[{"issue":"41","abstract":[{"lang":"eng","text":"Dissipative self-assembly leads to structures and materials that exist away from equilibrium by continuously exchanging energy and materials with the external environment. Although this mode of self-assembly is ubiquitous in nature, where it gives rise to functions such as signal processing, motility, self-healing, self-replication, and ultimately life, examples of dissipative self-assembly processes in man-made systems are few and far between. Herein, recent progress in developing diverse synthetic dissipative self-assembly systems is discussed. The systems reported thus far can be categorized into three classes, in which: i) the fuel chemically modifies the building blocks, thus triggering their self-assembly, ii) the fuel acts as a template interacting with the building blocks noncovalently, and iii) transient states are induced by the addition of two mutually exclusive stimuli. These early studies give rise to materials that would be difficult to obtain otherwise, including hydrogels with programmable lifetimes, vesicular nanoreactors, and membranes exhibiting transient conductivity."}],"volume":30,"date_published":"2018-10-11T00:00:00Z","author":[{"first_name":"Soumen","last_name":"De","full_name":"De, Soumen"},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"day":"11","year":"2018","language":[{"iso":"eng"}],"publication":"Advanced Materials","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"publisher":"Wiley","pmid":1,"scopus_import":"1","article_type":"original","date_created":"2023-08-01T09:39:46Z","article_number":"1706750","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","oa_version":"None","date_updated":"2023-08-07T10:56:26Z","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"publication_status":"published","article_processing_charge":"No","citation":{"apa":"De, S., &#38; Klajn, R. (2018). Dissipative self-assembly driven by the consumption of chemical fuels. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201706750\">https://doi.org/10.1002/adma.201706750</a>","mla":"De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption of Chemical Fuels.” <i>Advanced Materials</i>, vol. 30, no. 41, 1706750, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/adma.201706750\">10.1002/adma.201706750</a>.","ama":"De S, Klajn R. Dissipative self-assembly driven by the consumption of chemical fuels. <i>Advanced Materials</i>. 2018;30(41). doi:<a href=\"https://doi.org/10.1002/adma.201706750\">10.1002/adma.201706750</a>","chicago":"De, Soumen, and Rafal Klajn. “Dissipative Self-Assembly Driven by the Consumption of Chemical Fuels.” <i>Advanced Materials</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/adma.201706750\">https://doi.org/10.1002/adma.201706750</a>.","short":"S. De, R. Klajn, Advanced Materials 30 (2018).","ieee":"S. De and R. Klajn, “Dissipative self-assembly driven by the consumption of chemical fuels,” <i>Advanced Materials</i>, vol. 30, no. 41. Wiley, 2018.","ista":"De S, Klajn R. 2018. Dissipative self-assembly driven by the consumption of chemical fuels. Advanced Materials. 30(41), 1706750."},"extern":"1","status":"public","type":"journal_article","title":"Dissipative self-assembly driven by the consumption of chemical fuels","_id":"13375","intvolume":"        30","doi":"10.1002/adma.201706750","external_id":{"pmid":["29520846"]},"quality_controlled":"1"},{"article_type":"original","date_created":"2023-08-01T09:40:00Z","scopus_import":"1","publisher":"Proceedings of the National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1712787115"}],"pmid":1,"keyword":["Multidisciplinary"],"day":"01","language":[{"iso":"eng"}],"year":"2018","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","text":"Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light."}],"volume":115,"date_published":"2018-05-01T00:00:00Z","author":[{"first_name":"Dipak","last_name":"Samanta","full_name":"Samanta, Dipak"},{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"full_name":"Chu, Zonglin","last_name":"Chu","first_name":"Zonglin"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"last_name":"Shimon","first_name":"Linda J. W.","full_name":"Shimon, Linda J. W."},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","first_name":"Rafal"}],"issue":"38","quality_controlled":"1","_id":"13376","page":"9379-9384","intvolume":"       115","doi":"10.1073/pnas.1712787115","external_id":{"pmid":["29717041"]},"type":"journal_article","status":"public","title":"Reversible photoswitching of encapsulated azobenzenes in water","citation":{"short":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L.J.W. Shimon, R. Klajn, Proceedings of the National Academy of Sciences 115 (2018) 9379–9384.","ama":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. Reversible photoswitching of encapsulated azobenzenes in water. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(38):9379-9384. doi:<a href=\"https://doi.org/10.1073/pnas.1712787115\">10.1073/pnas.1712787115</a>","chicago":"Samanta, Dipak, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J. W. Shimon, and Rafal Klajn. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1712787115\">https://doi.org/10.1073/pnas.1712787115</a>.","mla":"Samanta, Dipak, et al. “Reversible Photoswitching of Encapsulated Azobenzenes in Water.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 38, Proceedings of the National Academy of Sciences, 2018, pp. 9379–84, doi:<a href=\"https://doi.org/10.1073/pnas.1712787115\">10.1073/pnas.1712787115</a>.","apa":"Samanta, D., Gemen, J., Chu, Z., Diskin-Posner, Y., Shimon, L. J. W., &#38; Klajn, R. (2018). Reversible photoswitching of encapsulated azobenzenes in water. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1712787115\">https://doi.org/10.1073/pnas.1712787115</a>","ista":"Samanta D, Gemen J, Chu Z, Diskin-Posner Y, Shimon LJW, Klajn R. 2018. Reversible photoswitching of encapsulated azobenzenes in water. Proceedings of the National Academy of Sciences. 115(38), 9379–9384.","ieee":"D. Samanta, J. Gemen, Z. Chu, Y. Diskin-Posner, L. J. W. Shimon, and R. Klajn, “Reversible photoswitching of encapsulated azobenzenes in water,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 38. Proceedings of the National Academy of Sciences, pp. 9379–9384, 2018."},"article_processing_charge":"No","extern":"1","date_updated":"2023-08-07T10:58:11Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","oa_version":"Published Version"},{"date_updated":"2023-08-07T11:14:28Z","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","oa_version":"Published Version","quality_controlled":"1","page":"7023-7027","_id":"13377","intvolume":"        57","doi":"10.1002/anie.201800673","external_id":{"pmid":["29673022"]},"type":"journal_article","status":"public","title":"“Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles","citation":{"ista":"Chu Z, Han Y, Král P, Klajn R. 2018. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. Angewandte Chemie International Edition. 57(24), 7023–7027.","ieee":"Z. Chu, Y. Han, P. Král, and R. Klajn, “‘Precipitation on nanoparticles’: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles,” <i>Angewandte Chemie International Edition</i>, vol. 57, no. 24. Wiley, pp. 7023–7027, 2018.","short":"Z. Chu, Y. Han, P. Král, R. Klajn, Angewandte Chemie International Edition 57 (2018) 7023–7027.","chicago":"Chu, Zonglin, Yanxiao Han, Petr Král, and Rafal Klajn. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” <i>Angewandte Chemie International Edition</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/anie.201800673\">https://doi.org/10.1002/anie.201800673</a>.","ama":"Chu Z, Han Y, Král P, Klajn R. “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. <i>Angewandte Chemie International Edition</i>. 2018;57(24):7023-7027. doi:<a href=\"https://doi.org/10.1002/anie.201800673\">10.1002/anie.201800673</a>","apa":"Chu, Z., Han, Y., Král, P., &#38; Klajn, R. (2018). “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201800673\">https://doi.org/10.1002/anie.201800673</a>","mla":"Chu, Zonglin, et al. “‘Precipitation on Nanoparticles’: Attractive Intermolecular Interactions Stabilize Specific Ligand Ratios on the Surfaces of Nanoparticles.” <i>Angewandte Chemie International Edition</i>, vol. 57, no. 24, Wiley, 2018, pp. 7023–27, doi:<a href=\"https://doi.org/10.1002/anie.201800673\">10.1002/anie.201800673</a>."},"article_processing_charge":"No","extern":"1","keyword":["General Chemistry","Catalysis"],"day":"11","language":[{"iso":"eng"}],"year":"2018","publication":"Angewandte Chemie International Edition","abstract":[{"lang":"eng","text":"Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self-assembled monolayers obtained by co-adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on-nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well-defined hybrid organic–inorganic nanostructures."}],"volume":57,"date_published":"2018-06-11T00:00:00Z","author":[{"last_name":"Chu","first_name":"Zonglin","full_name":"Chu, Zonglin"},{"full_name":"Han, Yanxiao","first_name":"Yanxiao","last_name":"Han"},{"full_name":"Král, Petr","last_name":"Král","first_name":"Petr"},{"last_name":"Klajn","first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"issue":"24","date_created":"2023-08-01T09:40:16Z","article_type":"original","scopus_import":"1","publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.201800673"}],"pmid":1},{"intvolume":"        39","_id":"13379","external_id":{"pmid":["29314396"]},"doi":"10.1002/marc.201700827","quality_controlled":"1","citation":{"ista":"Bléger D, Klajn R. 2018. Integrating macromolecules with molecular switches. Macromolecular Rapid Communications. 39(1), 1700827.","ieee":"D. Bléger and R. Klajn, “Integrating macromolecules with molecular switches,” <i>Macromolecular Rapid Communications</i>, vol. 39, no. 1. Wiley, 2018.","mla":"Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular Switches.” <i>Macromolecular Rapid Communications</i>, vol. 39, no. 1, 1700827, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/marc.201700827\">10.1002/marc.201700827</a>.","apa":"Bléger, D., &#38; Klajn, R. (2018). Integrating macromolecules with molecular switches. <i>Macromolecular Rapid Communications</i>. Wiley. <a href=\"https://doi.org/10.1002/marc.201700827\">https://doi.org/10.1002/marc.201700827</a>","chicago":"Bléger, David, and Rafal Klajn. “Integrating Macromolecules with Molecular Switches.” <i>Macromolecular Rapid Communications</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/marc.201700827\">https://doi.org/10.1002/marc.201700827</a>.","ama":"Bléger D, Klajn R. Integrating macromolecules with molecular switches. <i>Macromolecular Rapid Communications</i>. 2018;39(1). doi:<a href=\"https://doi.org/10.1002/marc.201700827\">10.1002/marc.201700827</a>","short":"D. Bléger, R. Klajn, Macromolecular Rapid Communications 39 (2018)."},"extern":"1","article_processing_charge":"No","status":"public","type":"journal_article","title":"Integrating macromolecules with molecular switches","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"01","publication_identifier":{"eissn":["1521-3927"],"issn":["1022-1336"]},"date_updated":"2023-08-07T11:16:49Z","oa":1,"publication_status":"published","article_number":"1700827","article_type":"letter_note","date_created":"2023-08-01T09:40:48Z","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/marc.201700827"}],"publisher":"Wiley","scopus_import":"1","year":"2018","language":[{"iso":"eng"}],"day":"08","publication":"Macromolecular Rapid Communications","keyword":["Materials Chemistry","Polymers and Plastics","Organic Chemistry"],"issue":"1","date_published":"2018-01-08T00:00:00Z","volume":39,"author":[{"full_name":"Bléger, David","last_name":"Bléger","first_name":"David"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}]},{"article_number":"94","alternative_title":["SIGGRAPH"],"has_accepted_license":"1","ddc":["000"],"date_updated":"2024-02-28T13:58:51Z","oa":1,"publication_status":"published","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/"}]},"publist_id":"7789","month":"07","oa_version":"Published Version","status":"public","type":"journal_article","tmp":{"image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"title":"Water surface wavelets","isi":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","citation":{"short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. <i>ACM Transactions on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., &#38; Wojtan, C. (2018). Water surface wavelets. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4, 94, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>.","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4. ACM, 2018.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94."},"department":[{"_id":"ChWo"}],"quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"134","intvolume":"        37","doi":"10.1145/3197517.3201336","external_id":{"isi":["000448185000055"]},"volume":37,"abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"date_published":"2018-07-30T00:00:00Z","author":[{"last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","first_name":"Tomas"},{"last_name":"Mueller Fischer","first_name":"Matthias","full_name":"Mueller Fischer, Matthias"},{"last_name":"Chentanez","first_name":"Nuttapong","full_name":"Chentanez, Nuttapong"},{"first_name":"Miles","last_name":"Macklin","full_name":"Macklin, Miles"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J"}],"issue":"4","file_date_updated":"2020-07-14T12:44:45Z","ec_funded":1,"day":"30","year":"2018","language":[{"iso":"eng"}],"publication":"ACM Transactions on Graphics","scopus_import":"1","publisher":"ACM","file":[{"access_level":"open_access","file_size":22185016,"file_name":"2018_ACM_Jeschke.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:45Z","checksum":"db75ebabe2ec432bf41389e614d6ef62","relation":"main_file","date_created":"2018-12-18T09:59:23Z","creator":"dernst","file_id":"5744"}],"date_created":"2018-12-11T11:44:48Z","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"638176"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"_id":"13473","intvolume":"       615","doi":"10.1051/0004-6361/201731194","external_id":{"arxiv":["1803.02379"]},"quality_controlled":"1","article_processing_charge":"No","extern":"1","citation":{"ista":"Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. 2018. Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. Astronomy &#38; Astrophysics. 615, A30.","ieee":"A. Schootemeijer, Y. L. L. Götberg, S. E. de Mink, D. Gies, and E. Zapartas, “Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei,” <i>Astronomy &#38; Astrophysics</i>, vol. 615. EDP Sciences, 2018.","mla":"Schootemeijer, A., et al. “Clues about the Scarcity of Stripped-Envelope Stars from the Evolutionary State of the SdO+Be Binary System φ Persei.” <i>Astronomy &#38; Astrophysics</i>, vol. 615, A30, EDP Sciences, 2018, doi:<a href=\"https://doi.org/10.1051/0004-6361/201731194\">10.1051/0004-6361/201731194</a>.","apa":"Schootemeijer, A., Götberg, Y. L. L., de Mink, S. E., Gies, D., &#38; Zapartas, E. (2018). Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201731194\">https://doi.org/10.1051/0004-6361/201731194</a>","short":"A. Schootemeijer, Y.L.L. Götberg, S.E. de Mink, D. Gies, E. Zapartas, Astronomy &#38; Astrophysics 615 (2018).","chicago":"Schootemeijer, A., Ylva Louise Linsdotter Götberg, S. E. de Mink, D. Gies, and E. Zapartas. “Clues about the Scarcity of Stripped-Envelope Stars from the Evolutionary State of the SdO+Be Binary System φ Persei.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2018. <a href=\"https://doi.org/10.1051/0004-6361/201731194\">https://doi.org/10.1051/0004-6361/201731194</a>.","ama":"Schootemeijer A, Götberg YLL, de Mink SE, Gies D, Zapartas E. Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei. <i>Astronomy &#38; Astrophysics</i>. 2018;615. doi:<a href=\"https://doi.org/10.1051/0004-6361/201731194\">10.1051/0004-6361/201731194</a>"},"status":"public","type":"journal_article","title":"Clues about the scarcity of stripped-envelope stars from the evolutionary state of the sdO+Be binary system φ Persei","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"07","date_updated":"2023-08-09T12:22:52Z","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","oa":1,"arxiv":1,"article_number":"A30","date_created":"2023-08-03T10:14:37Z","article_type":"original","publisher":"EDP Sciences","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201731194"}],"scopus_import":"1","day":"06","language":[{"iso":"eng"}],"year":"2018","publication":"Astronomy & Astrophysics","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"abstract":[{"lang":"eng","text":"Stripped-envelope stars form in binary systems after losing mass through Roche-lobe overflow. They bear astrophysical significance as sources of UV and ionizing radiation in older stellar populations and, if sufficiently massive, as stripped supernova progenitors. Binary evolutionary models predict that they are common, but only a handful of subdwarfs with B-type companions are known. The question is whether a large population of such systems has evaded detection as a result of biases, or whether the model predictions are wrong. We reanalyze the well-studied post-interaction binary φ Persei. Recently, new data have improved the orbital solution of the system, which contains an ~1.2M⊙ stripped-envelope star and a rapidly rotating ~9.6M⊙ Be star. We compare with an extensive grid of evolutionary models using a Bayesian approach and constrain the initial masses of the progenitor to 7.2 ± 0.4M⊙ for the stripped star and 3.8 ± 0.4M⊙ for the Be star. The system must have evolved through near-conservative mass transfer. These findings are consistent with earlier studies. The age we obtain, 57 ± 9 Myr, is in excellent agreement with the age of the α Persei cluster. We note that neither star was initially massive enough to produce a core-collapse supernova, but mass exchange pushed the Be star above the mass threshold. We find that the subdwarf is overluminous for its mass by almost an order of magnitude, compared to the expectations for a helium core burning star. We can only reconcile this if the subdwarf resides in a late phase of helium shell burning, which lasts only 2–3% of the total lifetime as a subdwarf. Assuming continuous star formation implies that up to ~50 less evolved, dimmer subdwarfs exist for each system similar to φ Persei, but have evaded detection so far. Our findings can be interpreted as a strong indication that a substantial population of stripped-envelope stars indeed exists, but has so far evaded detection because of observational biases and lack of large-scale systematic searches."}],"volume":615,"date_published":"2018-07-06T00:00:00Z","author":[{"first_name":"A.","last_name":"Schootemeijer","full_name":"Schootemeijer, A."},{"orcid":"0000-0002-6960-6911","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","full_name":"Götberg, Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"first_name":"S. E.","last_name":"de Mink","full_name":"de Mink, S. E."},{"first_name":"D.","last_name":"Gies","full_name":"Gies, D."},{"full_name":"Zapartas, E.","last_name":"Zapartas","first_name":"E."}]},{"article_type":"original","date_created":"2023-08-03T10:14:47Z","publisher":"Oxford University Press","main_file_link":[{"url":"https://doi.org/10.1093/mnras/stx3181","open_access":"1"}],"scopus_import":"1","publication":"Monthly Notices of the Royal Astronomical Society","day":"01","year":"2018","language":[{"iso":"eng"}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"issue":"1","author":[{"last_name":"Smith","first_name":"Nathan","full_name":"Smith, Nathan"},{"full_name":"Götberg, Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","first_name":"Ylva Louise Linsdotter","last_name":"Götberg","orcid":"0000-0002-6960-6911"},{"full_name":"de Mink, Selma E","first_name":"Selma E","last_name":"de Mink"}],"abstract":[{"lang":"eng","text":"Recent surveys of the Magellanic Clouds have revealed a subtype of Wolf–Rayet (WR) star with peculiar properties. WN3/O3 spectra exhibit both WR-like emission and O3 V-like absorption – but at lower luminosity than O3 V or WN stars. We examine the projected spatial distribution of WN3/O3 stars in the Large Magellanic Cloud as compared to O-type stars. Surprisingly, WN3/O3 stars are among the most isolated of all classes of massive stars; they have a distribution similar to red supergiants dominated by initial masses of 10–15 M⊙, and are far more dispersed than classical WR stars or luminous blue variables. Their lack of association with clusters of O-type stars suggests strongly that WN3/O3 stars are not the descendants of single massive stars (30 M⊙ or above). Instead, they are likely products of interacting binaries at lower initial mass (10–18 M⊙). Comparison with binary models suggests a probable origin with primaries in this mass range that were stripped of their H envelopes through non-conservative mass transfer by a low-mass secondary. We show that model spectra and positions on the Hertzsprung–Russell diagram for binary-stripped stars are consistent with WN3/O3 stars. Monitoring radial velocities with high-resolution spectra can test for low-mass companions or runaway velocities. With lower initial mass and environments that avoid very massive stars, the WN3/O3 stars fit expectations for progenitors of Type Ib and possibly Type Ibn supernovae."}],"volume":475,"date_published":"2018-03-01T00:00:00Z","doi":"10.1093/mnras/stx3181","external_id":{"arxiv":["1704.03516"]},"_id":"13474","page":"772-782","intvolume":"       475","quality_controlled":"1","article_processing_charge":"No","extern":"1","citation":{"chicago":"Smith, Nathan, Ylva Louise Linsdotter Götberg, and Selma E de Mink. “Extreme Isolation of WN3/O3 Stars and Implications for Their Evolutionary Origin as the Elusive Stripped Binaries.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/mnras/stx3181\">https://doi.org/10.1093/mnras/stx3181</a>.","short":"N. Smith, Y.L.L. Götberg, S.E. de Mink, Monthly Notices of the Royal Astronomical Society 475 (2018) 772–782.","ama":"Smith N, Götberg YLL, de Mink SE. Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. <i>Monthly Notices of the Royal Astronomical Society</i>. 2018;475(1):772-782. doi:<a href=\"https://doi.org/10.1093/mnras/stx3181\">10.1093/mnras/stx3181</a>","apa":"Smith, N., Götberg, Y. L. L., &#38; de Mink, S. E. (2018). Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stx3181\">https://doi.org/10.1093/mnras/stx3181</a>","mla":"Smith, Nathan, et al. “Extreme Isolation of WN3/O3 Stars and Implications for Their Evolutionary Origin as the Elusive Stripped Binaries.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 475, no. 1, Oxford University Press, 2018, pp. 772–82, doi:<a href=\"https://doi.org/10.1093/mnras/stx3181\">10.1093/mnras/stx3181</a>.","ista":"Smith N, Götberg YLL, de Mink SE. 2018. Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries. Monthly Notices of the Royal Astronomical Society. 475(1), 772–782.","ieee":"N. Smith, Y. L. L. Götberg, and S. E. de Mink, “Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 475, no. 1. Oxford University Press, pp. 772–782, 2018."},"title":"Extreme isolation of WN3/O3 stars and implications for their evolutionary origin as the elusive stripped binaries","type":"journal_article","status":"public","month":"03","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"date_updated":"2023-08-09T12:17:34Z","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"arxiv":1},{"extern":"1","article_processing_charge":"No","citation":{"ama":"Götberg YLL, de Mink SE, Groh JH, et al. Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. <i>Astronomy &#38;amp; Astrophysics</i>. 2018;615. doi:<a href=\"https://doi.org/10.1051/0004-6361/201732274\">10.1051/0004-6361/201732274</a>","short":"Y.L.L. Götberg, S.E. de Mink, J.H. Groh, T. Kupfer, P.A. Crowther, E. Zapartas, M. Renzo, Astronomy &#38;amp; Astrophysics 615 (2018).","chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, T. Kupfer, P. A. Crowther, E. Zapartas, and M. Renzo. “Spectral Models for Binary Products: Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.” <i>Astronomy &#38;amp; Astrophysics</i>. EDP Sciences, 2018. <a href=\"https://doi.org/10.1051/0004-6361/201732274\">https://doi.org/10.1051/0004-6361/201732274</a>.","mla":"Götberg, Ylva Louise Linsdotter, et al. “Spectral Models for Binary Products: Unifying Subdwarfs and Wolf-Rayet Stars as a Sequence of Stripped-Envelope Stars.” <i>Astronomy &#38;amp; Astrophysics</i>, vol. 615, A78, EDP Sciences, 2018, doi:<a href=\"https://doi.org/10.1051/0004-6361/201732274\">10.1051/0004-6361/201732274</a>.","apa":"Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Kupfer, T., Crowther, P. A., Zapartas, E., &#38; Renzo, M. (2018). Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. <i>Astronomy &#38;amp; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/201732274\">https://doi.org/10.1051/0004-6361/201732274</a>","ista":"Götberg YLL, de Mink SE, Groh JH, Kupfer T, Crowther PA, Zapartas E, Renzo M. 2018. Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars. Astronomy &#38;amp; Astrophysics. 615, A78.","ieee":"Y. L. L. Götberg <i>et al.</i>, “Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars,” <i>Astronomy &#38;amp; Astrophysics</i>, vol. 615. EDP Sciences, 2018."},"title":"Spectral models for binary products: Unifying subdwarfs and Wolf-Rayet stars as a sequence of stripped-envelope stars","type":"journal_article","status":"public","doi":"10.1051/0004-6361/201732274","external_id":{"arxiv":["1802.03018"]},"_id":"13475","intvolume":"       615","quality_controlled":"1","arxiv":1,"article_number":"A78","month":"07","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"date_updated":"2023-08-09T11:22:17Z","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publisher":"EDP Sciences","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201732274"}],"scopus_import":"1","article_type":"original","date_created":"2023-08-03T10:15:00Z","author":[{"last_name":"Götberg","first_name":"Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","full_name":"Götberg, Ylva Louise Linsdotter"},{"first_name":"S. E.","last_name":"de Mink","full_name":"de Mink, S. E."},{"first_name":"J. H.","last_name":"Groh","full_name":"Groh, J. H."},{"full_name":"Kupfer, T.","last_name":"Kupfer","first_name":"T."},{"full_name":"Crowther, P. A.","last_name":"Crowther","first_name":"P. A."},{"full_name":"Zapartas, E.","last_name":"Zapartas","first_name":"E."},{"full_name":"Renzo, M.","last_name":"Renzo","first_name":"M."}],"volume":615,"abstract":[{"lang":"eng","text":"Stars stripped of their hydrogen-rich envelope through interaction with a binary companion are generally not considered when accounting for ionizing radiation from stellar populations, despite the expectation that stripped stars emit hard ionizing radiation, form frequently, and live 10–100 times longer than single massive stars. We compute the first grid of evolutionary and spectral models specially made for stars stripped in binaries for a range of progenitor masses (2–20 M⊙) and metallicities ranging from solar to values representative for pop II stars. For stripped stars with masses in the range 0.3–7 M⊙, we find consistently high effective temperatures (20 000–100 000 K, increasing with mass), small radii (0.2–1 R⊙), and high bolometric luminosities, comparable to that of their progenitor before stripping. The spectra show a continuous sequence that naturally bridges subdwarf-type stars at the low-mass end and Wolf-Rayet-like spectra at the high-mass end. For intermediate masses we find hybrid spectral classes showing a mixture of absorption and emission lines. These appear for stars with mass-loss rates of 10−8−10−6 M⊙ yr−1, which have semi-transparent atmospheres. At low metallicity, substantial hydrogen-rich layers are left at the surface and we predict spectra that resemble O-type stars instead. We obtain spectra undistinguishable from subdwarfs for stripped stars with masses up to 1.7 M⊙, which questions whether the widely adopted canonical value of 0.47 M⊙ is uniformly valid. Only a handful of stripped stars of intermediate mass have currently been identified observationally. Increasing this sample will provide necessary tests for the physics of interaction, internal mixing, and stellar winds. We use our model spectra to investigate the feasibility to detect stripped stars next to an optically bright companion and recommend systematic searches for their UV excess and possible emission lines, most notably HeII λ4686 in the optical and HeII λ1640 in the UV. Our models are publicly available for further investigations or inclusion in spectral synthesis simulations."}],"date_published":"2018-07-17T00:00:00Z","publication":"Astronomy &amp; Astrophysics","day":"17","year":"2018","language":[{"iso":"eng"}],"keyword":["Space and Planetary Science","Astronomy and Astrophysics"]},{"scopus_import":"1","publisher":"Wiley","file":[{"date_updated":"2020-10-08T08:38:23Z","content_type":"application/pdf","file_name":"exnbflip.pdf","access_level":"open_access","file_size":54309947,"file_id":"8627","date_created":"2020-10-08T08:38:23Z","creator":"wojtan","relation":"main_file","checksum":"8edb90da8a72395eb5d970580e0925b6","success":1}],"project":[{"call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"article_type":"original","date_created":"2018-12-11T11:44:49Z","author":[{"last_name":"Sato","first_name":"Takahiro","full_name":"Sato, Takahiro"},{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"full_name":"Ando, Ryoichi","last_name":"Ando","first_name":"Ryoichi"}],"date_published":"2018-05-22T00:00:00Z","volume":37,"abstract":[{"text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.","lang":"eng"}],"file_date_updated":"2020-10-08T08:38:23Z","issue":"2","ec_funded":1,"publication":"Computer Graphics Forum","language":[{"iso":"eng"}],"year":"2018","day":"22","title":"Extended narrow band FLIP for liquid simulations","status":"public","type":"journal_article","citation":{"apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., &#38; Ando, R. (2018). Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>.","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. 2018;37(2):169-177. doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” <i>Computer Graphics Forum</i>, vol. 37, no. 2. Wiley, pp. 169–177, 2018."},"article_processing_charge":"No","isi":1,"quality_controlled":"1","department":[{"_id":"ChWo"}],"external_id":{"isi":["000434085600016"]},"doi":"10.1111/cgf.13351","intvolume":"        37","_id":"135","page":"169 - 177","has_accepted_license":"1","alternative_title":["Eurographics"],"publication_status":"published","oa":1,"publication_identifier":{"issn":["0167-7055"]},"date_updated":"2023-09-11T14:00:26Z","ddc":["006"],"month":"05","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"language":[{"iso":"eng"}],"year":"2018","day":"13","publication":"Physical Review E","issue":"2","date_published":"2018-08-13T00:00:00Z","volume":98,"abstract":[{"lang":"eng","text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space."}],"author":[{"last_name":"Suri","first_name":"Balachandra","full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jeffrey","last_name":"Tithof","full_name":"Tithof, Jeffrey"},{"full_name":"Grigoriev, Roman","last_name":"Grigoriev","first_name":"Roman"},{"full_name":"Schatz, Michael","first_name":"Michael","last_name":"Schatz"}],"date_created":"2018-12-11T11:44:49Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.02088"}],"publisher":"American Physical Society","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","oa_version":"Submitted Version","date_updated":"2023-10-10T13:29:10Z","oa":1,"publication_status":"published","arxiv":1,"intvolume":"        98","_id":"136","external_id":{"isi":["000441466800010"],"arxiv":["1808.02088"]},"doi":"10.1103/PhysRevE.98.023105","department":[{"_id":"BjHo"}],"quality_controlled":"1","isi":1,"article_processing_charge":"No","citation":{"ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” <i>Physical Review E</i>, vol. 98, no. 2. American Physical Society, 2018.","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. 2018;98(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>.","apa":"Suri, B., Tithof, J., Grigoriev, R., &#38; Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>, vol. 98, no. 2, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>."},"status":"public","type":"journal_article","title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow"},{"external_id":{"isi":["000442174500013"],"pmid":["30061718 "]},"doi":"10.1038/s41589-018-0108-2","intvolume":"        14","_id":"137","page":"861 - 869","quality_controlled":"1","department":[{"_id":"HaJa"}],"article_processing_charge":"No","citation":{"ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","ieee":"W. Zhang <i>et al.</i>, “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” <i>Nature Chemical Biology</i>, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0108-2\">https://doi.org/10.1038/s41589-018-0108-2</a>","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” <i>Nature Chemical Biology</i>, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:<a href=\"https://doi.org/10.1038/s41589-018-0108-2\">10.1038/s41589-018-0108-2</a>.","short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. <i>Nature Chemical Biology</i>. 2018;14(9):861-869. doi:<a href=\"https://doi.org/10.1038/s41589-018-0108-2\">10.1038/s41589-018-0108-2</a>","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0108-2\">https://doi.org/10.1038/s41589-018-0108-2</a>."},"isi":1,"title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","status":"public","type":"journal_article","month":"07","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7786","publication_status":"published","oa":1,"date_updated":"2023-09-13T08:58:05Z","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012"}],"article_type":"original","date_created":"2018-12-11T11:44:49Z","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718"}],"publisher":"Nature Publishing Group","scopus_import":"1","publication":"Nature Chemical Biology","year":"2018","language":[{"iso":"eng"}],"day":"30","issue":"9","author":[{"last_name":"Zhang","first_name":"William","full_name":"Zhang, William"},{"last_name":"Herde","first_name":"Michel","full_name":"Herde, Michel"},{"last_name":"Mitchell","first_name":"Joshua","full_name":"Mitchell, Joshua"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"last_name":"Wulff","first_name":"Andreas","full_name":"Wulff, Andreas"},{"full_name":"Vongsouthi, Vanessa","last_name":"Vongsouthi","first_name":"Vanessa"},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada","first_name":"Inmaculada","last_name":"Sanchez Romero"},{"full_name":"Gulakova, Polina","first_name":"Polina","last_name":"Gulakova"},{"last_name":"Minge","first_name":"Daniel","full_name":"Minge, Daniel"},{"full_name":"Breithausen, Björn","last_name":"Breithausen","first_name":"Björn"},{"full_name":"Schoch, Susanne","first_name":"Susanne","last_name":"Schoch"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"},{"first_name":"Colin","last_name":"Jackson","full_name":"Jackson, Colin"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"}],"date_published":"2018-07-30T00:00:00Z","volume":14,"abstract":[{"lang":"eng","text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli."}]},{"publication":"PeerJ","day":"30","year":"2018","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:48Z","issue":"7","author":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"full_name":"Gagnaire, Pierre","first_name":"Pierre","last_name":"Gagnaire"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"volume":2018,"date_published":"2018-07-30T00:00:00Z","date_created":"2018-12-11T11:44:50Z","file":[{"file_id":"5739","relation":"main_file","checksum":"7d55ae22598a1c70759cd671600cff53","date_created":"2018-12-18T09:42:11Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:44:48Z","access_level":"open_access","file_size":1480792,"file_name":"2018_PeerJ_Fraisse.pdf"}],"publisher":"PeerJ","scopus_import":"1","oa_version":"Published Version","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7784","oa":1,"publication_status":"published","date_updated":"2023-10-17T12:25:28Z","ddc":["576"],"has_accepted_license":"1","article_number":"30083438","doi":"10.7717/peerj.5198","external_id":{"isi":["000440484800002"]},"_id":"139","license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"      2018","quality_controlled":"1","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"citation":{"ieee":"C. Fraisse <i>et al.</i>, “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” <i>PeerJ</i>, vol. 2018, no. 7. PeerJ, 2018.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., &#38; Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>.","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. 2018;2018(7). doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018)."},"article_processing_charge":"No","isi":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)"},"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","status":"public","type":"journal_article"},{"title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","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)"},"status":"public","type":"journal_article","article_processing_charge":"No","citation":{"ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” <i>International Journal of Molecular Sciences</i>, vol. 19, no. 11. MDPI, 2018.","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” <i>International Journal of Molecular Sciences</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/ijms19113566\">https://doi.org/10.3390/ijms19113566</a>.","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. <i>International Journal of Molecular Sciences</i>. 2018;19(11). doi:<a href=\"https://doi.org/10.3390/ijms19113566\">10.3390/ijms19113566</a>","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., &#38; Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms19113566\">https://doi.org/10.3390/ijms19113566</a>","mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” <i>International Journal of Molecular Sciences</i>, vol. 19, no. 11, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/ijms19113566\">10.3390/ijms19113566</a>."},"isi":1,"quality_controlled":"1","acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"external_id":{"isi":["000451528500282"]},"doi":"10.3390/ijms19113566","intvolume":"        19","_id":"14","has_accepted_license":"1","publication_status":"published","oa":1,"publication_identifier":{"eissn":["1422-0067"]},"ddc":["580"],"date_updated":"2023-09-18T08:09:32Z","month":"11","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8042","scopus_import":"1","publisher":"MDPI","file":[{"file_size":2200593,"access_level":"open_access","file_name":"2018_IJMS_Hille.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:50Z","relation":"main_file","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","creator":"dernst","date_created":"2018-12-17T16:04:11Z","file_id":"5719"}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"}],"date_created":"2018-12-11T11:44:09Z","article_type":"original","author":[{"full_name":"Hille, Sander","last_name":"Hille","first_name":"Sander"},{"full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Akhmanova","orcid":"0000-0003-1522-3162"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-11-12T00:00:00Z","volume":19,"abstract":[{"text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:50Z","issue":"11","ec_funded":1,"publication":"International Journal of Molecular Sciences","year":"2018","language":[{"iso":"eng"}],"day":"12"},{"alternative_title":["LNCS"],"has_accepted_license":"1","publist_id":"7783","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"6894","relation":"dissertation_contains","status":"public"}]},"month":"07","oa_version":"Published Version","date_updated":"2023-09-19T09:30:43Z","ddc":["005"],"publication_identifier":{"issn":["03029743"]},"oa":1,"publication_status":"published","conference":{"end_date":"2018-07-17","name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, United Kingdom"},"isi":1,"citation":{"mla":"Frehse, Goran, et al. <i>Space-Time Interpolants</i>. Vol. 10981, Springer, 2018, pp. 468–86, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>.","apa":"Frehse, G., Giacobbe, M., &#38; Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>","chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>.","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486."},"article_processing_charge":"No","status":"public","type":"conference","pubrep_id":"1010","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)"},"title":"Space-time interpolants","_id":"140","page":"468 - 486","intvolume":"     10981","doi":"10.1007/978-3-319-96145-3_25","external_id":{"isi":["000491481600025"]},"department":[{"_id":"ToHe"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:44:50Z","volume":10981,"abstract":[{"lang":"eng","text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools."}],"date_published":"2018-07-18T00:00:00Z","author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"orcid":"0000-0001-8180-0904","first_name":"Mirco","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"}],"day":"18","language":[{"iso":"eng"}],"year":"2018","publisher":"Springer","file":[{"date_created":"2018-12-12T10:17:53Z","creator":"system","checksum":"6dca832f575d6b3f0ea9dff56f579142","relation":"main_file","file_id":"5310","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","access_level":"open_access","file_size":563710,"date_updated":"2020-07-14T12:44:50Z","content_type":"application/pdf"}],"scopus_import":"1","date_created":"2018-12-11T11:44:50Z","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}]},{"article_number":"031060","oa":1,"publication_status":"published","date_updated":"2023-08-22T07:42:07Z","publication_identifier":{"eissn":["2160-3308"]},"oa_version":"Published Version","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Chiral discrimination through bielliptical high-harmonic spectroscopy","status":"public","type":"journal_article","extern":"1","article_processing_charge":"No","citation":{"chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” <i>Physical Review X</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevx.8.031060\">https://doi.org/10.1103/physrevx.8.031060</a>.","short":"D.R. Baykusheva, H.J. Wörner, Physical Review X 8 (2018).","ama":"Baykusheva DR, Wörner HJ. Chiral discrimination through bielliptical high-harmonic spectroscopy. <i>Physical Review X</i>. 2018;8(3). doi:<a href=\"https://doi.org/10.1103/physrevx.8.031060\">10.1103/physrevx.8.031060</a>","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” <i>Physical Review X</i>, vol. 8, no. 3, 031060, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevx.8.031060\">10.1103/physrevx.8.031060</a>.","apa":"Baykusheva, D. R., &#38; Wörner, H. J. (2018). Chiral discrimination through bielliptical high-harmonic spectroscopy. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.8.031060\">https://doi.org/10.1103/physrevx.8.031060</a>","ista":"Baykusheva DR, Wörner HJ. 2018. Chiral discrimination through bielliptical high-harmonic spectroscopy. Physical Review X. 8(3), 031060.","ieee":"D. R. Baykusheva and H. J. Wörner, “Chiral discrimination through bielliptical high-harmonic spectroscopy,” <i>Physical Review X</i>, vol. 8, no. 3. American Physical Society, 2018."},"quality_controlled":"1","doi":"10.1103/physrevx.8.031060","_id":"14003","intvolume":"         8","author":[{"last_name":"Baykusheva","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"abstract":[{"text":"Molecular chirality plays an essential role in most biochemical processes. The observation and quantification of chirality-sensitive signals, however, remains extremely challenging, especially on ultrafast timescales and in dilute media. Here, we describe the experimental realization of an all-optical and ultrafast scheme for detecting chiral dynamics in molecules. This technique is based on high-harmonic generation by a combination of two-color counterrotating femtosecond laser pulses with polarization states tunable from linear to circular. We demonstrate two different implementations of chiral-sensitive high-harmonic spectroscopy on an ensemble of randomly oriented methyloxirane molecules in the gas phase. Using two elliptically polarized fields, we observe that the ellipticities maximizing the harmonic signal reach up to \r\n4.4\r\n±\r\n0.2\r\n%\r\n (at 17.6 eV). Using two circularly polarized fields, we observe circular dichroisms ranging up to \r\n13\r\n±\r\n6\r\n%\r\n (28.3–33.1 eV). Our theoretical analysis confirms that the observed chiral response originates from subfemtosecond electron dynamics driven by the magnetic component of the driving laser field. This assignment is supported by the experimental observation of a strong intensity dependence of the chiral effects and its agreement with theory. We moreover report and explain a pronounced variation of the signal strength and dichroism with the driving-field ellipticities and harmonic orders. Finally, we demonstrate the sensitivity of the experimental observables to the shape of the electron hole. This technique for chiral discrimination will yield femtosecond temporal resolution when integrated in a pump-probe scheme and subfemtosecond resolution on chiral charge migration in a self-probing scheme.","lang":"eng"}],"volume":8,"date_published":"2018-07-01T00:00:00Z","issue":"3","keyword":["General Physics and Astronomy"],"publication":"Physical Review X","day":"01","year":"2018","language":[{"iso":"eng"}],"scopus_import":"1","publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1103/PhysRevX.8.031060"}],"article_type":"original","date_created":"2023-08-10T06:34:48Z"},{"ec_funded":1,"year":"2018","language":[{"iso":"eng"}],"day":"18","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Loitzenbauer","first_name":"Veronika","full_name":"Loitzenbauer, Veronika"},{"full_name":"Oraee, Simin","first_name":"Simin","last_name":"Oraee"},{"full_name":"Toman, Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","last_name":"Toman","first_name":"Viktor"}],"date_published":"2018-07-18T00:00:00Z","abstract":[{"lang":"eng","text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples."}],"volume":10982,"file_date_updated":"2020-07-14T12:44:53Z","project":[{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"date_created":"2018-12-11T11:44:51Z","scopus_import":"1","file":[{"file_name":"2018_LNCS_Chatterjee.pdf","file_size":675606,"access_level":"open_access","date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","date_created":"2018-12-18T08:52:38Z","creator":"dernst","relation":"main_file","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","file_id":"5737"}],"publisher":"Springer","conference":{"location":"Oxford, United Kingdom","name":"CAV: Computer Aided Verification","start_date":"2018-07-14","end_date":"2018-07-17"},"oa":1,"publication_status":"published","date_updated":"2025-07-14T09:10:15Z","ddc":["000"],"month":"07","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"10199","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7782","has_accepted_license":"1","alternative_title":["LNCS"],"quality_controlled":"1","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","department":[{"_id":"KrCh"}],"external_id":{"isi":["000491469700013"]},"doi":"10.1007/978-3-319-96142-2_13","intvolume":"     10982","_id":"141","page":"178-197","title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","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)"},"type":"conference","status":"public","citation":{"short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>","mla":"Chatterjee, Krishnendu, et al. <i>Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives</i>. Vol. 10982, Springer, 2018, pp. 178–97, doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>.","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., &#38; Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197."},"article_processing_charge":"No","isi":1},{"status":"public","type":"conference","title":"SOM-VAE: Interpretable discrete representation learning on time series","article_processing_charge":"No","citation":{"short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In <i>International Conference on Learning Representations</i>, 2018.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: <i>International Conference on Learning Representations</i>. ; 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., &#38; Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In <i>International Conference on Learning Representations</i>. New Orleans, LA, United States.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” <i>International Conference on Learning Representations</i>, 2018.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in <i>International Conference on Learning Representations</i>, New Orleans, LA, United States, 2018.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02199"}],"extern":"1","department":[{"_id":"FrLo"}],"quality_controlled":"1","_id":"14198","external_id":{"arxiv":["1806.02199"]},"date_created":"2023-08-22T14:12:48Z","date_published":"2018-06-06T00:00:00Z","abstract":[{"text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data.","lang":"eng"}],"author":[{"full_name":"Fortuin, Vincent","first_name":"Vincent","last_name":"Fortuin"},{"first_name":"Matthias","last_name":"Hüser","full_name":"Hüser, Matthias"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"first_name":"Heiko","last_name":"Strathmann","full_name":"Strathmann, Heiko"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"}],"arxiv":1,"date_updated":"2023-09-13T06:35:12Z","conference":{"location":"New Orleans, LA, United States","name":"ICLR: International Conference on Learning Representations","start_date":"2019-05-06","end_date":"2019-05-09"},"publication_status":"published","oa":1,"year":"2018","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"06","month":"06","oa_version":"Preprint","publication":"International Conference on Learning Representations"},{"date_created":"2018-12-11T11:44:51Z","project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"scopus_import":"1","file":[{"file_id":"5718","checksum":"fd95e8026deacef3dc752a733bb9355f","relation":"main_file","creator":"dernst","date_created":"2018-12-17T15:57:06Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","file_size":5591566,"file_name":"2018_LNCS_Kong.pdf"}],"publisher":"Springer","day":"18","year":"2018","language":[{"iso":"eng"}],"author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"}],"abstract":[{"lang":"eng","text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective."}],"volume":10981,"date_published":"2018-07-18T00:00:00Z","file_date_updated":"2020-07-14T12:44:53Z","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","quality_controlled":"1","department":[{"_id":"ToHe"}],"doi":"10.1007/978-3-319-96145-3_24","external_id":{"isi":["000491481600024"]},"_id":"142","page":"449 - 467","intvolume":"     10981","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)"},"title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","status":"public","type":"conference","article_processing_charge":"No","citation":{"ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>.","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>","apa":"Kong, H., Bartocci, E., &#38; Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>","mla":"Kong, Hui, et al. <i>Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes</i>. Vol. 10981, Springer, 2018, pp. 449–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>."},"isi":1,"publication_status":"published","oa":1,"conference":{"end_date":"2018-07-17","name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, United Kingdom"},"ddc":["000"],"date_updated":"2023-09-15T12:12:08Z","month":"07","oa_version":"Published Version","publist_id":"7781","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","alternative_title":["LNCS"]},{"language":[{"iso":"eng"}],"year":"2018","day":"15","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","date_published":"2018-04-15T00:00:00Z","abstract":[{"text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties.","lang":"eng"}],"volume":84,"author":[{"orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Khanna","first_name":"Rajiv","full_name":"Khanna, Rajiv"},{"first_name":"Joydeep","last_name":"Ghosh","full_name":"Ghosh, Joydeep"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"}],"date_created":"2023-08-22T14:15:20Z","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1708.01733","open_access":"1"}],"publisher":"ML Research Press","date_updated":"2023-09-13T07:52:40Z","conference":{"location":"Playa Blanca, Lanzarote","name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2018-04-09","end_date":"2018-04-11"},"oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","oa_version":"Preprint","alternative_title":["PMLR"],"arxiv":1,"department":[{"_id":"FrLo"}],"quality_controlled":"1","intvolume":"        84","page":"464-472","_id":"14201","external_id":{"arxiv":["1708.01733"]},"type":"conference","status":"public","title":"Boosting variational inference: An optimization perspective","citation":{"ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, vol. 84, ML Research Press, 2018, pp. 464–72.","apa":"Locatello, F., Khanna, R., Ghosh, J., &#38; Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i> (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>. Vol 84. ML Research Press; 2018:464-472.","chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, 84:464–72. ML Research Press, 2018."},"extern":"1","article_processing_charge":"No"},{"department":[{"_id":"FrLo"}],"quality_controlled":"1","_id":"14202","intvolume":"        31","external_id":{"arxiv":["1806.02185"]},"status":"public","type":"conference","title":"Boosting black box variational inference","extern":"1","citation":{"ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 31.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: <i>Advances in Neural Information Processing Systems</i>. Vol 31. Neural Information Processing Systems Foundation; 2018.","chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 31. Neural Information Processing Systems Foundation, 2018.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., &#38; Rätsch, G. (2018). Boosting black box variational inference. In <i>Advances in Neural Information Processing Systems</i> (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” <i>Advances in Neural Information Processing Systems</i>, vol. 31, Neural Information Processing Systems Foundation, 2018."},"article_processing_charge":"No","date_updated":"2023-09-13T07:38:24Z","publication_identifier":{"isbn":["9781510884472"],"eissn":["1049-5258"]},"publication_status":"published","oa":1,"conference":{"end_date":"2018-12-08","name":"NeurIPS: Neural Information Processing Systems","start_date":"2018-12-03","location":"Montreal, Canada"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","oa_version":"Preprint","arxiv":1,"date_created":"2023-08-22T14:15:40Z","scopus_import":"1","publisher":"Neural Information Processing Systems Foundation","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02185"}],"day":"06","language":[{"iso":"eng"}],"year":"2018","publication":"Advances in Neural Information Processing Systems","abstract":[{"text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions.","lang":"eng"}],"volume":31,"date_published":"2018-06-06T00:00:00Z","author":[{"orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Dresdner, Gideon","last_name":"Dresdner","first_name":"Gideon"},{"full_name":"Khanna, Rajiv","last_name":"Khanna","first_name":"Rajiv"},{"first_name":"Isabel","last_name":"Valera","full_name":"Valera, Isabel"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}]}]