[{"date_created":"2021-09-05T22:01:24Z","ec_funded":1,"_id":"9987","year":"2021","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10199"}]},"abstract":[{"text":"Stateless model checking (SMC) is one of the standard approaches to the verification of concurrent programs. As scheduling non-determinism creates exponentially large spaces of thread interleavings, SMC attempts to partition this space into equivalence classes and explore only a few representatives from each class. The efficiency of this approach depends on two factors: (a) the coarseness of the partitioning, and (b) the time to generate representatives in each class. For this reason, the search for coarse partitionings that are efficiently explorable is an active research challenge. In this work we present   RVF-SMC , a new SMC algorithm that uses a novel reads-value-from (RVF) partitioning. Intuitively, two interleavings are deemed equivalent if they agree on the value obtained in each read event, and read events induce consistent causal orderings between them. The RVF partitioning is provably coarser than recent approaches based on Mazurkiewicz and “reads-from” partitionings. Our experimental evaluation reveals that RVF is quite often a very effective equivalence, as the underlying partitioning is exponentially coarser than other approaches. Moreover,   RVF-SMC  generates representatives very efficiently, as the reduction in the partitioning is often met with significant speed-ups in the model checking task.","lang":"eng"}],"file":[{"file_name":"2021_LNCS_Agarwal.pdf","success":1,"relation":"main_file","date_created":"2022-05-13T07:00:20Z","file_id":"11368","date_updated":"2022-05-13T07:00:20Z","checksum":"4b346e5fbaa8b9bdf107819c7b2aadee","content_type":"application/pdf","file_size":1516756,"creator":"dernst","access_level":"open_access"}],"quality_controlled":"1","article_processing_charge":"Yes","oa_version":"Published Version","citation":{"short":"P. Agarwal, K. Chatterjee, S. Pathak, A. Pavlogiannis, V. Toman, in:, 33rd International Conference on Computer-Aided Verification , Springer Nature, 2021, pp. 341–366.","mla":"Agarwal, Pratyush, et al. “Stateless Model Checking under a Reads-Value-from Equivalence.” <i>33rd International Conference on Computer-Aided Verification </i>, vol. 12759, Springer Nature, 2021, pp. 341–66, doi:<a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">10.1007/978-3-030-81685-8_16</a>.","ieee":"P. Agarwal, K. Chatterjee, S. Pathak, A. Pavlogiannis, and V. Toman, “Stateless model checking under a reads-value-from equivalence,” in <i>33rd International Conference on Computer-Aided Verification </i>, Virtual, 2021, vol. 12759, pp. 341–366.","apa":"Agarwal, P., Chatterjee, K., Pathak, S., Pavlogiannis, A., &#38; Toman, V. (2021). Stateless model checking under a reads-value-from equivalence. In <i>33rd International Conference on Computer-Aided Verification </i> (Vol. 12759, pp. 341–366). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">https://doi.org/10.1007/978-3-030-81685-8_16</a>","ama":"Agarwal P, Chatterjee K, Pathak S, Pavlogiannis A, Toman V. Stateless model checking under a reads-value-from equivalence. In: <i>33rd International Conference on Computer-Aided Verification </i>. Vol 12759. Springer Nature; 2021:341-366. doi:<a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">10.1007/978-3-030-81685-8_16</a>","chicago":"Agarwal, Pratyush, Krishnendu Chatterjee, Shreya Pathak, Andreas Pavlogiannis, and Viktor Toman. “Stateless Model Checking under a Reads-Value-from Equivalence.” In <i>33rd International Conference on Computer-Aided Verification </i>, 12759:341–66. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-81685-8_16\">https://doi.org/10.1007/978-3-030-81685-8_16</a>.","ista":"Agarwal P, Chatterjee K, Pathak S, Pavlogiannis A, Toman V. 2021. Stateless model checking under a reads-value-from equivalence. 33rd International Conference on Computer-Aided Verification . CAV: Computer Aided Verification , LNCS, vol. 12759, 341–366."},"author":[{"last_name":"Agarwal","first_name":"Pratyush","full_name":"Agarwal, Pratyush"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Pathak, Shreya","last_name":"Pathak","first_name":"Shreya"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor"}],"date_updated":"2025-07-14T09:10:15Z","day":"15","oa":1,"publication":"33rd International Conference on Computer-Aided Verification ","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-030-81684-1"],"eisbn":["978-3-030-81685-8"]},"external_id":{"arxiv":["2105.06424"],"isi":["000698732400016"]},"title":"Stateless model checking under a reads-value-from equivalence","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"has_accepted_license":"1","arxiv":1,"page":"341-366","conference":{"end_date":"2021-07-23","start_date":"2021-07-20","name":"CAV: Computer Aided Verification ","location":"Virtual"},"acknowledgement":"The research was partially funded by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science and Technology Fund (WWTF) through project ICT15-003.","scopus_import":"1","month":"07","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"isi":1,"type":"conference","volume":"12759 ","file_date_updated":"2022-05-13T07:00:20Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-07-15T00:00:00Z","doi":"10.1007/978-3-030-81685-8_16","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"ddc":["000"]},{"page":"168","degree_awarded":"PhD","month":"09","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-09-15T22:30:26Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","alternative_title":["ISTA Thesis"],"ddc":["575"],"date_published":"2021-09-13T00:00:00Z","doi":"10.15479/at:ista:9992","status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"language":[{"iso":"eng"}],"date_created":"2021-09-09T07:37:20Z","ec_funded":1,"_id":"9992","year":"2021","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"No","oa_version":"Published Version","related_material":{"record":[{"id":"6351","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6943","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8002"}]},"publication_status":"published","abstract":[{"text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. ","lang":"eng"}],"file":[{"creator":"lhoermaye","access_level":"closed","checksum":"c763064adaa720e16066c1a4f9682bbb","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":25179004,"date_updated":"2021-09-15T22:30:26Z","embargo_to":"open_access","file_name":"Thesis_vupload.docx","relation":"source_file","date_created":"2021-09-09T07:29:48Z","file_id":"9993"},{"access_level":"open_access","creator":"lhoermaye","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","content_type":"application/pdf","file_size":6246900,"date_updated":"2021-09-15T22:30:26Z","embargo":"2021-09-09","file_name":"Thesis_vfinal_pdfa.pdf","file_id":"9996","date_created":"2021-09-09T14:25:08Z","relation":"main_file"}],"day":"13","oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T13:38:33Z","citation":{"ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>.","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021."},"author":[{"orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer"}],"supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"has_accepted_license":"1","title":"Wound healing in the Arabidopsis root meristem","project":[{"grant_number":"P29988","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}]},{"publication_identifier":{"eissn":["2045-2322"]},"publication":"Scientific Reports","oa":1,"day":"31","citation":{"short":"L. Schmid, P. Shati, C. Hilbe, K. Chatterjee, Scientific Reports 11 (2021).","ista":"Schmid L, Shati P, Hilbe C, Chatterjee K. 2021. The evolution of indirect reciprocity under action and assessment generosity. Scientific Reports. 11(1), 17443.","chicago":"Schmid, Laura, Pouya Shati, Christian Hilbe, and Krishnendu Chatterjee. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>.","ama":"Schmid L, Shati P, Hilbe C, Chatterjee K. The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>","ieee":"L. Schmid, P. Shati, C. Hilbe, and K. Chatterjee, “The evolution of indirect reciprocity under action and assessment generosity,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","apa":"Schmid, L., Shati, P., Hilbe, C., &#38; Chatterjee, K. (2021). The evolution of indirect reciprocity under action and assessment generosity. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-96932-1\">https://doi.org/10.1038/s41598-021-96932-1</a>","mla":"Schmid, Laura, et al. “The Evolution of Indirect Reciprocity under Action and Assessment Generosity.” <i>Scientific Reports</i>, vol. 11, no. 1, 17443, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-96932-1\">10.1038/s41598-021-96932-1</a>."},"date_updated":"2025-07-14T09:10:09Z","author":[{"first_name":"Laura","last_name":"Schmid","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329"},{"full_name":"Shati, Pouya","last_name":"Shati","first_name":"Pouya"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","article_number":"17443","has_accepted_license":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"title":"The evolution of indirect reciprocity under action and assessment generosity","external_id":{"pmid":["34465830"],"isi":["000692406400018"]},"year":"2021","_id":"9997","pmid":1,"ec_funded":1,"date_created":"2021-09-11T16:22:02Z","oa_version":"Published Version","article_processing_charge":"Yes","keyword":["Multidisciplinary"],"quality_controlled":"1","file":[{"date_updated":"2021-09-13T10:31:21Z","date_created":"2021-09-13T10:31:21Z","relation":"main_file","success":1,"file_id":"10006","file_name":"2021_ScientificReports_Schmid.pdf","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","file_size":2424943,"checksum":"19df8816cf958b272b85841565c73182"}],"abstract":[{"lang":"eng","text":"Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms."}],"article_type":"original","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","id":"10293","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-09-13T10:31:21Z","volume":11,"type":"journal_article","ddc":["003"],"intvolume":"        11","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1038/s41598-021-96932-1","date_published":"2021-08-31T00:00:00Z","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under Grant Z211-N23 (Wittgenstein Award).","isi":1,"publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"month":"08"},{"date_created":"2021-09-12T22:01:22Z","_id":"9998","year":"2021","quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice."}],"file":[{"checksum":"beadc5a722ffb48190e1e63ee2dbfee5","content_type":"application/pdf","file_size":584648,"creator":"cchlebak","access_level":"open_access","file_name":"2021_SelectaMath_Koroteev.pdf","date_created":"2021-09-13T11:31:34Z","relation":"main_file","success":1,"file_id":"10010","date_updated":"2021-09-13T11:31:34Z"}],"day":"30","oa":1,"publication":"Selecta Mathematica","publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"date_updated":"2023-08-14T06:34:14Z","citation":{"ama":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. 2021;27(5). doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>","apa":"Koroteev, P., Pushkar, P., Smirnov, A. V., &#38; Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>","ieee":"P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” <i>Selecta Mathematica</i>, vol. 27, no. 5. Springer Nature, 2021.","mla":"Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>, vol. 27, no. 5, 87, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>.","ista":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87.","chicago":"Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>.","short":"P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021)."},"author":[{"last_name":"Koroteev","first_name":"Peter","full_name":"Koroteev, Peter"},{"id":"151DCEB6-9EC3-11E9-8480-ABECE5697425","full_name":"Pushkar, Petr","first_name":"Petr","last_name":"Pushkar"},{"full_name":"Smirnov, Andrey V.","last_name":"Smirnov","first_name":"Andrey V."},{"full_name":"Zeitlin, Anton M.","first_name":"Anton M.","last_name":"Zeitlin"}],"has_accepted_license":"1","article_number":"87","issue":"5","external_id":{"isi":["000692795200001"]},"title":"Quantum K-theory of quiver varieties and many-body systems","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"acknowledgement":"First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).","scopus_import":"1","isi":1,"month":"08","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"file_date_updated":"2021-09-13T11:31:34Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":27,"intvolume":"        27","ddc":["530"],"date_published":"2021-08-30T00:00:00Z","doi":"10.1007/s00029-021-00698-3","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}]},{"author":[{"full_name":"Pulgar, Eduardo","first_name":"Eduardo","last_name":"Pulgar"},{"full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia"},{"first_name":"Néstor","last_name":"Guerrero","full_name":"Guerrero, Néstor"},{"full_name":"López, Loreto","last_name":"López","first_name":"Loreto"},{"first_name":"Susana","last_name":"Márquez","full_name":"Márquez, Susana"},{"full_name":"Härtel, Steffen","first_name":"Steffen","last_name":"Härtel"},{"full_name":"Soto, Rodrigo","last_name":"Soto","first_name":"Rodrigo"},{"first_name":"Carl Philipp","last_name":"Heisenberg","full_name":"Heisenberg, Carl Philipp"},{"full_name":"Concha, Miguel L.","last_name":"Concha","first_name":"Miguel L."}],"citation":{"short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).","chicago":"Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>.","ista":"Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483.","mla":"Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>, vol. 10, e66483, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>.","ieee":"E. Pulgar <i>et al.</i>, “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>","ama":"Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>"},"date_updated":"2023-08-14T06:53:33Z","publication":"eLife","publication_identifier":{"eissn":["2050-084X"]},"oa":1,"day":"27","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","external_id":{"isi":["000700428500001"],"pmid":["34448451"]},"article_number":"e66483","has_accepted_license":"1","year":"2021","_id":"9999","pmid":1,"ec_funded":1,"date_created":"2021-09-12T22:01:23Z","file":[{"date_updated":"2022-05-13T08:03:37Z","file_id":"11371","success":1,"relation":"main_file","date_created":"2022-05-13T08:03:37Z","file_name":"2021_eLife_Pulgar.pdf","access_level":"open_access","creator":"dernst","file_size":9010446,"content_type":"application/pdf","checksum":"a3f82b0499cc822ac1eab48a01f3f57e"}],"abstract":[{"lang":"eng","text":"The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site."}],"publication_status":"published","article_type":"original","oa_version":"Published Version","article_processing_charge":"Yes","keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"quality_controlled":"1","volume":10,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2022-05-13T08:03:37Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.7554/eLife.66483","date_published":"2021-08-27T00:00:00Z","ddc":["570"],"intvolume":"        10","scopus_import":"1","publisher":"eLife Sciences Publications","department":[{"_id":"CaHe"}],"month":"08","isi":1},{"external_id":{"arxiv":["2003.05478"]},"title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","status":"public","language":[{"iso":"eng"}],"project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"date_published":"2020-03-11T00:00:00Z","article_number":"2003.05478","citation":{"ista":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.","chicago":"Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” <i>ArXiv</i>, n.d.","apa":"Fischer, J. L., Hensel, S., Laux, T., &#38; Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. <i>arXiv</i>.","ieee":"J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” <i>arXiv</i>. .","ama":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. <i>arXiv</i>.","mla":"Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” <i>ArXiv</i>, 2003.05478.","short":"J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.)."},"type":"preprint","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L"},{"last_name":"Hensel","first_name":"Sebastian","full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072"},{"first_name":"Tim","last_name":"Laux","full_name":"Laux, Tim"},{"full_name":"Simon, Thilo","last_name":"Simon","first_name":"Thilo"}],"date_updated":"2023-09-07T13:30:45Z","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"arXiv","day":"11","abstract":[{"lang":"eng","text":"We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a \"gradient flow calibration\" ensures that the route of steepest descent in the energy landscape is unique and stable."}],"month":"03","related_material":{"record":[{"status":"public","id":"10007","relation":"dissertation_contains"}]},"department":[{"_id":"JuFi"}],"publication_status":"submitted","article_processing_charge":"No","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/2003.05478","open_access":"1"}],"arxiv":1,"_id":"10012","year":"2020","acknowledgement":"Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385.","ec_funded":1,"date_created":"2021-09-13T12:17:11Z"},{"author":[{"full_name":"Forkert, Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","last_name":"Forkert","first_name":"Dominik L"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan"},{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","last_name":"Portinale"}],"citation":{"short":"D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>ArXiv</i>, n.d.","ista":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962.","mla":"Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>ArXiv</i>, 2008.10962.","ama":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>arXiv</i>.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” <i>arXiv</i>. .","apa":"Forkert, D. L., Maas, J., &#38; Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>arXiv</i>."},"date_updated":"2023-09-07T13:31:05Z","type":"preprint","day":"25","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"arXiv","oa":1,"date_published":"2020-08-25T00:00:00Z","project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"language":[{"iso":"eng"}],"title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","external_id":{"arxiv":["2008.10962"]},"status":"public","article_number":"2008.10962","arxiv":1,"page":"33","date_created":"2021-09-17T10:57:27Z","ec_funded":1,"acknowledgement":"This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245.","year":"2020","_id":"10022","related_material":{"record":[{"id":"11739","status":"public","relation":"later_version"},{"status":"public","id":"10030","relation":"dissertation_contains"}]},"department":[{"_id":"JaMa"}],"publication_status":"submitted","month":"08","abstract":[{"text":"We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2008.10962","open_access":"1"}],"oa_version":"Preprint","article_processing_charge":"No"},{"date_published":"2020-01-01T00:00:00Z","doi":"10.1364/QUANTUM.2020.QTu8A.1","status":"public","title":"New designs and noise channels in electro-optic microwave to optical up-conversion","language":[{"iso":"eng"}],"alternative_title":["OSA Technical Digest"],"article_number":"QTu8A.1","date_updated":"2023-10-18T08:32:34Z","citation":{"short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” <i>OSA Quantum 2.0 Conference</i>, QTu8A.1, Optica Publishing Group, 2020, doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group; 2020. doi:<a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">10.1364/QUANTUM.2020.QTu8A.1</a>","ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in <i>OSA Quantum 2.0 Conference</i>, Washington, DC, United States, 2020.","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., &#38; Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In <i>OSA Quantum 2.0 Conference</i>. Washington, DC, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>","chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In <i>OSA Quantum 2.0 Conference</i>. Optica Publishing Group, 2020. <a href=\"https://doi.org/10.1364/QUANTUM.2020.QTu8A.1\">https://doi.org/10.1364/QUANTUM.2020.QTu8A.1</a>.","ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1."},"author":[{"full_name":"Lambert, Nicholas J.","first_name":"Nicholas J.","last_name":"Lambert"},{"full_name":"Mobassem, Sonia","last_name":"Mobassem","first_name":"Sonia"},{"first_name":"Alfredo R","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwefel, Harald G.L.","last_name":"Schwefel","first_name":"Harald G.L."}],"type":"conference","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"publication":"OSA Quantum 2.0 Conference","month":"01","publisher":"Optica Publishing Group","publication_status":"published","department":[{"_id":"JoFi"}],"abstract":[{"text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","oa_version":"None","conference":{"location":"Washington, DC, United States","start_date":"2020-09-14","name":"OSA: Optical Society of America","end_date":"2020-09-17"},"date_created":"2021-11-21T23:01:31Z","_id":"10328","scopus_import":"1","year":"2020"},{"scopus_import":"1","acknowledgement":"We thank T. C. T. Michaels for reading the manuscript. This work was supported by the Academy of Medical Science (J.K. and A.Š.), the Cambridge Center for Misfolding Diseases (T.P.J.K.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council Grant PhysProt Agreement 337969, the Wellcome Trust (A.Š. and T.P.J.K.), the Royal Society (A.Š.), the Medical Research Council (J.K. and A.Š.), and the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by Engineering and Physical Sciences Research Council Grant EP/P020194/1.","page":"33090-33098","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2019.12.22.886267v2","open_access":"1"}],"publisher":"National Academy of Sciences","month":"12","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":117,"type":"journal_article","intvolume":"       117","extern":"1","language":[{"iso":"eng"}],"status":"public","doi":"10.1073/pnas.2007694117","date_published":"2020-12-16T00:00:00Z","year":"2020","_id":"10336","pmid":1,"date_created":"2021-11-25T15:07:09Z","oa_version":"Published Version","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context."}],"article_type":"original","publication_status":"published","publication":"Proceedings of the National Academy of Sciences","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa":1,"day":"16","date_updated":"2021-11-25T15:35:58Z","citation":{"short":"J. Krausser, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences 117 (2020) 33090–33098.","chicago":"Krausser, Johannes, Tuomas P. J. Knowles, and Anđela Šarić. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2007694117\">https://doi.org/10.1073/pnas.2007694117</a>.","ista":"Krausser J, Knowles TPJ, Šarić A. 2020. Physical mechanisms of amyloid nucleation on fluid membranes. Proceedings of the National Academy of Sciences. 117(52), 33090–33098.","mla":"Krausser, Johannes, et al. “Physical Mechanisms of Amyloid Nucleation on Fluid Membranes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 52, National Academy of Sciences, 2020, pp. 33090–98, doi:<a href=\"https://doi.org/10.1073/pnas.2007694117\">10.1073/pnas.2007694117</a>.","ama":"Krausser J, Knowles TPJ, Šarić A. Physical mechanisms of amyloid nucleation on fluid membranes. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(52):33090-33098. doi:<a href=\"https://doi.org/10.1073/pnas.2007694117\">10.1073/pnas.2007694117</a>","apa":"Krausser, J., Knowles, T. P. J., &#38; Šarić, A. (2020). Physical mechanisms of amyloid nucleation on fluid membranes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2007694117\">https://doi.org/10.1073/pnas.2007694117</a>","ieee":"J. Krausser, T. P. J. Knowles, and A. Šarić, “Physical mechanisms of amyloid nucleation on fluid membranes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 52. National Academy of Sciences, pp. 33090–33098, 2020."},"author":[{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"}],"issue":"52","title":"Physical mechanisms of amyloid nucleation on fluid membranes","external_id":{"pmid":["33328273"]}},{"extern":"1","intvolume":"        16","status":"public","language":[{"iso":"eng"}],"date_published":"2020-10-06T00:00:00Z","doi":"10.1039/d0sm00712a","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":16,"type":"journal_article","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1","open_access":"1"}],"month":"10","publisher":"Royal Society of Chemistry","scopus_import":"1","acknowledgement":"We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.).","page":"10628-10639","issue":"47","external_id":{"pmid":["33084724"]},"title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes","oa":1,"publication":"Soft Matter","publication_identifier":{"issn":["1744-683X","1744-6848"]},"day":"06","citation":{"apa":"Debets, V. E., Janssen, L. M. C., &#38; Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>","ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” <i>Soft Matter</i>, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. 2020;16(47):10628-10639. doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>","mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>.","ista":"Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639.","chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639."},"author":[{"last_name":"Debets","first_name":"V. E.","full_name":"Debets, V. E."},{"last_name":"Janssen","first_name":"L. M. C.","full_name":"Janssen, L. M. C."},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"date_updated":"2021-11-26T07:00:33Z","keyword":["condensed matter physics","general chemistry"],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.","lang":"eng"}],"article_type":"original","publication_status":"published","_id":"10341","year":"2020","date_created":"2021-11-26T06:29:41Z","pmid":1},{"keyword":["multidisciplinary"],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across."}],"file":[{"creator":"cchlebak","access_level":"open_access","checksum":"3ba2eca975930cdb0b1ce1ae876885a7","content_type":"application/pdf","file_size":10381298,"date_updated":"2021-11-26T06:50:09Z","file_name":"2020_SciAdv_Tian.pdf","relation":"main_file","date_created":"2021-11-26T06:50:09Z","success":1,"file_id":"10343"}],"publication_status":"published","article_type":"original","_id":"10342","year":"2020","date_created":"2021-11-26T06:40:28Z","pmid":1,"issue":"48","article_number":"eabc4397 ","has_accepted_license":"1","external_id":{"pmid":["33246953"]},"title":"On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias","oa":1,"publication_identifier":{"issn":["2375-2548"]},"publication":"Science Advances","day":"27","author":[{"full_name":"Tian, Xiaohe","first_name":"Xiaohe","last_name":"Tian"},{"first_name":"Diana M.","last_name":"Leite","full_name":"Leite, Diana M."},{"first_name":"Edoardo","last_name":"Scarpa","full_name":"Scarpa, Edoardo"},{"last_name":"Nyberg","first_name":"Sophie","full_name":"Nyberg, Sophie"},{"first_name":"Gavin","last_name":"Fullstone","full_name":"Fullstone, Gavin"},{"full_name":"Forth, Joe","last_name":"Forth","first_name":"Joe"},{"full_name":"Matias, Diana","last_name":"Matias","first_name":"Diana"},{"last_name":"Apriceno","first_name":"Azzurra","full_name":"Apriceno, Azzurra"},{"full_name":"Poma, Alessandro","last_name":"Poma","first_name":"Alessandro"},{"first_name":"Aroa","last_name":"Duro-Castano","full_name":"Duro-Castano, Aroa"},{"full_name":"Vuyyuru, Manish","first_name":"Manish","last_name":"Vuyyuru"},{"last_name":"Harker-Kirschneck","first_name":"Lena","full_name":"Harker-Kirschneck, Lena"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Zhang","first_name":"Zhongping","full_name":"Zhang, Zhongping"},{"last_name":"Xiang","first_name":"Pan","full_name":"Xiang, Pan"},{"full_name":"Fang, Bin","last_name":"Fang","first_name":"Bin"},{"first_name":"Yupeng","last_name":"Tian","full_name":"Tian, Yupeng"},{"full_name":"Luo, Lei","last_name":"Luo","first_name":"Lei"},{"last_name":"Rizzello","first_name":"Loris","full_name":"Rizzello, Loris"},{"full_name":"Battaglia, Giuseppe","first_name":"Giuseppe","last_name":"Battaglia"}],"citation":{"chicago":"Tian, Xiaohe, Diana M. Leite, Edoardo Scarpa, Sophie Nyberg, Gavin Fullstone, Joe Forth, Diana Matias, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” <i>Science Advances</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc4397\">https://doi.org/10.1126/sciadv.abc4397</a>.","ista":"Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. 2020. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Science Advances. 6(48), eabc4397.","mla":"Tian, Xiaohe, et al. “On the Shuttling across the Blood-Brain Barrier via Tubule Formation: Mechanism and Cargo Avidity Bias.” <i>Science Advances</i>, vol. 6, no. 48, eabc4397, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc4397\">10.1126/sciadv.abc4397</a>.","apa":"Tian, X., Leite, D. M., Scarpa, E., Nyberg, S., Fullstone, G., Forth, J., … Battaglia, G. (2020). On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abc4397\">https://doi.org/10.1126/sciadv.abc4397</a>","ieee":"X. Tian <i>et al.</i>, “On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias,” <i>Science Advances</i>, vol. 6, no. 48. American Association for the Advancement of Science, 2020.","ama":"Tian X, Leite DM, Scarpa E, et al. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. <i>Science Advances</i>. 2020;6(48). doi:<a href=\"https://doi.org/10.1126/sciadv.abc4397\">10.1126/sciadv.abc4397</a>","short":"X. Tian, D.M. Leite, E. Scarpa, S. Nyberg, G. Fullstone, J. Forth, D. Matias, A. Apriceno, A. Poma, A. Duro-Castano, M. Vuyyuru, L. Harker-Kirschneck, A. Šarić, Z. Zhang, P. Xiang, B. Fang, Y. Tian, L. Luo, L. Rizzello, G. Battaglia, Science Advances 6 (2020)."},"date_updated":"2021-11-26T07:00:24Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.04.04.025866v1"}],"month":"11","publisher":"American Association for the Advancement of Science","scopus_import":"1","acknowledgement":"Funding: G.B. thanks the ERC for the starting grant (MEViC 278793) and consolidator award (CheSSTaG 769798), EPSRC/BTG Healthcare Partnership (EP/I001697/1), EPSRC Established Career Fellowship (EP/N026322/1), EPSRC/SomaNautix Healthcare Partnership EP/R024723/1, and Children with Cancer UK for the research project (16-227). X.T. and G.B. thank that Anhui 100 Talent program for facilitating data sharing and research visits. A.D.-C. and L.R. acknowledge the Royal Society for a Newton fellowship and the Marie Skłodowska-Curie Actions for a European Fellowship. Author contributions: X.T. prepared and characterized POs, performed all the fast imaging in both conventional and STED microscopy, set up the initial BBB model, encapsulated the PtA2 in POs, and supervised the PtA2-PO animal work. D.M.L. prepared and characterized POs; performed all the permeability studies, PLA assays, WB and associated data analysis, and part of the colocalization assays; and performed experiments with the shRNA for knockdown of syndapin-2. E.S. prepared and characterized POs and performed part of colocalization assays and Cy7-labeled PO animal experiments. S.N. prepared and characterized POs and performed part of the colocalization and inhibition assays. G.F. designed, performed, and analyzed the agent-based simulations of transcytosis. J.F. designed the image-based algorithm to analyze the PLA data. D.M. prepared and characterized POs and helped with Cy7-labeled PO animal experiments. A.A. performed TEM imaging of the POs. A.P. and A.D.-C. synthesized the dye- and peptide-functionalized and pristine copolymers. M.V., L.H.-K., and A.Š. designed, performed, and analyzed the MD simulations. Z.Z. supervised and supported STED imaging. P.X., B.F., and Y.T. synthesized and characterized the PtA2 compound. L.L. performed some of the animal work. L.R. supported and helped with the BBB characterization. G.B. analyzed all fast imaging and supervised and coordinated the overall work. X.T., D.M.L., E.S., and G.B. wrote the manuscript. Competing interests: The authors declare that part of the work is associated with the UCL spin-out company SomaNautix Ltd. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.","extern":"1","intvolume":"         6","ddc":["611"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"date_published":"2020-11-27T00:00:00Z","doi":"10.1126/sciadv.abc4397","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2021-11-26T06:50:09Z","volume":6,"type":"journal_article"},{"day":"23","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication":"Physical Review Letters","oa":1,"author":[{"last_name":"Forster","first_name":"Joel C.","full_name":"Forster, Joel C."},{"first_name":"Johannes","last_name":"Krausser","full_name":"Krausser, Johannes"},{"first_name":"Manish R.","last_name":"Vuyyuru","full_name":"Vuyyuru, Manish R."},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"}],"citation":{"ista":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. 2020. Exploring the design rules for efficient membrane-reshaping nanostructures. Physical Review Letters. 125(22), 228101.","chicago":"Forster, Joel C., Johannes Krausser, Manish R. Vuyyuru, Buzz Baum, and Anđela Šarić. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevlett.125.228101\">https://doi.org/10.1103/physrevlett.125.228101</a>.","ama":"Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the design rules for efficient membrane-reshaping nanostructures. <i>Physical Review Letters</i>. 2020;125(22). doi:<a href=\"https://doi.org/10.1103/physrevlett.125.228101\">10.1103/physrevlett.125.228101</a>","apa":"Forster, J. C., Krausser, J., Vuyyuru, M. R., Baum, B., &#38; Šarić, A. (2020). Exploring the design rules for efficient membrane-reshaping nanostructures. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.125.228101\">https://doi.org/10.1103/physrevlett.125.228101</a>","ieee":"J. C. Forster, J. Krausser, M. R. Vuyyuru, B. Baum, and A. Šarić, “Exploring the design rules for efficient membrane-reshaping nanostructures,” <i>Physical Review Letters</i>, vol. 125, no. 22. American Physical Society, 2020.","mla":"Forster, Joel C., et al. “Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures.” <i>Physical Review Letters</i>, vol. 125, no. 22, 228101, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.125.228101\">10.1103/physrevlett.125.228101</a>.","short":"J.C. Forster, J. Krausser, M.R. Vuyyuru, B. Baum, A. Šarić, Physical Review Letters 125 (2020)."},"date_updated":"2021-11-30T08:33:14Z","has_accepted_license":"1","issue":"22","article_number":"228101","external_id":{"pmid":["33315453"]},"title":"Exploring the design rules for efficient membrane-reshaping nanostructures","date_created":"2021-11-26T07:10:43Z","pmid":1,"year":"2020","_id":"10344","quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","publication_status":"published","article_type":"original","file":[{"date_updated":"2021-11-26T07:16:49Z","file_id":"10345","success":1,"relation":"main_file","date_created":"2021-11-26T07:16:49Z","file_name":"2020_PhysRevLett_Forster.pdf","access_level":"open_access","creator":"cchlebak","file_size":844353,"content_type":"application/pdf","checksum":"fbf2e1415e332d6add90222d60401a1d"}],"abstract":[{"lang":"eng","text":"In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry."}],"file_date_updated":"2021-11-26T07:16:49Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":125,"ddc":["530"],"intvolume":"       125","extern":"1","doi":"10.1103/physrevlett.125.228101","date_published":"2020-11-23T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","acknowledgement":"We acknowledge support from EPSRC (J. C. F.), MRC (B. B. and A. Š.), the ERC StG 802960 “NEPA” (J. K. and A. Š.), the Royal Society (A. Š.), and the United Kingdom Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC (EP/P020194/1).","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.27.968149v1","open_access":"1"}],"publisher":"American Physical Society","month":"11"},{"month":"09","publisher":"Cell Press","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1","open_access":"1"}],"page":"1791-1799","acknowledgement":"We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu, Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.), Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).","scopus_import":"1","date_published":"2020-09-23T00:00:00Z","doi":"10.1016/j.bpj.2020.09.013","status":"public","language":[{"iso":"eng"}],"extern":"1","intvolume":"       119","type":"journal_article","volume":119,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","publication_status":"published","abstract":[{"text":"One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","keyword":["biophysics"],"oa_version":"Published Version","date_created":"2021-11-26T07:27:24Z","pmid":1,"_id":"10346","year":"2020","title":"Modeling fibrillogenesis of collagen-mimetic molecules","external_id":{"pmid":["33049216"]},"issue":"9","citation":{"mla":"Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>.","ama":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. 2020;119(9):1791-1799. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>","ieee":"A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” <i>Biophysical Journal</i>, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020.","apa":"Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., &#38; Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>","chicago":"Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>.","ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799."},"author":[{"full_name":"Hafner, Anne E.","first_name":"Anne E.","last_name":"Hafner"},{"full_name":"Gyori, Noemi G.","last_name":"Gyori","first_name":"Noemi G."},{"first_name":"Ciaran A.","last_name":"Bench","full_name":"Bench, Ciaran A."},{"full_name":"Davis, Luke K.","last_name":"Davis","first_name":"Luke K."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"date_updated":"2021-11-26T07:45:24Z","day":"23","oa":1,"publication_identifier":{"issn":["0006-3495"]},"publication":"Biophysical Journal"},{"page":"24251-24257","acknowledgement":"We acknowledge support from Peterhouse, Cambridge (T.C.T.M.); the Swiss National Science Foundation (T.C.T.M.); the Royal Society (A.S. and S.C.); the Academy of Medical Sciences (A.S.); Sidney Sussex College, Cambridge (G.M.); Newnham College, Cambridge (G.T.H.); the Wellcome Trust (T.P.J.K.); the Cambridge Center for Misfolding Diseases (T.P.J.K. and M.V.); the Biotechnology and Biological Sciences Research Council (T.P.J.K.); the Frances and Augustus Newman Foundation (T.P.J.K.); and the Synapsis Foundation for Alzheimer’s disease (P.A.). The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7/2007-2013) through the ERC Grant PhysProt (Agreement 337969).","scopus_import":"1","publisher":"National Academy of Sciences","month":"09","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.22.960716","open_access":"1"}],"type":"journal_article","volume":117,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1073/pnas.2006684117","date_published":"2020-09-14T00:00:00Z","language":[{"iso":"eng"}],"status":"public","intvolume":"       117","extern":"1","date_created":"2021-11-26T07:48:27Z","pmid":1,"year":"2020","_id":"10347","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors."}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","keyword":["multidisciplinary"],"author":[{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"full_name":"Heller, Gabriella T.","last_name":"Heller","first_name":"Gabriella T."},{"full_name":"Curk, Samo","first_name":"Samo","last_name":"Curk"},{"full_name":"Arosio, Paolo","last_name":"Arosio","first_name":"Paolo"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"citation":{"short":"T.C.T. Michaels, A. Šarić, G. Meisl, G.T. Heller, S. Curk, P. Arosio, S. Linse, C.M. Dobson, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences 117 (2020) 24251–24257.","apa":"Michaels, T. C. T., Šarić, A., Meisl, G., Heller, G. T., Curk, S., Arosio, P., … Knowles, T. P. J. (2020). Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006684117\">https://doi.org/10.1073/pnas.2006684117</a>","ama":"Michaels TCT, Šarić A, Meisl G, et al. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. <i>Proceedings of the National Academy of Sciences</i>. 2020;117(39):24251-24257. doi:<a href=\"https://doi.org/10.1073/pnas.2006684117\">10.1073/pnas.2006684117</a>","ieee":"T. C. T. Michaels <i>et al.</i>, “Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors,” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 39. National Academy of Sciences, pp. 24251–24257, 2020.","mla":"Michaels, Thomas C. T., et al. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” <i>Proceedings of the National Academy of Sciences</i>, vol. 117, no. 39, National Academy of Sciences, 2020, pp. 24251–57, doi:<a href=\"https://doi.org/10.1073/pnas.2006684117\">10.1073/pnas.2006684117</a>.","ista":"Michaels TCT, Šarić A, Meisl G, Heller GT, Curk S, Arosio P, Linse S, Dobson CM, Vendruscolo M, Knowles TPJ. 2020. Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors. Proceedings of the National Academy of Sciences. 117(39), 24251–24257.","chicago":"Michaels, Thomas C. T., Anđela Šarić, Georg Meisl, Gabriella T. Heller, Samo Curk, Paolo Arosio, Sara Linse, Christopher M. Dobson, Michele Vendruscolo, and Tuomas P. J. Knowles. “Thermodynamic and Kinetic Design Principles for Amyloid-Aggregation Inhibitors.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006684117\">https://doi.org/10.1073/pnas.2006684117</a>."},"date_updated":"2021-11-26T08:59:06Z","day":"14","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences","oa":1,"external_id":{"pmid":["32929030"]},"title":"Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors","issue":"39"},{"article_type":"original","publication_status":"published","abstract":[{"text":"The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity.","lang":"eng"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","keyword":["general biochemistry","genetics and molecular biology"],"date_created":"2021-11-26T08:02:27Z","pmid":1,"year":"2020","_id":"10348","title":"An ESCRT-III polymerization sequence drives membrane deformation and fission","external_id":{"pmid":["32814015"]},"issue":"5","author":[{"full_name":"Pfitzner, Anna-Katharina","first_name":"Anna-Katharina","last_name":"Pfitzner"},{"full_name":"Mercier, Vincent","first_name":"Vincent","last_name":"Mercier"},{"full_name":"Jiang, Xiuyun","first_name":"Xiuyun","last_name":"Jiang"},{"last_name":"Moser von Filseck","first_name":"Joachim","full_name":"Moser von Filseck, Joachim"},{"last_name":"Baum","first_name":"Buzz","full_name":"Baum, Buzz"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić"},{"full_name":"Roux, Aurélien","first_name":"Aurélien","last_name":"Roux"}],"citation":{"short":"A.-K. Pfitzner, V. Mercier, X. Jiang, J. Moser von Filseck, B. Baum, A. Šarić, A. Roux, Cell 182 (2020) 1140–1155.e18.","chicago":"Pfitzner, Anna-Katharina, Vincent Mercier, Xiuyun Jiang, Joachim Moser von Filseck, Buzz Baum, Anđela Šarić, and Aurélien Roux. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>.","ista":"Pfitzner A-K, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. 2020. An ESCRT-III polymerization sequence drives membrane deformation and fission. Cell. 182(5), 1140–1155.e18.","mla":"Pfitzner, Anna-Katharina, et al. “An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission.” <i>Cell</i>, vol. 182, no. 5, Elsevier, 2020, p. 1140–1155.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>.","ieee":"A.-K. Pfitzner <i>et al.</i>, “An ESCRT-III polymerization sequence drives membrane deformation and fission,” <i>Cell</i>, vol. 182, no. 5. Elsevier, p. 1140–1155.e18, 2020.","ama":"Pfitzner A-K, Mercier V, Jiang X, et al. An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. 2020;182(5):1140-1155.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">10.1016/j.cell.2020.07.021</a>","apa":"Pfitzner, A.-K., Mercier, V., Jiang, X., Moser von Filseck, J., Baum, B., Šarić, A., &#38; Roux, A. (2020). An ESCRT-III polymerization sequence drives membrane deformation and fission. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2020.07.021\">https://doi.org/10.1016/j.cell.2020.07.021</a>"},"date_updated":"2021-11-26T08:58:37Z","day":"18","publication_identifier":{"issn":["0092-8674"]},"publication":"Cell","oa":1,"publisher":"Elsevier","month":"08","main_file_link":[{"url":"https://www.sciencedirect.com/science/article/pii/S0092867420309296","open_access":"1"}],"page":"1140-1155.e18","acknowledgement":"The authors thank Nicolas Chiaruttini, Jean Gruenberg, and Lena Harker-Kirschneck for careful correction of this manuscript and helpful discussions. The authors want to thank the NCCR Chemical Biology for constant support during this project. A.R. acknowledges funding from the Swiss National Fund for Research (31003A_130520, 31003A_149975, and 31003A_173087) and the European Research Council Consolidator (311536). A.Š. acknowledges the European Research Council (802960). B.B. thanks the BBSRC (BB/K009001/1) and Wellcome Trust (203276/Z/16/Z) for support. J.M.v.F. acknowledges funding through an EMBO Long-Term Fellowship (ALTF 1065-2015), the European Commission FP7 (Marie Curie Actions, LTFCOFUND2013, and GA-2013-609409), and a Transitional Postdoc fellowship (2015/345) from the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation and Swiss National Science Foundation Research (SNSF SINERGIA 160728/1 [leader, Sophie Martin]).","scopus_import":"1","doi":"10.1016/j.cell.2020.07.021","date_published":"2020-08-18T00:00:00Z","language":[{"iso":"eng"}],"status":"public","intvolume":"       182","extern":"1","type":"journal_article","volume":182,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"issue":"6504","title":"The proteasome controls ESCRT-III–mediated cell division in an archaeon","external_id":{"pmid":["32764038"]},"day":"07","publication":"Science","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa":1,"author":[{"first_name":"Gabriel","last_name":"Tarrason Risa","full_name":"Tarrason Risa, Gabriel"},{"full_name":"Hurtig, Fredrik","last_name":"Hurtig","first_name":"Fredrik"},{"full_name":"Bray, Sian","first_name":"Sian","last_name":"Bray"},{"last_name":"Hafner","first_name":"Anne E.","full_name":"Hafner, Anne E."},{"last_name":"Harker-Kirschneck","first_name":"Lena","full_name":"Harker-Kirschneck, Lena"},{"last_name":"Faull","first_name":"Peter","full_name":"Faull, Peter"},{"full_name":"Davis, Colin","last_name":"Davis","first_name":"Colin"},{"full_name":"Papatziamou, Dimitra","last_name":"Papatziamou","first_name":"Dimitra"},{"last_name":"Mutavchiev","first_name":"Delyan R.","full_name":"Mutavchiev, Delyan R."},{"last_name":"Fan","first_name":"Catherine","full_name":"Fan, Catherine"},{"last_name":"Meneguello","first_name":"Leticia","full_name":"Meneguello, Leticia"},{"last_name":"Arashiro Pulschen","first_name":"Andre","full_name":"Arashiro Pulschen, Andre"},{"full_name":"Dey, Gautam","last_name":"Dey","first_name":"Gautam"},{"full_name":"Culley, Siân","last_name":"Culley","first_name":"Siân"},{"full_name":"Kilkenny, Mairi","first_name":"Mairi","last_name":"Kilkenny"},{"last_name":"Souza","first_name":"Diorge P.","full_name":"Souza, Diorge P."},{"first_name":"Luca","last_name":"Pellegrini","full_name":"Pellegrini, Luca"},{"full_name":"de Bruin, Robertus A. M.","first_name":"Robertus A. M.","last_name":"de Bruin"},{"first_name":"Ricardo","last_name":"Henriques","full_name":"Henriques, Ricardo"},{"full_name":"Snijders, Ambrosius P.","last_name":"Snijders","first_name":"Ambrosius P."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"full_name":"Lindås, Ann-Christin","first_name":"Ann-Christin","last_name":"Lindås"},{"full_name":"Robinson, Nicholas P.","last_name":"Robinson","first_name":"Nicholas P."},{"full_name":"Baum, Buzz","first_name":"Buzz","last_name":"Baum"}],"date_updated":"2021-11-26T08:58:33Z","citation":{"chicago":"Tarrason Risa, Gabriel, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” <i>Science</i>. American Association for the Advancement of Science, 2020. <a href=\"https://doi.org/10.1126/science.aaz2532\">https://doi.org/10.1126/science.aaz2532</a>.","ista":"Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås A-C, Robinson NP, Baum B. 2020. The proteasome controls ESCRT-III–mediated cell division in an archaeon. Science. 369(6504).","mla":"Tarrason Risa, Gabriel, et al. “The Proteasome Controls ESCRT-III–Mediated Cell Division in an Archaeon.” <i>Science</i>, vol. 369, no. 6504, American Association for the Advancement of Science, 2020, doi:<a href=\"https://doi.org/10.1126/science.aaz2532\">10.1126/science.aaz2532</a>.","apa":"Tarrason Risa, G., Hurtig, F., Bray, S., Hafner, A. E., Harker-Kirschneck, L., Faull, P., … Baum, B. (2020). The proteasome controls ESCRT-III–mediated cell division in an archaeon. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaz2532\">https://doi.org/10.1126/science.aaz2532</a>","ama":"Tarrason Risa G, Hurtig F, Bray S, et al. The proteasome controls ESCRT-III–mediated cell division in an archaeon. <i>Science</i>. 2020;369(6504). doi:<a href=\"https://doi.org/10.1126/science.aaz2532\">10.1126/science.aaz2532</a>","ieee":"G. Tarrason Risa <i>et al.</i>, “The proteasome controls ESCRT-III–mediated cell division in an archaeon,” <i>Science</i>, vol. 369, no. 6504. American Association for the Advancement of Science, 2020.","short":"G. Tarrason Risa, F. Hurtig, S. Bray, A.E. Hafner, L. Harker-Kirschneck, P. Faull, C. Davis, D. Papatziamou, D.R. Mutavchiev, C. Fan, L. Meneguello, A. Arashiro Pulschen, G. Dey, S. Culley, M. Kilkenny, D.P. Souza, L. Pellegrini, R.A.M. de Bruin, R. Henriques, A.P. Snijders, A. Šarić, A.-C. Lindås, N.P. Robinson, B. Baum, Science 369 (2020)."},"quality_controlled":"1","oa_version":"Preprint","keyword":["multidisciplinary"],"article_processing_charge":"No","article_type":"original","publication_status":"published","abstract":[{"text":"Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.","lang":"eng"}],"pmid":1,"date_created":"2021-11-26T08:21:34Z","year":"2020","_id":"10349","intvolume":"       369","extern":"1","doi":"10.1126/science.aaz2532","date_published":"2020-08-07T00:00:00Z","language":[{"iso":"eng"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":369,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/774273v1"}],"publisher":"American Association for the Advancement of Science","month":"08","acknowledgement":"We thank the MRC LMCB at UCL for their support; the flow cytometry STP at the Francis Crick Institute for assistance, with special thanks to S. Purewal and D. Davis; C. Bertoli for mentorship\r\nand advice; J. M. Garcia-Arcos for help early on in this project; the entire Baum lab for their input throughout the project; the Albers lab for advice and reagents, with special thanks to M. Van Wolferen and S. Albers; the members of the Wellcome consortium for archaeal cytoskeleton studies for advice and comments; and J. Löwe, S. Oliferenko, M. Balasubramanian, and D. Gerlich for discussions and advice on the manuscript. N.P.R. and S.B. would like to thank N. Rzechorzek, A. Simon, and S. Anjum for discussion and advice.","scopus_import":"1"},{"_id":"10350","year":"2020","pmid":1,"date_created":"2021-11-26T09:08:19Z","article_processing_charge":"No","keyword":["general chemistry"],"oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation."}],"article_type":"original","publication_status":"published","oa":1,"publication":"Chemical Science","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"day":"08","date_updated":"2021-11-26T11:21:20Z","author":[{"full_name":"Dear, Alexander J.","first_name":"Alexander J.","last_name":"Dear"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Michaels","first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T."},{"full_name":"Kjaergaard, Magnus","first_name":"Magnus","last_name":"Kjaergaard"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J.","last_name":"Knowles"}],"citation":{"short":"A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse, T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247.","ista":"Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. 2020. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 11(24), 6236–6247.","chicago":"Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>.","apa":"Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., &#38; Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>","ieee":"A. J. Dear <i>et al.</i>, “Identification of on- and off-pathway oligomers in amyloid fibril formation,” <i>Chemical Science</i>, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020.","ama":"Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. 2020;11(24):6236-6247. doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>","mla":"Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>."},"issue":"24","external_id":{"pmid":["32953019"]},"title":"Identification of on- and off-pathway oligomers in amyloid fibril formation","scopus_import":"1","acknowledgement":"We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge (TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship, Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation (MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus Newman Foundation (TPJK) for financial support. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL).","page":"6236-6247","main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f"}],"month":"06","publisher":"Royal Society of Chemistry","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":11,"type":"journal_article","extern":"1","intvolume":"        11","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)"},"language":[{"iso":"eng"}],"date_published":"2020-06-08T00:00:00Z","doi":"10.1039/c9sc06501f"},{"oa":1,"publication":"Nature Chemistry","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"day":"13","citation":{"chicago":"Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio, Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” <i>Nature Chemistry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41557-020-0452-1\">https://doi.org/10.1038/s41557-020-0452-1</a>.","ista":"Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 12(5), 445–451.","mla":"Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” <i>Nature Chemistry</i>, vol. 12, no. 5, Springer Nature, 2020, pp. 445–51, doi:<a href=\"https://doi.org/10.1038/s41557-020-0452-1\">10.1038/s41557-020-0452-1</a>.","ama":"Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. <i>Nature Chemistry</i>. 2020;12(5):445-451. doi:<a href=\"https://doi.org/10.1038/s41557-020-0452-1\">10.1038/s41557-020-0452-1</a>","ieee":"T. C. T. Michaels <i>et al.</i>, “Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide,” <i>Nature Chemistry</i>, vol. 12, no. 5. Springer Nature, pp. 445–451, 2020.","apa":"Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G., … Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-020-0452-1\">https://doi.org/10.1038/s41557-020-0452-1</a>","short":"T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J. Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Chemistry 12 (2020) 445–451."},"date_updated":"2021-11-26T11:21:08Z","author":[{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"last_name":"Curk","first_name":"Samo","full_name":"Curk, Samo"},{"first_name":"Katja","last_name":"Bernfur","full_name":"Bernfur, Katja"},{"first_name":"Paolo","last_name":"Arosio","full_name":"Arosio, Paolo"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"full_name":"Dear, Alexander J.","last_name":"Dear","first_name":"Alexander J."},{"first_name":"Samuel I. A.","last_name":"Cohen","full_name":"Cohen, Samuel I. A."},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}],"issue":"5","title":"Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide","external_id":{"pmid":["32303714"]},"_id":"10351","year":"2020","date_created":"2021-11-26T09:15:13Z","pmid":1,"keyword":["general chemical engineering","general chemistry"],"article_processing_charge":"No","oa_version":"None","quality_controlled":"1","abstract":[{"text":"Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases.","lang":"eng"}],"article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1038/s41557-020-0468-6","relation":"erratum"}]},"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":12,"type":"journal_article","extern":"1","intvolume":"        12","status":"public","language":[{"iso":"eng"}],"date_published":"2020-04-13T00:00:00Z","doi":"10.1038/s41557-020-0452-1","scopus_import":"1","acknowledgement":"We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V., C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant MAMBA (S.L., agreement no. 340890). The research that led to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969).","page":"445-451","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.01.08.897488"}],"month":"04","publisher":"Springer Nature"},{"article_number":"022420","issue":"2","title":"Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics","external_id":{"pmid":["32168597"]},"publication":"Physical Review E","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"oa":1,"day":"28","citation":{"short":"L.K. Davis, I.J. Ford, A. Šarić, B.W. Hoogenboom, Physical Review E 101 (2020).","apa":"Davis, L. K., Ford, I. J., Šarić, A., &#38; Hoogenboom, B. W. (2020). Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.101.022420\">https://doi.org/10.1103/physreve.101.022420</a>","ieee":"L. K. Davis, I. J. Ford, A. Šarić, and B. W. Hoogenboom, “Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics,” <i>Physical Review E</i>, vol. 101, no. 2. American Physical Society, 2020.","ama":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. <i>Physical Review E</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/physreve.101.022420\">10.1103/physreve.101.022420</a>","mla":"Davis, Luke K., et al. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” <i>Physical Review E</i>, vol. 101, no. 2, 022420, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physreve.101.022420\">10.1103/physreve.101.022420</a>.","ista":"Davis LK, Ford IJ, Šarić A, Hoogenboom BW. 2020. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Physical Review E. 101(2), 022420.","chicago":"Davis, Luke K., Ian J. Ford, Anđela Šarić, and Bart W. Hoogenboom. “Intrinsically Disordered Nuclear Pore Proteins Show Ideal-Polymer Morphologies and Dynamics.” <i>Physical Review E</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physreve.101.022420\">https://doi.org/10.1103/physreve.101.022420</a>."},"author":[{"first_name":"Luke K.","last_name":"Davis","full_name":"Davis, Luke K."},{"full_name":"Ford, Ian J.","last_name":"Ford","first_name":"Ian J."},{"last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139"},{"first_name":"Bart W.","last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W."}],"date_updated":"2021-11-26T11:21:16Z","oa_version":"Preprint","article_processing_charge":"No","quality_controlled":"1","abstract":[{"text":"In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events.","lang":"eng"}],"publication_status":"published","article_type":"original","year":"2020","_id":"10352","pmid":1,"date_created":"2021-11-26T09:41:04Z","intvolume":"       101","extern":"1","language":[{"iso":"eng"}],"status":"public","doi":"10.1103/physreve.101.022420","date_published":"2020-02-28T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":101,"type":"journal_article","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/571687","open_access":"1"}],"publisher":"American Physical Society","month":"02","scopus_import":"1","acknowledgement":"We thank Dino Osmanović (MIT), Roy Beck (Tel-Aviv), Larissa Kapinos (Basel), Roderick Lim (Basel), Ralf Richter (Leeds), and Anton Zilman (Toronto) for discussions. This work was funded by the Royal Society (A.Š.) and the UK Engineering and Physical Sciences Research Council (EP/L504889/1, B.W.H.)."},{"_id":"10353","year":"2020","date_created":"2021-11-26T09:57:01Z","pmid":1,"article_processing_charge":"No","keyword":["general physics and astronomy"],"oa_version":"Preprint","quality_controlled":"1","abstract":[{"text":"Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content.","lang":"eng"}],"article_type":"original","publication_status":"published","oa":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication":"Physical Review Letters","day":"31","author":[{"full_name":"Paraschiv, Alexandru","last_name":"Paraschiv","first_name":"Alexandru"},{"full_name":"Hegde, Smitha","first_name":"Smitha","last_name":"Hegde"},{"first_name":"Raman","last_name":"Ganti","full_name":"Ganti, Raman"},{"full_name":"Pilizota, Teuta","last_name":"Pilizota","first_name":"Teuta"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"}],"date_updated":"2021-11-26T11:21:12Z","citation":{"mla":"Paraschiv, Alexandru, et al. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” <i>Physical Review Letters</i>, vol. 124, no. 4, 048102, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevlett.124.048102\">10.1103/physrevlett.124.048102</a>.","ieee":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, and A. Šarić, “Dynamic clustering regulates activity of mechanosensitive membrane channels,” <i>Physical Review Letters</i>, vol. 124, no. 4. American Physical Society, 2020.","apa":"Paraschiv, A., Hegde, S., Ganti, R., Pilizota, T., &#38; Šarić, A. (2020). Dynamic clustering regulates activity of mechanosensitive membrane channels. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.124.048102\">https://doi.org/10.1103/physrevlett.124.048102</a>","ama":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic clustering regulates activity of mechanosensitive membrane channels. <i>Physical Review Letters</i>. 2020;124(4). doi:<a href=\"https://doi.org/10.1103/physrevlett.124.048102\">10.1103/physrevlett.124.048102</a>","chicago":"Paraschiv, Alexandru, Smitha Hegde, Raman Ganti, Teuta Pilizota, and Anđela Šarić. “Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels.” <i>Physical Review Letters</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevlett.124.048102\">https://doi.org/10.1103/physrevlett.124.048102</a>.","ista":"Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. 2020. Dynamic clustering regulates activity of mechanosensitive membrane channels. Physical Review Letters. 124(4), 048102.","short":"A. Paraschiv, S. Hegde, R. Ganti, T. Pilizota, A. Šarić, Physical Review Letters 124 (2020)."},"issue":"4","article_number":"048102","external_id":{"pmid":["32058787"]},"title":"Dynamic clustering regulates activity of mechanosensitive membrane channels","scopus_import":"1","acknowledgement":"We thank Samantha Miller, Bert Poolman, and the members of Šarić and Pilizota laboratories for useful discussion. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P. and A.Š.), Darwin Trust of University of Edinburgh (H.S.), Industrial Biotechnology Innovation Centre (H.S. and T.P.), BBSRC Council Crossing Biological Membrane Network (H.S. and T.P.), BBSRC/EPSRC/MRC Synthetic Biology Research Centre (T.P.), and the Royal Society (A.Š.).","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/553248","open_access":"1"}],"month":"01","publisher":"American Physical Society","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":124,"type":"journal_article","extern":"1","intvolume":"       124","status":"public","language":[{"iso":"eng"}],"date_published":"2020-01-31T00:00:00Z","doi":"10.1103/physrevlett.124.048102"}]