[{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1830"}]},"doi":"10.5061/dryad.dj2bf","date_published":"2015-12-29T00:00:00Z","date_created":"2021-07-26T09:38:36Z","day":"29","year":"2015","month":"12","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.dj2bf"}],"oa":1,"oa_version":"Published Version","abstract":[{"text":"To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.","lang":"eng"}],"title":"Data from: Opposing effects of allogrooming on disease transmission in ant societies","department":[{"_id":"SyCr"}],"author":[{"first_name":"Fabian","full_name":"Theis, Fabian","last_name":"Theis"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"first_name":"Carsten","full_name":"Marr, Carsten","last_name":"Marr"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Theis, Fabian, et al. Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies. Dryad, 2015, doi:10.5061/dryad.dj2bf.","apa":"Theis, F., Ugelvig, L. V., Marr, C., & Cremer, S. (2015). Data from: Opposing effects of allogrooming on disease transmission in ant societies. Dryad. https://doi.org/10.5061/dryad.dj2bf","ama":"Theis F, Ugelvig LV, Marr C, Cremer S. Data from: Opposing effects of allogrooming on disease transmission in ant societies. 2015. doi:10.5061/dryad.dj2bf","ieee":"F. Theis, L. V. Ugelvig, C. Marr, and S. Cremer, “Data from: Opposing effects of allogrooming on disease transmission in ant societies.” Dryad, 2015.","short":"F. Theis, L.V. Ugelvig, C. Marr, S. Cremer, (2015).","chicago":"Theis, Fabian, Line V Ugelvig, Carsten Marr, and Sylvia Cremer. “Data from: Opposing Effects of Allogrooming on Disease Transmission in Ant Societies.” Dryad, 2015. https://doi.org/10.5061/dryad.dj2bf.","ista":"Theis F, Ugelvig LV, Marr C, Cremer S. 2015. Data from: Opposing effects of allogrooming on disease transmission in ant societies, Dryad, 10.5061/dryad.dj2bf."},"date_updated":"2023-02-23T10:16:22Z","status":"public","type":"research_data_reference","_id":"9721"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001.","mla":"Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015)."},"date_updated":"2023-02-23T10:16:13Z","department":[{"_id":"GaTk"}],"title":"Supporting information text","article_processing_charge":"No","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"},{"full_name":"Mayo, Avraham E.","last_name":"Mayo","first_name":"Avraham E."},{"last_name":"Tlusty","full_name":"Tlusty, Tsvi","first_name":"Tsvi"},{"first_name":"Uri","full_name":"Alon, Uri","last_name":"Alon"}],"_id":"9718","status":"public","type":"research_data_reference","day":"23","year":"2015","date_created":"2021-07-26T08:35:23Z","doi":"10.1371/journal.pcbi.1004055.s001","related_material":{"record":[{"relation":"used_in_publication","id":"1827","status":"public"}]},"date_published":"2015-03-23T00:00:00Z","oa_version":"Published Version","month":"03","publisher":"Public Library of Science"},{"title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","author":[{"first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova","full_name":"Symonova, Olga"},{"last_name":"Topp","full_name":"Topp, Christopher","first_name":"Christopher"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"publist_id":"5318","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” PLoS One, vol. 10, no. 6. Public Library of Science, 2015.","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015).","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 2015;10(6). doi:10.1371/journal.pone.0127657","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” PLoS One, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:10.1371/journal.pone.0127657."},"article_number":"e0127657","date_published":"2015-06-01T00:00:00Z","doi":"10.1371/journal.pone.0127657","date_created":"2018-12-11T11:54:02Z","day":"01","publication":"PLoS One","has_accepted_license":"1","year":"2015","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"department":[{"_id":"MaJö"},{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:16Z","ddc":["000"],"date_updated":"2023-02-23T14:06:33Z","status":"public","pubrep_id":"454","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)"},"_id":"1793","issue":"6","related_material":{"record":[{"relation":"research_data","status":"public","id":"9737"}]},"volume":10,"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d20f26461ca575276ad3ed9ce4bfc787","file_id":"5150","date_updated":"2020-07-14T12:45:16Z","file_size":1850825,"creator":"system","date_created":"2018-12-12T10:15:30Z","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 10","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth."}]},{"day":"01","year":"2015","related_material":{"record":[{"relation":"used_in_publication","id":"1793","status":"public"}]},"doi":"10.1371/journal.pone.0127657.s001","date_published":"2015-06-01T00:00:00Z","date_created":"2021-07-28T06:20:13Z","oa_version":"Published Version","month":"06","publisher":"Public Library of Science","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001."},"date_updated":"2023-02-23T10:14:42Z","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","author":[{"full_name":"Symonova, Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga"},{"first_name":"Christopher","last_name":"Topp","full_name":"Topp, Christopher"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"article_processing_charge":"No","_id":"9737","status":"public","type":"research_data_reference"},{"related_material":{"record":[{"relation":"research_data","id":"9718","status":"public"},{"relation":"research_data","id":"9773","status":"public"}]},"issue":"3","volume":11,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-12T10:15:39Z","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","creator":"system","date_updated":"2020-07-14T12:45:17Z","file_size":1811647,"file_id":"5161","checksum":"b8aa66f450ff8de393014b87ec7d2efb","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"03","intvolume":" 11","abstract":[{"lang":"eng","text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"GaTk"}],"date_updated":"2023-02-23T14:07:51Z","ddc":["576"],"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":"452","_id":"1827","doi":"10.1371/journal.pcbi.1004055","date_published":"2015-03-23T00:00:00Z","date_created":"2018-12-11T11:54:14Z","has_accepted_license":"1","year":"2015","day":"23","publication":"PLoS Computational Biology","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"author":[{"last_name":"Friedlander","full_name":"Friedlander, Tamar","first_name":"Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Avraham","last_name":"Mayo","full_name":"Mayo, Avraham"},{"first_name":"Tsvi","full_name":"Tlusty, Tsvi","last_name":"Tlusty"},{"first_name":"Uri","last_name":"Alon","full_name":"Alon, Uri"}],"publist_id":"5278","article_processing_charge":"No","title":"Evolution of bow-tie architectures in biology","citation":{"ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055","apa":"Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]},{"date_updated":"2023-02-23T14:07:48Z","ddc":["570","576"],"file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"NiBa"}],"_id":"1809","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":"453","publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:45:17Z","file_size":2748982,"date_created":"2018-12-12T10:09:07Z","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_id":"4730"}],"language":[{"iso":"eng"}],"volume":10,"issue":"5","related_material":{"record":[{"id":"9715","status":"public","relation":"research_data"},{"status":"public","id":"9772","relation":"research_data"}]},"abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"oa_version":"Published Version","scopus_import":1,"month":"05","intvolume":" 10","citation":{"ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"publist_id":"5299","title":"Indirect genetic effects and the dynamics of social interactions","has_accepted_license":"1","year":"2015","day":"18","publication":"PLoS One","doi":"10.1371/journal.pone.0126907","date_published":"2015-05-18T00:00:00Z","date_created":"2018-12-11T11:54:07Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1},{"title":"Description of the agent based simulations","department":[{"_id":"NiBa"}],"article_processing_charge":"No","author":[{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967"},{"first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","short":"B. Trubenova, S. Novak, R. Hager, (2015).","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003."},"date_updated":"2023-02-23T10:15:25Z","status":"public","type":"research_data_reference","_id":"9772","date_created":"2021-08-05T12:55:20Z","date_published":"2015-05-18T00:00:00Z","related_material":{"record":[{"status":"public","id":"1809","relation":"used_in_publication"}]},"doi":"10.1371/journal.pone.0126907.s003","day":"18","year":"2015","month":"05","publisher":"Public Library of Science","oa_version":"Published Version"},{"title":"Evolutionary simulation code","department":[{"_id":"GaTk"}],"author":[{"last_name":"Friedlander","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"first_name":"Avraham E.","full_name":"Mayo, Avraham E.","last_name":"Mayo"},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"full_name":"Alon, Uri","last_name":"Alon","first_name":"Uri"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","mla":"Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002.","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002."},"date_updated":"2023-02-23T10:16:13Z","status":"public","type":"research_data_reference","_id":"9773","related_material":{"record":[{"relation":"used_in_publication","id":"1827","status":"public"}]},"date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s002","date_created":"2021-08-05T12:58:07Z","day":"23","year":"2015","month":"03","publisher":"Public Library of Science","oa_version":"Published Version"},{"issue":"3","volume":14,"doi":"10.1038/nmat4215","date_published":"2015-03-01T00:00:00Z","date_created":"2018-12-11T11:49:31Z","page":"318 - 324","day":"01","publication":"Nature Materials","year":"2015","publication_status":"published","month":"03","intvolume":" 14","quality_controlled":0,"publisher":"Nature Publishing Group","main_file_link":[{"url":"https://arxiv.org/abs/1403.4906","open_access":"1"}],"oa":1,"acknowledgement":"We thank R. Buczko, C. Chamon, J. C. Seamus Davis, M. El-Batanouny, A. Mesaros, Y. Ran and A. Soumyanarayanan for useful conversations and G. McMahon for help with EDS measurements. V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the support of I.Z., Y.O., W.Z. and D.W. for this project. Work at Massachusetts Institute of Technology is supported by US Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0010526 (L.F.), and NSF-DMR-1104498 (M.S.). H.L. acknowledges the Singapore National Research Foundation for support under NRF Award No. NRF-NRFF2013-03. Y.O. was partly supported by JSPS KAKENHI Grant Numbers 26707016 and 00707656. The work at Northeastern University is supported by the US Department of Energy grant number DE-FG02-07ER46352, and benefited from Northeastern University’s Advanced Scientific Computation Center (ASCC), theory support at the Advanced Light Source, Berkeley and the allocation of supercomputer time at the NERSC through DOE grant number DE-AC02-05CH11231. Work at Princeton University is supported by the US National Science Foundation Grant, NSF-DMR-1006492. F.C. acknowledges the support provided by MOST-Taiwan under project number NSC-102-2119-M-002-004.","abstract":[{"lang":"eng","text":"The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials."}],"title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","publist_id":"6419","author":[{"last_name":"Zeljkovic","full_name":"Zeljkovic, Ilija","first_name":"Ilija"},{"first_name":"Yoshinori","full_name":"Okada, Yoshinori","last_name":"Okada"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827"},{"first_name":"Raman","full_name":"Sankar, Raman","last_name":"Sankar"},{"first_name":"Daniel","full_name":"Walkup, Daniel","last_name":"Walkup"},{"first_name":"Wenwen","last_name":"Zhou","full_name":"Zhou, Wenwen"},{"first_name":"Junwei","full_name":"Liu, Junwei","last_name":"Liu"},{"first_name":"Guoqing","last_name":"Chang","full_name":"Chang, Guoqing"},{"last_name":"Wang","full_name":"Wang, Yungjui","first_name":"Yungjui"},{"first_name":"Md","last_name":"Hasan","full_name":"Hasan, Md Z"},{"last_name":"Chou","full_name":"Chou, Fangcheng","first_name":"Fangcheng"},{"first_name":"Hsin","last_name":"Lin","full_name":"Lin, Hsin"},{"first_name":"Arun","full_name":"Bansil, Arun","last_name":"Bansil"},{"first_name":"Liang","last_name":"Fu","full_name":"Fu, Liang"},{"first_name":"Vidya","last_name":"Madhavan","full_name":"Madhavan, Vidya"}],"extern":1,"citation":{"mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:10.1038/nmat4215.","ieee":"I. Zeljkovic et al., “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” Nature Materials, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","short":"I. Zeljkovic, Y. Okada, M. Serbyn, R. Sankar, D. Walkup, W. Zhou, J. Liu, G. Chang, Y. Wang, M. Hasan, F. Chou, H. Lin, A. Bansil, L. Fu, V. Madhavan, Nature Materials 14 (2015) 318–324.","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 2015;14(3):318-324. doi:10.1038/nmat4215","apa":"Zeljkovic, I., Okada, Y., Serbyn, M., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2015). Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. Nature Publishing Group. https://doi.org/10.1038/nmat4215","chicago":"Zeljkovic, Ilija, Yoshinori Okada, Maksym Serbyn, Raman Sankar, Daniel Walkup, Wenwen Zhou, Junwei Liu, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” Nature Materials. Nature Publishing Group, 2015. https://doi.org/10.1038/nmat4215.","ista":"Zeljkovic I, Okada Y, Serbyn M, Sankar R, Walkup D, Zhou W, Liu J, Chang G, Wang Y, Hasan M, Chou F, Lin H, Bansil A, Fu L, Madhavan V. 2015. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. Nature Materials. 14(3), 318–324."},"date_updated":"2021-01-12T08:22:24Z","status":"public","type":"journal_article","_id":"981"},{"abstract":[{"lang":"eng","text":"We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions."}],"acknowledgement":"We acknowledge helpful discussions with Sid Parameswaran, Andrew Potter, Antonello Scardicchio, Romain Vasseur, and especially with Ehud Altman and David Huse. We would like to thank Miles Stoudenmire for the assistance with ITensor library. Research at Perimeter Institute is supported by the Government of Canada through Industry Canada and by the Province of Ontario through the Ministry of Economic Development & Innovation. This research was supported by Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4307 (M. S.), Sloan Foundation, NSERC, and Early Researcher Award of Ontario (D. A.). This work made use of the facilities of N8 HPC Centre of Excellence, provided and funded by the N8 consortium and EPSRC (Grant No. EP/K000225/1). The Centre is coordinated by the Universities of Leeds and Manchester.","main_file_link":[{"url":"https://arxiv.org/abs/1507.01635","open_access":"1"}],"oa":1,"quality_controlled":0,"publisher":"American Physical Society","intvolume":" 5","month":"01","publication_status":"published","year":"2015","publication":"Physical Review X","day":"01","date_created":"2018-12-11T11:49:32Z","date_published":"2015-01-01T00:00:00Z","doi":"10.1103/PhysRevX.5.041047","issue":"4","volume":5,"_id":"982","type":"journal_article","status":"public","date_updated":"2021-01-12T08:22:25Z","citation":{"chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X. American Physical Society, 2015. https://doi.org/10.1103/PhysRevX.5.041047.","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4).","mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” Physical Review X, vol. 5, no. 4, American Physical Society, 2015, doi:10.1103/PhysRevX.5.041047.","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. Physical Review X. 2015;5(4). doi:10.1103/PhysRevX.5.041047","apa":"Serbyn, M., Papić, Z., & Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.5.041047","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” Physical Review X, vol. 5, no. 4. American Physical Society, 2015."},"extern":1,"author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A","first_name":"Dmitry"}],"publist_id":"6418","title":"Criterion for many-body localization-delocalization phase transition"}]