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Cell. 179(1), 51–53.","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047.","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047","apa":"Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["31539498"],"isi":["000486618500011"]},"article_processing_charge":"No","author":[{"last_name":"Kopf","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"title":"The neural crest pitches in to remove apoptotic debris"},{"date_updated":"2024-03-27T23:30:41Z","department":[{"_id":"SiHi"}],"_id":"6830","status":"public","article_type":"letter_note","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"7902","status":"public"}]},"issue":"5","volume":103,"pmid":1,"oa_version":"Published Version","month":"09","intvolume":" 103","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.021"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752."},"title":"Memo1 tiles the radial glial cell grid","author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"external_id":{"isi":["000484400200002"],"pmid":["31487522"]},"article_processing_charge":"No","day":"04","publication":"Neuron","isi":1,"year":"2019","doi":"10.1016/j.neuron.2019.08.021","date_published":"2019-09-04T00:00:00Z","date_created":"2019-08-25T22:00:50Z","page":"750-752","quality_controlled":"1","publisher":"Elsevier","oa":1},{"date_updated":"2024-03-27T23:30:43Z","ddc":["580"],"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"_id":"6627","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1422-0067"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:34Z","file_size":3330291,"date_created":"2019-07-17T06:17:15Z","file_name":"2019_JournalMolecularScience_Adamowski.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_id":"6645"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"volume":20,"issue":"13","ec_funded":1,"abstract":[{"text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 20","citation":{"mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"article_processing_charge":"Yes","external_id":{"isi":["000477041100221"],"pmid":["31284661"]},"title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","article_number":"3337","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"has_accepted_license":"1","isi":1,"year":"2019","day":"07","publication":"International Journal of Molecular Sciences","date_published":"2019-07-07T00:00:00Z","doi":"10.3390/ijms20133337","date_created":"2019-07-11T12:00:32Z","quality_controlled":"1","publisher":"MDPI","oa":1},{"ddc":["000"],"date_updated":"2024-03-27T23:30:46Z","file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"BeBi"}],"_id":"7117","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-26T14:24:26Z","title":"X-CAD Supplemental Material","file_name":"xcad_sup_mat_siga19.pdf","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","file_size":1673176,"checksum":"56a2fb019adcb556d2b022f5e5acb68c","file_id":"7119","access_level":"open_access","relation":"supplementary_material","content_type":"application/pdf"},{"content_type":"application/pdf","description":"This is the author's version of the work.","relation":"main_file","access_level":"open_access","file_id":"7120","checksum":"5f29d76aceb5102e766cbab9b17d776e","file_size":14563618,"date_updated":"2020-07-14T12:47:49Z","creator":"bbickel","file_name":"XCAD_authors_version.pdf","date_created":"2019-11-26T14:24:27Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements"},{"file_name":"XCAD_video.mp4","date_created":"2019-11-26T14:27:37Z","creator":"bbickel","file_size":259979129,"date_updated":"2020-07-14T12:47:49Z","checksum":"0d31e123286cbec9e28b2001c2bb0d55","file_id":"7121","relation":"main_file","access_level":"open_access","content_type":"video/mp4"}],"publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"ec_funded":1,"volume":38,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12897"}]},"issue":"6","oa_version":"Submitted Version","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"intvolume":" 38","month":"11","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576."},"title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","article_processing_charge":"No","external_id":{"isi":["000498397300007"]},"author":[{"full_name":"Hafner, Christian","last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Schumacher, Christian","last_name":"Schumacher"},{"first_name":"Espen","last_name":"Knoop","full_name":"Knoop, Espen"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","last_name":"Auzinger","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"full_name":"Bächer, Moritz","last_name":"Bächer","first_name":"Moritz"}],"article_number":"157","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"publication":"ACM Transactions on Graphics","day":"06","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-11-26T14:22:09Z","doi":"10.1145/3355089.3356576","date_published":"2019-11-06T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM"},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"doi":"10.1103/PhysRevLett.122.114502","date_published":"2019-03-22T00:00:00Z","date_created":"2019-03-31T21:59:12Z","isi":1,"year":"2019","day":"22","publication":"Physical Review Letters","article_number":"114502","author":[{"full_name":"Agrawal, Nishchal","last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Choueiri, George H","last_name":"Choueiri","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1809.06358"],"isi":["000461922000006"]},"title":"Transition to turbulence in particle laden flows","citation":{"chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"month":"03","intvolume":" 122","abstract":[{"text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations.","lang":"eng"}],"oa_version":"Preprint","issue":"11","volume":122,"related_material":{"record":[{"relation":"dissertation_contains","id":"9728","status":"public"}]},"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"6189","department":[{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:47Z"},{"publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2019","day":"03","page":"152","date_published":"2019-05-03T00:00:00Z","doi":"10.15479/AT:ISTA:6371","date_created":"2019-05-03T11:55:51Z","project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"05","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","embargo":"2020-05-02","file_id":"6373","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_size":12597663,"date_updated":"2021-02-11T11:17:13Z","creator":"cigler","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","date_created":"2019-05-03T11:54:52Z"},{"creator":"cigler","file_size":34644426,"date_updated":"2020-07-14T12:47:28Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","date_created":"2019-05-03T11:54:54Z","relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6374","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"67","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"5585","relation":"popular_science"}]},"_id":"6371","type":"dissertation","status":"public","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"supervisor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-21T13:45:52Z","ddc":["576","579"],"file_date_updated":"2021-02-11T11:17:13Z","department":[{"_id":"CaGu"}]},{"department":[{"_id":"KrPi"}],"file_date_updated":"2021-11-15T10:27:29Z","date_updated":"2021-11-15T10:48:49Z","ddc":["000"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"10286","volume":2018,"issue":"3","publication_identifier":{"eissn":["2569-2925"]},"publication_status":"published","file":[{"checksum":"b816b848f046c48a8357700d9305dce5","file_id":"10289","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-11-15T10:27:29Z","file_name":"2018_IACR_Allini.pdf","date_updated":"2021-11-15T10:27:29Z","file_size":955755,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 2018","abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"oa_version":"Published Version","author":[{"full_name":"Allini, Elie Noumon","last_name":"Allini","first_name":"Elie Noumon"},{"last_name":"Skórski","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"},{"first_name":"Oto","full_name":"Petura, Oto","last_name":"Petura"},{"full_name":"Bernard, Florent","last_name":"Bernard","first_name":"Florent"},{"first_name":"Marek","last_name":"Laban","full_name":"Laban, Marek"},{"last_name":"Fischer","full_name":"Fischer, Viktor","first_name":"Viktor"}],"article_processing_charge":"No","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","citation":{"chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"214-242","doi":"10.13154/tches.v2018.i3.214-242","date_published":"2018-01-01T00:00:00Z","date_created":"2021-11-14T23:01:25Z","has_accepted_license":"1","year":"2018","day":"01","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","publisher":"International Association for Cryptologic Research","quality_controlled":"1","oa":1},{"citation":{"ista":"Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. 2018. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 12(2), 1508–1518.","chicago":"Fisher, Patrick D. Ellis, Qi Shen, Bernice Akpinar, Luke K. Davis, Kenny Kwok Hin Chung, David Baddeley, Anđela Šarić, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano. American Chemical Society, 2018. https://doi.org/10.1021/acsnano.7b08044.","apa":"Fisher, P. D. E., Shen, Q., Akpinar, B., Davis, L. K., Chung, K. K. H., Baddeley, D., … Lusk, C. P. (2018). A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.7b08044","ama":"Fisher PDE, Shen Q, Akpinar B, et al. A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement. ACS Nano. 2018;12(2):1508-1518. doi:10.1021/acsnano.7b08044","short":"P.D.E. Fisher, Q. Shen, B. Akpinar, L.K. Davis, K.K.H. Chung, D. Baddeley, A. Šarić, T.J. Melia, B.W. Hoogenboom, C. Lin, C.P. Lusk, ACS Nano 12 (2018) 1508–1518.","ieee":"P. D. E. Fisher et al., “A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement,” ACS Nano, vol. 12, no. 2. American Chemical Society, pp. 1508–1518, 2018.","mla":"Fisher, Patrick D. Ellis, et al. “A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement.” ACS Nano, vol. 12, no. 2, American Chemical Society, 2018, pp. 1508–18, doi:10.1021/acsnano.7b08044."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Patrick D. Ellis","full_name":"Fisher, Patrick D. Ellis","last_name":"Fisher"},{"full_name":"Shen, Qi","last_name":"Shen","first_name":"Qi"},{"full_name":"Akpinar, Bernice","last_name":"Akpinar","first_name":"Bernice"},{"first_name":"Luke K.","last_name":"Davis","full_name":"Davis, Luke K."},{"full_name":"Chung, Kenny Kwok Hin","last_name":"Chung","first_name":"Kenny Kwok Hin"},{"first_name":"David","full_name":"Baddeley, David","last_name":"Baddeley"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Melia, Thomas J.","last_name":"Melia","first_name":"Thomas J."},{"first_name":"Bart W.","last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W."},{"full_name":"Lin, Chenxiang","last_name":"Lin","first_name":"Chenxiang"},{"first_name":"C. Patrick","full_name":"Lusk, C. Patrick","last_name":"Lusk"}],"external_id":{"pmid":["29350911"]},"article_processing_charge":"No","title":"A Programmable DNA origami platform for organizing intrinsically disordered nucleoporins within nanopore confinement","year":"2018","day":"19","publication":"ACS Nano","page":"1508-1518","doi":"10.1021/acsnano.7b08044","date_published":"2018-01-19T00:00:00Z","date_created":"2021-11-26T15:15:00Z","acknowledgement":"We thank J. Edel and members of the Lusk, Lin and Hoogenboom lab for discussion and acknowledge A. Pyne and R. Thorogate for support carrying out the AFM experiments. This work was funded by the NIH (R21GM109466 to CPL, CL and TJM, DP2GM114830 to CL, RO1GM105672 to CPL, and T32GM007223 to PDEF) and the UK Engineering and Physical Sciences Research Council (EP/L015277/1, EP/L504889/1, and EP/M028100/1).","quality_controlled":"1","publisher":"American Chemical Society","date_updated":"2021-11-26T15:57:02Z","extern":"1","_id":"10362","type":"journal_article","article_type":"original","status":"public","keyword":["general physics and astronomy"],"publication_identifier":{"eissn":["1936-086X"],"issn":["1936-0851"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"2","volume":12,"abstract":[{"lang":"eng","text":"Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties."}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"01","intvolume":" 12"},{"title":"Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide","author":[{"first_name":"Samuel I. A.","full_name":"Cohen, Samuel I. A.","last_name":"Cohen"},{"full_name":"Cukalevski, Risto","last_name":"Cukalevski","first_name":"Risto"},{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"first_name":"Mattias","full_name":"Törnquist, Mattias","last_name":"Törnquist"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"first_name":"Christopher M.","last_name":"Dobson","full_name":"Dobson, Christopher M."},{"full_name":"Buell, Alexander K.","last_name":"Buell","first_name":"Alexander K."},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"}],"external_id":{"pmid":["29581486"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"S. I. A. Cohen et al., “Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide,” Nature Chemistry, vol. 10, no. 5. Springer Nature, pp. 523–531, 2018.","short":"S.I.A. Cohen, R. Cukalevski, T.C.T. Michaels, A. Šarić, M. Törnquist, M. Vendruscolo, C.M. Dobson, A.K. Buell, T.P.J. Knowles, S. Linse, Nature Chemistry 10 (2018) 523–531.","ama":"Cohen SIA, Cukalevski R, Michaels TCT, et al. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 2018;10(5):523-531. doi:10.1038/s41557-018-0023-x","apa":"Cohen, S. I. A., Cukalevski, R., Michaels, T. C. T., Šarić, A., Törnquist, M., Vendruscolo, M., … Linse, S. (2018). Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-018-0023-x","mla":"Cohen, Samuel I. A., et al. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry, vol. 10, no. 5, Springer Nature, 2018, pp. 523–31, doi:10.1038/s41557-018-0023-x.","ista":"Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. 2018. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nature Chemistry. 10(5), 523–531.","chicago":"Cohen, Samuel I. A., Risto Cukalevski, Thomas C. T. Michaels, Anđela Šarić, Mattias Törnquist, Michele Vendruscolo, Christopher M. Dobson, Alexander K. Buell, Tuomas P. J. Knowles, and Sara Linse. “Distinct Thermodynamic Signatures of Oligomer Generation in the Aggregation of the Amyloid-β Peptide.” Nature Chemistry. Springer Nature, 2018. https://doi.org/10.1038/s41557-018-0023-x."},"date_published":"2018-03-26T00:00:00Z","doi":"10.1038/s41557-018-0023-x","date_created":"2021-11-26T12:41:38Z","page":"523-531","day":"26","publication":"Nature Chemistry","year":"2018","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank B. Jönsson and I. André for helpful discussions. We acknowledge financial support from the Schiff Foundation (S.I.A.C.), St John’s College, Cambridge (S.I.A.C.), the Royal Physiographic Society (R.C.), the Research School FLÄK of Lund University (S.L., R.C.), the Swedish Research Council (S.L.) and its Linneaus Centre Organizing Molecular Matter (S.L.), the Crafoord Foundation (S.L.), Alzheimerfonden (S.L.), the European Research Council (S.L.), NanoLund (S.L.), Knut and Alice Wallenberg Foundation (S.L.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science Foundation (T.C.T.M.), Magdalene College, Cambridge (A.K.B.), the Leverhulme Trust (A.K.B.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the Wellcome Trust (C.M.D., T.P.J.K., A.Š.), and the Centre for Misfolding Diseases (C.M.D., T.P.J.K, M.V.). A.K.B. thanks the Alzheimer Forschung Initiative (AFI).","extern":"1","date_updated":"2021-11-26T15:14:00Z","status":"public","keyword":["general chemical engineering","general chemistry"],"article_type":"original","type":"journal_article","_id":"10360","issue":"5","volume":10,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1755-4330"],"eissn":["1755-4349"]},"publication_status":"published","month":"03","intvolume":" 10","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.","lang":"eng"}]},{"date_updated":"2021-11-26T12:40:02Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["materials chemistry"],"_id":"10357","issue":"49","volume":122,"publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 122","abstract":[{"text":"The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.","lang":"eng"}],"oa_version":"None","pmid":1,"author":[{"first_name":"Alexander J.","full_name":"Dear, Alexander J.","last_name":"Dear"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Thomas C. T.","full_name":"Michaels, Thomas C. T.","last_name":"Michaels"},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"article_processing_charge":"No","external_id":{"pmid":["30336667"]},"title":"Statistical mechanics of globular oligomer formation by protein molecules","citation":{"chicago":"Dear, Alexander J., Anđela Šarić, Thomas C. T. Michaels, Christopher M. Dobson, and Tuomas P. J. Knowles. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B. American Chemical Society, 2018. https://doi.org/10.1021/acs.jpcb.8b07805.","ista":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. 2018. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 122(49), 11721–11730.","mla":"Dear, Alexander J., et al. “Statistical Mechanics of Globular Oligomer Formation by Protein Molecules.” The Journal of Physical Chemistry B, vol. 122, no. 49, American Chemical Society, 2018, pp. 11721–30, doi:10.1021/acs.jpcb.8b07805.","ieee":"A. J. Dear, A. Šarić, T. C. T. Michaels, C. M. Dobson, and T. P. J. Knowles, “Statistical mechanics of globular oligomer formation by protein molecules,” The Journal of Physical Chemistry B, vol. 122, no. 49. American Chemical Society, pp. 11721–11730, 2018.","short":"A.J. Dear, A. Šarić, T.C.T. Michaels, C.M. Dobson, T.P.J. Knowles, The Journal of Physical Chemistry B 122 (2018) 11721–11730.","apa":"Dear, A. J., Šarić, A., Michaels, T. C. T., Dobson, C. M., & Knowles, T. P. J. (2018). Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.8b07805","ama":"Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical mechanics of globular oligomer formation by protein molecules. The Journal of Physical Chemistry B. 2018;122(49):11721-11730. doi:10.1021/acs.jpcb.8b07805"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"11721-11730","date_published":"2018-10-18T00:00:00Z","doi":"10.1021/acs.jpcb.8b07805","date_created":"2021-11-26T11:55:12Z","year":"2018","day":"18","publication":"The Journal of Physical Chemistry B","quality_controlled":"1","publisher":"American Chemical Society","acknowledgement":"We acknowledge support from the Schiff Foundation (A.J.D.), the Royal Society (A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), Peterhouse, Cambridge (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Wellcome Trust (T.P.J.K.), the Cambridge Centre for Misfolding Diseases (T.P.J.K.), the BBSRC (T.P.J.K.), the Frances and Augustus Newman foundation (T.P.J.K.). The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (Grant FP7/2007-2013) through the ERC Grant PhysProt (Agreement No. 337969). We thank Daan Frenkel for several useful discussions."},{"issue":"9","volume":18,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"intvolume":" 18","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1712.10147","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","pmid":1,"abstract":[{"lang":"eng","text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets."}],"extern":"1","date_updated":"2021-11-26T15:14:08Z","keyword":["mechanical engineering","condensed matter physics"],"status":"public","article_type":"original","type":"journal_article","_id":"10359","date_created":"2021-11-26T12:15:47Z","doi":"10.1021/acs.nanolett.8b00786","date_published":"2018-04-18T00:00:00Z","page":"5350-5356","publication":"Nano Letters","day":"18","year":"2018","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1.","title":"Controlling cargo trafficking in multicomponent membranes","external_id":{"pmid":["29667410"]},"article_processing_charge":"No","author":[{"first_name":"Tine","full_name":"Curk, Tine","last_name":"Curk"},{"full_name":"Wirnsberger, Peter","last_name":"Wirnsberger","first_name":"Peter"},{"full_name":"Dobnikar, Jure","last_name":"Dobnikar","first_name":"Jure"},{"first_name":"Daan","last_name":"Frenkel","full_name":"Frenkel, Daan"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786.","apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786","ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356.","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:10.1021/acs.nanolett.8b00786."}},{"main_file_link":[{"url":"https://arxiv.org/abs/1803.04851","open_access":"1"}],"scopus_import":"1","intvolume":" 116","month":"05","abstract":[{"lang":"eng","text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements."}],"oa_version":"Preprint","issue":"21-22","volume":116,"publication_status":"published","publication_identifier":{"eissn":["1362-3028"],"issn":["0026-8976"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["physical chemistry"],"status":"public","_id":"10358","date_updated":"2021-11-26T12:39:58Z","extern":"1","oa":1,"quality_controlled":"1","publisher":"Taylor & Francis","acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","page":"3055-3065","date_created":"2021-11-26T12:08:02Z","doi":"10.1080/00268976.2018.1474280","date_published":"2018-05-24T00:00:00Z","year":"2018","publication":"Molecular Physics","day":"24","article_processing_charge":"No","external_id":{"arxiv":["1803.04851"]},"author":[{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"first_name":"Lucie X.","last_name":"Liu","full_name":"Liu, Lucie X."},{"last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"full_name":"Bolhuis, Peter G.","last_name":"Bolhuis","first_name":"Peter G."},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation","citation":{"mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22, Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor & Francis, pp. 3055–3065, 2018.","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., & Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280","chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics. Taylor & Francis, 2018. https://doi.org/10.1080/00268976.2018.1474280.","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"year":"2018","day":"28","publication":"Annual Review of Physical Chemistry","page":"273-298","date_published":"2018-02-28T00:00:00Z","doi":"10.1146/annurev-physchem-050317-021322","date_created":"2021-11-26T12:52:12Z","acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","quality_controlled":"1","publisher":"Annual Reviews","citation":{"chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews, 2018. https://doi.org/10.1146/annurev-physchem-050317-021322.","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298.","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.","apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322","ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","ieee":"T. C. T. Michaels et al., “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” Annual Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T.","last_name":"Michaels"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"Johnny","last_name":"Habchi","full_name":"Habchi, Johnny"},{"first_name":"Sean","full_name":"Chia, Sean","last_name":"Chia"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"article_processing_charge":"No","external_id":{"pmid":["29490200"]},"title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation","publication_identifier":{"issn":["0066-426X"],"eissn":["1545-1593"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":69,"abstract":[{"lang":"eng","text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation."}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"02","intvolume":" 69","date_updated":"2021-11-26T15:58:19Z","extern":"1","_id":"10361","type":"journal_article","article_type":"original","status":"public","keyword":["physical and theoretical chemistry"]},{"article_number":"226801","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801.","chicago":"Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.226801.","ieee":"H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22. American Physical Society, 2018.","short":"H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018).","ama":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801","apa":"Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.226801","mla":"Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801."},"title":"Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices","article_processing_charge":"No","external_id":{"arxiv":["1805.04199"]},"author":[{"last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"last_name":"Zhou","full_name":"Zhou, H.","first_name":"H."},{"first_name":"E. M.","last_name":"Spanton","full_name":"Spanton, E. M."},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"full_name":"Watanabe, K.","last_name":"Watanabe","first_name":"K."},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"acknowledgement":"We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation.","oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review Letters","day":"28","year":"2018","date_created":"2022-01-14T12:15:47Z","doi":"10.1103/physrevlett.121.226801","date_published":"2018-11-28T00:00:00Z","_id":"10626","keyword":["general physics and astronomy"],"status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2022-01-14T13:48:35Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4."}],"intvolume":" 121","month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.04199"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"volume":121,"issue":"22"},{"external_id":{"arxiv":["1703.08184"]},"article_processing_charge":"No","author":[{"last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy"},{"full_name":"Naibert, Tyler R.","last_name":"Naibert","first_name":"Tyler R."},{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"}],"title":"Imaging phase slip dynamics in micron-size superconducting rings","citation":{"mla":"Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:10.1103/physrevb.97.184501.","ieee":"H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” Physical Review B, vol. 97, no. 18. American Physical Society, 2018.","short":"H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).","apa":"Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.184501","ama":"Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501","chicago":"Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.","ista":"Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"184501","date_created":"2022-01-14T13:48:47Z","doi":"10.1103/physrevb.97.184501","date_published":"2018-05-08T00:00:00Z","year":"2018","publication":"Physical Review B","day":"08","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n","date_updated":"2022-01-14T13:58:24Z","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"10627","issue":"18","volume":97,"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1703.08184","open_access":"1"}],"scopus_import":"1","intvolume":" 97","month":"05","abstract":[{"text":"We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures.","lang":"eng"}],"oa_version":"Preprint"},{"abstract":[{"lang":"eng","text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space."}],"oa_version":"Published Version","alternative_title":["EPiC Series in Computing"],"scopus_import":"1","month":"10","intvolume":" 57","publication_identifier":{"issn":["2398-7340"]},"publication_status":"published","file":[{"date_updated":"2022-05-17T07:51:08Z","file_size":720893,"creator":"dernst","date_created":"2022-05-17T07:51:08Z","file_name":"2018_EPiCs_Chatterjee.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"11392","checksum":"1229aa8640bd6db610c85decf2265480","success":1}],"language":[{"iso":"eng"}],"volume":57,"ec_funded":1,"_id":"10883","type":"conference","conference":{"start_date":"2018-11-17","end_date":"2018-11-21","location":"Awassa, Ethiopia","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning"},"status":"public","date_updated":"2022-07-29T09:24:31Z","ddc":["000"],"file_date_updated":"2022-05-17T07:51:08Z","department":[{"_id":"KrCh"}],"acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","quality_controlled":"1","publisher":"EasyChair","oa":1,"has_accepted_license":"1","year":"2018","day":"23","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","page":"233-253","doi":"10.29007/5z5k","date_published":"2018-10-23T00:00:00Z","date_created":"2022-03-18T12:46:32Z","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"citation":{"ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Wolfgang","last_name":"Dvořák","full_name":"Dvořák, Wolfgang"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Alexander","last_name":"Svozil","full_name":"Svozil, Alexander"}],"article_processing_charge":"No","external_id":{"arxiv":["1909.04983"]},"title":"Quasipolynomial set-based symbolic algorithms for parity games"},{"date_updated":"2021-01-12T06:48:13Z","citation":{"mla":"Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:10.1137/16M107894X.","apa":"Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. SIAM. https://doi.org/10.1137/16M107894X","ama":"Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93. doi:10.1137/16M107894X","ieee":"F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” SIAM Journal on Discrete Mathematics, vol. 32, no. 1. SIAM, pp. 64–93, 2018.","short":"F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93.","chicago":"Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X.","ista":"Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93."},"extern":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","first_name":"Fatemeh","id":"2C29581E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler"},{"first_name":"Charles","full_name":"Wang, Charles","last_name":"Wang"},{"full_name":"Yu, Josephine","last_name":"Yu","first_name":"Josephine"}],"publist_id":"6284","title":"Generalized permutohedra from probabilistic graphical models","_id":"1092","type":"journal_article","status":"public","year":"2018","publication_status":"published","day":"01","publication":"SIAM Journal on Discrete Mathematics","language":[{"iso":"eng"}],"page":"64-93","volume":32,"date_published":"2018-01-01T00:00:00Z","issue":"1","doi":"10.1137/16M107894X","date_created":"2018-12-11T11:50:06Z","abstract":[{"lang":"eng","text":"A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. "}],"oa_version":"Preprint","quality_controlled":"1","publisher":"SIAM","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1606.01814","open_access":"1"}],"month":"01","intvolume":" 32"},{"external_id":{"arxiv":["1806.10843"]},"author":[{"orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"publist_id":"8045","title":"Mean-field limits of particles in interaction with quantised radiation fields","citation":{"ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"page":"185 - 214","date_created":"2018-12-11T11:44:08Z","date_published":"2018-10-27T00:00:00Z","doi":"10.1007/978-3-030-01602-9_9","year":"2018","day":"27","oa":1,"quality_controlled":"1","publisher":"Springer","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:48:16Z","conference":{"location":"Munich, Germany","end_date":"2017-04-01","start_date":"2017-03-30","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"type":"conference","status":"public","_id":"11","ec_funded":1,"volume":270,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"scopus_import":1,"intvolume":" 270","month":"10","abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"oa_version":"Preprint"},{"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory","oa":1,"year":"2018","day":"18","publication":"Genes & Development","page":"1321-1331","date_published":"2018-09-18T00:00:00Z","doi":"10.1101/gad.315523.118","date_created":"2022-04-07T07:45:30Z","citation":{"ama":"McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331. doi:10.1101/gad.315523.118","apa":"McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118","ieee":"A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” Genes & Development, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.","short":"A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.","mla":"McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.","ista":"McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331.","chicago":"McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development. Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","author":[{"first_name":"Asako","full_name":"McCloskey, Asako","last_name":"McCloskey"},{"first_name":"Arkaitz","full_name":"Ibarra, Arkaitz","last_name":"Ibarra"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"external_id":{"pmid":["30228202"]},"article_processing_charge":"No","title":"Tpr regulates the total number of nuclear pore complexes per cell nucleus","abstract":[{"lang":"eng","text":"The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.315523.118"}],"month":"09","intvolume":" 32","publication_identifier":{"issn":["0890-9369","1549-5477"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":32,"issue":"19-20","_id":"11063","article_type":"original","type":"journal_article","status":"public","keyword":["Developmental Biology","Genetics"],"date_updated":"2022-07-18T08:32:32Z","extern":"1"},{"month":"12","intvolume":" 19","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-018-1599-6"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients."}],"volume":19,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1474-760X"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"11064","extern":"1","date_updated":"2022-07-18T08:32:34Z","quality_controlled":"1","publisher":"BioMed Central","oa":1,"date_published":"2018-12-20T00:00:00Z","doi":"10.1186/s13059-018-1599-6","date_created":"2022-04-07T07:45:40Z","day":"20","publication":"Genome Biology","year":"2018","article_number":"221","title":"Predicting age from the transcriptome of human dermal fibroblasts","author":[{"full_name":"Fleischer, Jason G.","last_name":"Fleischer","first_name":"Jason G."},{"last_name":"Schulte","full_name":"Schulte, Roberta","first_name":"Roberta"},{"first_name":"Hsiao H.","last_name":"Tsai","full_name":"Tsai, Hsiao H."},{"last_name":"Tyagi","full_name":"Tyagi, Swati","first_name":"Swati"},{"full_name":"Ibarra, Arkaitz","last_name":"Ibarra","first_name":"Arkaitz"},{"first_name":"Maxim N.","full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev"},{"last_name":"Huang","full_name":"Huang, Ling","first_name":"Ling"},{"last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"full_name":"Navlakha, Saket","last_name":"Navlakha","first_name":"Saket"}],"external_id":{"pmid":["30567591"]},"article_processing_charge":"No","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"mla":"Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018, doi:10.1186/s13059-018-1599-6.","ama":"Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6","apa":"Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6","ieee":"J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018.","short":"J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).","chicago":"Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6.","ista":"Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221."}}]