":"P3.18","month":"07","ddc":["000"],"type":"journal_article","publisher":"International Press","publication":"Electronic Journal of Combinatorics","scopus_import":"1","file_date_updated":"2020-07-14T12:48:06Z","file":[{"checksum":"ef320cff0f062051e858f929be6a3581","content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_id":"5853","relation":"main_file","file_size":236944,"date_created":"2019-01-18T14:04:08Z","file_name":"2017_ElectrCombi_Fulek.pdf","date_updated":"2020-07-14T12:48:06Z"}],"abstract":[{"lang":"eng","text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof."}],"language":[{"iso":"eng"}],"publist_id":"6859","department":[{"_id":"UlWa"}],"article_type":"original","publication_status":"published","quality_controlled":"1","citation":{"ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” <i>Electronic Journal of Combinatorics</i>, vol. 24, no. 3. International Press, 2017.","ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” <i>Electronic Journal of Combinatorics</i>, vol. 24, no. 3, P3.18, International Press, 2017, doi:<a href=\"https://doi.org/10.37236/6663\">10.37236/6663</a>.","short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017).","ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. <i>Electronic Journal of Combinatorics</i>. 2017;24(3). doi:<a href=\"https://doi.org/10.37236/6663\">10.37236/6663</a>","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” <i>Electronic Journal of Combinatorics</i>. International Press, 2017. <a href=\"https://doi.org/10.37236/6663\">https://doi.org/10.37236/6663</a>.","apa":"Fulek, R., Kynčl, J., &#38; Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. <i>Electronic Journal of Combinatorics</i>. International Press. <a href=\"https://doi.org/10.37236/6663\">https://doi.org/10.37236/6663</a>"},"oa":1,"publication_identifier":{"issn":["10778926"]},"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"year":"2017","has_accepted_license":"1","date_updated":"2022-03-18T12:58:53Z","_id":"795","article_processing_charge":"No","title":"Unified Hanani Tutte theorem","day":"28","date_published":"2017-07-28T00:00:00Z","doi":"10.37236/6663","date_created":"2018-12-11T11:48:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":24,"oa_version":"Published Version","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kynčl","full_name":"Kynčl, Jan","first_name":"Jan"},{"last_name":"Pálvölgyi","first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör"}],"status":"public"},{"date_updated":"2023-09-27T12:13:36Z","_id":"796","article_processing_charge":"No","title":"Al transmon qubits on silicon on insulator for quantum device integration","publication_identifier":{"issn":["00036951"]},"oa":1,"acknowledgement":"This work was supported by the AFOSR MURI Quantum Photonic Matter (Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers (Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.J.K. acknowledges the IQIM Postdoctoral Fellowship.","year":"2017","date_created":"2018-12-11T11:48:33Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":111,"doi":"10.1063/1.4994661","author":[{"first_name":"Andrew J","full_name":"Keller, Andrew J","last_name":"Keller"},{"full_name":"Dieterle, Paul","first_name":"Paul","last_name":"Dieterle"},{"first_name":"Michael","full_name":"Fang, Michael","last_name":"Fang"},{"last_name":"Berger","full_name":"Berger, Brett","first_name":"Brett"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"}],"status":"public","oa_version":"Submitted Version","date_published":"2017-07-01T00:00:00Z","day":"01","external_id":{"isi":["000406779700031"]},"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1703.10195","open_access":"1"}],"issue":"4","month":"07","isi":1,"intvolume":"       111","article_number":"042603","publication_status":"published","quality_controlled":"1","citation":{"ista":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 111(4), 042603.","ieee":"A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter, “Al transmon qubits on silicon on insulator for quantum device integration,” <i>Applied Physics Letters</i>, vol. 111, no. 4. American Institute of Physics, 2017.","short":"A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied Physics Letters 111 (2017).","mla":"Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>, vol. 111, no. 4, 042603, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>.","ama":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. 2017;111(4). doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>","chicago":"Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>.","apa":"Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., &#38; Painter, O. (2017). Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>"},"publication":"Applied Physics Letters","scopus_import":"1","publisher":"American Institute of Physics","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"publist_id":"6857","abstract":[{"text":"We present the fabrication and characterization of an aluminum transmon qubit on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This process in principle permits the co-fabrication of silicon photonic and mechanical elements, providing a route towards chip-scale integration of electro-opto-mechanical transducers for quantum networking of superconducting microwave quantum circuits. The additional processing steps are compatible with established fabrication techniques for aluminum transmon qubits on silicon.","lang":"eng"}]},{"date_created":"2018-12-11T11:48:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","volume":48,"doi":"10.1002/piuz.201770305","article_type":"original","author":[{"first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"status":"public","quality_controlled":"1","citation":{"ama":"Fink JM. Photonenblockade aufgelöst. <i>Physik in unserer Zeit</i>. 2017;48(3):111-113. doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. <i>Physik in Unserer Zeit</i>. Wiley. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” <i>Physik in unserer Zeit</i>, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>."},"oa_version":"None","date_published":"2017-05-01T00:00:00Z","publication":"Physik in unserer Zeit","day":"01","publisher":"Wiley","language":[{"iso":"eng"}],"publist_id":"6856","department":[{"_id":"JoFi"}],"abstract":[{"text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden.","lang":"ger"}],"date_updated":"2022-03-24T09:16:20Z","type":"journal_article","_id":"797","article_processing_charge":"No","title":"Photonenblockade aufgelöst","issue":"3","page":"111 - 113","month":"05","year":"2017","intvolume":"        48"},{"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","citation":{"apa":"Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., &#38; Fink, J. M. (2017). Mechanical on chip microwave circulator. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>","chicago":"Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>.","ama":"Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>","short":"S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017).","mla":"Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>.","ieee":"S. Barzanjeh <i>et al.</i>, “Mechanical on chip microwave circulator,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304."},"quality_controlled":"1","file":[{"file_id":"5145","access_level":"open_access","creator":"system","checksum":"b68dafa71d1834c23b742cd9987a3d5f","content_type":"application/pdf","date_updated":"2020-07-14T12:48:06Z","file_name":"IST-2017-867-v1+1_s41467-017-01304-x.pdf","file_size":1467696,"date_created":"2018-12-12T10:15:25Z","relation":"main_file"}],"file_date_updated":"2020-07-14T12:48:06Z","scopus_import":"1","publication":"Nature Communications","publisher":"Nature Publishing Group","department":[{"_id":"JoFi"}],"publist_id":"6855","language":[{"iso":"eng"}],"abstract":[{"text":"Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout.","lang":"eng"}],"type":"journal_article","ddc":["539"],"issue":"1","ec_funded":1,"month":"10","isi":1,"article_number":"1304","pubrep_id":"867","intvolume":"         8","volume":8,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:33Z","doi":"10.1038/s41467-017-01304-x","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"orcid":"0000-0003-0415-1423","first_name":"Shabir","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","first_name":"Matthias"},{"first_name":"Matilda","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo"},{"last_name":"Kalaee","first_name":"Mahmoud","full_name":"Kalaee, Mahmoud"},{"first_name":"Paul","full_name":"Dieterle, Paul","last_name":"Dieterle"},{"last_name":"Painter","first_name":"Oskar","full_name":"Painter, Oskar"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","orcid":"0000-0001-8112-028X"}],"oa_version":"Published Version","date_published":"2017-10-16T00:00:00Z","day":"16","external_id":{"isi":["000412999700021"]},"_id":"798","date_updated":"2023-09-27T12:11:28Z","article_processing_charge":"Yes (in subscription journal)","title":"Mechanical on chip microwave circulator","publication_identifier":{"issn":["20411723"]},"oa":1,"has_accepted_license":"1","project":[{"call_identifier":"H2020","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","call_identifier":"H2020"}],"year":"2017"},{"external_id":{"pmid":["29016942"],"isi":["000413220400019"]},"day":"21","date_published":"2017-08-21T00:00:00Z","oa_version":"Submitted Version","author":[{"last_name":"Kitakura","full_name":"Kitakura, Saeko","first_name":"Saeko"},{"last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek"},{"last_name":"Matsuura","full_name":"Matsuura, Yuki","first_name":"Yuki"},{"last_name":"Santuari","full_name":"Santuari, Luca","first_name":"Luca"},{"last_name":"Kouno","full_name":"Kouno, Hirotaka","first_name":"Hirotaka"},{"last_name":"Arima","full_name":"Arima, Kohei","first_name":"Kohei"},{"full_name":"Hardtke, Christian","first_name":"Christian","last_name":"Hardtke"},{"full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"full_name":"Kakimoto, Tatsuo","first_name":"Tatsuo","last_name":"Kakimoto"},{"last_name":"Tanaka","full_name":"Tanaka, Hirokazu","first_name":"Hirokazu"}],"status":"public","doi":"10.1093/pcp/pcx118","pmid":1,"volume":58,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:34Z","year":"2017","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["00320781"]},"article_processing_charge":"No","title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","_id":"799","date_updated":"2023-09-27T11:00:19Z","abstract":[{"lang":"eng","text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis."}],"publist_id":"6854","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","file":[{"file_id":"6333","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"bd3e3a94d55416739cbb19624bb977f8","file_name":"2017_PlantCellPhysio_Kitakura.pdf","date_updated":"2020-07-14T12:48:06Z","date_created":"2019-04-17T07:52:34Z","file_size":1352913,"relation":"main_file"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:06Z","publication":"Plant and Cell Physiology","citation":{"short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>.","ieee":"S. Kitakura <i>et al.</i>, “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” <i>Plant and Cell Physiology</i>, vol. 58, no. 10. Oxford University Press, 2017.","ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811.","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>.","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. 2017;58(10). doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>"},"quality_controlled":"1","publication_status":"published","article_number":"1801-1811","pubrep_id":"1009","intvolume":"        58","isi":1,"month":"08","issue":"10","type":"journal_article","ddc":["581"]},{"article_number":"758","pubrep_id":"914","intvolume":"         8","month":"10","isi":1,"ec_funded":1,"issue":"1","type":"journal_article","ddc":["571"],"abstract":[{"text":"Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"publist_id":"6853","publisher":"Nature Publishing Group","scopus_import":"1","file":[{"file_id":"5135","creator":"system","access_level":"open_access","checksum":"7e2c7621afd5f802338e92e8619f024d","content_type":"application/pdf","file_name":"IST-2017-914-v1+1_s41467-017-00936-3.pdf","date_updated":"2020-07-14T12:48:07Z","date_created":"2018-12-12T10:15:17Z","file_size":4261832,"relation":"main_file"}],"file_date_updated":"2020-07-14T12:48:07Z","publication":"Nature Communications","citation":{"ama":"Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>","apa":"Strüber, M., Sauer, J., Jonas, P. M., &#38; Bartos, M. (2017). Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>","chicago":"Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00936-3\">https://doi.org/10.1038/s41467-017-00936-3</a>.","ieee":"M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications. 8(1), 758.","mla":"Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” <i>Nature Communications</i>, vol. 8, no. 1, 758, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00936-3\">10.1038/s41467-017-00936-3</a>.","short":"M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017)."},"quality_controlled":"1","publication_status":"published","year":"2017","project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","call_identifier":"FP7"}],"has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["20411723"]},"article_processing_charge":"No","title":"Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus","_id":"800","date_updated":"2023-09-27T10:59:41Z","external_id":{"isi":["000412053100004"]},"day":"02","date_published":"2017-10-02T00:00:00Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Strüber","full_name":"Strüber, Michael","first_name":"Michael"},{"full_name":"Sauer, Jonas","first_name":"Jonas","last_name":"Sauer"},{"first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"},{"last_name":"Bartos","first_name":"Marlene","full_name":"Bartos, Marlene"}],"status":"public","doi":"10.1038/s41467-017-00936-3","volume":8,"date_created":"2018-12-11T11:48:34Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"page":"956 - 972","acknowledged_ssus":[{"_id":"Bio"}],"issue":"5","intvolume":"       170","month":"08","isi":1,"type":"journal_article","ddc":["570"],"publisher":"Cell Press","file":[{"file_id":"5852","checksum":"64897b0c5373f22273f598e4672c60ff","content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_size":17666637,"date_created":"2019-01-18T13:45:40Z","file_name":"2017_Cell_Samwer.pdf","date_updated":"2020-07-14T12:48:08Z","relation":"main_file"}],"publication":"Cell","scopus_import":"1","file_date_updated":"2020-07-14T12:48:08Z","abstract":[{"lang":"eng","text":"Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function."}],"language":[{"iso":"eng"}],"publist_id":"6848","department":[{"_id":"CaHe"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_status":"published","citation":{"ieee":"M. Samwer <i>et al.</i>, “DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes,” <i>Cell</i>, vol. 170, no. 5. Cell Press, pp. 956–972, 2017.","ista":"Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. Cell. 170(5), 956–972.","short":"M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber, D. Gerlic, Cell 170 (2017) 956–972.","mla":"Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>, vol. 170, no. 5, Cell Press, 2017, pp. 956–72, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>.","ama":"Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. 2017;170(5):956-972. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">10.1016/j.cell.2017.07.038</a>","apa":"Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber, J., &#38; Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>","chicago":"Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst, Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.07.038\">https://doi.org/10.1016/j.cell.2017.07.038</a>."},"quality_controlled":"1","oa":1,"publication_identifier":{"issn":["00928674"]},"year":"2017","has_accepted_license":"1","_id":"803","date_updated":"2023-09-27T10:59:14Z","title":"DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes","article_processing_charge":"No","day":"24","date_published":"2017-08-24T00:00:00Z","external_id":{"isi":["000408372400014"]},"doi":"10.1016/j.cell.2017.07.038","volume":170,"date_created":"2018-12-11T11:48:35Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"author":[{"last_name":"Samwer","full_name":"Samwer, Matthias","first_name":"Matthias"},{"first_name":"Maximilian","full_name":"Schneider, Maximilian","last_name":"Schneider"},{"last_name":"Hoefler","first_name":"Rudolf","full_name":"Hoefler, Rudolf"},{"last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5795-0133","full_name":"Schmalhorst, Philipp S","first_name":"Philipp S"},{"last_name":"Jude","full_name":"Jude, Julian","first_name":"Julian"},{"last_name":"Zuber","first_name":"Johannes","full_name":"Zuber, Johannes"},{"last_name":"Gerlic","first_name":"Daniel","full_name":"Gerlic, Daniel"}],"status":"public"},{"article_processing_charge":"No","title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","_id":"804","date_updated":"2023-09-27T10:58:45Z","year":"2017","acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the  Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","publication_identifier":{"issn":["15499618"]},"oa":1,"author":[{"full_name":"Schmalhorst, Philipp S","first_name":"Philipp S","orcid":"0000-0002-5795-0133","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","last_name":"Schmalhorst"},{"full_name":"Deluweit, Felix","first_name":"Felix","last_name":"Deluweit"},{"full_name":"Scherrers, Roger","first_name":"Roger","last_name":"Scherrers"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora"}],"status":"public","oa_version":"Submitted Version","volume":13,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:35Z","doi":"10.1021/acs.jctc.7b00374","external_id":{"isi":["000412965700036"]},"date_published":"2017-10-10T00:00:00Z","day":"10","main_file_link":[{"url":"https://arxiv.org/abs/1704.03773","open_access":"1"}],"type":"journal_article","month":"10","isi":1,"intvolume":"        13","issue":"10","page":"5039 - 5053","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. 2017;13(10):5039-5053. doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>","apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &#38; Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>","chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>.","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017.","ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053.","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053.","mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>."},"quality_controlled":"1","publication_status":"published","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"publist_id":"6847","abstract":[{"lang":"eng","text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides."}],"publication":"Journal of Chemical Theory and Computation","scopus_import":"1","publisher":"American Chemical Society"},{"date_created":"2018-12-11T11:48:36Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","volume":144,"doi":"10.1242/dev.145698","status":"public","author":[{"last_name":"Pfurr","full_name":"Pfurr, Sabrina","first_name":"Sabrina"},{"last_name":"Chu","full_name":"Chu, Yu","first_name":"Yu"},{"full_name":"Bohrer, Christian","first_name":"Christian","last_name":"Bohrer"},{"last_name":"Greulich","full_name":"Greulich, Franziska","first_name":"Franziska"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","full_name":"Beattie, Robert J","first_name":"Robert J","orcid":"0000-0002-8483-8753"},{"full_name":"Mammadzada, Könül","first_name":"Könül","last_name":"Mammadzada"},{"full_name":"Hils, Miriam","first_name":"Miriam","last_name":"Hils"},{"full_name":"Arnold, Sebastian","first_name":"Sebastian","last_name":"Arnold"},{"full_name":"Taylor, Verdon","first_name":"Verdon","last_name":"Taylor"},{"full_name":"Schachtrup, Kristina","first_name":"Kristina","last_name":"Schachtrup"},{"last_name":"Uhlenhaut","first_name":"N Henriette","full_name":"Uhlenhaut, N Henriette"},{"full_name":"Schachtrup, Christian","first_name":"Christian","last_name":"Schachtrup"}],"quality_controlled":"1","citation":{"mla":"Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” <i>Development</i>, vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:<a href=\"https://doi.org/10.1242/dev.145698\">10.1242/dev.145698</a>.","short":"S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M. Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development 144 (2017) 3917–3931.","ieee":"S. Pfurr <i>et al.</i>, “The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development,” <i>Development</i>, vol. 144. Company of Biologists, pp. 3917–3931, 2017.","ista":"Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. Development. 144, 3917–3931.","apa":"Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K., … Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.145698\">https://doi.org/10.1242/dev.145698</a>","chicago":"Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.145698\">https://doi.org/10.1242/dev.145698</a>.","ama":"Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development. <i>Development</i>. 2017;144:3917-3931. doi:<a href=\"https://doi.org/10.1242/dev.145698\">10.1242/dev.145698</a>"},"oa_version":"None","date_published":"2017-10-31T00:00:00Z","scopus_import":"1","publication":"Development","publisher":"Company of Biologists","day":"31","external_id":{"isi":["000414025600007"]},"language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"publist_id":"6846","abstract":[{"text":"During corticogenesis, distinct classes of neurons are born from progenitor cells located in the ventricular and subventricular zones, from where they migrate towards the pial surface to assemble into highly organized layer-specific circuits. However, the precise and coordinated transcriptional network activity defining neuronal identity is still not understood. Here, we show that genetic depletion of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47 increased the number of Tbr1-positive deep layer and Satb2-positive upper layer neurons at E14.5, while depletion of the alternatively spliced E12 variant did not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap for E12- and E47-specific binding sites in embryonic NSCs, including sites at the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed a unique transcriptional regulation by each splice variant. E47 activated the expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression in vivo by in utero electroporation disturbed proper layer-specific neurogenesis and upregulated p57(KIP2) expression. Overall, this study identified E2A target genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation via p57(KIP2).","lang":"eng"}],"date_updated":"2023-09-26T16:20:09Z","type":"journal_article","_id":"805","title":"The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development","article_processing_charge":"No","page":"3917 - 3931","month":"10","isi":1,"year":"2017","intvolume":"       144"},{"publisher":"VÖB","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","checksum":"558c18bcf5580d87dd371ec626d52075","file_id":"5851","relation":"main_file","date_updated":"2020-07-14T12:48:09Z","file_name":"2017_VOEB_Andrae.pdf","file_size":125065,"date_created":"2019-01-18T13:39:26Z"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:48:09Z","abstract":[{"lang":"eng","text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group &quot;Springer Compact Evaluierung&quot; made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do."}],"department":[{"_id":"E-Lib"}],"language":[{"iso":"eng"}],"publist_id":"6843","publication_status":"published","citation":{"ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>.","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2017;70(2):274-280. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">10.31263/voebm.v70i2.1898</a>","apa":"Andrae, M., &#38; Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>","chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare</i>. VÖB, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1898\">https://doi.org/10.31263/voebm.v70i2.1898</a>."},"page":"274 - 280","popular_science":"1","issue":"2","intvolume":"        70","month":"08","type":"journal_article","ddc":["020"],"day":"01","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1898","volume":70,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:36Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"first_name":"Magdalena","full_name":"Andrae, Magdalena","last_name":"Andrae"},{"last_name":"Villányi","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton","first_name":"Márton"}],"oa":1,"publication_identifier":{"issn":["10222588"]},"year":"2017","has_accepted_license":"1","_id":"807","date_updated":"2021-01-12T08:16:45Z","title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung"},{"language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"publist_id":"6831","abstract":[{"text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:09Z","file":[{"file_name":"Thesis_KarinMitosch.docx","date_updated":"2020-07-14T12:48:09Z","file_size":6331071,"date_created":"2019-04-05T08:48:51Z","relation":"source_file","file_id":"6210","creator":"dernst","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"da3993c5f90f59a8e8623cc31ad501dd"},{"date_created":"2019-04-05T08:48:51Z","file_size":9289852,"date_updated":"2020-07-14T12:48:09Z","file_name":"Thesis_KarinMitosch.pdf","relation":"main_file","file_id":"6211","content_type":"application/pdf","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","access_level":"open_access","creator":"dernst"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>.","apa":"Mitosch, K. (2017). <i>Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017.","mla":"Mitosch, Karin. <i>Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017."},"publication_status":"published","supervisor":[{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"month":"09","pubrep_id":"862","degree_awarded":"PhD","page":"113","ddc":["571","579"],"type":"dissertation","date_published":"2017-09-27T00:00:00Z","day":"27","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:48:40Z","doi":"10.15479/AT:ISTA:th_862","has_accepted_license":"1","year":"2017","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","publication_identifier":{"issn":["2663-337X"]},"oa":1,"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","article_processing_charge":"No","related_material":{"record":[{"id":"2001","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"666"}]},"date_updated":"2023-09-07T12:00:26Z","_id":"818"},{"_id":"819","date_updated":"2023-09-28T11:31:32Z","related_material":{"record":[{"id":"616","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"806"},{"relation":"part_of_dissertation","id":"734","status":"public"},{"id":"732","status":"public","relation":"part_of_dissertation"}]},"article_processing_charge":"No","title":"Disease defence in garden ants","oa":1,"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","year":"2017","has_accepted_license":"1","doi":"10.15479/AT:ISTA:th_861","date_created":"2018-12-11T11:48:40Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","first_name":"Christopher"}],"day":"26","date_published":"2017-09-26T00:00:00Z","type":"dissertation","ddc":["576","577","578","579","590","592"],"page":"122","degree_awarded":"PhD","pubrep_id":"861","month":"09","supervisor":[{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M","first_name":"Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","citation":{"chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>.","apa":"Pull, C. (2017). <i>Disease defence in garden ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>","ama":"Pull C. Disease defence in garden ants. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>","mla":"Pull, Christopher. <i>Disease Defence in Garden Ants</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>.","short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017.","ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017."},"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2019-04-05T07:53:04Z","file_size":18580400,"date_updated":"2020-07-14T12:48:09Z","file_name":"2017_Thesis_Pull.docx","relation":"source_file","file_id":"6199","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"4993cdd5382295758ecc3ecbd2a9aaff","access_level":"closed","creator":"dernst"},{"file_id":"6200","content_type":"application/pdf","checksum":"ee2e3ebb5b53c154c866f5b052b25153","access_level":"open_access","creator":"dernst","date_created":"2019-04-05T07:53:04Z","file_size":14400681,"date_updated":"2020-07-14T12:48:09Z","file_name":"2017_Thesis_Pull.pdf","relation":"main_file"}],"file_date_updated":"2020-07-14T12:48:09Z","abstract":[{"text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. ","lang":"eng"}],"publist_id":"6830","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}]},{"intvolume":"       167","pubrep_id":"489","month":"04","isi":1,"page":"673 - 776","ec_funded":1,"issue":"3-4","ddc":["530"],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized."}],"department":[{"_id":"LaEr"}],"publist_id":"5644","language":[{"iso":"eng"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:45:00Z","publication":"Probability Theory and Related Fields","file":[{"date_updated":"2020-07-14T12:45:00Z","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf","file_size":1615755,"date_created":"2018-12-12T10:08:05Z","relation":"main_file","file_id":"4665","access_level":"open_access","creator":"system","checksum":"67afa85ff1e220cbc1f9f477a828513c","content_type":"application/pdf"}],"scopus_import":"1","quality_controlled":"1","citation":{"ieee":"Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4. Springer, pp. 673–776, 2017.","ista":"Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776.","mla":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>.","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.","ama":"Bao Z, Erdös L. Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. 2017;167(3-4):673-776. doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>","apa":"Bao, Z., &#38; Erdös, L. (2017). Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>","chicago":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>."},"article_type":"original","publication_status":"published","year":"2017","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"}],"acknowledgement":"Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization.","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["01788051"]},"article_processing_charge":"Yes (via OA deal)","title":"Delocalization for a class of random block band matrices","date_updated":"2023-09-20T09:42:12Z","_id":"1528","external_id":{"isi":["000398842700004"]},"day":"01","date_published":"2017-04-01T00:00:00Z","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","first_name":"Zhigang"},{"orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1007/s00440-015-0692-y","date_created":"2018-12-11T11:52:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":167},{"type":"journal_article","arxiv":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.1242","open_access":"1"}],"page":"285 - 306","issue":"2","intvolume":"        44","month":"06","isi":1,"publication_status":"published","citation":{"ieee":"A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.","ista":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","mla":"Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>.","ama":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. 2017;44(2):285-306. doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>","apa":"Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., &#38; Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>","chicago":"Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>."},"quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":"1","publication":"Scandinavian Journal of Statistics","abstract":[{"lang":"eng","text":"The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane."}],"department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"publist_id":"5060","_id":"2016","date_updated":"2023-09-19T15:13:27Z","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"article_processing_charge":"No","title":"Exact goodness-of-fit testing for the Ising model","oa":1,"publication_identifier":{"issn":["03036898"]},"year":"2017","doi":"10.1111/sjos.12251","volume":44,"date_created":"2018-12-11T11:55:13Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","author":[{"last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham","first_name":"Abraham"},{"full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","full_name":"Uhler, Caroline","first_name":"Caroline","orcid":"0000-0002-7008-0216"}],"status":"public","day":"01","date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000400985000001"],"arxiv":["1410.1242"]}},{"abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"publist_id":"7711","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:45:24Z","file":[{"relation":"main_file","date_created":"2018-12-12T10:08:48Z","file_size":18569590,"date_updated":"2020-07-14T12:45:24Z","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","content_type":"application/pdf","checksum":"33cfb59674e91f82e3738396d3fb3776","access_level":"open_access","creator":"system","file_id":"4710"},{"file_id":"6204","creator":"dernst","access_level":"closed","checksum":"dcc239968decb233e7f98cf1083d8c26","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2017_Pleska_Maros_Thesis.docx","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-04-05T08:33:14Z","file_size":2801649,"relation":"source_file"}],"alternative_title":["ISTA Thesis"],"citation":{"short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","mla":"Pleska, Maros. <i>Biology of Restriction-Modification Systems at the Single-Cell and Population Level</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>.","apa":"Pleska, M. (2017). <i>Biology of restriction-modification systems at the single-cell and population level</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">https://doi.org/10.15479/AT:ISTA:th_916</a>","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_916\">10.15479/AT:ISTA:th_916</a>"},"publication_status":"published","supervisor":[{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"916","month":"10","page":"126","degree_awarded":"PhD","ddc":["576","579"],"type":"dissertation","day":"01","date_published":"2017-10-01T00:00:00Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"}],"status":"public","doi":"10.15479/AT:ISTA:th_916","date_created":"2018-12-11T11:45:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","year":"2017","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["2663-337X"]},"title":"Biology of restriction-modification systems at the single-cell and population level","article_processing_charge":"No","date_updated":"2023-09-15T12:04:56Z","_id":"202","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1243"},{"status":"public","id":"561","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"457"}]}},{"publication_status":"published","quality_controlled":"1","citation":{"chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>.","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713."},"publisher":"Springer","scopus_import":"1","file_date_updated":"2020-07-14T12:44:44Z","publication":"Algorithmica","file":[{"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","date_created":"2018-12-12T10:10:19Z","file_size":710206,"relation":"main_file","file_id":"4805","access_level":"open_access","creator":"system","content_type":"application/pdf","checksum":"7873f665a0c598ac747c908f34cb14b9"}],"abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"language":[{"iso":"eng"}],"publist_id":"5931","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"ddc":["576"],"type":"journal_article","page":"681 - 713","ec_funded":1,"issue":"2","intvolume":"        78","pubrep_id":"658","month":"06","isi":1,"doi":"10.1007/s00453-016-0212-1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:51:27Z","volume":78,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","full_name":"Paixao, Tiago"},{"last_name":"Pérez Heredia","first_name":"Jorge","full_name":"Pérez Heredia, Jorge"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"status":"public","day":"01","date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000400379500013"]},"date_updated":"2023-09-20T11:14:42Z","_id":"1336","title":"Towards a runtime comparison of natural and artificial evolution","article_processing_charge":"No","oa":1,"publication_identifier":{"issn":["01784617"]},"year":"2017","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091"}],"has_accepted_license":"1"},{"quality_controlled":"1","citation":{"mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2017). Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>","ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. 2017;169(3-4):667-727. doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes."}],"publist_id":"5930","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:44:44Z","scopus_import":"1","publication":"Probability Theory and Related Fields","file":[{"file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","date_updated":"2020-07-14T12:44:44Z","file_size":988843,"date_created":"2018-12-12T10:08:25Z","relation":"main_file","file_id":"4686","creator":"system","access_level":"open_access","checksum":"29f5a72c3f91e408aeb9e78344973803","content_type":"application/pdf"}],"ddc":["510","530"],"type":"journal_article","pubrep_id":"657","intvolume":"       169","isi":1,"month":"12","page":"667 - 727","ec_funded":1,"issue":"3-4","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Ajanki, Oskari H","first_name":"Oskari H","last_name":"Ajanki","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H","full_name":"Krüger, Torben H"}],"status":"public","doi":"10.1007/s00440-016-0740-2","date_created":"2018-12-11T11:51:27Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":169,"external_id":{"isi":["000414358400002"]},"day":"01","date_published":"2017-12-01T00:00:00Z","title":"Universality for general Wigner-type matrices","article_processing_charge":"Yes (via OA deal)","date_updated":"2023-09-20T11:14:17Z","_id":"1337","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).  ","year":"2017","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["01788051"]}}]