[{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1707.02922","open_access":"1"}],"date_published":"2017-07-13T00:00:00Z","publication_status":"published","arxiv":1,"date_created":"2024-03-26T10:41:24Z","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"intvolume":"       471","author":[{"first_name":"C.","last_name":"Elenbaas","full_name":"Elenbaas, C."},{"full_name":"Huppenkothen, D.","first_name":"D.","last_name":"Huppenkothen"},{"first_name":"C.","last_name":"Omand","full_name":"Omand, C."},{"first_name":"A. L.","last_name":"Watts","full_name":"Watts, A. L."},{"last_name":"Bissaldi","first_name":"E.","full_name":"Bissaldi, E."},{"first_name":"Ilaria","last_name":"Caiazzo","orcid":"0000-0002-4770-5388","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","full_name":"Caiazzo, Ilaria"},{"last_name":"Heyl","first_name":"J.","full_name":"Heyl, J."}],"year":"2017","month":"07","status":"public","scopus_import":"1","quality_controlled":"1","title":"Magnetar giant flare high-energy emission","external_id":{"arxiv":["1707.02922"]},"doi":"10.1093/mnras/stx1727","oa_version":"Preprint","publication":"Monthly Notices of the Royal Astronomical Society","article_processing_charge":"No","page":"1856-1872","day":"13","publisher":"Oxford University Press","extern":"1","article_type":"original","_id":"15243","issue":"2","citation":{"ista":"Elenbaas C, Huppenkothen D, Omand C, Watts AL, Bissaldi E, Caiazzo I, Heyl J. 2017. Magnetar giant flare high-energy emission. Monthly Notices of the Royal Astronomical Society. 471(2), 1856–1872.","apa":"Elenbaas, C., Huppenkothen, D., Omand, C., Watts, A. L., Bissaldi, E., Caiazzo, I., &#38; Heyl, J. (2017). Magnetar giant flare high-energy emission. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stx1727\">https://doi.org/10.1093/mnras/stx1727</a>","ieee":"C. Elenbaas <i>et al.</i>, “Magnetar giant flare high-energy emission,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 471, no. 2. Oxford University Press, pp. 1856–1872, 2017.","chicago":"Elenbaas, C., D. Huppenkothen, C. Omand, A. L. Watts, E. Bissaldi, Ilaria Caiazzo, and J. Heyl. “Magnetar Giant Flare High-Energy Emission.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/mnras/stx1727\">https://doi.org/10.1093/mnras/stx1727</a>.","short":"C. Elenbaas, D. Huppenkothen, C. Omand, A.L. Watts, E. Bissaldi, I. Caiazzo, J. Heyl, Monthly Notices of the Royal Astronomical Society 471 (2017) 1856–1872.","ama":"Elenbaas C, Huppenkothen D, Omand C, et al. Magnetar giant flare high-energy emission. <i>Monthly Notices of the Royal Astronomical Society</i>. 2017;471(2):1856-1872. doi:<a href=\"https://doi.org/10.1093/mnras/stx1727\">10.1093/mnras/stx1727</a>","mla":"Elenbaas, C., et al. “Magnetar Giant Flare High-Energy Emission.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 471, no. 2, Oxford University Press, 2017, pp. 1856–72, doi:<a href=\"https://doi.org/10.1093/mnras/stx1727\">10.1093/mnras/stx1727</a>."},"date_updated":"2024-04-08T07:05:47Z","language":[{"iso":"eng"}],"abstract":[{"text":"High-energy (>250 keV) emission has been detected persisting for several tens of seconds after the initial spike of magnetar giant flares (GFs). It has been conjectured that this emission might arise via inverse Compton scattering in a highly extended corona generated by super-Eddington outflows high up in the magnetosphere. In this paper, we undertake a detailed examination of this model. We investigate the properties of the required scatterers, and whether the mechanism is consistent with the degree of pulsed emission observed in the tail of the GF. We conclude that the mechanism is consistent with current data, although the origin of the scattering population remains an open question. We propose an alternative picture in which the emission is closer to that star and is dominated by synchrotron radiation. The Reuven Ramaty High Energy Solar Spectroscopic Imager observations of the 2004 December flare modestly favour this latter picture. We assess the prospects for the Fermi Gamma-ray Space Telescope to detect and characterize a similar high-energy component in a future GF. Such a detection should help to resolve some of the outstanding issues.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":471,"type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics"]},{"quality_controlled":"1","title":"Ethylene production with engineered Synechocystis sp PCC 6803 strains","scopus_import":"1","ddc":["579"],"external_id":{"isi":["000397733000001"],"pmid":["28231787"]},"doi":"10.1186/s12934-017-0645-5","file_date_updated":"2018-12-12T10:16:50Z","oa_version":"Published Version","file":[{"relation":"main_file","content_type":"application/pdf","file_id":"5240","creator":"system","file_size":1361313,"file_name":"IST-2017-792-v1+1_s12934-017-0645-5.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:50Z","date_updated":"2018-12-12T10:16:50Z"}],"pmid":1,"publication":"Microbial Cell Factories","article_processing_charge":"No","date_published":"2017-02-23T00:00:00Z","pubrep_id":"792","publication_status":"published","intvolume":"        16","publist_id":"6325","publication_identifier":{"issn":["14752859"]},"author":[{"first_name":"Vinod","last_name":"Veetil","full_name":"Veetil, Vinod"},{"last_name":"Angermayr","first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","full_name":"Angermayr, Andreas","orcid":"0000-0001-8619-2223"},{"full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf","first_name":"Klaas"}],"isi":1,"date_created":"2018-12-11T11:49:56Z","month":"02","status":"public","year":"2017","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"34","issue":"1","citation":{"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>","ista":"Veetil V, Angermayr A, Hellingwerf K. 2017. Ethylene production with engineered Synechocystis sp PCC 6803 strains. Microbial Cell Factories. 16(1), 34.","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>.","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>","short":"V. Veetil, A. Angermayr, K. Hellingwerf, Microbial Cell Factories 16 (2017)."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"date_updated":"2023-09-20T12:09:21Z","volume":16,"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"extern":"1","publisher":"BioMed Central","day":"23","_id":"1061"},{"issue":"8","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","quality_controlled":"1","oa_version":"None","external_id":{"isi":["000399430300022"]},"doi":"10.1113/JP273735","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>","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>.","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.","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>","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>."},"date_updated":"2023-09-20T12:09:47Z","publication":"Journal of Physiology","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."}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","volume":595,"type":"journal_article","date_published":"2017-04-15T00:00:00Z","publication_status":"published","page":"2587 - 2609 ","isi":1,"date_created":"2018-12-11T11:49:56Z","publisher":"Wiley-Blackwell","day":"15","extern":"1","author":[{"full_name":"Guarina, Laura","last_name":"Guarina","first_name":"Laura"},{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H"},{"full_name":"Carabelli, Valentina","last_name":"Carabelli","first_name":"Valentina"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"}],"intvolume":"       595","publist_id":"6326","year":"2017","status":"public","month":"04","_id":"1062"},{"publication_status":"published","department":[{"_id":"NiBa"}],"date_published":"2017-04-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://biorxiv.org/content/early/2016/10/14/081042"}],"ec_funded":1,"year":"2017","month":"04","status":"public","date_created":"2018-12-11T11:49:57Z","isi":1,"publication_identifier":{"issn":["0014-3820"]},"intvolume":"        71","publist_id":"6327","author":[{"last_name":"Uecker","first_name":"Hildegard","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813"}],"external_id":{"isi":["000398545200003"]},"oa_version":"Submitted Version","doi":"10.1111/evo.13191","scopus_import":"1","quality_controlled":"1","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","article_processing_charge":"No","publication":"Evolution","page":"845 - 858","_id":"1063","publisher":"Wiley-Blackwell","day":"01","citation":{"ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” <i>Evolution</i>, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>.","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/evo.13191\">https://doi.org/10.1111/evo.13191</a>","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. <i>Evolution</i>. 2017;71(4):845-858. doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>","short":"H. Uecker, Evolution 71 (2017) 845–858.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” <i>Evolution</i>, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:<a href=\"https://doi.org/10.1111/evo.13191\">10.1111/evo.13191</a>."},"issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"oa":1,"type":"journal_article","volume":71,"date_updated":"2025-07-10T11:49:52Z","language":[{"iso":"eng"}],"abstract":[{"text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.","lang":"eng"}]},{"date_published":"2017-06-01T00:00:00Z","ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"pubrep_id":"991","date_created":"2018-12-11T11:49:57Z","isi":1,"publication_identifier":{"issn":["0020-0190"]},"publist_id":"6323","intvolume":"       122","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F"}],"year":"2017","month":"06","status":"public","scopus_import":"1","quality_controlled":"1","title":"Pushdown reachability with constant treewidth","file":[{"relation":"main_file","access_level":"open_access","file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","date_created":"2018-12-12T10:13:17Z","date_updated":"2019-10-15T07:44:51Z","file_id":"4998","creator":"system","content_type":"application/pdf","file_size":247657}],"ddc":["000"],"doi":"10.1016/j.ipl.2017.02.003","oa_version":"Submitted Version","file_date_updated":"2019-10-15T07:44:51Z","external_id":{"isi":["000399506600005"]},"publication":"Information Processing Letters","article_processing_charge":"No","page":"25 - 29","publisher":"Elsevier","day":"01","_id":"1065","has_accepted_license":"1","citation":{"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>.","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>","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","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>.","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>","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29."},"date_updated":"2025-07-10T11:49:53Z","language":[{"iso":"eng"}],"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."}],"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":122,"type":"journal_article"},{"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.","publication":"Information and Computation","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","title":"Quantitative fair simulation games","OA_place":"publisher","external_id":{"isi":["000402025600002"]},"oa_version":"Published Version","doi":"10.1016/j.ic.2016.10.006","date_created":"2018-12-11T11:49:58Z","isi":1,"intvolume":"       254","publist_id":"6322","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"year":"2017","month":"06","status":"public","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ic.2016.10.006"}],"date_published":"2017-06-01T00:00:00Z","ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2025-06-25T11:18:09Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"volume":254,"type":"journal_article","issue":"2","citation":{"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>.","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>","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>","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.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166."},"day":"01","publisher":"Elsevier","related_material":{"record":[{"id":"5428","status":"public","relation":"earlier_version"}]},"_id":"1066","article_type":"original","OA_type":"free access","page":"143 - 166"},{"date_published":"2017-09-18T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/2142/99178"}],"publication_status":"published","page":"103","degree_awarded":"PhD","date_created":"2022-01-25T14:54:14Z","day":"18","publisher":"University of Illinois at Urbana-Champaign","extern":"1","author":[{"last_name":"Polshyn","first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"}],"supervisor":[{"full_name":"Budakian, Raffi","last_name":"Budakian","first_name":"Raffi"}],"year":"2017","status":"public","_id":"10663","month":"09","alternative_title":["Graduate Dissertations and Theses at Illinois"],"title":"Magnetic force microscopy studies of mesoscopic superconducting structures","oa_version":"Published Version","citation":{"chicago":"Polshyn, Hryhoriy. “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.","apa":"Polshyn, H. (2017). <i>Magnetic force microscopy studies of mesoscopic superconducting structures</i>. University of Illinois at Urbana-Champaign.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","mla":"Polshyn, Hryhoriy. <i>Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures</i>. University of Illinois at Urbana-Champaign, 2017.","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."},"date_updated":"2024-10-14T11:13:43Z","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"type":"dissertation","article_processing_charge":"No"},{"publication":"Developmental Cell","article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","acknowledged_ssus":[{"_id":"PreCl"}],"title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","file":[{"relation":"main_file","date_created":"2018-12-12T10:10:57Z","date_updated":"2018-12-12T10:10:57Z","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","access_level":"open_access","file_size":6866187,"file_id":"4849","content_type":"application/pdf","creator":"system"}],"ddc":["572","597"],"oa_version":"Published Version","external_id":{"isi":["000395368300007"]},"file_date_updated":"2018-12-12T10:10:57Z","doi":"10.1016/j.devcel.2017.01.010","isi":1,"date_created":"2018-12-11T11:49:58Z","publist_id":"6320","intvolume":"        40","publication_identifier":{"issn":["1534-5807"]},"author":[{"first_name":"Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"full_name":"Bock, Martin","first_name":"Martin","last_name":"Bock"},{"last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"year":"2017","month":"02","status":"public","corr_author":"1","date_published":"2017-02-27T00:00:00Z","ec_funded":1,"publication_status":"published","department":[{"_id":"CaHe"}],"pubrep_id":"869","date_updated":"2025-07-10T11:49:55Z","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"project":[{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","grant_number":"201439","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":40,"type":"journal_article","issue":"4","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","citation":{"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.","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.","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>.","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>","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>","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 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>."},"day":"27","publisher":"Cell Press","_id":"1067","page":"354 - 366"},{"issue":"5","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>.","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.","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>","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>.","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>","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762."},"date_updated":"2025-04-15T08:37:54Z","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":369,"type":"journal_article","page":"3741 - 3762","day":"01","publisher":"American Mathematical Society","article_type":"original","_id":"1072","scopus_import":"1","title":"The Morse theory of Čech and delaunay complexes","quality_controlled":"1","doi":"10.1090/tran/6991","oa_version":"Preprint","external_id":{"arxiv":["1312.1231"],"isi":["000398030400024"]},"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”.","publication":"Transactions of the American Mathematical Society","article_processing_charge":"No","ec_funded":1,"date_published":"2017-05-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.1231"}],"publication_status":"published","department":[{"_id":"HeEd"}],"isi":1,"date_created":"2018-12-11T11:49:59Z","arxiv":1,"author":[{"first_name":"Ulrich","last_name":"Bauer","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       369","publist_id":"6311","year":"2017","status":"public","month":"05"},{"article_processing_charge":"No","publication":"Discrete & Computational Geometry","doi":"10.1007/s00454-016-9855-6","oa_version":"Submitted Version","external_id":{"isi":["000400072700008"],"arxiv":["1307.6444"]},"quality_controlled":"1","title":"Algorithmic solvability of the lifting extension problem","scopus_import":"1","month":"06","status":"public","year":"2017","intvolume":"        54","publication_identifier":{"issn":["01795376"]},"publist_id":"6309","author":[{"last_name":"Čadek","first_name":"Martin","full_name":"Čadek, Martin"},{"full_name":"Krcál, Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","first_name":"Marek"},{"full_name":"Vokřínek, Lukáš","first_name":"Lukáš","last_name":"Vokřínek"}],"arxiv":1,"isi":1,"date_created":"2018-12-11T11:50:00Z","department":[{"_id":"UlWa"}],"publication_status":"published","date_published":"2017-06-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1307.6444"}],"volume":54,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"date_updated":"2025-06-04T08:11:10Z","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>.","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","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>.","short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","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>"},"issue":"4","_id":"1073","day":"01","publisher":"Springer","page":"915 - 965"},{"main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11"}],"date_published":"2017-03-01T00:00:00Z","publication_status":"published","publication_identifier":{"issn":["0003-0503"]},"intvolume":"        62","author":[{"full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","last_name":"Polshyn","first_name":"Hryhoriy"},{"first_name":"Tyler","last_name":"Naibert","full_name":"Naibert, Tyler"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"date_created":"2022-02-08T09:49:17Z","month":"03","status":"public","year":"2017","quality_controlled":"1","title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","alternative_title":["Bulletin of the American Physical Society"],"oa_version":"Published Version","publication":"APS March Meeting 2017","article_processing_charge":"No","extern":"1","day":"01","publisher":"American Physical Society","_id":"10745","conference":{"location":"New Orleans, LA, United States","end_date":"2017-03-17","name":"APS: American Physical Society","start_date":"2017-03-13"},"article_number":"P39.00011","issue":"4","citation":{"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.","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.","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.","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.","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."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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"}],"date_updated":"2022-02-08T10:44:35Z","type":"conference","volume":62,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1},{"extern":"1","publisher":"LIT Verlag Berlin-Münster-Wien-Zürich-London","day":"01","_id":"1075","page":"73 - 80","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:48:06Z","type":"book_chapter","volume":15,"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","oa":1,"has_accepted_license":"1","citation":{"apa":"Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In J. Parker &#38; R. Poole (Eds.), <i>Austria and America: 20th-Century Cross-Cultural Encounters</i> (Vol. 15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.","chicago":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” In <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.","ieee":"B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;,” in <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ista":"Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.","mla":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","short":"B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ama":"Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In: Parker J, Poole R, eds. <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80."},"publication_identifier":{"isbn":["978-3643908124"]},"publist_id":"6306","intvolume":"        15","author":[{"full_name":"Wenzl, Bernhard","id":"479E9046-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","last_name":"Wenzl"}],"date_created":"2018-12-11T11:50:00Z","month":"02","status":"public","year":"2017","date_published":"2017-02-01T00:00:00Z","editor":[{"first_name":"Joshua","last_name":"Parker","full_name":"Parker, Joshua"},{"last_name":"Poole","first_name":"Ralph","full_name":"Poole, Ralph"}],"publication_status":"published","publication":"Austria and America: 20th-Century Cross-Cultural Encounters","title":"An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;","alternative_title":["American Studies in Austria"],"ddc":["001"],"oa_version":"None","file_date_updated":"2018-12-12T10:08:06Z","file":[{"relation":"main_file","date_updated":"2018-12-12T10:08:06Z","date_created":"2018-12-12T10:08:06Z","access_level":"open_access","file_name":"IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf","file_size":380624,"creator":"system","file_id":"4666","content_type":"application/pdf"}]},{"ec_funded":1,"date_published":"2017-02-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.07018"}],"department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"first_name":"Jiří","last_name":"Daněk","full_name":"Daněk, Jiří"},{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu","first_name":"Enderalp"},{"last_name":"Hatsagortsyan","first_name":"Karen","full_name":"Hatsagortsyan, Karen"},{"first_name":"Christoph","last_name":"Keitel","full_name":"Keitel, Christoph"}],"publication_identifier":{"issn":["2469-9926"]},"publist_id":"6305","intvolume":"        95","isi":1,"date_created":"2018-12-11T11:50:01Z","arxiv":1,"status":"public","month":"02","year":"2017","title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","quality_controlled":"1","scopus_import":"1","oa_version":"Submitted Version","doi":"10.1103/PhysRevA.95.023403","external_id":{"isi":["000400571700011"],"arxiv":["1609.07018"]},"publication":" Physical Review A - Atomic, Molecular, and Optical Physics","article_processing_charge":"No","day":"01","publisher":"American Physical Society","_id":"1076","issue":"2","article_number":"023403","citation":{"mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>.","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2017;95(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel,  Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2. American Physical Society, 2017.","chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>.","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., &#38; Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation.  Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403."},"abstract":[{"text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-06-04T08:11:30Z","type":"journal_article","volume":95,"oa":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"date_updated":"2025-07-10T11:49:59Z","type":"journal_article","volume":14,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","article_number":"20160139","issue":"126","citation":{"ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society of London, 2017.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>."},"related_material":{"record":[{"status":"public","id":"9864","relation":"research_data"}]},"day":"04","publisher":"Royal Society of London","_id":"1077","publication":"Journal of the Royal Society Interface","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","scopus_import":"1","ddc":["570"],"doi":"10.1098/rsif.2016.0139","file_date_updated":"2019-01-18T09:14:02Z","external_id":{"isi":["000393380400001"]},"oa_version":"Published Version","file":[{"relation":"main_file","file_size":1092015,"success":1,"creator":"dernst","file_id":"5843","content_type":"application/pdf","date_updated":"2019-01-18T09:14:02Z","date_created":"2019-01-18T09:14:02Z","file_name":"2017_JRSI_Redondo.pdf","access_level":"open_access"}],"publication_identifier":{"issn":["1742-5689"]},"publist_id":"6303","intvolume":"        14","author":[{"last_name":"Fernandes Redondo","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","last_name":"Vladar","first_name":"Harold"},{"last_name":"Włodarski","first_name":"Tomasz","full_name":"Włodarski, Tomasz"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback"}],"date_created":"2018-12-11T11:50:01Z","isi":1,"month":"01","status":"public","year":"2017","date_published":"2017-01-04T00:00:00Z","ec_funded":1,"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publication_status":"published"},{"ec_funded":1,"date_published":"2017-01-18T00:00:00Z","publication_status":"published","pubrep_id":"808","department":[{"_id":"JiFr"},{"_id":"Bio"}],"isi":1,"date_created":"2018-12-11T11:50:01Z","author":[{"first_name":"Daniel","last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"intvolume":"      2017","publist_id":"6302","year":"2017","status":"public","month":"01","scopus_import":"1","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"file":[{"relation":"main_file","access_level":"open_access","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","date_updated":"2018-12-12T10:16:31Z","date_created":"2018-12-12T10:16:31Z","creator":"system","file_id":"5219","content_type":"application/pdf","file_size":57678},{"date_updated":"2018-12-12T10:16:32Z","date_created":"2018-12-12T10:16:32Z","access_level":"open_access","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","file_size":1317820,"creator":"system","content_type":"application/pdf","file_id":"5220","relation":"main_file"}],"file_date_updated":"2018-12-12T10:16:32Z","oa_version":"Published Version","external_id":{"isi":["000397847200041"]},"doi":"10.3791/55044","ddc":["580"],"publication":"Journal of visualized experiments JoVE","article_processing_charge":"No","publisher":"Journal of Visualized Experiments","day":"18","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5565"}]},"_id":"1078","issue":"119","article_number":"e55044","has_accepted_license":"1","citation":{"chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of visualized experiments JoVE</i>, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of visualized experiments JoVE</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017)."},"date_updated":"2025-04-15T06:50:23Z","abstract":[{"text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. ","lang":"eng"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"volume":2017,"type":"journal_article"},{"quality_controlled":"1","title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","scopus_import":"1","external_id":{"isi":["000401270000004"],"arxiv":["1603.07368"]},"doi":"10.1007/s11040-017-9238-0","oa_version":"Submitted Version","publication":"Mathematical Physics, Analysis and Geometry","article_processing_charge":"No","date_published":"2017-06-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"department":[{"_id":"RoSe"}],"publication_status":"published","publication_identifier":{"issn":["1385-0172"]},"publist_id":"6300","intvolume":"        20","author":[{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","first_name":"Phan"},{"last_name":"Van Den Bosch","first_name":"Hanne","full_name":"Van Den Bosch, Hanne"}],"arxiv":1,"isi":1,"date_created":"2018-12-11T11:50:02Z","month":"06","status":"public","year":"2017","article_number":"6","issue":"2","citation":{"mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2, 6, Springer, 2017, doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>.","short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. 2017;20(2). doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>","apa":"Nam, P., &#38; Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>.","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2. Springer, 2017.","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6."},"language":[{"iso":"eng"}],"abstract":[{"text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers.","lang":"eng"}],"date_updated":"2025-06-04T08:11:50Z","type":"journal_article","volume":20,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"oa":1,"day":"01","publisher":"Springer","_id":"1079"},{"publication":"Nature Communications","article_processing_charge":"No","quality_controlled":"1","title":"Reconstructing metastatic seeding patterns of human cancers","scopus_import":"1","ddc":["004","006"],"doi":"10.1038/ncomms14114","file_date_updated":"2018-12-12T10:15:15Z","external_id":{"isi":["000393096600001"]},"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","date_created":"2018-12-12T10:15:15Z","date_updated":"2018-12-12T10:15:15Z","file_id":"5133","content_type":"application/pdf","creator":"system","file_size":897050,"relation":"main_file"}],"intvolume":"         8","publist_id":"6301","publication_identifier":{"issn":["2041-1723"]},"author":[{"last_name":"Reiter","first_name":"Johannes","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353"},{"full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore","first_name":"Alvin"},{"full_name":"Gerold, Jeffrey","first_name":"Jeffrey","last_name":"Gerold"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Christine","last_name":"Iacobuzio Donahue","full_name":"Iacobuzio Donahue, Christine"},{"last_name":"Vogelstein","first_name":"Bert","full_name":"Vogelstein, Bert"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"isi":1,"date_created":"2018-12-11T11:50:02Z","month":"01","status":"public","year":"2017","date_published":"2017-01-31T00:00:00Z","ec_funded":1,"department":[{"_id":"KrCh"}],"pubrep_id":"786","publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods."}],"date_updated":"2025-07-10T11:50:00Z","type":"journal_article","volume":8,"project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"14114","citation":{"chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>.","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>.","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017)."},"day":"31","publisher":"Nature Publishing Group","_id":"1080"},{"article_number":"14251","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"ieee":"A. Wright <i>et al.</i>, “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","chicago":"Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>.","apa":"Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14251\">https://doi.org/10.1038/ncomms14251</a>","ista":"Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251.","mla":"Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” <i>Nature Communications</i>, vol. 8, 14251, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>.","ama":"Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14251\">10.1038/ncomms14251</a>","short":"A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017)."},"date_updated":"2025-07-10T11:50:01Z","language":[{"iso":"eng"}],"abstract":[{"text":"Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"journal_article","volume":8,"day":"31","publisher":"Nature Publishing Group","_id":"1085","scopus_import":"1","quality_controlled":"1","title":"Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation","file":[{"file_size":955256,"creator":"system","file_id":"5141","content_type":"application/pdf","date_created":"2018-12-12T10:15:22Z","date_updated":"2018-12-12T10:15:22Z","file_name":"IST-2017-791-v1+1_ncomms14251.pdf","access_level":"open_access","relation":"main_file"}],"ddc":["570","576"],"file_date_updated":"2018-12-12T10:15:22Z","doi":"10.1038/ncomms14251","external_id":{"isi":["000392953700001"]},"oa_version":"Published Version","publication":"Nature Communications","article_processing_charge":"No","date_published":"2017-01-31T00:00:00Z","publication_status":"published","department":[{"_id":"BeVi"}],"pubrep_id":"791","date_created":"2018-12-11T11:50:04Z","isi":1,"publist_id":"6292","intvolume":"         8","publication_identifier":{"issn":["2041-1723"]},"author":[{"full_name":"Wright, Alison","first_name":"Alison","last_name":"Wright"},{"last_name":"Darolti","first_name":"Iulia","full_name":"Darolti, Iulia"},{"first_name":"Natasha","last_name":"Bloch","full_name":"Bloch, Natasha"},{"first_name":"Vicencio","last_name":"Oostra","full_name":"Oostra, Vicencio"},{"full_name":"Sandkam, Benjamin","first_name":"Benjamin","last_name":"Sandkam"},{"full_name":"Buechel, Séverine","last_name":"Buechel","first_name":"Séverine"},{"first_name":"Niclas","last_name":"Kolm","full_name":"Kolm, Niclas"},{"full_name":"Breden, Felix","last_name":"Breden","first_name":"Felix"},{"first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"},{"first_name":"Judith","last_name":"Mank","full_name":"Mank, Judith"}],"year":"2017","month":"01","status":"public"},{"publication":"Scientific Reports","article_processing_charge":"No","title":"Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide","quality_controlled":"1","scopus_import":"1","oa_version":"Published Version","file_date_updated":"2018-12-12T10:14:59Z","doi":"10.1038/srep41002","external_id":{"isi":["000393163800001"]},"ddc":["570","590"],"file":[{"file_name":"IST-2017-790-v1+1_srep41002_1_.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:59Z","date_updated":"2018-12-12T10:14:59Z","content_type":"application/pdf","creator":"system","file_id":"5115","file_size":1994139,"relation":"main_file"}],"author":[{"full_name":"Di Giglio, Maria","last_name":"Di Giglio","first_name":"Maria"},{"full_name":"Muttenthaler, Markus","first_name":"Markus","last_name":"Muttenthaler"},{"first_name":"Kasper","last_name":"Harpsøe","full_name":"Harpsøe, Kasper"},{"first_name":"Zita","last_name":"Liutkeviciute","full_name":"Liutkeviciute, Zita"},{"last_name":"Keov","first_name":"Peter","full_name":"Keov, Peter"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"full_name":"Rattei, Thomas","first_name":"Thomas","last_name":"Rattei"},{"full_name":"Arrowsmith, Sarah","last_name":"Arrowsmith","first_name":"Sarah"},{"last_name":"Wray","first_name":"Susan","full_name":"Wray, Susan"},{"full_name":"Marek, Ales","last_name":"Marek","first_name":"Ales"},{"full_name":"Elbert, Tomas","last_name":"Elbert","first_name":"Tomas"},{"first_name":"Paul","last_name":"Alewood","full_name":"Alewood, Paul"},{"last_name":"Gloriam","first_name":"David","full_name":"Gloriam, David"},{"first_name":"Christian","last_name":"Gruber","full_name":"Gruber, Christian"}],"publist_id":"6291","intvolume":"         7","isi":1,"date_created":"2018-12-11T11:50:04Z","status":"public","month":"02","year":"2017","date_published":"2017-02-01T00:00:00Z","pubrep_id":"790","publication_status":"published","abstract":[{"text":"Characterisation of G protein-coupled receptors (GPCR) relies on the availability of a toolbox of ligands that selectively modulate different functional states of the receptors. To uncover such molecules, we explored a unique strategy for ligand discovery that takes advantage of the evolutionary conservation of the 600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger), identified and cloned its cognate receptor and determined its pharmacological properties on the insect and human oxytocin/vasopressin receptors. Subsequently, we identified a functional dichotomy: inotocin activated the insect inotocin and the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist ([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor interaction, which led to the identification of key residues of the receptors that are important for ligand functionality and selectivity. These observations could play an important role for development of oxytocin/vasopressin receptor modulators that would enable clear distinction of the physiological and pathological responses of the individual receptor subtypes.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2023-09-20T11:47:47Z","type":"journal_article","volume":7,"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"ieee":"M. Di Giglio <i>et al.</i>, “Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide,” <i>Scientific Reports</i>, vol. 7. Nature Publishing Group, p. 41002, 2017.","chicago":"Di Giglio, Maria, Markus Muttenthaler, Kasper Harpsøe, Zita Liutkeviciute, Peter Keov, Thomas Eder, Thomas Rattei, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” <i>Scientific Reports</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/srep41002\">https://doi.org/10.1038/srep41002</a>.","apa":"Di Giglio, M., Muttenthaler, M., Harpsøe, K., Liutkeviciute, Z., Keov, P., Eder, T., … Gruber, C. (2017). Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep41002\">https://doi.org/10.1038/srep41002</a>","ista":"Di Giglio M, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood P, Gloriam D, Gruber C. 2017. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. Scientific Reports. 7, 41002.","mla":"Di Giglio, Maria, et al. “Development of a Human Vasopressin V1a-Receptor Antagonist from an Evolutionary-Related Insect Neuropeptide.” <i>Scientific Reports</i>, vol. 7, Nature Publishing Group, 2017, p. 41002, doi:<a href=\"https://doi.org/10.1038/srep41002\">10.1038/srep41002</a>.","ama":"Di Giglio M, Muttenthaler M, Harpsøe K, et al. Development of a human vasopressin V1a-receptor antagonist from an evolutionary-related insect neuropeptide. <i>Scientific Reports</i>. 2017;7:41002. doi:<a href=\"https://doi.org/10.1038/srep41002\">10.1038/srep41002</a>","short":"M. Di Giglio, M. Muttenthaler, K. Harpsøe, Z. Liutkeviciute, P. Keov, T. Eder, T. Rattei, S. Arrowsmith, S. Wray, A. Marek, T. Elbert, P. Alewood, D. Gloriam, C. Gruber, Scientific Reports 7 (2017) 41002."},"day":"01","publisher":"Nature Publishing Group","_id":"1086","page":"41002"},{"page":"1045 - 1059","day":"25","publisher":"Cambridge University Press","_id":"1087","citation":{"ama":"Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;813:1045-1059. doi:<a href=\"https://doi.org/10.1017/jfm.2017.14\">10.1017/jfm.2017.14</a>","short":"B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059.","mla":"Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:<a href=\"https://doi.org/10.1017/jfm.2017.14\">10.1017/jfm.2017.14</a>.","ista":"Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.","chicago":"Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.14\">https://doi.org/10.1017/jfm.2017.14</a>.","ieee":"B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 813. Cambridge University Press, pp. 1045–1059, 2017.","apa":"Song, B., Barkley, D., Hof, B., &#38; Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.14\">https://doi.org/10.1017/jfm.2017.14</a>"},"abstract":[{"text":"Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-06-04T08:35:11Z","volume":813,"type":"journal_article","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"ec_funded":1,"date_published":"2017-02-25T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1603.04077","open_access":"1"}],"department":[{"_id":"BjHo"}],"publication_status":"published","author":[{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"full_name":"Barkley, Dwight","last_name":"Barkley","first_name":"Dwight"},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"publication_identifier":{"issn":["0022-1120"]},"publist_id":"6290","intvolume":"       813","date_created":"2018-12-11T11:50:04Z","isi":1,"arxiv":1,"status":"public","month":"02","year":"2017","title":"Speed and structure of turbulent fronts in pipe flow","quality_controlled":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","external_id":{"isi":["000394376400044"],"arxiv":["1603.04077"]},"doi":"10.1017/jfm.2017.14","oa_version":"Submitted Version","publication":"Journal of Fluid Mechanics","article_processing_charge":"No"}]