[{"month":"10","file":[{"file_id":"5769","creator":"dernst","file_size":7202224,"checksum":"1e4024b3161adcae4a53a0b3dc8a946e","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","relation":"main_file","access_level":"open_access","file_name":"2015_eLife_Sehring.pdf","date_created":"2018-12-20T15:50:56Z"}],"status":"public","publist_id":"6512","date_created":"2018-12-11T11:49:15Z","doi":"10.7554/eLife.09206","language":[{"iso":"eng"}],"oa":1,"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","_id":"928","fulldoi":"https://doi.org/10.7554/eLife.09206","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","article_number":"e09206","file_date_updated":"2020-07-14T12:48:15Z","citation":{"ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” <i>ELife</i>. eLife Sciences Publications, 2015. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. <i>eLife</i>. 2015;4. doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>","ieee":"I. Sehring <i>et al.</i>, “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” <i>eLife</i>, vol. 4. eLife Sciences Publications, 2015.","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” <i>ELife</i>, vol. 4, e09206, eLife Sciences Publications, 2015, doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>.","short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"21","quality_controlled":"1","ddc":["539","570"],"has_accepted_license":"1","publication":"eLife","date_published":"2015-10-21T00:00:00Z","intvolume":"         4","publisher":"eLife Sciences Publications","abstract":[{"text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events.","lang":"eng"}],"date_updated":"2021-01-12T08:21:58Z","author":[{"last_name":"Sehring","first_name":"Ivonne","full_name":"Sehring, Ivonne"},{"last_name":"Recho","full_name":"Recho, Pierre","first_name":"Pierre"},{"last_name":"Denker","full_name":"Denker, Elsa","first_name":"Elsa"},{"last_name":"Kourakis","first_name":"Matthew","full_name":"Kourakis, Matthew"},{"full_name":"Mathiesen, Birthe","first_name":"Birthe","last_name":"Mathiesen"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dong","first_name":"Bo","full_name":"Dong, Bo"},{"last_name":"Jiang","full_name":"Jiang, Di","first_name":"Di"}],"year":"2015","type":"journal_article","volume":4,"extern":"1"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1504762112","publisher":"National Academy of Sciences","intvolume":"       112","page":"8620 - 8625","abstract":[{"text":"An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. ","lang":"eng"}],"month":"07","issue":"28","date_created":"2018-12-11T11:49:15Z","publist_id":"6513","date_published":"2015-07-14T00:00:00Z","status":"public","publication":"PNAS","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1504762112\">https://doi.org/10.1073/pnas.1504762112</a>.","ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. <i>PNAS</i>. 2015;112(28):8620-8625. doi:<a href=\"https://doi.org/10.1073/pnas.1504762112\">10.1073/pnas.1504762112</a>","ista":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” <i>PNAS</i>, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:<a href=\"https://doi.org/10.1073/pnas.1504762112\">10.1073/pnas.1504762112</a>.","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., &#38; Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1504762112\">https://doi.org/10.1073/pnas.1504762112</a>","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” <i>PNAS</i>, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015."},"article_processing_charge":"No","extern":"1","day":"14","acknowledgement":"We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.","year":"2015","oa_version":"None","date_updated":"2021-01-12T08:21:59Z","author":[{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"full_name":"Dong, Bo","first_name":"Bo","last_name":"Dong"},{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"last_name":"Joanny","full_name":"Joanny, Jean","first_name":"Jean"},{"full_name":"Hayashi, Shigeo","first_name":"Shigeo","last_name":"Hayashi"}],"publication_status":"published","volume":112,"title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","fulldoi":"https://doi.org/10.1073/pnas.1504762112","type":"journal_article","_id":"929"},{"day":"15","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., &#38; Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” <i>PNAS</i>, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>.","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>.","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. 2015;112(50):15314-15319. doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319."},"fulldoi":"https://doi.org/10.1073/pnas.1510973112","title":"Physics of active jamming during collective cellular motion in a monolayer","_id":"933","oa_version":"Published Version","pmid":1,"publication_status":"published","OA_type":"hybrid","page":"15314 - 15319","external_id":{"pmid":["26627719"]},"oa":1,"doi":"10.1073/pnas.1510973112","article_type":"original","language":[{"iso":"eng"}],"publist_id":"6511","date_created":"2018-12-11T11:49:16Z","publication_identifier":{"issn":[" 0027-8424"],"eissn":["1091-6490"]},"status":"public","month":"12","issue":"50","article_processing_charge":"No","extern":"1","volume":112,"type":"journal_article","scopus_import":"1","year":"2015","date_updated":"2026-05-19T10:19:15Z","author":[{"first_name":"Simón","full_name":"García, Simón","last_name":"García"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Elgeti, Jens","first_name":"Jens","last_name":"Elgeti"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"},{"first_name":"Pascal","full_name":"Silberzan, Pascal","last_name":"Silberzan"},{"full_name":"Gov, Nir","first_name":"Nir","last_name":"Gov"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1510973112","open_access":"1"}],"abstract":[{"text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.","lang":"eng"}],"publisher":"National Academy of Sciences","intvolume":"       112","OA_place":"publisher","date_published":"2015-12-15T00:00:00Z","publication":"PNAS","quality_controlled":"1"},{"abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"intvolume":"        29","publisher":"Cold Spring Harbor Laboratory Press","date_published":"2015-12-15T00:00:00Z","publication":"Genes and Development","ddc":["570"],"quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","has_accepted_license":"1","article_processing_charge":"No","extern":"1","scopus_import":"1","type":"journal_article","department":[{"_id":"DaZi"}],"volume":29,"year":"2015","author":[{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"date_updated":"2021-12-14T07:58:15Z","page":"2517–2531","external_id":{"pmid":["26680300"]},"oa":1,"doi":"10.1101/gad.269902.115","article_type":"review","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","date_updated":"2021-06-08T09:55:10Z","access_level":"open_access","file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","date_created":"2021-06-08T09:55:10Z","file_id":"9533","creator":"asandaue","success":1,"file_size":1116846,"checksum":"086a88cfca4677646da26ed960cb02e9"}],"date_created":"2021-06-08T09:56:24Z","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"status":"public","issue":"24","month":"12","day":"15","citation":{"mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531."},"file_date_updated":"2021-06-08T09:55:10Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Evolution and function of genomic imprinting in plants","fulldoi":"https://doi.org/10.1101/gad.269902.115","_id":"9532","pmid":1,"publication_status":"published","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"}},{"main_file_link":[{"url":"https://arxiv.org/abs/1501.04816","open_access":"1"}],"date_updated":"2023-02-23T14:01:28Z","author":[{"last_name":"Krivelevich","first_name":"Michael","full_name":"Krivelevich, Michael"},{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","last_name":"Kwan","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan"},{"last_name":"Sudakov","first_name":"Benny","full_name":"Sudakov, Benny"}],"year":"2015","scopus_import":"1","type":"journal_article","volume":49,"arxiv":1,"extern":"1","article_processing_charge":"No","quality_controlled":"1","publication":"Electronic Notes in Discrete Mathematics","date_published":"2015-11-01T00:00:00Z","intvolume":"        49","publisher":"Elsevier","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"publication_status":"published","oa_version":"Preprint","_id":"9575","title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","fulldoi":"https://doi.org/10.1016/j.endm.2015.06.027","citation":{"ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. 2015;49:181-187. doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49, Elsevier, 2015, pp. 181–87, doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>.","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49. Elsevier, pp. 181–187, 2015."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"01","month":"11","status":"public","date_created":"2021-06-21T06:40:34Z","publication_identifier":{"issn":["1571-0653"]},"doi":"10.1016/j.endm.2015.06.027","article_type":"original","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1501.04816"]},"page":"181-187"},{"type":"journal_article","_id":"9673","scopus_import":"1","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","fulldoi":"https://doi.org/10.1016/j.ijplas.2014.09.009","volume":67,"publication_status":"published","date_updated":"2023-02-23T14:04:28Z","oa_version":"None","author":[{"first_name":"H.S.","full_name":"Leung, H.S.","last_name":"Leung"},{"last_name":"Leung","full_name":"Leung, P.S.S.","first_name":"P.S.S."},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632"},{"last_name":"Ngan","full_name":"Ngan, A.H.W.","first_name":"A.H.W."}],"year":"2015","article_processing_charge":"No","day":"01","extern":"1","citation":{"ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. <i>International Journal of Plasticity</i>. 2015;67:1-25. doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” <i>International Journal of Plasticity</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>.","ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., &#38; Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. <i>International Journal of Plasticity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” <i>International Journal of Plasticity</i>, vol. 67. Elsevier, pp. 1–25, 2015.","short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” <i>International Journal of Plasticity</i>, vol. 67, Elsevier, 2015, pp. 1–25, doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","publication":"International Journal of Plasticity","date_published":"2015-04-01T00:00:00Z","date_created":"2021-07-15T14:09:32Z","publication_identifier":{"issn":["0749-6419"]},"month":"04","abstract":[{"text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation.","lang":"eng"}],"page":"1-25","intvolume":"        67","publisher":"Elsevier","article_type":"original","doi":"10.1016/j.ijplas.2014.09.009","language":[{"iso":"eng"}]},{"extern":"1","article_processing_charge":"No","scopus_import":"1","type":"journal_article","volume":23,"author":[{"last_name":"Leung","full_name":"Leung, P S S","first_name":"P S S"},{"last_name":"Leung","first_name":"H S","full_name":"Leung, H S"},{"first_name":"Bingqing","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632"},{"full_name":"Ngan, A H W","first_name":"A H W","last_name":"Ngan"}],"date_updated":"2023-02-23T14:04:54Z","year":"2015","abstract":[{"text":"The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.","lang":"eng"}],"intvolume":"        23","publisher":"IOP Publishing","publication":"Modelling and Simulation in Materials Science and Engineering","date_published":"2015-04-01T00:00:00Z","quality_controlled":"1","day":"01","citation":{"mla":"Leung, P. S. S., et al. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” <i>Modelling and Simulation in Materials Science and Engineering</i>, vol. 23, no. 3, 035001, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">10.1088/0965-0393/23/3/035001</a>.","short":"P.S.S. Leung, H.S. Leung, B. Cheng, A.H.W. Ngan, Modelling and Simulation in Materials Science and Engineering 23 (2015).","apa":"Leung, P. S. S., Leung, H. S., Cheng, B., &#38; Ngan, A. H. W. (2015). Size dependence of yield strength simulated by a dislocation-density function dynamics approach. <i>Modelling and Simulation in Materials Science and Engineering</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">https://doi.org/10.1088/0965-0393/23/3/035001</a>","ieee":"P. S. S. Leung, H. S. Leung, B. Cheng, and A. H. W. Ngan, “Size dependence of yield strength simulated by a dislocation-density function dynamics approach,” <i>Modelling and Simulation in Materials Science and Engineering</i>, vol. 23, no. 3. IOP Publishing, 2015.","chicago":"Leung, P S S, H S Leung, Bingqing Cheng, and A H W Ngan. “Size Dependence of Yield Strength Simulated by a Dislocation-Density Function Dynamics Approach.” <i>Modelling and Simulation in Materials Science and Engineering</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">https://doi.org/10.1088/0965-0393/23/3/035001</a>.","ama":"Leung PSS, Leung HS, Cheng B, Ngan AHW. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. <i>Modelling and Simulation in Materials Science and Engineering</i>. 2015;23(3). doi:<a href=\"https://doi.org/10.1088/0965-0393/23/3/035001\">10.1088/0965-0393/23/3/035001</a>","ista":"Leung PSS, Leung HS, Cheng B, Ngan AHW. 2015. Size dependence of yield strength simulated by a dislocation-density function dynamics approach. Modelling and Simulation in Materials Science and Engineering. 23(3), 035001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9684","article_number":"035001","title":"Size dependence of yield strength simulated by a dislocation-density function dynamics approach","fulldoi":"https://doi.org/10.1088/0965-0393/23/3/035001","publication_status":"published","oa_version":"None","doi":"10.1088/0965-0393/23/3/035001","article_type":"original","language":[{"iso":"eng"}],"status":"public","publication_identifier":{"eissn":["1361-651X"],"issn":["0965-0393"]},"date_created":"2021-07-19T09:11:12Z","issue":"3","month":"04"},{"abstract":[{"text":"The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.","lang":"eng"}],"publisher":"American Physical Society","intvolume":"        92","date_published":"2015-11-01T00:00:00Z","publication":"Physical Review B - Condensed Matter and Materials Physics","quality_controlled":"1","article_processing_charge":"No","extern":"1","arxiv":1,"volume":92,"scopus_import":"1","type":"journal_article","year":"2015","date_updated":"2021-08-09T12:38:49Z","author":[{"first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"last_name":"Tribello","full_name":"Tribello, Gareth A.","first_name":"Gareth A."},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"}],"main_file_link":[{"url":"https://arxiv.org/abs/1511.08668","open_access":"1"}],"external_id":{"arxiv":["1511.08668"]},"oa":1,"doi":"10.1103/physrevb.92.180102","language":[{"iso":"eng"}],"article_type":"original","date_created":"2021-07-19T10:07:22Z","publication_identifier":{"issn":["1098-0121"],"eissn":["1550-235X"]},"status":"public","month":"11","issue":"18","day":"01","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Cheng B, Tribello GA, Ceriotti M. 2015. Solid-liquid interfacial free energy out of equilibrium. Physical Review B - Condensed Matter and Materials Physics. 92(18), 180102.","ama":"Cheng B, Tribello GA, Ceriotti M. Solid-liquid interfacial free energy out of equilibrium. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2015;92(18). doi:<a href=\"https://doi.org/10.1103/physrevb.92.180102\">10.1103/physrevb.92.180102</a>","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/physrevb.92.180102\">https://doi.org/10.1103/physrevb.92.180102</a>.","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “Solid-liquid interfacial free energy out of equilibrium,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 92, no. 18. American Physical Society, 2015.","apa":"Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2015). Solid-liquid interfacial free energy out of equilibrium. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.92.180102\">https://doi.org/10.1103/physrevb.92.180102</a>","short":"B. Cheng, G.A. Tribello, M. Ceriotti, Physical Review B - Condensed Matter and Materials Physics 92 (2015).","mla":"Cheng, Bingqing, et al. “Solid-Liquid Interfacial Free Energy out of Equilibrium.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 92, no. 18, 180102, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/physrevb.92.180102\">10.1103/physrevb.92.180102</a>."},"fulldoi":"https://doi.org/10.1103/physrevb.92.180102","article_number":"180102","title":"Solid-liquid interfacial free energy out of equilibrium","_id":"9688","oa_version":"Preprint","publication_status":"published"},{"publisher":"Public Library of Science","doi":"10.1371/journal.pbio.1002299.s001","status":"public","date_published":"2015-11-18T00:00:00Z","date_created":"2021-07-23T11:53:50Z","month":"11","day":"18","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>.","mla":"Chevereau, Guillaume, et al. <i>Excel File Containing the Raw Data for All Figures</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","ieee":"G. Chevereau <i>et al.</i>, “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>"},"related_material":{"record":[{"status":"public","id":"1619","relation":"used_in_publication"}]},"department":[{"_id":"ToBo"}],"_id":"9711","type":"research_data_reference","title":"Excel file containing the raw data for all figures","fulldoi":"https://doi.org/10.1371/journal.pbio.1002299.s001","oa_version":"Published Version","author":[{"first_name":"Guillaume","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau"},{"full_name":"Lukacisinova, Marta","first_name":"Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Batur","full_name":"Batur, Tugce","first_name":"Tugce"},{"last_name":"Guvenek","first_name":"Aysegul","full_name":"Guvenek, Aysegul"},{"last_name":"Ayhan","first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal"},{"last_name":"Toprak","first_name":"Erdal","full_name":"Toprak, Erdal"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias"}],"date_updated":"2025-09-23T09:58:54Z","year":"2015"},{"_id":"9712","type":"research_data_reference","title":"Other fitness models for comparison & for interacting TFBSs","fulldoi":"https://doi.org/10.1371/journal.pgen.1005639.s001","related_material":{"record":[{"relation":"used_in_publication","id":"1666","status":"public"}]},"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"full_name":"Tugrul, Murat","first_name":"Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455"}],"oa_version":"Published Version","date_updated":"2025-09-23T08:31:14Z","year":"2015","article_processing_charge":"No","day":"06","citation":{"ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison &#38; for interacting TFBSs.” Public Library of Science, 2015.","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Other fitness models for comparison &#38; for interacting TFBSs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>","mla":"Tugrul, Murat, et al. <i>Other Fitness Models for Comparison &#38; for Interacting TFBSs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison &#38; for interacting TFBSs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison &#38; for interacting TFBSs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">10.1371/journal.pgen.1005639.s001</a>","chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison &#38; for Interacting TFBSs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639.s001\">https://doi.org/10.1371/journal.pgen.1005639.s001</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","date_published":"2015-11-06T00:00:00Z","date_created":"2021-07-23T12:00:37Z","month":"11","publisher":"Public Library of Science","doi":"10.1371/journal.pgen.1005639.s001"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. <i>Mathematical Inference of the Results</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Mathematical inference of the results.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Mathematical inference of the results. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>","ista":"Trubenova B, Novak S, Hager R. 2015. Mathematical inference of the results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>.","ama":"Trubenova B, Novak S, Hager R. Mathematical inference of the results. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">10.1371/journal.pone.0126907.s001</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Mathematical Inference of the Results.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s001\">https://doi.org/10.1371/journal.pone.0126907.s001</a>."},"day":"18","article_processing_charge":"No","oa_version":"Published Version","date_updated":"2025-09-23T09:21:54Z","author":[{"first_name":"Barbora","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","last_name":"Trubenova"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","first_name":"Sebastian"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"year":"2015","department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"1809","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","_id":"9715","title":"Mathematical inference of the results","fulldoi":"https://doi.org/10.1371/journal.pone.0126907.s001","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0126907.s001","month":"05","status":"public","date_published":"2015-05-18T00:00:00Z","date_created":"2021-07-23T12:11:30Z"},{"month":"03","status":"public","date_created":"2021-07-26T08:35:23Z","date_published":"2015-03-23T00:00:00Z","publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1004055.s001","date_updated":"2025-09-23T08:43:16Z","author":[{"first_name":"Tamar","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","last_name":"Friedlander"},{"full_name":"Mayo, Avraham E.","first_name":"Avraham E.","last_name":"Mayo"},{"last_name":"Tlusty","full_name":"Tlusty, Tsvi","first_name":"Tsvi"},{"last_name":"Alon","first_name":"Uri","full_name":"Alon, Uri"}],"oa_version":"Published Version","year":"2015","department":[{"_id":"GaTk"}],"related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"_id":"9718","type":"research_data_reference","title":"Supporting information text","fulldoi":"https://doi.org/10.1371/journal.pcbi.1004055.s001","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. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Supporting information text. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">https://doi.org/10.1371/journal.pcbi.1004055.s001</a>","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015.","mla":"Friedlander, Tamar, et al. <i>Supporting Information Text</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s001\">10.1371/journal.pcbi.1004055.s001</a>.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015)."},"day":"23","article_processing_charge":"No"},{"month":"12","date_created":"2021-07-26T08:44:04Z","date_published":"2015-12-21T00:00:00Z","status":"public","doi":"10.5061/dryad.cj910","publisher":"Dryad","abstract":[{"text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cj910"}],"year":"2015","oa_version":"Published Version","date_updated":"2026-04-29T05:57:01Z","author":[{"last_name":"Wielgoss","full_name":"Wielgoss, Sébastien","first_name":"Sébastien"},{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","first_name":"Tobias"},{"last_name":"Bischofberger","first_name":"Anna M.","full_name":"Bischofberger, Anna M."},{"last_name":"Hall","full_name":"Hall, Alex R.","first_name":"Alex R."}],"fulldoi":"https://doi.org/10.5061/dryad.cj910","title":"Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria","_id":"9719","type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"5749"}]},"department":[{"_id":"CaGu"}],"citation":{"short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, (2015).","mla":"Wielgoss, Sébastien, et al. <i>Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2015). Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. Dryad. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria.” Dryad, 2015.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2015. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria, Dryad, <a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"21","article_processing_charge":"No"},{"month":"06","status":"public","date_published":"2015-06-01T00:00:00Z","date_created":"2021-07-28T06:20:13Z","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0127657.s001","oa_version":"Published Version","author":[{"orcid":"0000-0003-2012-9947","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","full_name":"Symonova, Olga"},{"first_name":"Christopher","full_name":"Topp, Christopher","last_name":"Topp"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-09-23T08:30:43Z","year":"2015","related_material":{"record":[{"id":"1793","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"MaJö"},{"_id":"HeEd"}],"_id":"9737","type":"research_data_reference","fulldoi":"https://doi.org/10.1371/journal.pone.0127657.s001","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"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., &#38; Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>","mla":"Symonova, Olga, et al. <i>Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","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, <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>.","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. <a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">https://doi.org/10.1371/journal.pone.0127657.s001</a>.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657.s001\">10.1371/journal.pone.0127657.s001</a>"},"article_processing_charge":"No","day":"01"},{"month":"07","date_created":"2021-07-28T08:52:53Z","date_published":"2015-07-09T00:00:00Z","status":"public","doi":"10.5061/dryad.7kc79","publisher":"Dryad","abstract":[{"lang":"eng","text":"Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects."}],"oa":1,"year":"2015","oa_version":"Published Version","date_updated":"2025-09-29T11:42:25Z","author":[{"full_name":"Westhus, Claudia","first_name":"Claudia","last_name":"Westhus"},{"full_name":"Ugelvig, Line V","first_name":"Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tourdot","first_name":"Edouard","full_name":"Tourdot, Edouard"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"full_name":"Doums, Claudie","first_name":"Claudie","last_name":"Doums"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.7kc79","open_access":"1"}],"related_material":{"record":[{"status":"public","id":"2161","relation":"used_in_publication"}]},"department":[{"_id":"SyCr"}],"fulldoi":"https://doi.org/10.5061/dryad.7kc79","title":"Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant","_id":"9742","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Westhus, Claudia, Line V Ugelvig, Edouard Tourdot, Jürgen Heinze, Claudie Doums, and Sylvia Cremer. “Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>.","ama":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>","ista":"Westhus C, Ugelvig LV, Tourdot E, Heinze J, Doums C, Cremer S. 2015. Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant, Dryad, <a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>.","apa":"Westhus, C., Ugelvig, L. V., Tourdot, E., Heinze, J., Doums, C., &#38; Cremer, S. (2015). Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant. Dryad. <a href=\"https://doi.org/10.5061/dryad.7kc79\">https://doi.org/10.5061/dryad.7kc79</a>","ieee":"C. Westhus, L. V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, and S. Cremer, “Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant.” Dryad, 2015.","short":"C. Westhus, L.V. Ugelvig, E. Tourdot, J. Heinze, C. Doums, S. Cremer, (2015).","mla":"Westhus, Claudia, et al. <i>Data from: Increased Grooming after Repeated Brood Care Provides Sanitary Benefits in a Clonal Ant</i>. Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.7kc79\">10.5061/dryad.7kc79</a>."},"day":"09","article_processing_charge":"No"},{"related_material":{"record":[{"status":"public","id":"1619","relation":"used_in_publication"}]},"department":[{"_id":"ToBo"}],"type":"research_data_reference","_id":"9765","title":"Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs","fulldoi":"https://doi.org/10.1371/journal.pbio.1002299.s008","oa_version":"Published Version","author":[{"id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","full_name":"Chevereau, Guillaume","first_name":"Guillaume"},{"full_name":"Lukacisinova, Marta","first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004"},{"full_name":"Batur, Tugce","first_name":"Tugce","last_name":"Batur"},{"last_name":"Guvenek","first_name":"Aysegul","full_name":"Guvenek, Aysegul"},{"full_name":"Ayhan, Dilay Hazal","first_name":"Dilay Hazal","last_name":"Ayhan"},{"first_name":"Erdal","full_name":"Toprak, Erdal","last_name":"Toprak"},{"first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-09-23T09:58:54Z","year":"2015","day":"18","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","mla":"Chevereau, Guillaume, et al. <i>Gene Ontology Enrichment Analysis for the Most Sensitive Gene Deletion Strains for All Drugs</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">10.1371/journal.pbio.1002299.s008</a>.","ieee":"G. Chevereau <i>et al.</i>, “Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs.” Public Library of Science, 2015.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s008\">https://doi.org/10.1371/journal.pbio.1002299.s008</a>"},"status":"public","date_published":"2015-11-18T00:00:00Z","date_created":"2021-08-03T07:05:16Z","month":"11","publisher":"Public Library of Science","doi":"10.1371/journal.pbio.1002299.s008"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1809"}]},"department":[{"_id":"NiBa"}],"_id":"9772","type":"research_data_reference","fulldoi":"https://doi.org/10.1371/journal.pone.0126907.s003","title":"Description of the agent based simulations","author":[{"first_name":"Barbora","full_name":"Trubenova, Barbora","last_name":"Trubenova","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X","last_name":"Novak"},{"last_name":"Hager","full_name":"Hager, Reinmar","first_name":"Reinmar"}],"date_updated":"2025-09-23T09:21:54Z","oa_version":"Published Version","year":"2015","article_processing_charge":"No","day":"18","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Description of the agent based simulations. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>","short":"B. Trubenova, S. Novak, R. Hager, (2015).","mla":"Trubenova, Barbora, et al. <i>Description of the Agent Based Simulations</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">10.1371/journal.pone.0126907.s003</a>","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907.s003\">https://doi.org/10.1371/journal.pone.0126907.s003</a>."},"status":"public","date_published":"2015-05-18T00:00:00Z","date_created":"2021-08-05T12:55:20Z","month":"05","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0126907.s003"},{"citation":{"ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>.","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A. E., Tlusty, T., &#38; Alon, U. (2015). Evolutionary simulation code. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">https://doi.org/10.1371/journal.pcbi.1004055.s002</a>","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. <i>Evolutionary Simulation Code</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055.s002\">10.1371/journal.pcbi.1004055.s002</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"23","year":"2015","oa_version":"Published Version","date_updated":"2025-09-23T08:43:16Z","author":[{"full_name":"Friedlander, Tamar","first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mayo","full_name":"Mayo, Avraham E.","first_name":"Avraham E."},{"first_name":"Tsvi","full_name":"Tlusty, Tsvi","last_name":"Tlusty"},{"full_name":"Alon, Uri","first_name":"Uri","last_name":"Alon"}],"fulldoi":"https://doi.org/10.1371/journal.pcbi.1004055.s002","title":"Evolutionary simulation code","_id":"9773","type":"research_data_reference","related_material":{"record":[{"id":"1827","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"GaTk"}],"doi":"10.1371/journal.pcbi.1004055.s002","publisher":"Public Library of Science","month":"03","date_published":"2015-03-23T00:00:00Z","date_created":"2021-08-05T12:58:07Z","status":"public"},{"citation":{"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.","ama":"Zeljkovic I, Okada Y, Serbyn M, et al. Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators. <i>Nature Materials</i>. 2015;14(3):318-324. doi:<a href=\"https://doi.org/10.1038/nmat4215\">10.1038/nmat4215</a>","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.” <i>Nature Materials</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nmat4215\">https://doi.org/10.1038/nmat4215</a>.","mla":"Zeljkovic, Ilija, et al. “Dirac Mass Generation from Crystal Symmetry Breaking on the Surfaces of Topological Crystalline Insulators.” <i>Nature Materials</i>, vol. 14, no. 3, Nature Publishing Group, 2015, pp. 318–24, doi:<a href=\"https://doi.org/10.1038/nmat4215\">10.1038/nmat4215</a>.","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.","ieee":"I. Zeljkovic <i>et al.</i>, “Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators,” <i>Nature Materials</i>, vol. 14, no. 3. Nature Publishing Group, pp. 318–324, 2015.","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. <i>Nature Materials</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nmat4215\">https://doi.org/10.1038/nmat4215</a>"},"extern":1,"day":"01","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.","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.4906"}],"author":[{"last_name":"Zeljkovic","full_name":"Zeljkovic, Ilija","first_name":"Ilija"},{"last_name":"Okada","full_name":"Okada, Yoshinori","first_name":"Yoshinori"},{"full_name":"Maksym Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"full_name":"Sankar, Raman","first_name":"Raman","last_name":"Sankar"},{"first_name":"Daniel","full_name":"Walkup, Daniel","last_name":"Walkup"},{"last_name":"Zhou","full_name":"Zhou, Wenwen","first_name":"Wenwen"},{"last_name":"Liu","first_name":"Junwei","full_name":"Liu, Junwei"},{"last_name":"Chang","full_name":"Chang, Guoqing","first_name":"Guoqing"},{"last_name":"Wang","first_name":"Yungjui","full_name":"Wang, Yungjui"},{"full_name":"Hasan, Md Z","first_name":"Md","last_name":"Hasan"},{"first_name":"Fangcheng","full_name":"Chou, Fangcheng","last_name":"Chou"},{"last_name":"Lin","first_name":"Hsin","full_name":"Lin, Hsin"},{"last_name":"Bansil","full_name":"Bansil, Arun","first_name":"Arun"},{"full_name":"Fu, Liang","first_name":"Liang","last_name":"Fu"},{"first_name":"Vidya","full_name":"Madhavan, Vidya","last_name":"Madhavan"}],"date_updated":"2021-01-12T08:22:24Z","year":"2015","type":"journal_article","_id":"981","title":"Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators","fulldoi":"https://doi.org/10.1038/nmat4215","volume":14,"intvolume":"        14","publisher":"Nature Publishing Group","doi":"10.1038/nmat4215","abstract":[{"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.","lang":"eng"}],"oa":1,"page":"318 - 324","issue":"3","quality_controlled":0,"month":"03","status":"public","publication":"Nature Materials","publist_id":"6419","date_published":"2015-03-01T00:00:00Z","date_created":"2018-12-11T11:49:31Z"},{"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.","day":"01","extern":1,"citation":{"short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review X 5 (2015).","mla":"Serbyn, Maksym, et al. “Criterion for Many-Body Localization-Delocalization Phase Transition.” <i>Physical Review X</i>, vol. 5, no. 4, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">10.1103/PhysRevX.5.041047</a>.","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Criterion for many-body localization-delocalization phase transition,” <i>Physical Review X</i>, vol. 5, no. 4. American Physical Society, 2015.","apa":"Serbyn, M., Papić, Z., &#38; Abanin, D. (2015). Criterion for many-body localization-delocalization phase transition. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">https://doi.org/10.1103/PhysRevX.5.041047</a>","ista":"Serbyn M, Papić Z, Abanin D. 2015. Criterion for many-body localization-delocalization phase transition. Physical Review X. 5(4).","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Criterion for Many-Body Localization-Delocalization Phase Transition.” <i>Physical Review X</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">https://doi.org/10.1103/PhysRevX.5.041047</a>.","ama":"Serbyn M, Papić Z, Abanin D. Criterion for many-body localization-delocalization phase transition. <i>Physical Review X</i>. 2015;5(4). doi:<a href=\"https://doi.org/10.1103/PhysRevX.5.041047\">10.1103/PhysRevX.5.041047</a>"},"volume":5,"fulldoi":"https://doi.org/10.1103/PhysRevX.5.041047","title":"Criterion for many-body localization-delocalization phase transition","_id":"982","type":"journal_article","year":"2015","author":[{"first_name":"Maksym","full_name":"Maksym Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"last_name":"Papić","full_name":"Papić, Zlatko","first_name":"Zlatko"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A","first_name":"Dmitry"}],"date_updated":"2021-01-12T08:22:25Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.01635"}],"publication_status":"published","oa":1,"abstract":[{"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.","lang":"eng"}],"doi":"10.1103/PhysRevX.5.041047","publisher":"American Physical Society","intvolume":"         5","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:49:32Z","publist_id":"6418","status":"public","publication":"Physical Review X","month":"01","issue":"4","quality_controlled":0}]