[{"publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"01","publication":"Computer Physics Communications","year":"2019","date_published":"2019-03-01T00:00:00Z","doi":"10.1016/j.cpc.2018.09.020","date_created":"2021-07-16T08:53:01Z","page":"214-223","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 236, 214–223.","chicago":"Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications. Elsevier, 2019. https://doi.org/10.1016/j.cpc.2018.09.020.","apa":"Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T., … Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020","ama":"Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 2019;236:214-223. doi:10.1016/j.cpc.2018.09.020","short":"V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng, A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue, W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf, T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko, G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications 236 (2019) 214–223.","ieee":"V. Kapil et al., “i-PI 2.0: A universal force engine for advanced molecular simulations,” Computer Physics Communications, vol. 236. Elsevier, pp. 214–223, 2019.","mla":"Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications, vol. 236, Elsevier, 2019, pp. 214–23, doi:10.1016/j.cpc.2018.09.020."},"title":"i-PI 2.0: A universal force engine for advanced molecular simulations","author":[{"last_name":"Kapil","full_name":"Kapil, Venkat","first_name":"Venkat"},{"last_name":"Rossi","full_name":"Rossi, Mariana","first_name":"Mariana"},{"full_name":"Marsalek, Ondrej","last_name":"Marsalek","first_name":"Ondrej"},{"full_name":"Petraglia, Riccardo","last_name":"Petraglia","first_name":"Riccardo"},{"first_name":"Yair","last_name":"Litman","full_name":"Litman, Yair"},{"last_name":"Spura","full_name":"Spura, Thomas","first_name":"Thomas"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng"},{"first_name":"Alice","full_name":"Cuzzocrea, Alice","last_name":"Cuzzocrea"},{"first_name":"Robert H.","last_name":"Meißner","full_name":"Meißner, Robert H."},{"last_name":"Wilkins","full_name":"Wilkins, David M.","first_name":"David M."},{"first_name":"Benjamin A.","full_name":"Helfrecht, Benjamin A.","last_name":"Helfrecht"},{"first_name":"Przemysław","full_name":"Juda, Przemysław","last_name":"Juda"},{"first_name":"Sébastien P.","full_name":"Bienvenue, Sébastien P.","last_name":"Bienvenue"},{"first_name":"Wei","last_name":"Fang","full_name":"Fang, Wei"},{"first_name":"Jan","last_name":"Kessler","full_name":"Kessler, Jan"},{"first_name":"Igor","last_name":"Poltavsky","full_name":"Poltavsky, Igor"},{"last_name":"Vandenbrande","full_name":"Vandenbrande, Steven","first_name":"Steven"},{"full_name":"Wieme, Jelle","last_name":"Wieme","first_name":"Jelle"},{"first_name":"Clemence","full_name":"Corminboeuf, Clemence","last_name":"Corminboeuf"},{"full_name":"Kühne, Thomas D.","last_name":"Kühne","first_name":"Thomas D."},{"first_name":"David E.","last_name":"Manolopoulos","full_name":"Manolopoulos, David E."},{"first_name":"Thomas E.","full_name":"Markland, Thomas E.","last_name":"Markland"},{"last_name":"Richardson","full_name":"Richardson, Jeremy O.","first_name":"Jeremy O."},{"first_name":"Alexandre","last_name":"Tkatchenko","full_name":"Tkatchenko, Alexandre"},{"first_name":"Gareth A.","last_name":"Tribello","full_name":"Tribello, Gareth A."},{"first_name":"Veronique","last_name":"Van Speybroeck","full_name":"Van Speybroeck, Veronique"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"article_processing_charge":"No","external_id":{"arxiv":["1808.03824"]},"oa_version":"Preprint","abstract":[{"text":"Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.","lang":"eng"}],"month":"03","intvolume":" 236","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.03824"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0010-4655"]},"publication_status":"published","volume":236,"_id":"9677","status":"public","type":"journal_article","article_type":"original","extern":"1","date_updated":"2021-08-09T12:37:16Z"},{"oa":1,"publisher":"American Chemical Society","quality_controlled":"1","publication":"Journal of Chemical Theory and Computation","day":"14","year":"2019","date_created":"2021-07-19T06:56:45Z","doi":"10.1021/acs.jctc.9b00907","date_published":"2019-01-14T00:00:00Z","page":"100-107","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society, 2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907.","apa":"Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907","ama":"Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107. doi:10.1021/acs.jctc.9b00907","short":"F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107.","ieee":"F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation, vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019.","chicago":"Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation. American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907.","ista":"Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1), 100–107."},"title":"Iterative unbiasing of quasi-equilibrium sampling","external_id":{"pmid":["31743021"],"arxiv":["1911.01140"]},"article_processing_charge":"No","author":[{"first_name":"F.","full_name":"Giberti, F.","last_name":"Giberti"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng"},{"last_name":"Tribello","full_name":"Tribello, G. A.","first_name":"G. A."},{"last_name":"Ceriotti","full_name":"Ceriotti, M.","first_name":"M."}],"oa_version":"Preprint","pmid":1,"abstract":[{"lang":"eng","text":"Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality."}],"intvolume":" 16","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1911.01140","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"issue":"1","volume":16,"_id":"9680","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2021-08-09T12:37:37Z"},{"intvolume":" 55","month":"08","main_file_link":[{"url":"https://doi.org/10.1029/2019WR024935","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The snow cover dynamics of High Mountain Asia are usually assessed at spatial resolutions of 250 m or greater, but this scale is too coarse to clearly represent the rugged topography common to the region. Higher-resolution measurement of snow-covered area often results in biased sampling due to cloud cover and deep shadows. We therefore develop a Normalized Difference Snow Index-based workflow to delineate snow lines from Landsat Thematic Mapper/Enhanced Thematic Mapper+ imagery and apply it to the upper Langtang Valley in Nepal, processing 194 scenes spanning 1999 to 2013. For each scene, we determine the spatial distribution of snow line altitudes (SLAs) with respect to aspect and across six subcatchments. Our results show that the mean SLA exhibits distinct seasonal behavior based on aspect and subcatchment position. We find that SLA dynamics respond to spatial and seasonal trade-offs in precipitation, temperature, and solar radiation, which act as primary controls. We identify two SLA spatial gradients, which we attribute to the effect of spatially variable precipitation. Our results also reveal that aspect-related SLA differences vary seasonally and are influenced by solar radiation. In terms of seasonal dominant controls, we demonstrate that the snow line is controlled by snow precipitation in winter, melt in premonsoon, a combination of both in postmonsoon, and temperature in monsoon, explaining to a large extent the spatial and seasonal variability of the SLA in the upper Langtang Valley. We conclude that while SLA and snow-covered area are complementary metrics, the SLA has a strong potential for understanding local-scale snow cover dynamics and their controlling mechanisms.","lang":"eng"}],"issue":"8","volume":55,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"keyword":["Water Science and Technology"],"status":"public","type":"journal_article","article_type":"original","_id":"12600","extern":"1","date_updated":"2023-02-28T12:14:18Z","oa":1,"quality_controlled":"1","publisher":"American Geophysical Union","date_created":"2023-02-20T08:12:59Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1029/2019wr024935","page":"6754-6772","publication":"Water Resources Research","day":"01","year":"2019","title":"High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment","article_processing_charge":"No","author":[{"last_name":"Girona‐Mata","full_name":"Girona‐Mata, Marc","first_name":"Marc"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"full_name":"Ragettli, Silvan","last_name":"Ragettli","first_name":"Silvan"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. 2019. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 55(8), 6754–6772.","chicago":"Girona‐Mata, Marc, Evan S. Miles, Silvan Ragettli, and Francesca Pellicciotti. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research. American Geophysical Union, 2019. https://doi.org/10.1029/2019wr024935.","apa":"Girona‐Mata, M., Miles, E. S., Ragettli, S., & Pellicciotti, F. (2019). High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. American Geophysical Union. https://doi.org/10.1029/2019wr024935","ama":"Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 2019;55(8):6754-6772. doi:10.1029/2019wr024935","short":"M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources Research 55 (2019) 6754–6772.","ieee":"M. Girona‐Mata, E. S. Miles, S. Ragettli, and F. Pellicciotti, “High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment,” Water Resources Research, vol. 55, no. 8. American Geophysical Union, pp. 6754–6772, 2019.","mla":"Girona‐Mata, Marc, et al. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research, vol. 55, no. 8, American Geophysical Union, 2019, pp. 6754–72, doi:10.1029/2019wr024935."}},{"abstract":[{"text":"This study aims at developing and applying a spatially-distributed coupled glacier mass balance and ice-flow model to attribute the response of glaciers to natural and anthropogenic climate change. We focus on two glaciers with contrasting surface characteristics: a debris-covered glacier (Langtang Glacier in Nepal) and a clean-ice glacier (Hintereisferner in Austria). The model is applied from the end of the Little Ice Age (1850) to the present-day (2016) and is forced with four bias-corrected General Circulation Models (GCMs) from the historical experiment of the CMIP5 archive. The selected GCMs represent region-specific warm-dry, warm-wet, cold-dry, and cold-wet climate conditions. To isolate the effects of anthropogenic climate change on glacier mass balance and flow runs from these GCMs with and without further anthropogenic forcing after 1970 until 2016 are selected. The outcomes indicate that both glaciers experience the largest reduction in area and volume under warm climate conditions, whereas area and volume reductions are smaller under cold climate conditions. Simultaneously with changes in glacier area and volume, surface velocities generally decrease over time. Without further anthropogenic forcing the results reveal a 3% (9%) smaller decline in glacier area (volume) for the debris-covered glacier and a 18% (39%) smaller decline in glacier area (volume) for the clean-ice glacier. The difference in the magnitude between the two glaciers can mainly be attributed to differences in the response time of the glaciers, where the clean-ice glacier shows a much faster response to climate change. We conclude that the response of the two glaciers can mainly be attributed to anthropogenic climate change and that the impact is larger on the clean-ice glacier. The outcomes show that the model performs well under different climate conditions and that the developed approach can be used for regional-scale glacio-hydrological modeling.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3389/feart.2019.00143"}],"month":"06","intvolume":" 7","publication_identifier":{"issn":["2296-6463"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":7,"_id":"12602","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-02-28T12:04:48Z","extern":"1","quality_controlled":"1","publisher":"Frontiers Media","oa":1,"year":"2019","day":"04","publication":"Frontiers in Earth Science","date_published":"2019-06-04T00:00:00Z","doi":"10.3389/feart.2019.00143","date_created":"2023-02-20T08:13:08Z","article_number":"143","citation":{"mla":"Wijngaard, René R., et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science, vol. 7, 143, Frontiers Media, 2019, doi:10.3389/feart.2019.00143.","apa":"Wijngaard, R. R., Steiner, J. F., Kraaijenbrink, P. D. A., Klug, C., Adhikari, S., Banerjee, A., … Immerzeel, W. W. (2019). Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. Frontiers Media. https://doi.org/10.3389/feart.2019.00143","ama":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, et al. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 2019;7. doi:10.3389/feart.2019.00143","ieee":"R. R. Wijngaard et al., “Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age,” Frontiers in Earth Science, vol. 7. Frontiers Media, 2019.","short":"R.R. Wijngaard, J.F. Steiner, P.D.A. Kraaijenbrink, C. Klug, S. Adhikari, A. Banerjee, F. Pellicciotti, L.P.H. van Beek, M.F.P. Bierkens, A.F. Lutz, W.W. Immerzeel, Frontiers in Earth Science 7 (2019).","chicago":"Wijngaard, René R., Jakob F. Steiner, Philip D. A. Kraaijenbrink, Christoph Klug, Surendra Adhikari, Argha Banerjee, Francesca Pellicciotti, et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science. Frontiers Media, 2019. https://doi.org/10.3389/feart.2019.00143.","ista":"Wijngaard RR, Steiner JF, Kraaijenbrink PDA, Klug C, Adhikari S, Banerjee A, Pellicciotti F, van Beek LPH, Bierkens MFP, Lutz AF, Immerzeel WW. 2019. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 7, 143."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Wijngaard, René R.","last_name":"Wijngaard","first_name":"René R."},{"full_name":"Steiner, Jakob F.","last_name":"Steiner","first_name":"Jakob F."},{"first_name":"Philip D. A.","last_name":"Kraaijenbrink","full_name":"Kraaijenbrink, Philip D. A."},{"first_name":"Christoph","full_name":"Klug, Christoph","last_name":"Klug"},{"full_name":"Adhikari, Surendra","last_name":"Adhikari","first_name":"Surendra"},{"last_name":"Banerjee","full_name":"Banerjee, Argha","first_name":"Argha"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"},{"first_name":"Ludovicus P. H.","full_name":"van Beek, Ludovicus P. H.","last_name":"van Beek"},{"first_name":"Marc F. P.","last_name":"Bierkens","full_name":"Bierkens, Marc F. P."},{"first_name":"Arthur F.","last_name":"Lutz","full_name":"Lutz, Arthur F."},{"last_name":"Immerzeel","full_name":"Immerzeel, Walter W.","first_name":"Walter W."}],"article_processing_charge":"No","title":"Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age"},{"date_updated":"2023-02-28T12:11:07Z","extern":"1","_id":"12601","type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"language":[{"iso":"eng"}],"issue":"252","volume":65,"abstract":[{"lang":"eng","text":"Ice cliffs and ponds on debris-covered glaciers have received increased attention due to their role in amplifying local melt. However, very few studies have looked at these features on the catchment scale to determine their patterns and changes in space and time. We have compiled a detailed inventory of cliffs and ponds in the Langtang catchment, central Himalaya, from six high-resolution satellite orthoimages and DEMs between 2006 and 2015, and a historic orthophoto from 1974. Cliffs cover between 1.4% (± 0.4%) in the dry and 3.4% (± 0.9%) in the wet seasons and ponds between 0.6% (± 0.1%) and 1.6% (± 0.3%) of the total debris-covered tongues. We find large variations between seasons, as cliffs and ponds tend to grow in the wetter monsoon period, but there is no obvious trend in total area over the study period. The inventory further shows that cliffs are predominately north-facing irrespective of the glacier flow direction. Both cliffs and ponds appear in higher densities several hundred metres from the terminus in areas where tributaries reach the main glacier tongue. On the largest glacier in the catchment ~10% of all cliffs and ponds persisted over nearly a decade."}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1017/jog.2019.40","open_access":"1"}],"scopus_import":"1","intvolume":" 65","month":"08","citation":{"chicago":"STEINER, JAKOB F., PASCAL BURI, EVAN S. MILES, SILVAN RAGETTLI, and Francesca Pellicciotti. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology. Cambridge University Press, 2019. https://doi.org/10.1017/jog.2019.40.","ista":"STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. 2019. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 65(252), 617–632.","mla":"STEINER, JAKOB F., et al. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology, vol. 65, no. 252, Cambridge University Press, 2019, pp. 617–32, doi:10.1017/jog.2019.40.","ieee":"J. F. STEINER, P. BURI, E. S. MILES, S. RAGETTLI, and F. Pellicciotti, “Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics,” Journal of Glaciology, vol. 65, no. 252. Cambridge University Press, pp. 617–632, 2019.","short":"J.F. STEINER, P. BURI, E.S. MILES, S. RAGETTLI, F. Pellicciotti, Journal of Glaciology 65 (2019) 617–632.","apa":"STEINER, J. F., BURI, P., MILES, E. S., RAGETTLI, S., & Pellicciotti, F. (2019). Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. Cambridge University Press. https://doi.org/10.1017/jog.2019.40","ama":"STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 2019;65(252):617-632. doi:10.1017/jog.2019.40"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"JAKOB F.","last_name":"STEINER","full_name":"STEINER, JAKOB F."},{"full_name":"BURI, PASCAL","last_name":"BURI","first_name":"PASCAL"},{"full_name":"MILES, EVAN S.","last_name":"MILES","first_name":"EVAN S."},{"last_name":"RAGETTLI","full_name":"RAGETTLI, SILVAN","first_name":"SILVAN"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"}],"title":"Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics","year":"2019","publication":"Journal of Glaciology","day":"01","page":"617-632","date_created":"2023-02-20T08:13:03Z","date_published":"2019-08-01T00:00:00Z","doi":"10.1017/jog.2019.40","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press"},{"intvolume":" 8","month":"05","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation."}],"volume":8,"language":[{"iso":"eng"}],"file":[{"date_created":"2023-02-07T09:42:46Z","file_name":"2019_elife_He.pdf","creator":"alisjak","date_updated":"2023-02-07T09:42:46Z","file_size":2493837,"checksum":"ea6b89c20d59e5eb3646916fe5d568ad","file_id":"12525","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"12192","file_date_updated":"2023-02-07T09:42:46Z","department":[{"_id":"XiFe"}],"ddc":["580"],"extern":"1","date_updated":"2023-05-08T10:54:12Z","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications, Ltd","acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","date_created":"2023-01-16T09:17:21Z","doi":"10.7554/elife.42530","date_published":"2019-05-28T00:00:00Z","publication":"eLife","day":"28","year":"2019","has_accepted_license":"1","article_number":"42530","title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","external_id":{"unknown":["31135340"]},"article_processing_charge":"No","author":[{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"last_name":"Zhang","full_name":"Zhang, Jingyi","first_name":"Jingyi"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530.","ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530.","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019."}},{"acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","publisher":"Elsevier BV","quality_controlled":"1","year":"2019","publication":"Current Biology","day":"19","page":"2676-2686.e3","date_created":"2023-01-16T09:16:33Z","doi":"10.1016/j.cub.2019.06.084","date_published":"2019-08-19T00:00:00Z","citation":{"mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3.","ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084","apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084.","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["31378616"]},"author":[{"full_name":"Lawrence, Emma J.","last_name":"Lawrence","first_name":"Emma J."},{"last_name":"Gao","full_name":"Gao, Hongbo","first_name":"Hongbo"},{"first_name":"Andrew J.","last_name":"Tock","full_name":"Tock, Andrew J."},{"full_name":"Lambing, Christophe","last_name":"Lambing","first_name":"Christophe"},{"first_name":"Alexander R.","last_name":"Blackwell","full_name":"Blackwell, Alexander R."},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Henderson","full_name":"Henderson, Ian R.","first_name":"Ian R."}],"title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","abstract":[{"lang":"eng","text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor."}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 29","month":"08","publication_status":"published","publication_identifier":{"issn":["0960-9822"]},"language":[{"iso":"eng"}],"issue":"16","volume":29,"_id":"12190","type":"journal_article","article_type":"original","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"status":"public","date_updated":"2023-05-08T10:54:54Z","extern":"1","department":[{"_id":"XiFe"}]},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1Cryptology EPrint Archive, n.d.","ista":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive, 2019/1015.","mla":"Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, 2019/1015.","short":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint Archive (n.d.).","ieee":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation,” Cryptology ePrint Archive. .","ama":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive.","apa":"Kokoris Kogias, E., Spiegelman, A., Malkhi, D., & Abraham, I. (n.d.). Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive."},"date_updated":"2023-05-10T09:27:54Z","title":"Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation","author":[{"last_name":"KOKORIS KOGIAS","full_name":"KOKORIS KOGIAS, Eleftherios","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"},{"last_name":"Malkhi","full_name":"Malkhi, Dahlia","first_name":"Dahlia"},{"full_name":"Abraham, Ittai","last_name":"Abraham","first_name":"Ittai"}],"article_processing_charge":"No"},{"page":"25","date_created":"2023-05-05T12:48:48Z","date_published":"2019-02-27T00:00:00Z","year":"2019","publication_status":"published","has_accepted_license":"1","publication":"AHPC19 - Austrian HPC Meeting 2019 ","language":[{"iso":"eng"}],"day":"27","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12970","checksum":"acc8272027faaf30709c51ac5c58ffa4","creator":"dernst","file_size":1097603,"date_updated":"2023-05-16T07:27:09Z","file_name":"2019_AHPC_Schloegl.pdf","date_created":"2023-05-16T07:27:09Z"}],"oa":1,"main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf","open_access":"1"}],"publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","month":"02","oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"full_name":"Kiss, Janos","last_name":"Kiss","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","first_name":"Janos"},{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ScienComp"}],"title":"Is Debian suitable for running an HPC Cluster?","file_date_updated":"2023-05-16T07:27:09Z","citation":{"ista":"Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.","ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25."},"date_updated":"2023-05-16T07:29:32Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"AHPC: Austrian HPC Meeting","location":"Grundlsee, Austria","end_date":"2019-02-27","start_date":"2019-02-25"},"type":"conference_abstract","status":"public","_id":"12901"},{"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.49796.","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 8, e49796.","mla":"Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” ELife, vol. 8, e49796, eLife Sciences Publications, 2019, doi:10.7554/elife.49796.","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. eLife. 2019;8. doi:10.7554/elife.49796","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.49796","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress,” eLife, vol. 8. eLife Sciences Publications, 2019."},"title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","author":[{"first_name":"Abigail","last_name":"Buchwalter","full_name":"Buchwalter, Abigail"},{"last_name":"Schulte","full_name":"Schulte, Roberta","first_name":"Roberta"},{"full_name":"Tsai, Hsiao","last_name":"Tsai","first_name":"Hsiao"},{"last_name":"Capitanio","full_name":"Capitanio, Juliana","first_name":"Juliana"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER"}],"external_id":{"pmid":["31599721"]},"article_processing_charge":"No","article_number":"e49796","day":"10","publication":"eLife","has_accepted_license":"1","year":"2019","doi":"10.7554/elife.49796","date_published":"2019-10-10T00:00:00Z","date_created":"2022-04-07T07:45:02Z","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"extern":"1","ddc":["570"],"date_updated":"2023-05-31T06:36:22Z","file_date_updated":"2022-04-08T08:18:01Z","_id":"11060","status":"public","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"11138","checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2022-04-08T08:18:01Z","file_name":"2019_eLife_Buchwalter.pdf","creator":"dernst","date_updated":"2022-04-08T08:18:01Z","file_size":6984654}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","volume":8,"related_material":{"record":[{"id":"13079","status":"public","relation":"research_data"}]},"oa_version":"Published Version","pmid":1,"abstract":[{"text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.","lang":"eng"}],"month":"10","intvolume":" 8","scopus_import":"1"},{"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","_id":"13079","article_processing_charge":"No","author":[{"last_name":"Buchwalter","full_name":"Buchwalter, Abigail","first_name":"Abigail"},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"first_name":"Hsiao","full_name":"Tsai, Hsiao","last_name":"Tsai"},{"last_name":"Capitanio","full_name":"Capitanio, Juliana","first_name":"Juliana"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER"}],"title":"Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","citation":{"mla":"Buchwalter, Abigail, et al. Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress. Dryad, 2019, doi:10.5061/DRYAD.N0R525H.","apa":"Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019). Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. Dryad. https://doi.org/10.5061/DRYAD.N0R525H","ama":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. 2019. doi:10.5061/DRYAD.N0R525H","ieee":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress.” Dryad, 2019.","short":"A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, (2019).","chicago":"Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and Martin Hetzer. “Data from: Selective Clearance of the Inner Nuclear Membrane Protein Emerin by Vesicular Transport during ER Stress.” Dryad, 2019. https://doi.org/10.5061/DRYAD.N0R525H.","ista":"Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress, Dryad, 10.5061/DRYAD.N0R525H."},"date_updated":"2023-05-31T06:36:23Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.n0r525h"}],"publisher":"Dryad","month":"10","abstract":[{"text":"The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum (ER) that is gated by the nuclear pore complex. It is unknown whether proteins of the INM and ER are degraded through shared or distinct pathways in mammalian cells. We applied dynamic proteomics to profile protein half-lives and report that INM and ER residents turn over at similar rates, indicating that the INM’s unique topology is not a barrier to turnover. Using a microscopy approach, we observed that the proteasome can degrade INM proteins in situ. However, we also uncovered evidence for selective, vesicular transport-mediated turnover of a single INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular trafficking to lysosomes. This work demonstrates that the INM can be dynamically remodeled in response to environmental inputs.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T17:09:30Z","date_published":"2019-10-28T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11060"}]},"doi":"10.5061/DRYAD.N0R525H","year":"2019","day":"28"},{"related_material":{"record":[{"relation":"extended_version","status":"public","id":"8317"}]},"date_published":"2019-08-01T00:00:00Z","date_created":"2019-11-04T16:46:11Z","page":"164-170","day":"01","publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","language":[{"iso":"eng"}],"year":"2019","publication_status":"published","month":"08","publisher":"Canadian Conference on Computational Geometry","quality_controlled":"1","scopus_import":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://cccg.ca/proceedings/2019/proceedings.pdf"}],"oa_version":"Published Version","acknowledgement":"This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere.","abstract":[{"lang":"eng","text":"When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. "}],"title":"Folding polyominoes with holes into a cube","department":[{"_id":"HeEd"}],"author":[{"first_name":"Oswin","last_name":"Aichholzer","full_name":"Aichholzer, Oswin"},{"last_name":"Akitaya","full_name":"Akitaya, Hugo A","first_name":"Hugo A"},{"last_name":"Cheung","full_name":"Cheung, Kenneth C","first_name":"Kenneth C"},{"first_name":"Erik D","full_name":"Demaine, Erik D","last_name":"Demaine"},{"full_name":"Demaine, Martin L","last_name":"Demaine","first_name":"Martin L"},{"first_name":"Sandor P","last_name":"Fekete","full_name":"Fekete, Sandor P"},{"first_name":"Linda","full_name":"Kleist, Linda","last_name":"Kleist"},{"first_name":"Irina","last_name":"Kostitsyna","full_name":"Kostitsyna, Irina"},{"first_name":"Maarten","full_name":"Löffler, Maarten","last_name":"Löffler"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana","last_name":"Masárová"},{"first_name":"Klara","last_name":"Mundilova","full_name":"Mundilova, Klara"},{"first_name":"Christiane","full_name":"Schmidt, Christiane","last_name":"Schmidt"}],"article_processing_charge":"No","external_id":{"arxiv":["1910.09917"]},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2023-08-04T10:57:42Z","citation":{"ieee":"O. Aichholzer et al., “Folding polyominoes with holes into a cube,” in Proceedings of the 31st Canadian Conference on Computational Geometry, Edmonton, Canada, 2019, pp. 164–170.","short":"O. Aichholzer, H.A. Akitaya, K.C. Cheung, E.D. Demaine, M.L. Demaine, S.P. Fekete, L. Kleist, I. Kostitsyna, M. Löffler, Z. Masárová, K. Mundilova, C. Schmidt, in:, Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–170.","ama":"Aichholzer O, Akitaya HA, Cheung KC, et al. Folding polyominoes with holes into a cube. In: Proceedings of the 31st Canadian Conference on Computational Geometry. Canadian Conference on Computational Geometry; 2019:164-170.","apa":"Aichholzer, O., Akitaya, H. A., Cheung, K. C., Demaine, E. D., Demaine, M. L., Fekete, S. P., … Schmidt, C. (2019). Folding polyominoes with holes into a cube. In Proceedings of the 31st Canadian Conference on Computational Geometry (pp. 164–170). Edmonton, Canada: Canadian Conference on Computational Geometry.","mla":"Aichholzer, Oswin, et al. “Folding Polyominoes with Holes into a Cube.” Proceedings of the 31st Canadian Conference on Computational Geometry, Canadian Conference on Computational Geometry, 2019, pp. 164–70.","ista":"Aichholzer O, Akitaya HA, Cheung KC, Demaine ED, Demaine ML, Fekete SP, Kleist L, Kostitsyna I, Löffler M, Masárová Z, Mundilova K, Schmidt C. 2019. Folding polyominoes with holes into a cube. Proceedings of the 31st Canadian Conference on Computational Geometry. CCCG: Canadian Conference in Computational Geometry, 164–170.","chicago":"Aichholzer, Oswin, Hugo A Akitaya, Kenneth C Cheung, Erik D Demaine, Martin L Demaine, Sandor P Fekete, Linda Kleist, et al. “Folding Polyominoes with Holes into a Cube.” In Proceedings of the 31st Canadian Conference on Computational Geometry, 164–70. Canadian Conference on Computational Geometry, 2019."},"status":"public","type":"conference","conference":{"name":"CCCG: Canadian Conference in Computational Geometry","end_date":"2019-08-10","location":"Edmonton, Canada","start_date":"2019-08-08"},"_id":"6989"},{"article_number":"1905866","title":"The many ways to assemble nanoparticles using light","author":[{"first_name":"Tong","full_name":"Bian, Tong","last_name":"Bian"},{"full_name":"Chu, Zonglin","last_name":"Chu","first_name":"Zonglin"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"}],"external_id":{"pmid":["31709655"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bian, Tong, et al. “The Many Ways to Assemble Nanoparticles Using Light.” Advanced Materials, vol. 32, no. 20, 1905866, Wiley, 2019, doi:10.1002/adma.201905866.","apa":"Bian, T., Chu, Z., & Klajn, R. (2019). The many ways to assemble nanoparticles using light. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201905866","ama":"Bian T, Chu Z, Klajn R. The many ways to assemble nanoparticles using light. Advanced Materials. 2019;32(20). doi:10.1002/adma.201905866","ieee":"T. Bian, Z. Chu, and R. Klajn, “The many ways to assemble nanoparticles using light,” Advanced Materials, vol. 32, no. 20. Wiley, 2019.","short":"T. Bian, Z. Chu, R. Klajn, Advanced Materials 32 (2019).","chicago":"Bian, Tong, Zonglin Chu, and Rafal Klajn. “The Many Ways to Assemble Nanoparticles Using Light.” Advanced Materials. Wiley, 2019. https://doi.org/10.1002/adma.201905866.","ista":"Bian T, Chu Z, Klajn R. 2019. The many ways to assemble nanoparticles using light. Advanced Materials. 32(20), 1905866."},"quality_controlled":"1","publisher":"Wiley","date_published":"2019-11-19T00:00:00Z","doi":"10.1002/adma.201905866","date_created":"2023-08-01T09:37:26Z","day":"19","publication":"Advanced Materials","year":"2019","status":"public","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"type":"journal_article","article_type":"original","_id":"13366","extern":"1","date_updated":"2023-08-07T10:23:41Z","month":"11","intvolume":" 32","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"The ability to reversibly assemble nanoparticles using light is both fundamentally interesting and important for applications ranging from reversible data storage to controlled drug delivery. Here, the diverse approaches that have so far been developed to control the self-assembly of nanoparticles using light are reviewed and compared. These approaches include functionalizing nanoparticles with monolayers of photoresponsive molecules, placing them in photoresponsive media capable of reversibly protonating the particles under light, and decorating plasmonic nanoparticles with thermoresponsive polymers, to name just a few. The applicability of these methods to larger, micrometer-sized particles is also discussed. Finally, several perspectives on further developments in the field are offered."}],"volume":32,"issue":"20","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"publication_status":"published"},{"month":"02","intvolume":" 141","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene’s hydrophobic nature, most of these examples have been realized only in organic solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-soluble. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amount of azobenzene on the functionalized nanoparticles. Molecular dynamics simulations helped us to identify two distinct supramolecular architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aqueous solubilities. Azobenzenes adsorbed on these water-soluble nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aqueous media and, in the long run, in biological environments."}],"issue":"5","volume":141,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"publication_status":"published","status":"public","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"article_type":"original","type":"journal_article","_id":"13373","extern":"1","date_updated":"2023-08-07T10:51:12Z","quality_controlled":"1","publisher":"American Chemical Society","doi":"10.1021/jacs.8b09638","date_published":"2019-02-06T00:00:00Z","date_created":"2023-08-01T09:39:19Z","page":"1949-1960","day":"06","publication":"Journal of the American Chemical Society","year":"2019","title":"Supramolecular control of azobenzene switching on nanoparticles","author":[{"first_name":"Zonglin","full_name":"Chu, Zonglin","last_name":"Chu"},{"first_name":"Yanxiao","full_name":"Han, Yanxiao","last_name":"Han"},{"first_name":"Tong","full_name":"Bian, Tong","last_name":"Bian"},{"full_name":"De, Soumen","last_name":"De","first_name":"Soumen"},{"first_name":"Petr","last_name":"Král","full_name":"Král, Petr"},{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"external_id":{"pmid":["30595017"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. 2019. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 141(5), 1949–1960.","chicago":"Chu, Zonglin, Yanxiao Han, Tong Bian, Soumen De, Petr Král, and Rafal Klajn. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09638.","ieee":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, and R. Klajn, “Supramolecular control of azobenzene switching on nanoparticles,” Journal of the American Chemical Society, vol. 141, no. 5. American Chemical Society, pp. 1949–1960, 2019.","short":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, R. Klajn, Journal of the American Chemical Society 141 (2019) 1949–1960.","apa":"Chu, Z., Han, Y., Bian, T., De, S., Král, P., & Klajn, R. (2019). Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09638","ama":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 2019;141(5):1949-1960. doi:10.1021/jacs.8b09638","mla":"Chu, Zonglin, et al. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” Journal of the American Chemical Society, vol. 141, no. 5, American Chemical Society, 2019, pp. 1949–60, doi:10.1021/jacs.8b09638."}},{"date_updated":"2023-08-07T10:48:31Z","extern":"1","type":"journal_article","article_type":"original","keyword":["General Chemistry"],"status":"public","_id":"13372","issue":"5","volume":48,"publication_status":"published","publication_identifier":{"issn":["0306-0012"],"eissn":["1460-4744"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1039/C8CS00787J","open_access":"1"}],"scopus_import":"1","intvolume":" 48","month":"01","abstract":[{"lang":"eng","text":"The capacity to respond or adapt to environmental changes is an intrinsic property of living systems that comprise highly-connected subcomponents communicating through chemical networks. The development of responsive synthetic systems is a relatively new research area that covers different disciplines, among which nanochemistry brings conceptually new demonstrations. Especially attractive are ligand-protected gold nanoparticles, which have been extensively used over the last decade as building blocks in constructing superlattices or dynamic aggregates, under the effect of an applied stimulus. To reflect the importance of surface chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles, we provide here an overview of various available stimuli, as tools for synthetic chemists to exploit. Along with this task, the review starts with the use of chemical stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses on physical stimuli: temperature, magnetic and electric fields, as well as light. To reflect on the increasing complexity of current architectures, we discuss systems that are responsive to more than one stimulus, to finally encourage further research by proposing future challenges."}],"pmid":1,"oa_version":"Published Version","article_processing_charge":"No","external_id":{"pmid":["30688963"]},"author":[{"full_name":"Grzelczak, Marek","last_name":"Grzelczak","first_name":"Marek"},{"last_name":"Liz-Marzán","full_name":"Liz-Marzán, Luis M.","first_name":"Luis M."},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"title":"Stimuli-responsive self-assembly of nanoparticles","citation":{"ama":"Grzelczak M, Liz-Marzán LM, Klajn R. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 2019;48(5):1342-1361. doi:10.1039/c8cs00787j","apa":"Grzelczak, M., Liz-Marzán, L. M., & Klajn, R. (2019). Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. Royal Society of Chemistry. https://doi.org/10.1039/c8cs00787j","short":"M. Grzelczak, L.M. Liz-Marzán, R. Klajn, Chemical Society Reviews 48 (2019) 1342–1361.","ieee":"M. Grzelczak, L. M. Liz-Marzán, and R. Klajn, “Stimuli-responsive self-assembly of nanoparticles,” Chemical Society Reviews, vol. 48, no. 5. Royal Society of Chemistry, pp. 1342–1361, 2019.","mla":"Grzelczak, Marek, et al. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews, vol. 48, no. 5, Royal Society of Chemistry, 2019, pp. 1342–61, doi:10.1039/c8cs00787j.","ista":"Grzelczak M, Liz-Marzán LM, Klajn R. 2019. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 48(5), 1342–1361.","chicago":"Grzelczak, Marek, Luis M. Liz-Marzán, and Rafal Klajn. “Stimuli-Responsive Self-Assembly of Nanoparticles.” Chemical Society Reviews. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8cs00787j."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1342-1361","date_created":"2023-08-01T09:38:52Z","doi":"10.1039/c8cs00787j","date_published":"2019-01-28T00:00:00Z","year":"2019","publication":"Chemical Society Reviews","day":"28","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1"},{"author":[{"first_name":"Anton I","full_name":"Hanopolskyi, Anton I","last_name":"Hanopolskyi"},{"full_name":"De, Soumen","last_name":"De","first_name":"Soumen"},{"last_name":"Białek","full_name":"Białek, Michał J","first_name":"Michał J"},{"last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael","first_name":"Yael"},{"full_name":"Avram, Liat","last_name":"Avram","first_name":"Liat"},{"first_name":"Moran","last_name":"Feller","full_name":"Feller, Moran"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"}],"external_id":{"pmid":["31666874"]},"article_processing_charge":"No","title":"Reversible switching of arylazopyrazole within a metal–organic cage","citation":{"short":"A.I. Hanopolskyi, S. De, M.J. Białek, Y. Diskin-Posner, L. Avram, M. Feller, R. Klajn, Beilstein Journal of Organic Chemistry 15 (2019) 2398–2407.","ieee":"A. I. Hanopolskyi et al., “Reversible switching of arylazopyrazole within a metal–organic cage,” Beilstein Journal of Organic Chemistry, vol. 15. Beilstein Institut, pp. 2398–2407, 2019.","ama":"Hanopolskyi AI, De S, Białek MJ, et al. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 2019;15:2398-2407. doi:10.3762/bjoc.15.232","apa":"Hanopolskyi, A. I., De, S., Białek, M. J., Diskin-Posner, Y., Avram, L., Feller, M., & Klajn, R. (2019). Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. Beilstein Institut. https://doi.org/10.3762/bjoc.15.232","mla":"Hanopolskyi, Anton I., et al. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry, vol. 15, Beilstein Institut, 2019, pp. 2398–407, doi:10.3762/bjoc.15.232.","ista":"Hanopolskyi AI, De S, Białek MJ, Diskin-Posner Y, Avram L, Feller M, Klajn R. 2019. Reversible switching of arylazopyrazole within a metal–organic cage. Beilstein Journal of Organic Chemistry. 15, 2398–2407.","chicago":"Hanopolskyi, Anton I, Soumen De, Michał J Białek, Yael Diskin-Posner, Liat Avram, Moran Feller, and Rafal Klajn. “Reversible Switching of Arylazopyrazole within a Metal–Organic Cage.” Beilstein Journal of Organic Chemistry. Beilstein Institut, 2019. https://doi.org/10.3762/bjoc.15.232."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2398-2407","date_published":"2019-10-10T00:00:00Z","doi":"10.3762/bjoc.15.232","date_created":"2023-08-01T09:38:06Z","year":"2019","day":"10","publication":"Beilstein Journal of Organic Chemistry","publisher":"Beilstein Institut","quality_controlled":"1","oa":1,"date_updated":"2023-08-07T10:34:56Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Organic Chemistry"],"_id":"13369","volume":15,"publication_identifier":{"eissn":["1860-5397"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.3762/bjoc.15.232","open_access":"1"}],"month":"10","intvolume":" 15","abstract":[{"text":"Arylazopyrazoles represent a new family of molecular photoswitches characterized by a near-quantitative conversion between two states and long thermal half-lives of the metastable state. Here, we investigated the behavior of a model arylazopyrazole in the presence of a self-assembled cage based on Pd–imidazole coordination. Owing to its high water solubility, the cage can solubilize the E isomer of arylazopyrazole, which, by itself, is not soluble in water. NMR spectroscopy and X-ray crystallography have independently demonstrated that each cage can encapsulate two molecules of E-arylazopyrazole. UV-induced switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calculations suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with green light and resulted in the initial 1:2 cage/E-arylazopyrazole complex. This back-isomerization reaction also proceeded in the dark, with a rate significantly higher than in the absence of the cage.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"date_created":"2023-08-01T09:38:23Z","date_published":"2019-09-20T00:00:00Z","doi":"10.1021/acs.nanolett.9b02642","page":"7106-7111","publication":"Nano Letters","day":"20","year":"2019","publisher":"American Chemical Society","quality_controlled":"1","title":"Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules","article_processing_charge":"No","external_id":{"pmid":["31539469"]},"author":[{"full_name":"Chu, Zonglin","last_name":"Chu","first_name":"Zonglin"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chu Z, Klajn R. 2019. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. 19(10), 7106–7111.","chicago":"Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano Letters. American Chemical Society, 2019. https://doi.org/10.1021/acs.nanolett.9b02642.","apa":"Chu, Z., & Klajn, R. (2019). Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b02642","ama":"Chu Z, Klajn R. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. 2019;19(10):7106-7111. doi:10.1021/acs.nanolett.9b02642","ieee":"Z. Chu and R. Klajn, “Polysilsesquioxane nanowire networks as an ‘Artificial Solvent’ for reversible operation of photochromic molecules,” Nano Letters, vol. 19, no. 10. American Chemical Society, pp. 7106–7111, 2019.","short":"Z. Chu, R. Klajn, Nano Letters 19 (2019) 7106–7111.","mla":"Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” Nano Letters, vol. 19, no. 10, American Chemical Society, 2019, pp. 7106–11, doi:10.1021/acs.nanolett.9b02642."},"volume":19,"issue":"10","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"intvolume":" 19","month":"09","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Efficient isomerization of photochromic molecules often requires conformational freedom and is typically not available under solvent-free conditions. Here, we report a general methodology allowing for reversible switching of such molecules on the surfaces of solid materials. Our method is based on dispersing photochromic compounds within polysilsesquioxane nanowire networks (PNNs), which can be fabricated as transparent, highly porous, micrometer-thick layers on various substrates. We found that azobenzene switching within the PNNs proceeded unusually fast compared with the same molecules in liquid solvents. Efficient isomerization of another photochromic system, spiropyran, from a colorless to a colored form was used to create reversible images in PNN-coated glass. The coloration reaction could be induced with sunlight and is of interest for developing “smart” windows."}],"extern":"1","date_updated":"2023-08-07T10:39:34Z","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"status":"public","type":"journal_article","article_type":"original","_id":"13370"},{"extern":"1","date_updated":"2023-08-07T10:46:50Z","_id":"13371","status":"public","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2451-9308"],"eissn":["2451-9294"]},"publication_status":"published","volume":5,"issue":"9","oa_version":"Published Version","abstract":[{"text":"Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials.","lang":"eng"}],"month":"09","intvolume":" 5","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2019.08.012"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Białek MJ, Klajn R. 2019. Diamond grows up. Chem. 5(9), 2283–2285.","chicago":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem. Elsevier, 2019. https://doi.org/10.1016/j.chempr.2019.08.012.","ieee":"M. J. Białek and R. Klajn, “Diamond grows up,” Chem, vol. 5, no. 9. Elsevier, pp. 2283–2285, 2019.","short":"M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285.","ama":"Białek MJ, Klajn R. Diamond grows up. Chem. 2019;5(9):2283-2285. doi:10.1016/j.chempr.2019.08.012","apa":"Białek, M. J., & Klajn, R. (2019). Diamond grows up. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2019.08.012","mla":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” Chem, vol. 5, no. 9, Elsevier, 2019, pp. 2283–85, doi:10.1016/j.chempr.2019.08.012."},"title":"Diamond grows up","author":[{"first_name":"Michał J.","full_name":"Białek, Michał J.","last_name":"Białek"},{"full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"article_processing_charge":"No","day":"12","publication":"Chem","year":"2019","doi":"10.1016/j.chempr.2019.08.012","date_published":"2019-09-12T00:00:00Z","date_created":"2023-08-01T09:38:38Z","page":"2283-2285","quality_controlled":"1","publisher":"Elsevier","oa":1},{"author":[{"last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde"}],"external_id":{"arxiv":["1905.03835"]},"title":"Bidding mechanisms in graph games","citation":{"short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","ieee":"G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138.","ama":"Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.MFCS.2019.11","apa":"Avni, G., Henzinger, T. A., & Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: nternational Symposium on Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2019.11","mla":"Avni, Guy, et al. Bidding Mechanisms in Graph Games. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.MFCS.2019.11.","ista":"Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: nternational Symposium on Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.","chicago":"Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.MFCS.2019.11."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"}],"article_number":"11","date_published":"2019-08-01T00:00:00Z","doi":"10.4230/LIPICS.MFCS.2019.11","date_created":"2019-09-18T08:04:26Z","has_accepted_license":"1","year":"2019","day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:42Z","date_updated":"2023-08-07T14:08:34Z","ddc":["004"],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Aachen, Germany","end_date":"2019-08-30","start_date":"2019-08-26","name":"MFCS: nternational Symposium on Mathematical Foundations of Computer Science"},"status":"public","_id":"6884","related_material":{"record":[{"id":"9239","status":"public","relation":"later_version"}]},"volume":138,"ec_funded":1,"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","file_id":"6913","creator":"kschuh","date_updated":"2020-07-14T12:47:42Z","file_size":554457,"date_created":"2019-09-27T11:45:15Z","file_name":"2019_LIPIcs_Avni.pdf"}],"language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["LIPIcs"],"month":"08","intvolume":" 138","abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the \"bank\" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. "}],"oa_version":"Published Version"},{"_id":"13471","type":"journal_article","article_type":"original","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","date_updated":"2023-08-09T12:26:08Z","extern":"1","abstract":[{"lang":"eng","text":"We perform an extensive numerical study of the evolution of massive binary systems to predict the peculiar velocities that stars obtain when their companion collapses and disrupts the system. Our aim is to (i) identify which predictions are robust against model uncertainties and assess their implications, (ii) investigate which physical processes leave a clear imprint and may therefore be constrained observationally, and (iii) provide a suite of publicly available model predictions to allow for the use of kinematic constraints from the Gaia mission. We find that 22+26−8% of all massive binary systems merge prior to the first core-collapse in the system. Of the remainder, 86+11−9% become unbound because of the core-collapse. Remarkably, this rarely produces runaway stars (observationally defined as stars with velocities above 30 km s−1). These are outnumbered by more than an order of magnitude by slower unbound companions, or “walkaway stars”. This is a robust outcome of our simulations and is due to the reversal of the mass ratio prior to the explosion and widening of the orbit, as we show analytically and numerically. For stars more massive than 15 M⊙, we estimate that 10+5−8% are walkaways and only 0.5+1.0−0.4% are runaways, nearly all of which have accreted mass from their companion. Our findings are consistent with earlier studies; however, the low runaway fraction we find is in tension with observed fractions of about 10%. Thus, astrometric data on presently single massive stars can potentially constrain the physics of massive binary evolution. Finally, we show that the high end of the mass distributions of runaway stars is very sensitive to the assumed black hole natal kicks, and we propose this as a potentially stringent test for the explosion mechanism. We also discuss companions remaining bound that can evolve into X-ray and gravitational wave sources."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201833297"}],"scopus_import":"1","intvolume":" 624","month":"04","publication_status":"published","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"language":[{"iso":"eng"}],"volume":624,"article_number":"A66","citation":{"ista":"Renzo M, Zapartas E, de Mink SE, Götberg YLL, Justham S, Farmer RJ, Izzard RG, Toonen S, Sana H. 2019. Massive runaway and walkaway stars. Astronomy & Astrophysics. 624, A66.","chicago":"Renzo, M., E. Zapartas, S. E. de Mink, Ylva Louise Linsdotter Götberg, S. Justham, R. J. Farmer, R. G. Izzard, S. Toonen, and H. Sana. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201833297.","ama":"Renzo M, Zapartas E, de Mink SE, et al. Massive runaway and walkaway stars. Astronomy & Astrophysics. 2019;624. doi:10.1051/0004-6361/201833297","apa":"Renzo, M., Zapartas, E., de Mink, S. E., Götberg, Y. L. L., Justham, S., Farmer, R. J., … Sana, H. (2019). Massive runaway and walkaway stars. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833297","ieee":"M. Renzo et al., “Massive runaway and walkaway stars,” Astronomy & Astrophysics, vol. 624. EDP Sciences, 2019.","short":"M. Renzo, E. Zapartas, S.E. de Mink, Y.L.L. Götberg, S. Justham, R.J. Farmer, R.G. Izzard, S. Toonen, H. Sana, Astronomy & Astrophysics 624 (2019).","mla":"Renzo, M., et al. “Massive Runaway and Walkaway Stars.” Astronomy & Astrophysics, vol. 624, A66, EDP Sciences, 2019, doi:10.1051/0004-6361/201833297."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1804.09164"]},"author":[{"last_name":"Renzo","full_name":"Renzo, M.","first_name":"M."},{"last_name":"Zapartas","full_name":"Zapartas, E.","first_name":"E."},{"first_name":"S. E.","last_name":"de Mink","full_name":"de Mink, S. E."},{"first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d","last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911"},{"first_name":"S.","full_name":"Justham, S.","last_name":"Justham"},{"last_name":"Farmer","full_name":"Farmer, R. J.","first_name":"R. J."},{"last_name":"Izzard","full_name":"Izzard, R. G.","first_name":"R. G."},{"full_name":"Toonen, S.","last_name":"Toonen","first_name":"S."},{"full_name":"Sana, H.","last_name":"Sana","first_name":"H."}],"title":"Massive runaway and walkaway stars","oa":1,"quality_controlled":"1","publisher":"EDP Sciences","year":"2019","publication":"Astronomy & Astrophysics","day":"11","date_created":"2023-08-03T10:14:18Z","date_published":"2019-04-11T00:00:00Z","doi":"10.1051/0004-6361/201833297"},{"quality_controlled":"1","publisher":"EDP Sciences","oa":1,"date_published":"2019-07-16T00:00:00Z","doi":"10.1051/0004-6361/201935684","date_created":"2023-08-03T10:14:09Z","day":"16","publication":"Astronomy & Astrophysics","year":"2019","article_number":"A151","title":"The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud","author":[{"first_name":"T.","full_name":"Shenar, T.","last_name":"Shenar"},{"first_name":"D. P.","full_name":"Sablowski, D. P.","last_name":"Sablowski"},{"full_name":"Hainich, R.","last_name":"Hainich","first_name":"R."},{"first_name":"H.","last_name":"Todt","full_name":"Todt, H."},{"first_name":"A. F. J.","last_name":"Moffat","full_name":"Moffat, A. F. J."},{"first_name":"L. M.","full_name":"Oskinova, L. M.","last_name":"Oskinova"},{"last_name":"Ramachandran","full_name":"Ramachandran, V.","first_name":"V."},{"first_name":"H.","full_name":"Sana, H.","last_name":"Sana"},{"last_name":"Sander","full_name":"Sander, A. A. C.","first_name":"A. A. C."},{"first_name":"O.","full_name":"Schnurr, O.","last_name":"Schnurr"},{"first_name":"N.","full_name":"St-Louis, N.","last_name":"St-Louis"},{"first_name":"D.","last_name":"Vanbeveren","full_name":"Vanbeveren, D."},{"last_name":"Götberg","full_name":"Götberg, Ylva Louise Linsdotter","orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"first_name":"W.-R.","last_name":"Hamann","full_name":"Hamann, W.-R."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Shenar, T., D. P. Sablowski, R. Hainich, H. Todt, A. F. J. Moffat, L. M. Oskinova, V. Ramachandran, et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935684.","ista":"Shenar T, Sablowski DP, Hainich R, Todt H, Moffat AFJ, Oskinova LM, Ramachandran V, Sana H, Sander AAC, Schnurr O, St-Louis N, Vanbeveren D, Götberg YLL, Hamann W-R. 2019. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 627, A151.","mla":"Shenar, T., et al. “The Wolf–Rayet Binaries of the Nitrogen Sequence in the Large Magellanic Cloud.” Astronomy & Astrophysics, vol. 627, A151, EDP Sciences, 2019, doi:10.1051/0004-6361/201935684.","apa":"Shenar, T., Sablowski, D. P., Hainich, R., Todt, H., Moffat, A. F. J., Oskinova, L. M., … Hamann, W.-R. (2019). The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935684","ama":"Shenar T, Sablowski DP, Hainich R, et al. The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud. Astronomy & Astrophysics. 2019;627. doi:10.1051/0004-6361/201935684","short":"T. Shenar, D.P. Sablowski, R. Hainich, H. Todt, A.F.J. Moffat, L.M. Oskinova, V. Ramachandran, H. Sana, A.A.C. Sander, O. Schnurr, N. St-Louis, D. Vanbeveren, Y.L.L. Götberg, W.-R. Hamann, Astronomy & Astrophysics 627 (2019).","ieee":"T. Shenar et al., “The Wolf–Rayet binaries of the nitrogen sequence in the Large Magellanic Cloud,” Astronomy & Astrophysics, vol. 627. EDP Sciences, 2019."},"month":"07","intvolume":" 627","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201935684","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Context. Massive Wolf–Rayet (WR) stars dominate the radiative and mechanical energy budget of galaxies and probe a critical phase in the evolution of massive stars prior to core collapse. It is not known whether core He-burning WR stars (classical WR; cWR) form predominantly through wind stripping (w-WR) or binary stripping (b-WR). Whereas spectroscopy of WR binaries has so-far largely been avoided because of its complexity, our study focuses on the 44 WR binaries and binary candidates of the Large Magellanic Cloud (LMC; metallicity Z ≈ 0.5 Z⊙), which were identified on the basis of radial velocity variations, composite spectra, or high X-ray luminosities.\r\n\r\nAims. Relying on a diverse spectroscopic database, we aim to derive the physical and orbital parameters of our targets, confronting evolution models of evolved massive stars at subsolar metallicity and constraining the impact of binary interaction in forming these stars.\r\n\r\nMethods. Spectroscopy was performed using the Potsdam Wolf–Rayet (PoWR) code and cross-correlation techniques. Disentanglement was performed using the code Spectangular or the shift-and-add algorithm. Evolutionary status was interpreted using the Binary Population and Spectral Synthesis (BPASS) code, exploring binary interaction and chemically homogeneous evolution.\r\n\r\nResults. Among our sample, 28/44 objects show composite spectra and are analyzed as such. An additional five targets show periodically moving WR primaries but no detected companions (SB1); two (BAT99 99 and 112) are potential WR + compact-object candidates owing to their high X-ray luminosities. We cannot confirm the binary nature of the remaining 11 candidates. About two-thirds of the WN components in binaries are identified as cWR, and one-third as hydrogen-burning WR stars. We establish metallicity-dependent mass-loss recipes, which broadly agree with those recently derived for single WN stars, and in which so-called WN3/O3 stars are clear outliers. We estimate that 45 ± 30% of the cWR stars in our sample have interacted with a companion via mass transfer. However, only ≈12 ± 7% of the cWR stars in our sample naively appear to have formed purely owing to stripping via a companion (12% b-WR). Assuming that apparently single WR stars truly formed as single stars, this comprises ≈4% of the whole LMC WN population, which is about ten times less than expected. No obvious differences in the properties of single and binary WN stars, whose luminosities extend down to log L ≈ 5.2 [L⊙], are apparent. With the exception of a few systems (BAT99 19, 49, and 103), the equatorial rotational velocities of the OB-type companions are moderate (veq ≲ 250 km s−1) and challenge standard formalisms of angular-momentum accretion. For most objects, chemically homogeneous evolution can be rejected for the secondary, but not for the WR progenitor.\r\n\r\nConclusions. No obvious dichotomy in the locations of apparently single and binary WN stars on the Hertzsprung-Russell diagram is apparent. According to commonly used stellar evolution models (BPASS, Geneva), most apparently single WN stars could not have formed as single stars, implying that they were stripped by an undetected companion. Otherwise, it must follow that pre-WR mass-loss/mixing (e.g., during the red supergiant phase) are strongly underestimated in standard stellar evolution models.","lang":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1051/0004-6361/201935684e"}]},"volume":627,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"publication_status":"published","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"type":"journal_article","article_type":"original","_id":"13470","extern":"1","date_updated":"2023-08-09T12:29:58Z"},{"volume":623,"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201732206","open_access":"1"}],"month":"03","intvolume":" 623","abstract":[{"text":"Massive stars in binaries can give rise to extreme phenomena such as X-ray binaries and gravitational wave sources after one or both stars end their lives as core-collapse supernovae. Stars in close orbit around a stellar or compact companion are expected to explode as “stripped-envelope supernovae”, showing no (Type Ib/c) or little (Type IIb) signs of hydrogen in the spectra, because hydrogen-rich progenitors are too large to fit. The physical processes responsible for the stripping process and the fate of the companion are still very poorly understood. Aiming to find new clues, we investigate Cas A, which is a very young (∼340 yr) and near (∼3.4 kpc) remnant of a core-collapse supernova. Cas A has been subject to several searches for possible companions, all unsuccessfully. We present new measurements of the proper motions and photometry of stars in the vicinity based on deep HST ACS/WFC and WFC3-IR data. We identify stellar sources that are close enough in projection but using their proper motions we show that none are compatible with being at the location of center at the time of explosion, in agreement with earlier findings. Our photometric measurements allow us to place much deeper (order-of-magnitude) upper limits on the brightness of possible undetected companions. We systematically compare them with model predictions for a wide variety of scenarios. We can confidently rule out the presence of any stellar companion of any reasonable mass and age (main sequence, pre main sequence or stripped) ruling out what many considered to be likely evolutionary scenarios for Type IIb supernova (SN IIb). More exotic scenarios that predict the presence of a compact companion (white dwarf, neutron star or black hole) are still possible as well as scenarios where the progenitor of Cas A was single at the moment of explosion (either because it was truly single, or resulted from a binary that was disrupted, or from a binary merger). The presence of a compact companion would imply that Cas A is of interest to study exotic outcomes of binary evolution. The single-at-death solution would still require fine-tuning of the process that removed most of the envelope through a mass-loss mechanism yet to be identified. We discuss how future constraints from Gaia and even deeper photometric studies may help to place further constraints.","lang":"eng"}],"oa_version":"Published Version","date_updated":"2023-08-09T12:28:17Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"13472","date_published":"2019-03-27T00:00:00Z","doi":"10.1051/0004-6361/201732206","date_created":"2023-08-03T10:14:27Z","year":"2019","day":"27","publication":"Astronomy & Astrophysics","publisher":"EDP Sciences","quality_controlled":"1","oa":1,"author":[{"full_name":"Kerzendorf, Wolfgang E.","last_name":"Kerzendorf","first_name":"Wolfgang E."},{"full_name":"Do, Tuan","last_name":"Do","first_name":"Tuan"},{"first_name":"Selma E.","full_name":"de Mink, Selma E.","last_name":"de Mink"},{"orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Milisavljevic, Dan","last_name":"Milisavljevic","first_name":"Dan"},{"first_name":"Emmanouil","full_name":"Zapartas, Emmanouil","last_name":"Zapartas"},{"last_name":"Renzo","full_name":"Renzo, Mathieu","first_name":"Mathieu"},{"full_name":"Justham, Stephen","last_name":"Justham","first_name":"Stephen"},{"first_name":"Philipp","last_name":"Podsiadlowski","full_name":"Podsiadlowski, Philipp"},{"first_name":"Robert A.","last_name":"Fesen","full_name":"Fesen, Robert A."}],"article_processing_charge":"No","external_id":{"arxiv":["1711.00055"]},"title":"No surviving non-compact stellar companion to Cassiopeia A","citation":{"mla":"Kerzendorf, Wolfgang E., et al. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics, vol. 623, A34, EDP Sciences, 2019, doi:10.1051/0004-6361/201732206.","ama":"Kerzendorf WE, Do T, de Mink SE, et al. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 2019;623. doi:10.1051/0004-6361/201732206","apa":"Kerzendorf, W. E., Do, T., de Mink, S. E., Götberg, Y. L. L., Milisavljevic, D., Zapartas, E., … Fesen, R. A. (2019). No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201732206","ieee":"W. E. Kerzendorf et al., “No surviving non-compact stellar companion to Cassiopeia A,” Astronomy & Astrophysics, vol. 623. EDP Sciences, 2019.","short":"W.E. Kerzendorf, T. Do, S.E. de Mink, Y.L.L. Götberg, D. Milisavljevic, E. Zapartas, M. Renzo, S. Justham, P. Podsiadlowski, R.A. Fesen, Astronomy & Astrophysics 623 (2019).","chicago":"Kerzendorf, Wolfgang E., Tuan Do, Selma E. de Mink, Ylva Louise Linsdotter Götberg, Dan Milisavljevic, Emmanouil Zapartas, Mathieu Renzo, Stephen Justham, Philipp Podsiadlowski, and Robert A. Fesen. “No Surviving Non-Compact Stellar Companion to Cassiopeia A.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201732206.","ista":"Kerzendorf WE, Do T, de Mink SE, Götberg YLL, Milisavljevic D, Zapartas E, Renzo M, Justham S, Podsiadlowski P, Fesen RA. 2019. No surviving non-compact stellar companion to Cassiopeia A. Astronomy & Astrophysics. 623, A34."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A34"},{"article_number":"A5","external_id":{"arxiv":["1907.06687"]},"article_processing_charge":"No","author":[{"first_name":"Emmanouil","full_name":"Zapartas, Emmanouil","last_name":"Zapartas"},{"last_name":"de Mink","full_name":"de Mink, Selma E.","first_name":"Selma E."},{"last_name":"Justham","full_name":"Justham, Stephen","first_name":"Stephen"},{"first_name":"Nathan","full_name":"Smith, Nathan","last_name":"Smith"},{"first_name":"Alex","full_name":"de Koter, Alex","last_name":"de Koter"},{"first_name":"Mathieu","full_name":"Renzo, Mathieu","last_name":"Renzo"},{"full_name":"Arcavi, Iair","last_name":"Arcavi","first_name":"Iair"},{"first_name":"Rob","last_name":"Farmer","full_name":"Farmer, Rob"},{"last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Toonen, Silvia","last_name":"Toonen","first_name":"Silvia"}],"title":"The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction","citation":{"mla":"Zapartas, Emmanouil, et al. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics, vol. 631, A5, EDP Sciences, 2019, doi:10.1051/0004-6361/201935854.","short":"E. Zapartas, S.E. de Mink, S. Justham, N. Smith, A. de Koter, M. Renzo, I. Arcavi, R. Farmer, Y.L.L. Götberg, S. Toonen, Astronomy & Astrophysics 631 (2019).","ieee":"E. Zapartas et al., “The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction,” Astronomy & Astrophysics, vol. 631. EDP Sciences, 2019.","apa":"Zapartas, E., de Mink, S. E., Justham, S., Smith, N., de Koter, A., Renzo, M., … Toonen, S. (2019). The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201935854","ama":"Zapartas E, de Mink SE, Justham S, et al. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 2019;631. doi:10.1051/0004-6361/201935854","chicago":"Zapartas, Emmanouil, Selma E. de Mink, Stephen Justham, Nathan Smith, Alex de Koter, Mathieu Renzo, Iair Arcavi, Rob Farmer, Ylva Louise Linsdotter Götberg, and Silvia Toonen. “The Diverse Lives of Progenitors of Hydrogen-Rich Core-Collapse Supernovae: The Role of Binary Interaction.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201935854.","ista":"Zapartas E, de Mink SE, Justham S, Smith N, de Koter A, Renzo M, Arcavi I, Farmer R, Götberg YLL, Toonen S. 2019. The diverse lives of progenitors of hydrogen-rich core-collapse supernovae: The role of binary interaction. Astronomy & Astrophysics. 631, A5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"EDP Sciences","quality_controlled":"1","date_created":"2023-08-03T10:13:52Z","doi":"10.1051/0004-6361/201935854","date_published":"2019-11-20T00:00:00Z","year":"2019","publication":"Astronomy & Astrophysics","day":"20","article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","_id":"13468","date_updated":"2023-08-09T12:36:09Z","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201935854"}],"scopus_import":"1","intvolume":" 631","month":"11","abstract":[{"lang":"eng","text":"Hydrogen-rich supernovae, known as Type II (SNe II), are the most common class of explosions observed following the collapse of the core of massive stars. We used analytical estimates and population synthesis simulations to assess the fraction of SNe II progenitors that are expected to have exchanged mass with a companion prior to explosion. We estimate that 1/3 to 1/2 of SN II progenitors have a history of mass exchange with a binary companion before exploding. The dominant binary channels leading to SN II progenitors involve the merger of binary stars. Mergers are expected to produce a diversity of SN II progenitor characteristics, depending on the evolutionary timing and properties of the merger. Alternatively, SN II progenitors from interacting binaries may have accreted mass from their companion, and subsequently been ejected from the binary system after their companion exploded. We show that the overall fraction of SN II progenitors that are predicted to have experienced binary interaction is robust against the main physical uncertainties in our models. However, the relative importance of different binary evolutionary channels is affected by changing physical assumptions. We further discuss ways in which binarity might contribute to the observed diversity of SNe II by considering potential observational signatures arising from each binary channel. For supernovae which have a substantial H-rich envelope at explosion (i.e., excluding Type IIb SNe), a surviving non-compact companion would typically indicate that the supernova progenitor star was in a wide, non-interacting binary. We argue that a significant fraction of even Type II-P SNe are expected to have gained mass from a companion prior to explosion."}],"oa_version":"Published Version","volume":631,"publication_status":"published","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"language":[{"iso":"eng"}]},{"author":[{"last_name":"Götberg","orcid":"0000-0002-6960-6911","full_name":"Götberg, Ylva Louise Linsdotter","first_name":"Ylva Louise Linsdotter","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"last_name":"de Mink","full_name":"de Mink, S. E.","first_name":"S. E."},{"first_name":"J. H.","full_name":"Groh, J. H.","last_name":"Groh"},{"last_name":"Leitherer","full_name":"Leitherer, C.","first_name":"C."},{"first_name":"C.","last_name":"Norman","full_name":"Norman, C."}],"external_id":{"arxiv":["1908.06102"]},"article_processing_charge":"No","title":"The impact of stars stripped in binaries on the integrated spectra of stellar populations","citation":{"mla":"Götberg, Ylva Louise Linsdotter, et al. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics, vol. 629, A134, EDP Sciences, 2019, doi:10.1051/0004-6361/201834525.","ieee":"Y. L. L. Götberg, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman, “The impact of stars stripped in binaries on the integrated spectra of stellar populations,” Astronomy & Astrophysics, vol. 629. EDP Sciences, 2019.","short":"Y.L.L. Götberg, S.E. de Mink, J.H. Groh, C. Leitherer, C. Norman, Astronomy & Astrophysics 629 (2019).","apa":"Götberg, Y. L. L., de Mink, S. E., Groh, J. H., Leitherer, C., & Norman, C. (2019). The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201834525","ama":"Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 2019;629. doi:10.1051/0004-6361/201834525","chicago":"Götberg, Ylva Louise Linsdotter, S. E. de Mink, J. H. Groh, C. Leitherer, and C. Norman. “The Impact of Stars Stripped in Binaries on the Integrated Spectra of Stellar Populations.” Astronomy & Astrophysics. EDP Sciences, 2019. https://doi.org/10.1051/0004-6361/201834525.","ista":"Götberg YLL, de Mink SE, Groh JH, Leitherer C, Norman C. 2019. The impact of stars stripped in binaries on the integrated spectra of stellar populations. Astronomy & Astrophysics. 629, A134."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A134","date_published":"2019-09-17T00:00:00Z","doi":"10.1051/0004-6361/201834525","date_created":"2023-08-03T10:14:00Z","year":"2019","day":"17","publication":"Astronomy & Astrophysics","publisher":"EDP Sciences","quality_controlled":"1","oa":1,"date_updated":"2023-08-09T12:34:11Z","extern":"1","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"_id":"13469","volume":629,"publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1051/0004-6361/201834525","open_access":"1"}],"month":"09","intvolume":" 629","abstract":[{"lang":"eng","text":"Stars stripped of their envelopes from interaction with a binary companion emit a significant fraction of their radiation as ionizing photons. They are potentially important stellar sources of ionizing radiation, however, they are still often neglected in spectral synthesis simulations or simulations of stellar feedback. In anticipating the large datasets of galaxy spectra from the upcoming James Webb Space Telescope, we modeled the radiative contribution from stripped stars by using detailed evolutionary and spectral models. We estimated their impact on the integrated spectra and specifically on the emission rates of H I-, He I-, and He II-ionizing photons from stellar populations. We find that stripped stars have the largest impact on the ionizing spectrum of a population in which star formation halted several Myr ago. In such stellar populations, stripped stars dominate the emission of ionizing photons, mimicking a younger stellar population in which massive stars are still present. Our models also suggest that stripped stars have harder ionizing spectra than massive stars. The additional ionizing radiation, with which stripped stars contribute affects observable properties that are related to the emission of ionizing photons from stellar populations. In co-eval stellar populations, the ionizing radiation from stripped stars increases the ionization parameter and the production efficiency of hydrogen ionizing photons. They also cause high values for these parameters for about ten times longer than what is predicted for massive stars. The effect on properties related to non-ionizing wavelengths is less pronounced, such as on the ultraviolet continuum slope or stellar contribution to emission lines. However, the hard ionizing radiation from stripped stars likely introduces a characteristic ionization structure of the nebula, which leads to the emission of highly ionized elements such as O2+ and C3+. We, therefore, expect that the presence of stripped stars affects the location in the BPT diagram and the diagnostic ratio of O III to O II nebular emission lines. Our models are publicly available through CDS database and on the STARBURST99 website."}],"oa_version":"Published Version"},{"title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","department":[{"_id":"EdHa"}],"article_processing_charge":"No","author":[{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"full_name":"Lipowsky, Reinhard","last_name":"Lipowsky","first_name":"Reinhard"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-17T14:07:52Z","citation":{"mla":"Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","short":"M.C. Ucar, R. Lipowsky, (2019).","apa":"Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001."},"status":"public","type":"research_data_reference","_id":"9726","date_created":"2021-07-27T09:51:46Z","related_material":{"record":[{"status":"public","id":"7166","relation":"used_in_publication"}]},"doi":"10.1021/acs.nanolett.9b04445.s001","date_published":"2019-12-19T00:00:00Z","day":"19","year":"2019","month":"12","publisher":"American Chemical Society ","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)"}]},{"article_type":"original","type":"journal_article","keyword":["Multidisciplinary"],"status":"public","_id":"14001","date_updated":"2023-08-22T07:40:05Z","extern":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1907189116","open_access":"1"}],"scopus_import":"1","intvolume":" 116","month":"11","abstract":[{"text":"Chiral molecules interact and react differently with other chiral objects, depending on their handedness. Therefore, it is essential to understand and ultimately control the evolution of molecular chirality during chemical reactions. Although highly sophisticated techniques for the controlled synthesis of chiral molecules have been developed, the observation of chirality on the natural femtosecond time scale of a chemical reaction has so far remained out of reach in the gas phase. Here, we demonstrate a general experimental technique, based on high-harmonic generation in tailored laser fields, and apply it to probe the time evolution of molecular chirality during the photodissociation of 2-iodobutane. These measurements show a change in sign and a pronounced increase in the magnitude of the chiral response over the first 100 fs, followed by its decay within less than 500 fs, revealing the photodissociation to achiral products. The observed time evolution is explained in terms of the variation of the electric and magnetic transition-dipole moments between the lowest electronic states of the cation as a function of the reaction coordinate. These results open the path to investigations of the chirality of molecular-reaction pathways, light-induced chirality in chemical processes, and the control of molecular chirality through tailored laser pulses.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","issue":"48","volume":116,"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"arxiv":["1906.10818"],"pmid":["31723044"]},"author":[{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"last_name":"Zindel","full_name":"Zindel, Daniel","first_name":"Daniel"},{"last_name":"Svoboda","full_name":"Svoboda, Vít","first_name":"Vít"},{"last_name":"Bommeli","full_name":"Bommeli, Elias","first_name":"Elias"},{"last_name":"Ochsner","full_name":"Ochsner, Manuel","first_name":"Manuel"},{"first_name":"Andres","full_name":"Tehlar, Andres","last_name":"Tehlar"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"title":"Real-time probing of chirality during a chemical reaction","citation":{"short":"D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar, H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929.","ieee":"D. R. Baykusheva et al., “Real-time probing of chirality during a chemical reaction,” Proceedings of the National Academy of Sciences, vol. 116, no. 48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.","apa":"Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar, A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116","ama":"Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929. doi:10.1073/pnas.1907189116","mla":"Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences, vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29, doi:10.1073/pnas.1907189116.","ista":"Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings of the National Academy of Sciences. 116(48), 23923–23929.","chicago":"Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli, Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality during a Chemical Reaction.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","page":"23923-23929","date_created":"2023-08-09T13:10:36Z","doi":"10.1073/pnas.1907189116","date_published":"2019-11-13T00:00:00Z","year":"2019","publication":"Proceedings of the National Academy of Sciences","day":"13"},{"conference":{"name":"CLEO: European Conference on Lasers and Electro-Optics","start_date":"2019-06-23","end_date":"2019-06-27","location":"Munich, Germany"},"type":"conference","status":"public","_id":"14002","article_number":"8871819","article_processing_charge":"No","author":[{"first_name":"Shubhadeep","last_name":"Biswas","full_name":"Biswas, Shubhadeep"},{"first_name":"I.","last_name":"Liontos","full_name":"Liontos, I."},{"last_name":"Kamal","full_name":"Kamal, A. M.","first_name":"A. M."},{"last_name":"Kling","full_name":"Kling, N. G.","first_name":"N. G."},{"full_name":"Alharbi, A. F.","last_name":"Alharbi","first_name":"A. F."},{"last_name":"Alharbi","full_name":"Alharbi, M.","first_name":"M."},{"last_name":"Azzeer","full_name":"Azzeer, A. M.","first_name":"A. M."},{"last_name":"Worner","full_name":"Worner, H. J.","first_name":"H. J."},{"first_name":"A. S.","last_name":"Landsman","full_name":"Landsman, A. S."},{"first_name":"M. F.","full_name":"Kling, M. F.","last_name":"Kling"},{"first_name":"B.","last_name":"Forg","full_name":"Forg, B."},{"last_name":"Schotz","full_name":"Schotz, J.","first_name":"J."},{"last_name":"Schweinberger","full_name":"Schweinberger, W.","first_name":"W."},{"first_name":"L.","full_name":"Ortmann, L.","last_name":"Ortmann"},{"full_name":"Zimmermann, T.","last_name":"Zimmermann","first_name":"T."},{"first_name":"L.-W.","full_name":"Pi, L.-W.","last_name":"Pi"},{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"first_name":"H. A.","full_name":"Masood, H. A.","last_name":"Masood"}],"title":"Probing molecular influence on photoemission delays","date_updated":"2023-08-22T09:32:56Z","citation":{"short":"S. Biswas, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi, A.M. Azzeer, H.J. Worner, A.S. Landsman, M.F. Kling, B. Forg, J. Schotz, W. Schweinberger, L. Ortmann, T. Zimmermann, L.-W. Pi, D.R. Baykusheva, H.A. Masood, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Institute of Electrical and Electronics Engineers, 2019.","ieee":"S. Biswas et al., “Probing molecular influence on photoemission delays,” in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 2019.","ama":"Biswas S, Liontos I, Kamal AM, et al. Probing molecular influence on photoemission delays. In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers; 2019. doi:10.1109/cleoe-eqec.2019.8871819","apa":"Biswas, S., Liontos, I., Kamal, A. M., Kling, N. G., Alharbi, A. F., Alharbi, M., … Masood, H. A. (2019). Probing molecular influence on photoemission delays. In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Munich, Germany: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/cleoe-eqec.2019.8871819","mla":"Biswas, Shubhadeep, et al. “Probing Molecular Influence on Photoemission Delays.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8871819, Institute of Electrical and Electronics Engineers, 2019, doi:10.1109/cleoe-eqec.2019.8871819.","ista":"Biswas S, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM, Worner HJ, Landsman AS, Kling MF, Forg B, Schotz J, Schweinberger W, Ortmann L, Zimmermann T, Pi L-W, Baykusheva DR, Masood HA. 2019. Probing molecular influence on photoemission delays. 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. CLEO: European Conference on Lasers and Electro-Optics, 8871819.","chicago":"Biswas, Shubhadeep, I. Liontos, A. M. Kamal, N. G. Kling, A. F. Alharbi, M. Alharbi, A. M. Azzeer, et al. “Probing Molecular Influence on Photoemission Delays.” In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Institute of Electrical and Electronics Engineers, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8871819."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","scopus_import":"1","publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","month":"10","abstract":[{"lang":"eng","text":"The advancement of attosecond chronoscopy has made it possible to reveal ultrashort time dynamics of photoionization [1]. Ionization delay measurements in atomic targets provide a wealth of information about the timing of the photoelectric effect [2], resonances, electron correlations and transport. The extension of this approach to molecules, however, presents great challenges. In addition to the difficulty of identifying correct ionization channels, it is hard to disentangle the role of the anisotropic molecular landscape from the delays inherent to the excitation process itself. Here, we present the measurements of ionization delays from ethyl iodide around the 4d giant dipole resonance of iodine. We employ attosecond streaking spectroscopy, which enables to disentangle the contribution to the delay from the functional ethyl group, being responsible for the characteristic chemical reactivity of the molecule. An attosecond extreme ultraviolet (XUV) pulse ionizes the molecule around the energy of the giant resonance and the released electron is exposed to the ponderomotive force of a synchronized near-infrared (NIR) field, which yields a streaking spectrogram (see figure). Comparative phase analysis of the spectrograms corresponding to iodine 4d and neon 2p emission permits extracting overall photoemission delays for ethyl iodide. The data is recorded for multiple photon energies around the iodine 4d resonance and compared to classical Wigner propagation [3] and quantum scattering [4] calculations. Here the outgoing electron, produced via inner shell ionization of the iodine atom in ethyl iodide, and thereby hardly influenced by the molecular potential during the birth process, acquires the necessary information about the influence of the functional ethyl group during its propagation. We find significant delay contributions that can distinguish between different functional groups, providing a sensitive probe of the local molecular environment [5]. This would stimulate to perform further angle resolved measurements in molecules to probe the potential landscape in three dimension."}],"oa_version":"None","date_created":"2023-08-09T13:10:49Z","date_published":"2019-10-17T00:00:00Z","doi":"10.1109/cleoe-eqec.2019.8871819","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781728104706"],"eisbn":["9781728104690"]},"language":[{"iso":"eng"}],"publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","day":"17"},{"date_updated":"2023-08-22T12:37:47Z","ddc":["000"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:47:36Z","_id":"6671","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"a5b244db9f751221409cf09c97ee0935","file_id":"6741","creator":"dernst","file_size":2215157,"date_updated":"2020-07-14T12:47:36Z","file_name":"2019_JournAppliedComputTopol_Boissonnat.pdf","date_created":"2019-07-31T08:09:56Z"}],"language":[{"iso":"eng"}],"volume":3,"issue":"1-2","ec_funded":1,"abstract":[{"text":"In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.","lang":"eng"}],"oa_version":"Published Version","month":"06","intvolume":" 3","citation":{"ista":"Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58.","chicago":"Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8.","ieee":"J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.","short":"J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58.","ama":"Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8","apa":"Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8","mla":"Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs"}],"article_processing_charge":"Yes (via OA deal)","title":"The reach, metric distortion, geodesic convexity and the variation of tangent spaces","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"has_accepted_license":"1","year":"2019","day":"01","publication":"Journal of Applied and Computational Topology","page":"29–58","date_published":"2019-06-01T00:00:00Z","doi":"10.1007/s41468-019-00029-8","date_created":"2019-07-24T08:37:29Z","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","date_created":"2018-12-11T11:45:42Z","doi":"10.1016/j.spa.2018.04.003","date_published":"2019-03-01T00:00:00Z","page":"995-1012","publication":"Stochastic Processes and their Applications","day":"01","year":"2019","isi":1,"title":"A Feynman–Kac formula for stochastic Dirichlet problems","article_processing_charge":"No","external_id":{"arxiv":["1611.04177"],"isi":["000458945300012"]},"author":[{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gyöngy","full_name":"Gyöngy, István","first_name":"István"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003.","ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012.","mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.","apa":"Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019.","short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012."},"intvolume":" 129","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.04177"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.","lang":"eng"}],"issue":"3","volume":129,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"301","department":[{"_id":"JaMa"}],"date_updated":"2023-08-24T14:20:49Z"},{"abstract":[{"lang":"eng","text":"We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 368","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c7e9880b43ac726712c1365e9f2f73a6","file_id":"5688","creator":"dernst","date_updated":"2020-07-14T12:48:07Z","file_size":893902,"date_created":"2018-12-17T10:34:06Z","file_name":"2018_CommunMathPhys_Deuchert.pdf"}],"ec_funded":1,"volume":368,"issue":"2","_id":"80","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","date_updated":"2023-08-24T14:27:51Z","ddc":["530"],"file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"RoSe"}],"oa":1,"publisher":"Springer","quality_controlled":"1","year":"2019","has_accepted_license":"1","isi":1,"publication":"Communications in Mathematical Physics","day":"01","page":"723-776","date_created":"2018-12-11T11:44:31Z","date_published":"2019-06-01T00:00:00Z","doi":"10.1007/s00220-018-3239-0","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ista":"Deuchert A, Seiringer R, Yngvason J. 2019. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 368(2), 723–776.","chicago":"Deuchert, Andreas, Robert Seiringer, and Jakob Yngvason. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics. Springer, 2019. https://doi.org/10.1007/s00220-018-3239-0.","short":"A. Deuchert, R. Seiringer, J. Yngvason, Communications in Mathematical Physics 368 (2019) 723–776.","ieee":"A. Deuchert, R. Seiringer, and J. Yngvason, “Bose–Einstein condensation in a dilute, trapped gas at positive temperature,” Communications in Mathematical Physics, vol. 368, no. 2. Springer, pp. 723–776, 2019.","ama":"Deuchert A, Seiringer R, Yngvason J. Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. 2019;368(2):723-776. doi:10.1007/s00220-018-3239-0","apa":"Deuchert, A., Seiringer, R., & Yngvason, J. (2019). Bose–Einstein condensation in a dilute, trapped gas at positive temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-018-3239-0","mla":"Deuchert, Andreas, et al. “Bose–Einstein Condensation in a Dilute, Trapped Gas at Positive Temperature.” Communications in Mathematical Physics, vol. 368, no. 2, Springer, 2019, pp. 723–76, doi:10.1007/s00220-018-3239-0."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000467796800007"]},"author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","last_name":"Deuchert"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Yngvason","full_name":"Yngvason, Jakob","first_name":"Jakob"}],"publist_id":"7974","title":"Bose–Einstein condensation in a dilute, trapped gas at positive temperature"},{"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"NiBa"}],"ddc":["570"],"date_updated":"2023-08-24T14:29:48Z","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","_id":"5911","ec_funded":1,"volume":34,"issue":"3","language":[{"iso":"eng"}],"file":[{"creator":"cziletti","date_updated":"2020-07-14T12:47:13Z","file_size":1946795,"date_created":"2020-01-09T10:55:58Z","file_name":"2019_Trends_Evolution_Faria.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7245","checksum":"ef24572d6ebcc1452c067e05410cc4a2"}],"publication_status":"published","publication_identifier":{"issn":["01695347"]},"intvolume":" 34","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved."}],"title":"Evolving inversions","external_id":{"isi":["000459899000013"]},"article_processing_charge":"No","author":[{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005.","apa":"Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005","ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","mla":"Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_created":"2019-02-03T22:59:15Z","date_published":"2019-03-01T00:00:00Z","doi":"10.1016/j.tree.2018.12.005","page":"239-248","publication":"Trends in Ecology and Evolution","day":"01","year":"2019","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"ec_funded":1,"volume":21,"issue":"10","publication_status":"published","publication_identifier":{"eissn":["1435-9855"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.03382"}],"scopus_import":"1","intvolume":" 21","month":"10","abstract":[{"lang":"eng","text":"We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system."}],"oa_version":"Preprint","department":[{"_id":"TaHa"}],"date_updated":"2023-08-24T14:24:49Z","article_type":"original","type":"journal_article","status":"public","_id":"439","page":"2995-3052","date_created":"2018-12-11T11:46:29Z","date_published":"2019-10-01T00:00:00Z","doi":"10.4171/JEMS/896","year":"2019","isi":1,"publication":"Journal of the European Mathematical Society","day":"01","oa":1,"quality_controlled":"1","publisher":"European Mathematical Society","external_id":{"isi":["000480413600002"],"arxiv":["1604.03382"]},"article_processing_charge":"No","publist_id":"7384","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","last_name":"Hausel","full_name":"Hausel, Tamas"},{"id":"43D735EE-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Mereb, Martin","last_name":"Mereb"},{"last_name":"Wong","full_name":"Wong, Michael","first_name":"Michael"}],"title":"Arithmetic and representation theory of wild character varieties","citation":{"chicago":"Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society. European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896.","ista":"Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.","mla":"Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” Journal of the European Mathematical Society, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896.","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","ieee":"T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” Journal of the European Mathematical Society, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.","ama":"Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052. doi:10.4171/JEMS/896","apa":"Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/896"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces"}]},{"page":"161-166","date_published":"2019-01-01T00:00:00Z","doi":"10.1038/s41431-018-0231-2","date_created":"2018-12-11T11:44:39Z","isi":1,"year":"2019","day":"01","publication":"European Journal of Human Genetics","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.","author":[{"full_name":"Marsh, Ashley","last_name":"Marsh","first_name":"Ashley"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"},{"last_name":"Lockhart","full_name":"Lockhart, Paul","first_name":"Paul"},{"first_name":"Richard","full_name":"Leventer, Richard","last_name":"Leventer"}],"publist_id":"7949","article_processing_charge":"No","external_id":{"isi":["000454111500019"],"pmid":["30089829"]},"title":"CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63","citation":{"chicago":"Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2.","ista":"Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166.","mla":"Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2.","short":"A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166.","ieee":"A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019.","apa":"Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2","ama":"Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":27,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41431-018-0231-2","open_access":"1"}],"month":"01","intvolume":" 27","abstract":[{"text":"Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"GaNo"}],"date_updated":"2023-08-24T14:28:24Z","type":"journal_article","article_type":"original","status":"public","_id":"105"},{"article_type":"original","type":"journal_article","status":"public","_id":"65","department":[{"_id":"JaMa"}],"date_updated":"2023-08-24T14:30:16Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1803.06953"}],"month":"03","intvolume":" 266","abstract":[{"text":"We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2.","lang":"eng"}],"oa_version":"Preprint","issue":"6","volume":266,"publication_status":"published","language":[{"iso":"eng"}],"author":[{"full_name":"Dareiotis, Konstantinos","last_name":"Dareiotis","first_name":"Konstantinos"},{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate"},{"first_name":"Benjamin","full_name":"Gess, Benjamin","last_name":"Gess"}],"publist_id":"7989","article_processing_charge":"No","external_id":{"isi":["000456332500026"],"arxiv":["1803.06953"]},"title":"Entropy solutions for stochastic porous media equations","citation":{"ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","chicago":"Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012.","short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","ieee":"K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” Journal of Differential Equations, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019.","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012","apa":"Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for stochastic porous media equations. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.09.012","mla":"Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","quality_controlled":"1","oa":1,"page":"3732-3763","date_published":"2019-03-05T00:00:00Z","doi":"10.1016/j.jde.2018.09.012","date_created":"2018-12-11T11:44:26Z","isi":1,"year":"2019","day":"5","publication":"Journal of Differential Equations"},{"issue":"1","volume":9,"publication_status":"published","file":[{"file_name":"2019_ScientificReports_Mocsai.pdf","date_created":"2019-02-05T13:10:02Z","file_size":2124292,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","checksum":"4129c7d7663d1f8a1edf8c4232372f66","file_id":"5923","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 9","abstract":[{"lang":"eng","text":"Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins."}],"oa_version":"Published Version","department":[{"_id":"FlSc"}],"file_date_updated":"2020-07-14T12:47:13Z","date_updated":"2023-08-24T14:33:16Z","ddc":["580"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"5907","date_published":"2019-01-23T00:00:00Z","doi":"10.1038/s41598-018-36884-1","date_created":"2019-02-03T22:59:13Z","isi":1,"has_accepted_license":"1","year":"2019","day":"23","publication":"Scientific Reports","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"author":[{"first_name":"Réka","full_name":"Mócsai, Réka","last_name":"Mócsai"},{"first_name":"Rudolf","full_name":"Figl, Rudolf","last_name":"Figl"},{"last_name":"Troschl","full_name":"Troschl, Clemens","first_name":"Clemens"},{"first_name":"Richard","full_name":"Strasser, Richard","last_name":"Strasser"},{"full_name":"Svehla, Elisabeth","last_name":"Svehla","first_name":"Elisabeth"},{"full_name":"Windwarder, Markus","last_name":"Windwarder","first_name":"Markus"},{"last_name":"Thader","full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"last_name":"Altmann","full_name":"Altmann, Friedrich","first_name":"Friedrich"}],"external_id":{"isi":["000456392400012"]},"article_processing_charge":"No","title":"N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated","citation":{"chicago":"Mócsai, Réka, Rudolf Figl, Clemens Troschl, Richard Strasser, Elisabeth Svehla, Markus Windwarder, Andreas Thader, and Friedrich Altmann. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports. Nature Publishing Group, 2019. https://doi.org/10.1038/s41598-018-36884-1.","ista":"Mócsai R, Figl R, Troschl C, Strasser R, Svehla E, Windwarder M, Thader A, Altmann F. 2019. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 9(1), 331.","mla":"Mócsai, Réka, et al. “N-Glycans of the Microalga Chlorella Vulgaris Are of the Oligomannosidic Type but Highly Methylated.” Scientific Reports, vol. 9, no. 1, 331, Nature Publishing Group, 2019, doi:10.1038/s41598-018-36884-1.","apa":"Mócsai, R., Figl, R., Troschl, C., Strasser, R., Svehla, E., Windwarder, M., … Altmann, F. (2019). N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-36884-1","ama":"Mócsai R, Figl R, Troschl C, et al. N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated. Scientific Reports. 2019;9(1). doi:10.1038/s41598-018-36884-1","ieee":"R. Mócsai et al., “N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated,” Scientific Reports, vol. 9, no. 1. Nature Publishing Group, 2019.","short":"R. Mócsai, R. Figl, C. Troschl, R. Strasser, E. Svehla, M. Windwarder, A. Thader, F. Altmann, Scientific Reports 9 (2019)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"331"},{"title":"Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis","external_id":{"pmid":["30610176"],"isi":["000456336100050"]},"article_processing_charge":"No","author":[{"last_name":"Lee","full_name":"Lee, Eunkyoung","first_name":"Eunkyoung"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Pérez-Sancho","full_name":"Pérez-Sancho, Jessica","first_name":"Jessica"},{"first_name":"Francisco","full_name":"Benitez-Fuente, Francisco","last_name":"Benitez-Fuente"},{"first_name":"Matthew","full_name":"Strelau, Matthew","last_name":"Strelau"},{"full_name":"Macho, Alberto P.","last_name":"Macho","first_name":"Alberto P."},{"first_name":"Miguel A.","last_name":"Botella","full_name":"Botella, Miguel A."},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Abel","full_name":"Rosado, Abel","last_name":"Rosado"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Lee E, Vanneste S, Pérez-Sancho J, Benitez-Fuente F, Strelau M, Macho AP, Botella MA, Friml J, Rosado A. 2019. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 116(4), 1420–1429.","chicago":"Lee, Eunkyoung, Steffen Vanneste, Jessica Pérez-Sancho, Francisco Benitez-Fuente, Matthew Strelau, Alberto P. Macho, Miguel A. Botella, Jiří Friml, and Abel Rosado. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1818099116.","ama":"Lee E, Vanneste S, Pérez-Sancho J, et al. Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(4):1420-1429. doi:10.1073/pnas.1818099116","apa":"Lee, E., Vanneste, S., Pérez-Sancho, J., Benitez-Fuente, F., Strelau, M., Macho, A. P., … Rosado, A. (2019). Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1818099116","short":"E. Lee, S. Vanneste, J. Pérez-Sancho, F. Benitez-Fuente, M. Strelau, A.P. Macho, M.A. Botella, J. Friml, A. Rosado, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 1420–1429.","ieee":"E. Lee et al., “Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4. National Academy of Sciences, pp. 1420–1429, 2019.","mla":"Lee, Eunkyoung, et al. “Ionic Stress Enhances ER–PM Connectivity via Phosphoinositide-Associated SYT1 Contact Site Expansion in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1420–29, doi:10.1073/pnas.1818099116."},"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","date_created":"2019-02-03T22:59:14Z","date_published":"2019-01-22T00:00:00Z","doi":"10.1073/pnas.1818099116","page":"1420-1429","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"22","year":"2019","isi":1,"status":"public","article_type":"original","type":"journal_article","_id":"5908","department":[{"_id":"JiFr"}],"date_updated":"2023-08-24T14:31:09Z","intvolume":" 116","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1818099116"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants.","lang":"eng"}],"issue":"4","volume":116,"language":[{"iso":"eng"}],"publication_status":"published"},{"date_updated":"2023-08-24T14:34:12Z","department":[{"_id":"NiBa"}],"_id":"5680","type":"journal_article","status":"public","publication_identifier":{"issn":["23818107"],"eissn":["23818115"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":166,"abstract":[{"lang":"eng","text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones."}],"oa_version":"None","scopus_import":"1","month":"01","intvolume":" 166","citation":{"ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92.","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142.","ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142","short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Andalo, Christophe","last_name":"Andalo","first_name":"Christophe"},{"last_name":"Burrus","full_name":"Burrus, Monique","first_name":"Monique"},{"last_name":"Paute","full_name":"Paute, Sandrine","first_name":"Sandrine"},{"first_name":"Christine","last_name":"Lauzeral","full_name":"Lauzeral, Christine"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"}],"external_id":{"isi":["000463802800009"]},"article_processing_charge":"No","title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","isi":1,"year":"2019","day":"01","publication":"Botany Letters","page":"80-92","doi":"10.1080/23818107.2018.1545142","date_published":"2019-01-01T00:00:00Z","date_created":"2018-12-16T22:59:20Z","quality_controlled":"1","publisher":"Taylor and Francis"},{"publisher":"Wiley","quality_controlled":"1","oa":1,"page":"365-394","date_published":"2019-08-01T00:00:00Z","doi":"10.1002/jgt.22436","date_created":"2018-12-30T22:59:15Z","isi":1,"year":"2019","day":"01","publication":"Journal of Graph Theory","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Chaplick","full_name":"Chaplick, Steven","first_name":"Steven"},{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"last_name":"Klavík","full_name":"Klavík, Pavel","first_name":"Pavel"}],"external_id":{"isi":["000485392800004"],"arxiv":["1309.2399"]},"article_processing_charge":"No","title":"Extending partial representations of circle graphs","citation":{"chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436.","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394.","mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.","ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019.","short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436","apa":"Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1309.2399","open_access":"1"}],"month":"08","intvolume":" 91","abstract":[{"lang":"eng","text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest."}],"oa_version":"Preprint","issue":"4","volume":91,"ec_funded":1,"publication_identifier":{"issn":["03649024"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"5790","department":[{"_id":"UlWa"}],"date_updated":"2023-08-24T14:30:43Z"},{"language":[{"iso":"eng"}],"publication_status":"published","volume":576,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently."}],"month":"09","intvolume":" 576","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.05324","open_access":"1"}],"date_updated":"2023-08-24T14:31:47Z","department":[{"_id":"LaEr"}],"_id":"405","status":"public","article_type":"original","type":"journal_article","day":"01","publication":"Linear Algebra and Its Applications","isi":1,"year":"2019","doi":"10.1016/j.laa.2018.03.002","date_published":"2019-09-01T00:00:00Z","date_created":"2018-12-11T11:46:17Z","page":"67-78","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152)","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002.","ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.","ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002","ama":"Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002"},"title":"Jointly convex quantum Jensen divergences","author":[{"first_name":"Daniel","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","last_name":"Virosztek"}],"publist_id":"7424","article_processing_charge":"No","external_id":{"isi":["000470955300005"],"arxiv":["1712.05324"]},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"intvolume":" 371","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1705.01999","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points."}],"issue":"8","volume":371,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00029947"],"eissn":["10886850"]},"status":"public","type":"journal_article","_id":"175","department":[{"_id":"TiBr"}],"date_updated":"2023-08-24T14:34:56Z","oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","date_created":"2018-12-11T11:45:01Z","date_published":"2019-04-15T00:00:00Z","doi":"10.1090/tran/7514","page":"5757-5785","publication":"Transactions of the American Mathematical Society","day":"15","year":"2019","isi":1,"title":"Sieving rational points on varieties","external_id":{"isi":["000464034200019"],"arxiv":["1705.01999"]},"article_processing_charge":"No","publist_id":"7746","author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"},{"first_name":"Daniel","full_name":"Loughran, Daniel","last_name":"Loughran"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Browning, Timothy D., and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society, vol. 371, no. 8, American Mathematical Society, 2019, pp. 5757–85, doi:10.1090/tran/7514.","ieee":"T. D. Browning and D. Loughran, “Sieving rational points on varieties,” Transactions of the American Mathematical Society, vol. 371, no. 8. American Mathematical Society, pp. 5757–5785, 2019.","short":"T.D. Browning, D. Loughran, Transactions of the American Mathematical Society 371 (2019) 5757–5785.","ama":"Browning TD, Loughran D. Sieving rational points on varieties. Transactions of the American Mathematical Society. 2019;371(8):5757-5785. doi:10.1090/tran/7514","apa":"Browning, T. D., & Loughran, D. (2019). Sieving rational points on varieties. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7514","chicago":"Browning, Timothy D, and Daniel Loughran. “Sieving Rational Points on Varieties.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7514.","ista":"Browning TD, Loughran D. 2019. Sieving rational points on varieties. Transactions of the American Mathematical Society. 371(8), 5757–5785."}},{"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Probability Theory and Related Fields","page":"697–758","date_published":"2019-04-01T00:00:00Z","doi":"10.1007/s00440-018-0841-1","date_created":"2018-12-11T11:45:48Z","acknowledgement":"MG thanks the support of the LMS Postdoctoral Mobility Grant.\r\n\r\n","quality_controlled":"1","publisher":"Springer","oa":1,"citation":{"ista":"Gerencser M, Hairer M. 2019. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 173(3–4), 697–758.","chicago":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0841-1.","apa":"Gerencser, M., & Hairer, M. (2019). Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0841-1","ama":"Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. Probability Theory and Related Fields. 2019;173(3-4):697–758. doi:10.1007/s00440-018-0841-1","ieee":"M. Gerencser and M. Hairer, “Singular SPDEs in domains with boundaries,” Probability Theory and Related Fields, vol. 173, no. 3–4. Springer, pp. 697–758, 2019.","short":"M. Gerencser, M. Hairer, Probability Theory and Related Fields 173 (2019) 697–758.","mla":"Gerencser, Mate, and Martin Hairer. “Singular SPDEs in Domains with Boundaries.” Probability Theory and Related Fields, vol. 173, no. 3–4, Springer, 2019, pp. 697–758, doi:10.1007/s00440-018-0841-1."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publist_id":"7546","author":[{"full_name":"Gerencser, Mate","last_name":"Gerencser","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hairer","full_name":"Hairer, Martin","first_name":"Martin"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000463613800001"]},"title":"Singular SPDEs in domains with boundaries","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication_identifier":{"eissn":["14322064"],"issn":["01788051"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:03Z","file_size":893182,"date_created":"2018-12-17T16:25:24Z","file_name":"2018_ProbTheory_Gerencser.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5722","checksum":"288d16ef7291242f485a9660979486e3"}],"language":[{"iso":"eng"}],"issue":"3-4","volume":173,"abstract":[{"lang":"eng","text":"We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 173","date_updated":"2023-08-24T14:38:32Z","ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:46:03Z","_id":"319","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"429","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"LaEr"}],"date_updated":"2023-08-24T14:39:00Z","ddc":["510"],"scopus_import":"1","month":"02","intvolume":" 173","abstract":[{"lang":"eng","text":"We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent."}],"oa_version":"Published Version","volume":173,"issue":"1-2","ec_funded":1,"publication_identifier":{"issn":["01788051"],"eissn":["14322064"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"f9354fa5c71f9edd17132588f0dc7d01","file_id":"5720","creator":"dernst","file_size":1201840,"date_updated":"2020-07-14T12:46:26Z","file_name":"2018_ProbTheory_Ajanki.pdf","date_created":"2018-12-17T16:12:08Z"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","full_name":"Ajanki, Oskari H","last_name":"Ajanki"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H"}],"publist_id":"7394","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000459396500007"]},"title":"Stability of the matrix Dyson equation and random matrices with correlations","citation":{"chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z.","ista":"Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373.","mla":"Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory and Related Fields, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z.","ama":"Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373. doi:10.1007/s00440-018-0835-z","apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” Probability Theory and Related Fields, vol. 173, no. 1–2. Springer, pp. 293–373, 2019.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","page":"293–373","date_published":"2019-02-01T00:00:00Z","doi":"10.1007/s00440-018-0835-z","date_created":"2018-12-11T11:46:25Z","isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Probability Theory and Related Fields"},{"isi":1,"year":"2019","day":"04","publication":"ACM International Conference Proceeding Series","page":"168-177","date_published":"2019-01-04T00:00:00Z","doi":"10.1145/3288599.3288617","date_created":"2019-02-10T22:59:17Z","quality_controlled":"1","publisher":"ACM","oa":1,"citation":{"ieee":"B. Chatterjee, S. Peri, M. Sa, and N. Singhal, “A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries,” in ACM International Conference Proceeding Series, Bangalore, India, 2019, pp. 168–177.","short":"B. Chatterjee, S. Peri, M. Sa, N. Singhal, in:, ACM International Conference Proceeding Series, ACM, 2019, pp. 168–177.","ama":"Chatterjee B, Peri S, Sa M, Singhal N. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In: ACM International Conference Proceeding Series. ACM; 2019:168-177. doi:10.1145/3288599.3288617","apa":"Chatterjee, B., Peri, S., Sa, M., & Singhal, N. (2019). A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. In ACM International Conference Proceeding Series (pp. 168–177). Bangalore, India: ACM. https://doi.org/10.1145/3288599.3288617","mla":"Chatterjee, Bapi, et al. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” ACM International Conference Proceeding Series, ACM, 2019, pp. 168–77, doi:10.1145/3288599.3288617.","ista":"Chatterjee B, Peri S, Sa M, Singhal N. 2019. A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries. ACM International Conference Proceeding Series. ICDCN: Conference on Distributed Computing and Networking, 168–177.","chicago":"Chatterjee, Bapi, Sathya Peri, Muktikanta Sa, and Nandini Singhal. “A Simple and Practical Concurrent Non-Blocking Unbounded Graph with Linearizable Reachability Queries.” In ACM International Conference Proceeding Series, 168–77. ACM, 2019. https://doi.org/10.1145/3288599.3288617."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-2742-4028","full_name":"Chatterjee, Bapi","last_name":"Chatterjee","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi"},{"first_name":"Sathya","full_name":"Peri, Sathya","last_name":"Peri"},{"full_name":"Sa, Muktikanta","last_name":"Sa","first_name":"Muktikanta"},{"first_name":"Nandini","full_name":"Singhal, Nandini","last_name":"Singhal"}],"external_id":{"arxiv":["1809.00896"],"isi":["000484491600019"]},"article_processing_charge":"No","title":"A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries","publication_identifier":{"isbn":["978-1-4503-6094-4 "]},"publication_status":"published","language":[{"iso":"eng"}],"abstract":[{"text":"Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00896"}],"month":"01","date_updated":"2023-08-24T14:41:53Z","department":[{"_id":"DaAl"}],"_id":"5947","type":"conference","conference":{"location":"Bangalore, India","end_date":"2019-01-07","start_date":"2019-01-04","name":"ICDCN: Conference on Distributed Computing and Networking"},"status":"public"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n."}],"month":"04","intvolume":" 259","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0166218X"]},"publication_status":"published","issue":"4","related_material":{"record":[{"id":"433","status":"public","relation":"earlier_version"}]},"volume":259,"_id":"5857","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-08-24T14:39:33Z","department":[{"_id":"UlWa"}],"publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"30","publication":"Discrete Applied Mathematics","isi":1,"year":"2019","date_published":"2019-04-30T00:00:00Z","doi":"10.1016/j.dam.2018.12.025","date_created":"2019-01-20T22:59:17Z","page":"266-231","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics, vol. 259, no. 4, Elsevier, 2019, pp. 266–231, doi:10.1016/j.dam.2018.12.025.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” Discrete Applied Mathematics, vol. 259, no. 4. Elsevier, pp. 266–231, 2019.","short":"R. Fulek, J. Pach, Discrete Applied Mathematics 259 (2019) 266–231.","apa":"Fulek, R., & Pach, J. (2019). Thrackles: An improved upper bound. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2018.12.025","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. Discrete Applied Mathematics. 2019;259(4):266-231. doi:10.1016/j.dam.2018.12.025","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound.” Discrete Applied Mathematics. Elsevier, 2019. https://doi.org/10.1016/j.dam.2018.12.025.","ista":"Fulek R, Pach J. 2019. Thrackles: An improved upper bound. Discrete Applied Mathematics. 259(4), 266–231."},"title":"Thrackles: An improved upper bound","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"last_name":"Pach","full_name":"Pach, János","first_name":"János"}],"external_id":{"isi":["000466061100020"],"arxiv":["1708.08037"]},"article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 9","month":"01","publication_status":"published","publication_identifier":{"eissn":["20751729"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:13Z","file_size":963454,"creator":"dernst","date_created":"2019-02-11T10:45:27Z","file_name":"2019_Life_Corominas.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5951","checksum":"7d2322cd96ace41959909b66702d5cf4"}],"issue":"1","volume":9,"_id":"5944","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-08-24T14:43:41Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"EdHa"}],"oa":1,"publisher":"MDPI","quality_controlled":"1","year":"2019","has_accepted_license":"1","isi":1,"publication":"Life","day":"15","date_created":"2019-02-10T22:59:15Z","date_published":"2019-01-15T00:00:00Z","doi":"10.3390/life9010009","article_number":"9","citation":{"short":"B. Corominas-Murtra, Life 9 (2019).","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.","ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009","mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000464125500001"]},"author":[{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra"}],"title":"Thermodynamics of duplication thresholds in synthetic protocell systems"},{"_id":"6029","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-08-24T14:45:38Z","ddc":["540"],"file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"JoDa"}],"abstract":[{"text":"Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 6","publication_identifier":{"eissn":["22962646"]},"publication_status":"published","file":[{"checksum":"7841301d7c53b56ef873791b4b6f7b24","file_id":"6039","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_frontiers_Lindner.pdf","date_created":"2019-02-18T15:10:34Z","file_size":1766820,"date_updated":"2020-07-14T12:47:17Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":6,"article_number":"655","citation":{"chicago":"Lindner, Marco, Aliz Tresztenyak, Gergö Fülöp, Wiebke Jahr, Adrian Prinz, Iris Prinz, Johann G Danzl, Gerhard J. Schütz, and Eva Sevcsik. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry. Frontiers Media S.A., 2019. https://doi.org/10.3389/fchem.2018.00655.","ista":"Lindner M, Tresztenyak A, Fülöp G, Jahr W, Prinz A, Prinz I, Danzl JG, Schütz GJ, Sevcsik E. 2019. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 6, 655.","mla":"Lindner, Marco, et al. “A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns.” Frontiers in Chemistry, vol. 6, 655, Frontiers Media S.A., 2019, doi:10.3389/fchem.2018.00655.","apa":"Lindner, M., Tresztenyak, A., Fülöp, G., Jahr, W., Prinz, A., Prinz, I., … Sevcsik, E. (2019). A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. Frontiers Media S.A. https://doi.org/10.3389/fchem.2018.00655","ama":"Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. Frontiers in Chemistry. 2019;6. doi:10.3389/fchem.2018.00655","ieee":"M. Lindner et al., “A fast and simple contact printing approach to generate 2D protein nanopatterns,” Frontiers in Chemistry, vol. 6. Frontiers Media S.A., 2019.","short":"M. Lindner, A. Tresztenyak, G. Fülöp, W. Jahr, A. Prinz, I. Prinz, J.G. Danzl, G.J. Schütz, E. Sevcsik, Frontiers in Chemistry 6 (2019)."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Lindner","full_name":"Lindner, Marco","first_name":"Marco"},{"first_name":"Aliz","full_name":"Tresztenyak, Aliz","last_name":"Tresztenyak"},{"first_name":"Gergö","full_name":"Fülöp, Gergö","last_name":"Fülöp"},{"first_name":"Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","full_name":"Jahr, Wiebke","last_name":"Jahr"},{"first_name":"Adrian","full_name":"Prinz, Adrian","last_name":"Prinz"},{"full_name":"Prinz, Iris","last_name":"Prinz","first_name":"Iris"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"last_name":"Schütz","full_name":"Schütz, Gerhard J.","first_name":"Gerhard J."},{"first_name":"Eva","last_name":"Sevcsik","full_name":"Sevcsik, Eva"}],"article_processing_charge":"No","external_id":{"isi":["000456718000001"]},"title":"A fast and simple contact printing approach to generate 2D protein nanopatterns","publisher":"Frontiers Media S.A.","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"24","publication":"Frontiers in Chemistry","date_published":"2019-01-24T00:00:00Z","doi":"10.3389/fchem.2018.00655","date_created":"2019-02-17T22:59:24Z"},{"publication":"Communications on Pure and Applied Mathematics","day":"08","year":"2019","isi":1,"has_accepted_license":"1","date_created":"2019-02-17T22:59:24Z","date_published":"2019-02-08T00:00:00Z","doi":"10.1002/cpa.21816","page":"1983-2005","oa":1,"publisher":"Wiley","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816.","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","apa":"Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816"},"title":"A solution theory for quasilinear singular SPDEs","external_id":{"isi":["000475465000003"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","full_name":"Gerencser, Mate"},{"last_name":"Hairer","full_name":"Hairer, Martin","first_name":"Martin"}],"language":[{"iso":"eng"}],"file":[{"file_name":"2019_Wiley_Gerencser.pdf","date_created":"2020-01-07T13:25:55Z","file_size":381350,"date_updated":"2020-07-14T12:47:17Z","creator":"kschuh","file_id":"7237","checksum":"09aec427eb48c0f96a1cce9ff53f013b","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","volume":72,"issue":"9","oa_version":"Published Version","abstract":[{"text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small.","lang":"eng"}],"intvolume":" 72","month":"02","scopus_import":"1","ddc":["500"],"date_updated":"2023-08-24T14:44:31Z","file_date_updated":"2020-07-14T12:47:17Z","department":[{"_id":"JaMa"}],"_id":"6028","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article"},{"status":"public","type":"conference","conference":{"start_date":"2019-01-13","location":"Cascais, Portugal","end_date":"2019-01-15","name":"VMCAI: Verification, Model Checking, and Abstract Interpretation"},"_id":"5948","department":[{"_id":"KrCh"}],"date_updated":"2023-08-24T14:42:22Z","month":"01","intvolume":" 11388","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1701.02944"}],"oa_version":"Preprint","abstract":[{"text":"We study the termination problem for nondeterministic probabilistic programs. We consider the bounded termination problem that asks whether the supremum of the expected termination time over all schedulers is bounded. First, we show that ranking supermartingales (RSMs) are both sound and complete for proving bounded termination over nondeterministic probabilistic programs. For nondeterministic probabilistic programs a previous result claimed that RSMs are not complete for bounded termination, whereas our result corrects the previous flaw and establishes completeness with a rigorous proof. Second, we present the first sound approach to establish lower bounds on expected termination time through RSMs.","lang":"eng"}],"volume":11388,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Termination of nondeterministic probabilistic programs","author":[{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"external_id":{"isi":["000931943000022"],"arxiv":["1701.02944"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Fu, H., & Chatterjee, K. (2019). Termination of nondeterministic probabilistic programs. In International Conference on Verification, Model Checking, and Abstract Interpretation (Vol. 11388, pp. 468–490). Cascais, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-11245-5_22","ama":"Fu H, Chatterjee K. Termination of nondeterministic probabilistic programs. In: International Conference on Verification, Model Checking, and Abstract Interpretation. Vol 11388. Springer Nature; 2019:468-490. doi:10.1007/978-3-030-11245-5_22","short":"H. Fu, K. Chatterjee, in:, International Conference on Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2019, pp. 468–490.","ieee":"H. Fu and K. Chatterjee, “Termination of nondeterministic probabilistic programs,” in International Conference on Verification, Model Checking, and Abstract Interpretation, Cascais, Portugal, 2019, vol. 11388, pp. 468–490.","mla":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” International Conference on Verification, Model Checking, and Abstract Interpretation, vol. 11388, Springer Nature, 2019, pp. 468–90, doi:10.1007/978-3-030-11245-5_22.","ista":"Fu H, Chatterjee K. 2019. Termination of nondeterministic probabilistic programs. International Conference on Verification, Model Checking, and Abstract Interpretation. VMCAI: Verification, Model Checking, and Abstract Interpretation, LNCS, vol. 11388, 468–490.","chicago":"Fu, Hongfei, and Krishnendu Chatterjee. “Termination of Nondeterministic Probabilistic Programs.” In International Conference on Verification, Model Checking, and Abstract Interpretation, 11388:468–90. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-11245-5_22."},"publisher":"Springer Nature","quality_controlled":"1","date_published":"2019-01-11T00:00:00Z","doi":"10.1007/978-3-030-11245-5_22","date_created":"2019-02-10T22:59:17Z","page":"468-490","day":"11","publication":"International Conference on Verification, Model Checking, and Abstract Interpretation","isi":1,"year":"2019"},{"abstract":[{"lang":"eng","text":"In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy."}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.007"}],"scopus_import":"1","intvolume":" 176","month":"02","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-find-their-identity-using-a-mathematically-optimal-strategy/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"4","volume":176,"_id":"5945","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-24T14:42:47Z","department":[{"_id":"GaTk"}],"oa":1,"publisher":"Cell Press","quality_controlled":"1","year":"2019","isi":1,"publication":"Cell","day":"07","page":"844-855.e15","date_created":"2019-02-10T22:59:16Z","date_published":"2019-02-07T00:00:00Z","doi":"10.1016/j.cell.2019.01.007","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"citation":{"mla":"Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.","short":"M.D. Petkova, G. Tkačik, W. Bialek, E.F. Wieschaus, T. Gregor, Cell 176 (2019) 844–855.e15.","ieee":"M. D. Petkova, G. Tkačik, W. Bialek, E. F. Wieschaus, and T. Gregor, “Optimal decoding of cellular identities in a genetic network,” Cell, vol. 176, no. 4. Cell Press, p. 844–855.e15, 2019.","apa":"Petkova, M. D., Tkačik, G., Bialek, W., Wieschaus, E. F., & Gregor, T. (2019). Optimal decoding of cellular identities in a genetic network. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.01.007","ama":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. Optimal decoding of cellular identities in a genetic network. Cell. 2019;176(4):844-855.e15. doi:10.1016/j.cell.2019.01.007","chicago":"Petkova, Mariela D., Gašper Tkačik, William Bialek, Eric F. Wieschaus, and Thomas Gregor. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.01.007.","ista":"Petkova MD, Tkačik G, Bialek W, Wieschaus EF, Gregor T. 2019. Optimal decoding of cellular identities in a genetic network. Cell. 176(4), 844–855.e15."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["30712870"],"isi":["000457969200015"]},"article_processing_charge":"No","author":[{"first_name":"Mariela D.","last_name":"Petkova","full_name":"Petkova, Mariela D."},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"full_name":"Wieschaus, Eric F.","last_name":"Wieschaus","first_name":"Eric F."},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"}],"title":"Optimal decoding of cellular identities in a genetic network"},{"date_updated":"2023-08-24T14:43:13Z","department":[{"_id":"BjHo"}],"_id":"5943","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":863,"ec_funded":1,"abstract":[{"lang":"eng","text":"The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07931"}],"month":"03","intvolume":" 863","citation":{"chicago":"Klotz, Lukasz, Konrad Gumowski, and José Eduardo Wesfreid. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2018.974.","ista":"Klotz L, Gumowski K, Wesfreid JE. 2019. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 863, 386–406.","mla":"Klotz, Lukasz, et al. “Experiments on a Jet in a Crossflow in the Low-Velocity-Ratio Regime.” Journal of Fluid Mechanics, vol. 863, Cambridge University Press, 2019, pp. 386–406, doi:10.1017/jfm.2018.974.","ama":"Klotz L, Gumowski K, Wesfreid JE. Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. 2019;863:386-406. doi:10.1017/jfm.2018.974","apa":"Klotz, L., Gumowski, K., & Wesfreid, J. E. (2019). Experiments on a jet in a crossflow in the low-velocity-ratio regime. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2018.974","ieee":"L. Klotz, K. Gumowski, and J. E. Wesfreid, “Experiments on a jet in a crossflow in the low-velocity-ratio regime,” Journal of Fluid Mechanics, vol. 863. Cambridge University Press, pp. 386–406, 2019.","short":"L. Klotz, K. Gumowski, J.E. Wesfreid, Journal of Fluid Mechanics 863 (2019) 386–406."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Klotz, Lukasz","orcid":"0000-0003-1740-7635","last_name":"Klotz","first_name":"Lukasz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gumowski","full_name":"Gumowski, Konrad","first_name":"Konrad"},{"first_name":"José Eduardo","full_name":"Wesfreid, José Eduardo","last_name":"Wesfreid"}],"article_processing_charge":"No","external_id":{"isi":["000526029100016"],"arxiv":["1902.07931"]},"title":"Experiments on a jet in a crossflow in the low-velocity-ratio regime","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"isi":1,"year":"2019","day":"25","publication":"Journal of Fluid Mechanics","page":"386-406","date_published":"2019-03-25T00:00:00Z","doi":"10.1017/jfm.2018.974","date_created":"2019-02-10T22:59:15Z","quality_controlled":"1","publisher":"Cambridge University Press","oa":1}]