[{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/559898"}],"external_id":{"pmid":["31640700"]},"quality_controlled":"1","doi":"10.1186/s12915-019-0700-2","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1741-7007"]},"month":"10","pmid":1,"year":"2019","acknowledgement":"We thank Jeremy Carlton, Mike Staddon, Geraint Harker, and the Wellcome Trust Consortium “Archaeal Origins of Eukaryotic Cell Organisation” for fruitful conversations. We thank Peter Wirnsberger and Tine Curk for discussions about the membrane model implementation.","publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","first_name":"Lena"},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"},{"full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"volume":17,"date_created":"2021-11-26T11:25:03Z","date_updated":"2021-11-26T11:54:29Z","article_number":"82","file_date_updated":"2021-11-26T11:37:54Z","extern":"1","citation":{"chicago":"Harker-Kirschneck, Lena, Buzz Baum, and Anđela Šarić. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology. Springer Nature, 2019. https://doi.org/10.1186/s12915-019-0700-2.","short":"L. Harker-Kirschneck, B. Baum, A. Šarić, BMC Biology 17 (2019).","mla":"Harker-Kirschneck, Lena, et al. “Changes in ESCRT-III Filament Geometry Drive Membrane Remodelling and Fission in Silico.” BMC Biology, vol. 17, no. 1, 82, Springer Nature, 2019, doi:10.1186/s12915-019-0700-2.","ieee":"L. Harker-Kirschneck, B. Baum, and A. Šarić, “Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico,” BMC Biology, vol. 17, no. 1. Springer Nature, 2019.","apa":"Harker-Kirschneck, L., Baum, B., & Šarić, A. (2019). Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0700-2","ista":"Harker-Kirschneck L, Baum B, Šarić A. 2019. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 17(1), 82.","ama":"Harker-Kirschneck L, Baum B, Šarić A. Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico. BMC Biology. 2019;17(1). doi:10.1186/s12915-019-0700-2"},"publication":"BMC Biology","article_type":"original","date_published":"2019-10-22T00:00:00Z","scopus_import":"1","keyword":["cell biology"],"article_processing_charge":"No","has_accepted_license":"1","day":"22","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10354","intvolume":" 17","title":"Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":1648926,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_BMCBio_Harker_Kirschneck.pdf","success":1,"checksum":"31d8bae55a376d30925f53f7e1a02396","date_created":"2021-11-26T11:37:54Z","date_updated":"2021-11-26T11:37:54Z","file_id":"10356","relation":"main_file"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Background\r\nESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling.\r\nResults\r\nHere we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles.\r\nConclusions\r\nOur model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems."}]},{"date_published":"2019-06-18T00:00:00Z","page":"43-52","article_type":"original","citation":{"chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018.","mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52.","ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019.","apa":"Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018","ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018"},"publication":"Current Opinion in Structural Biology","article_processing_charge":"No","day":"18","keyword":["molecular biology","structural biology"],"scopus_import":"1","oa_version":"Preprint","intvolume":" 58","status":"public","title":"Minimal coarse-grained models for molecular self-organisation in biology","_id":"10355","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.sbi.2019.05.018","quality_controlled":"1","external_id":{"pmid":["31226513"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1906.09349","open_access":"1"}],"publication_identifier":{"issn":["0959-440X"]},"month":"06","volume":58,"date_updated":"2021-11-26T11:54:25Z","date_created":"2021-11-26T11:33:21Z","author":[{"full_name":"Hafner, Anne E","last_name":"Hafner","first_name":"Anne E"},{"first_name":"Johannes","last_name":"Krausser","full_name":"Krausser, Johannes"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","year":"2019","extern":"1"},{"extern":"1","year":"2019","acknowledgement":"The authors thank S. Das Sarma and F. Wu for sharing their unpublished theoretical results, and acknowledge further discussions with L. Balents and T. Senthil. Work at both Columbia and UCSB was funded by the Army Research Office under award W911NF-17-1-0323. Sample device design and fabrication was partially supported by DoE Pro-QM EFRC (DE-SC0019443). A.F.Y. and C.R.D. separately acknowledge the support of the David and Lucile Packard Foundation. K.W. and T.T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan and the CREST (JPMJCR15F3), JST. A portion of this work was carried out at the KITP, Santa Barbara, supported by the National Science Foundation under grant number NSF PHY-1748958.","publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","last_name":"Polshyn","first_name":"Hryhoriy"},{"full_name":"Yankowitz, Matthew","last_name":"Yankowitz","first_name":"Matthew"},{"last_name":"Chen","first_name":"Shaowen","full_name":"Chen, Shaowen"},{"full_name":"Zhang, Yuxuan","last_name":"Zhang","first_name":"Yuxuan"},{"full_name":"Watanabe, K.","first_name":"K.","last_name":"Watanabe"},{"full_name":"Taniguchi, T.","first_name":"T.","last_name":"Taniguchi"},{"last_name":"Dean","first_name":"Cory R.","full_name":"Dean, Cory R."},{"first_name":"Andrea F.","last_name":"Young","full_name":"Young, Andrea F."}],"volume":15,"date_created":"2022-01-13T15:00:58Z","date_updated":"2022-01-20T09:33:38Z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1902.00763","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1902.00763"]},"quality_controlled":"1","doi":"10.1038/s41567-019-0596-3","language":[{"iso":"eng"}],"type":"journal_article","issue":"10","abstract":[{"text":"Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity.","lang":"eng"}],"_id":"10621","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","intvolume":" 15","status":"public","title":"Large linear-in-temperature resistivity in twisted bilayer graphene","oa_version":"Preprint","scopus_import":"1","keyword":["general physics and astronomy"],"article_processing_charge":"No","day":"05","citation":{"chicago":"Polshyn, Hryhoriy, Matthew Yankowitz, Shaowen Chen, Yuxuan Zhang, K. Watanabe, T. Taniguchi, Cory R. Dean, and Andrea F. Young. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics. Springer Nature, 2019. https://doi.org/10.1038/s41567-019-0596-3.","short":"H. Polshyn, M. Yankowitz, S. Chen, Y. Zhang, K. Watanabe, T. Taniguchi, C.R. Dean, A.F. Young, Nature Physics 15 (2019) 1011–1016.","mla":"Polshyn, Hryhoriy, et al. “Large Linear-in-Temperature Resistivity in Twisted Bilayer Graphene.” Nature Physics, vol. 15, no. 10, Springer Nature, 2019, pp. 1011–16, doi:10.1038/s41567-019-0596-3.","apa":"Polshyn, H., Yankowitz, M., Chen, S., Zhang, Y., Watanabe, K., Taniguchi, T., … Young, A. F. (2019). Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-019-0596-3","ieee":"H. Polshyn et al., “Large linear-in-temperature resistivity in twisted bilayer graphene,” Nature Physics, vol. 15, no. 10. Springer Nature, pp. 1011–1016, 2019.","ista":"Polshyn H, Yankowitz M, Chen S, Zhang Y, Watanabe K, Taniguchi T, Dean CR, Young AF. 2019. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 15(10), 1011–1016.","ama":"Polshyn H, Yankowitz M, Chen S, et al. Large linear-in-temperature resistivity in twisted bilayer graphene. Nature Physics. 2019;15(10):1011-1016. doi:10.1038/s41567-019-0596-3"},"publication":"Nature Physics","page":"1011-1016","article_type":"original","date_published":"2019-08-05T00:00:00Z"},{"year":"2019","acknowledgement":"We are grateful to Nadya Mason, Taylor Hughes, and Alexey Bezryadin for useful discussions. This work was supported by the DOE Basic Energy Sciences under DE-SC0012649 and the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.","pmid":1,"publication_status":"published","publisher":"American Chemical Society","author":[{"full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn"},{"full_name":"Naibert, Tyler","last_name":"Naibert","first_name":"Tyler"},{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"date_updated":"2022-01-13T15:41:24Z","date_created":"2022-01-13T15:11:14Z","volume":19,"extern":"1","external_id":{"arxiv":["1905.06303"],"pmid":["31246034"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.06303"}],"oa":1,"quality_controlled":"1","doi":"10.1021/acs.nanolett.9b01983","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","_id":"10622","title":"Manipulating multivortex states in superconducting structures","status":"public","intvolume":" 19","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing.","lang":"eng"}],"issue":"8","publication":"Nano Letters","citation":{"short":"H. Polshyn, T. Naibert, R. Budakian, Nano Letters 19 (2019) 5476–5482.","mla":"Polshyn, Hryhoriy, et al. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters, vol. 19, no. 8, American Chemical Society, 2019, pp. 5476–82, doi:10.1021/acs.nanolett.9b01983.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “Manipulating Multivortex States in Superconducting Structures.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b01983.","ama":"Polshyn H, Naibert T, Budakian R. Manipulating multivortex states in superconducting structures. Nano Letters. 2019;19(8):5476-5482. doi:10.1021/acs.nanolett.9b01983","apa":"Polshyn, H., Naibert, T., & Budakian, R. (2019). Manipulating multivortex states in superconducting structures. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b01983","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “Manipulating multivortex states in superconducting structures,” Nano Letters, vol. 19, no. 8. American Chemical Society, pp. 5476–5482, 2019.","ista":"Polshyn H, Naibert T, Budakian R. 2019. Manipulating multivortex states in superconducting structures. Nano Letters. 19(8), 5476–5482."},"article_type":"original","page":"5476-5482","date_published":"2019-06-27T00:00:00Z","scopus_import":"1","keyword":["mechanical engineering","condensed matter physics","general materials science","general chemistry","bioengineering"],"day":"27","article_processing_charge":"No"},{"extern":"1","author":[{"full_name":"Yankowitz, Matthew","last_name":"Yankowitz","first_name":"Matthew"},{"full_name":"Chen, Shaowen","first_name":"Shaowen","last_name":"Chen"},{"last_name":"Polshyn","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy"},{"full_name":"Zhang, Yuxuan","first_name":"Yuxuan","last_name":"Zhang"},{"first_name":"K.","last_name":"Watanabe","full_name":"Watanabe, K."},{"full_name":"Taniguchi, T.","last_name":"Taniguchi","first_name":"T."},{"first_name":"David","last_name":"Graf","full_name":"Graf, David"},{"full_name":"Young, Andrea F.","last_name":"Young","first_name":"Andrea F."},{"last_name":"Dean","first_name":"Cory R.","full_name":"Dean, Cory R."}],"volume":363,"date_updated":"2022-01-14T13:48:32Z","date_created":"2022-01-14T12:14:58Z","pmid":1,"year":"2019","acknowledgement":"We thank J. Zhu and H. Zhou for experimental assistance and D. Shahar, A. Millis, O. Vafek, M. Zaletel, L. Balents, C. Xu, A. Bernevig, L. Fu, M. Koshino, and P. Moon for helpful discussions.","publisher":"American Association for the Advancement of Science (AAAS)","publication_status":"published","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"01","doi":"10.1126/science.aav1910","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07865"}],"external_id":{"arxiv":["1808.07865"],"pmid":["30679385 "]},"oa":1,"quality_controlled":"1","issue":"6431","abstract":[{"lang":"eng","text":"The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures."}],"type":"journal_article","oa_version":"Preprint","_id":"10625","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 363","title":"Tuning superconductivity in twisted bilayer graphene","status":"public","article_processing_charge":"No","day":"24","scopus_import":"1","keyword":["multidisciplinary"],"date_published":"2019-01-24T00:00:00Z","citation":{"short":"M. Yankowitz, S. Chen, H. Polshyn, Y. Zhang, K. Watanabe, T. Taniguchi, D. Graf, A.F. Young, C.R. Dean, Science 363 (2019) 1059–1064.","mla":"Yankowitz, Matthew, et al. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science, vol. 363, no. 6431, American Association for the Advancement of Science (AAAS), 2019, pp. 1059–64, doi:10.1126/science.aav1910.","chicago":"Yankowitz, Matthew, Shaowen Chen, Hryhoriy Polshyn, Yuxuan Zhang, K. Watanabe, T. Taniguchi, David Graf, Andrea F. Young, and Cory R. Dean. “Tuning Superconductivity in Twisted Bilayer Graphene.” Science. American Association for the Advancement of Science (AAAS), 2019. https://doi.org/10.1126/science.aav1910.","ama":"Yankowitz M, Chen S, Polshyn H, et al. Tuning superconductivity in twisted bilayer graphene. Science. 2019;363(6431):1059-1064. doi:10.1126/science.aav1910","ieee":"M. Yankowitz et al., “Tuning superconductivity in twisted bilayer graphene,” Science, vol. 363, no. 6431. American Association for the Advancement of Science (AAAS), pp. 1059–1064, 2019.","apa":"Yankowitz, M., Chen, S., Polshyn, H., Zhang, Y., Watanabe, K., Taniguchi, T., … Dean, C. R. (2019). Tuning superconductivity in twisted bilayer graphene. Science. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aav1910","ista":"Yankowitz M, Chen S, Polshyn H, Zhang Y, Watanabe K, Taniguchi T, Graf D, Young AF, Dean CR. 2019. Tuning superconductivity in twisted bilayer graphene. Science. 363(6431), 1059–1064."},"publication":"Science","page":"1059-1064","article_type":"original"}]