[{"year":"2018","abstract":[{"lang":"eng","text":"An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate."}],"publication":"Nature Physics","date_updated":"2021-01-12T08:07:15Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","language":[{"iso":"eng"}],"extern":"1","month":"10","oa_version":"Preprint","oa":1,"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1712.06535","open_access":"1"}],"publication_identifier":{"issn":["1745-2473","1745-2481"]},"status":"public","citation":{"ista":"Higginbotham AP, Burns PS, Urmey MD, Peterson RW, Kampel NS, Brubaker BM, Smith G, Lehnert KW, Regal CA. 2018. Harnessing electro-optic correlations in an efficient mechanical converter. Nature Physics. 14(10), 1038–1042.","ieee":"A. P. Higginbotham <i>et al.</i>, “Harnessing electro-optic correlations in an efficient mechanical converter,” <i>Nature Physics</i>, vol. 14, no. 10. Springer Nature, pp. 1038–1042, 2018.","apa":"Higginbotham, A. P., Burns, P. S., Urmey, M. D., Peterson, R. W., Kampel, N. S., Brubaker, B. M., … Regal, C. A. (2018). Harnessing electro-optic correlations in an efficient mechanical converter. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-018-0210-0\">https://doi.org/10.1038/s41567-018-0210-0</a>","short":"A.P. Higginbotham, P.S. Burns, M.D. Urmey, R.W. Peterson, N.S. Kampel, B.M. Brubaker, G. Smith, K.W. Lehnert, C.A. Regal, Nature Physics 14 (2018) 1038–1042.","mla":"Higginbotham, Andrew P., et al. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” <i>Nature Physics</i>, vol. 14, no. 10, Springer Nature, 2018, pp. 1038–42, doi:<a href=\"https://doi.org/10.1038/s41567-018-0210-0\">10.1038/s41567-018-0210-0</a>.","ama":"Higginbotham AP, Burns PS, Urmey MD, et al. Harnessing electro-optic correlations in an efficient mechanical converter. <i>Nature Physics</i>. 2018;14(10):1038-1042. doi:<a href=\"https://doi.org/10.1038/s41567-018-0210-0\">10.1038/s41567-018-0210-0</a>","chicago":"Higginbotham, Andrew P, P. S. Burns, M. D. Urmey, R. W. Peterson, N. S. Kampel, B. M. Brubaker, G. Smith, K. W. Lehnert, and C. A. Regal. “Harnessing Electro-Optic Correlations in an Efficient Mechanical Converter.” <i>Nature Physics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41567-018-0210-0\">https://doi.org/10.1038/s41567-018-0210-0</a>."},"volume":14,"author":[{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham"},{"full_name":"Burns, P. S.","last_name":"Burns","first_name":"P. S."},{"full_name":"Urmey, M. D.","first_name":"M. D.","last_name":"Urmey"},{"last_name":"Peterson","first_name":"R. W.","full_name":"Peterson, R. W."},{"first_name":"N. S.","last_name":"Kampel","full_name":"Kampel, N. S."},{"last_name":"Brubaker","first_name":"B. M.","full_name":"Brubaker, B. M."},{"first_name":"G.","last_name":"Smith","full_name":"Smith, G."},{"last_name":"Lehnert","first_name":"K. W.","full_name":"Lehnert, K. W."},{"last_name":"Regal","first_name":"C. A.","full_name":"Regal, C. A."}],"intvolume":"        14","external_id":{"arxiv":["1712.06535"]},"date_published":"2018-10-01T00:00:00Z","quality_controlled":"1","page":"1038-1042","date_created":"2019-05-03T09:17:20Z","_id":"6368","publisher":"Springer Nature","type":"journal_article","doi":"10.1038/s41567-018-0210-0","publication_status":"published","issue":"10","title":"Harnessing electro-optic correlations in an efficient mechanical converter"},{"publication_status":"published","publisher":"American Physical Society (APS)","doi":"10.1103/physrevb.97.220301","type":"journal_article","title":"Topological phase transition measured in a dissipative metamaterial","issue":"22","external_id":{"arxiv":["1802.02243"]},"date_published":"2018-06-04T00:00:00Z","quality_controlled":"1","author":[{"last_name":"Rosenthal","first_name":"Eric I.","full_name":"Rosenthal, Eric I."},{"full_name":"Ehrlich, Nicole K.","last_name":"Ehrlich","first_name":"Nicole K."},{"last_name":"Rudner","first_name":"Mark S.","full_name":"Rudner, Mark S."},{"last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P"},{"last_name":"Lehnert","first_name":"K. W.","full_name":"Lehnert, K. W."}],"intvolume":"        97","_id":"6369","date_created":"2019-05-03T09:29:49Z","publication_identifier":{"issn":["2469-9950","2469-9969"]},"article_number":"220301","status":"public","oa_version":"Preprint","oa":1,"arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.02243","open_access":"1"}],"citation":{"chicago":"Rosenthal, Eric I., Nicole K. Ehrlich, Mark S. Rudner, Andrew P Higginbotham, and K. W. Lehnert. “Topological Phase Transition Measured in a Dissipative Metamaterial.” <i>Physical Review B</i>. American Physical Society (APS), 2018. <a href=\"https://doi.org/10.1103/physrevb.97.220301\">https://doi.org/10.1103/physrevb.97.220301</a>.","mla":"Rosenthal, Eric I., et al. “Topological Phase Transition Measured in a Dissipative Metamaterial.” <i>Physical Review B</i>, vol. 97, no. 22, 220301, American Physical Society (APS), 2018, doi:<a href=\"https://doi.org/10.1103/physrevb.97.220301\">10.1103/physrevb.97.220301</a>.","ama":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. Topological phase transition measured in a dissipative metamaterial. <i>Physical Review B</i>. 2018;97(22). doi:<a href=\"https://doi.org/10.1103/physrevb.97.220301\">10.1103/physrevb.97.220301</a>","ieee":"E. I. Rosenthal, N. K. Ehrlich, M. S. Rudner, A. P. Higginbotham, and K. W. Lehnert, “Topological phase transition measured in a dissipative metamaterial,” <i>Physical Review B</i>, vol. 97, no. 22. American Physical Society (APS), 2018.","apa":"Rosenthal, E. I., Ehrlich, N. K., Rudner, M. S., Higginbotham, A. P., &#38; Lehnert, K. W. (2018). Topological phase transition measured in a dissipative metamaterial. <i>Physical Review B</i>. American Physical Society (APS). <a href=\"https://doi.org/10.1103/physrevb.97.220301\">https://doi.org/10.1103/physrevb.97.220301</a>","short":"E.I. Rosenthal, N.K. Ehrlich, M.S. Rudner, A.P. Higginbotham, K.W. Lehnert, Physical Review B 97 (2018).","ista":"Rosenthal EI, Ehrlich NK, Rudner MS, Higginbotham AP, Lehnert KW. 2018. Topological phase transition measured in a dissipative metamaterial. Physical Review B. 97(22), 220301."},"volume":97,"publication":"Physical Review B","date_updated":"2021-01-12T08:07:16Z","year":"2018","abstract":[{"lang":"eng","text":"We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before."}],"month":"06","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"04","language":[{"iso":"eng"}],"extern":"1"},{"publication_status":"published","department":[{"_id":"TaHa"}],"type":"journal_article","doi":"10.1073/pnas.1805847115","publisher":"National Academy of Sciences","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","issue":"35","quality_controlled":"1","date_published":"2018-08-28T00:00:00Z","external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"intvolume":"       115","author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"first_name":"Aldo","last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo"},{"first_name":"Y","last_name":"Prieto","full_name":"Prieto, Y"},{"last_name":"Shkolnikov","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail"},{"full_name":"Kalinina, V","first_name":"V","last_name":"Kalinina"},{"last_name":"Lupercio","first_name":"Ernesto","full_name":"Lupercio, Ernesto"}],"_id":"64","date_created":"2018-12-11T11:44:26Z","article_processing_charge":"No","page":"E8135 - E8142","status":"public","publication_identifier":{"issn":["0027-8424"]},"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1806.09153","open_access":"1"}],"arxiv":1,"oa_version":"Preprint","publist_id":"7990","oa":1,"ec_funded":1,"volume":115,"citation":{"chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1805847115\">https://doi.org/10.1073/pnas.1805847115</a>.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:<a href=\"https://doi.org/10.1073/pnas.1805847115\">10.1073/pnas.1805847115</a>.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(35):E8135-E8142. doi:<a href=\"https://doi.org/10.1073/pnas.1805847115\">10.1073/pnas.1805847115</a>","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., &#38; Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1805847115\">https://doi.org/10.1073/pnas.1805847115</a>","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142."},"date_updated":"2025-06-03T11:21:16Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","abstract":[{"text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation.","lang":"eng"}],"year":"2018","isi":1,"month":"08","article_type":"original","language":[{"iso":"eng"}],"day":"28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2025-06-10T11:12:41Z","publication":"Nature Materials","abstract":[{"text":"Transition-metal dichalcogenides (TMDs) are renowned for their rich and varied bulk properties, while their single-layer variants have become one of the most prominent examples of two-dimensional materials beyond graphene. Their disparate ground states largely depend on transition metal d-electron-derived electronic states, on which the vast majority of attention has been concentrated to date. Here, we focus on the chalcogen-derived states. From density-functional theory calculations together with spin- and angle-resolved photoemission, we find that these generically host a co-existence of type-I and type-II three-dimensional bulk Dirac fermions as well as ladders of topological surface states and surface resonances. We demonstrate how these naturally arise within a single p-orbital manifold as a general consequence of a trigonal crystal field, and as such can be expected across a large number of compounds. Already, we demonstrate their existence in six separate TMDs, opening routes to tune, and ultimately exploit, their topological physics.","lang":"eng"}],"year":"2018","month":"01","article_type":"original","extern":"1","language":[{"iso":"eng"}],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.08177"}],"OA_place":"repository","arxiv":1,"oa":1,"oa_version":"Preprint","volume":17,"citation":{"apa":"Bahramy, M. S., Clark, O. J., Yang, B.-J., Feng, J., Bawden, L., Riley, J. M., … King, P. D. C. (2018). Ubiquitous formation of bulk Dirac cones and topological surface states from a single orbital manifold in transition-metal dichalcogenides. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nmat5031\">https://doi.org/10.1038/nmat5031</a>","ieee":"M. S. Bahramy <i>et al.</i>, “Ubiquitous formation of bulk Dirac cones and topological surface states from a single orbital manifold in transition-metal dichalcogenides,” <i>Nature Materials</i>, vol. 17. Springer Nature, pp. 21–28, 2018.","short":"M.S. Bahramy, O.J. Clark, B.-J. Yang, J. Feng, L. Bawden, J.M. Riley, I. Marković, F. Mazzola, V. Sunko, D. Biswas, S.P. Cooil, M. Jorge, J.W. Wells, M. Leandersson, T. Balasubramanian, J. Fujii, I. Vobornik, J.E. Rault, T.K. Kim, M. Hoesch, K. Okawa, M. Asakawa, T. Sasagawa, T. Eknapakul, W. Meevasana, P.D.C. King, Nature Materials 17 (2018) 21–28.","ista":"Bahramy MS, Clark OJ, Yang B-J, Feng J, Bawden L, Riley JM, Marković I, Mazzola F, Sunko V, Biswas D, Cooil SP, Jorge M, Wells JW, Leandersson M, Balasubramanian T, Fujii J, Vobornik I, Rault JE, Kim TK, Hoesch M, Okawa K, Asakawa M, Sasagawa T, Eknapakul T, Meevasana W, King PDC. 2018. Ubiquitous formation of bulk Dirac cones and topological surface states from a single orbital manifold in transition-metal dichalcogenides. Nature Materials. 17, 21–28.","chicago":"Bahramy, M. S., O. J. Clark, B.-J. Yang, J. Feng, L. Bawden, J. M. Riley, I. Marković, et al. “Ubiquitous Formation of Bulk Dirac Cones and Topological Surface States from a Single Orbital Manifold in Transition-Metal Dichalcogenides.” <i>Nature Materials</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/nmat5031\">https://doi.org/10.1038/nmat5031</a>.","mla":"Bahramy, M. S., et al. “Ubiquitous Formation of Bulk Dirac Cones and Topological Surface States from a Single Orbital Manifold in Transition-Metal Dichalcogenides.” <i>Nature Materials</i>, vol. 17, Springer Nature, 2018, pp. 21–28, doi:<a href=\"https://doi.org/10.1038/nmat5031\">10.1038/nmat5031</a>.","ama":"Bahramy MS, Clark OJ, Yang B-J, et al. Ubiquitous formation of bulk Dirac cones and topological surface states from a single orbital manifold in transition-metal dichalcogenides. <i>Nature Materials</i>. 2018;17:21-28. doi:<a href=\"https://doi.org/10.1038/nmat5031\">10.1038/nmat5031</a>"},"pmid":1,"OA_type":"green","quality_controlled":"1","date_published":"2018-01-01T00:00:00Z","external_id":{"pmid":["29180775"],"arxiv":["1702.08177"]},"intvolume":"        17","author":[{"last_name":"Bahramy","first_name":"M. S.","full_name":"Bahramy, M. S."},{"full_name":"Clark, O. J.","last_name":"Clark","first_name":"O. J."},{"full_name":"Yang, B.-J.","last_name":"Yang","first_name":"B.-J."},{"last_name":"Feng","first_name":"J.","full_name":"Feng, J."},{"first_name":"L.","last_name":"Bawden","full_name":"Bawden, L."},{"last_name":"Riley","first_name":"J. M.","full_name":"Riley, J. M."},{"full_name":"Marković, I.","last_name":"Marković","first_name":"I."},{"first_name":"F.","last_name":"Mazzola","full_name":"Mazzola, F."},{"first_name":"Veronika","orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","last_name":"Sunko","full_name":"Sunko, Veronika"},{"full_name":"Biswas, D.","last_name":"Biswas","first_name":"D."},{"last_name":"Cooil","first_name":"S. P.","full_name":"Cooil, S. P."},{"full_name":"Jorge, M.","last_name":"Jorge","first_name":"M."},{"full_name":"Wells, J. W.","last_name":"Wells","first_name":"J. W."},{"full_name":"Leandersson, M.","first_name":"M.","last_name":"Leandersson"},{"full_name":"Balasubramanian, T.","last_name":"Balasubramanian","first_name":"T."},{"last_name":"Fujii","first_name":"J.","full_name":"Fujii, J."},{"full_name":"Vobornik, I.","first_name":"I.","last_name":"Vobornik"},{"first_name":"J. E.","last_name":"Rault","full_name":"Rault, J. E."},{"last_name":"Kim","first_name":"T. K.","full_name":"Kim, T. K."},{"full_name":"Hoesch, M.","last_name":"Hoesch","first_name":"M."},{"full_name":"Okawa, K.","first_name":"K.","last_name":"Okawa"},{"last_name":"Asakawa","first_name":"M.","full_name":"Asakawa, M."},{"full_name":"Sasagawa, T.","first_name":"T.","last_name":"Sasagawa"},{"first_name":"T.","last_name":"Eknapakul","full_name":"Eknapakul, T."},{"first_name":"W.","last_name":"Meevasana","full_name":"Meevasana, W."},{"first_name":"P. D. C.","last_name":"King","full_name":"King, P. D. C."}],"_id":"19806","date_created":"2025-06-10T09:11:05Z","article_processing_charge":"No","page":"21-28","publication_status":"published","doi":"10.1038/nmat5031","type":"journal_article","publisher":"Springer Nature","title":"Ubiquitous formation of bulk Dirac cones and topological surface states from a single orbital manifold in transition-metal dichalcogenides"},{"_id":"19808","date_created":"2025-06-10T09:12:15Z","article_processing_charge":"No","OA_type":"gold","quality_controlled":"1","date_published":"2018-12-18T00:00:00Z","external_id":{"arxiv":["1804.01896"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"intvolume":"         3","author":[{"full_name":"Nandi, Nabhanila","first_name":"Nabhanila","last_name":"Nandi"},{"first_name":"Thomas","last_name":"Scaffidi","full_name":"Scaffidi, Thomas"},{"full_name":"Kushwaha, Pallavi","first_name":"Pallavi","last_name":"Kushwaha"},{"full_name":"Khim, Seunghyun","last_name":"Khim","first_name":"Seunghyun"},{"first_name":"Mark E.","last_name":"Barber","full_name":"Barber, Mark E."},{"full_name":"Sunko, Veronika","last_name":"Sunko","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523","first_name":"Veronika"},{"full_name":"Mazzola, Federico","first_name":"Federico","last_name":"Mazzola"},{"last_name":"King","first_name":"Philip D. C.","full_name":"King, Philip D. C."},{"first_name":"Helge","last_name":"Rosner","full_name":"Rosner, Helge"},{"first_name":"Philip J. W.","last_name":"Moll","full_name":"Moll, Philip J. W."},{"last_name":"König","first_name":"Markus","full_name":"König, Markus"},{"first_name":"Joel E.","last_name":"Moore","full_name":"Moore, Joel E."},{"first_name":"Sean","last_name":"Hartnoll","full_name":"Hartnoll, Sean"},{"last_name":"Mackenzie","first_name":"Andrew P.","full_name":"Mackenzie, Andrew P."}],"title":"Unconventional magneto-transport in ultrapure PdCoO2 and PtCoO2","publication_status":"published","doi":"10.1038/s41535-018-0138-8","type":"journal_article","publisher":"Springer Nature","month":"12","article_type":"original","language":[{"iso":"eng"}],"extern":"1","day":"18","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-10T11:39:41Z","publication":"npj Quantum Materials","abstract":[{"lang":"eng","text":"The single-band, quasi-two dimensional metals PdCoO2 and PtCoO2 have recently come to prominence because of their extremely long mean free paths, which establish them as some of the most electronically pure materials known, and as potential hosts of previously unobservable regimes of electronic transport. To fully establish their magnetotransport properties, we have studied the magnetoresistance and Hall effect in bulk single crystals to which electrical contacts have been made with high precision using focused ion beam machining. We observe a strong temperature dependence of the Hall resistivity in small applied fields, linked to a large violation of Kohler’s rule in the magnetoresistance. We discuss the extent to which these observations can be accounted for by standard transport theory."}],"year":"2018","volume":3,"citation":{"chicago":"Nandi, Nabhanila, Thomas Scaffidi, Pallavi Kushwaha, Seunghyun Khim, Mark E. Barber, Veronika Sunko, Federico Mazzola, et al. “Unconventional Magneto-Transport in Ultrapure PdCoO2 and PtCoO2.” <i>Npj Quantum Materials</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41535-018-0138-8\">https://doi.org/10.1038/s41535-018-0138-8</a>.","ama":"Nandi N, Scaffidi T, Kushwaha P, et al. Unconventional magneto-transport in ultrapure PdCoO2 and PtCoO2. <i>npj Quantum Materials</i>. 2018;3. doi:<a href=\"https://doi.org/10.1038/s41535-018-0138-8\">10.1038/s41535-018-0138-8</a>","mla":"Nandi, Nabhanila, et al. “Unconventional Magneto-Transport in Ultrapure PdCoO2 and PtCoO2.” <i>Npj Quantum Materials</i>, vol. 3, 66, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41535-018-0138-8\">10.1038/s41535-018-0138-8</a>.","ieee":"N. Nandi <i>et al.</i>, “Unconventional magneto-transport in ultrapure PdCoO2 and PtCoO2,” <i>npj Quantum Materials</i>, vol. 3. Springer Nature, 2018.","apa":"Nandi, N., Scaffidi, T., Kushwaha, P., Khim, S., Barber, M. E., Sunko, V., … Mackenzie, A. P. (2018). Unconventional magneto-transport in ultrapure PdCoO2 and PtCoO2. <i>Npj Quantum Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41535-018-0138-8\">https://doi.org/10.1038/s41535-018-0138-8</a>","short":"N. Nandi, T. Scaffidi, P. Kushwaha, S. Khim, M.E. Barber, V. Sunko, F. Mazzola, P.D.C. King, H. Rosner, P.J.W. Moll, M. König, J.E. Moore, S. Hartnoll, A.P. Mackenzie, Npj Quantum Materials 3 (2018).","ista":"Nandi N, Scaffidi T, Kushwaha P, Khim S, Barber ME, Sunko V, Mazzola F, King PDC, Rosner H, Moll PJW, König M, Moore JE, Hartnoll S, Mackenzie AP. 2018. Unconventional magneto-transport in ultrapure PdCoO2 and PtCoO2. npj Quantum Materials. 3, 66."},"status":"public","article_number":"66","publication_identifier":{"issn":["2397-4648"]},"scopus_import":"1","OA_place":"publisher","main_file_link":[{"url":"https://doi.org/10.1038/s41535-018-0138-8","open_access":"1"}],"arxiv":1,"oa":1,"has_accepted_license":"1","oa_version":"Published Version"},{"date_updated":"2025-06-10T12:16:08Z","publication":"Physical Review Letters","abstract":[{"text":"We study the low-energy surface electronic structure of the transition-metal dichalcogenide superconductor PdTe2 by spin- and angle-resolved photoemission, scanning tunneling microscopy, and density-functional theory-based supercell calculations. Comparing PdTe2 with its sister compound PtSe2, we demonstrate how enhanced interlayer hopping in the Te-based material drives a band inversion within the antibonding 𝑝-orbital manifold well above the Fermi level. We show how this mediates spin-polarized topological surface states which form rich multivalley Fermi surfaces with complex spin textures. Scanning tunneling spectroscopy reveals type-II superconductivity at the surface, and moreover shows no evidence for an unconventional component of its superconducting order parameter, despite the presence of topological surface states.","lang":"eng"}],"year":"2018","month":"04","language":[{"iso":"eng"}],"extern":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","article_number":"156401","status":"public","scopus_import":"1","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"arxiv":1,"OA_place":"repository","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1712.04184","open_access":"1"}],"oa_version":"Preprint","oa":1,"volume":120,"citation":{"short":"O.J. Clark, M.J. Neat, K. Okawa, L. Bawden, I. Marković, F. Mazzola, J. Feng, V. Sunko, J.M. Riley, W. Meevasana, J. Fujii, I. Vobornik, T.K. Kim, M. Hoesch, T. Sasagawa, P. Wahl, M.S. Bahramy, P.D.C. King, Physical Review Letters 120 (2018).","apa":"Clark, O. J., Neat, M. J., Okawa, K., Bawden, L., Marković, I., Mazzola, F., … King, P. D. C. (2018). Fermiology and superconductivity of topological surface states in PdTe2. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.120.156401\">https://doi.org/10.1103/physrevlett.120.156401</a>","ieee":"O. J. Clark <i>et al.</i>, “Fermiology and superconductivity of topological surface states in PdTe2,” <i>Physical Review Letters</i>, vol. 120, no. 15. American Physical Society, 2018.","ista":"Clark OJ, Neat MJ, Okawa K, Bawden L, Marković I, Mazzola F, Feng J, Sunko V, Riley JM, Meevasana W, Fujii J, Vobornik I, Kim TK, Hoesch M, Sasagawa T, Wahl P, Bahramy MS, King PDC. 2018. Fermiology and superconductivity of topological surface states in PdTe2. Physical Review Letters. 120(15), 156401.","chicago":"Clark, O. J., M. J. Neat, K. Okawa, L. Bawden, I. Marković, F. Mazzola, J. Feng, et al. “Fermiology and Superconductivity of Topological Surface States in PdTe2.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevlett.120.156401\">https://doi.org/10.1103/physrevlett.120.156401</a>.","ama":"Clark OJ, Neat MJ, Okawa K, et al. Fermiology and superconductivity of topological surface states in PdTe2. <i>Physical Review Letters</i>. 2018;120(15). doi:<a href=\"https://doi.org/10.1103/physrevlett.120.156401\">10.1103/physrevlett.120.156401</a>","mla":"Clark, O. J., et al. “Fermiology and Superconductivity of Topological Surface States in PdTe2.” <i>Physical Review Letters</i>, vol. 120, no. 15, 156401, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevlett.120.156401\">10.1103/physrevlett.120.156401</a>."},"pmid":1,"quality_controlled":"1","OA_type":"green","external_id":{"pmid":["29756894"],"arxiv":["1712.04184"]},"date_published":"2018-04-09T00:00:00Z","author":[{"full_name":"Clark, O. J.","first_name":"O. J.","last_name":"Clark"},{"first_name":"M. J.","last_name":"Neat","full_name":"Neat, M. J."},{"first_name":"K.","last_name":"Okawa","full_name":"Okawa, K."},{"full_name":"Bawden, L.","first_name":"L.","last_name":"Bawden"},{"full_name":"Marković, I.","last_name":"Marković","first_name":"I."},{"first_name":"F.","last_name":"Mazzola","full_name":"Mazzola, F."},{"full_name":"Feng, J.","last_name":"Feng","first_name":"J."},{"full_name":"Sunko, Veronika","last_name":"Sunko","first_name":"Veronika","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523"},{"last_name":"Riley","first_name":"J. M.","full_name":"Riley, J. M."},{"full_name":"Meevasana, W.","last_name":"Meevasana","first_name":"W."},{"full_name":"Fujii, J.","first_name":"J.","last_name":"Fujii"},{"first_name":"I.","last_name":"Vobornik","full_name":"Vobornik, I."},{"full_name":"Kim, T. K.","first_name":"T. K.","last_name":"Kim"},{"full_name":"Hoesch, M.","last_name":"Hoesch","first_name":"M."},{"full_name":"Sasagawa, T.","last_name":"Sasagawa","first_name":"T."},{"last_name":"Wahl","first_name":"P.","full_name":"Wahl, P."},{"full_name":"Bahramy, M. S.","first_name":"M. S.","last_name":"Bahramy"},{"last_name":"King","first_name":"P. D. C.","full_name":"King, P. D. C."}],"intvolume":"       120","_id":"19813","article_processing_charge":"No","date_created":"2025-06-10T09:14:51Z","publication_status":"published","publisher":"American Physical Society","type":"journal_article","doi":"10.1103/physrevlett.120.156401","title":"Fermiology and superconductivity of topological surface states in PdTe2","issue":"15"},{"pmid":1,"citation":{"mla":"Mazzola, Federico, et al. “Itinerant Ferromagnetism of the Pd-Terminated Polar Surface of PdCoO2.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 51, National Academy of Sciences, 2018, pp. 12956–60, doi:<a href=\"https://doi.org/10.1073/pnas.1811873115\">10.1073/pnas.1811873115</a>.","ama":"Mazzola F, Sunko V, Khim S, et al. Itinerant ferromagnetism of the Pd-terminated polar surface of PdCoO2. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(51):12956-12960. doi:<a href=\"https://doi.org/10.1073/pnas.1811873115\">10.1073/pnas.1811873115</a>","chicago":"Mazzola, Federico, Veronika Sunko, Seunghyun Khim, Helge Rosner, Pallavi Kushwaha, Oliver J. Clark, Lewis Bawden, et al. “Itinerant Ferromagnetism of the Pd-Terminated Polar Surface of PdCoO2.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1811873115\">https://doi.org/10.1073/pnas.1811873115</a>.","ista":"Mazzola F, Sunko V, Khim S, Rosner H, Kushwaha P, Clark OJ, Bawden L, Marković I, Kim TK, Hoesch M, Mackenzie AP, King PDC. 2018. Itinerant ferromagnetism of the Pd-terminated polar surface of PdCoO2. Proceedings of the National Academy of Sciences. 115(51), 12956–12960.","short":"F. Mazzola, V. Sunko, S. Khim, H. Rosner, P. Kushwaha, O.J. Clark, L. Bawden, I. Marković, T.K. Kim, M. Hoesch, A.P. Mackenzie, P.D.C. King, Proceedings of the National Academy of Sciences 115 (2018) 12956–12960.","ieee":"F. Mazzola <i>et al.</i>, “Itinerant ferromagnetism of the Pd-terminated polar surface of PdCoO2,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 51. National Academy of Sciences, pp. 12956–12960, 2018.","apa":"Mazzola, F., Sunko, V., Khim, S., Rosner, H., Kushwaha, P., Clark, O. J., … King, P. D. C. (2018). Itinerant ferromagnetism of the Pd-terminated polar surface of PdCoO2. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1811873115\">https://doi.org/10.1073/pnas.1811873115</a>"},"volume":115,"oa":1,"oa_version":"Preprint","OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1710.05392"}],"arxiv":1,"scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","day":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","language":[{"iso":"eng"}],"extern":"1","month":"12","year":"2018","abstract":[{"text":"The ability to modulate the collective properties of correlated electron systems at their interfaces and surfaces underpins the burgeoning field of “designer” quantum materials. Here, we show how an electronic reconstruction driven by surface polarity mediates a Stoner-like magnetic instability to itinerant ferromagnetism at the Pd-terminated surface of the nonmagnetic delafossite oxide metal PdCoO2. Combining angle-resolved photoemission spectroscopy and density-functional theory calculations, we show how this leads to a rich multiband surface electronic structure. We find similar surface state dispersions in PdCrO2, suggesting surface ferromagnetism persists in this sister compound despite its bulk antiferromagnetic order.","lang":"eng"}],"publication":"Proceedings of the National Academy of Sciences","date_updated":"2025-06-10T12:40:00Z","issue":"51","title":"Itinerant ferromagnetism of the Pd-terminated polar surface of PdCoO2","doi":"10.1073/pnas.1811873115","type":"journal_article","publisher":"National Academy of Sciences","publication_status":"published","page":"12956-12960","date_created":"2025-06-10T09:19:14Z","article_processing_charge":"No","_id":"19819","intvolume":"       115","author":[{"last_name":"Mazzola","first_name":"Federico","full_name":"Mazzola, Federico"},{"last_name":"Sunko","first_name":"Veronika","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","orcid":"0000-0003-2724-3523","full_name":"Sunko, Veronika"},{"full_name":"Khim, Seunghyun","first_name":"Seunghyun","last_name":"Khim"},{"last_name":"Rosner","first_name":"Helge","full_name":"Rosner, Helge"},{"first_name":"Pallavi","last_name":"Kushwaha","full_name":"Kushwaha, Pallavi"},{"first_name":"Oliver J.","last_name":"Clark","full_name":"Clark, Oliver J."},{"full_name":"Bawden, Lewis","last_name":"Bawden","first_name":"Lewis"},{"full_name":"Marković, Igor","first_name":"Igor","last_name":"Marković"},{"first_name":"Timur K.","last_name":"Kim","full_name":"Kim, Timur K."},{"first_name":"Moritz","last_name":"Hoesch","full_name":"Hoesch, Moritz"},{"full_name":"Mackenzie, Andrew P.","last_name":"Mackenzie","first_name":"Andrew P."},{"first_name":"Phil D. C.","last_name":"King","full_name":"King, Phil D. C."}],"date_published":"2018-12-04T00:00:00Z","external_id":{"arxiv":["1710.05392"],"pmid":["30514820"]},"OA_type":"green","quality_controlled":"1"},{"publication_status":"published","department":[{"_id":"BeVi"}],"doi":"10.3390/genes9060294","type":"journal_article","publisher":"MDPI","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","issue":"6","file":[{"date_created":"2019-02-01T07:52:28Z","content_type":"application/pdf","file_name":"2018_Genes_Ma.pdf","file_id":"5905","access_level":"open_access","file_size":3985796,"creator":"dernst","date_updated":"2020-07-14T12:45:22Z","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","relation":"main_file"}],"quality_controlled":"1","date_published":"2018-06-12T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"isi":["000436494200026"]},"intvolume":"         9","author":[{"last_name":"Ma","first_name":"Wen","full_name":"Ma, Wen"},{"last_name":"Veltsos","first_name":"Paris","full_name":"Veltsos, Paris"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"full_name":"Rodrigues, Nicolas","last_name":"Rodrigues","first_name":"Nicolas"},{"last_name":"Sermier","first_name":"Roberto","full_name":"Sermier, Roberto"},{"full_name":"Jeffries, Daniel","last_name":"Jeffries","first_name":"Daniel"},{"full_name":"Perrin, Nicolas","first_name":"Nicolas","last_name":"Perrin"}],"_id":"199","date_created":"2018-12-11T11:45:09Z","article_processing_charge":"No","status":"public","article_number":"294","scopus_import":"1","publist_id":"7714","oa":1,"has_accepted_license":"1","oa_version":"Published Version","volume":9,"citation":{"chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. 2018;9(6). doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>, vol. 9, no. 6, 294, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., &#38; Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>","ieee":"W. Ma <i>et al.</i>, “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” <i>Genes</i>, vol. 9, no. 6. MDPI, 2018.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294."},"ddc":["570"],"date_updated":"2024-12-11T13:13:35Z","publication":"Genes","abstract":[{"text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.","lang":"eng"}],"year":"2018","isi":1,"month":"06","language":[{"iso":"eng"}],"day":"12","file_date_updated":"2020-07-14T12:45:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file":[{"file_name":"2018_BMCGenomics_Higareda.pdf","content_type":"application/pdf","date_created":"2018-12-17T14:52:57Z","creator":"dernst","file_size":4629784,"access_level":"open_access","file_id":"5712","relation":"main_file","checksum":"a56516e734dab589dc7f3e1915973b4d","date_updated":"2020-07-14T12:45:23Z"}],"issue":"1","title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","publisher":"BioMed Central","doi":"10.1186/s12864-018-5173-0","type":"journal_article","department":[{"_id":"SiHi"}],"publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T11:44:12Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9807"},{"id":"9808","relation":"research_data","status":"public"}]},"_id":"20","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","author":[{"full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz","first_name":"Juan"},{"full_name":"Karbiener, Michael","last_name":"Karbiener","first_name":"Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"first_name":"Teresa","last_name":"Gerhalter","full_name":"Gerhalter, Teresa"},{"full_name":"Herzig, Stephan","first_name":"Stephan","last_name":"Herzig"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"intvolume":"        19","external_id":{"isi":["000450976700002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2018-11-03T00:00:00Z","quality_controlled":"1","ddc":["570"],"citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>, vol. 19, no. 1, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. 2018;19(1). doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>","ieee":"J. Higareda Almaraz <i>et al.</i>, “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” <i>BMC Genomics</i>, vol. 19, no. 1. BioMed Central, 2018.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1)."},"volume":19,"publist_id":"8035","has_accepted_license":"1","oa_version":"Published Version","oa":1,"publication_identifier":{"issn":["1471-2164"]},"scopus_import":"1","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:45:23Z","day":"03","language":[{"iso":"eng"}],"article_type":"original","month":"11","isi":1,"year":"2018","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"publication":"BMC Genomics","date_updated":"2023-09-13T09:10:47Z"},{"month":"02","language":[{"iso":"eng"}],"day":"21","file_date_updated":"2020-07-14T12:45:23Z","pubrep_id":"963","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T14:06:37Z","supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"year":"2018","citation":{"ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","apa":"Ringbauer, H. (2018). <i>Inferring recent demography from spatial genetic structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","mla":"Ringbauer, Harald. <i>Inferring Recent Demography from Spatial Genetic Structure</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>."},"ddc":["576"],"status":"public","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","degree_awarded":"PhD","has_accepted_license":"1","oa":1,"publist_id":"7713","oa_version":"Published Version","_id":"200","date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"id":"563","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1074"}]},"article_processing_charge":"No","corr_author":"1","page":"146","date_published":"2018-02-21T00:00:00Z","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"author":[{"full_name":"Ringbauer, Harald","last_name":"Ringbauer","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald"}],"title":"Inferring recent demography from spatial genetic structure","file":[{"file_id":"5111","access_level":"open_access","file_size":5792935,"creator":"system","date_created":"2018-12-12T10:14:55Z","content_type":"application/pdf","file_name":"IST-2018-963-v1+1_thesis.pdf","date_updated":"2020-07-14T12:45:23Z","checksum":"8cc534d2b528ae017acf80874cce48c9","relation":"main_file"},{"date_created":"2019-04-05T09:30:12Z","file_name":"2018_thesis_ringbauer_source.zip","content_type":"application/zip","file_id":"6224","file_size":113365,"creator":"dernst","access_level":"closed","date_updated":"2020-07-14T12:45:23Z","relation":"source_file","checksum":"6af18d7e5a7e2728ceda2f41ee24f628"}],"publication_status":"published","department":[{"_id":"NiBa"}],"doi":"10.15479/AT:ISTA:th_963","type":"dissertation","publisher":"Institute of Science and Technology Austria"},{"doi":"10.1002/sta4.183","type":"journal_article","publisher":"Wiley","publication_status":"published","issue":"1","title":"Learning directed acyclic graphs based on sparsest permutations","intvolume":"         7","author":[{"full_name":"Raskutti, Garvesh","last_name":"Raskutti","first_name":"Garvesh"},{"full_name":"Uhler, Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline"}],"date_published":"2018-04-17T00:00:00Z","external_id":{"arxiv":["1307.0366"]},"quality_controlled":"1","date_created":"2018-12-11T11:55:13Z","article_processing_charge":"No","_id":"2015","oa_version":"Preprint","publist_id":"5061","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1307.0366","open_access":"1"}],"arxiv":1,"status":"public","article_number":"e183","citation":{"apa":"Raskutti, G., &#38; Uhler, C. (2018). Learning directed acyclic graphs based on sparsest permutations. <i>STAT</i>. Wiley. <a href=\"https://doi.org/10.1002/sta4.183\">https://doi.org/10.1002/sta4.183</a>","ieee":"G. Raskutti and C. Uhler, “Learning directed acyclic graphs based on sparsest permutations,” <i>STAT</i>, vol. 7, no. 1. Wiley, 2018.","short":"G. Raskutti, C. Uhler, STAT 7 (2018).","ista":"Raskutti G, Uhler C. 2018. Learning directed acyclic graphs based on sparsest permutations. STAT. 7(1), e183.","chicago":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” <i>STAT</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/sta4.183\">https://doi.org/10.1002/sta4.183</a>.","mla":"Raskutti, Garvesh, and Caroline Uhler. “Learning Directed Acyclic Graphs Based on Sparsest Permutations.” <i>STAT</i>, vol. 7, no. 1, e183, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/sta4.183\">10.1002/sta4.183</a>.","ama":"Raskutti G, Uhler C. Learning directed acyclic graphs based on sparsest permutations. <i>STAT</i>. 2018;7(1). doi:<a href=\"https://doi.org/10.1002/sta4.183\">10.1002/sta4.183</a>"},"volume":7,"year":"2018","abstract":[{"text":"We consider the problem of learning a Bayesian network or directed acyclic graph model from observational data. A number of constraint‐based, score‐based and hybrid algorithms have been developed for this purpose. Statistical consistency guarantees of these algorithms rely on the faithfulness assumption, which has been shown to be restrictive especially for graphs with cycles in the skeleton. We here propose the sparsest permutation (SP) algorithm, showing that learning Bayesian networks is possible under strictly weaker assumptions than faithfulness. This comes at a computational price, thereby indicating a statistical‐computational trade‐off for causal inference algorithms. In the Gaussian noiseless setting, we prove that the SP algorithm boils down to finding the permutation of the variables with the sparsest Cholesky decomposition of the inverse covariance matrix, which is equivalent to ℓ0‐penalized maximum likelihood estimation. We end with a simulation study showing that in line with the proven stronger consistency guarantees, and the SP algorithm compares favourably to standard causal inference algorithms in terms of accuracy for a given sample size.","lang":"eng"}],"publication":"STAT","date_updated":"2021-01-12T06:54:44Z","day":"17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","extern":"1","language":[{"iso":"eng"}],"month":"04"},{"publication":"PNAS","date_updated":"2026-04-28T08:29:26Z","isi":1,"year":"2018","abstract":[{"lang":"eng","text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses."}],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"26","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","status":"public","oa":1,"oa_version":"Submitted Version","publist_id":"7710","main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"OA_place":"repository","citation":{"mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. 2018;115(26):6864-6869. doi:<a href=\"https://doi.org/10.1073/pnas.1806565115\">10.1073/pnas.1806565115</a>","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ieee":"M. Abbas <i>et al.</i>, “Auxin methylation is required for differential growth in Arabidopsis,” <i>PNAS</i>, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1806565115\">https://doi.org/10.1073/pnas.1806565115</a>","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869."},"volume":115,"ec_funded":1,"external_id":{"isi":["000436245000096"]},"date_published":"2018-06-26T00:00:00Z","quality_controlled":"1","OA_type":"green","author":[{"last_name":"Abbas","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","first_name":"Mohamad","full_name":"Abbas, Mohamad"},{"full_name":"Hernández, García J","first_name":"García J","last_name":"Hernández"},{"full_name":"Pollmann, Stephan","last_name":"Pollmann","first_name":"Stephan"},{"full_name":"Samodelov, Sophia L","last_name":"Samodelov","first_name":"Sophia L"},{"full_name":"Kolb, Martina","first_name":"Martina","last_name":"Kolb"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ulrich Z","last_name":"Hammes","full_name":"Hammes, Ulrich Z"},{"full_name":"Zurbriggen, Matias D","last_name":"Zurbriggen","first_name":"Matias D"},{"first_name":"Miguel","last_name":"Blázquez","full_name":"Blázquez, Miguel"},{"full_name":"Alabadí, David","first_name":"David","last_name":"Alabadí"}],"intvolume":"       115","_id":"203","page":"6864-6869","article_processing_charge":"No","date_created":"2018-12-11T11:45:11Z","department":[{"_id":"JiFr"}],"publication_status":"published","publisher":"National Academy of Sciences","type":"journal_article","doi":"10.1073/pnas.1806565115","title":"Auxin methylation is required for differential growth in Arabidopsis","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"issue":"26"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"18","language":[{"iso":"eng"}],"extern":"1","article_type":"original","month":"10","year":"2018","abstract":[{"lang":"eng","text":"The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements."}],"publication":"The Journal of Physical Chemistry B","date_updated":"2021-11-26T12:40:02Z","pmid":1,"citation":{"chicago":"Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">https://doi.org/10.1021/acs.jpcb.8b07805</a>.","mla":"Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” <i>The Journal of Physical Chemistry B</i>, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">10.1021/acs.jpcb.8b07805</a>.","ama":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. <i>The Journal of Physical Chemistry B</i>. 2018;122(49):11721-11730. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">10.1021/acs.jpcb.8b07805</a>","short":"A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730.","apa":"Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., &#38; Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.8b07805\">https://doi.org/10.1021/acs.jpcb.8b07805</a>","ieee":"A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” <i>The Journal of Physical Chemistry B</i>, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018.","ista":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730."},"volume":122,"oa_version":"None","scopus_import":"1","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"status":"public","page":"11721-11730","article_processing_charge":"No","date_created":"2021-11-26T11:55:12Z","keyword":["materials chemistry"],"_id":"10357","acknowledgement":"We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions.","author":[{"full_name":"Dear, Alexander J.","last_name":"Dear","first_name":"Alexander J."},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."}],"intvolume":"       122","external_id":{"pmid":["30336667"]},"date_published":"2018-10-18T00:00:00Z","quality_controlled":"1","issue":"49","title":"Statistical mechanics of globular oligomer formation by protein molecules","publisher":"American Chemical Society","doi":"10.1021/acs.jpcb.8b07805","type":"journal_article","publication_status":"published"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"24","extern":"1","language":[{"iso":"eng"}],"article_type":"original","month":"05","year":"2018","abstract":[{"text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements.","lang":"eng"}],"publication":"Molecular Physics","date_updated":"2021-11-26T12:39:58Z","citation":{"mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” <i>Molecular Physics</i>, vol. 116, no. 21–22, Taylor &#38; Francis, 2018, pp. 3055–65, doi:<a href=\"https://doi.org/10.1080/00268976.2018.1474280\">10.1080/00268976.2018.1474280</a>.","ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. <i>Molecular Physics</i>. 2018;116(21-22):3055-3065. doi:<a href=\"https://doi.org/10.1080/00268976.2018.1474280\">10.1080/00268976.2018.1474280</a>","chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” <i>Molecular Physics</i>. Taylor &#38; Francis, 2018. <a href=\"https://doi.org/10.1080/00268976.2018.1474280\">https://doi.org/10.1080/00268976.2018.1474280</a>.","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065.","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., &#38; Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. <i>Molecular Physics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00268976.2018.1474280\">https://doi.org/10.1080/00268976.2018.1474280</a>","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” <i>Molecular Physics</i>, vol. 116, no. 21–22. Taylor &#38; Francis, pp. 3055–3065, 2018."},"volume":116,"oa":1,"oa_version":"Preprint","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1803.04851","open_access":"1"}],"scopus_import":"1","publication_identifier":{"eissn":["1362-3028"],"issn":["0026-8976"]},"status":"public","page":"3055-3065","article_processing_charge":"No","keyword":["physical chemistry"],"date_created":"2021-11-26T12:08:02Z","_id":"10358","acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","author":[{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"first_name":"Lucie X.","last_name":"Liu","full_name":"Liu, Lucie X."},{"last_name":"Curk","first_name":"Samo","full_name":"Curk, Samo"},{"last_name":"Bolhuis","first_name":"Peter G.","full_name":"Bolhuis, Peter G."},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"intvolume":"       116","external_id":{"arxiv":["1803.04851"]},"date_published":"2018-05-24T00:00:00Z","quality_controlled":"1","issue":"21-22","title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation","publisher":"Taylor & Francis","doi":"10.1080/00268976.2018.1474280","type":"journal_article","publication_status":"published"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"18","language":[{"iso":"eng"}],"extern":"1","article_type":"original","month":"04","year":"2018","abstract":[{"lang":"eng","text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets."}],"publication":"Nano Letters","date_updated":"2021-11-26T15:14:08Z","pmid":1,"citation":{"ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356.","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” <i>Nano Letters</i>, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., &#38; Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">https://doi.org/10.1021/acs.nanolett.8b00786</a>","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” <i>Nano Letters</i>, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">10.1021/acs.nanolett.8b00786</a>.","ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. <i>Nano Letters</i>. 2018;18(9):5350-5356. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">10.1021/acs.nanolett.8b00786</a>","chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” <i>Nano Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.nanolett.8b00786\">https://doi.org/10.1021/acs.nanolett.8b00786</a>."},"volume":18,"oa":1,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1712.10147","open_access":"1"}],"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"scopus_import":"1","status":"public","page":"5350-5356","article_processing_charge":"No","date_created":"2021-11-26T12:15:47Z","keyword":["mechanical engineering","condensed matter physics"],"_id":"10359","acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1.","author":[{"last_name":"Curk","first_name":"Tine","full_name":"Curk, Tine"},{"first_name":"Peter","last_name":"Wirnsberger","full_name":"Wirnsberger, Peter"},{"last_name":"Dobnikar","first_name":"Jure","full_name":"Dobnikar, Jure"},{"last_name":"Frenkel","first_name":"Daan","full_name":"Frenkel, Daan"},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"intvolume":"        18","external_id":{"pmid":["29667410"]},"date_published":"2018-04-18T00:00:00Z","quality_controlled":"1","issue":"9","title":"Controlling cargo trafficking in multicomponent membranes","publisher":"American Chemical Society","type":"journal_article","doi":"10.1021/acs.nanolett.8b00786","publication_status":"published"},{"intvolume":"        10","author":[{"full_name":"Cohen, Samuel I. A.","last_name":"Cohen","first_name":"Samuel I. A."},{"last_name":"Cukalevski","first_name":"Risto","full_name":"Cukalevski, Risto"},{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Törnquist","first_name":"Mattias","full_name":"Törnquist, Mattias"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"last_name":"Buell","first_name":"Alexander K.","full_name":"Buell, Alexander K."},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"},{"last_name":"Linse","first_name":"Sara","full_name":"Linse, Sara"}],"date_published":"2018-03-26T00:00:00Z","external_id":{"pmid":["29581486"]},"quality_controlled":"1","page":"523-531","keyword":["general chemical engineering","general chemistry"],"date_created":"2021-11-26T12:41:38Z","article_processing_charge":"No","_id":"10360","acknowledgement":"We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).","type":"journal_article","doi":"10.1038/s41557-018-0023-x","publisher":"Springer Nature","publication_status":"published","issue":"5","title":"Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide","year":"2018","abstract":[{"lang":"eng","text":"Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation."}],"publication":"Nature Chemistry","date_updated":"2021-11-26T15:14:00Z","day":"26","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","extern":"1","language":[{"iso":"eng"}],"month":"03","oa_version":"None","scopus_import":"1","publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"status":"public","pmid":1,"citation":{"chicago":"Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” <i>Nature Chemistry</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41557-018-0023-x\">https://doi.org/10.1038/s41557-018-0023-x</a>.","mla":"Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” <i>Nature Chemistry</i>, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:<a href=\"https://doi.org/10.1038/s41557-018-0023-x\">10.1038/s41557-018-0023-x</a>.","ama":"Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. <i>Nature Chemistry</i>. 2018;10(5):523-531. doi:<a href=\"https://doi.org/10.1038/s41557-018-0023-x\">10.1038/s41557-018-0023-x</a>","apa":"Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-018-0023-x\">https://doi.org/10.1038/s41557-018-0023-x</a>","ieee":"S. I. A. Cohen <i>et al.</i>, “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” <i>Nature Chemistry</i>, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.","short":"S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531.","ista":"Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531."},"volume":10},{"year":"2018","abstract":[{"lang":"eng","text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation."}],"publication":"Annual Review of Physical Chemistry","date_updated":"2021-11-26T15:58:19Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"28","language":[{"iso":"eng"}],"extern":"1","article_type":"original","month":"02","oa_version":"None","publication_identifier":{"eissn":["1545-1593"],"issn":["0066-426X"]},"scopus_import":"1","status":"public","pmid":1,"citation":{"chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” <i>Annual Review of Physical Chemistry</i>. Annual Reviews, 2018. <a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">https://doi.org/10.1146/annurev-physchem-050317-021322</a>.","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” <i>Annual Review of Physical Chemistry</i>, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:<a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">10.1146/annurev-physchem-050317-021322</a>.","ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. <i>Annual Review of Physical Chemistry</i>. 2018;69(1):273-298. doi:<a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">10.1146/annurev-physchem-050317-021322</a>","ieee":"T. C. T. Michaels <i>et al.</i>, “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” <i>Annual Review of Physical Chemistry</i>, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018.","apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. <i>Annual Review of Physical Chemistry</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-physchem-050317-021322\">https://doi.org/10.1146/annurev-physchem-050317-021322</a>","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298."},"volume":69,"author":[{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Habchi","first_name":"Johnny","full_name":"Habchi, Johnny"},{"first_name":"Sean","last_name":"Chia","full_name":"Chia, Sean"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"intvolume":"        69","external_id":{"pmid":["29490200"]},"date_published":"2018-02-28T00:00:00Z","quality_controlled":"1","page":"273-298","article_processing_charge":"No","keyword":["physical and theoretical chemistry"],"date_created":"2021-11-26T12:52:12Z","_id":"10361","acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","publisher":"Annual Reviews","type":"journal_article","doi":"10.1146/annurev-physchem-050317-021322","publication_status":"published","issue":"1","title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation"},{"page":"1508-1518","article_processing_charge":"No","date_created":"2021-11-26T15:15:00Z","keyword":["general physics and astronomy"],"_id":"10362","acknowledgement":"We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1).","author":[{"first_name":"Patrick D. Ellis","last_name":"Fisher","full_name":"Fisher, Patrick D. Ellis"},{"first_name":"Qi","last_name":"Shen","full_name":"Shen, Qi"},{"full_name":"Akpinar, Bernice","last_name":"Akpinar","first_name":"Bernice"},{"last_name":"Davis","first_name":"Luke K.","full_name":"Davis, Luke K."},{"full_name":"Chung, Kenny Kwok Hin","first_name":"Kenny Kwok Hin","last_name":"Chung"},{"full_name":"Baddeley, David","first_name":"David","last_name":"Baddeley"},{"full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"full_name":"Melia, Thomas J.","last_name":"Melia","first_name":"Thomas J."},{"last_name":"Hoogenboom","first_name":"Bart W.","full_name":"Hoogenboom, Bart W."},{"first_name":"Chenxiang","last_name":"Lin","full_name":"Lin, Chenxiang"},{"full_name":"Lusk, C. Patrick","last_name":"Lusk","first_name":"C. Patrick"}],"intvolume":"        12","external_id":{"pmid":["29350911"]},"date_published":"2018-01-19T00:00:00Z","quality_controlled":"1","issue":"2","title":"A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement","publisher":"American Chemical Society","type":"journal_article","doi":"10.1021/acsnano.7b08044","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"19","extern":"1","language":[{"iso":"eng"}],"article_type":"original","month":"01","year":"2018","abstract":[{"lang":"eng","text":"Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties."}],"publication":"ACS Nano","date_updated":"2021-11-26T15:57:02Z","pmid":1,"citation":{"ieee":"P. D. E. Fisher <i>et al.</i>, “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” <i>ACS Nano</i>, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.","apa":"Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.7b08044\">https://doi.org/10.1021/acsnano.7b08044</a>","short":"P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.","ista":"Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518.","chicago":"Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” <i>ACS Nano</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acsnano.7b08044\">https://doi.org/10.1021/acsnano.7b08044</a>.","mla":"Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” <i>ACS Nano</i>, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:<a href=\"https://doi.org/10.1021/acsnano.7b08044\">10.1021/acsnano.7b08044</a>.","ama":"Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. <i>ACS Nano</i>. 2018;12(2):1508-1518. doi:<a href=\"https://doi.org/10.1021/acsnano.7b08044\">10.1021/acsnano.7b08044</a>"},"volume":12,"oa_version":"None","publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"scopus_import":"1","status":"public"},{"citation":{"short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","apa":"Seitner, D., Uhse, S., Gallei, M. C., &#38; Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” <i>Molecular Plant Pathology</i>, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/mpp.12698\">https://doi.org/10.1111/mpp.12698</a>.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” <i>Molecular Plant Pathology</i>, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>.","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. <i>Molecular Plant Pathology</i>. 2018;19(10):2277-2287. doi:<a href=\"https://doi.org/10.1111/mpp.12698\">10.1111/mpp.12698</a>"},"volume":19,"ddc":["580"],"scopus_import":"1","status":"public","oa":1,"has_accepted_license":"1","publist_id":"7950","oa_version":"Published Version","month":"10","file_date_updated":"2018-12-18T09:46:00Z","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"publication":"Molecular Plant Pathology","date_updated":"2023-09-19T10:06:42Z","year":"2018","isi":1,"abstract":[{"text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host.","lang":"eng"}],"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","file":[{"file_name":"2018_MolecPlantPath_Seitner.pdf","content_type":"application/pdf","date_created":"2018-12-18T09:46:00Z","file_size":682335,"creator":"dernst","access_level":"open_access","file_id":"5740","success":1,"relation":"main_file","date_updated":"2018-12-18T09:46:00Z"}],"issue":"10","department":[{"_id":"GradSch"}],"publication_status":"published","type":"journal_article","doi":"10.1111/mpp.12698","publisher":"Wiley","_id":"104","acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","page":"2277 - 2287","date_created":"2018-12-11T11:44:39Z","article_processing_charge":"No","date_published":"2018-10-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"external_id":{"isi":["000445624100006"]},"quality_controlled":"1","intvolume":"        19","author":[{"first_name":"Denise","last_name":"Seitner","full_name":"Seitner, Denise"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"last_name":"Djamei","first_name":"Armin","full_name":"Djamei, Armin"}]},{"abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence."}],"year":"2018","date_updated":"2025-05-20T09:45:10Z","publication":"Proceedings of the ACM on Programming Languages","language":[{"iso":"eng"}],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","file_date_updated":"2025-05-20T09:44:47Z","month":"01","arxiv":1,"OA_place":"publisher","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_number":"31","status":"public","publication_identifier":{"eissn":["2475-1421"]},"scopus_import":"1","ddc":["000"],"volume":2,"ec_funded":1,"citation":{"chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2018. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. 2018;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 31, Association for Computing Machinery, 2018, doi:<a href=\"https://doi.org/10.1145/3158119\">10.1145/3158119</a>.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., &#38; Vaidya, K. (2018). Data-centric dynamic partial order reduction. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158119\">https://doi.org/10.1145/3158119</a>","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2018.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2018).","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2018. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31."},"author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Sinha, Nishant","first_name":"Nishant","last_name":"Sinha"},{"full_name":"Vaidya, Kapil","first_name":"Kapil","last_name":"Vaidya"}],"intvolume":"         2","quality_controlled":"1","OA_type":"hybrid","external_id":{"arxiv":["1610.01188"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"conference":{"location":"Los Angeles, CA, United States","end_date":"2018-01-13","start_date":"2018-01-07","name":"POPL: Programming Languages"},"date_published":"2018-01-01T00:00:00Z","article_processing_charge":"No","related_material":{"record":[{"id":"5448","status":"public","relation":"earlier_version"},{"id":"5456","status":"public","relation":"earlier_version"}]},"date_created":"2021-12-05T23:01:49Z","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","_id":"10417","publisher":"Association for Computing Machinery","type":"journal_article","doi":"10.1145/3158119","publication_status":"published","department":[{"_id":"KrCh"}],"issue":"POPL","file":[{"date_created":"2025-05-20T09:44:47Z","content_type":"application/pdf","file_name":"2018_ACM_Chalupa.pdf","file_id":"19716","access_level":"open_access","creator":"dernst","file_size":388891,"success":1,"date_updated":"2025-05-20T09:44:47Z","checksum":"b27ab1745f6dba2387deb785798a657c","relation":"main_file"}],"title":"Data-centric dynamic partial order reduction","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}]}]