[{"year":"2017","has_accepted_license":"1","day":"01","page":"38:1-38-21","date_created":"2018-12-11T11:50:33Z","doi":"10.4230/LIPIcs.ITCS.2017.38","date_published":"2017-01-01T00:00:00Z","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","citation":{"mla":"Alwen, Joel F., et al. Cumulative Space in Black-White Pebbling and Resolution. Edited by Christos Papadimitriou, vol. 67, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21, doi:10.4230/LIPIcs.ITCS.2017.38.","short":"J.F. Alwen, S. De Rezende, J. Nordstrom, M. Vinyals, in:, C. Papadimitriou (Ed.), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, p. 38:1-38-21.","ieee":"J. F. Alwen, S. De Rezende, J. Nordstrom, and M. Vinyals, “Cumulative space in black-white pebbling and resolution,” presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States, 2017, vol. 67, p. 38:1-38-21.","apa":"Alwen, J. F., De Rezende, S., Nordstrom, J., & Vinyals, M. (2017). Cumulative space in black-white pebbling and resolution. In C. Papadimitriou (Ed.) (Vol. 67, p. 38:1-38-21). Presented at the ITCS: Innovations in Theoretical Computer Science, Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2017.38","ama":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. Cumulative space in black-white pebbling and resolution. In: Papadimitriou C, ed. Vol 67. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:38:1-38-21. doi:10.4230/LIPIcs.ITCS.2017.38","chicago":"Alwen, Joel F, Susanna De Rezende, Jakob Nordstrom, and Marc Vinyals. “Cumulative Space in Black-White Pebbling and Resolution.” edited by Christos Papadimitriou, 67:38:1-38-21. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ITCS.2017.38.","ista":"Alwen JF, De Rezende S, Nordstrom J, Vinyals M. 2017. Cumulative space in black-white pebbling and resolution. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 67, 38:1-38-21."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"full_name":"De Rezende, Susanna","last_name":"De Rezende","first_name":"Susanna"},{"full_name":"Nordstrom, Jakob","last_name":"Nordstrom","first_name":"Jakob"},{"full_name":"Vinyals, Marc","last_name":"Vinyals","first_name":"Marc"}],"publist_id":"6179","title":"Cumulative space in black-white pebbling and resolution","editor":[{"first_name":"Christos","last_name":"Papadimitriou","full_name":"Papadimitriou, Christos"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"dbc94810be07c2fb1945d5c2a6130e6c","file_id":"5263","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_size":557769,"date_created":"2018-12-12T10:17:11Z","file_name":"IST-2018-927-v1+1_LIPIcs-ITCS-2017-38.pdf"}],"volume":67,"abstract":[{"text":"We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 67","month":"01","date_updated":"2021-01-12T06:48:51Z","ddc":["005","600"],"file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"KrPi"}],"_id":"1175","conference":{"location":"Berkeley, CA, United States","end_date":"2017-01-11","start_date":"2017-01-09","name":"ITCS: Innovations in Theoretical Computer Science"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"927","status":"public"},{"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:48:58Z","status":"public","type":"journal_article","_id":"1191","ec_funded":1,"volume":79,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 79","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1607.00944","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed."}],"title":"Existence of traveling waves for the generalized F–KPP equation","author":[{"first_name":"Richard","last_name":"Kollár","full_name":"Kollár, Richard"},{"last_name":"Novak","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"publist_id":"6160","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3.","apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3","ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3."},"project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:38Z","doi":"10.1007/s11538-016-0244-3","date_published":"2017-03-01T00:00:00Z","page":"525-559","publication":"Bulletin of Mathematical Biology","day":"01","year":"2017","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project."},{"volume":167,"issue":"3-4","publication_status":"published","file":[{"file_size":2820207,"date_updated":"2020-07-14T12:44:39Z","creator":"system","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","date_created":"2018-12-12T10:18:01Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5319","checksum":"3e971d09eb167761aa0888ed415b0056"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"05","intvolume":" 167","abstract":[{"text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:44:39Z","date_updated":"2021-01-12T06:49:07Z","ddc":["530"],"type":"journal_article","status":"public","pubrep_id":"782","_id":"1211","page":"636-655","doi":"10.1007/s10955-016-1672-z","date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:50:44Z","has_accepted_license":"1","year":"2017","day":"01","publication":"Journal of Statistical Physics","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","publist_id":"6136","author":[{"last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"full_name":"Cvitanović, Predrag","last_name":"Cvitanović","first_name":"Predrag"}],"title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","citation":{"chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z.","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:10.1007/s10955-016-1672-z.","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655, 2017.","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z","apa":"Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408.","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408","mla":"Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408."},"title":"Hanani-Tutte for radial planarity","external_id":{"arxiv":["1608.08662"]},"article_processing_charge":"No","publist_id":"6254","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek"},{"last_name":"Pelsmajer","full_name":"Pelsmajer, Michael","first_name":"Michael"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication":"Journal of Graph Algorithms and Applications","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:50:13Z","date_published":"2017-01-01T00:00:00Z","doi":"10.7155/jgaa.00408","page":"135 - 154","oa":1,"quality_controlled":"1","publisher":"Brown University","ddc":["510"],"date_updated":"2023-02-23T10:05:57Z","department":[{"_id":"UlWa"}],"file_date_updated":"2019-10-24T10:54:37Z","_id":"1113","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"6967","creator":"dernst","file_size":573623,"date_updated":"2019-10-24T10:54:37Z","file_name":"2017_JournalGraphAlgorithms_Fulek.pdf","date_created":"2019-10-24T10:54:37Z"}],"publication_status":"published","ec_funded":1,"issue":"1","related_material":{"record":[{"relation":"earlier_version","id":"1164","status":"public"},{"id":"1595","status":"public","relation":"earlier_version"}]},"volume":21,"oa_version":"Published Version","abstract":[{"text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth.","lang":"eng"}],"intvolume":" 21","month":"01","scopus_import":1},{"publist_id":"7379","author":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"department":[{"_id":"LeSa"}],"editor":[{"first_name":"Mårten","last_name":"Wikström","full_name":"Wikström, Mårten"}],"title":"Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions","date_updated":"2021-01-12T07:56:59Z","citation":{"ista":"Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59.","chicago":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025.","short":"L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59.","ieee":"L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.","apa":"Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025","ama":"Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025","mla":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:10.1039/9781788010405-00025."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","status":"public","series_title":"Mechanisms of Primary Energy Transduction in Biology ","_id":"444","page":"25 - 59","date_published":"2017-11-29T00:00:00Z","doi":"10.1039/9781788010405-00025","date_created":"2018-12-11T11:46:30Z","publication_identifier":{"isbn":["978-1-78262-865-1"]},"year":"2017","publication_status":"published","day":"29","publication":"Mechanisms of primary energy transduction in biology ","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Royal Society of Chemistry","month":"11","abstract":[{"lang":"eng","text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations."}],"oa_version":"None"},{"status":"public","pubrep_id":"965","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"453","department":[{"_id":"MaLo"}],"file_date_updated":"2020-07-14T12:46:31Z","ddc":["570"],"date_updated":"2021-01-12T07:59:28Z","month":"11","intvolume":" 113","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor."}],"volume":113,"issue":"9","file":[{"date_updated":"2020-07-14T12:46:31Z","file_size":977192,"creator":"system","date_created":"2018-12-12T10:14:03Z","file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"99a2474088e20ac74b1882c4fbbb45b1","file_id":"5052"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement","publist_id":"7369","author":[{"full_name":"Fallesen, Todd","last_name":"Fallesen","first_name":"Todd"},{"first_name":"Johanna","full_name":"Roostalu, Johanna","last_name":"Roostalu"},{"orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F","last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian F"},{"last_name":"Pruessner","full_name":"Pruessner, Gunnar","first_name":"Gunnar"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006","ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006","short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006.","ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067.","chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006."},"quality_controlled":"1","publisher":"Biophysical Society","oa":1,"acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). 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Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017.","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017).","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 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We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). 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Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. 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By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings."}],"month":"04","intvolume":" 26","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229.","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications. 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Research supported by Austrian Science Fund (FWF): P25816-N15.","publisher":"World Scientific Publishing","quality_controlled":"1","oa":1},{"citation":{"mla":"Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.","short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738.","ieee":"P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017.","ama":"Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4","apa":"Nam, P., & Napiórkowski, M. M. (2017). 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For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.04631"}],"month":"01","intvolume":" 21"},{"year":"2017","publication":"Advances in Theoretical and Mathematical Physics","day":"25","page":"739 - 800","date_created":"2018-12-11T11:46:43Z","doi":"10.4310/ATMP.2017.v21.n3.a5","date_published":"2017-08-25T00:00:00Z","oa":1,"publisher":"International Press","quality_controlled":"1","citation":{"ista":"Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.","chicago":"Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800.","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5","ama":"Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5","mla":"Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Paul","last_name":"Bourgade","full_name":"Bourgade, Paul"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"},{"first_name":"Horng","full_name":"Yau, Horng","last_name":"Yau"},{"last_name":"Yin","full_name":"Yin, Jun","first_name":"Jun"}],"publist_id":"7337","title":"Universality for a class of random band matrices","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"publication_status":"published","publication_identifier":{"issn":["10950761"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":21,"issue":"3","abstract":[{"lang":"eng","text":"We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1602.02312","open_access":"1"}],"scopus_import":1,"intvolume":" 21","month":"08","date_updated":"2021-01-12T08:00:57Z","department":[{"_id":"LaEr"}],"_id":"483","type":"journal_article","status":"public"},{"month":"11","scopus_import":1,"quality_controlled":"1","publisher":"ACM","oa_version":"None","abstract":[{"text":"In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x.","lang":"eng"}],"date_published":"2017-11-28T00:00:00Z","doi":"10.1145/3143361.3143367","date_created":"2018-12-11T11:46:45Z","page":"2 - 14","day":"28","language":[{"iso":"eng"}],"publication":"Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies","publication_identifier":{"isbn":["978-145035422-6"]},"year":"2017","publication_status":"published","status":"public","type":"conference","conference":{"name":"CoNEXT: Conference on emerging Networking EXperiments and Technologies","start_date":"2017-12-12","end_date":"2017-12-15","location":"Incheon, South Korea"},"_id":"487","department":[{"_id":"DaAl"}],"title":"Towards unlicensed cellular networks in TV white spaces","author":[{"first_name":"Ghufran","last_name":"Baig","full_name":"Baig, Ghufran"},{"first_name":"Bozidar","last_name":"Radunovic","full_name":"Radunovic, Bozidar"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"full_name":"Balkwill, Matthew","last_name":"Balkwill","first_name":"Matthew"},{"last_name":"Karagiannis","full_name":"Karagiannis, Thomas","first_name":"Thomas"},{"first_name":"Lili","full_name":"Qiu, Lili","last_name":"Qiu"}],"publist_id":"7333","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:21:11Z","citation":{"mla":"Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.” Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367.","apa":"Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., & Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367","ama":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies. ACM; 2017:2-14. doi:10.1145/3143361.3143367","ieee":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L. Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies, Incheon, South Korea, 2017, pp. 2–14.","short":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu, in:, Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14.","chicago":"Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill, Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV White Spaces.” In Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367.","ista":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017. Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies. CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14."}},{"status":"public","pubrep_id":"937","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"514","department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:46:36Z","ddc":["571"],"date_updated":"2021-01-12T08:01:16Z","month":"07","intvolume":" 8","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum."}],"volume":8,"file":[{"file_id":"5083","checksum":"76d8a2b72a58e56adb410ec37dfa7eee","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:14:31Z","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","creator":"system","date_updated":"2020-07-14T12:46:36Z","file_size":2948357}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["20411723"]},"publication_status":"published","article_number":"16032","title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","publist_id":"7305","author":[{"full_name":"Simonnet, Jean","last_name":"Simonnet","first_name":"Jean"},{"last_name":"Nassar","full_name":"Nassar, Mérie","first_name":"Mérie"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico","orcid":"0000-0001-9439-3148","full_name":"Stella, Federico","last_name":"Stella"},{"full_name":"Cohen, Ivan","last_name":"Cohen","first_name":"Ivan"},{"full_name":"Mathon, Bertrand","last_name":"Mathon","first_name":"Bertrand"},{"first_name":"Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte","last_name":"Boccara"},{"last_name":"Miles","full_name":"Miles, Richard","first_name":"Richard"},{"first_name":"Desdemona","last_name":"Fricker","full_name":"Fricker, Desdemona"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032.","ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032","apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032","ieee":"J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032.","ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032."},"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"date_published":"2017-07-01T00:00:00Z","doi":"10.1038/ncomms16032","date_created":"2018-12-11T11:46:54Z","day":"01","publication":"Nature Communications","has_accepted_license":"1","year":"2017"},{"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","page":"800 - 808","date_created":"2018-12-11T11:46:54Z","doi":"10.1038/nsmb.3460","date_published":"2017-10-05T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Nature Structural and Molecular Biology","day":"05","project":[{"grant_number":"701309","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-9864-3586","full_name":"Letts, James A","last_name":"Letts","first_name":"James A","id":"322DA418-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov"}],"publist_id":"7304","title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","citation":{"ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460","apa":"Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808.","ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460.","ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 24","month":"10","abstract":[{"lang":"eng","text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport."}],"oa_version":"Submitted Version","ec_funded":1,"volume":24,"issue":"10","publication_status":"published","publication_identifier":{"issn":["15459993"]},"language":[{"iso":"eng"}],"file":[{"file_name":"29893_2_merged_1501257589_red.pdf","date_created":"2019-11-07T12:51:07Z","creator":"lsazanov","file_size":4118385,"date_updated":"2020-07-14T12:46:36Z","file_id":"6993","checksum":"9bc7e8c41b43636dd7566289e511f096","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","article_type":"original","status":"public","_id":"515","file_date_updated":"2020-07-14T12:46:36Z","department":[{"_id":"LeSa"}],"date_updated":"2021-01-12T08:01:17Z","ddc":["572"]},{"year":"2017","publication_status":"published","language":[{"iso":"eng"}],"publication":"Physical Review Fluids","day":"01","date_created":"2018-12-11T11:46:54Z","volume":2,"issue":"4","date_published":"2017-04-01T00:00:00Z","doi":"10.1103/PhysRevFluids.2.043904","abstract":[{"lang":"eng","text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction."}],"oa_version":"Preprint","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.02619"}],"publisher":"American Physical Society","quality_controlled":"1","scopus_import":1,"intvolume":" 2","month":"04","citation":{"mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.","short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904","ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904","chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.","ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904."},"date_updated":"2021-01-12T08:01:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7306","author":[{"full_name":"Klotz, Lukasz","orcid":"0000-0003-1740-7635","last_name":"Klotz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","first_name":"Lukasz"},{"last_name":"Lemoult","full_name":"Lemoult, Grégoire M","first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Frontczak, Idalia","last_name":"Frontczak","first_name":"Idalia"},{"last_name":"Tuckerman","full_name":"Tuckerman, Laurette","first_name":"Laurette"},{"first_name":"José","last_name":"Wesfreid","full_name":"Wesfreid, José"}],"title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","department":[{"_id":"BjHo"}],"_id":"513","article_number":"043904","type":"journal_article","status":"public"},{"quality_controlled":"1","publisher":"American Chemical Society","year":"2017","publication":"ACS Synthetic Biology","day":"17","page":"395 - 401","date_created":"2018-12-11T11:46:56Z","date_published":"2017-03-17T00:00:00Z","doi":"10.1021/acssynbio.6b00235","citation":{"ista":"Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401.","chicago":"Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235.","ieee":"W. Du et al., “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” ACS Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017.","short":"W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.","apa":"Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235","ama":"Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235","mla":"Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["27936615"]},"author":[{"first_name":"Wei","last_name":"Du","full_name":"Du, Wei"},{"orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","last_name":"Angermayr","first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jongbloets, Joeri","last_name":"Jongbloets","first_name":"Joeri"},{"full_name":"Molenaar, Douwe","last_name":"Molenaar","first_name":"Douwe"},{"first_name":"Herwig","last_name":"Bachmann","full_name":"Bachmann, Herwig"},{"first_name":"Klaas","last_name":"Hellingwerf","full_name":"Hellingwerf, Klaas"},{"full_name":"Branco Dos Santos, Filipe","last_name":"Branco Dos Santos","first_name":"Filipe"}],"publist_id":"7298","title":"Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803","abstract":[{"lang":"eng","text":"Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here."}],"pmid":1,"oa_version":"None","scopus_import":1,"intvolume":" 6","month":"03","publication_status":"published","publication_identifier":{"issn":["21615063"]},"language":[{"iso":"eng"}],"issue":"3","volume":6,"_id":"520","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2021-01-12T08:01:21Z","department":[{"_id":"ToBo"}]},{"author":[{"first_name":"Kyle","last_name":"Austin","full_name":"Austin, Kyle"},{"first_name":"Ziga","id":"2E36B656-F248-11E8-B48F-1D18A9856A87","last_name":"Virk","full_name":"Virk, Ziga"}],"publist_id":"7299","department":[{"_id":"HeEd"}],"title":"Higson compactification and dimension raising","date_updated":"2021-01-12T08:01:21Z","citation":{"ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.","ama":"Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005","apa":"Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005","mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"521","page":"45 - 57","date_created":"2018-12-11T11:46:56Z","volume":215,"date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.topol.2016.10.005","year":"2017","publication_status":"published","publication_identifier":{"issn":["01668641"]},"language":[{"iso":"eng"}],"publication":"Topology and its Applications","day":"01","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1608.03954v1","open_access":"1"}],"publisher":"Elsevier","quality_controlled":"1","intvolume":" 215","month":"01","abstract":[{"lang":"eng","text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension."}],"oa_version":"Submitted Version"},{"citation":{"ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888.","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0.","ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7283","author":[{"first_name":"Benjamin","full_name":"Burton, Benjamin","last_name":"Burton"},{"full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay","first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"external_id":{"arxiv":["1602.07907"]},"article_processing_charge":"No","title":"Finding non-orientable surfaces in 3-Manifolds","quality_controlled":"1","publisher":"Springer","oa":1,"year":"2017","day":"09","publication":"Discrete & Computational Geometry","page":"871 - 888","date_published":"2017-06-09T00:00:00Z","doi":"10.1007/s00454-017-9900-0","date_created":"2018-12-11T11:47:01Z","_id":"534","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-21T17:01:34Z","department":[{"_id":"UlWa"}],"abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.07907"}],"month":"06","intvolume":" 58","publication_identifier":{"issn":["01795376"]},"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"1379","status":"public"}]},"issue":"4","volume":58},{"day":"20","publication":"Angewandte Chemie","has_accepted_license":"1","year":"2017","date_published":"2017-05-20T00:00:00Z","doi":"10.1002/ange.201611998","date_created":"2018-12-11T11:47:02Z","page":"4679 - 4682","quality_controlled":"1","publisher":"Wiley","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998"},"title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","publist_id":"7279","author":[{"full_name":"Kainrath, Stephanie","last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Manuela","last_name":"Stadler","full_name":"Stadler, Manuela"},{"first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart"},{"first_name":"Martin","full_name":"Distel, Martin","last_name":"Distel"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"file":[{"file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","date_created":"2018-12-12T10:13:24Z","file_size":1668557,"date_updated":"2020-07-14T12:46:39Z","creator":"system","file_id":"5007","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":129,"issue":"16","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"ger","text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. "}],"month":"05","intvolume":" 129","ddc":["571"],"date_updated":"2021-01-12T08:01:33Z","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:46:39Z","_id":"538","status":"public","pubrep_id":"932","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}}]