[{"_id":"1026","department":[{"_id":"HaJa"}],"publist_id":"6365","scopus_import":"1","publication_identifier":{"issn":["0958-1669"]},"doi":"10.1016/j.copbio.2017.02.006","ec_funded":1,"abstract":[{"text":"The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function.","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Optogenetic methods in drug screening: Technologies and applications","acknowledgement":"This work was supported by grants of the European Union Seventh Framework Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the Austrian Science Fund FWF (W1232 MolecularDrugTargets).","month":"12","type":"journal_article","external_id":{"isi":["000418313200003"]},"year":"2017","isi":1,"author":[{"last_name":"Agus","first_name":"Viviana","full_name":"Agus, Viviana"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"}],"status":"public","intvolume":"        48","quality_controlled":"1","date_updated":"2026-04-16T09:57:03Z","article_type":"original","oa_version":"None","page":"8 - 14","publication":"Current Opinion in Biotechnology","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:45Z","publisher":"Elsevier","date_published":"2017-12-01T00:00:00Z","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","grant_number":"RGY0084/2012"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","call_identifier":"FP7"},{"name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"}],"corr_author":"1","volume":48,"citation":{"short":"V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.","ista":"Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 48, 8–14.","ama":"Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and applications. <i>Current Opinion in Biotechnology</i>. 2017;48:8-14. doi:<a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">10.1016/j.copbio.2017.02.006</a>","mla":"Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” <i>Current Opinion in Biotechnology</i>, vol. 48, Elsevier, 2017, pp. 8–14, doi:<a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">10.1016/j.copbio.2017.02.006</a>.","chicago":"Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” <i>Current Opinion in Biotechnology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">https://doi.org/10.1016/j.copbio.2017.02.006</a>.","ieee":"V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies and applications,” <i>Current Opinion in Biotechnology</i>, vol. 48. Elsevier, pp. 8–14, 2017.","apa":"Agus, V., &#38; Janovjak, H. L. (2017). Optogenetic methods in drug screening: Technologies and applications. <i>Current Opinion in Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.copbio.2017.02.006\">https://doi.org/10.1016/j.copbio.2017.02.006</a>"},"article_processing_charge":"No","publication_status":"published","day":"01"},{"doi":"10.1103/PhysRevLett.118.137701","issue":"13","publist_id":"7951","_id":"103","type":"journal_article","month":"03","year":"2017","extern":"1","external_id":{"arxiv":["1612.05748"]},"title":"Transport signatures of quasiparticle poisoning in a majorana island","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We investigate effects of quasiparticle poisoning in a Majorana island with strong tunnel coupling to normal-metal leads. In addition to the main Coulomb blockade diamonds, &quot;shadow&quot; diamonds appear, shifted by 1e in gate voltage, consistent with transport through an excited (poisoned) state of the island. Comparison to a simple model yields an estimate of parity lifetime for the strongly coupled island (∼1 μs) and sets a bound for a weakly coupled island (&gt;10 μs). Fluctuations in the gate-voltage spacing of Coulomb peaks at high field, reflecting Majorana hybridization, are enhanced by the reduced lever arm at strong coupling. When converted from gate voltage to energy units, fluctuations are consistent with previous measurements."}],"acknowledgement":"Research supported by Microsoft, the Danish National Research Foundation, the Lundbeck Foundation, Carlsberg Foundation, Villum Foundation, and the European Commission.","article_number":"137701","arxiv":1,"oa_version":"Preprint","publisher":"American Physical Society","date_created":"2018-12-11T11:44:39Z","language":[{"iso":"eng"}],"publication":"APS Physics, Physical Review Letters","status":"public","oa":1,"author":[{"first_name":"S M","full_name":"Albrecht, S M","last_name":"Albrecht"},{"first_name":"Esben","full_name":"Hansen, Esben","last_name":"Hansen"},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kuemmeth","first_name":"Ferdinand","full_name":"Kuemmeth, Ferdinand"},{"full_name":"Jespersen, Thomas","first_name":"Thomas","last_name":"Jespersen"},{"full_name":"Nygård, Jesper","first_name":"Jesper","last_name":"Nygård"},{"full_name":"Krogstrup, Peter","first_name":"Peter","last_name":"Krogstrup"},{"full_name":"Danon, Jeroen","first_name":"Jeroen","last_name":"Danon"},{"full_name":"Flensberg, Karsten","first_name":"Karsten","last_name":"Flensberg"},{"last_name":"Marcus","full_name":"Marcus, Charles","first_name":"Charles"}],"date_updated":"2021-01-12T06:47:47Z","quality_controlled":"1","intvolume":"       118","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.05748"}],"date_published":"2017-03-31T00:00:00Z","day":"31","publication_status":"published","citation":{"short":"S.M. Albrecht, E. Hansen, A.P. Higginbotham, F. Kuemmeth, T. Jespersen, J. Nygård, P. Krogstrup, J. Danon, K. Flensberg, C. Marcus, APS Physics, Physical Review Letters 118 (2017).","mla":"Albrecht, S. M., et al. “Transport Signatures of Quasiparticle Poisoning in a Majorana Island.” <i>APS Physics, Physical Review Letters</i>, vol. 118, no. 13, 137701, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.137701\">10.1103/PhysRevLett.118.137701</a>.","ista":"Albrecht SM, Hansen E, Higginbotham AP, Kuemmeth F, Jespersen T, Nygård J, Krogstrup P, Danon J, Flensberg K, Marcus C. 2017. Transport signatures of quasiparticle poisoning in a majorana island. APS Physics, Physical Review Letters. 118(13), 137701.","ama":"Albrecht SM, Hansen E, Higginbotham AP, et al. Transport signatures of quasiparticle poisoning in a majorana island. <i>APS Physics, Physical Review Letters</i>. 2017;118(13). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.137701\">10.1103/PhysRevLett.118.137701</a>","apa":"Albrecht, S. M., Hansen, E., Higginbotham, A. P., Kuemmeth, F., Jespersen, T., Nygård, J., … Marcus, C. (2017). Transport signatures of quasiparticle poisoning in a majorana island. <i>APS Physics, Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.118.137701\">https://doi.org/10.1103/PhysRevLett.118.137701</a>","chicago":"Albrecht, S M, Esben Hansen, Andrew P Higginbotham, Ferdinand Kuemmeth, Thomas Jespersen, Jesper Nygård, Peter Krogstrup, Jeroen Danon, Karsten Flensberg, and Charles Marcus. “Transport Signatures of Quasiparticle Poisoning in a Majorana Island.” <i>APS Physics, Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.118.137701\">https://doi.org/10.1103/PhysRevLett.118.137701</a>.","ieee":"S. M. Albrecht <i>et al.</i>, “Transport signatures of quasiparticle poisoning in a majorana island,” <i>APS Physics, Physical Review Letters</i>, vol. 118, no. 13. American Physical Society, 2017."},"volume":118},{"article_type":"original","oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"Informationspraxis","date_created":"2018-12-11T11:49:46Z","publisher":"Verein Informationspraxis ","author":[{"last_name":"Villányi","orcid":"0000-0001-8126-0426","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","full_name":"Villányi, Márton","first_name":"Márton"}],"oa":1,"file":[{"date_updated":"2018-12-12T10:08:20Z","relation":"main_file","creator":"system","file_size":201163,"content_type":"application/pdf","date_created":"2018-12-12T10:08:20Z","access_level":"open_access","file_id":"4680","file_name":"IST-2017-799-v1+1_35227-112025-1-PB.pdf"}],"status":"public","intvolume":"         3","date_updated":"2024-10-09T20:57:18Z","date_published":"2017-01-01T00:00:00Z","corr_author":"1","volume":3,"ddc":["020"],"publication_status":"published","day":"01","pubrep_id":"799","citation":{"ista":"Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 3(1).","ama":"Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. <i>Informationspraxis</i>. 2017;3(1). doi:<a href=\"https://doi.org/10.11588/ip.2017.1.35227\">10.11588/ip.2017.1.35227</a>","mla":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” <i>Informationspraxis</i>, vol. 3, no. 1, Verein Informationspraxis , 2017, doi:<a href=\"https://doi.org/10.11588/ip.2017.1.35227\">10.11588/ip.2017.1.35227</a>.","short":"M. Villányi, Informationspraxis 3 (2017).","chicago":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” <i>Informationspraxis</i>. Verein Informationspraxis , 2017. <a href=\"https://doi.org/10.11588/ip.2017.1.35227\">https://doi.org/10.11588/ip.2017.1.35227</a>.","ieee":"M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library,” <i>Informationspraxis</i>, vol. 3, no. 1. Verein Informationspraxis , 2017.","apa":"Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. <i>Informationspraxis</i>. Verein Informationspraxis . <a href=\"https://doi.org/10.11588/ip.2017.1.35227\">https://doi.org/10.11588/ip.2017.1.35227</a>"},"article_processing_charge":"No","has_accepted_license":"1","publist_id":"6360","publication_identifier":{"issn":["2297-3249"]},"doi":"10.11588/ip.2017.1.35227","issue":"1","file_date_updated":"2018-12-12T10:08:20Z","_id":"1030","department":[{"_id":"E-Lib"}],"type":"journal_article","month":"01","popular_science":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2017","abstract":[{"text":"Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die Bibliothek auf eine erfolgreiche Implementierung zurückblicken.","lang":"ger"},{"lang":"eng","text":"IST Austria was looking for a new library system until 2014 when the research institute decided\r\nto implement Koha. The library first activated basic functions of the open-source product and\r\nthen brought additional tools into operation. The high flexibility of the system allows customized\r\nsolutions for different institutions. Although the library faced some challenges, it can now look\r\nback on a successful implementation."}],"title":"Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by/4.0/"},{"main_file_link":[{"url":"https://pubs.acs.org/doi/10.1021/acscentsci.7b00392","open_access":"1"}],"intvolume":"         3","quality_controlled":"1","date_updated":"2021-11-29T09:28:06Z","author":[{"first_name":"Mijo","full_name":"Simunovic, Mijo","last_name":"Simunovic"},{"full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"first_name":"J. Michael","full_name":"Henderson, J. Michael","last_name":"Henderson"},{"full_name":"Lee, Ka Yee C.","first_name":"Ka Yee C.","last_name":"Lee"},{"full_name":"Voth, Gregory A.","first_name":"Gregory A.","last_name":"Voth"}],"oa":1,"file":[{"file_size":2635263,"content_type":"application/pdf","relation":"main_file","creator":"cchlebak","date_updated":"2021-11-29T09:00:40Z","success":1,"file_name":"2017_ACSCentSci_Simunovic.pdf","checksum":"1cf3e5e5342f2d728f47560acc3ec560","file_id":"10371","access_level":"open_access","date_created":"2021-11-29T09:00:40Z"}],"status":"public","language":[{"iso":"eng"}],"publication":"ACS Central Science","date_created":"2021-11-29T08:49:50Z","publisher":"American Chemical Society","article_type":"original","page":"1246-1253","oa_version":"Published Version","has_accepted_license":"1","volume":3,"publication_status":"published","ddc":["540"],"day":"21","article_processing_charge":"No","citation":{"apa":"Simunovic, M., Šarić, A., Henderson, J. M., Lee, K. Y. C., &#38; Voth, G. A. (2017). Long-range organization of membrane-curving proteins. <i>ACS Central Science</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acscentsci.7b00392\">https://doi.org/10.1021/acscentsci.7b00392</a>","ieee":"M. Simunovic, A. Šarić, J. M. Henderson, K. Y. C. Lee, and G. A. Voth, “Long-range organization of membrane-curving proteins,” <i>ACS Central Science</i>, vol. 3, no. 12. American Chemical Society, pp. 1246–1253, 2017.","chicago":"Simunovic, Mijo, Anđela Šarić, J. Michael Henderson, Ka Yee C. Lee, and Gregory A. Voth. “Long-Range Organization of Membrane-Curving Proteins.” <i>ACS Central Science</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acscentsci.7b00392\">https://doi.org/10.1021/acscentsci.7b00392</a>.","short":"M. Simunovic, A. Šarić, J.M. Henderson, K.Y.C. Lee, G.A. Voth, ACS Central Science 3 (2017) 1246–1253.","mla":"Simunovic, Mijo, et al. “Long-Range Organization of Membrane-Curving Proteins.” <i>ACS Central Science</i>, vol. 3, no. 12, American Chemical Society, 2017, pp. 1246–53, doi:<a href=\"https://doi.org/10.1021/acscentsci.7b00392\">10.1021/acscentsci.7b00392</a>.","ama":"Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-range organization of membrane-curving proteins. <i>ACS Central Science</i>. 2017;3(12):1246-1253. doi:<a href=\"https://doi.org/10.1021/acscentsci.7b00392\">10.1021/acscentsci.7b00392</a>","ista":"Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. 2017. Long-range organization of membrane-curving proteins. ACS Central Science. 3(12), 1246–1253."},"date_published":"2017-11-21T00:00:00Z","_id":"10369","keyword":["general chemical engineering","general chemistry"],"file_date_updated":"2021-11-29T09:00:40Z","scopus_import":"1","issue":"12","doi":"10.1021/acscentsci.7b00392","publication_identifier":{"issn":["2374-7943"],"eissn":["2374-7951"]},"acknowledgement":"M.S. and G.A.V. acknowledge their research reported in this publication as being supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01-GM063796. Computational resources were provided to M.S. and G.A.V. by the National Science Foundation through XSEDE (Grant TG-MCA94P017, supercomputers Stampede and Gordon), and also by the Blue Waters computing project at the National Center for Supercomputing Applications (University of Illinois at Urbana–Champaign, NSF Awards OCI-0725070 and ACI-1238993). A.Š. acknowledges support from the Human Frontier Science Program and Royal Society. J.M.H. and K.Y.C.L. acknowledge the support from the National Science Foundation (Grant MCB-1413613) and the NSF-supported MRSEC program at the University of Chicago (Grant DMR-1420709). We are grateful to Carsten Mim and Vinzenz Unger of Northwestern University for generously providing us with the protein. We thank all the members of the Voth group for fruitful discussions, especially John M. A. Grime.","pmid":1,"abstract":[{"lang":"eng","text":"Biological membranes have a central role in mediating the organization of membrane-curving proteins, a dynamic process that has proven to be challenging to probe experimentally. Using atomic force microscopy, we capture the hierarchically organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid membranes. Their structure reveals distinct long linear aggregates of proteins, regularly spaced by up to 300 nm. Employing accurate free-energy calculations from large-scale coarse-grained computer simulations, we found that the membrane mediates the interaction among protein filaments as a combination of short- and long-ranged interactions. The long-ranged component acts at strikingly long distances, giving rise to a variety of micron-sized ordered patterns. This mechanism may contribute to the long-ranged spatiotemporal control of membrane remodeling by proteins in the cell."}],"title":"Long-range organization of membrane-curving proteins","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"extern":"1","year":"2017","external_id":{"pmid":["29296664"]},"type":"journal_article","month":"11"},{"quality_controlled":"1","intvolume":"         6","main_file_link":[{"open_access":"1","url":"https://elifesciences.org/articles/30292"}],"date_updated":"2021-11-29T09:28:14Z","file":[{"content_type":"application/pdf","file_size":6120157,"relation":"main_file","creator":"cchlebak","success":1,"date_updated":"2021-11-29T09:07:41Z","checksum":"c35f42dcfb007f6d6c761a27e24c26d3","file_name":"2017_eLife_Helle.pdf","file_id":"10372","access_level":"open_access","date_created":"2021-11-29T09:07:41Z"}],"oa":1,"author":[{"first_name":"Sebastian Carsten Johannes","full_name":"Helle, Sebastian Carsten Johannes","last_name":"Helle"},{"first_name":"Qian","full_name":"Feng, Qian","last_name":"Feng"},{"full_name":"Aebersold, Mathias J","first_name":"Mathias J","last_name":"Aebersold"},{"first_name":"Luca","full_name":"Hirt, Luca","last_name":"Hirt"},{"full_name":"Grüter, Raphael R","first_name":"Raphael R","last_name":"Grüter"},{"last_name":"Vahid","full_name":"Vahid, Afshin","first_name":"Afshin"},{"last_name":"Sirianni","first_name":"Andrea","full_name":"Sirianni, Andrea"},{"last_name":"Mostowy","full_name":"Mostowy, Serge","first_name":"Serge"},{"full_name":"Snedeker, Jess G","first_name":"Jess G","last_name":"Snedeker"},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Idema","first_name":"Timon","full_name":"Idema, Timon"},{"full_name":"Zambelli, Tomaso","first_name":"Tomaso","last_name":"Zambelli"},{"last_name":"Kornmann","full_name":"Kornmann, Benoît","first_name":"Benoît"}],"status":"public","publication":"eLife","language":[{"iso":"eng"}],"date_created":"2021-11-29T08:51:38Z","publisher":"eLife Sciences Publications","article_type":"original","oa_version":"Published Version","has_accepted_license":"1","volume":6,"citation":{"mla":"Helle, Sebastian Carsten Johannes, et al. “Mechanical Force Induces Mitochondrial Fission.” <i>ELife</i>, vol. 6, e30292, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/elife.30292\">10.7554/elife.30292</a>.","ama":"Helle SCJ, Feng Q, Aebersold MJ, et al. Mechanical force induces mitochondrial fission. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.30292\">10.7554/elife.30292</a>","ista":"Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. 2017. Mechanical force induces mitochondrial fission. eLife. 6, e30292.","short":"S.C.J. Helle, Q. Feng, M.J. Aebersold, L. Hirt, R.R. Grüter, A. Vahid, A. Sirianni, S. Mostowy, J.G. Snedeker, A. Šarić, T. Idema, T. Zambelli, B. Kornmann, ELife 6 (2017).","apa":"Helle, S. C. J., Feng, Q., Aebersold, M. J., Hirt, L., Grüter, R. R., Vahid, A., … Kornmann, B. (2017). Mechanical force induces mitochondrial fission. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.30292\">https://doi.org/10.7554/elife.30292</a>","ieee":"S. C. J. Helle <i>et al.</i>, “Mechanical force induces mitochondrial fission,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","chicago":"Helle, Sebastian Carsten Johannes, Qian Feng, Mathias J Aebersold, Luca Hirt, Raphael R Grüter, Afshin Vahid, Andrea Sirianni, et al. “Mechanical Force Induces Mitochondrial Fission.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/elife.30292\">https://doi.org/10.7554/elife.30292</a>."},"article_processing_charge":"No","day":"09","ddc":["572"],"publication_status":"published","date_published":"2017-11-09T00:00:00Z","_id":"10370","keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"file_date_updated":"2021-11-29T09:07:41Z","scopus_import":"1","doi":"10.7554/elife.30292","publication_identifier":{"issn":["2050-084X"]},"article_number":"e30292","abstract":[{"lang":"eng","text":"Eukaryotic cells are densely packed with macromolecular complexes and intertwining organelles, continually transported and reshaped. Intriguingly, organelles avoid clashing and entangling with each other in such limited space. Mitochondria form extensive networks constantly remodeled by fission and fusion. Here, we show that mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of mitochondria – via encounter with motile intracellular pathogens, via external pressure applied by an atomic force microscope, or via cell migration across uneven microsurfaces – results in the recruitment of the mitochondrial fission machinery, and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria, acts as a membrane-bound force sensor to recruit the fission machinery to mechanically strained sites. Thus, mitochondria adapt to the environment by sensing and responding to biomechanical cues. Our findings that mechanical triggers can be coupled to biochemical responses in membrane dynamics may explain how organelles orderly cohabit in the crowded cytoplasm."}],"pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Mechanical force induces mitochondrial fission","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["29119945"]},"extern":"1","year":"2017","month":"11","type":"journal_article"},{"quality_controlled":"1","main_file_link":[{"url":"https://www.pnas.org/content/114/19/4911","open_access":"1"}],"intvolume":"       114","date_updated":"2021-11-29T09:59:12Z","author":[{"full_name":"Wirnsberger, Peter","first_name":"Peter","last_name":"Wirnsberger"},{"last_name":"Fijan","first_name":"Domagoj","full_name":"Fijan, Domagoj"},{"last_name":"Lightwood","full_name":"Lightwood, Roger A.","first_name":"Roger A."},{"first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139"},{"last_name":"Dellago","full_name":"Dellago, Christoph","first_name":"Christoph"},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"}],"oa":1,"status":"public","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","date_created":"2021-11-29T09:28:24Z","article_type":"original","oa_version":"Published Version","page":"4911-4914","arxiv":1,"volume":114,"citation":{"short":"P. Wirnsberger, D. Fijan, R.A. Lightwood, A. Šarić, C. Dellago, D. Frenkel, Proceedings of the National Academy of Sciences 114 (2017) 4911–4914.","mla":"Wirnsberger, Peter, et al. “Numerical Evidence for Thermally Induced Monopoles.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 19, National Academy of Sciences, 2017, pp. 4911–14, doi:<a href=\"https://doi.org/10.1073/pnas.1621494114\">10.1073/pnas.1621494114</a>.","ista":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. 2017. Numerical evidence for thermally induced monopoles. Proceedings of the National Academy of Sciences. 114(19), 4911–4914.","ama":"Wirnsberger P, Fijan D, Lightwood RA, Šarić A, Dellago C, Frenkel D. Numerical evidence for thermally induced monopoles. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(19):4911-4914. doi:<a href=\"https://doi.org/10.1073/pnas.1621494114\">10.1073/pnas.1621494114</a>","ieee":"P. Wirnsberger, D. Fijan, R. A. Lightwood, A. Šarić, C. Dellago, and D. Frenkel, “Numerical evidence for thermally induced monopoles,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 19. National Academy of Sciences, pp. 4911–4914, 2017.","chicago":"Wirnsberger, Peter, Domagoj Fijan, Roger A. Lightwood, Anđela Šarić, Christoph Dellago, and Daan Frenkel. “Numerical Evidence for Thermally Induced Monopoles.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1621494114\">https://doi.org/10.1073/pnas.1621494114</a>.","apa":"Wirnsberger, P., Fijan, D., Lightwood, R. A., Šarić, A., Dellago, C., &#38; Frenkel, D. (2017). Numerical evidence for thermally induced monopoles. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1621494114\">https://doi.org/10.1073/pnas.1621494114</a>"},"article_processing_charge":"No","publication_status":"published","day":"24","date_published":"2017-04-24T00:00:00Z","_id":"10373","keyword":["multidisciplinary"],"scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"issue":"19","doi":"10.1073/pnas.1621494114","acknowledgement":"P.W. acknowledges many invaluable discussions with Martin Neumann, Chao Zhang, Michiel Sprik, Aleks Reinhardt, Carl Pölking, and Tine Curk. We acknowledge financial support from the Austrian Academy of Sciences through a doctoral (DOC) fellowship (to P.W.), the Austrian Science Fund (FWF) within the Spezialforschungsbereich Vienna Computational Materials Laboratory (Project F41) (C.D.), and the European Union Early Training Network NANOTRANS (Grant 674979 to D. Frenkel). The results presented here have been achieved in part using the Vienna Scientific Cluster.","abstract":[{"lang":"eng","text":"Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis."}],"pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Numerical evidence for thermally induced monopoles","external_id":{"arxiv":["1610.06840"],"pmid":["28439003"]},"year":"2017","extern":"1","month":"04","type":"journal_article"},{"date_published":"2017-08-31T00:00:00Z","volume":8,"ddc":["540"],"day":"31","publication_status":"published","citation":{"mla":"Meisl, Georg, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” <i>Chemical Science</i>, vol. 8, no. 10, Royal Society of Chemistry, 2017, pp. 7087–97, doi:<a href=\"https://doi.org/10.1039/c7sc01965c\">10.1039/c7sc01965c</a>.","ista":"Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK, Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. 2017. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chemical Science. 8(10), 7087–7097.","ama":"Meisl G, Rajah L, Cohen SAI, et al. Scaling behaviour and rate-determining steps in filamentous self-assembly. <i>Chemical Science</i>. 2017;8(10):7087-7097. doi:<a href=\"https://doi.org/10.1039/c7sc01965c\">10.1039/c7sc01965c</a>","short":"G. Meisl, L. Rajah, S.A.I. Cohen, M. Pfammatter, A. Šarić, E. Hellstrand, A.K. Buell, A. Aguzzi, S. Linse, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Chemical Science 8 (2017) 7087–7097.","chicago":"Meisl, Georg, Luke Rajah, Samuel A. I. Cohen, Manuela Pfammatter, Anđela Šarić, Erik Hellstrand, Alexander K. Buell, et al. “Scaling Behaviour and Rate-Determining Steps in Filamentous Self-Assembly.” <i>Chemical Science</i>. Royal Society of Chemistry, 2017. <a href=\"https://doi.org/10.1039/c7sc01965c\">https://doi.org/10.1039/c7sc01965c</a>.","ieee":"G. Meisl <i>et al.</i>, “Scaling behaviour and rate-determining steps in filamentous self-assembly,” <i>Chemical Science</i>, vol. 8, no. 10. Royal Society of Chemistry, pp. 7087–7097, 2017.","apa":"Meisl, G., Rajah, L., Cohen, S. A. I., Pfammatter, M., Šarić, A., Hellstrand, E., … Knowles, T. P. J. (2017). Scaling behaviour and rate-determining steps in filamentous self-assembly. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c7sc01965c\">https://doi.org/10.1039/c7sc01965c</a>"},"article_processing_charge":"No","oa":1,"author":[{"first_name":"Georg","full_name":"Meisl, Georg","last_name":"Meisl"},{"full_name":"Rajah, Luke","first_name":"Luke","last_name":"Rajah"},{"last_name":"Cohen","full_name":"Cohen, Samuel A. I.","first_name":"Samuel A. I."},{"first_name":"Manuela","full_name":"Pfammatter, Manuela","last_name":"Pfammatter"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"full_name":"Hellstrand, Erik","first_name":"Erik","last_name":"Hellstrand"},{"first_name":"Alexander K.","full_name":"Buell, Alexander K.","last_name":"Buell"},{"full_name":"Aguzzi, Adriano","first_name":"Adriano","last_name":"Aguzzi"},{"first_name":"Sara","full_name":"Linse, Sara","last_name":"Linse"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"full_name":"Dobson, Christopher M.","first_name":"Christopher M.","last_name":"Dobson"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"}],"status":"public","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlelanding/2017/SC/C7SC01965C"}],"intvolume":"         8","date_updated":"2021-11-29T10:00:00Z","article_type":"original","page":"7087-7097","oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"Chemical Science","date_created":"2021-11-29T09:29:31Z","publisher":"Royal Society of Chemistry","pmid":1,"abstract":[{"lang":"eng","text":"The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins. Here we show that this range of behaviour can be quantitatively captured by a single unifying Petri net that describes filamentous growth in terms of aggregate number and aggregate mass concentrations. By considering general features associated with a particular network connectivity, we are able to establish directly the rate-determining steps of the overall aggregation reaction from the system's scaling behaviour. We illustrate the power of this framework on a range of different experimental and simulated aggregating systems. The approach is general and will be applicable to any future extensions of the reaction network of filamentous self-assembly."}],"title":"Scaling behaviour and rate-determining steps in filamentous self-assembly","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"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 grant PhysProt (agreement no. 337969) (SL, TPJK), Sidney Sussex College Cambridge (GM), the Frances and Augusta Newman Foundation (TPJK), the Biotechnology and Biological Science Research Council (TPJK), the Swedish Research Council (SL), the Academy of Medical Sciences (AŠ), Wellcome Trust (AŠ), and the Cambridge Centre for Misfolding Diseases (CMD, TPJK, MV).","license":"https://creativecommons.org/licenses/by-nc/3.0/","type":"journal_article","month":"08","tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"extern":"1","year":"2017","external_id":{"pmid":["29147538"]},"keyword":["general chemistry"],"_id":"10374","scopus_import":"1","issue":"10","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"doi":"10.1039/c7sc01965c"},{"date_updated":"2021-11-29T10:33:36Z","quality_controlled":"1","intvolume":"        13","main_file_link":[{"open_access":"1","url":"https://pubs.rsc.org/en/content/articlelanding/2017/SM/C7SM00433H"}],"status":"public","author":[{"last_name":"Vahid","first_name":"Afshin","full_name":"Vahid, Afshin"},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"last_name":"Idema","first_name":"Timon","full_name":"Idema, Timon"}],"oa":1,"date_created":"2021-11-29T10:00:39Z","publisher":"Royal Society of Chemistry","publication":"Soft Matter","language":[{"iso":"eng"}],"oa_version":"Published Version","arxiv":1,"page":"4924-4930","article_type":"original","article_processing_charge":"No","citation":{"short":"A. Vahid, A. Šarić, T. Idema, Soft Matter 13 (2017) 4924–4930.","ista":"Vahid A, Šarić A, Idema T. 2017. Curvature variation controls particle aggregation on fluid vesicles. Soft Matter. 13(28), 4924–4930.","ama":"Vahid A, Šarić A, Idema T. Curvature variation controls particle aggregation on fluid vesicles. <i>Soft Matter</i>. 2017;13(28):4924-4930. doi:<a href=\"https://doi.org/10.1039/c7sm00433h\">10.1039/c7sm00433h</a>","mla":"Vahid, Afshin, et al. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” <i>Soft Matter</i>, vol. 13, no. 28, Royal Society of Chemistry, 2017, pp. 4924–30, doi:<a href=\"https://doi.org/10.1039/c7sm00433h\">10.1039/c7sm00433h</a>.","chicago":"Vahid, Afshin, Anđela Šarić, and Timon Idema. “Curvature Variation Controls Particle Aggregation on Fluid Vesicles.” <i>Soft Matter</i>. Royal Society of Chemistry, 2017. <a href=\"https://doi.org/10.1039/c7sm00433h\">https://doi.org/10.1039/c7sm00433h</a>.","ieee":"A. Vahid, A. Šarić, and T. Idema, “Curvature variation controls particle aggregation on fluid vesicles,” <i>Soft Matter</i>, vol. 13, no. 28. Royal Society of Chemistry, pp. 4924–4930, 2017.","apa":"Vahid, A., Šarić, A., &#38; Idema, T. (2017). Curvature variation controls particle aggregation on fluid vesicles. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c7sm00433h\">https://doi.org/10.1039/c7sm00433h</a>"},"publication_status":"published","day":"15","volume":13,"date_published":"2017-06-15T00:00:00Z","_id":"10375","keyword":["condensed matter physics","general chemistry"],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"issue":"28","doi":"10.1039/c7sm00433h","scopus_import":"1","license":"https://creativecommons.org/licenses/by/3.0/","acknowledgement":"This work was supported by the Netherlands Organisation for Scientific Research (NWO/OCW), as part of the Frontiers of Nanoscience program.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Curvature variation controls particle aggregation on fluid vesicles","abstract":[{"lang":"eng","text":"Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins influence the membrane shape, the membrane shape affects the interactions between the proteins. To study these membrane-mediated interactions on closed and anisotropically curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as a model system. We find that two particles on a closed system always attract each other, and tend to align with the direction of largest curvature. Multiple particles form arcs, or, at large enough numbers, a complete ring surrounding the vesicle in its equatorial plane. The resulting vesicle shape resembles a snowman. Our results indicate that these physical interactions on membranes with anisotropic shapes can be exploited by cells to drive macromolecules to preferred regions of cellular or intracellular membranes, and utilized to initiate dynamic processes such as cell division. The same principle could be used to find the midplane of an artificial vesicle, as a first step towards dividing it into two equal parts."}],"pmid":1,"external_id":{"arxiv":["1703.00776"],"pmid":["28677712"]},"year":"2017","extern":"1","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","short":"CC BY (3.0)"},"month":"06","type":"journal_article"},{"file":[{"file_id":"10421","file_name":"2017_ACMProgLang_Chatterjee.pdf","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","date_created":"2021-12-07T08:06:28Z","access_level":"open_access","file_size":460188,"content_type":"application/pdf","success":1,"date_updated":"2021-12-07T08:06:28Z","creator":"cchlebak","relation":"main_file"}],"oa":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Bhavya","full_name":"Choudhary, Bhavya","last_name":"Choudhary"},{"first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"}],"status":"public","intvolume":"         2","quality_controlled":"1","date_updated":"2025-04-15T07:26:20Z","article_type":"original","related_material":{"record":[{"status":"public","id":"5455","relation":"earlier_version"}]},"oa_version":"Published Version","arxiv":1,"publication":"Proceedings of the ACM on Programming Languages","language":[{"iso":"eng"}],"date_created":"2021-12-05T23:01:48Z","publisher":"Association for Computing Machinery","has_accepted_license":"1","project":[{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"}],"date_published":"2017-12-27T00:00:00Z","corr_author":"1","volume":2,"citation":{"short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:<a href=\"https://doi.org/10.1145/3158118\">10.1145/3158118</a>.","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. <i>Proceedings of the ACM on Programming Languages</i>. 2017;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158118\">10.1145/3158118</a>","apa":"Chatterjee, K., Choudhary, B., &#38; Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158118\">https://doi.org/10.1145/3158118</a>","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2017.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2017. <a href=\"https://doi.org/10.1145/3158118\">https://doi.org/10.1145/3158118</a>."},"article_processing_charge":"No","publication_status":"published","day":"27","ddc":["000"],"_id":"10416","department":[{"_id":"KrCh"}],"scopus_import":"1","conference":{"start_date":"2018-01-07","name":"POPL: Programming Languages","end_date":"2018-01-13","location":"Los Angeles, CA, United States"},"doi":"10.1145/3158118","issue":"POPL","publication_identifier":{"eissn":["2475-1421"]},"ec_funded":1,"file_date_updated":"2021-12-07T08:06:28Z","abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Optimal Dyck reachability for data-dependence and Alias analysis","article_number":"30","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","month":"12","type":"journal_article","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"arxiv":["1910.00241"]},"year":"2017"},{"date_published":"2017-12-07T00:00:00Z","corr_author":"1","volume":2,"citation":{"apa":"Mciver, A., Morgan, C., Kaminski, B. L., &#38; Katoen, J. P. (2017). A new proof rule for almost-sure termination. <i>Proceedings of the ACM on Programming Languages</i>. Los Angeles, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3158121\">https://doi.org/10.1145/3158121</a>","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL. Association for Computing Machinery, 2017.","chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2017. <a href=\"https://doi.org/10.1145/3158121\">https://doi.org/10.1145/3158121</a>.","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. <i>Proceedings of the ACM on Programming Languages</i>. 2017;2(POPL). doi:<a href=\"https://doi.org/10.1145/3158121\">10.1145/3158121</a>","mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:<a href=\"https://doi.org/10.1145/3158121\">10.1145/3158121</a>."},"article_processing_charge":"No","day":"07","publication_status":"published","ddc":["000"],"author":[{"last_name":"Mciver","first_name":"Annabelle","full_name":"Mciver, Annabelle"},{"last_name":"Morgan","first_name":"Carroll","full_name":"Morgan, Carroll"},{"first_name":"Benjamin Lucien","full_name":"Kaminski, Benjamin Lucien","last_name":"Kaminski"},{"orcid":"0000-0002-6143-1926","last_name":"Katoen","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P","first_name":"Joost P"}],"oa":1,"status":"public","intvolume":"         2","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3158121"}],"quality_controlled":"1","date_updated":"2026-06-18T08:40:04Z","article_type":"original","oa_version":"Published Version","arxiv":1,"publication":"Proceedings of the ACM on Programming Languages","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","date_created":"2021-12-05T23:01:49Z","abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A new proof rule for almost-sure termination","article_number":"33","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","month":"12","type":"journal_article","external_id":{"arxiv":["1711.03588"]},"year":"2017","_id":"10418","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"scopus_import":"1","conference":{"name":"POPL: Programming Languages","start_date":"2018-01-07","end_date":"2018-01-13","location":"Los Angeles, CA, United States"},"publication_identifier":{"eissn":["2475-1421"]},"doi":"10.1145/3158121","issue":"POPL"},{"oa_version":"Published Version","language":[{"iso":"eng"}],"publication":"Microbial Cell Factories","date_created":"2018-12-11T11:49:56Z","publisher":"BioMed Central","author":[{"first_name":"Vinod","full_name":"Veetil, Vinod","last_name":"Veetil"},{"full_name":"Angermayr, Andreas","first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr","orcid":"0000-0001-8619-2223"},{"first_name":"Klaas","full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf"}],"oa":1,"isi":1,"file":[{"date_created":"2018-12-12T10:16:50Z","access_level":"open_access","file_id":"5240","file_name":"IST-2017-792-v1+1_s12934-017-0645-5.pdf","date_updated":"2018-12-12T10:16:50Z","relation":"main_file","creator":"system","file_size":1361313,"content_type":"application/pdf"}],"status":"public","quality_controlled":"1","intvolume":"        16","date_updated":"2023-09-20T12:09:21Z","date_published":"2017-02-23T00:00:00Z","volume":16,"pubrep_id":"792","ddc":["579"],"publication_status":"published","day":"23","citation":{"short":"V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017).","mla":"Veetil, Vinod, et al. “Ethylene Production with Engineered Synechocystis Sp PCC 6803 Strains.” <i>Microbial Cell Factories</i>, vol. 16, no. 1, 34, BioMed Central, 2017, doi:<a href=\"https://doi.org/10.1186/s12934-017-0645-5\">10.1186/s12934-017-0645-5</a>.","ista":"Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.","ama":"Veetil V, Angermayr A, Hellingwerf K. Ethylene production with engineered Synechocystis sp PCC 6803 strains. <i>Microbial Cell Factories</i>. 2017;16(1). doi:<a href=\"https://doi.org/10.1186/s12934-017-0645-5\">10.1186/s12934-017-0645-5</a>","ieee":"V. Veetil, A. Angermayr, and K. Hellingwerf, “Ethylene production with engineered Synechocystis sp PCC 6803 strains,” <i>Microbial Cell Factories</i>, vol. 16, no. 1. BioMed Central, 2017.","chicago":"Veetil, Vinod, Andreas Angermayr, and Klaas Hellingwerf. “Ethylene Production with Engineered Synechocystis Sp PCC 6803 Strains.” <i>Microbial Cell Factories</i>. BioMed Central, 2017. <a href=\"https://doi.org/10.1186/s12934-017-0645-5\">https://doi.org/10.1186/s12934-017-0645-5</a>.","apa":"Veetil, V., Angermayr, A., &#38; Hellingwerf, K. (2017). Ethylene production with engineered Synechocystis sp PCC 6803 strains. <i>Microbial Cell Factories</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12934-017-0645-5\">https://doi.org/10.1186/s12934-017-0645-5</a>"},"article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","publist_id":"6325","issue":"1","publication_identifier":{"issn":["14752859"]},"doi":"10.1186/s12934-017-0645-5","file_date_updated":"2018-12-12T10:16:50Z","_id":"1061","type":"journal_article","month":"02","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"extern":"1","year":"2017","external_id":{"isi":["000397733000001"],"pmid":["28231787"]},"pmid":1,"abstract":[{"text":"Background: Metabolic engineering and synthetic biology of cyanobacteria offer a promising sustainable alternative approach for fossil-based ethylene production, by using sunlight via oxygenic photosynthesis, to convert carbon dioxide directly into ethylene. Towards this, both well-studied cyanobacteria, i.e., Synechocystis sp PCC 6803 and Synechococcus elongatus PCC 7942, have been engineered to produce ethylene by introducing the ethylene-forming enzyme (Efe) from Pseudomonas syringae pv. phaseolicola PK2 (the Kudzu strain), which catalyzes the conversion of the ubiquitous tricarboxylic acid cycle intermediate 2-oxoglutarate into ethylene. Results: This study focuses on Synechocystis sp PCC 6803 and shows stable ethylene production through the integration of a codon-optimized version of the efe gene under control of the Ptrc promoter and the core Shine-Dalgarno sequence (5\\'-AGGAGG-3\\') as the ribosome-binding site (RBS), at the slr0168 neutral site. We have increased ethylene production twofold by RBS screening and further investigated improving ethylene production from a single gene copy of efe, using multiple tandem promoters and by putting our best construct on an RSF1010-based broad-host-self-replicating plasmid, which has a higher copy number than the genome. Moreover, to raise the intracellular amounts of the key Efe substrate, 2-oxoglutarate, from which ethylene is formed, we constructed a glycogen-synthesis knockout mutant (glgC) and introduced the ethylene biosynthetic pathway in it. Under nitrogen limiting conditions, the glycogen knockout strain has increased intracellular 2-oxoglutarate levels; however, surprisingly, ethylene production was lower in this strain than in the wild-type background. Conclusion: Making use of different RBS sequences, production of ethylene ranging over a 20-fold difference has been achieved. However, a further increase of production through multiple tandem promoters and a broad-host plasmid was not achieved speculating that the transcription strength and the gene copy number are not the limiting factors in our system.","lang":"eng"}],"title":"Ethylene production with engineered Synechocystis sp PCC 6803 strains","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"34"},{"date_updated":"2023-09-20T12:09:47Z","quality_controlled":"1","intvolume":"       595","_id":"1062","status":"public","isi":1,"author":[{"last_name":"Guarina","full_name":"Guarina, Laura","first_name":"Laura"},{"orcid":"0000-0001-7577-1676","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","first_name":"David H"},{"last_name":"Carabelli","first_name":"Valentina","full_name":"Carabelli, Valentina"},{"last_name":"Carbone","full_name":"Carbone, Emilio","first_name":"Emilio"}],"date_created":"2018-12-11T11:49:56Z","publisher":"Wiley-Blackwell","publication":"Journal of Physiology","language":[{"iso":"eng"}],"oa_version":"None","issue":"8","doi":"10.1113/JP273735","page":"2587 - 2609 ","publist_id":"6326","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells","abstract":[{"lang":"eng","text":"Mouse chromaffin cells (MCCs) generate action potential (AP) firing that regulates the Ca2+‐dependent release of catecholamines (CAs). Recent findings indicate that MCCs possess a variety of spontaneous firing modes that span from the common ‘tonic‐irregular’ to the less frequent ‘burst’ firing. This latter is evident in a small fraction of MCCs but occurs regularly when Nav1.3/1.7 channels are made less available or when the Slo1β2‐subunit responsible for BK channel inactivation is deleted. Burst firing causes large increases of Ca2+‐entry and potentiates CA release by ∼3.5‐fold and thus may be a key mechanism for regulating MCC function. With the aim to uncover a physiological role for burst‐firing we investigated the effects of acidosis on MCC activity. Lowering the extracellular pH (pHo) from 7.4 to 7.0 and 6.6 induces cell depolarizations of 10–15 mV that generate repeated bursts. Bursts at pHo 6.6 lasted ∼330 ms, occurred at 1–2 Hz and caused an ∼7‐fold increase of CA cumulative release. Burst firing originates from the inhibition of the pH‐sensitive TASK‐1/TASK‐3 channels and from a 40% BK channel conductance reduction at pHo 7.0. The same pHo had little or no effect on Nav, Cav, Kv and SK channels that support AP firing in MCCs. Burst firing of pHo 6.6 could be mimicked by mixtures of the TASK‐1 blocker A1899 (300 nm) and BK blocker paxilline (300 nm) and could be prevented by blocking L‐type channels by adding 3 μm nifedipine. Mixtures of the two blockers raised cumulative CA‐secretion even more than low pHo (∼12‐fold), showing that the action of protons on vesicle release is mainly a result of the ionic conductance changes that increase Ca2+‐entry during bursts. Our data provide direct evidence suggesting that MCCs respond to low pHo with sustained depolarization, burst firing and enhanced CA‐secretion, thus mimicking the physiological response of CCs to acute acidosis and hyperkalaemia generated during heavy exercise and muscle fatigue."}],"citation":{"short":"L. Guarina, D.H. Vandael, V. Carabelli, E. Carbone, Journal of Physiology 595 (2017) 2587–2609.","ama":"Guarina L, Vandael DH, Carabelli V, Carbone E. Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. <i>Journal of Physiology</i>. 2017;595(8):2587-2609. doi:<a href=\"https://doi.org/10.1113/JP273735\">10.1113/JP273735</a>","ista":"Guarina L, Vandael DH, Carabelli V, Carbone E. 2017. Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. Journal of Physiology. 595(8), 2587–2609.","mla":"Guarina, Laura, et al. “Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>, vol. 595, no. 8, Wiley-Blackwell, 2017, pp. 2587–609, doi:<a href=\"https://doi.org/10.1113/JP273735\">10.1113/JP273735</a>.","ieee":"L. Guarina, D. H. Vandael, V. Carabelli, and E. Carbone, “Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells,” <i>Journal of Physiology</i>, vol. 595, no. 8. Wiley-Blackwell, pp. 2587–2609, 2017.","chicago":"Guarina, Laura, David H Vandael, Valentina Carabelli, and Emilio Carbone. “Low PH Inf o Boosts Burst Firing and Catecholamine Release by Blocking TASK-1 and BK Channels While Preserving Cav1 Channels in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1113/JP273735\">https://doi.org/10.1113/JP273735</a>.","apa":"Guarina, L., Vandael, D. H., Carabelli, V., &#38; Carbone, E. (2017). Low pH inf o boosts burst firing and catecholamine release by blocking TASK-1 and BK channels while preserving Cav1 channels in mouse chromaffin cells. <i>Journal of Physiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1113/JP273735\">https://doi.org/10.1113/JP273735</a>"},"article_processing_charge":"No","external_id":{"isi":["000399430300022"]},"publication_status":"published","day":"15","year":"2017","extern":"1","volume":595,"month":"04","type":"journal_article","date_published":"2017-04-15T00:00:00Z"},{"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"}],"date_published":"2017-06-01T00:00:00Z","volume":122,"citation":{"apa":"Chatterjee, K., &#38; Osang, G. F. (2017). Pushdown reachability with constant treewidth. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">https://doi.org/10.1016/j.ipl.2017.02.003</a>","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” <i>Information Processing Letters</i>, vol. 122. Elsevier, pp. 25–29, 2017.","chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” <i>Information Processing Letters</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">https://doi.org/10.1016/j.ipl.2017.02.003</a>.","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29.","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. <i>Information Processing Letters</i>. 2017;122:25-29. doi:<a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">10.1016/j.ipl.2017.02.003</a>","mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” <i>Information Processing Letters</i>, vol. 122, Elsevier, 2017, pp. 25–29, doi:<a href=\"https://doi.org/10.1016/j.ipl.2017.02.003\">10.1016/j.ipl.2017.02.003</a>.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29."},"article_processing_charge":"No","publication_status":"published","ddc":["000"],"day":"01","pubrep_id":"991","has_accepted_license":"1","oa_version":"Submitted Version","page":"25 - 29","publication":"Information Processing Letters","language":[{"iso":"eng"}],"publisher":"Elsevier","date_created":"2018-12-11T11:49:57Z","isi":1,"file":[{"file_id":"4998","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","date_created":"2018-12-12T10:13:17Z","access_level":"open_access","content_type":"application/pdf","file_size":247657,"date_updated":"2019-10-15T07:44:51Z","relation":"main_file","creator":"system"}],"oa":1,"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Osang","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","full_name":"Osang, Georg F"}],"status":"public","intvolume":"       122","quality_controlled":"1","date_updated":"2025-07-10T11:49:53Z","month":"06","type":"journal_article","external_id":{"isi":["000399506600005"]},"year":"2017","abstract":[{"lang":"eng","text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Pushdown reachability with constant treewidth","scopus_import":"1","publist_id":"6323","publication_identifier":{"issn":["0020-0190"]},"doi":"10.1016/j.ipl.2017.02.003","ec_funded":1,"file_date_updated":"2019-10-15T07:44:51Z","_id":"1065","department":[{"_id":"KrCh"},{"_id":"HeEd"}]},{"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreements 267989 (QUAREM), 279307 (Graph Games), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), S11407-N23 (RiSE), P23499-N23, and Microsoft faculty fellows award.","abstract":[{"text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms.","lang":"eng"}],"title":"Quantitative fair simulation games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","external_id":{"isi":["000402025600002"]},"type":"journal_article","month":"06","_id":"1066","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ec_funded":1,"publist_id":"6322","scopus_import":"1","doi":"10.1016/j.ic.2016.10.006","issue":"2","OA_type":"free access","volume":254,"publication_status":"published","day":"01","ddc":["000"],"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” <i>Information and Computation</i>, vol. 254, no. 2. Elsevier, pp. 143–166, 2017.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2017). Quantitative fair simulation games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. <i>Information and Computation</i>. 2017;254(2):143-166. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>."},"article_processing_charge":"No","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_published":"2017-06-01T00:00:00Z","corr_author":"1","intvolume":"       254","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ic.2016.10.006"}],"quality_controlled":"1","OA_place":"publisher","date_updated":"2026-06-18T08:47:01Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"oa":1,"isi":1,"status":"public","language":[{"iso":"eng"}],"publication":"Information and Computation","publisher":"Elsevier","date_created":"2018-12-11T11:49:58Z","article_type":"original","page":"143 - 166","related_material":{"record":[{"id":"5428","status":"public","relation":"earlier_version"}]},"oa_version":"Published Version"},{"abstract":[{"text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures.","lang":"eng"}],"title":"Magnetic force microscopy studies of mesoscopic superconducting structures","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"dissertation","date_published":"2017-09-18T00:00:00Z","month":"09","alternative_title":["Graduate Dissertations and Theses at Illinois"],"degree_awarded":"PhD","day":"18","year":"2017","publication_status":"published","extern":"1","citation":{"mla":"Polshyn, Hryhoriy. <i>Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures</i>. University of Illinois at Urbana-Champaign, 2017.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","ama":"Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017.","short":"H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017.","ieee":"H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017.","chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017.","apa":"Polshyn, H. (2017). <i>Magnetic force microscopy studies of mesoscopic superconducting structures</i>. University of Illinois at Urbana-Champaign."},"article_processing_charge":"No","oa":1,"author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn"}],"keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"status":"public","_id":"10663","main_file_link":[{"url":"http://hdl.handle.net/2142/99178","open_access":"1"}],"date_updated":"2024-10-14T11:13:43Z","page":"103","oa_version":"Published Version","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"}],"date_created":"2022-01-25T14:54:14Z","publisher":"University of Illinois at Urbana-Champaign"},{"ec_funded":1,"file_date_updated":"2018-12-12T10:10:57Z","doi":"10.1016/j.devcel.2017.01.010","issue":"4","publication_identifier":{"issn":["1534-5807"]},"publist_id":"6320","scopus_import":"1","department":[{"_id":"CaHe"}],"_id":"1067","acknowledged_ssus":[{"_id":"PreCl"}],"external_id":{"isi":["000395368300007"]},"year":"2017","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"month":"02","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","abstract":[{"lang":"eng","text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction."}],"publisher":"Cell Press","date_created":"2018-12-11T11:49:58Z","publication":"Developmental Cell","language":[{"iso":"eng"}],"oa_version":"Published Version","page":"354 - 366","date_updated":"2025-07-10T11:49:55Z","intvolume":"        40","quality_controlled":"1","status":"public","file":[{"date_created":"2018-12-12T10:10:57Z","access_level":"open_access","file_id":"4849","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","date_updated":"2018-12-12T10:10:57Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":6866187}],"isi":1,"oa":1,"author":[{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","first_name":"Hitoshi","last_name":"Morita"},{"last_name":"Grigolon","full_name":"Grigolon, Silvia","first_name":"Silvia"},{"last_name":"Bock","first_name":"Martin","full_name":"Bock, Martin"},{"first_name":"Gabriel","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","orcid":"0000-0003-4761-5996"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","citation":{"chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>.","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” <i>Developmental Cell</i>, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., &#38; Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. 2017;40(4):354-366. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>."},"publication_status":"published","day":"27","pubrep_id":"869","ddc":["572","597"],"volume":40,"corr_author":"1","date_published":"2017-02-27T00:00:00Z","project":[{"_id":"2524F500-B435-11E9-9278-68D0E5697425","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","call_identifier":"FP7","grant_number":"201439"}],"has_accepted_license":"1"},{"year":"2017","external_id":{"arxiv":["1312.1231"],"isi":["000398030400024"]},"type":"journal_article","month":"05","acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”.","abstract":[{"text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field.","lang":"eng"}],"title":"The Morse theory of Čech and delaunay complexes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"scopus_import":"1","publist_id":"6311","issue":"5","doi":"10.1090/tran/6991","_id":"1072","department":[{"_id":"HeEd"}],"volume":369,"day":"01","publication_status":"published","article_processing_charge":"No","citation":{"chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>.","apa":"Bauer, U., &#38; Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. 2017;369(5):3741-3762. doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>."},"date_published":"2017-05-01T00:00:00Z","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493"}],"language":[{"iso":"eng"}],"publication":"Transactions of the American Mathematical Society","date_created":"2018-12-11T11:49:59Z","publisher":"American Mathematical Society","article_type":"original","arxiv":1,"page":"3741 - 3762","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"quality_controlled":"1","intvolume":"       369","date_updated":"2025-04-15T08:37:54Z","author":[{"last_name":"Bauer","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","full_name":"Bauer, Ulrich"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"}],"oa":1,"isi":1,"status":"public"},{"oa_version":"Submitted Version","arxiv":1,"page":"915 - 965","date_created":"2018-12-11T11:50:00Z","publisher":"Springer","publication":"Discrete & Computational Geometry","language":[{"iso":"eng"}],"status":"public","isi":1,"author":[{"last_name":"Čadek","full_name":"Čadek, Martin","first_name":"Martin"},{"last_name":"Krcál","full_name":"Krcál, Marek","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukáš","full_name":"Vokřínek, Lukáš","last_name":"Vokřínek"}],"oa":1,"date_updated":"2025-06-04T08:11:10Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1307.6444"}],"quality_controlled":"1","intvolume":"        54","date_published":"2017-06-01T00:00:00Z","citation":{"apa":"Čadek, M., Krcál, M., &#38; Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4. Springer, pp. 915–965, 2017.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>.","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. 2017;54(4):915-965. doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965."},"article_processing_charge":"No","publication_status":"published","day":"01","volume":54,"publication_identifier":{"issn":["01795376"]},"issue":"4","doi":"10.1007/s00454-016-9855-6","publist_id":"6309","scopus_import":"1","department":[{"_id":"UlWa"}],"_id":"1073","month":"06","type":"journal_article","external_id":{"isi":["000400072700008"],"arxiv":["1307.6444"]},"year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Algorithmic solvability of the lifting extension problem","abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}]},{"abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","month":"03","type":"journal_article","external_id":{"isi":["000395807200023"]},"year":"2017","_id":"1074","department":[{"_id":"NiBa"}],"scopus_import":"1","publist_id":"6307","issue":"3","publication_identifier":{"issn":["0016-6731"]},"doi":"10.1534/genetics.116.196220","ec_funded":1,"project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"date_published":"2017-03-01T00:00:00Z","volume":205,"article_processing_charge":"No","citation":{"chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>.","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” <i>Genetics</i>, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","apa":"Ringbauer, H., Coop, G., &#38; Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. 2017;205(3):1335-1351. doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>","ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351."},"publication_status":"published","day":"01","isi":1,"oa":1,"author":[{"first_name":"Harald","full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","orcid":"0000-0002-4884-9682"},{"first_name":"Graham","full_name":"Coop, Graham","last_name":"Coop"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"status":"public","intvolume":"       205","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"date_updated":"2026-04-08T14:06:35Z","related_material":{"record":[{"relation":"dissertation_contains","id":"200","status":"public"}]},"oa_version":"Preprint","page":"1335 - 1351","publication":"Genetics","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:00Z","publisher":"Genetics Society of America"},{"date_published":"2017-03-01T00:00:00Z","volume":62,"citation":{"apa":"Polshyn, H., Naibert, T., &#38; Budakian, R. (2017).  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In <i>APS March Meeting 2017</i> (Vol. 62). New Orleans, LA, United States: American Physical Society.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in <i>APS March Meeting 2017</i>, New Orleans, LA, United States, 2017, vol. 62, no. 4.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In <i>APS March Meeting 2017</i>, Vol. 62. American Physical Society, 2017.","short":"H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017.","mla":"Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” <i>APS March Meeting 2017</i>, vol. 62, no. 4, P39.00011, American Physical Society, 2017.","ista":"Polshyn H, Naibert T, Budakian R. 2017.  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. APS March Meeting 2017. APS: American Physical Society, Bulletin of the American Physical Society, vol. 62, P39.00011.","ama":"Polshyn H, Naibert T, Budakian R.  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In: <i>APS March Meeting 2017</i>. Vol 62. American Physical Society; 2017."},"article_processing_charge":"No","publication_status":"published","day":"01","oa_version":"Published Version","publication":"APS March Meeting 2017","language":[{"iso":"eng"}],"publisher":"American Physical Society","date_created":"2022-02-08T09:49:17Z","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn"},{"last_name":"Naibert","full_name":"Naibert, Tyler","first_name":"Tyler"},{"last_name":"Budakian","full_name":"Budakian, Raffi","first_name":"Raffi"}],"oa":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11"}],"quality_controlled":"1","intvolume":"        62","date_updated":"2022-02-08T10:44:35Z","month":"03","type":"conference","alternative_title":["Bulletin of the American Physical Society"],"year":"2017","extern":"1","abstract":[{"text":"New ways to investigate and manipulate fluxoid and vortex states of mesoscopic superconducting structures are of great interest. The states with multiple vortices or winding numbers could be useful for the study of vortex interactions and interference effects, the braiding of Majorana bound states by winding vortices, and the development of novel superconducting devices. We demonstrate a methodology based on magnetic force microscopy that allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. By using micro-magnet as a source of inhomogeneous magnetic field, we can efficiently explore the configuration space of fluxoid states. Scanning over the structure reveals the energy crossing points of the lowest laying fluxoid states. This is due the strong interaction of cantilever with thermally activated fluxoid transitions at points of degeneracy. We show that measured patterns of fluxoid transitions allow to identify the states, investigate their energetics, and manipulate them. Further, we show that the dynamics of driven fluxoid transitions can be described by stochastic resonance model, which provides a unique way of measuring fluxoid transition rate and related energy barrier for chosen transitions even in complicated structures","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","article_number":"P39.00011","conference":{"location":"New Orleans, LA, United States","end_date":"2017-03-17","start_date":"2017-03-13","name":"APS: American Physical Society"},"publication_identifier":{"issn":["0003-0503"]},"issue":"4","_id":"10745"}]