[{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","ieee":"C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z"},"title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","article_processing_charge":"No","external_id":{"pmid":["30061750"],"isi":["000443861300016"]},"publist_id":"7777","author":[{"full_name":"Shi, Chun Lin","last_name":"Shi","first_name":"Chun Lin"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247"},{"last_name":"Herrmann","full_name":"Herrmann, Ullrich","first_name":"Ullrich"},{"first_name":"Mari","last_name":"Wildhagen","full_name":"Wildhagen, Mari"},{"id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","first_name":"Ivan","last_name":"Kulik","full_name":"Kulik, Ivan"},{"last_name":"Kopf","full_name":"Kopf, Andreas","first_name":"Andreas"},{"first_name":"Takashi","last_name":"Ishida","full_name":"Ishida, Takashi"},{"last_name":"Olsson","full_name":"Olsson, Vilde","first_name":"Vilde"},{"first_name":"Mari Kristine","full_name":"Anker, Mari Kristine","last_name":"Anker"},{"first_name":"Markus","full_name":"Albert, Markus","last_name":"Albert"},{"first_name":"Melinka A","last_name":"Butenko","full_name":"Butenko, Melinka A"},{"first_name":"Georg","last_name":"Felix","full_name":"Felix, Georg"},{"full_name":"Sawa, Shinichiro","last_name":"Sawa","first_name":"Shinichiro"},{"first_name":"Manfred","full_name":"Claassen, Manfred","last_name":"Claassen"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Reidunn B","last_name":"Aalen","full_name":"Aalen, Reidunn B"}],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Plants","day":"30","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:52Z","date_published":"2018-07-30T00:00:00Z","doi":"10.1038/s41477-018-0212-z","page":"596 - 604","_id":"146","status":"public","article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2023-09-19T10:08:45Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:56Z","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity.","lang":"eng"}],"intvolume":" 4","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:44:56Z","file_size":226829,"date_created":"2019-11-18T16:24:07Z","file_name":"2018_NaturePlants_Shi.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7043","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0"}],"publication_status":"published","issue":"8","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/","relation":"press_release"}]},"volume":4},{"acknowledgement":"This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"28","publication":"Nature Human Behaviour","page":"397 - 404","doi":"10.1038/s41562-018-0354-z","date_published":"2018-05-28T00:00:00Z","date_created":"2018-12-11T11:45:39Z","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"mla":"Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:10.1038/s41562-018-0354-z.","ama":"Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2018;2:397-404. doi:10.1038/s41562-018-0354-z","apa":"Hoffman, M., Hilbe, C., & Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0354-z","short":"M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404.","ieee":"M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 397–404, 2018.","chicago":"Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0354-z.","ista":"Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Hoffman","full_name":"Hoffman, Moshe","first_name":"Moshe"},{"last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"publist_id":"7588","external_id":{"isi":["000435551300009"]},"article_processing_charge":"No","title":"The signal-burying game can explain why we obscure positive traits and good deeds","abstract":[{"lang":"eng","text":"People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness."}],"oa_version":"Submitted Version","scopus_import":"1","month":"05","intvolume":" 2","publication_status":"published","file":[{"file_name":"2018_NatureHumanBeh_Hoffman.pdf","date_created":"2019-11-19T08:17:23Z","creator":"dernst","file_size":194734,"date_updated":"2020-07-14T12:45:54Z","checksum":"32efaf06a597495c184df91b3fbb19c0","file_id":"7051","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/","relation":"press_release"}]},"volume":2,"ec_funded":1,"_id":"293","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-19T10:12:03Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:54Z","department":[{"_id":"KrCh"}]},{"license":"https://creativecommons.org/licenses/by/4.0/","issue":"4","volume":19,"language":[{"iso":"eng"}],"file":[{"file_id":"4914","checksum":"883eeccba8384ad7fcaa28761d99a0fa","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:11:57Z","file_name":"IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf","date_updated":"2020-07-14T12:46:31Z","file_size":923252,"creator":"system"}],"publication_status":"published","intvolume":" 19","month":"04","scopus_import":"1","alternative_title":["Annales Henri Poincare"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities"}],"department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:46:31Z","ddc":["510","539"],"date_updated":"2023-09-19T10:07:41Z","pubrep_id":"993","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"455","date_created":"2018-12-11T11:46:34Z","date_published":"2018-04-01T00:00:00Z","doi":"10.1007/s00023-018-0644-z","page":"1167 - 1214","publication":"Annales Henri Poincare","day":"01","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Birkhäuser","quality_controlled":"1","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations.","title":"The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations","article_processing_charge":"No","external_id":{"isi":["000427578900006"]},"publist_id":"7367","author":[{"first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091","last_name":"Benedikter"},{"last_name":"Sok","full_name":"Sok, Jérémy","first_name":"Jérémy"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214.","chicago":"Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z.","apa":"Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z","ama":"Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z","short":"N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214.","ieee":"N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018.","mla":"Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z."}},{"volume":6,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2405-4712"]},"intvolume":" 6","month":"04","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cels.2018.04.003"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations."}],"department":[{"_id":"AnKi"}],"date_updated":"2023-09-19T10:11:25Z","status":"public","article_type":"letter_note","type":"journal_article","_id":"314","date_created":"2018-12-11T11:45:46Z","date_published":"2018-04-25T00:00:00Z","doi":"10.1016/j.cels.2018.04.003","page":"400 - 402","publication":"Cell Systems","day":"25","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Cell Press","title":"The science of living matter for tomorrow","article_processing_charge":"No","external_id":{"pmid":["29698645"],"isi":["000432192100003"]},"publist_id":"7551","author":[{"last_name":"Bauer","full_name":"Bauer, Guntram","first_name":"Guntram"},{"first_name":"Nikta","full_name":"Fakhri, Nikta","last_name":"Fakhri"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"last_name":"Kondev","full_name":"Kondev, Jané","first_name":"Jané"},{"first_name":"Karsten","last_name":"Kruse","full_name":"Kruse, Karsten"},{"last_name":"Noji","full_name":"Noji, Hiroyuki","first_name":"Hiroyuki"},{"last_name":"Riveline","full_name":"Riveline, Daniel","first_name":"Daniel"},{"last_name":"Saunders","full_name":"Saunders, Timothy","first_name":"Timothy"},{"last_name":"Thatta","full_name":"Thatta, Mukund","first_name":"Mukund"},{"first_name":"Eric","last_name":"Wieschaus","full_name":"Wieschaus, Eric"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” Cell Systems, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:10.1016/j.cels.2018.04.003.","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2018.04.003","ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. Cell Systems. 2018;6(4):400-402. doi:10.1016/j.cels.2018.04.003","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","ieee":"G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” Cell Systems. Cell Press, 2018. https://doi.org/10.1016/j.cels.2018.04.003.","ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402."}},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"intvolume":" 208","month":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":208,"_id":"565","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-19T10:12:31Z","department":[{"_id":"NiBa"}],"oa":1,"quality_controlled":"1","publisher":"Genetics ","publication":"Genetics","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:47:12Z","doi":"10.1534/genetics.117.300426","date_published":"2018-01-01T00:00:00Z","page":"377 - 382","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426"},"title":"The spread of an inversion with migration and selection","article_processing_charge":"No","external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"publist_id":"7249","author":[{"first_name":"Brian","full_name":"Charlesworth, Brian","last_name":"Charlesworth"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}]},{"status":"public","type":"journal_article","article_type":"original","_id":"446","department":[{"_id":"RoSe"}],"date_updated":"2023-09-19T10:09:40Z","intvolume":" 71","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.07355"}],"oa_version":"Preprint","abstract":[{"text":"We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential.","lang":"eng"}],"issue":"3","volume":71,"language":[{"iso":"eng"}],"publication_status":"published","title":"The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory","external_id":{"isi":["000422675800004"],"arxiv":["1606.07355"]},"article_processing_charge":"No","publist_id":"7377","author":[{"first_name":"Rupert","full_name":"Frank, Rupert","last_name":"Frank"},{"first_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan Thanh, Nam","last_name":"Phan Thanh"},{"last_name":"Van Den Bosch","full_name":"Van Den Bosch, Hanne","first_name":"Hanne"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614.","chicago":"Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717.","apa":"Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717","ama":"Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717","short":"R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614.","ieee":"R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018.","mla":"Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717."},"oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","acknowledgement":"We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n","date_created":"2018-12-11T11:46:31Z","doi":"10.1002/cpa.21717","date_published":"2018-03-01T00:00:00Z","page":"577 - 614","publication":"Communications on Pure and Applied Mathematics","day":"01","year":"2018","isi":1},{"quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Genetics","page":"1351 - 1355","doi":"10.1534/genetics.118.300786","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:46:26Z","citation":{"mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7393","author":[{"last_name":"Novembre","full_name":"Novembre, John","first_name":"John"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"article_processing_charge":"No","external_id":{"isi":["000429094400005"]},"title":"Tread lightly interpreting polygenic tests of selection","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 208","publication_status":"published","file":[{"file_id":"4958","checksum":"3d838dc285df394376555b794b6a5ad1","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","date_created":"2018-12-12T10:12:40Z","file_size":500129,"date_updated":"2020-07-14T12:46:26Z","creator":"system"}],"language":[{"iso":"eng"}],"volume":208,"issue":"4","_id":"430","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"1012","date_updated":"2023-09-19T10:17:30Z","ddc":["576"],"file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"NiBa"}]},{"_id":"199","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-09-19T10:15:31Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"BeVi"}],"abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":3985796,"date_updated":"2020-07-14T12:45:22Z","file_name":"2018_Genes_Ma.pdf","date_created":"2019-02-01T07:52:28Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","file_id":"5905"}],"issue":"6","volume":9,"article_number":"294","citation":{"chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294.","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000436494200026"]},"publist_id":"7714","author":[{"full_name":"Ma, Wen","last_name":"Ma","first_name":"Wen"},{"full_name":"Veltsos, Paris","last_name":"Veltsos","first_name":"Paris"},{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rodrigues, Nicolas","last_name":"Rodrigues","first_name":"Nicolas"},{"full_name":"Sermier, Roberto","last_name":"Sermier","first_name":"Roberto"},{"first_name":"Daniel","full_name":"Jeffries, Daniel","last_name":"Jeffries"},{"first_name":"Nicolas","last_name":"Perrin","full_name":"Perrin, Nicolas"}],"title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","oa":1,"quality_controlled":"1","publisher":"MDPI AG","year":"2018","isi":1,"has_accepted_license":"1","publication":"Genes","day":"12","date_created":"2018-12-11T11:45:09Z","date_published":"2018-06-12T00:00:00Z","doi":"10.3390/genes9060294"},{"month":"01","intvolume":" 115","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits."}],"volume":115,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"543","department":[{"_id":"GaTk"}],"date_updated":"2023-09-19T10:16:35Z","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"doi":"10.1073/pnas.1711114115","date_published":"2018-01-02T00:00:00Z","date_created":"2018-12-11T11:47:04Z","page":"186 - 191","day":"02","publication":"PNAS","isi":1,"year":"2018","project":[{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26"}],"title":"Toward a unified theory of efficient, predictive, and sparse coding","author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"publist_id":"7273","external_id":{"isi":["000419128700049"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115."}},{"department":[{"_id":"EdHa"}],"date_updated":"2023-09-19T10:13:55Z","status":"public","type":"journal_article","_id":"421","issue":"4","volume":114,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 114","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.01486"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","external_id":{"arxiv":["1709.01486"],"isi":["000428016700021"]},"article_processing_charge":"No","publist_id":"7403","author":[{"first_name":"Kinjal","full_name":"Dasbiswas, Kinjal","last_name":"Dasbiswas"},{"full_name":"Hannezo, Claude-Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022.","short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022","apa":"Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022."},"date_created":"2018-12-11T11:46:23Z","date_published":"2018-02-27T00:00:00Z","doi":"10.1016/j.bpj.2017.12.022","page":"968 - 977","publication":"Biophysical Journal","day":"27","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Biophysical Society"},{"department":[{"_id":"BeVi"}],"file_date_updated":"2020-07-14T12:47:27Z","ddc":["570"],"date_updated":"2023-09-19T10:37:03Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"63","ec_funded":1,"issue":"10","volume":9,"language":[{"iso":"eng"}],"file":[{"file_name":"2018_Genes_Gammerdinger.pdf","date_created":"2018-12-18T09:54:46Z","file_size":1415791,"date_updated":"2020-07-14T12:47:27Z","creator":"dernst","file_id":"5743","checksum":"bec527692e2c9b56919c0429634ff337","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","intvolume":" 9","month":"10","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.","lang":"eng"}],"title":"Unusual diversity of sex chromosomes in African cichlid fishes","article_processing_charge":"No","external_id":{"isi":["000448656700018"]},"publist_id":"7991","author":[{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220"},{"full_name":"Kocher, Thomas","last_name":"Kocher","first_name":"Thomas"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480.","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018, doi:10.3390/genes9100480.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480"},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"480","date_created":"2018-12-11T11:44:26Z","doi":"10.3390/genes9100480","date_published":"2018-10-04T00:00:00Z","publication":"Genes","day":"04","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"MDPI AG","quality_controlled":"1","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship"},{"date_updated":"2023-09-19T10:37:55Z","department":[{"_id":"MaSe"}],"_id":"296","article_type":"original","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":14,"abstract":[{"text":"The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/130860/"}],"month":"05","intvolume":" 14","citation":{"chicago":"Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5.","ista":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749.","mla":"Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:10.1038/s41567-018-0137-5.","ieee":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature Publishing Group, pp. 745–749, 2018.","short":"C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749.","ama":"Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5","apa":"Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Turner","full_name":"Turner, Christopher","first_name":"Christopher"},{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis"},{"full_name":"Abanin, Dmitry","last_name":"Abanin","first_name":"Dmitry"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"}],"publist_id":"7585","article_processing_charge":"No","external_id":{"isi":["000438253600028"]},"title":"Weak ergodicity breaking from quantum many-body scars","isi":1,"year":"2018","day":"14","publication":"Nature Physics","page":"745 - 749","doi":"10.1038/s41567-018-0137-5","date_published":"2018-05-14T00:00:00Z","date_created":"2018-12-11T11:45:40Z","acknowledgement":"C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation.","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1},{"year":"2018","isi":1,"publication":"Physica D: Nonlinear Phenomena","day":"01","page":"108-120","date_created":"2018-12-11T11:47:28Z","date_published":"2018-08-01T00:00:00Z","doi":"10.1016/j.physd.2017.10.015","acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.","apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"article_processing_charge":"No","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Bodova","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171"},{"first_name":"Jan","full_name":"Haskovec, Jan","last_name":"Haskovec"},{"last_name":"Markowich","full_name":"Markowich, Peter","first_name":"Peter"}],"publist_id":"7198","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","publication_status":"published","language":[{"iso":"eng"}],"volume":"376-377","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1704.08757","open_access":"1"}],"scopus_import":"1","month":"08","date_updated":"2023-09-19T10:38:34Z","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"_id":"607","type":"journal_article","status":"public"},{"title":"Two-photon processes based on quantum commutators","article_processing_charge":"No","external_id":{"arxiv":["1801.06892"],"isi":["000430296800008"]},"publist_id":"7587","author":[{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"},{"full_name":"Safari, Laleh","last_name":"Safari","first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pedro","full_name":"Amaro, Pedro","last_name":"Amaro"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842.","ista":"Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4).","mla":"Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842.","ama":"Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043842","apa":"Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842","ieee":"F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","short":"F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018)."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:40Z","doi":"10.1103/PhysRevA.97.043842","date_published":"2018-04-18T00:00:00Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","day":"18","year":"2018","isi":1,"oa":1,"publisher":"American Physical Society","quality_controlled":"1","department":[{"_id":"MiLe"}],"date_updated":"2023-09-19T10:17:56Z","status":"public","type":"journal_article","_id":"294","ec_funded":1,"issue":"4","volume":97,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 97","month":"04","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.06892"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed.","lang":"eng"}]},{"volume":35,"issue":"5","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00268"}],"scopus_import":"1","intvolume":" 35","month":"08","abstract":[{"text":"We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"JuFi"}],"date_updated":"2023-09-19T10:39:09Z","type":"journal_article","status":"public","_id":"606","page":"1267-1319","date_created":"2018-12-11T11:47:27Z","date_published":"2018-08-01T00:00:00Z","doi":"10.1016/j.anihpc.2017.11.004","year":"2018","isi":1,"publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","day":"01","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n","external_id":{"arxiv":["1607.00268"],"isi":["000437975500005"]},"article_processing_charge":"No","publist_id":"7199","author":[{"last_name":"Duerinckx","full_name":"Duerinckx, Mitia","first_name":"Mitia"},{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X"}],"title":"Well-posedness for mean-field evolutions arising in superconductivity","citation":{"ista":"Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319.","chicago":"Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004.","apa":"Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004","ama":"Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004","short":"M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319.","ieee":"M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018.","mla":"Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"quality_controlled":"1","publisher":"IEEE","oa":1,"doi":"10.1109/emsoft.2018.8537203","date_published":"2018-09-30T00:00:00Z","date_created":"2019-02-13T09:19:28Z","page":"1-10","day":"30","publication":"2018 International Conference on Embedded Software","isi":1,"has_accepted_license":"1","year":"2018","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"title":"Keynote: The first-order logic of signals","author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Nickovicl","full_name":"Nickovicl, Deian","first_name":"Deian"}],"external_id":{"isi":["000492828500005"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In 2018 International Conference on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203.","ista":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software, 1–10.","mla":"Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.","short":"A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10.","ieee":"A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in 2018 International Conference on Embedded Software, Turin, Italy, 2018, pp. 1–10.","ama":"Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: 2018 International Conference on Embedded Software. IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203","apa":"Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018). Keynote: The first-order logic of signals. In 2018 International Conference on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203"},"month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain."}],"file":[{"date_created":"2020-05-14T16:01:29Z","file_name":"2018_EMSOFT_Bakhirkin.pdf","date_updated":"2020-07-14T12:47:13Z","file_size":338006,"creator":"dernst","file_id":"7839","checksum":"234a33ad9055b3458fcdda6af251b33a","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781538655603"]},"publication_status":"published","status":"public","type":"conference","conference":{"location":"Turin, Italy","end_date":"2018-10-05","start_date":"2018-09-30","name":"EMSOFT: International Conference on Embedded Software"},"_id":"5959","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-09-19T10:41:29Z"},{"date_updated":"2023-09-19T10:42:53Z","department":[{"_id":"DaAl"}],"_id":"5962","type":"conference","conference":{"end_date":"2018-07-27","location":"Egham, United Kingdom","start_date":"2018-07-23","name":"PODC: Principles of Distributed Computing"},"status":"public","publication_identifier":{"isbn":["9781450357951"]},"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"text":"Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard shared-memory model are still not well-understood. In this work, we address this gap, and provide new convergence bounds for lock-free concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the \"price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental trade-off between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.08841","open_access":"1"}],"month":"07","citation":{"mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763.","short":"D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 169–178.","ieee":"D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic gradient descent in asynchronous shared memory,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 169–178.","ama":"Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:169-178. doi:10.1145/3212734.3212763","apa":"Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence of stochastic gradient descent in asynchronous shared memory. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763","chicago":"Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763.","ista":"Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 169–178."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"De Sa","full_name":"De Sa, Christopher","first_name":"Christopher"},{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H"}],"article_processing_charge":"No","external_id":{"isi":["000458186900022"],"arxiv":["1803.08841"]},"title":"The convergence of stochastic gradient descent in asynchronous shared memory","isi":1,"year":"2018","day":"23","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","page":"169-178","date_published":"2018-07-23T00:00:00Z","doi":"10.1145/3212734.3212763","date_created":"2019-02-13T09:58:58Z","publisher":"ACM Press","quality_controlled":"1","oa":1},{"oa":1,"quality_controlled":"1","publisher":"Royal Society Publishing","date_created":"2019-01-20T22:59:19Z","doi":"10.1098/rsif.2018.0395","date_published":"2018-12-12T00:00:00Z","year":"2018","isi":1,"publication":"Journal of the Royal Society Interface","day":"12","article_number":"20180395","article_processing_charge":"No","external_id":{"isi":["000456783800002"],"arxiv":["1612.01605"]},"author":[{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","first_name":"Bernat"},{"last_name":"Seoane","full_name":"Seoane, Luís F.","first_name":"Luís F."},{"last_name":"Solé","full_name":"Solé, Ricard","first_name":"Ricard"}],"title":"Zipf's Law, unbounded complexity and open-ended evolution","citation":{"ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395","ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395.","ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/1612.01605","open_access":"1"}],"scopus_import":"1","intvolume":" 15","month":"12","abstract":[{"text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.","lang":"eng"}],"oa_version":"Preprint","issue":"149","volume":15,"publication_status":"published","publication_identifier":{"issn":["17425689"]},"language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"5860","department":[{"_id":"EdHa"}],"date_updated":"2023-09-19T10:40:38Z"},{"citation":{"ieee":"S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” The International Journal of Robotics Research, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018.","short":"S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516.","apa":"Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. SAGE Publications. https://doi.org/10.1177/0278364918808367","ama":"Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516. doi:10.1177/0278364918808367","mla":"Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:10.1177/0278364918808367.","ista":"Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516.","chicago":"Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Simon","full_name":"Rohou, Simon","last_name":"Rohou"},{"orcid":"0000-0001-8878-8397","full_name":"Franek, Peter","last_name":"Franek","id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Clément","full_name":"Aubry, Clément","last_name":"Aubry"},{"first_name":"Luc","full_name":"Jaulin, Luc","last_name":"Jaulin"}],"external_id":{"isi":["000456881100004"],"arxiv":["1712.01341"]},"article_processing_charge":"No","title":"Proving the existence of loops in robot trajectories","quality_controlled":"1","publisher":"SAGE Publications","oa":1,"isi":1,"year":"2018","day":"24","publication":"The International Journal of Robotics Research","page":"1500-1516","date_published":"2018-10-24T00:00:00Z","doi":"10.1177/0278364918808367","date_created":"2019-02-13T09:36:20Z","_id":"5960","type":"journal_article","status":"public","date_updated":"2023-09-19T10:41:59Z","department":[{"_id":"UlWa"}],"abstract":[{"text":"In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.01341"}],"month":"10","intvolume":" 37","publication_identifier":{"issn":["0278-3649"],"eissn":["1741-3176"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":37,"issue":"12"},{"title":"Relaxed schedulers can efficiently parallelize iterative algorithms","external_id":{"isi":["000458186900048"],"arxiv":["1808.04155"]},"article_processing_charge":"No","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Brown, Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A"},{"full_name":"Kopinsky, Justin","last_name":"Kopinsky","first_name":"Justin"},{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","first_name":"Giorgi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–86, doi:10.1145/3212734.3212756.","short":"D.-A. Alistarh, T.A. Brown, J. Kopinsky, G. Nadiradze, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, ACM Press, 2018, pp. 377–386.","ieee":"D.-A. Alistarh, T. A. Brown, J. Kopinsky, and G. Nadiradze, “Relaxed schedulers can efficiently parallelize iterative algorithms,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, Egham, United Kingdom, 2018, pp. 377–386.","ama":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. Relaxed schedulers can efficiently parallelize iterative algorithms. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. ACM Press; 2018:377-386. doi:10.1145/3212734.3212756","apa":"Alistarh, D.-A., Brown, T. A., Kopinsky, J., & Nadiradze, G. (2018). Relaxed schedulers can efficiently parallelize iterative algorithms. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18 (pp. 377–386). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212756","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, Justin Kopinsky, and Giorgi Nadiradze. “Relaxed Schedulers Can Efficiently Parallelize Iterative Algorithms.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18, 377–86. ACM Press, 2018. https://doi.org/10.1145/3212734.3212756.","ista":"Alistarh D-A, Brown TA, Kopinsky J, Nadiradze G. 2018. Relaxed schedulers can efficiently parallelize iterative algorithms. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC ’18. PODC: Principles of Distributed Computing, 377–386."},"oa":1,"quality_controlled":"1","publisher":"ACM Press","date_created":"2019-02-13T10:03:25Z","date_published":"2018-07-23T00:00:00Z","doi":"10.1145/3212734.3212756","page":"377-386","publication":"Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18","day":"23","year":"2018","isi":1,"status":"public","conference":{"start_date":"2018-07-23","location":"Egham, United Kingdom","end_date":"2018-07-27","name":"PODC: Principles of Distributed Computing"},"type":"conference","_id":"5963","department":[{"_id":"DaAl"}],"date_updated":"2023-09-19T10:43:21Z","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.04155"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"There has been significant progress in understanding the parallelism inherent to iterative sequential algorithms: for many classic algorithms, the depth of the dependence structure is now well understood, and scheduling techniques have been developed to exploit this shallow dependence structure for efficient parallel implementations. A related, applied research strand has studied methods by which certain iterative task-based algorithms can be efficiently parallelized via relaxed concurrent priority schedulers. These allow for high concurrency when inserting and removing tasks, at the cost of executing superfluous work due to the relaxed semantics of the scheduler. In this work, we take a step towards unifying these two research directions, by showing that there exists a family of relaxed priority schedulers that can efficiently and deterministically execute classic iterative algorithms such as greedy maximal independent set (MIS) and matching. Our primary result shows that, given a randomized scheduler with an expected relaxation factor of k in terms of the maximum allowed priority inversions on a task, and any graph on n vertices, the scheduler is able to execute greedy MIS with only an additive factor of \\poly(k) expected additional iterations compared to an exact (but not scalable) scheduler. This counter-intuitive result demonstrates that the overhead of relaxation when computing MIS is not dependent on the input size or structure of the input graph. Experimental results show that this overhead can be clearly offset by the gain in performance due to the highly scalable scheduler. In sum, we present an efficient method to deterministically parallelize iterative sequential algorithms, with provable runtime guarantees in terms of the number of executed tasks to completion.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781450357951"]}}]