[{"oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","external_id":{"arxiv":["1412.0897"],"pmid":["25453085"]},"month":"12","year":"2014","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","pmid":1,"day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["multidisciplinary"],"doi":"10.1073/pnas.1410159111","arxiv":1,"publication":"Proceedings of the National Academy of Sciences","volume":111,"oa":1,"author":[{"first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"full_name":"Chebaro, Yassmine C.","first_name":"Yassmine C.","last_name":"Chebaro"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"}],"main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","issue":"50","article_type":"original","page":"17869-17874","abstract":[{"lang":"eng","text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory."}],"date_updated":"2021-11-29T13:29:05Z","type":"journal_article","intvolume":"       111","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publisher":"National Academy of Sciences","title":"Crucial role of nonspecific interactions in amyloid nucleation","_id":"10382","date_published":"2014-12-01T00:00:00Z","extern":"1","date_created":"2021-11-29T13:09:53Z","publication_status":"published","citation":{"ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(50):17869-17874. doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., &#38; Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>.","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>.","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874."}},{"citation":{"ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” <i>Physical Review E</i>, vol. 89, no. 5. American Physical Society, 2014.","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. 2014;89(5). doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>","apa":"Mallory, S. A., Šarić, A., Valeriani, C., &#38; Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>.","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>.","short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014)."},"publication_status":"published","date_created":"2021-11-29T13:10:33Z","_id":"10383","extern":"1","date_published":"2014-05-06T00:00:00Z","title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","publisher":"American Physical Society","publication_identifier":{"issn":["1539-3755"],"eissn":["1550-2376"]},"intvolume":"        89","type":"journal_article","date_updated":"2021-11-29T13:29:01Z","abstract":[{"text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.","lang":"eng"}],"article_number":"052303","article_type":"original","issue":"5","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"author":[{"full_name":"Mallory, S. A.","first_name":"S. A.","last_name":"Mallory"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Valeriani","first_name":"C.","full_name":"Valeriani, C."},{"first_name":"A.","full_name":"Cacciuto, A.","last_name":"Cacciuto"}],"oa":1,"volume":89,"publication":"Physical Review E","arxiv":1,"doi":"10.1103/physreve.89.052303","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"06","pmid":1,"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"year":"2014","month":"05","external_id":{"pmid":["25353796"],"arxiv":["1310.0826"]},"quality_controlled":"1","scopus_import":"1","oa_version":"Preprint"},{"type":"journal_article","intvolume":"        54","publication_identifier":{"issn":["0914-3505"]},"issue":"1","main_file_link":[{"url":"https://doi.org/10.1111/cga.12039","open_access":"1"}],"author":[{"full_name":"Hashimoto, Masakazu","first_name":"Masakazu","last_name":"Hashimoto"},{"full_name":"Morita, Hitoshi","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita"},{"last_name":"Ueno","first_name":"Naoto","full_name":"Ueno, Naoto"}],"acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","date_updated":"2022-03-04T08:26:05Z","page":"1-7","abstract":[{"text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest.","lang":"eng"}],"article_type":"original","_id":"10815","date_published":"2014-02-01T00:00:00Z","title":"Molecular and cellular mechanisms of development underlying congenital diseases","date_created":"2022-03-04T08:17:25Z","citation":{"short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>.","mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>.","apa":"Hashimoto, M., Morita, H., &#38; Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. Wiley. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>","ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” <i>Congenital Anomalies</i>, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. 2014;54(1):1-7. doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>","ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7."},"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Wiley","year":"2014","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"day":"01","scopus_import":"1","oa_version":"None","external_id":{"pmid":["24666178"]},"quality_controlled":"1","volume":54,"oa":1,"keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"doi":"10.1111/cga.12039","publication":"Congenital Anomalies"},{"publication":"Cell","doi":"10.1016/j.cell.2014.01.029","oa":1,"volume":156,"quality_controlled":"1","external_id":{"pmid":["24630728"]},"oa_version":"Published Version","scopus_import":"1","day":"13","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"03","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"year":"2014","publisher":"Elsevier","department":[{"_id":"DaZi"}],"publication_status":"published","citation":{"short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297."},"date_created":"2021-06-04T12:00:16Z","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","extern":"1","_id":"9458","date_published":"2014-03-13T00:00:00Z","article_type":"original","abstract":[{"lang":"eng","text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints."}],"page":"1286-1297","date_updated":"2021-12-14T08:22:36Z","author":[{"last_name":"Huff","full_name":"Huff, Jason T.","first_name":"Jason T."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2014.01.029"}],"issue":"6","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"type":"journal_article","intvolume":"       156"},{"quality_controlled":"1","external_id":{"pmid":["25344531"]},"oa_version":"Published Version","scopus_import":"1","day":"11","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"11","article_processing_charge":"No","year":"2014","language":[{"iso":"eng"}],"status":"public","publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.1418564111","oa":1,"volume":111,"abstract":[{"text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.","lang":"eng"}],"page":"16166-16171","article_type":"original","date_updated":"2021-12-14T08:23:26Z","author":[{"last_name":"Mérai","first_name":"Zsuzsanna","full_name":"Mérai, Zsuzsanna"},{"full_name":"Chumak, Nina","first_name":"Nina","last_name":"Chumak"},{"first_name":"Marcelina","full_name":"García-Aguilar, Marcelina","last_name":"García-Aguilar"},{"first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh"},{"last_name":"Nishimura","full_name":"Nishimura, Toshiro","first_name":"Toshiro"},{"last_name":"Schoft","full_name":"Schoft, Vera K.","first_name":"Vera K."},{"full_name":"Bindics, János","first_name":"János","last_name":"Bindics"},{"last_name":"Ślusarz","first_name":"Lucyna","full_name":"Ślusarz, Lucyna"},{"first_name":"Stéphanie","full_name":"Arnoux, Stéphanie","last_name":"Arnoux"},{"first_name":"Susanne","full_name":"Opravil, Susanne","last_name":"Opravil"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"last_name":"Fischer","full_name":"Fischer, Robert L.","first_name":"Robert L."},{"last_name":"Tamaru","full_name":"Tamaru, Hisashi","first_name":"Hisashi"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"issue":"45","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"type":"journal_article","intvolume":"       111","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"publication_status":"published","citation":{"ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171."},"date_created":"2021-06-07T07:23:43Z","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","date_published":"2014-11-11T00:00:00Z","_id":"9479","extern":"1"},{"oa":1,"volume":21,"publication":"The Electronic Journal of Combinatorics","arxiv":1,"doi":"10.37236/3752","day":"28","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"02","article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2014","status":"public","quality_controlled":"1","external_id":{"arxiv":["1309.6710"]},"oa_version":"Published Version","scopus_import":"1","citation":{"ista":"Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.","chicago":"Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics, 2014. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>.","mla":"Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular Graphs.” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1, P1.45, The Electronic Journal of Combinatorics, 2014, doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>.","short":"C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics 21 (2014).","ieee":"C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in random regular graphs,” <i>The Electronic Journal of Combinatorics</i>, vol. 21, no. 1. The Electronic Journal of Combinatorics, 2014.","ama":"Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. 2014;21(1). doi:<a href=\"https://doi.org/10.37236/3752\">10.37236/3752</a>","apa":"Greenhill, C., Kwan, M. A., &#38; Wind, D. (2014). On the number of spanning trees in random regular graphs. <i>The Electronic Journal of Combinatorics</i>. The Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/3752\">https://doi.org/10.37236/3752</a>"},"publication_status":"published","date_created":"2021-06-23T06:29:35Z","title":"On the number of spanning trees in random regular graphs","_id":"9594","extern":"1","date_published":"2014-02-28T00:00:00Z","publisher":"The Electronic Journal of Combinatorics","publication_identifier":{"eissn":["1077-8926"]},"intvolume":"        21","type":"journal_article","article_type":"original","abstract":[{"lang":"eng","text":"Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture."}],"article_number":"P1.45","date_updated":"2023-02-23T14:02:12Z","author":[{"last_name":"Greenhill","full_name":"Greenhill, Catherine","first_name":"Catherine"},{"full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Wind","first_name":"David","full_name":"Wind, David"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.37236/3752"}],"issue":"1"},{"day":"14","publist_id":"7958","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"01","status":"public","language":[{"iso":"eng"}],"year":"2014","quality_controlled":"1","external_id":{"arxiv":["1306.2720"]},"oa_version":"Preprint","volume":112,"oa":1,"arxiv":1,"publication":"APS Physics, Physical Review Letters","doi":"10.1103/PhysRevLett.112.026801","type":"journal_article","intvolume":"       112","abstract":[{"text":"Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (&gt;1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range.","lang":"eng"}],"article_number":"026801","date_updated":"2021-01-12T08:22:14Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1306.2720"}],"author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"},{"first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth"},{"first_name":"Micah","full_name":"Hanson, Micah","last_name":"Hanson"},{"first_name":"Arthur","full_name":"Gossard, Arthur","last_name":"Gossard"},{"full_name":"Marcus, Charles","first_name":"Charles","last_name":"Marcus"}],"acknowledgement":"The research is supported by the Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Grant No. W911NF-12-1-0354, the DARPA QuEST Program, the Department of Energy, Office of Science, and the Danish National Research Foundation.","issue":"2","date_created":"2018-12-11T11:44:36Z","citation":{"short":"A.P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Micah Hanson, Arthur Gossard, and Charles Marcus. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>. American Physiological Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>.","mla":"Higginbotham, Andrew P., et al. “Coherent Operations and Screening in Multielectron Spin Qubits.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2, 026801, American Physiological Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>.","apa":"Higginbotham, A. P., Kuemmeth, F., Hanson, M., Gossard, A., &#38; Marcus, C. (2014). Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. American Physiological Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">https://doi.org/10.1103/PhysRevLett.112.026801</a>","ama":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. Coherent operations and screening in multielectron spin qubits. <i>APS Physics, Physical Review Letters</i>. 2014;112(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.026801\">10.1103/PhysRevLett.112.026801</a>","ieee":"A. P. Higginbotham, F. Kuemmeth, M. Hanson, A. Gossard, and C. Marcus, “Coherent operations and screening in multielectron spin qubits,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 2. American Physiological Society, 2014.","ista":"Higginbotham AP, Kuemmeth F, Hanson M, Gossard A, Marcus C. 2014. Coherent operations and screening in multielectron spin qubits. APS Physics, Physical Review Letters. 112(2), 026801."},"publication_status":"published","title":"Coherent operations and screening in multielectron spin qubits","_id":"96","extern":"1","date_published":"2014-01-14T00:00:00Z","publisher":"American Physiological Society"},{"publication_identifier":{"issn":["1047-8477"]},"ddc":["570"],"intvolume":"       186","type":"journal_article","date_updated":"2021-07-22T08:26:32Z","abstract":[{"lang":"eng","text":"Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells."}],"article_type":"original","page":"205-213","file_date_updated":"2021-07-22T08:06:34Z","issue":"2","author":[{"full_name":"Perkovic, Mario","first_name":"Mario","last_name":"Perkovic"},{"last_name":"Kunz","full_name":"Kunz, Michael","first_name":"Michael"},{"last_name":"Endesfelder","first_name":"Ulrike","full_name":"Endesfelder, Ulrike"},{"first_name":"Stefanie","full_name":"Bunse, Stefanie","last_name":"Bunse"},{"last_name":"Wigge","first_name":"Christoph","full_name":"Wigge, Christoph"},{"last_name":"Yu","full_name":"Yu, Zhou","first_name":"Zhou"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Margot P.","full_name":"Scheffer, Margot P.","last_name":"Scheffer"},{"last_name":"Seybert","full_name":"Seybert, Anja","first_name":"Anja"},{"full_name":"Malkusch, Sebastian","first_name":"Sebastian","last_name":"Malkusch"},{"full_name":"Schuman, Erin M.","first_name":"Erin M.","last_name":"Schuman"},{"last_name":"Heilemann","first_name":"Mike","full_name":"Heilemann, Mike"},{"full_name":"Frangakis, Achilleas S.","first_name":"Achilleas S.","last_name":"Frangakis"}],"date_created":"2021-07-14T09:05:42Z","publication_status":"published","citation":{"apa":"Perkovic, M., Kunz, M., Endesfelder, U., Bunse, S., Wigge, C., Yu, Z., … Frangakis, A. S. (2014). Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>","ama":"Perkovic M, Kunz M, Endesfelder U, et al. Correlative light- and electron microscopy with chemical tags. <i>Journal of Structural Biology</i>. 2014;186(2):205-213. doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>","ieee":"M. Perkovic <i>et al.</i>, “Correlative light- and electron microscopy with chemical tags,” <i>Journal of Structural Biology</i>, vol. 186, no. 2. Elsevier, pp. 205–213, 2014.","short":"M. Perkovic, M. Kunz, U. Endesfelder, S. Bunse, C. Wigge, Z. Yu, V.-V. Hodirnau, M.P. Scheffer, A. Seybert, S. Malkusch, E.M. Schuman, M. Heilemann, A.S. Frangakis, Journal of Structural Biology 186 (2014) 205–213.","mla":"Perkovic, Mario, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>, vol. 186, no. 2, Elsevier, 2014, pp. 205–13, doi:<a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">10.1016/j.jsb.2014.03.018</a>.","chicago":"Perkovic, Mario, Michael Kunz, Ulrike Endesfelder, Stefanie Bunse, Christoph Wigge, Zhou Yu, Victor-Valentin Hodirnau, et al. “Correlative Light- and Electron Microscopy with Chemical Tags.” <i>Journal of Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.jsb.2014.03.018\">https://doi.org/10.1016/j.jsb.2014.03.018</a>.","ista":"Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau V-V, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. 2014. Correlative light- and electron microscopy with chemical tags. Journal of Structural Biology. 186(2), 205–213."},"date_published":"2014-05-01T00:00:00Z","_id":"9655","extern":"1","title":"Correlative light- and electron microscopy with chemical tags","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","file":[{"content_type":"application/pdf","file_name":"2014_JournalOfStructuralBiology_Perkovic.pdf","date_created":"2021-07-22T08:06:34Z","creator":"asandaue","file_id":"9701","file_size":3454628,"success":1,"date_updated":"2021-07-22T08:06:34Z","checksum":"a322991b43cdc5935c99db88d285aa3a","relation":"main_file","access_level":"open_access"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png"},"publisher":"Elsevier","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","pmid":1,"day":"01","language":[{"iso":"eng"}],"year":"2014","status":"public","article_processing_charge":"No","month":"05","has_accepted_license":"1","external_id":{"pmid":["24698954"]},"quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","volume":186,"oa":1,"publication":"Journal of Structural Biology","doi":"10.1016/j.jsb.2014.03.018"},{"arxiv":1,"publication":"The Journal of Chemical Physics","doi":"10.1063/1.4904293","volume":141,"oa":1,"quality_controlled":"1","external_id":{"arxiv":["1412.1308"],"pmid":["25554138"]},"oa_version":"Preprint","scopus_import":"1","pmid":1,"day":"28","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","language":[{"iso":"eng"}],"year":"2014","status":"public","article_processing_charge":"No","publisher":"AIP Publishing","date_created":"2021-07-15T09:22:49Z","citation":{"ista":"Cheng B, Ceriotti M. 2014. Direct path integral estimators for isotope fractionation ratios. The Journal of Chemical Physics. 141(24), 244112.","apa":"Cheng, B., &#38; Ceriotti, M. (2014). Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>","ieee":"B. Cheng and M. Ceriotti, “Direct path integral estimators for isotope fractionation ratios,” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24. AIP Publishing, 2014.","ama":"Cheng B, Ceriotti M. Direct path integral estimators for isotope fractionation ratios. <i>The Journal of Chemical Physics</i>. 2014;141(24). doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>","short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 141 (2014).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2014. <a href=\"https://doi.org/10.1063/1.4904293\">https://doi.org/10.1063/1.4904293</a>.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Direct Path Integral Estimators for Isotope Fractionation Ratios.” <i>The Journal of Chemical Physics</i>, vol. 141, no. 24, 244112, AIP Publishing, 2014, doi:<a href=\"https://doi.org/10.1063/1.4904293\">10.1063/1.4904293</a>."},"publication_status":"published","title":"Direct path integral estimators for isotope fractionation ratios","extern":"1","_id":"9662","date_published":"2014-12-28T00:00:00Z","article_type":"original","article_number":"244112","abstract":[{"lang":"eng","text":"Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons."}],"date_updated":"2021-08-09T12:32:24Z","author":[{"orcid":"0000-0002-3584-9632","first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.1308"}],"issue":"24","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"type":"journal_article","intvolume":"       141"},{"author":[{"orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"},{"full_name":"Kuemmeth, Ferdinand","first_name":"Ferdinand","last_name":"Kuemmeth"},{"last_name":"Larsen","first_name":"Thorvald","full_name":"Larsen, Thorvald"},{"full_name":"Fitzpatrick, Mattias","first_name":"Mattias","last_name":"Fitzpatrick"},{"first_name":"Jun","full_name":"Yao, Jun","last_name":"Yao"},{"last_name":"Yan","first_name":"Hao","full_name":"Yan, Hao"},{"last_name":"Lieber","full_name":"Lieber, Charles","first_name":"Charles"},{"last_name":"Marcus","full_name":"Marcus, Charles","first_name":"Charles"}],"acknowledgement":"Research supported by the Danish National Research Foundation, the Office of Science at the U.S. Department of Energy, the National Science Foundation (PHY-1104528), and the Defense Advanced Research Projects Agency through the QuEST Program.","main_file_link":[{"url":"https://arxiv.org/abs/1401.2948","open_access":"1"}],"issue":"21","abstract":[{"lang":"eng","text":"The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm)."}],"article_number":"216806","date_updated":"2021-01-12T08:22:19Z","type":"journal_article","intvolume":"       112","publisher":"American Physical Society","title":"Antilocalization of coulomb blockade in a Ge/Si nanowire","_id":"97","date_published":"2014-05-29T00:00:00Z","extern":"1","publication_status":"published","citation":{"ista":"Higginbotham AP, Kuemmeth F, Larsen T, Fitzpatrick M, Yao J, Yan H, Lieber C, Marcus C. 2014. Antilocalization of coulomb blockade in a Ge/Si nanowire. APS Physics, Physical Review Letters. 112(21), 216806.","mla":"Higginbotham, Andrew P., et al. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 21, 216806, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">10.1103/PhysRevLett.112.216806</a>.","chicago":"Higginbotham, Andrew P, Ferdinand Kuemmeth, Thorvald Larsen, Mattias Fitzpatrick, Jun Yao, Hao Yan, Charles Lieber, and Charles Marcus. “Antilocalization of Coulomb Blockade in a Ge/Si Nanowire.” <i>APS Physics, Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">https://doi.org/10.1103/PhysRevLett.112.216806</a>.","short":"A.P. Higginbotham, F. Kuemmeth, T. Larsen, M. Fitzpatrick, J. Yao, H. Yan, C. Lieber, C. Marcus, APS Physics, Physical Review Letters 112 (2014).","ama":"Higginbotham AP, Kuemmeth F, Larsen T, et al. Antilocalization of coulomb blockade in a Ge/Si nanowire. <i>APS Physics, Physical Review Letters</i>. 2014;112(21). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">10.1103/PhysRevLett.112.216806</a>","ieee":"A. P. Higginbotham <i>et al.</i>, “Antilocalization of coulomb blockade in a Ge/Si nanowire,” <i>APS Physics, Physical Review Letters</i>, vol. 112, no. 21. American Physical Society, 2014.","apa":"Higginbotham, A. P., Kuemmeth, F., Larsen, T., Fitzpatrick, M., Yao, J., Yan, H., … Marcus, C. (2014). Antilocalization of coulomb blockade in a Ge/Si nanowire. <i>APS Physics, Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.112.216806\">https://doi.org/10.1103/PhysRevLett.112.216806</a>"},"date_created":"2018-12-11T11:44:36Z","oa_version":"None","quality_controlled":"1","external_id":{"arxiv":["1401.2948"]},"month":"05","year":"2014","language":[{"iso":"eng"}],"status":"public","day":"29","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7957","doi":"10.1103/PhysRevLett.112.216806","publication":"APS Physics, Physical Review Letters","arxiv":1,"oa":1,"volume":112},{"month":"11","status":"public","type":"research_data_reference","year":"2014","article_processing_charge":"No","day":"13","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"author":[{"id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias","full_name":"Konrad, Matthias"},{"last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V"},{"first_name":"Simon","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"1993","relation":"used_in_publication"}]},"abstract":[{"text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.","lang":"eng"}],"date_updated":"2023-02-23T10:23:32Z","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","oa":1,"_id":"9740","date_published":"2014-11-13T00:00:00Z","date_created":"2021-07-28T08:38:40Z","citation":{"apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014).","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>."},"department":[{"_id":"SyCr"}],"doi":"10.5061/dryad.vm0vc","publisher":"Dryad"},{"type":"research_data_reference","status":"public","year":"2014","article_processing_charge":"No","month":"08","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"21","related_material":{"record":[{"relation":"used_in_publication","id":"2036","status":"public"}]},"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"last_name":"Colegrave","first_name":"Nick","full_name":"Colegrave, Nick"},{"full_name":"Neve, Paul","first_name":"Paul","last_name":"Neve"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.85dn7","open_access":"1"}],"oa_version":"Published Version","date_updated":"2023-02-23T10:25:31Z","abstract":[{"lang":"eng","text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments."}],"_id":"9741","date_published":"2014-08-21T00:00:00Z","title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","oa":1,"date_created":"2021-07-28T08:48:06Z","citation":{"apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>","ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","mla":"Lagator, Mato, et al. <i>Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>.","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, <a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>."},"department":[{"_id":"CaGu"}],"publisher":"Dryad","doi":"10.5061/dryad.85dn7"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"17","year":"2014","type":"research_data_reference","status":"public","article_processing_charge":"No","month":"04","date_updated":"2023-02-23T10:27:31Z","abstract":[{"lang":"eng","text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment."}],"related_material":{"record":[{"relation":"used_in_publication","id":"2083","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"oa_version":"Published Version","author":[{"last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","first_name":"Mato"},{"last_name":"Morgan","first_name":"Andrew","full_name":"Morgan, Andrew"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"},{"last_name":"Colegrave","first_name":"Nick","full_name":"Colegrave, Nick"}],"date_created":"2021-07-28T15:32:55Z","citation":{"short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>."},"date_published":"2014-04-17T00:00:00Z","_id":"9747","title":"Data from: Role of sex and migration in adaptation to sink environments","oa":1,"department":[{"_id":"CaGu"}],"publisher":"Dryad","doi":"10.5061/dryad.s42n1"},{"date_updated":"2023-02-23T10:35:57Z","abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"related_material":{"record":[{"id":"2277","status":"public","relation":"used_in_publication"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.246qg","open_access":"1"}],"author":[{"last_name":"Simmons","first_name":"Kristina","full_name":"Simmons, Kristina"},{"first_name":"Jason","full_name":"Prentice, Jason","last_name":"Prentice"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik"},{"full_name":"Homann, Jan","first_name":"Jan","last_name":"Homann"},{"first_name":"Heather","full_name":"Yee, Heather","last_name":"Yee"},{"full_name":"Palmer, Stephanie","first_name":"Stephanie","last_name":"Palmer"},{"last_name":"Nelson","full_name":"Nelson, Philip","first_name":"Philip"},{"last_name":"Balasubramanian","first_name":"Vijay","full_name":"Balasubramanian, Vijay"}],"oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"07","article_processing_charge":"No","status":"public","year":"2014","type":"research_data_reference","month":"11","doi":"10.5061/dryad.246qg","publisher":"Dryad","department":[{"_id":"GaTk"}],"citation":{"ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>."},"date_created":"2021-07-30T08:13:52Z","_id":"9752","date_published":"2014-11-07T00:00:00Z","oa":1,"title":"Data from: Transformation of stimulus correlations by the retina"},{"date_updated":"2023-02-23T10:36:17Z","abstract":[{"text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.","lang":"eng"}],"related_material":{"record":[{"id":"2284","status":"public","relation":"used_in_publication"}]},"oa_version":"Published Version","author":[{"last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Tragust, Simon"},{"last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V","first_name":"Line V"},{"last_name":"Chapuisat","first_name":"Michel","full_name":"Chapuisat, Michel"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.nc0gc"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"08","article_processing_charge":"No","status":"public","type":"research_data_reference","year":"2014","month":"10","doi":"10.5061/dryad.nc0gc","publisher":"Dryad","department":[{"_id":"SyCr"}],"citation":{"ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2014. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies.” Dryad, 2014.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2014). Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>","mla":"Tragust, Simon, et al. <i>Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.nc0gc\">10.5061/dryad.nc0gc</a>.","chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Data from: Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.nc0gc\">https://doi.org/10.5061/dryad.nc0gc</a>.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, (2014)."},"date_created":"2021-07-30T08:24:11Z","date_published":"2014-10-08T00:00:00Z","_id":"9753","oa":1,"title":"Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies"},{"author":[{"full_name":"Maksym Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"last_name":"Knap","full_name":"Knap, Michael J","first_name":"Michael"},{"last_name":"Gopalakrishnan","first_name":"Sarang","full_name":"Gopalakrishnan, Sarang"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"},{"full_name":"Yao, Norman Y","first_name":"Norman","last_name":"Yao"},{"first_name":"Chris","full_name":"Laumann, Chris R","last_name":"Laumann"},{"full_name":"Abanin, Dmitry A","first_name":"Dmitry","last_name":"Abanin"},{"last_name":"Lukin","full_name":"Lukin, Mikhail D","first_name":"Mikhail"},{"full_name":"Demler, Eugene A","first_name":"Eugene","last_name":"Demler"}],"acknowledgement":"We thank E. Altman, Y. Bahri, I. Bloch, T. Giamarchi, D. Huse, V. Oganesyan, A. Pal, D. Pekker, and G. Refael for insightful discussions. The authors acknowledge support from the Harvard Quantum Optics Center, Harvard-MIT CUA, the DARPA OLE program, AFOSR Quantum Simulation MURI, ARO-MURI on Atomtronics, the ARO-MURI Quism program, the Austrian Science Fund (FWF) Project No. J 3361-N20, NSERC grant, and Sloan Research Fellowship. Simulations presented in this article were performed on computational resources supported by the High Performance Computing Center (PICSciE) at Princeton University and the Research Computing Center at Harvard University. Research at Perimeter Institute was supported by the Government of Canada and by the Province of Ontario.\n\nM. S., M. K., and S. G. contributed equally to this work.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.0693"}],"issue":"14","abstract":[{"lang":"eng","text":"We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems."}],"quality_controlled":0,"date_updated":"2021-01-12T08:22:22Z","month":"10","type":"journal_article","intvolume":"       113","status":"public","year":"2014","day":"03","publist_id":"6421","publisher":"American Physical Society","doi":"10.1103/PhysRevLett.113.147204","publication":"Physical Review Letters","title":"Interferometric probes of many-body localization","volume":113,"oa":1,"_id":"977","extern":1,"date_published":"2014-10-03T00:00:00Z","date_created":"2018-12-11T11:49:30Z","citation":{"chicago":"Serbyn, Maksym, Michael Knap, Sarang Gopalakrishnan, Zlatko Papić, Norman Yao, Chris Laumann, Dmitry Abanin, Mikhail Lukin, and Eugene Demler. “Interferometric Probes of Many-Body Localization.” <i>Physical Review Letters</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">https://doi.org/10.1103/PhysRevLett.113.147204</a>.","mla":"Serbyn, Maksym, et al. “Interferometric Probes of Many-Body Localization.” <i>Physical Review Letters</i>, vol. 113, no. 14, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">10.1103/PhysRevLett.113.147204</a>.","short":"M. Serbyn, M. Knap, S. Gopalakrishnan, Z. Papić, N. Yao, C. Laumann, D. Abanin, M. Lukin, E. Demler, Physical Review Letters 113 (2014).","ieee":"M. Serbyn <i>et al.</i>, “Interferometric probes of many-body localization,” <i>Physical Review Letters</i>, vol. 113, no. 14. American Physical Society, 2014.","ama":"Serbyn M, Knap M, Gopalakrishnan S, et al. Interferometric probes of many-body localization. <i>Physical Review Letters</i>. 2014;113(14). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">10.1103/PhysRevLett.113.147204</a>","apa":"Serbyn, M., Knap, M., Gopalakrishnan, S., Papić, Z., Yao, N., Laumann, C., … Demler, E. (2014). Interferometric probes of many-body localization. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.113.147204\">https://doi.org/10.1103/PhysRevLett.113.147204</a>","ista":"Serbyn M, Knap M, Gopalakrishnan S, Papić Z, Yao N, Laumann C, Abanin D, Lukin M, Demler E. 2014. Interferometric probes of many-body localization. Physical Review Letters. 113(14)."},"publication_status":"published"},{"publication":"Nature Physics","publisher":"Nature Publishing Group","doi":"10.1038/nphys3012","date_created":"2018-12-11T11:49:30Z","publication_status":"published","citation":{"ista":"Zeljkovic I, Okada Y, Huang C, Sankar R, Walkup D, Zhou W, Serbyn M, Chou F, Tsai W, Lin H, Bansil A, Fu L, Hasan M, Madhavan V. 2014. Mapping the unconventional orbital texture in topological crystalline insulators. Nature Physics. 10(8), 572–577.","ama":"Zeljkovic I, Okada Y, Huang C, et al. Mapping the unconventional orbital texture in topological crystalline insulators. <i>Nature Physics</i>. 2014;10(8):572-577. doi:<a href=\"https://doi.org/10.1038/nphys3012\">10.1038/nphys3012</a>","ieee":"I. Zeljkovic <i>et al.</i>, “Mapping the unconventional orbital texture in topological crystalline insulators,” <i>Nature Physics</i>, vol. 10, no. 8. Nature Publishing Group, pp. 572–577, 2014.","apa":"Zeljkovic, I., Okada, Y., Huang, C., Sankar, R., Walkup, D., Zhou, W., … Madhavan, V. (2014). Mapping the unconventional orbital texture in topological crystalline insulators. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys3012\">https://doi.org/10.1038/nphys3012</a>","mla":"Zeljkovic, Ilija, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” <i>Nature Physics</i>, vol. 10, no. 8, Nature Publishing Group, 2014, pp. 572–77, doi:<a href=\"https://doi.org/10.1038/nphys3012\">10.1038/nphys3012</a>.","chicago":"Zeljkovic, Ilija, Yoshinori Okada, Chengyi Huang, Raman Sankar, Daniel Walkup, Wenwen Zhou, Maksym Serbyn, et al. “Mapping the Unconventional Orbital Texture in Topological Crystalline Insulators.” <i>Nature Physics</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nphys3012\">https://doi.org/10.1038/nphys3012</a>.","short":"I. Zeljkovic, Y. Okada, C. Huang, R. Sankar, D. Walkup, W. Zhou, M. Serbyn, F. Chou, W. Tsai, H. Lin, A. Bansil, L. Fu, M. Hasan, V. Madhavan, Nature Physics 10 (2014) 572–577."},"volume":10,"title":"Mapping the unconventional orbital texture in topological crystalline insulators","oa":1,"extern":1,"_id":"978","date_published":"2014-08-01T00:00:00Z","abstract":[{"text":"The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications.","lang":"eng"}],"quality_controlled":0,"page":"572 - 577","date_updated":"2021-01-12T08:22:23Z","main_file_link":[{"url":"https://arxiv.org/abs/1312.0164","open_access":"1"}],"author":[{"last_name":"Zeljkovic","full_name":"Zeljkovic, Ilija","first_name":"Ilija"},{"last_name":"Okada","first_name":"Yoshinori","full_name":"Okada, Yoshinori"},{"last_name":"Huang","full_name":"Huang, Chengyi","first_name":"Chengyi"},{"full_name":"Sankar, Raman","first_name":"Raman","last_name":"Sankar"},{"full_name":"Walkup, Daniel","first_name":"Daniel","last_name":"Walkup"},{"last_name":"Zhou","first_name":"Wenwen","full_name":"Zhou, Wenwen"},{"orcid":"0000-0002-2399-5827","full_name":"Maksym Serbyn","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn"},{"last_name":"Chou","first_name":"Fangcheng","full_name":"Chou, Fangcheng"},{"first_name":"Wei","full_name":"Tsai, Wei-Feng","last_name":"Tsai"},{"first_name":"Hsin","full_name":"Lin, Hsin","last_name":"Lin"},{"last_name":"Bansil","first_name":"Arun","full_name":"Bansil, Arun"},{"last_name":"Fu","first_name":"Liang","full_name":"Fu, Liang"},{"full_name":"Hasan, Md Z","first_name":"Md","last_name":"Hasan"},{"last_name":"Madhavan","full_name":"Madhavan, Vidya","first_name":"Vidya"}],"acknowledgement":"V.M. gratefully acknowledges funding from the US Department of Energy, Scanned Probe Division under Award Number DE-FG02-12ER46880 for the primary support of I.Z. and Y.O. (experiments, data analysis and writing the paper) and NSF-ECCS-1232105 for the partial support of W.Z. and D.W. (data acquisition). 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. 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 time at the NERSC supercomputing centre through DOE grant number DE-AC02-05CH11231. W-F.T. and C-Y.H. were supported by the NSC in Taiwan under Grant No. 102-2112-M-110-009. W-F.T. also thanks C. Fang for useful discussions. 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.","issue":"8","day":"01","publist_id":"6423","month":"08","intvolume":"        10","type":"journal_article","status":"public","year":"2014"},{"date_created":"2018-12-11T11:49:31Z","publication_status":"published","citation":{"ista":"Serbyn M, Fu L. 2014. Symmetry breaking and Landau quantization in topological crystalline insulators. Physical Review B - Condensed Matter and Materials Physics. 90(3).","short":"M. Serbyn, L. Fu, Physical Review B - Condensed Matter and Materials Physics 90 (2014).","mla":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 3, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">10.1103/PhysRevB.90.035402</a>.","chicago":"Serbyn, Maksym, and Liang Fu. “Symmetry Breaking and Landau Quantization in Topological Crystalline Insulators.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">https://doi.org/10.1103/PhysRevB.90.035402</a>.","apa":"Serbyn, M., &#38; Fu, L. (2014). Symmetry breaking and Landau quantization in topological crystalline insulators. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">https://doi.org/10.1103/PhysRevB.90.035402</a>","ieee":"M. Serbyn and L. Fu, “Symmetry breaking and Landau quantization in topological crystalline insulators,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 3. American Physical Society, 2014.","ama":"Serbyn M, Fu L. Symmetry breaking and Landau quantization in topological crystalline insulators. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2014;90(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.035402\">10.1103/PhysRevB.90.035402</a>"},"volume":90,"title":"Symmetry breaking and Landau quantization in topological crystalline insulators","oa":1,"date_published":"2014-07-03T00:00:00Z","_id":"979","extern":1,"publication":"Physical Review B - Condensed Matter and Materials Physics","publisher":"American Physical Society","doi":"10.1103/PhysRevB.90.035402","day":"03","publist_id":"6422","month":"07","type":"journal_article","intvolume":"        90","year":"2014","status":"public","abstract":[{"text":"In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators.","lang":"eng"}],"quality_controlled":0,"date_updated":"2021-01-12T08:22:23Z","acknowledgement":"We thank V. Madhavan and Y. Okada for related collaborations, and P. A. Lee for discussions. M.S. was supported by P. A. Lee via Grant No. NSF DMR 1104498. L.F. is supported by the DOE Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under award DE-SC0010526.","author":[{"full_name":"Maksym Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fu","full_name":"Fu, Liang","first_name":"Liang"}],"main_file_link":[{"url":"https://arxiv.org/abs/1403.8153","open_access":"1"}],"issue":"3"},{"volume":14,"oa":1,"doi":"10.1021/nl501242b","arxiv":1,"publication":"Nano Letters","month":"05","language":[{"iso":"eng"}],"year":"2014","status":"public","day":"05","publist_id":"7956","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","quality_controlled":"1","external_id":{"arxiv":["1403.2093"]},"title":"Hole spin coherence in a Ge/Si heterostructure nanowire","extern":"1","_id":"98","date_published":"2014-05-05T00:00:00Z","date_created":"2018-12-11T11:44:37Z","publication_status":"published","citation":{"chicago":"Higginbotham, Andrew P, Thorvald Larsen, Jun Yao, Hao Yan, Charles Lieber, Charles Marcus, and Ferdinand Kuemmeth. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>.","mla":"Higginbotham, Andrew P., et al. “Hole Spin Coherence in a Ge/Si Heterostructure Nanowire.” <i>Nano Letters</i>, vol. 14, no. 6, American Chemical Society, 2014, pp. 3582–86, doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>.","short":"A.P. Higginbotham, T. Larsen, J. Yao, H. Yan, C. Lieber, C. Marcus, F. Kuemmeth, Nano Letters 14 (2014) 3582–3586.","ama":"Higginbotham AP, Larsen T, Yao J, et al. Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. 2014;14(6):3582-3586. doi:<a href=\"https://doi.org/10.1021/nl501242b\">10.1021/nl501242b</a>","ieee":"A. P. Higginbotham <i>et al.</i>, “Hole spin coherence in a Ge/Si heterostructure nanowire,” <i>Nano Letters</i>, vol. 14, no. 6. American Chemical Society, pp. 3582–3586, 2014.","apa":"Higginbotham, A. P., Larsen, T., Yao, J., Yan, H., Lieber, C., Marcus, C., &#38; Kuemmeth, F. (2014). Hole spin coherence in a Ge/Si heterostructure nanowire. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl501242b\">https://doi.org/10.1021/nl501242b</a>","ista":"Higginbotham AP, Larsen T, Yao J, Yan H, Lieber C, Marcus C, Kuemmeth F. 2014. Hole spin coherence in a Ge/Si heterostructure nanowire. Nano Letters. 14(6), 3582–3586."},"publisher":"American Chemical Society","intvolume":"        14","type":"journal_article","acknowledgement":"Funding from the Department of Energy, Office of Science & SCGF, the EC FP7-ICT project SiSPIN no. 323841, and the Danish National Research Foundation is acknowledged.","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1403.2093"}],"author":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"},{"last_name":"Larsen","first_name":"Thorvald","full_name":"Larsen, Thorvald"},{"last_name":"Yao","first_name":"Jun","full_name":"Yao, Jun"},{"first_name":"Hao","full_name":"Yan, Hao","last_name":"Yan"},{"last_name":"Lieber","full_name":"Lieber, Charles","first_name":"Charles"},{"first_name":"Charles","full_name":"Marcus, Charles","last_name":"Marcus"},{"first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand","last_name":"Kuemmeth"}],"issue":"6","page":"3582 - 3586","abstract":[{"text":"Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.","lang":"eng"}],"date_updated":"2021-01-12T08:22:24Z"},{"author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn","orcid":"0000-0002-2399-5827"},{"last_name":"Papić","first_name":"Zlatko","full_name":"Papić, Zlatko"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A","first_name":"Dmitry"}],"main_file_link":[{"url":"https://arxiv.org/abs/1408.4105","open_access":"1"}],"acknowledgement":"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. We acknowledge support by NSERC Discovery Grant (D.A.).","issue":"17","quality_controlled":0,"abstract":[{"text":"Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization.","lang":"eng"}],"date_updated":"2021-01-12T08:22:24Z","month":"11","year":"2014","intvolume":"        90","type":"journal_article","status":"public","day":"06","publist_id":"6420","doi":"10.1103/PhysRevB.90.174302","publisher":"American Physical Society","publication":"Physical Review B - Condensed Matter and Materials Physics","oa":1,"volume":90,"title":"Quantum quenches in the many-body localized phase","extern":1,"_id":"980","date_published":"2014-11-06T00:00:00Z","citation":{"ista":"Serbyn M, Papić Z, Abanin D. 2014. Quantum quenches in the many-body localized phase. Physical Review B - Condensed Matter and Materials Physics. 90(17).","ieee":"M. Serbyn, Z. Papić, and D. Abanin, “Quantum quenches in the many-body localized phase,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 17. American Physical Society, 2014.","ama":"Serbyn M, Papić Z, Abanin D. Quantum quenches in the many-body localized phase. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2014;90(17). doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">10.1103/PhysRevB.90.174302</a>","apa":"Serbyn, M., Papić, Z., &#38; Abanin, D. (2014). Quantum quenches in the many-body localized phase. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">https://doi.org/10.1103/PhysRevB.90.174302</a>","chicago":"Serbyn, Maksym, Zlatko Papić, and Dmitry Abanin. “Quantum Quenches in the Many-Body Localized Phase.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">https://doi.org/10.1103/PhysRevB.90.174302</a>.","mla":"Serbyn, Maksym, et al. “Quantum Quenches in the Many-Body Localized Phase.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 90, no. 17, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevB.90.174302\">10.1103/PhysRevB.90.174302</a>.","short":"M. Serbyn, Z. Papić, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 90 (2014)."},"publication_status":"published","date_created":"2018-12-11T11:49:31Z"}]