[{"oa":1,"publisher":"Elsevier","quality_controlled":"1","page":"214-223","date_created":"2021-07-16T08:53:01Z","date_published":"2019-03-01T00:00:00Z","doi":"10.1016/j.cpc.2018.09.020","year":"2019","publication":"Computer Physics Communications","day":"01","external_id":{"arxiv":["1808.03824"]},"article_processing_charge":"No","author":[{"first_name":"Venkat","last_name":"Kapil","full_name":"Kapil, Venkat"},{"full_name":"Rossi, Mariana","last_name":"Rossi","first_name":"Mariana"},{"full_name":"Marsalek, Ondrej","last_name":"Marsalek","first_name":"Ondrej"},{"last_name":"Petraglia","full_name":"Petraglia, Riccardo","first_name":"Riccardo"},{"full_name":"Litman, Yair","last_name":"Litman","first_name":"Yair"},{"first_name":"Thomas","full_name":"Spura, Thomas","last_name":"Spura"},{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing"},{"first_name":"Alice","full_name":"Cuzzocrea, Alice","last_name":"Cuzzocrea"},{"full_name":"Meißner, Robert H.","last_name":"Meißner","first_name":"Robert H."},{"first_name":"David M.","full_name":"Wilkins, David M.","last_name":"Wilkins"},{"full_name":"Helfrecht, Benjamin A.","last_name":"Helfrecht","first_name":"Benjamin A."},{"last_name":"Juda","full_name":"Juda, Przemysław","first_name":"Przemysław"},{"last_name":"Bienvenue","full_name":"Bienvenue, Sébastien P.","first_name":"Sébastien P."},{"first_name":"Wei","full_name":"Fang, Wei","last_name":"Fang"},{"first_name":"Jan","full_name":"Kessler, Jan","last_name":"Kessler"},{"first_name":"Igor","last_name":"Poltavsky","full_name":"Poltavsky, Igor"},{"first_name":"Steven","last_name":"Vandenbrande","full_name":"Vandenbrande, Steven"},{"last_name":"Wieme","full_name":"Wieme, Jelle","first_name":"Jelle"},{"first_name":"Clemence","last_name":"Corminboeuf","full_name":"Corminboeuf, Clemence"},{"full_name":"Kühne, Thomas D.","last_name":"Kühne","first_name":"Thomas D."},{"first_name":"David E.","full_name":"Manolopoulos, David E.","last_name":"Manolopoulos"},{"first_name":"Thomas E.","full_name":"Markland, Thomas E.","last_name":"Markland"},{"first_name":"Jeremy O.","full_name":"Richardson, Jeremy O.","last_name":"Richardson"},{"first_name":"Alexandre","full_name":"Tkatchenko, Alexandre","last_name":"Tkatchenko"},{"first_name":"Gareth A.","last_name":"Tribello","full_name":"Tribello, Gareth A."},{"first_name":"Veronique","full_name":"Van Speybroeck, Veronique","last_name":"Van Speybroeck"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"title":"i-PI 2.0: A universal force engine for advanced molecular simulations","citation":{"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.","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.","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.","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.","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.","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","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"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.03824"}],"scopus_import":"1","intvolume":" 236","month":"03","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","volume":236,"publication_status":"published","publication_identifier":{"issn":["0010-4655"]},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"9677","date_updated":"2021-08-09T12:37:16Z","extern":"1"},{"year":"2019","publication":"Journal of Chemical Theory and Computation","day":"14","page":"100-107","date_created":"2021-07-19T06:56:45Z","doi":"10.1021/acs.jctc.9b00907","date_published":"2019-01-14T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","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.","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.","short":"F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107.","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","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","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","external_id":{"pmid":["31743021"],"arxiv":["1911.01140"]},"author":[{"first_name":"F.","full_name":"Giberti, F.","last_name":"Giberti"},{"first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"first_name":"G. A.","last_name":"Tribello","full_name":"Tribello, G. A."},{"first_name":"M.","full_name":"Ceriotti, M.","last_name":"Ceriotti"}],"title":"Iterative unbiasing of quasi-equilibrium sampling","publication_status":"published","publication_identifier":{"eissn":["1549-9626"],"issn":["1549-9618"]},"language":[{"iso":"eng"}],"issue":"1","volume":16,"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"main_file_link":[{"url":"https://arxiv.org/abs/1911.01140","open_access":"1"}],"scopus_import":"1","intvolume":" 16","month":"01","date_updated":"2021-08-09T12:37:37Z","extern":"1","_id":"9680","article_type":"original","type":"journal_article","status":"public"},{"volume":55,"issue":"8","publication_status":"published","publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1029/2019WR024935","open_access":"1"}],"scopus_import":"1","intvolume":" 55","month":"08","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"}],"oa_version":"Published Version","date_updated":"2023-02-28T12:14:18Z","extern":"1","article_type":"original","type":"journal_article","keyword":["Water Science and Technology"],"status":"public","_id":"12600","page":"6754-6772","date_created":"2023-02-20T08:12:59Z","doi":"10.1029/2019wr024935","date_published":"2019-08-01T00:00:00Z","year":"2019","publication":"Water Resources Research","day":"01","oa":1,"quality_controlled":"1","publisher":"American Geophysical Union","article_processing_charge":"No","author":[{"last_name":"Girona‐Mata","full_name":"Girona‐Mata, Marc","first_name":"Marc"},{"first_name":"Evan S.","full_name":"Miles, Evan S.","last_name":"Miles"},{"first_name":"Silvan","full_name":"Ragettli, Silvan","last_name":"Ragettli"},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti"}],"title":"High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment","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.","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","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","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.","short":"M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources Research 55 (2019) 6754–6772.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.3389/feart.2019.00143"}],"scopus_import":"1","intvolume":" 7","month":"06","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","volume":7,"publication_status":"published","publication_identifier":{"issn":["2296-6463"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"12602","date_updated":"2023-02-28T12:04:48Z","extern":"1","oa":1,"publisher":"Frontiers Media","quality_controlled":"1","date_created":"2023-02-20T08:13:08Z","doi":"10.3389/feart.2019.00143","date_published":"2019-06-04T00:00:00Z","year":"2019","publication":"Frontiers in Earth Science","day":"04","article_number":"143","article_processing_charge":"No","author":[{"full_name":"Wijngaard, René R.","last_name":"Wijngaard","first_name":"René R."},{"first_name":"Jakob F.","last_name":"Steiner","full_name":"Steiner, Jakob F."},{"last_name":"Kraaijenbrink","full_name":"Kraaijenbrink, Philip D. A.","first_name":"Philip D. A."},{"first_name":"Christoph","last_name":"Klug","full_name":"Klug, Christoph"},{"first_name":"Surendra","last_name":"Adhikari","full_name":"Adhikari, Surendra"},{"first_name":"Argha","last_name":"Banerjee","full_name":"Banerjee, Argha"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"full_name":"van Beek, Ludovicus P. H.","last_name":"van Beek","first_name":"Ludovicus P. H."},{"full_name":"Bierkens, Marc F. P.","last_name":"Bierkens","first_name":"Marc F. P."},{"full_name":"Lutz, Arthur F.","last_name":"Lutz","first_name":"Arthur F."},{"first_name":"Walter W.","last_name":"Immerzeel","full_name":"Immerzeel, Walter W."}],"title":"Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age","citation":{"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.","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.","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).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","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.","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."},"title":"Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics","author":[{"last_name":"STEINER","full_name":"STEINER, JAKOB F.","first_name":"JAKOB F."},{"full_name":"BURI, PASCAL","last_name":"BURI","first_name":"PASCAL"},{"first_name":"EVAN S.","last_name":"MILES","full_name":"MILES, EVAN S."},{"last_name":"RAGETTLI","full_name":"RAGETTLI, SILVAN","first_name":"SILVAN"},{"full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca"}],"article_processing_charge":"No","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"day":"01","publication":"Journal of Glaciology","year":"2019","date_published":"2019-08-01T00:00:00Z","doi":"10.1017/jog.2019.40","date_created":"2023-02-20T08:13:03Z","page":"617-632","_id":"12601","status":"public","article_type":"original","type":"journal_article","extern":"1","date_updated":"2023-02-28T12:11:07Z","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"08","intvolume":" 65","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jog.2019.40"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"publication_status":"published","volume":65,"issue":"252"},{"date_updated":"2023-05-08T10:54:12Z","extern":"1","ddc":["580"],"department":[{"_id":"XiFe"}],"file_date_updated":"2023-02-07T09:42:46Z","_id":"12192","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","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","file":[{"creator":"alisjak","file_size":2493837,"date_updated":"2023-02-07T09:42:46Z","file_name":"2019_elife_He.pdf","date_created":"2023-02-07T09:42:46Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"ea6b89c20d59e5eb3646916fe5d568ad","file_id":"12525"}],"language":[{"iso":"eng"}],"volume":8,"license":"https://creativecommons.org/licenses/by/4.0/","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."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/"}],"month":"05","intvolume":" 8","citation":{"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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"He","full_name":"He, Shengbo","first_name":"Shengbo"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"first_name":"Jingyi","last_name":"Zhang","full_name":"Zhang, Jingyi"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"}],"article_processing_charge":"No","external_id":{"unknown":["31135340"]},"title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","article_number":"42530","has_accepted_license":"1","year":"2019","day":"28","publication":"eLife","date_published":"2019-05-28T00:00:00Z","doi":"10.7554/elife.42530","date_created":"2023-01-16T09:17:21Z","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).","publisher":"eLife Sciences Publications, Ltd","quality_controlled":"1","oa":1},{"article_type":"original","type":"journal_article","status":"public","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"_id":"12190","department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:54:54Z","extern":"1","scopus_import":"1","month":"08","intvolume":" 29","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"None","volume":29,"issue":"16","publication_identifier":{"issn":["0960-9822"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Lawrence","full_name":"Lawrence, Emma J.","first_name":"Emma J."},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"full_name":"Tock, Andrew J.","last_name":"Tock","first_name":"Andrew J."},{"last_name":"Lambing","full_name":"Lambing, Christophe","first_name":"Christophe"},{"first_name":"Alexander R.","full_name":"Blackwell, Alexander R.","last_name":"Blackwell"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"first_name":"Ian R.","last_name":"Henderson","full_name":"Henderson, Ian R."}],"article_processing_charge":"No","external_id":{"pmid":["31378616"]},"title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis","citation":{"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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier BV","quality_controlled":"1","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.).","page":"2676-2686.e3","date_published":"2019-08-19T00:00:00Z","doi":"10.1016/j.cub.2019.06.084","date_created":"2023-01-16T09:16:33Z","year":"2019","day":"19","publication":"Current Biology"},{"article_number":"2019/1015","_id":"8305","status":"public","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, 2019/1015.","ieee":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation,” Cryptology ePrint Archive. .","short":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint Archive (n.d.).","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.","chicago":"Kokoris Kogias, Eleftherios, Alexander Spiegelman, Dahlia Malkhi, and Ittai Abraham. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology 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."},"date_updated":"2023-05-10T09:27:54Z","title":"Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation","author":[{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"KOKORIS KOGIAS, Eleftherios","last_name":"KOKORIS KOGIAS"},{"last_name":"Spiegelman","full_name":"Spiegelman, Alexander","first_name":"Alexander"},{"first_name":"Dahlia","full_name":"Malkhi, Dahlia","last_name":"Malkhi"},{"first_name":"Ittai","last_name":"Abraham","full_name":"Abraham, Ittai"}],"article_processing_charge":"No","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+1AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","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.","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.","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.","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.","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.","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."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","first_name":"Janos","full_name":"Kiss, Janos","last_name":"Kiss"},{"last_name":"Elefante","full_name":"Elefante, Stefano","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Is Debian suitable for running an HPC Cluster?","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-16T07:27:09Z","oa_version":"Published Version","publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","oa":1,"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf"}],"month":"02","has_accepted_license":"1","publication_status":"published","year":"2019","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"}],"language":[{"iso":"eng"}],"publication":"AHPC19 - Austrian HPC Meeting 2019 ","page":"25","date_published":"2019-02-27T00:00:00Z","date_created":"2023-05-05T12:48:48Z"},{"scopus_import":"1","intvolume":" 8","month":"10","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","pmid":1,"related_material":{"record":[{"status":"public","id":"13079","relation":"research_data"}]},"volume":8,"publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2022-04-08T08:18:01Z","file_size":6984654,"date_created":"2022-04-08T08:18:01Z","file_name":"2019_eLife_Buchwalter.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1e8672a1e9c3dc0a2d3d0dad89673616","file_id":"11138","success":1}],"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)"},"article_type":"original","type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"status":"public","_id":"11060","file_date_updated":"2022-04-08T08:18:01Z","date_updated":"2023-05-31T06:36:22Z","ddc":["570"],"extern":"1","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_created":"2022-04-07T07:45:02Z","date_published":"2019-10-10T00:00:00Z","doi":"10.7554/elife.49796","year":"2019","has_accepted_license":"1","publication":"eLife","day":"10","article_number":"e49796","article_processing_charge":"No","external_id":{"pmid":["31599721"]},"author":[{"full_name":"Buchwalter, Abigail","last_name":"Buchwalter","first_name":"Abigail"},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"last_name":"Tsai","full_name":"Tsai, Hsiao","first_name":"Hsiao"},{"last_name":"Capitanio","full_name":"Capitanio, Juliana","first_name":"Juliana"},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"title":"Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","citation":{"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.","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","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","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.","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."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd"},{"date_created":"2023-05-23T17:09:30Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2019-10-28T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"11060","status":"public"}]},"doi":"10.5061/DRYAD.N0R525H","day":"28","year":"2019","month":"10","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.n0r525h","open_access":"1"}],"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"title":"Data from: Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress","article_processing_charge":"No","author":[{"full_name":"Buchwalter, Abigail","last_name":"Buchwalter","first_name":"Abigail"},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"full_name":"Tsai, Hsiao","last_name":"Tsai","first_name":"Hsiao"},{"full_name":"Capitanio, Juliana","last_name":"Capitanio","first_name":"Juliana"},{"last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"extern":"1","citation":{"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.","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.","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","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","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).","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."},"date_updated":"2023-05-31T06:36:23Z","status":"public","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","_id":"13079"},{"date_created":"2019-11-04T16:46:11Z","related_material":{"record":[{"relation":"extended_version","status":"public","id":"8317"}]},"date_published":"2019-08-01T00:00:00Z","page":"164-170","language":[{"iso":"eng"}],"publication":"Proceedings of the 31st Canadian Conference on Computational Geometry","day":"01","publication_status":"published","year":"2019","month":"08","main_file_link":[{"url":"https://cccg.ca/proceedings/2019/proceedings.pdf","open_access":"1"}],"oa":1,"quality_controlled":"1","scopus_import":"1","publisher":"Canadian Conference on Computational Geometry","acknowledgement":"This research was performed in part at the 33rd BellairsWinter Workshop on Computational Geometry. Wethank all other participants for a fruitful atmosphere.","oa_version":"Published Version","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. "}],"department":[{"_id":"HeEd"}],"title":"Folding polyominoes with holes into a cube","article_processing_charge":"No","external_id":{"arxiv":["1910.09917"]},"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"},{"full_name":"Demaine, Erik D","last_name":"Demaine","first_name":"Erik D"},{"last_name":"Demaine","full_name":"Demaine, Martin L","first_name":"Martin L"},{"first_name":"Sandor P","last_name":"Fekete","full_name":"Fekete, Sandor P"},{"first_name":"Linda","last_name":"Kleist","full_name":"Kleist, Linda"},{"full_name":"Kostitsyna, Irina","last_name":"Kostitsyna","first_name":"Irina"},{"first_name":"Maarten","last_name":"Löffler","full_name":"Löffler, Maarten"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová"},{"first_name":"Klara","full_name":"Mundilova, Klara","last_name":"Mundilova"},{"last_name":"Schmidt","full_name":"Schmidt, Christiane","first_name":"Christiane"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","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.","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.","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.","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."},"date_updated":"2023-08-04T10:57:42Z","status":"public","conference":{"name":"CCCG: Canadian Conference in Computational Geometry","location":"Edmonton, Canada","end_date":"2019-08-10","start_date":"2019-08-08"},"type":"conference","_id":"6989"},{"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","short":"T. Bian, Z. Chu, R. Klajn, Advanced Materials 32 (2019).","ieee":"T. Bian, Z. Chu, and R. Klajn, “The many ways to assemble nanoparticles using light,” Advanced Materials, vol. 32, no. 20. Wiley, 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Tong","full_name":"Bian, Tong","last_name":"Bian"},{"first_name":"Zonglin","last_name":"Chu","full_name":"Chu, Zonglin"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"}],"external_id":{"pmid":["31709655"]},"article_processing_charge":"No","title":"The many ways to assemble nanoparticles using light","article_number":"1905866","year":"2019","day":"19","publication":"Advanced Materials","date_published":"2019-11-19T00:00:00Z","doi":"10.1002/adma.201905866","date_created":"2023-08-01T09:37:26Z","publisher":"Wiley","quality_controlled":"1","date_updated":"2023-08-07T10:23:41Z","extern":"1","_id":"13366","type":"journal_article","article_type":"original","status":"public","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":32,"issue":"20","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"11","intvolume":" 32"},{"date_created":"2023-08-01T09:39:19Z","doi":"10.1021/jacs.8b09638","date_published":"2019-02-06T00:00:00Z","page":"1949-1960","publication":"Journal of the American Chemical Society","day":"06","year":"2019","quality_controlled":"1","publisher":"American Chemical Society","title":"Supramolecular control of azobenzene switching on nanoparticles","external_id":{"pmid":["30595017"]},"article_processing_charge":"No","author":[{"full_name":"Chu, Zonglin","last_name":"Chu","first_name":"Zonglin"},{"last_name":"Han","full_name":"Han, Yanxiao","first_name":"Yanxiao"},{"full_name":"Bian, Tong","last_name":"Bian","first_name":"Tong"},{"full_name":"De, Soumen","last_name":"De","first_name":"Soumen"},{"last_name":"Král","full_name":"Král, Petr","first_name":"Petr"},{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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."},"volume":141,"issue":"5","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"intvolume":" 141","month":"02","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"extern":"1","date_updated":"2023-08-07T10:51:12Z","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","type":"journal_article","article_type":"original","_id":"13373"},{"extern":"1","date_updated":"2023-08-07T10:48:31Z","_id":"13372","keyword":["General Chemistry"],"status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"issue":"5","volume":48,"oa_version":"Published Version","pmid":1,"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."}],"intvolume":" 48","month":"01","main_file_link":[{"url":"https://doi.org/10.1039/C8CS00787J","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","short":"M. Grzelczak, L.M. Liz-Marzán, R. Klajn, Chemical Society Reviews 48 (2019) 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.","ista":"Grzelczak M, Liz-Marzán LM, Klajn R. 2019. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 48(5), 1342–1361."},"title":"Stimuli-responsive self-assembly of nanoparticles","article_processing_charge":"No","external_id":{"pmid":["30688963"]},"author":[{"full_name":"Grzelczak, Marek","last_name":"Grzelczak","first_name":"Marek"},{"first_name":"Luis M.","full_name":"Liz-Marzán, Luis M.","last_name":"Liz-Marzán"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}],"publication":"Chemical Society Reviews","day":"28","year":"2019","date_created":"2023-08-01T09:38:52Z","doi":"10.1039/c8cs00787j","date_published":"2019-01-28T00:00:00Z","page":"1342-1361","oa":1,"quality_controlled":"1","publisher":"Royal Society of Chemistry"},{"oa":1,"quality_controlled":"1","publisher":"Beilstein Institut","date_created":"2023-08-01T09:38:06Z","doi":"10.3762/bjoc.15.232","date_published":"2019-10-10T00:00:00Z","page":"2398-2407","publication":"Beilstein Journal of Organic Chemistry","day":"10","year":"2019","title":"Reversible switching of arylazopyrazole within a metal–organic cage","article_processing_charge":"No","external_id":{"pmid":["31666874"]},"author":[{"last_name":"Hanopolskyi","full_name":"Hanopolskyi, Anton I","first_name":"Anton I"},{"first_name":"Soumen","last_name":"De","full_name":"De, Soumen"},{"first_name":"Michał J","full_name":"Białek, Michał J","last_name":"Białek"},{"first_name":"Yael","full_name":"Diskin-Posner, Yael","last_name":"Diskin-Posner"},{"last_name":"Avram","full_name":"Avram, Liat","first_name":"Liat"},{"last_name":"Feller","full_name":"Feller, Moran","first_name":"Moran"},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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."},"intvolume":" 15","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3762/bjoc.15.232"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":15,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1860-5397"]},"keyword":["Organic Chemistry"],"status":"public","type":"journal_article","article_type":"original","_id":"13369","extern":"1","date_updated":"2023-08-07T10:34:56Z"},{"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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chu, Zonglin","last_name":"Chu","first_name":"Zonglin"},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"external_id":{"pmid":["31539469"]},"article_processing_charge":"No","title":"Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules","year":"2019","day":"20","publication":"Nano Letters","page":"7106-7111","doi":"10.1021/acs.nanolett.9b02642","date_published":"2019-09-20T00:00:00Z","date_created":"2023-08-01T09:38:23Z","quality_controlled":"1","publisher":"American Chemical Society","date_updated":"2023-08-07T10:39:34Z","extern":"1","_id":"13370","article_type":"original","type":"journal_article","status":"public","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":19,"issue":"10","abstract":[{"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.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","month":"09","intvolume":" 19"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2451-9308"],"eissn":["2451-9294"]},"issue":"9","volume":5,"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"}],"intvolume":" 5","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2019.08.012"}],"scopus_import":"1","extern":"1","date_updated":"2023-08-07T10:46:50Z","_id":"13371","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"status":"public","type":"journal_article","article_type":"original","publication":"Chem","day":"12","year":"2019","date_created":"2023-08-01T09:38:38Z","date_published":"2019-09-12T00:00:00Z","doi":"10.1016/j.chempr.2019.08.012","page":"2283-2285","oa":1,"quality_controlled":"1","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285.","ieee":"M. J. Białek and R. Klajn, “Diamond grows up,” Chem, vol. 5, no. 9. Elsevier, pp. 2283–2285, 2019.","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.","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."},"title":"Diamond grows up","article_processing_charge":"No","author":[{"last_name":"Białek","full_name":"Białek, Michał J.","first_name":"Michał J."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"}]},{"oa_version":"Published Version","abstract":[{"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. ","lang":"eng"}],"intvolume":" 138","month":"08","alternative_title":["LIPIcs"],"scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:42Z","file_size":554457,"creator":"kschuh","date_created":"2019-09-27T11:45:15Z","file_name":"2019_LIPIcs_Avni.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","file_id":"6913"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"status":"public","id":"9239","relation":"later_version"}]},"volume":138,"_id":"6884","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)"},"conference":{"location":"Aachen, Germany","end_date":"2019-08-30","start_date":"2019-08-26","name":"MFCS: nternational Symposium on Mathematical Foundations of Computer Science"},"type":"conference","ddc":["004"],"date_updated":"2023-08-07T14:08:34Z","file_date_updated":"2020-07-14T12:47:42Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"01","year":"2019","has_accepted_license":"1","date_created":"2019-09-18T08:04:26Z","doi":"10.4230/LIPICS.MFCS.2019.11","date_published":"2019-08-01T00:00:00Z","article_number":"11","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","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."},"title":"Bidding mechanisms in graph games","external_id":{"arxiv":["1905.03835"]},"author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}]},{"_id":"13471","article_type":"original","type":"journal_article","status":"public","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"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","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1051/0004-6361/201833297"}],"month":"04","intvolume":" 624","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"publication_status":"published","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.","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","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","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","author":[{"first_name":"M.","full_name":"Renzo, M.","last_name":"Renzo"},{"first_name":"E.","full_name":"Zapartas, E.","last_name":"Zapartas"},{"first_name":"S. E.","last_name":"de Mink","full_name":"de Mink, S. E."},{"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"},{"first_name":"S.","last_name":"Justham","full_name":"Justham, S."},{"first_name":"R. J.","last_name":"Farmer","full_name":"Farmer, R. J."},{"first_name":"R. G.","full_name":"Izzard, R. G.","last_name":"Izzard"},{"first_name":"S.","full_name":"Toonen, S.","last_name":"Toonen"},{"first_name":"H.","full_name":"Sana, H.","last_name":"Sana"}],"external_id":{"arxiv":["1804.09164"]},"article_processing_charge":"No","title":"Massive runaway and walkaway stars","publisher":"EDP Sciences","quality_controlled":"1","oa":1,"year":"2019","day":"11","publication":"Astronomy & Astrophysics","doi":"10.1051/0004-6361/201833297","date_published":"2019-04-11T00:00:00Z","date_created":"2023-08-03T10:14:18Z"}]