[{"page":"124","_id":"839","language":[{"iso":"eng"}],"pubrep_id":"855","acknowledgement":"ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all, let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for supporting me throughout my PhD. Obviously, none of this work would\r\nhave been possible without you.\r\nFurthermore, Thank You to all the people who have contributed to this work in various\r\nways, in particular Martin Schanz and his group for providing and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel, and all the members – past and present – of his\r\nand Chris’ research groups at IST Austria for always providing honest and insightful\r\nfeedback throughout many joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs only virtual objects have been harmed in the process of creating this work, I would\r\nlike to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo” models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different ways.\r\n","degree_awarded":"PhD","file":[{"file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","relation":"main_file","checksum":"6c1ae8c90bfaba5e089417fefbc4a272","creator":"system","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:13Z","date_created":"2018-12-12T10:14:46Z","file_size":14596191,"file_id":"5100"},{"access_level":"closed","date_created":"2019-04-05T08:40:30Z","date_updated":"2020-07-14T12:48:13Z","file_size":15060566,"file_id":"6207","relation":"source_file","file_name":"2017_thesis_Hahn_source.zip","checksum":"421672f68d563b029869c5cf1713f919","creator":"dernst","content_type":"application/zip"}],"author":[{"full_name":"Hahn, David","first_name":"David","last_name":"Hahn","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"}],"month":"08","file_date_updated":"2020-07-14T12:48:13Z","ddc":["004","005","006","531","621"],"citation":{"ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>.","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","mla":"Hahn, David. <i>Brittle Fracture Simulation with Boundary Elements for Computer Graphics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>.","ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>","apa":"Hahn, D. (2017). <i>Brittle fracture simulation with boundary elements for computer graphics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>","ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria."},"year":"2017","ec_funded":1,"has_accepted_license":"1","related_material":{"record":[{"id":"1362","relation":"part_of_dissertation","status":"public"},{"id":"1633","relation":"part_of_dissertation","status":"public"},{"relation":"popular_science","id":"5568","status":"public"}]},"oa":1,"article_processing_charge":"No","doi":"10.15479/AT:ISTA:th_855","title":"Brittle fracture simulation with boundary elements for computer graphics","date_updated":"2024-02-21T13:48:02Z","day":"14","publication_identifier":{"issn":["2663-337X"]},"publist_id":"6809","date_published":"2017-08-14T00:00:00Z","status":"public","abstract":[{"text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. ","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","tmp":{"image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","date_created":"2018-12-11T11:48:47Z","alternative_title":["ISTA Thesis"],"type":"dissertation","project":[{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"supervisor":[{"last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"department":[{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"page":"1709 - 1735","abstract":[{"text":"The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind.","lang":"eng"}],"publication":"Handbook of Discrete and Computational Geometry, Third Edition","publist_id":"7970","status":"public","date_published":"2017-11-09T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"84","language":[{"iso":"eng"}],"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Koehl","first_name":"Patrice","full_name":"Koehl, Patrice"}],"oa_version":"None","month":"11","scopus_import":"1","date_created":"2018-12-11T11:44:32Z","citation":{"ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735.","apa":"Edelsbrunner, H., &#38; Koehl, P. (2017). Computational topology for structural molecular biology. In C. Toth, J. O’Rourke, &#38; J. Goodman (Eds.), <i>Handbook of Discrete and Computational Geometry, Third Edition</i> (pp. 1709–1735). Taylor &#38; Francis. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>","ama":"Edelsbrunner H, Koehl P. Computational topology for structural molecular biology. In: Toth C, O’Rourke J, Goodman J, eds. <i>Handbook of Discrete and Computational Geometry, Third Edition</i>. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis; 2017:1709-1735. doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>","short":"H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition, Taylor &#38; Francis, 2017, pp. 1709–1735.","mla":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth et al., Taylor &#38; Francis, 2017, pp. 1709–35, doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>.","chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” In <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis, 2017. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>.","ieee":"H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular biology,” in <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor &#38; Francis, 2017, pp. 1709–1735."},"series_title":"Handbook of Discrete and Computational Geometry","year":"2017","type":"book_chapter","article_processing_charge":"No","doi":"10.1201/9781315119601","editor":[{"last_name":"Toth","first_name":"Csaba","full_name":"Toth, Csaba"},{"full_name":"O'Rourke, Joseph","first_name":"Joseph","last_name":"O'Rourke"},{"last_name":"Goodman","first_name":"Jacob","full_name":"Goodman, Jacob"}],"title":"Computational topology for structural molecular biology","department":[{"_id":"HeEd"}],"quality_controlled":"1","day":"09","publication_status":"published","publication_identifier":{"eisbn":["9781498711425"]},"date_updated":"2023-10-16T11:15:22Z","publisher":"Taylor & Francis"},{"publication_identifier":{"issn":["15306984"]},"day":"10","date_updated":"2023-09-26T15:50:22Z","title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","doi":"10.1021/acs.nanolett.7b02627","isi":1,"external_id":{"isi":["000411043500078"]},"article_processing_charge":"No","oa":1,"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"id":"69","relation":"dissertation_contains","status":"public"},{"status":"public","id":"7996","relation":"dissertation_contains"}]},"has_accepted_license":"1","year":"2017","ec_funded":1,"citation":{"ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., &#38; Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. 2017;17(9):5706-5710. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>.","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” <i>Nano Letters</i>, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017."},"ddc":["539"],"month":"08","file_date_updated":"2020-07-14T12:48:13Z","file":[{"relation":"main_file","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","checksum":"761371a0129b2aa442424b9561450ece","creator":"system","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:13Z","date_created":"2018-12-12T10:12:33Z","file_size":2449546,"file_id":"4951"}],"author":[{"orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada","first_name":"Lada","last_name":"Vukusic","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"_id":"840","pubrep_id":"865","page":"5706 - 5710","issue":"9","publication_status":"published","publisher":"American Chemical Society","acknowledged_ssus":[{"_id":"M-Shop"}],"department":[{"_id":"GeKa"}],"project":[{"call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497"}],"quality_controlled":"1","volume":17,"type":"journal_article","scopus_import":"1","date_created":"2018-12-11T11:48:47Z","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        17","abstract":[{"text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.","lang":"eng"}],"status":"public","date_published":"2017-08-10T00:00:00Z","publication":"Nano Letters","publist_id":"6808"},{"oa_version":"Submitted Version","scopus_import":"1","date_created":"2018-12-11T11:49:09Z","abstract":[{"text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor &amp;#xbd; cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.","lang":"eng"}],"publist_id":"6534","publication":"The American Mathematical Monthly","status":"public","date_published":"2017-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       124","department":[{"_id":"HeEd"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","publisher":"Mathematical Association of America","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07997"}],"type":"journal_article","volume":124,"author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"last_name":"Vysotsky","first_name":"Vladislav","full_name":"Vysotsky, Vladislav"}],"month":"01","article_type":"original","arxiv":1,"citation":{"ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. 2017;124(7):588-596. doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>","apa":"Akopyan, A., &#38; Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. Mathematical Association of America. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>","ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.","ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” <i>The American Mathematical Monthly</i>, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>. Mathematical Association of America, 2017. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>."},"page":"588 - 596","issue":"7","_id":"909","language":[{"iso":"eng"}],"doi":"10.4169/amer.math.monthly.124.7.588","title":"On the lengths of curves passing through boundary points of a planar convex shape","external_id":{"isi":["000413947300002"],"arxiv":["1605.07997"]},"isi":1,"day":"01","publication_identifier":{"issn":["00029890"]},"date_updated":"2023-10-17T11:24:57Z","ec_funded":1,"year":"2017","article_processing_charge":"No","oa":1},{"page":"653 - 668","issue":"2","_id":"910","pubrep_id":"974","language":[{"iso":"eng"}],"file":[{"file_id":"5264","file_size":494268,"date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-12T10:17:12Z","access_level":"open_access","content_type":"application/pdf","checksum":"f7c32dabf52e6d9e709d9203761e39fd","creator":"system","relation":"main_file","file_name":"IST-2018-974-v1+1_manuscript.pdf"}],"author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"file_date_updated":"2020-07-14T12:48:15Z","month":"10","ddc":["576"],"citation":{"ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. 2017;207(2):653-668. doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","apa":"Novak, S., &#38; Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” <i>Genetics</i>, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668."},"has_accepted_license":"1","ec_funded":1,"year":"2017","oa":1,"article_processing_charge":"No","doi":"10.1534/genetics.117.300129","title":"When does frequency-independent selection maintain genetic variation?","external_id":{"isi":["000412232600019"]},"isi":1,"day":"01","date_updated":"2023-09-26T15:49:15Z","abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"publication":"Genetics","publist_id":"6533","date_published":"2017-10-01T00:00:00Z","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       207","oa_version":"Submitted Version","scopus_import":"1","date_created":"2018-12-11T11:49:09Z","type":"journal_article","volume":207,"department":[{"_id":"NiBa"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"publication_status":"published","publisher":"Genetics Society of America"},{"date_created":"2018-12-11T11:49:09Z","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-09-01T00:00:00Z","status":"public","publist_id":"6532","abstract":[{"lang":"eng","text":"We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset."}],"publisher":"BMVA Press","publication_status":"published","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"quality_controlled":"1","department":[{"_id":"ChLa"}],"type":"conference","citation":{"chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>.","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","mla":"Royer, Amélie, et al. <i>Probabilistic Image Colorization</i>. BMVA Press, 2017, p. 85.1-85.12, doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>.","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>","ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","apa":"Royer, A., Kolesnikov, A., &#38; Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>"},"arxiv":1,"ddc":["000"],"month":"09","file_date_updated":"2020-08-10T07:14:33Z","author":[{"orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","first_name":"Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kolesnikov, Alexander","first_name":"Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"file":[{"content_type":"application/pdf","file_name":"2017_BMVC_Royer.pdf","relation":"main_file","creator":"dernst","file_size":1625363,"file_id":"8224","success":1,"access_level":"open_access","date_created":"2020-08-10T07:14:33Z","date_updated":"2020-08-10T07:14:33Z"}],"language":[{"iso":"eng"}],"_id":"911","page":"85.1-85.12","date_updated":"2023-10-16T10:04:02Z","publication_identifier":{"eisbn":["190172560X"]},"day":"01","external_id":{"arxiv":["1705.04258"]},"title":"Probabilistic image colorization","doi":"10.5244/c.31.85","article_processing_charge":"No","oa":1,"year":"2017","ec_funded":1,"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"8390","relation":"dissertation_contains"}]},"conference":{"start_date":"2017-09-04","end_date":"2017-09-07","location":"London, United Kingdom","name":"BMVC: British Machine Vision Conference"}},{"main_file_link":[{"url":"https://arxiv.org/abs/1703.04616","open_access":"1"}],"type":"journal_article","volume":58,"department":[{"_id":"RoSe"}],"quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"}],"publication_status":"published","publisher":"AIP Publishing","abstract":[{"text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n","lang":"eng"}],"publist_id":"6531","publication":" Journal of Mathematical Physics","status":"public","date_published":"2017-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        58","oa_version":"Submitted Version","scopus_import":"1","date_created":"2018-12-11T11:49:10Z","ec_funded":1,"year":"2017","article_processing_charge":"No","oa":1,"doi":"10.1063/1.4996580","title":"A lower bound for the BCS functional with boundary conditions at infinity","external_id":{"isi":["000409197200015"]},"isi":1,"day":"01","publication_identifier":{"issn":["00222488"]},"date_updated":"2024-02-28T13:07:56Z","issue":"8","language":[{"iso":"eng"}],"_id":"912","author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","first_name":"Andreas","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746"}],"month":"08","article_number":"081901","citation":{"short":"A. Deuchert,  Journal of Mathematical Physics 58 (2017).","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>.","ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8. AIP Publishing, 2017.","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>.","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity.  Journal of Mathematical Physics. 58(8), 081901.","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. 2017;58(8). doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>"}},{"status":"public","date_published":"2017-07-05T00:00:00Z","publist_id":"6527","publication":"Royal Society Open Science","abstract":[{"text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.","lang":"eng"}],"intvolume":"         4","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","date_created":"2018-12-11T11:49:10Z","scopus_import":"1","volume":4,"type":"journal_article","quality_controlled":"1","department":[{"_id":"SyCr"}],"publisher":"Royal Society, The","publication_status":"published","issue":"7","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","_id":"914","pubrep_id":"849","language":[{"iso":"eng"}],"month":"07","article_number":"170547","file_date_updated":"2020-07-14T12:48:15Z","file":[{"file_size":530412,"file_id":"4684","access_level":"open_access","date_created":"2018-12-12T10:08:24Z","date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","creator":"system","checksum":"351ae5e7a37e6e7d9295cd41146c4190"}],"author":[{"first_name":"Julia","last_name":"Giehr","full_name":"Giehr, Julia"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer"},{"last_name":"Heinze","first_name":"Jürgen","full_name":"Heinze, Jürgen"},{"full_name":"Schrempf, Alexandra","first_name":"Alexandra","last_name":"Schrempf"}],"citation":{"ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. 2017;4(7). doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., &#38; Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547.","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” <i>Royal Society Open Science</i>, vol. 4, no. 7. Royal Society, The, 2017.","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>. Royal Society, The, 2017. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>.","mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>.","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017)."},"ddc":["576","592"],"year":"2017","related_material":{"record":[{"status":"public","relation":"research_data","id":"9853"}]},"has_accepted_license":"1","oa":1,"article_processing_charge":"No","isi":1,"external_id":{"isi":["000406670000025"]},"title":"Ant queens increase their reproductive efforts after pathogen infection","doi":"10.1098/rsos.170547","date_updated":"2023-09-26T15:45:47Z","publication_identifier":{"issn":["20545703"]},"day":"05"},{"abstract":[{"lang":"eng","text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes.  We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining."}],"date_published":"2017-07-01T00:00:00Z","status":"public","publist_id":"6526","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"      2017","oa_version":"Submitted Version","scopus_import":"1","date_created":"2018-12-11T11:49:11Z","volume":2017,"type":"conference","department":[{"_id":"VlKo"}],"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"quality_controlled":"1","publication_status":"published","publisher":"IEEE","page":"4990-4999","language":[{"iso":"eng"}],"_id":"915","file_date_updated":"2020-07-14T12:48:15Z","month":"07","file":[{"checksum":"7e51dacefa693574581a32da3eff63dc","creator":"dernst","relation":"main_file","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-01-18T12:52:46Z","access_level":"open_access","file_id":"5849","file_size":883264}],"author":[{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul"},{"full_name":"Andres, Bjoern","last_name":"Andres","first_name":"Bjoern"}],"citation":{"short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","mla":"Swoboda, Paul, and Bjoern Andres. <i>A Message Passing Algorithm for the Minimum Cost Multicut Problem</i>. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.530\">10.1109/CVPR.2017.530</a>.","ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.","chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.530\">https://doi.org/10.1109/CVPR.2017.530</a>.","apa":"Swoboda, P., &#38; Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.530\">https://doi.org/10.1109/CVPR.2017.530</a>","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.","ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.530\">10.1109/CVPR.2017.530</a>"},"ddc":["000"],"has_accepted_license":"1","conference":{"start_date":"2017-07-21","end_date":"2017-07-26","location":"Honolulu, HA, United States","name":"CVPR: Computer Vision and Pattern Recognition"},"year":"2017","ec_funded":1,"article_processing_charge":"No","oa":1,"title":"A message passing algorithm for the minimum cost multicut problem","doi":"10.1109/CVPR.2017.530","isi":1,"external_id":{"isi":["000418371405009"]},"publication_identifier":{"isbn":["978-153860457-1"]},"day":"01","date_updated":"2023-09-26T15:43:27Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"      2017","abstract":[{"text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each.","lang":"eng"}],"date_published":"2017-01-01T00:00:00Z","status":"public","publist_id":"6525","scopus_import":"1","date_created":"2018-12-11T11:49:11Z","oa_version":"Submitted Version","volume":2017,"type":"conference","publication_status":"published","publisher":"IEEE","department":[{"_id":"VlKo"}],"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"quality_controlled":"1","_id":"916","language":[{"iso":"eng"}],"page":"7062-7071","citation":{"chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.747\">https://doi.org/10.1109/CVPR.2017.747</a>.","ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071.","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","mla":"Swoboda, Paul, et al. <i>A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching</i>. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.747\">10.1109/CVPR.2017.747</a>.","ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.747\">10.1109/CVPR.2017.747</a>","ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., &#38; Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.747\">https://doi.org/10.1109/CVPR.2017.747</a>"},"ddc":["000"],"file_date_updated":"2020-07-14T12:48:15Z","month":"01","file":[{"access_level":"open_access","date_created":"2019-01-18T12:49:38Z","date_updated":"2020-07-14T12:48:15Z","file_size":944332,"file_id":"5848","relation":"main_file","file_name":"2017_CVPR_Swoboda2.pdf","creator":"dernst","checksum":"e38a2740daad1ea178465843b5072906","content_type":"application/pdf"}],"author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"},{"first_name":"Carsten","last_name":"Abu Alhaija","full_name":"Abu Alhaija, Carsten"},{"full_name":"Kainmueller, Dagmar","last_name":"Kainmueller","first_name":"Dagmar"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"article_processing_charge":"No","oa":1,"has_accepted_license":"1","conference":{"start_date":"2017-07-21","end_date":"2017-07-26","location":"Honolulu, HA, United States","name":"CVPR: Computer Vision and Pattern Recognition"},"ec_funded":1,"year":"2017","publication_identifier":{"isbn":["978-153860457-1"]},"day":"01","date_updated":"2023-09-26T15:41:40Z","title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","doi":"10.1109/CVPR.2017.747","isi":1,"external_id":{"isi":["000418371407018"]}},{"conference":{"start_date":"2017-07-21","end_date":"2017-07-26","location":"Honolulu, HA, United States","name":"CVPR: Computer Vision and Pattern Recognition"},"has_accepted_license":"1","ec_funded":1,"year":"2017","article_processing_charge":"No","oa":1,"doi":"10.1109/CVPR.2017.526","title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","external_id":{"isi":["000418371405005"]},"isi":1,"day":"01","publication_identifier":{"isbn":["978-153860457-1"]},"date_updated":"2023-09-26T15:41:11Z","page":"4950-4960","_id":"917","language":[{"iso":"eng"}],"file":[{"checksum":"72fd291046bd8e5717961bd68f6b6f03","creator":"dernst","relation":"main_file","file_name":"2017_CVPR_Swoboda.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-01-18T12:45:55Z","access_level":"open_access","file_id":"5847","file_size":898652}],"author":[{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul"},{"full_name":"Kuske, Jan","last_name":"Kuske","first_name":"Jan"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"month":"07","file_date_updated":"2020-07-14T12:48:15Z","ddc":["000"],"citation":{"mla":"Swoboda, Paul, et al. <i>A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems</i>. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.526\">10.1109/CVPR.2017.526</a>.","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","ieee":"P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.","chicago":"Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.526\">https://doi.org/10.1109/CVPR.2017.526</a>.","apa":"Swoboda, P., Kuske, J., &#38; Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.526\">https://doi.org/10.1109/CVPR.2017.526</a>","ista":"Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960.","ama":"Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.526\">10.1109/CVPR.2017.526</a>"},"type":"conference","volume":2017,"department":[{"_id":"VlKo"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"publication_status":"published","publisher":"IEEE","abstract":[{"lang":"eng","text":"We  propose  a  general  dual  ascent  framework  for  Lagrangean decomposition of combinatorial problems.  Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers."}],"publist_id":"6524","date_published":"2017-07-01T00:00:00Z","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"      2017","oa_version":"Submitted Version","scopus_import":"1","date_created":"2018-12-11T11:49:11Z"},{"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","doi":"10.15479/AT:ISTA:th_842","date_updated":"2023-09-07T12:06:09Z","publication_identifier":{"issn":["2663-337X"]},"day":"02","year":"2017","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"1591","relation":"part_of_dissertation"}]},"oa":1,"article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:15Z","month":"06","file":[{"file_name":"2017_Adamowski-Thesis_Source.docx","relation":"source_file","creator":"dernst","checksum":"193425764d9aaaed3ac57062a867b315","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","file_size":46903863,"file_id":"6215"},{"access_level":"open_access","date_created":"2019-04-05T09:03:19Z","date_updated":"2020-07-14T12:48:15Z","file_size":8698888,"file_id":"6216","file_name":"2017_Adamowski-Thesis.pdf","relation":"main_file","checksum":"df5ab01be81f821e1b958596a1ec8d21","creator":"dernst","content_type":"application/pdf"}],"author":[{"last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257"}],"citation":{"ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">10.15479/AT:ISTA:th_842</a>","apa":"Adamowski, M. (2017). <i>Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">https://doi.org/10.15479/AT:ISTA:th_842</a>","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">https://doi.org/10.15479/AT:ISTA:th_842</a>.","mla":"Adamowski, Maciek. <i>Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana </i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">10.15479/AT:ISTA:th_842</a>.","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017."},"ddc":["581","583","580"],"page":"117","_id":"938","pubrep_id":"842","language":[{"iso":"eng"}],"degree_awarded":"PhD","department":[{"_id":"JiFr"}],"supervisor":[{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","type":"dissertation","oa_version":"Published Version","date_created":"2018-12-11T11:49:18Z","alternative_title":["ISTA Thesis"],"date_published":"2017-06-02T00:00:00Z","status":"public","publist_id":"6483","abstract":[{"lang":"eng","text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"isi":1,"external_id":{"isi":["000405718200012"]},"title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","doi":"10.1103/PhysRevLett.119.033905","date_updated":"2023-09-26T15:39:46Z","publication_identifier":{"issn":["00319007"]},"day":"18","year":"2017","ec_funded":1,"oa":1,"article_processing_charge":"No","article_number":"033905","month":"07","author":[{"full_name":"Midya, Bikashkali","first_name":"Bikashkali","last_name":"Midya","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konotop, Vladimir","last_name":"Konotop","first_name":"Vladimir"}],"citation":{"short":"B. Midya, V. Konotop, Physical Review Letters 119 (2017).","mla":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” <i>Physical Review Letters</i>, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">10.1103/PhysRevLett.119.033905</a>.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">https://doi.org/10.1103/PhysRevLett.119.033905</a>.","ieee":"B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” <i>Physical Review Letters</i>, vol. 119, no. 3. American Physical Society, 2017.","ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.","apa":"Midya, B., &#38; Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">https://doi.org/10.1103/PhysRevLett.119.033905</a>","ama":"Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. <i>Physical Review Letters</i>. 2017;119(3). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">10.1103/PhysRevLett.119.033905</a>"},"issue":"3","_id":"939","language":[{"iso":"eng"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.04085 "}],"volume":119,"type":"journal_article","oa_version":"Submitted Version","date_created":"2018-12-11T11:49:18Z","scopus_import":"1","date_published":"2017-07-18T00:00:00Z","status":"public","publist_id":"6481","publication":"Physical Review Letters","abstract":[{"lang":"eng","text":"We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding."}],"intvolume":"       119","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"day":"27","publication_identifier":{"issn":["00278424"]},"date_updated":"2023-02-23T12:54:57Z","doi":"10.1073/pnas.1704470114","title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","external_id":{"pmid":["28607047"]},"oa":1,"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","year":"2017","ddc":["570"],"citation":{"ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. 2017;114(26):E5246-E5255. doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","ieee":"T. Miki <i>et al.</i>, “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” <i>PNAS</i>, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255."},"author":[{"full_name":"Miki, Takafumi","last_name":"Miki","first_name":"Takafumi"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"full_name":"Malagon, Gerardo","first_name":"Gerardo","last_name":"Malagon"},{"last_name":"Gomez","first_name":"Laura","full_name":"Gomez, Laura"},{"full_name":"Tabuchi, Katsuhiko","last_name":"Tabuchi","first_name":"Katsuhiko"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marty, Alain","last_name":"Marty","first_name":"Alain"}],"file":[{"file_size":2721544,"file_id":"7223","access_level":"open_access","date_updated":"2020-07-14T12:47:44Z","date_created":"2020-01-03T13:27:29Z","content_type":"application/pdf","file_name":"2017_PNAS_Miki.pdf","relation":"main_file","checksum":"2ab75d554f3df4a34d20fa8040589b7e","creator":"kschuh"}],"month":"06","file_date_updated":"2020-07-14T12:47:44Z","_id":"693","language":[{"iso":"eng"}],"page":"E5246 - E5255","issue":"26","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"quality_controlled":"1","pmid":1,"type":"journal_article","volume":114,"scopus_import":1,"date_created":"2018-12-11T11:47:57Z","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"       114","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"publication":"PNAS","publist_id":"7013","date_published":"2017-06-27T00:00:00Z","status":"public"},{"oa_version":"Published Version","date_created":"2018-12-11T11:47:58Z","scopus_import":1,"publist_id":"7008","publication":"Journal of Cell Science","status":"public","date_published":"2017-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells."}],"intvolume":"       130","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","pmid":1,"department":[{"_id":"MiSi"}],"publisher":"Company of Biologists","publication_status":"published","type":"journal_article","volume":130,"file":[{"checksum":"42c81a0a4fc3128883b391c3af3f74bc","creator":"dernst","file_name":"2017_CellScience_Vess.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2019-10-24T09:43:56Z","date_updated":"2020-07-14T12:47:45Z","access_level":"open_access","file_id":"6966","file_size":10847596}],"author":[{"first_name":"Astrid","last_name":"Veß","full_name":"Veß, Astrid"},{"full_name":"Blache, Ulrich","first_name":"Ulrich","last_name":"Blache"},{"full_name":"Leitner, Laura","last_name":"Leitner","first_name":"Laura"},{"last_name":"Kurz","first_name":"Angela","full_name":"Kurz, Angela"},{"last_name":"Ehrenpfordt","first_name":"Anja","full_name":"Ehrenpfordt, Anja"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"first_name":"Guido","last_name":"Posern","full_name":"Posern, Guido"}],"month":"07","file_date_updated":"2020-07-14T12:47:45Z","ddc":["570"],"citation":{"mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","ieee":"A. Veß <i>et al.</i>, “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” <i>Journal of Cell Science</i>, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., &#38; Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. 2017;130(13):2172-2184. doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>"},"article_type":"original","issue":"13","page":"2172 - 2184","language":[{"iso":"eng"}],"_id":"694","external_id":{"pmid":["28515231"]},"doi":"10.1242/jcs.200899","title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","date_updated":"2021-01-12T08:09:41Z","day":"01","publication_identifier":{"issn":["00219533"]},"year":"2017","has_accepted_license":"1","oa":1},{"doi":"10.1371/journal.pcbi.1005609","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","day":"18","publication_identifier":{"issn":["1553734X"]},"date_updated":"2024-03-25T23:30:14Z","related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"relation":"research_data","id":"9850","status":"public"},{"status":"public","id":"9851","relation":"research_data"},{"status":"public","relation":"research_data","id":"9852"},{"status":"public","id":"6263","relation":"dissertation_contains"}]},"has_accepted_license":"1","ec_funded":1,"year":"2017","oa":1,"file":[{"file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","relation":"main_file","creator":"system","checksum":"9143c290fa6458ed2563bff4b295554a","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:15:01Z","date_updated":"2020-07-14T12:47:46Z","file_size":3775716,"file_id":"5117"}],"author":[{"full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X"},{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao"}],"article_number":"e1005609","month":"07","file_date_updated":"2020-07-14T12:47:46Z","article_type":"original","ddc":["576"],"citation":{"mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>"},"issue":"7","_id":"696","pubrep_id":"894","language":[{"iso":"eng"}],"department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"quality_controlled":"1","project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","publisher":"Public Library of Science","type":"journal_article","volume":13,"oa_version":"Published Version","scopus_import":1,"date_created":"2018-12-11T11:47:58Z","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"publication":"PLoS Computational Biology","publist_id":"7004","date_published":"2017-07-18T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        13"},{"_id":"697","language":[{"iso":"eng"}],"pubrep_id":"893","ddc":["005"],"citation":{"apa":"Pietrzak, K. Z., &#38; Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. <i>Non Uniform Attacks against Pseudoentropy</i>. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>."},"file":[{"file_id":"4701","file_size":601004,"date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:08:40Z","access_level":"open_access","content_type":"application/pdf","creator":"system","checksum":"e95618a001692f1af2d68f5fde43bc1f","relation":"main_file","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf"}],"author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"article_number":"39","file_date_updated":"2020-07-14T12:47:46Z","month":"07","oa":1,"year":"2017","ec_funded":1,"conference":{"start_date":"2017-07-10","end_date":"2017-07-14","location":"Warsaw, Poland","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"has_accepted_license":"1","date_updated":"2021-01-12T08:11:15Z","day":"01","publication_identifier":{"issn":["18688969"]},"doi":"10.4230/LIPIcs.ICALP.2017.39","title":"Non uniform attacks against pseudoentropy","intvolume":"        80","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7003","date_published":"2017-07-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. "}],"date_created":"2018-12-11T11:47:59Z","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","type":"conference","volume":80,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrPi"}]},{"issue":"14","page":"1997 - 2009","_id":"698","pubrep_id":"892","language":[{"iso":"eng"}],"author":[{"first_name":"Yejun","last_name":"Wang","full_name":"Wang, Yejun"},{"full_name":"Nagarajan, Mallika","first_name":"Mallika","last_name":"Nagarajan"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gv","last_name":"Shivashankar","full_name":"Shivashankar, Gv"}],"file":[{"checksum":"de01dac9e30970cfa6ae902480a4e04d","creator":"system","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:53Z","date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","file_id":"4844","file_size":1086097}],"file_date_updated":"2020-07-14T12:47:46Z","month":"07","ddc":["519"],"citation":{"short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>.","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2017. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>.","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","apa":"Wang, Y., Nagarajan, M., Uhler, C., &#38; Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. 2017;28(14):1997-2009. doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>"},"year":"2017","has_accepted_license":"1","oa":1,"doi":"10.1091/mbc.E16-12-0825","title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","date_updated":"2021-01-12T08:11:17Z","day":"07","publication_identifier":{"issn":["10591524"]},"publication":"Molecular Biology of the Cell","publist_id":"7001","date_published":"2017-07-07T00:00:00Z","status":"public","abstract":[{"text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. ","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","intvolume":"        28","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2018-12-11T11:47:59Z","scopus_import":1,"type":"journal_article","volume":28,"quality_controlled":"1","project":[{"name":"Gaussian Graphical Models: Theory and Applications","_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35","call_identifier":"FWF"}],"department":[{"_id":"CaUh"}],"publisher":"American Society for Cell Biology","publication_status":"published"},{"department":[{"_id":"KrCh"}],"pmid":1,"quality_controlled":"1","publication_status":"published","publisher":"National Academy of Sciences","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"volume":114,"type":"journal_article","oa_version":"Submitted Version","scopus_import":1,"date_created":"2018-12-11T11:48:00Z","abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"status":"public","date_published":"2017-07-03T00:00:00Z","publication":"PNAS","publist_id":"7002","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       114","title":"The red queen and king in finite populations","doi":"10.1073/pnas.1702020114","external_id":{"pmid":["28630336"]},"publication_identifier":{"issn":["00278424"]},"day":"03","date_updated":"2021-01-12T08:11:21Z","year":"2017","oa":1,"month":"07","author":[{"last_name":"Veller","first_name":"Carl","full_name":"Veller, Carl"},{"full_name":"Hayward, Laura","first_name":"Laura","last_name":"Hayward"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"}],"citation":{"ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” <i>PNAS</i>, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” <i>PNAS</i>, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. <i>PNAS</i>. 2017;114(27):E5396-E5405. doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>","apa":"Veller, C., Hayward, L., Nowak, M., &#38; Hilbe, C. (2017). The red queen and king in finite populations. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405."},"page":"E5396 - E5405","issue":"27","_id":"699","language":[{"iso":"eng"}]},{"date_created":"2018-12-11T11:48:00Z","scopus_import":1,"oa_version":"Submitted Version","intvolume":"        96","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2017-07-12T00:00:00Z","status":"public","publist_id":"6997","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","abstract":[{"lang":"eng","text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs."}],"publisher":"American Institute of Physics","publication_status":"published","project":[{"grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"quality_controlled":"1","department":[{"_id":"JoFi"}],"volume":96,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1612.07061.pdf"}],"citation":{"ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1. American Institute of Physics, 2017.","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>.","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., &#38; Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404."},"article_number":"012404","month":"07","author":[{"first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"full_name":"Salari, Vahid","last_name":"Salari","first_name":"Vahid"},{"last_name":"Tuszynski","first_name":"Jack","full_name":"Tuszynski, Jack"},{"full_name":"Cifra, Michal","first_name":"Michal","last_name":"Cifra"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"_id":"700","language":[{"iso":"eng"}],"issue":"1","date_updated":"2023-02-23T12:56:35Z","publication_identifier":{"issn":["24700045"]},"day":"12","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","doi":"10.1103/PhysRevE.96.012404","oa":1,"year":"2017","ec_funded":1}]