[{"quality_controlled":"1","arxiv":1,"month":"12","publication":"Astronomy & Astrophysics","date_created":"2023-08-03T10:15:09Z","oa_version":"Published Version","citation":{"ista":"Götberg YLL, de Mink SE, Groh JH. 2017. Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity. Astronomy & Astrophysics. 608, A11.","chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, and J. H. Groh. “Ionizing Spectra of Stars That Lose Their Envelope through Interaction with a Binary Companion: Role of Metallicity.” Astronomy & Astrophysics. EDP Sciences, 2017. https://doi.org/10.1051/0004-6361/201730472.","short":"Y.L.L. Götberg, S.E. de Mink, J.H. Groh, Astronomy & Astrophysics 608 (2017).","ieee":"Y. L. L. Götberg, S. E. de Mink, and J. H. Groh, “Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity,” Astronomy & Astrophysics, vol. 608. EDP Sciences, 2017.","apa":"Götberg, Y. L. L., de Mink, S. E., & Groh, J. H. (2017). Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201730472","mla":"Götberg, Ylva Louise Linsdotter, et al. “Ionizing Spectra of Stars That Lose Their Envelope through Interaction with a Binary Companion: Role of Metallicity.” Astronomy & Astrophysics, vol. 608, A11, EDP Sciences, 2017, doi:10.1051/0004-6361/201730472.","ama":"Götberg YLL, de Mink SE, Groh JH. Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity. Astronomy & Astrophysics. 2017;608. doi:10.1051/0004-6361/201730472"},"type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201730472"}],"day":"01","external_id":{"arxiv":["1701.07439"]},"extern":"1","oa":1,"status":"public","intvolume":" 608","date_published":"2017-12-01T00:00:00Z","doi":"10.1051/0004-6361/201730472","article_number":"A11","date_updated":"2023-08-09T11:27:06Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Understanding ionizing fluxes of stellar populations is crucial for various astrophysical problems including the epoch of reionization. Short-lived massive stars are generally considered as the main stellar sources. We examine the potential role of less massive stars that lose their envelope through interaction with a binary companion. Here, we focus on the role of metallicity (Z). For this purpose we used the evolutionary code MESA and created tailored atmosphere models with the radiative transfer code CMFGEN. We show that typical progenitors, with initial masses of 12 M⊙, produce hot and compact stars (~ 4 M⊙, 60–80 kK, ~1 R⊙). These stripped stars copiously produce ionizing photons, emitting 60–85% and 30–60% of their energy as HI and HeI ionizing radiation, for Z = 0.0001–0.02, respectively. Their output is comparable to what massive stars emit during their Wolf-Rayet phase, if we account for their longer lifetimes and the favorable slope of the initial mass function. Their relative importance for reionization may be further favored since they emit their photons with a time delay (~ 20 Myr after birth in our fiducial model). This allows time for the dispersal of the birth clouds, allowing the ionizing photons to escape into the intergalactic medium. At low Z, we find that Roche stripping fails to fully remove the H-rich envelope, because of the reduced opacity in the subsurface layers. This is in sharp contrast with the assumption of complete stripping that is made in rapid population synthesis simulations, which are widely used to simulate the binary progenitors of supernovae and gravitational waves. Finally, we discuss the urgency to increase the observed sample of stripped stars to test these models and we discuss how our predictions can help to design efficient observational campaigns."}],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","first_name":"Ylva Louise Linsdotter"},{"last_name":"de Mink","full_name":"de Mink, S. E.","first_name":"S. E."},{"first_name":"J. H.","full_name":"Groh, J. H.","last_name":"Groh"}],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"year":"2017","scopus_import":"1","volume":608,"title":"Ionizing spectra of stars that lose their envelope through interaction with a binary companion: Role of metallicity","publication_status":"published","article_type":"original","publisher":"EDP Sciences","_id":"13476"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201629685"}],"day":"01","extern":"1","external_id":{"arxiv":["1701.07032"]},"status":"public","article_number":"A29","intvolume":" 601","doi":"10.1051/0004-6361/201629685","date_published":"2017-05-01T00:00:00Z","quality_controlled":"1","month":"05","arxiv":1,"date_created":"2023-08-03T10:15:18Z","oa_version":"Published Version","citation":{"ieee":"E. Zapartas et al., “Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction,” Astronomy & Astrophysics, vol. 601, no. A&A. EDP Sciences, 2017.","short":"E. Zapartas, S.E. de Mink, R.G. Izzard, S.-C. Yoon, C. Badenes, Y.L.L. Götberg, A. de Koter, C.J. Neijssel, M. Renzo, A. Schootemeijer, T.S. Shrotriya, Astronomy & Astrophysics 601 (2017).","chicago":"Zapartas, E., S. E. de Mink, R. G. Izzard, S.-C. Yoon, C. Badenes, Ylva Louise Linsdotter Götberg, A. de Koter, et al. “Delay-Time Distribution of Core-Collapse Supernovae with Late Events Resulting from Binary Interaction.” Astronomy & Astrophysics. EDP Sciences, 2017. https://doi.org/10.1051/0004-6361/201629685.","ista":"Zapartas E, de Mink SE, Izzard RG, Yoon S-C, Badenes C, Götberg YLL, de Koter A, Neijssel CJ, Renzo M, Schootemeijer A, Shrotriya TS. 2017. Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction. Astronomy & Astrophysics. 601(A&A), A29.","ama":"Zapartas E, de Mink SE, Izzard RG, et al. Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction. Astronomy & Astrophysics. 2017;601(A&A). doi:10.1051/0004-6361/201629685","mla":"Zapartas, E., et al. “Delay-Time Distribution of Core-Collapse Supernovae with Late Events Resulting from Binary Interaction.” Astronomy & Astrophysics, vol. 601, no. A&A, A29, EDP Sciences, 2017, doi:10.1051/0004-6361/201629685.","apa":"Zapartas, E., de Mink, S. E., Izzard, R. G., Yoon, S.-C., Badenes, C., Götberg, Y. L. L., … Shrotriya, T. S. (2017). Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201629685"},"publication":"Astronomy & Astrophysics","type":"journal_article","title":"Delay-time distribution of core-collapse supernovae with late events resulting from binary interaction","publication_status":"published","_id":"13477","article_type":"original","publisher":"EDP Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Most massive stars, the progenitors of core-collapse supernovae, are in close binary systems and may interact with their companion through mass transfer or merging. We undertake a population synthesis study to compute the delay-time distribution of core-collapse supernovae, that is, the supernova rate versus time following a starburst, taking into account binary interactions. We test the systematic robustness of our results by running various simulations to account for the uncertainties in our standard assumptions. We find that a significant fraction, 15+9-8%, of core-collapse supernovae are “late”, that is, they occur 50–200 Myr after birth, when all massive single stars have already exploded. These late events originate predominantly from binary systems with at least one, or, in most cases, with both stars initially being of intermediate mass (4–8 M⊙). The main evolutionary channels that contribute often involve either the merging of the initially more massive primary star with its companion or the engulfment of the remaining core of the primary by the expanding secondary that has accreted mass at an earlier evolutionary stage. Also, the total number of core-collapse supernovae increases by 14+15-14% because of binarity for the same initial stellar mass. The high rate implies that we should have already observed such late core-collapse supernovae, but have not recognized them as such. We argue that φ Persei is a likely progenitor and that eccentric neutron star – white dwarf systems are likely descendants. Late events can help explain the discrepancy in the delay-time distributions derived from supernova remnants in the Magellanic Clouds and extragalactic type Ia events, lowering the contribution of prompt Ia events. We discuss ways to test these predictions and speculate on the implications for supernova feedback in simulations of galaxy evolution."}],"date_updated":"2023-08-09T11:15:49Z","article_processing_charge":"No","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"author":[{"first_name":"E.","last_name":"Zapartas","full_name":"Zapartas, E."},{"last_name":"de Mink","full_name":"de Mink, S. E.","first_name":"S. E."},{"full_name":"Izzard, R. G.","last_name":"Izzard","first_name":"R. G."},{"last_name":"Yoon","full_name":"Yoon, S.-C.","first_name":"S.-C."},{"first_name":"C.","last_name":"Badenes","full_name":"Badenes, C."},{"orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"first_name":"A.","full_name":"de Koter, A.","last_name":"de Koter"},{"first_name":"C. J.","last_name":"Neijssel","full_name":"Neijssel, C. J."},{"first_name":"M.","last_name":"Renzo","full_name":"Renzo, M."},{"first_name":"A.","last_name":"Schootemeijer","full_name":"Schootemeijer, A."},{"first_name":"T. S.","last_name":"Shrotriya","full_name":"Shrotriya, T. S."}],"language":[{"iso":"eng"}],"year":"2017","issue":"A&A","scopus_import":"1","volume":601},{"year":"2017","issue":"8","tmp":{"short":"CC BY (4.0)","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)"},"scopus_import":"1","has_accepted_license":"1","volume":54,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"date_updated":"2025-05-28T11:57:04Z","file":[{"content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"5841","relation":"main_file","file_size":755241,"date_created":"2019-01-17T15:57:29Z","file_name":"2017_ActaInformatica_Giacobbe.pdf","date_updated":"2020-07-14T12:44:46Z","checksum":"4e661d9135d7f8c342e8e258dee76f3e"}],"article_processing_charge":"No","author":[{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco","last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet"},{"last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","first_name":"Ashutosh"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Paixao","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","orcid":"0000-0002-9041-0905"}],"publication_identifier":{"issn":["00015903"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:46Z","publication_status":"published","ddc":["006","576"],"_id":"1351","ec_funded":1,"publist_id":"5898","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"title":"Model checking the evolution of gene regulatory networks","page":"765 - 787","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"date_created":"2018-12-11T11:51:32Z","oa_version":"Published Version","citation":{"ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x"},"publication":"Acta Informatica","type":"journal_article","quality_controlled":"1","pubrep_id":"649","month":"12","related_material":{"record":[{"status":"public","id":"1835","relation":"earlier_version"}]},"status":"public","isi":1,"intvolume":" 54","date_published":"2017-12-01T00:00:00Z","doi":"10.1007/s00236-016-0278-x","oa":1,"day":"01","external_id":{"isi":["000414343200003"]}},{"page":"312 - 337","title":"Adaptive physically based models in computer graphics","department":[{"_id":"ChWo"}],"_id":"1367","publisher":"Wiley-Blackwell","publist_id":"5873","ddc":["000"],"file_date_updated":"2020-07-14T12:44:47Z","publication_status":"published","publication_identifier":{"issn":["01677055"]},"author":[{"first_name":"Pierre","full_name":"Manteaux, Pierre","last_name":"Manteaux"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546"},{"first_name":"Rahul","full_name":"Narain, Rahul","last_name":"Narain"},{"first_name":"Stéphane","last_name":"Redon","full_name":"Redon, Stéphane"},{"full_name":"Faure, François","last_name":"Faure","first_name":"François"},{"first_name":"Marie","last_name":"Cani","full_name":"Cani, Marie"}],"language":[{"iso":"eng"}],"abstract":[{"text":"One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-20T11:05:36Z","file":[{"creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5208","date_created":"2018-12-12T10:16:21Z","file_size":1434439,"date_updated":"2020-07-14T12:44:47Z","file_name":"IST-2016-634-v1+1_starAdaptivity-cgf.pdf","checksum":"7676e9a9ead6d58c3000988c97deb2ef"}],"has_accepted_license":"1","volume":36,"scopus_import":"1","issue":"6","year":"2017","oa":1,"external_id":{"isi":["000408634200019"]},"day":"01","isi":1,"doi":"10.1111/cgf.12941","date_published":"2017-09-01T00:00:00Z","intvolume":" 36","status":"public","pubrep_id":"634","month":"09","acknowledgement":"This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209).","quality_controlled":"1","type":"journal_article","citation":{"ista":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.","chicago":"Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941.","short":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337.","ieee":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” Computer Graphics Forum, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017.","apa":"Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M. (2017). Adaptive physically based models in computer graphics. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941","mla":"Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:10.1111/cgf.12941.","ama":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically based models in computer graphics. Computer Graphics Forum. 2017;36(6):312-337. doi:10.1111/cgf.12941"},"oa_version":"Submitted Version","date_created":"2018-12-11T11:51:37Z","publication":"Computer Graphics Forum"},{"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"author":[{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"last_name":"Brennecke","full_name":"Brennecke, Simon","first_name":"Simon"},{"full_name":"Lein, Manfred","last_name":"Lein","first_name":"Manfred"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy."}],"date_updated":"2023-08-22T08:21:10Z","article_processing_charge":"No","volume":119,"year":"2017","scopus_import":"1","issue":"20","title":"Signatures of electronic structure in bicircular high-harmonic spectroscopy","_id":"14004","article_type":"original","publisher":"American Physical Society","publication_status":"published","month":"11","arxiv":1,"quality_controlled":"1","type":"journal_article","date_created":"2023-08-10T06:35:51Z","citation":{"mla":"Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters, vol. 119, no. 20, 203201, American Physical Society, 2017, doi:10.1103/physrevlett.119.203201.","apa":"Baykusheva, D. R., Brennecke, S., Lein, M., & Wörner, H. J. (2017). Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.119.203201","ama":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 2017;119(20). doi:10.1103/physrevlett.119.203201","chicago":"Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/physrevlett.119.203201.","ista":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20), 203201.","ieee":"D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of electronic structure in bicircular high-harmonic spectroscopy,” Physical Review Letters, vol. 119, no. 20. American Physical Society, 2017.","short":"D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters 119 (2017)."},"oa_version":"Preprint","publication":"Physical Review Letters","oa":1,"day":"17","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.04474"}],"extern":"1","external_id":{"arxiv":["1710.04474"]},"keyword":["General Physics and Astronomy"],"article_number":"203201","intvolume":" 119","doi":"10.1103/physrevlett.119.203201","date_published":"2017-11-17T00:00:00Z","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Strong-field photoelectron holography and laser-induced electron diffraction (LIED) are two powerful emerging methods for probing the ultrafast dynamics of molecules. However, both of them have remained restricted to static systems and to nuclear dynamics induced by strong-field ionization. Here we extend these promising methods to image purely electronic valence-shell dynamics in molecules using photoelectron holography. In the same experiment, we use LIED and photoelectron holography simultaneously, to observe coupled electronic-rotational dynamics taking place on similar timescales. These results offer perspectives for imaging ultrafast dynamics of molecules on femtosecond to attosecond timescales."}],"date_updated":"2023-08-22T08:26:06Z","article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"author":[{"full_name":"Walt, Samuel G.","last_name":"Walt","first_name":"Samuel G."},{"first_name":"Niraghatam","last_name":"Bhargava Ram","full_name":"Bhargava Ram, Niraghatam"},{"last_name":"Atala","full_name":"Atala, Marcos","first_name":"Marcos"},{"first_name":"Nikolay I","full_name":"Shvetsov-Shilovski, Nikolay I","last_name":"Shvetsov-Shilovski"},{"full_name":"von Conta, Aaron","last_name":"von Conta","first_name":"Aaron"},{"last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova"},{"full_name":"Lein, Manfred","last_name":"Lein","first_name":"Manfred"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"language":[{"iso":"eng"}],"pmid":1,"year":"2017","scopus_import":"1","volume":8,"title":"Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering","publication_status":"published","_id":"14005","article_type":"original","publisher":"Springer Nature","quality_controlled":"1","month":"06","date_created":"2023-08-10T06:36:09Z","citation":{"mla":"Walt, Samuel G., et al. “Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography and Rescattering.” Nature Communications, vol. 8, 15651, Springer Nature, 2017, doi:10.1038/ncomms15651.","apa":"Walt, S. G., Bhargava Ram, N., Atala, M., Shvetsov-Shilovski, N. I., von Conta, A., Baykusheva, D. R., … Wörner, H. J. (2017). Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms15651","ama":"Walt SG, Bhargava Ram N, Atala M, et al. Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. Nature Communications. 2017;8. doi:10.1038/ncomms15651","chicago":"Walt, Samuel G., Niraghatam Bhargava Ram, Marcos Atala, Nikolay I Shvetsov-Shilovski, Aaron von Conta, Denitsa Rangelova Baykusheva, Manfred Lein, and Hans Jakob Wörner. “Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography and Rescattering.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/ncomms15651.","ista":"Walt SG, Bhargava Ram N, Atala M, Shvetsov-Shilovski NI, von Conta A, Baykusheva DR, Lein M, Wörner HJ. 2017. Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. Nature Communications. 8, 15651.","ieee":"S. G. Walt et al., “Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering,” Nature Communications, vol. 8. Springer Nature, 2017.","short":"S.G. Walt, N. Bhargava Ram, M. Atala, N.I. Shvetsov-Shilovski, A. von Conta, D.R. Baykusheva, M. Lein, H.J. Wörner, Nature Communications 8 (2017)."},"oa_version":"Published Version","publication":"Nature Communications","type":"journal_article","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/ncomms15651","open_access":"1"}],"day":"15","external_id":{"pmid":["28643771"]},"extern":"1","status":"public","article_number":"15651","intvolume":" 8","doi":"10.1038/ncomms15651","date_published":"2017-06-15T00:00:00Z"},{"keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"external_id":{"arxiv":["1611.09352"]},"extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.09352"}],"day":"15","oa":1,"status":"public","doi":"10.1088/1361-6455/aa62b5","date_published":"2017-03-15T00:00:00Z","intvolume":" 50","article_number":"078002","quality_controlled":"1","arxiv":1,"month":"03","publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","citation":{"ista":"Baykusheva DR, Wörner HJ. 2017. Comment on ‘Time delays in molecular photoionization’. Journal of Physics B: Atomic, Molecular and Optical Physics. 50(7), 078002.","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time Delays in Molecular Photoionization.’” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing, 2017. https://doi.org/10.1088/1361-6455/aa62b5.","short":"D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 50 (2017).","ieee":"D. R. Baykusheva and H. J. Wörner, “Comment on ‘Time delays in molecular photoionization,’” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 50, no. 7. IOP Publishing, 2017.","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time Delays in Molecular Photoionization.’” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 50, no. 7, 078002, IOP Publishing, 2017, doi:10.1088/1361-6455/aa62b5.","apa":"Baykusheva, D. R., & Wörner, H. J. (2017). Comment on ‘Time delays in molecular photoionization.’ Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing. https://doi.org/10.1088/1361-6455/aa62b5","ama":"Baykusheva DR, Wörner HJ. Comment on ‘Time delays in molecular photoionization.’ Journal of Physics B: Atomic, Molecular and Optical Physics. 2017;50(7). doi:10.1088/1361-6455/aa62b5"},"oa_version":"Preprint","date_created":"2023-08-10T06:36:29Z","type":"journal_article","title":"Comment on ‘Time delays in molecular photoionization’","publication_status":"published","publisher":"IOP Publishing","article_type":"letter_note","_id":"14007","article_processing_charge":"No","date_updated":"2023-08-22T08:32:43Z","abstract":[{"text":"In a recent article by Hockett et al (2016 J. Phys. B: At. Mol. Opt. Phys. 49 095602), time delays arising in the context of molecular single-photon ionization are investigated from a theoretical point of view. We argue that one of the central equations given in this article is incorrect and present a reformulation that is consistent with the established treatment of angle-dependent scattering delays (Eisenbud 1948 PhD Thesis Princeton University; Wigner 1955 Phys. Rev. 98 145–7; Smith 1960 Phys. Rev. 118 349–6; Nussenzveig 1972 Phys. Rev. D 6 1534–42).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0953-4075"],"eissn":["1361-6455"]},"author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"issue":"7","scopus_import":"1","year":"2017","volume":50},{"status":"public","article_number":"203201","doi":"10.1103/physrevlett.119.203201","date_published":"2017-11-17T00:00:00Z","intvolume":" 119","keyword":["General Physics and Astronomy"],"oa":1,"extern":"1","external_id":{"arxiv":["1710.04474"],"pmid":["29219334"]},"day":"17","main_file_link":[{"url":"https://arxiv.org/abs/1710.04474","open_access":"1"}],"citation":{"apa":"Baykusheva, D. R., Brennecke, S., Lein, M., & Wörner, H. J. (2017). Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.119.203201","mla":"Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters, vol. 119, no. 20, 203201, American Physical Society, 2017, doi:10.1103/physrevlett.119.203201.","ama":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 2017;119(20). doi:10.1103/physrevlett.119.203201","chicago":"Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/physrevlett.119.203201.","ista":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20), 203201.","short":"D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters 119 (2017).","ieee":"D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of electronic structure in bicircular high-harmonic spectroscopy,” Physical Review Letters, vol. 119, no. 20. American Physical Society, 2017."},"oa_version":"Preprint","date_created":"2023-08-10T06:48:12Z","publication":"Physical Review Letters","type":"journal_article","quality_controlled":"1","month":"11","arxiv":1,"publication_status":"published","_id":"14031","publisher":"American Physical Society","article_type":"original","title":"Signatures of electronic structure in bicircular high-harmonic spectroscopy","scopus_import":"1","issue":"20","year":"2017","volume":119,"abstract":[{"text":"High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2023-08-22T06:48:28Z","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"first_name":"Simon","full_name":"Brennecke, Simon","last_name":"Brennecke"},{"last_name":"Lein","full_name":"Lein, Manfred","first_name":"Manfred"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"pmid":1,"language":[{"iso":"eng"}]},{"month":"02","arxiv":1,"quality_controlled":"1","type":"journal_article","date_created":"2018-12-11T11:51:50Z","citation":{"ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006."},"oa_version":"Preprint","publication":"Nonlinear Analysis: Hybrid Systems","oa":1,"day":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.5387"}],"external_id":{"arxiv":["1410.5387"],"isi":["000390637000014"]},"isi":1,"intvolume":" 23","doi":"10.1016/j.nahs.2016.04.006","date_published":"2017-02-01T00:00:00Z","related_material":{"record":[{"id":"1689","relation":"earlier_version","status":"public"}]},"status":"public","author":[{"first_name":"Mária","full_name":"Svoreňová, Mária","last_name":"Svoreňová"},{"orcid":"0000-0002-8122-2881","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","first_name":"Jan"},{"first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Ivana","last_name":"Cěrná","full_name":"Cěrná, Ivana"},{"first_name":"Cǎlin","last_name":"Belta","full_name":"Belta, Cǎlin"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study.","lang":"eng"}],"date_updated":"2023-09-20T09:43:09Z","article_processing_charge":"No","volume":23,"year":"2017","scopus_import":"1","issue":"2","title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","page":"230 - 253","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"1407","ec_funded":1,"publist_id":"5800","publisher":"Elsevier","publication_status":"published"},{"department":[{"_id":"FrLo"}],"page":"860-868","title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","publication_status":"published","_id":"14205","publisher":"ML Research Press","abstract":[{"text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-13T09:49:10Z","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"full_name":"Khanna, Rajiv","last_name":"Khanna","first_name":"Rajiv"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2017-04-20","location":"Fort Lauderdale, FL, United States","end_date":"2017-04-22"},"language":[{"iso":"eng"}],"year":"2017","volume":54,"oa":1,"extern":"1","external_id":{"arxiv":["1702.06457"]},"day":"21","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.06457"}],"status":"public","date_published":"2017-02-21T00:00:00Z","intvolume":" 54","quality_controlled":"1","month":"02","arxiv":1,"oa_version":"Preprint","citation":{"ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.","short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 54:860–68. ML Research Press, 2017.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.","ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. Vol 54. ML Research Press; 2017:860-868.","apa":"Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.","mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017, pp. 860–68."},"date_created":"2023-08-22T14:17:19Z","publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","type":"conference"},{"day":"31","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.11041"}],"external_id":{"arxiv":["1705.11041"]},"extern":"1","oa":1,"title":"Greedy algorithms for cone constrained optimization with convergence guarantees","department":[{"_id":"FrLo"}],"date_published":"2017-05-31T00:00:00Z","_id":"14206","status":"public","publication_status":"published","language":[{"iso":"eng"}],"arxiv":1,"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"first_name":"Martin","full_name":"Jaggi, Martin","last_name":"Jaggi"}],"conference":{"start_date":"2017-12-04","name":"NeurIPS: Neural Information Processing Systems","location":"Long Beach, CA, United States","end_date":"2017-12-09"},"publication_identifier":{"isbn":["9781510860964"]},"month":"05","date_updated":"2023-09-13T08:32:23Z","quality_controlled":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings.","lang":"eng"}],"type":"conference","publication":"Advances in Neural Information Processing Systems","year":"2017","date_created":"2023-08-22T14:17:38Z","citation":{"apa":"Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In Advances in Neural Information Processing Systems. Long Beach, CA, United States.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” Advances in Neural Information Processing Systems, 2017.","ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: Advances in Neural Information Processing Systems. ; 2017.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In Advances in Neural Information Processing Systems, 2017.","ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in Advances in Neural Information Processing Systems, Long Beach, CA, United States, 2017.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017."},"oa_version":"Preprint"},{"arxiv":1,"month":"05","quality_controlled":"1","type":"journal_article","publication":"Nature Materials","oa_version":"Preprint","citation":{"ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of chiral colloidal liquid crystals using DNA origami,” Nature Materials, vol. 16, no. 8. Springer Nature, pp. 849–856, 2017.","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, Nature Materials 16 (2017) 849–856.","ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. 16(8), 849–856.","chicago":"Siavashpouri, M, CH Wachauf, MJ Zakhary, Florian M Praetorius, H Dietz, and Z Dogic. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” Nature Materials. Springer Nature, 2017. https://doi.org/10.1038/nmat4909.","ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. 2017;16(8):849-856. doi:10.1038/nmat4909","mla":"Siavashpouri, M., et al. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” Nature Materials, vol. 16, no. 8, Springer Nature, 2017, pp. 849–56, doi:10.1038/nmat4909.","apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., & Dogic, Z. (2017). Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat4909"},"date_created":"2023-09-06T13:37:27Z","external_id":{"arxiv":["1705.08944"],"pmid":["28530665"]},"extern":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1705.08944","open_access":"1"}],"day":"22","oa":1,"doi":"10.1038/nmat4909","date_published":"2017-05-22T00:00:00Z","intvolume":" 16","status":"public","pmid":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"author":[{"first_name":"M","full_name":"Siavashpouri, M","last_name":"Siavashpouri"},{"first_name":"CH","full_name":"Wachauf, CH","last_name":"Wachauf"},{"full_name":"Zakhary, MJ","last_name":"Zakhary","first_name":"MJ"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"},{"full_name":"Dietz, H","last_name":"Dietz","first_name":"H"},{"first_name":"Z","last_name":"Dogic","full_name":"Dogic, Z"}],"article_processing_charge":"No","date_updated":"2023-11-07T11:40:00Z","abstract":[{"lang":"eng","text":"Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":16,"scopus_import":"1","issue":"8","year":"2017","title":"Molecular engineering of chiral colloidal liquid crystals using DNA origami","page":"849-856","publisher":"Springer Nature","article_type":"original","_id":"14309","publication_status":"published"},{"title":"Phat - Persistent homology algorithms toolbox","page":"76 - 90","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems"}],"department":[{"_id":"HeEd"}],"ec_funded":1,"_id":"1433","publisher":"Academic Press","article_type":"original","publist_id":"5765","publication_status":"published","author":[{"first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich"},{"first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael"},{"last_name":"Reininghaus","full_name":"Reininghaus, Jan","first_name":"Jan"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","last_name":"Wagner"}],"publication_identifier":{"issn":[" 07477171"]},"language":[{"iso":"eng"}],"abstract":[{"text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","date_updated":"2023-09-20T09:42:40Z","volume":78,"scopus_import":"1","year":"2017","oa":1,"external_id":{"isi":["000384396000005"]},"day":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jsc.2016.03.008"}],"isi":1,"doi":"10.1016/j.jsc.2016.03.008","date_published":"2017-01-01T00:00:00Z","intvolume":" 78","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10894"}]},"status":"public","month":"01","quality_controlled":"1","type":"journal_article","oa_version":"Published Version","citation":{"apa":"Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. Academic Press. https://doi.org/10.1016/j.jsc.2016.03.008","mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation. Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic Press, pp. 76–90, 2017.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90."},"date_created":"2018-12-11T11:51:59Z","publication":"Journal of Symbolic Computation"},{"department":[{"_id":"GaNo"}],"title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","publication_status":"published","file_date_updated":"2020-07-14T12:46:44Z","ddc":["576","616"],"_id":"540","publisher":"Public Library of Science","publist_id":"7276","abstract":[{"text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"1aa20f19a1e90664fadce6e7d5284fdc","file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","date_updated":"2020-07-14T12:46:44Z","file_id":"4944","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system","file_size":4106772,"date_created":"2018-12-12T10:12:26Z"}],"date_updated":"2021-01-12T08:01:48Z","author":[{"first_name":"Kseniya","full_name":"Khamina, Kseniya","last_name":"Khamina"},{"first_name":"Alexander","last_name":"Lercher","full_name":"Lercher, Alexander"},{"first_name":"Michael","last_name":"Caldera","full_name":"Caldera, Michael"},{"first_name":"Christopher","last_name":"Schliehe","full_name":"Schliehe, Christopher"},{"first_name":"Bojan","last_name":"Vilagos","full_name":"Vilagos, Bojan"},{"first_name":"Mehmet","last_name":"Sahin","full_name":"Sahin, Mehmet"},{"last_name":"Kosack","full_name":"Kosack, Lindsay","first_name":"Lindsay"},{"full_name":"Bhattacharya, Anannya","last_name":"Bhattacharya","first_name":"Anannya"},{"last_name":"Májek","full_name":"Májek, Peter","first_name":"Peter"},{"full_name":"Stukalov, Alexey","last_name":"Stukalov","first_name":"Alexey"},{"first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto","last_name":"Sacco"},{"last_name":"James","full_name":"James, Leo","first_name":"Leo"},{"first_name":"Daniel","full_name":"Pinschewer, Daniel","last_name":"Pinschewer"},{"first_name":"Keiryn","last_name":"Bennett","full_name":"Bennett, Keiryn"},{"first_name":"Jörg","full_name":"Menche, Jörg","last_name":"Menche"},{"last_name":"Bergthaler","full_name":"Bergthaler, Andreas","first_name":"Andreas"}],"publication_identifier":{"issn":["15537366"]},"language":[{"iso":"eng"}],"scopus_import":1,"tmp":{"short":"CC BY (4.0)","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)"},"issue":"12","year":"2017","has_accepted_license":"1","volume":13,"oa":1,"day":"01","status":"public","article_number":"e1006758","doi":"10.1371/journal.ppat.1006758","date_published":"2017-12-01T00:00:00Z","intvolume":" 13","quality_controlled":"1","pubrep_id":"931","month":"12","oa_version":"Published Version","citation":{"ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758."},"date_created":"2018-12-11T11:47:03Z","publication":"PLoS Pathogens","type":"journal_article"},{"month":"12","pubrep_id":"959","quality_controlled":"1","type":"journal_article","publication":"PLoS Genetics","date_created":"2018-12-11T11:47:04Z","oa_version":"Published Version","citation":{"apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122","mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","ieee":"N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017."},"day":"18","oa":1,"intvolume":" 13","date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122","article_number":"e1007122","status":"public","related_material":{"record":[{"id":"9844","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9845"},{"id":"9846","relation":"research_data","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15537390"]},"author":[{"full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090"},{"first_name":"Frank","last_name":"Schreiber","full_name":"Schreiber, Frank"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346"},{"first_name":"Sten","full_name":"Littmann, Sten","last_name":"Littmann"},{"last_name":"Kuypers","full_name":"Kuypers, Marcel","first_name":"Marcel"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"file":[{"date_updated":"2020-07-14T12:46:46Z","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","checksum":"22426d9382f21554bad5fa5967afcfd0","creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"5088","date_created":"2018-12-12T10:14:35Z","file_size":1308475}],"date_updated":"2023-02-23T14:10:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"volume":13,"has_accepted_license":"1","year":"2017","scopus_import":1,"tmp":{"short":"CC BY (4.0)","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)"},"issue":"12","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","department":[{"_id":"CaGu"}],"publist_id":"7275","publisher":"Public Library of Science","_id":"541","ec_funded":1,"publication_status":"published","file_date_updated":"2020-07-14T12:46:46Z","ddc":["576","579"]},{"year":"2017","tmp":{"short":"CC BY (4.0)","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)"},"has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:46:58Z","file_name":"IST-2018-929-v1+1_56106.pdf","checksum":"e1f05e5850dfd9f9434d2d373ca61941","date_created":"2018-12-12T10:12:49Z","file_size":7443683,"creator":"system","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"4969"}],"date_updated":"2024-02-12T12:03:42Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis.","lang":"eng"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"series_title":"Plant Engineering","publication_status":"published","file_date_updated":"2020-07-14T12:46:58Z","ddc":["581"],"publist_id":"7269","publisher":"InTech","_id":"545","ec_funded":1,"department":[{"_id":"JiFr"}],"alternative_title":["Agricultural and Biological Sciences"],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"page":"113 - 140","title":"Vascular tissue development and regeneration in the model plant arabidopsis","publication":"Plant Engineering","date_created":"2018-12-11T11:47:05Z","oa_version":"Published Version","citation":{"mla":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” Plant Engineering, edited by Snježana Jurić, InTech, 2017, pp. 113–40, doi:10.5772/intechopen.69712.","apa":"Mazur, E., & Friml, J. (2017). Vascular tissue development and regeneration in the model plant arabidopsis. In S. Jurić (Ed.), Plant Engineering (pp. 113–140). InTech. https://doi.org/10.5772/intechopen.69712","ama":"Mazur E, Friml J. Vascular tissue development and regeneration in the model plant arabidopsis. In: Jurić S, ed. Plant Engineering. Plant Engineering. InTech; 2017:113-140. doi:10.5772/intechopen.69712","ista":"Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences, , 113–140.","chicago":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” In Plant Engineering, edited by Snježana Jurić, 113–40. Plant Engineering. InTech, 2017. https://doi.org/10.5772/intechopen.69712.","short":"E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, InTech, 2017, pp. 113–140.","ieee":"E. Mazur and J. Friml, “Vascular tissue development and regeneration in the model plant arabidopsis,” in Plant Engineering, S. Jurić, Ed. InTech, 2017, pp. 113–140."},"type":"book_chapter","quality_controlled":"1","pubrep_id":"929","month":"11","status":"public","related_material":{"record":[{"status":"public","id":"1274","relation":"earlier_version"}]},"doi":"10.5772/intechopen.69712","date_published":"2017-11-17T00:00:00Z","day":"17","oa":1,"editor":[{"first_name":"Snježana","last_name":"Jurić","full_name":"Jurić, Snježana"}]},{"publication_date":"2017-06-26","type":"report","year":"2017","date_created":"2018-12-12T11:39:24Z","citation":{"mla":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","apa":"Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria.","ama":"Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017.","chicago":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017.","ieee":"B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017."},"month":"06","pubrep_id":"724","author":[{"orcid":"0000-0003-2724-4614","first_name":"Barbara","full_name":"Barbara Petritsch","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2020-07-14T23:05:03Z","file":[{"file_id":"5483","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system","file_size":3460985,"date_created":"2018-12-12T11:53:22Z","checksum":"6321792dcfa82bf490f17615a9b22355","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","date_updated":"2020-07-14T12:46:59Z"}],"abstract":[{"text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.","lang":"eng"}],"date_published":"2017-06-26T00:00:00Z","publisher":"IST Austria","_id":"5450","status":"public","file_date_updated":"2020-07-14T12:46:59Z","day":"26","main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/724.","open_access":"1"}],"extern":0,"title":"Implementing the institutional data repository IST DataRep","oa":1,"department":[{"_id":"E-Lib"}]},{"date_created":"2018-12-12T11:39:26Z","citation":{"ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1","mla":"Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017.","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1.","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p."},"oa_version":"Published Version","type":"technical_report","pubrep_id":"870","month":"10","status":"public","related_material":{"record":[{"status":"public","id":"10416","relation":"later_version"}]},"date_published":"2017-10-23T00:00:00Z","doi":"10.15479/AT:IST-2017-870-v1-1","day":"23","oa":1,"year":"2017","has_accepted_license":"1","file":[{"date_created":"2018-12-12T11:54:02Z","file_size":960491,"relation":"main_file","file_id":"5524","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"177a84a46e3ac17e87b31534ad16a4c9","date_updated":"2020-07-14T12:46:59Z","file_name":"IST-2017-870-v1+1_main.pdf"}],"date_updated":"2023-02-21T15:54:10Z","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks.","lang":"eng"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Bhavya","full_name":"Choudhary, Bhavya","last_name":"Choudhary"},{"first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"}],"publication_status":"published","file_date_updated":"2020-07-14T12:46:59Z","ddc":["000"],"publisher":"IST Austria","_id":"5455","department":[{"_id":"KrCh"}],"alternative_title":["IST Austria Technical Report"],"page":"37","title":"Optimal Dyck reachability for data-dependence and alias analysis"},{"file_date_updated":"2020-07-14T12:46:59Z","related_material":{"record":[{"relation":"later_version","id":"10417","status":"public"},{"relation":"earlier_version","id":"5448","status":"public"}]},"ddc":["000"],"publication_status":"published","status":"public","_id":"5456","doi":"10.15479/AT:IST-2017-872-v1-1","date_published":"2017-10-23T00:00:00Z","publisher":"IST Austria","department":[{"_id":"KrCh"}],"alternative_title":["IST Austria Technical Report"],"title":"Data-centric dynamic partial order reduction","page":"36","oa":1,"day":"23","date_created":"2018-12-12T11:39:26Z","citation":{"ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1","mla":"Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p."},"oa_version":"Published Version","year":"2017","has_accepted_license":"1","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.","lang":"eng"}],"file":[{"date_created":"2018-12-12T11:53:26Z","file_size":910347,"relation":"main_file","file_id":"5487","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","date_updated":"2020-07-14T12:46:59Z","file_name":"IST-2017-872-v1+1_main.pdf"}],"date_updated":"2023-02-23T12:26:54Z","month":"10","author":[{"last_name":"Chalupa","full_name":"Chalupa, Marek","first_name":"Marek"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas"},{"first_name":"Nishant","last_name":"Sinha","full_name":"Sinha, Nishant"},{"first_name":"Kapil","full_name":"Vaidya, Kapil","last_name":"Vaidya"}],"publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"872","language":[{"iso":"eng"}]},{"ec_funded":1,"_id":"548","publisher":"American Physical Society","publist_id":"7266","publication_status":"published","title":"Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"alternative_title":["Rapid Communications"],"department":[{"_id":"GaTk"}],"volume":96,"scopus_import":"1","issue":"6","year":"2017","author":[{"orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"}],"publication_identifier":{"issn":["2470-0045"]},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2023-10-10T13:29:38Z","article_number":"060401","date_published":"2017-12-21T00:00:00Z","doi":"10.1103/PhysRevE.96.060401","intvolume":" 96","status":"public","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1707.00320","open_access":"1"}],"day":"21","type":"journal_article","oa_version":"Submitted Version","citation":{"ieee":"D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” Physical Review E, vol. 96, no. 6. American Physical Society, 2017.","short":"D. De Martino, Physical Review E 96 (2017).","chicago":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E. American Physical Society, 2017. https://doi.org/10.1103/PhysRevE.96.060401.","ista":"De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.","ama":"De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 2017;96(6). doi:10.1103/PhysRevE.96.060401","apa":"De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.96.060401","mla":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” Physical Review E, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:10.1103/PhysRevE.96.060401."},"date_created":"2018-12-11T11:47:06Z","publication":"Physical Review E","month":"12","quality_controlled":"1"}]