[{"intvolume":" 35","page":"225 - 232","language":[{"iso":"eng"}],"publisher":"Wiley-Blackwell","month":"05","publication_status":"published","day":"01","status":"public","issue":"2","publist_id":"5793","doi":"10.1111/cgf.12825","abstract":[{"text":"The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation.","lang":"eng"}],"date_created":"2018-12-11T11:51:53Z","ddc":["000"],"year":"2016","volume":35,"publication":"Computer Graphics Forum","title":"Narrow band FLIP for liquid simulations","date_published":"2016-05-01T00:00:00Z","quality_controlled":"1","pubrep_id":"611","type":"journal_article","department":[{"_id":"ChWo"}],"file":[{"checksum":"984afbe510ed48019025dff1dcc7baad","relation":"main_file","creator":"system","file_name":"IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","file_size":5938324,"access_level":"open_access","file_id":"4940","date_created":"2018-12-12T10:12:22Z"}],"date_updated":"2023-02-21T10:38:38Z","oa_version":"Submitted Version","oa":1,"author":[{"first_name":"Florian","full_name":"Ferstl, Florian","last_name":"Ferstl"},{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Westermann, Rüdiger","first_name":"Rüdiger","last_name":"Westermann"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"}],"citation":{"ieee":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, and N. Thuerey, “Narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 225–232, 2016.","ama":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 2016;35(2):225-232. doi:10.1111/cgf.12825","short":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232.","chicago":"Ferstl, Florian, Ryoichi Ando, Chris Wojtan, Rüdiger Westermann, and Nils Thuerey. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12825.","ista":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. 2016. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 35(2), 225–232.","apa":"Ferstl, F., Ando, R., Wojtan, C., Westermann, R., & Thuerey, N. (2016). Narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12825","mla":"Ferstl, Florian, et al. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 225–32, doi:10.1111/cgf.12825."},"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1415","scopus_import":1,"file_date_updated":"2020-07-14T12:44:53Z"},{"date_created":"2018-12-11T11:51:54Z","intvolume":" 93","article_number":"195145","language":[{"iso":"eng"}],"volume":93,"publication":"Physical Review B - Condensed Matter and Materials Physics","year":"2016","main_file_link":[{"url":"http://arxiv.org/abs/1603.09358","open_access":"1"}],"publisher":"American Physical Society","quality_controlled":"1","date_published":"2016-05-15T00:00:00Z","title":"Interaction-driven Lifshitz transition with dipolar fermions in optical lattices","month":"05","type":"journal_article","oa":1,"author":[{"last_name":"Van Loon","full_name":"Van Loon, Erik","first_name":"Erik"},{"last_name":"Katsnelson","first_name":"Mikhail","full_name":"Katsnelson, Mikhail"},{"last_name":"Chomaz","first_name":"Lauriane","full_name":"Chomaz, Lauriane"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"day":"15","citation":{"ieee":"E. Van Loon, M. Katsnelson, L. Chomaz, and M. Lemeshko, “Interaction-driven Lifshitz transition with dipolar fermions in optical lattices,” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19. American Physical Society, 2016.","short":"E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 93 (2016).","ama":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 2016;93(19). doi:10.1103/PhysRevB.93.195145","chicago":"Van Loon, Erik, Mikhail Katsnelson, Lauriane Chomaz, and Mikhail Lemeshko. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.195145.","ista":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. 2016. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 93(19), 195145.","mla":"Van Loon, Erik, et al. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19, 195145, American Physical Society, 2016, doi:10.1103/PhysRevB.93.195145.","apa":"Van Loon, E., Katsnelson, M., Chomaz, L., & Lemeshko, M. (2016). Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.93.195145"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:50:36Z","publication_status":"published","oa_version":"Preprint","_id":"1416","status":"public","scopus_import":1,"abstract":[{"text":"Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven.","lang":"eng"}],"doi":"10.1103/PhysRevB.93.195145","publist_id":"5791","issue":"19"},{"language":[{"iso":"eng"}],"intvolume":" 211","page":"65 - 74","publisher":"Wiley-Blackwell","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","publication_status":"published","day":"01","month":"07","issue":"1","doi":"10.1111/nph.14019","publist_id":"5790","abstract":[{"text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.","lang":"eng"}],"status":"public","year":"2016","volume":211,"publication":"New Phytologist","date_created":"2018-12-11T11:51:54Z","ddc":["581"],"title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","date_published":"2016-07-01T00:00:00Z","quality_controlled":"1","department":[{"_id":"JiFr"}],"file":[{"relation":"main_file","checksum":"23522ced3508ffe7a4f247c4230e6493","creator":"system","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf","file_size":3828383,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","date_created":"2018-12-12T10:13:32Z","file_id":"5016"}],"oa_version":"Submitted Version","date_updated":"2021-01-12T06:50:36Z","oa":1,"author":[{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon"},{"last_name":"Skůpa","full_name":"Skůpa, Petr","first_name":"Petr"},{"last_name":"Viaene","full_name":"Viaene, Tom","first_name":"Tom"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"first_name":"Petr","full_name":"Klíma, Petr","last_name":"Klíma"},{"full_name":"Čarná, Mária","first_name":"Mária","last_name":"Čarná"},{"last_name":"Rolčík","first_name":"Jakub","full_name":"Rolčík, Jakub"},{"last_name":"De Rycke","first_name":"Riet","full_name":"De Rycke, Riet"},{"last_name":"Moreno","first_name":"Ignacio","full_name":"Moreno, Ignacio"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre"},{"first_name":"Ariel","full_name":"Orellana, Ariel","last_name":"Orellana"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml"}],"citation":{"ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019"},"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pubrep_id":"1004","type":"journal_article","scopus_import":1,"file_date_updated":"2020-07-14T12:44:53Z","_id":"1417"},{"_id":"1419","status":"public","scopus_import":1,"abstract":[{"text":"We study the superconducting phase of the Hubbard model using the Gutzwiller variational wave function (GWF) and the recently proposed diagrammatic expansion technique (DE-GWF). The DE-GWF method works on the level of the full GWF and in the thermodynamic limit. Here, we consider a finite-size system to study the accuracy of the results as a function of the system size (which is practically unrestricted). We show that the finite-size scaling used, e.g. in the variational Monte Carlo method can lead to significant, uncontrolled errors. The presented research is the first step towards applying the DE-GWF method in studies of inhomogeneous situations, including systems with impurities, defects, inhomogeneous phases, or disorder.","lang":"eng"}],"doi":"10.1088/0953-8984/28/17/175701","publist_id":"5788","issue":"17","month":"03","type":"journal_article","author":[{"full_name":"Tomski, Andrzej","first_name":"Andrzej","last_name":"Tomski"},{"last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Kaczmarczyk, Jan"}],"ec_funded":1,"day":"29","citation":{"ama":"Tomski A, Kaczmarczyk J. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 2016;28(17). doi:10.1088/0953-8984/28/17/175701","short":"A. Tomski, J. Kaczmarczyk, Journal of Physics: Condensed Matter 28 (2016).","chicago":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2016. https://doi.org/10.1088/0953-8984/28/17/175701.","ieee":"A. Tomski and J. Kaczmarczyk, “Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model,” Journal of Physics: Condensed Matter, vol. 28, no. 17. IOP Publishing Ltd., 2016.","ista":"Tomski A, Kaczmarczyk J. 2016. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 28(17), 175701.","apa":"Tomski, A., & Kaczmarczyk, J. (2016). Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/0953-8984/28/17/175701","mla":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter, vol. 28, no. 17, 175701, IOP Publishing Ltd., 2016, doi:10.1088/0953-8984/28/17/175701."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:50:36Z","publication_status":"published","oa_version":"None","publisher":"IOP Publishing Ltd.","quality_controlled":"1","title":"Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model","date_published":"2016-03-29T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"intvolume":" 28","date_created":"2018-12-11T11:51:55Z","article_number":"175701","language":[{"iso":"eng"}],"volume":28,"publication":"Journal of Physics: Condensed Matter","year":"2016"},{"page":"1523 - 1548","intvolume":" 202","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Genetics Society of America","month":"04","ec_funded":1,"day":"06","publication_status":"published","status":"public","publist_id":"5787","doi":"10.1534/genetics.115.184127","abstract":[{"lang":"eng","text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. "}],"issue":"4","date_created":"2018-12-11T11:51:55Z","article_processing_charge":"No","volume":202,"publication":"Genetics","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"year":"2016","quality_controlled":"1","date_published":"2016-04-06T00:00:00Z","title":"A general approximation for the dynamics of quantitative traits","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}],"type":"journal_article","oa":1,"author":[{"last_name":"Bod'ová","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"citation":{"mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"oa_version":"Preprint","date_updated":"2025-05-28T11:42:47Z","_id":"1420","scopus_import":"1","external_id":{"arxiv":["1510.08344"]}},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"11","citation":{"ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, T. Johnson, and P. Prakash, “Scalable static hybridization methods for analysis of nonlinear systems,” presented at the HSCC 2016: International Conference on Hybrid Systems: Computation and Control, Vienna, Austria, 2016, pp. 155–164.","chicago":"Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, Taylor Johnson, and Pradyot Prakash. “Scalable Static Hybridization Methods for Analysis of Nonlinear Systems,” 155–64. Springer, 2016. https://doi.org/10.1145/2883817.2883837.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164.","ama":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. Scalable static hybridization methods for analysis of nonlinear systems. In: Springer; 2016:155-164. doi:10.1145/2883817.2883837","mla":"Bak, Stanley, et al. Scalable Static Hybridization Methods for Analysis of Nonlinear Systems. Springer, 2016, pp. 155–64, doi:10.1145/2883817.2883837.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., Johnson, T., & Prakash, P. (2016). Scalable static hybridization methods for analysis of nonlinear systems (pp. 155–164). Presented at the HSCC 2016: International Conference on Hybrid Systems: Computation and Control, Vienna, Austria: Springer. https://doi.org/10.1145/2883817.2883837","ista":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. 2016. Scalable static hybridization methods for analysis of nonlinear systems. HSCC 2016: International Conference on Hybrid Systems: Computation and Control, 155–164."},"ec_funded":1,"author":[{"last_name":"Bak","first_name":"Stanley","full_name":"Bak, Stanley"},{"orcid":"0000-0002-0686-0365","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Johnson","first_name":"Taylor","full_name":"Johnson, Taylor"},{"last_name":"Prakash","full_name":"Prakash, Pradyot","first_name":"Pradyot"}],"publication_status":"published","date_updated":"2021-01-12T06:50:37Z","oa_version":"None","department":[{"_id":"ToHe"}],"type":"conference","month":"04","abstract":[{"text":"Hybridization methods enable the analysis of hybrid automata with complex, nonlinear dynamics through a sound abstraction process. Complex dynamics are converted to simpler ones with added noise, and then analysis is done using a reachability method for the simpler dynamics. Several such recent approaches advocate that only "dynamic" hybridization techniquesi.e., those where the dynamics are abstracted on-The-fly during a reachability computation are effective. In this paper, we demonstrate this is not the case, and create static hybridization methods that are more scalable than earlier approaches. The main insight in our approach is that quick, numeric simulations can be used to guide the process, eliminating the need for an exponential number of hybridization domains. Transitions between domains are generally timetriggered, avoiding accumulated error from geometric intersections. We enhance our static technique by combining time-Triggered transitions with occasional space-Triggered transitions, and demonstrate the benefits of the combined approach in what we call mixed-Triggered hybridization. Finally, error modes are inserted to confirm that the reachable states stay within the hybridized regions. The developed techniques can scale to higher dimensions than previous static approaches, while enabling the parallelization of the main performance bottleneck for many dynamic hybridization approaches: The nonlinear optimization required for sound dynamics abstraction. We implement our method as a model transformation pass in the HYST tool, and perform reachability analysis and evaluation using an unmodified version of SpaceEx on nonlinear models with up to six dimensions.","lang":"eng"}],"publist_id":"5786","doi":"10.1145/2883817.2883837","scopus_import":1,"status":"public","_id":"1421","language":[{"iso":"eng"}],"year":"2016","page":"155 - 164","date_created":"2018-12-11T11:51:55Z","quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"date_published":"2016-04-11T00:00:00Z","title":"Scalable static hybridization methods for analysis of nonlinear systems","publisher":"Springer","conference":{"location":"Vienna, Austria","start_date":"2016-04-12","end_date":"2016-04-14","name":"HSCC 2016: International Conference on Hybrid Systems: Computation and Control"}},{"file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"_id":"1422","oa_version":"Published Version","date_updated":"2021-01-12T06:50:38Z","file":[{"creator":"system","checksum":"fb404923d8ca9a1faeb949561f26cbea","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","file_size":458968,"file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","file_id":"5181","date_created":"2018-12-12T10:15:57Z","access_level":"open_access"}],"department":[{"_id":"RoSe"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016.","chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5","apa":"Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5","mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5.","ista":"Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 106(7), 913–923."},"author":[{"full_name":"Frank, Rupert","first_name":"Rupert","last_name":"Frank"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"},{"last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"oa":1,"pubrep_id":"591","type":"journal_article","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"date_published":"2016-07-01T00:00:00Z","title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016","publication":"Letters in Mathematical Physics","article_processing_charge":"Yes (via OA deal)","volume":106,"ddc":["510","530"],"date_created":"2018-12-11T11:51:56Z","issue":"7","publist_id":"5785","doi":"10.1007/s11005-016-0847-5","abstract":[{"lang":"eng","text":"We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior."}],"status":"public","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","publication_status":"published","day":"01","month":"07","publisher":"Springer","language":[{"iso":"eng"}],"intvolume":" 106","page":"913 - 923"},{"article_number":"25676","intvolume":" 6","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","month":"05","publication_status":"published","acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","day":"10","status":"public","doi":"10.1038/srep25676","publist_id":"5784","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation."}],"ddc":["000"],"date_created":"2018-12-11T11:51:56Z","year":"2016","publication":"Scientific Reports","volume":6,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Comparing reactive and memory-one strategies of direct reciprocity","date_published":"2016-05-10T00:00:00Z","quality_controlled":"1","pubrep_id":"590","type":"journal_article","oa_version":"Published Version","date_updated":"2021-01-12T06:50:38Z","file":[{"checksum":"ee17c482370d2e1b3add393710d3c696","relation":"main_file","creator":"system","file_name":"IST-2016-590-v1+1_srep25676.pdf","date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","file_size":1349915,"access_level":"open_access","file_id":"5327","date_created":"2018-12-12T10:18:08Z"}],"department":[{"_id":"KrCh"}],"citation":{"ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","apa":"Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep25676","mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group, 2016, doi:10.1038/srep25676.","ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676","chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676."},"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"last_name":"Baek","first_name":"Seung","full_name":"Baek, Seung"},{"last_name":"Jeong","first_name":"Hyeongchai","full_name":"Jeong, Hyeongchai"},{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"_id":"1423","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1},{"publication":"Royal Society Open Science","volume":3,"year":"2016","ddc":["000"],"date_created":"2018-12-11T11:51:57Z","quality_controlled":"1","date_published":"2016-05-01T00:00:00Z","title":"Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","citation":{"mla":"Chakra, Maria, et al. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science, vol. 3, no. 5, 160036, Royal Society, The, 2016, doi:10.1098/rsos.160036.","apa":"Chakra, M., Hilbe, C., & Traulsen, A. (2016). Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160036","ista":"Chakra M, Hilbe C, Traulsen A. 2016. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 3(5), 160036.","chicago":"Chakra, Maria, Christian Hilbe, and Arne Traulsen. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160036.","short":"M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).","ama":"Chakra M, Hilbe C, Traulsen A. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 2016;3(5). doi:10.1098/rsos.160036","ieee":"M. Chakra, C. Hilbe, and A. Traulsen, “Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites,” Royal Society Open Science, vol. 3, no. 5. Royal Society, The, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"last_name":"Chakra","full_name":"Chakra, Maria","first_name":"Maria"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"last_name":"Traulsen","full_name":"Traulsen, Arne","first_name":"Arne"}],"date_updated":"2021-01-12T06:50:39Z","oa_version":"Published Version","department":[{"_id":"KrCh"}],"file":[{"date_created":"2018-12-12T10:14:49Z","file_id":"5104","access_level":"open_access","file_size":937002,"date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","file_name":"IST-2016-589-v1+1_160036.full.pdf","creator":"system","relation":"main_file","checksum":"bf84211b31fe87451e738ba301d729c3"}],"type":"journal_article","pubrep_id":"589","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"_id":"1426","language":[{"iso":"eng"}],"article_number":"160036","intvolume":" 3","publisher":"Royal Society, The","day":"01","acknowledgement":"C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","publication_status":"published","month":"05","publist_id":"5776","abstract":[{"lang":"eng","text":"Brood parasites exploit their host in order to increase their own fitness. Typically, this results in an arms race between parasite trickery and host defence. Thus, it is puzzling to observe hosts that accept parasitism without any resistance. The ‘mafia’ hypothesis suggests that these hosts accept parasitism to avoid retaliation. Retaliation has been shown to evolve when the hosts condition their response to mafia parasites, who use depredation as a targeted response to rejection. However, it is unclear if acceptance would also emerge when ‘farming’ parasites are present in the population. Farming parasites use depredation to synchronize the timing with the host, destroying mature clutches to force the host to re-nest. Herein, we develop an evolutionary model to analyse the interaction between depredatory parasites and their hosts. We show that coevolutionary cycles between farmers and mafia can still induce host acceptance of brood parasites. However, this equilibrium is unstable and in the long-run the dynamics of this host–parasite interaction exhibits strong oscillations: when farmers are the majority, accepters conditional to mafia (the host will reject first and only accept after retaliation by the parasite) have a higher fitness than unconditional accepters (the host always accepts parasitism). This leads to an increase in mafia parasites’ fitness and in turn induce an optimal environment for accepter hosts."}],"doi":"10.1098/rsos.160036","issue":"5","status":"public"},{"_id":"1427","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"pubrep_id":"588","type":"journal_article","oa_version":"Published Version","date_updated":"2021-01-12T06:50:39Z","file":[{"file_id":"4751","date_created":"2018-12-12T10:09:27Z","access_level":"open_access","date_updated":"2020-07-14T12:44:53Z","content_type":"application/pdf","file_size":648115,"file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf","creator":"system","checksum":"1f456ce1d2aa2f67176a1709f9702ecf","relation":"main_file"}],"department":[{"_id":"CaGu"},{"_id":"JoBo"}],"citation":{"apa":"Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269","mla":"Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.","ista":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769.","ieee":"M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016.","chicago":"Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269.","ama":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269","short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","full_name":"Lagator, Mato","last_name":"Lagator"},{"last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","full_name":"Igler, Claudia"},{"last_name":"Moreno","full_name":"Moreno, Anaisa","first_name":"Anaisa"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}],"oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_published":"2016-03-01T00:00:00Z","title":"Epistatic interactions in the arabinose cis-regulatory element","quality_controlled":"1","ddc":["570","576"],"date_created":"2018-12-11T11:51:57Z","year":"2016","publication":"Molecular Biology and Evolution","volume":33,"status":"public","issue":"3","publist_id":"5772","doi":"10.1093/molbev/msv269","abstract":[{"text":"Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.","lang":"eng"}],"month":"03","publication_status":"published","day":"01","ec_funded":1,"publisher":"Oxford University Press","intvolume":" 33","page":"761 - 769","language":[{"iso":"eng"}]},{"article_number":"012016","intvolume":" 691","language":[{"iso":"eng"}],"publisher":"IOP Publishing Ltd.","month":"03","publication_status":"published","day":"07","status":"public","issue":"1","publist_id":"5770","abstract":[{"lang":"eng","text":"We report on a mathematically rigorous analysis of the superfluid properties of a Bose- Einstein condensate in the many-body ground state of a one-dimensional model of interacting bosons in a random potential."}],"doi":"10.1088/1742-6596/691/1/012016","ddc":["510","530"],"date_created":"2018-12-11T11:51:58Z","year":"2016","publication":"Journal of Physics: Conference Series","volume":691,"conference":{"end_date":"2015-08-25","location":"Shanghai, China","start_date":"2015-08-21","name":"24th International Laser Physics Workshop (LPHYS'15)"},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"date_published":"2016-03-07T00:00:00Z","title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential","quality_controlled":"1","pubrep_id":"585","type":"conference","date_updated":"2021-01-12T06:50:40Z","oa_version":"Published Version","department":[{"_id":"RoSe"}],"file":[{"file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf","file_size":1434688,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","date_created":"2018-12-12T10:10:55Z","file_id":"4847","relation":"main_file","checksum":"109db801749072c3f6c8f1a1848700fa","creator":"system"}],"has_accepted_license":"1","citation":{"ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In: Journal of Physics: Conference Series. Vol 691. IOP Publishing Ltd.; 2016. doi:10.1088/1742-6596/691/1/012016","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing Ltd., 2016.","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” In Journal of Physics: Conference Series, Vol. 691. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1742-6596/691/1/012016.","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential,” in Journal of Physics: Conference Series, Shanghai, China, 2016, vol. 691, no. 1.","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2016. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. Journal of Physics: Conference Series. 24th International Laser Physics Workshop (LPHYS’15) vol. 691, 012016.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2016). Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In Journal of Physics: Conference Series (Vol. 691). Shanghai, China: IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/691/1/012016","mla":"Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” Journal of Physics: Conference Series, vol. 691, no. 1, 012016, IOP Publishing Ltd., 2016, doi:10.1088/1742-6596/691/1/012016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"last_name":"Könenberg","first_name":"Martin","full_name":"Könenberg, Martin"},{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Moser, Thomas","last_name":"Moser"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"_id":"1428","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1},{"language":[{"iso":"eng"}],"intvolume":" 7","article_number":"11332 (2016)","publisher":"Nature Publishing Group","day":"15","acknowledgement":"This research was supported by the Australian Research Council (ARC) Center of Excellence CUDOS (CE110001018), ARC Laureate Fellowship (FL120100029), ARC Discovery Early Career Researcher Award (DECRA DE120102069), the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO). L.K. acknowledges funding from ERC Advanced Investigator Grant (no. 240438-CONSTANS). A.D.R, S.C., and G.L. acknowledge financial support from the ERC-Pharos programme lead by A. P. Mosk.","publication_status":"published","month":"04","abstract":[{"lang":"eng","text":"Solitons are localized waves formed by a balance of focusing and defocusing effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar properties including stability, periodic recurrence and particle-like trajectories. One important property is soliton fission, a process by which an energetic higher-order soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate through both experiment and theory that nonlinear photocarrier generation can induce soliton fission. Using near-field measurements, we directly observe the nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic semiconductor waveguide. We develop an analytic formalism describing the free-carrier dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold by an order of magnitude. We confirm these observations with a numerical nonlinear Schrödinger equation model. These results provide a fundamental explanation and physical scaling of optical pulse evolution in free-carrier media and could enable improved supercontinuum sources in gas based and integrated semiconductor waveguides."}],"publist_id":"5769","doi":"10.1038/ncomms11332","status":"public","volume":7,"publication":"Nature Communications","year":"2016","date_created":"2018-12-11T11:51:58Z","ddc":["530"],"quality_controlled":"1","title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","date_published":"2016-04-15T00:00:00Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Husko","full_name":"Husko, Chad","first_name":"Chad"},{"orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Wulf"},{"last_name":"Lefrançois","first_name":"Simon","full_name":"Lefrançois, Simon"},{"first_name":"Sylvain","full_name":"Combrié, Sylvain","last_name":"Combrié"},{"first_name":"Gaëlle","full_name":"Lehoucq, Gaëlle","last_name":"Lehoucq"},{"full_name":"De Rossi, Alfredo","first_name":"Alfredo","last_name":"De Rossi"},{"full_name":"Eggleton, Benjamin","first_name":"Benjamin","last_name":"Eggleton"},{"full_name":"Kuipers, Laurens","first_name":"Laurens","last_name":"Kuipers"}],"oa":1,"has_accepted_license":"1","citation":{"ista":"Husko C, Wulf M, Lefrançois S, Combrié S, Lehoucq G, De Rossi A, Eggleton B, Kuipers L. 2016. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 7, 11332 (2016).","mla":"Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications, vol. 7, 11332 (2016), Nature Publishing Group, 2016, doi:10.1038/ncomms11332.","apa":"Husko, C., Wulf, M., Lefrançois, S., Combrié, S., Lehoucq, G., De Rossi, A., … Kuipers, L. (2016). Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11332","ieee":"C. Husko et al., “Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016).","ama":"Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 2016;7. doi:10.1038/ncomms11332","chicago":"Husko, Chad, Matthias Wulf, Simon Lefrançois, Sylvain Combrié, Gaëlle Lehoucq, Alfredo De Rossi, Benjamin Eggleton, and Laurens Kuipers. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11332."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoFi"}],"file":[{"relation":"main_file","checksum":"6484fa81a2e52e4fdd7935e1ae6091d4","creator":"system","file_name":"IST-2016-583-v1+1_ncomms11332.pdf","file_size":965176,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","date_created":"2018-12-12T10:15:53Z","file_id":"5177"}],"date_updated":"2021-01-12T06:50:40Z","oa_version":"Published Version","type":"journal_article","pubrep_id":"583","scopus_import":1,"file_date_updated":"2020-07-14T12:44:53Z","_id":"1429"},{"external_id":{"pmid":["27583560"]},"scopus_import":"1","_id":"14302","oa_version":"None","date_updated":"2023-11-07T12:08:46Z","citation":{"short":"E. Stahl, F.M. Praetorius, C.C. de Oliveira Mann, K.-P. Hopfner, H. Dietz, ACS Nano 10 (2016) 9156–9164.","ama":"Stahl E, Praetorius FM, de Oliveira Mann CC, Hopfner K-P, Dietz H. Impact of heterogeneity and lattice bond strength on DNA triangle crystal growth. ACS Nano. 2016;10(10):9156-9164. doi:10.1021/acsnano.6b04787","chicago":"Stahl, Evi, Florian M Praetorius, Carina C. de Oliveira Mann, Karl-Peter Hopfner, and Hendrik Dietz. “Impact of Heterogeneity and Lattice Bond Strength on DNA Triangle Crystal Growth.” ACS Nano. American Chemical Society, 2016. https://doi.org/10.1021/acsnano.6b04787.","ieee":"E. Stahl, F. M. Praetorius, C. C. de Oliveira Mann, K.-P. Hopfner, and H. Dietz, “Impact of heterogeneity and lattice bond strength on DNA triangle crystal growth,” ACS Nano, vol. 10, no. 10. American Chemical Society, pp. 9156–9164, 2016.","ista":"Stahl E, Praetorius FM, de Oliveira Mann CC, Hopfner K-P, Dietz H. 2016. Impact of heterogeneity and lattice bond strength on DNA triangle crystal growth. ACS Nano. 10(10), 9156–9164.","mla":"Stahl, Evi, et al. “Impact of Heterogeneity and Lattice Bond Strength on DNA Triangle Crystal Growth.” ACS Nano, vol. 10, no. 10, American Chemical Society, 2016, pp. 9156–64, doi:10.1021/acsnano.6b04787.","apa":"Stahl, E., Praetorius, F. M., de Oliveira Mann, C. C., Hopfner, K.-P., & Dietz, H. (2016). Impact of heterogeneity and lattice bond strength on DNA triangle crystal growth. ACS Nano. American Chemical Society. https://doi.org/10.1021/acsnano.6b04787"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Stahl","first_name":"Evi","full_name":"Stahl, Evi"},{"first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","last_name":"Praetorius"},{"last_name":"de Oliveira Mann","full_name":"de Oliveira Mann, Carina C.","first_name":"Carina C."},{"last_name":"Hopfner","full_name":"Hopfner, Karl-Peter","first_name":"Karl-Peter"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"}],"type":"journal_article","title":"Impact of heterogeneity and lattice bond strength on DNA triangle crystal growth","date_published":"2016-09-01T00:00:00Z","quality_controlled":"1","year":"2016","publication":"ACS Nano","article_processing_charge":"No","volume":10,"date_created":"2023-09-06T12:52:00Z","issue":"10","abstract":[{"text":"One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and co-workers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson–Crick base pairing. However, 3D crystallization of larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem. Larger objects would offer more degrees of freedom and design options with respect to tailoring lattice geometry and for positioning other objects within a crystal lattice. The greater rigidity of multilayer DNA origami could also positively influence the diffractive properties of crystals composed of such particles. Here, we rationally explore the role of heterogeneity and Watson–Crick interaction strengths in crystal growth using 40 variants of the original DNA triangle as model multichain objects. Crystal growth of the triangle was remarkably robust despite massive chemical, geometrical, and thermodynamical sample heterogeneity that we introduced, but the crystal growth sensitively depended on the sequences of base pairs next to the Watson–Crick sticky ends of the triangle. Our results point to weak lattice interactions and high concentrations as decisive factors for achieving productive crystallization, while sample heterogeneity and impurities played a minor role.","lang":"eng"}],"doi":"10.1021/acsnano.6b04787","pmid":1,"status":"public","publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"publication_status":"published","day":"01","extern":"1","month":"09","publisher":"American Chemical Society","language":[{"iso":"eng"}],"intvolume":" 10","article_type":"original","page":"9156-9164"},{"_id":"14304","external_id":{"pmid":["27821763"]},"scopus_import":"1","type":"journal_article","date_updated":"2023-11-07T11:53:06Z","oa_version":"Published Version","author":[{"last_name":"Martin","first_name":"Thomas G.","full_name":"Martin, Thomas G."},{"last_name":"Bharat","full_name":"Bharat, Tanmay A. M.","first_name":"Tanmay A. M."},{"full_name":"Joerger, Andreas C.","first_name":"Andreas C.","last_name":"Joerger"},{"last_name":"Bai","full_name":"Bai, Xiao-chen","first_name":"Xiao-chen"},{"last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"full_name":"Fersht, Alan R.","first_name":"Alan R.","last_name":"Fersht"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"},{"first_name":"Sjors H. W.","full_name":"Scheres, Sjors H. W.","last_name":"Scheres"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Martin, Thomas G., et al. “Design of a Molecular Support for Cryo-EM Structure Determination.” PNAS, vol. 113, no. 47, Proceedings of the National Academy of Sciences, 2016, pp. E7456–63, doi:10.1073/pnas.1612720113.","apa":"Martin, T. G., Bharat, T. A. M., Joerger, A. C., Bai, X., Praetorius, F. M., Fersht, A. R., … Scheres, S. H. W. (2016). Design of a molecular support for cryo-EM structure determination. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1612720113","ista":"Martin TG, Bharat TAM, Joerger AC, Bai X, Praetorius FM, Fersht AR, Dietz H, Scheres SHW. 2016. Design of a molecular support for cryo-EM structure determination. PNAS. 113(47), E7456–E7463.","ieee":"T. G. Martin et al., “Design of a molecular support for cryo-EM structure determination,” PNAS, vol. 113, no. 47. Proceedings of the National Academy of Sciences, pp. E7456–E7463, 2016.","chicago":"Martin, Thomas G., Tanmay A. M. Bharat, Andreas C. Joerger, Xiao-chen Bai, Florian M Praetorius, Alan R. Fersht, Hendrik Dietz, and Sjors H. W. Scheres. “Design of a Molecular Support for Cryo-EM Structure Determination.” PNAS. Proceedings of the National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1612720113.","short":"T.G. Martin, T.A.M. Bharat, A.C. Joerger, X. Bai, F.M. Praetorius, A.R. Fersht, H. Dietz, S.H.W. Scheres, PNAS 113 (2016) E7456–E7463.","ama":"Martin TG, Bharat TAM, Joerger AC, et al. Design of a molecular support for cryo-EM structure determination. PNAS. 2016;113(47):E7456-E7463. doi:10.1073/pnas.1612720113"},"date_published":"2016-10-13T00:00:00Z","title":"Design of a molecular support for cryo-EM structure determination","quality_controlled":"1","date_created":"2023-09-06T12:53:48Z","year":"2016","article_processing_charge":"No","volume":113,"publication":"PNAS","pmid":1,"status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"issue":"47","abstract":[{"lang":"eng","text":"Despite the recent rapid progress in cryo-electron microscopy (cryo-EM), there still exist ample opportunities for improvement in sample preparation. Macromolecular complexes may disassociate or adopt nonrandom orientations against the extended air–water interface that exists for a short time before the sample is frozen. We designed a hollow support structure using 3D DNA origami to protect complexes from the detrimental effects of cryo-EM sample preparation. For a first proof-of-principle, we concentrated on the transcription factor p53, which binds to specific DNA sequences on double-stranded DNA. The support structures spontaneously form monolayers of preoriented particles in a thin film of water, and offer advantages in particle picking and sorting. By controlling the position of the binding sequence on a single helix that spans the hollow support structure, we also sought to control the orientation of individual p53 complexes. Although the latter did not yet yield the desired results, the support structures did provide partial information about the relative orientations of individual p53 complexes. We used this information to calculate a tomographic 3D reconstruction, and refined this structure to a final resolution of ∼15 Å. This structure settles an ongoing debate about the symmetry of the p53 tetramer bound to DNA."}],"doi":"10.1073/pnas.1612720113","month":"10","publication_status":"published","extern":"1","day":"13","publisher":"Proceedings of the National Academy of Sciences","intvolume":" 113","article_type":"original","page":"E7456-E7463","language":[{"iso":"eng"}]},{"month":"02","publication_status":"published","day":"06","extern":"1","status":"public","publication_identifier":{"issn":["1631-0748"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"1-2","abstract":[{"text":"Targeting protein–protein interactions has long been considered as a very difficult if impossible task, but over the past decade, front lines have moved. The number of successful examples is exponentially growing. This review presents a rapid overview of recent advances in this field considering the strengths and weaknesses of the small molecule approaches and alternative strategies such as the selection or design of artificial antibodies, peptides or peptidomimetics.","lang":"eng"},{"text":"Cibler les interactions protéine–protéine a longtemps été considéré comme une tâche très difficile, voire impossible, mais, depuis les dix dernières années, les lignes ont bougé. Le nombre d’exemples de réussites s’accroît exponentiellement. Cette revue présente un rapide panorama des avancées récentes dans ce domaine, considérant les forces et les faiblesses de l’approche « petite molécule » ainsi que des stratégies alternatives comme la sélection ou le design d’anticorps artificiels, de peptides ou de peptidomimétiques.","lang":"fre"}],"doi":"10.1016/j.crci.2015.12.004","intvolume":" 19","article_type":"original","page":"19-27","language":[{"iso":"eng"}],"publisher":"Elsevier","type":"journal_article","date_updated":"2023-02-23T13:46:55Z","oa_version":"Published Version","file":[{"relation":"main_file","checksum":"c262814ffdbfe95900256ab9ff42cdf5","creator":"dernst","file_name":"2016_ComptesRendueChimie_Bakail.pdf","file_size":2045260,"date_updated":"2021-01-22T12:36:52Z","content_type":"application/pdf","access_level":"open_access","success":1,"date_created":"2021-01-22T12:36:52Z","file_id":"9035"}],"citation":{"ieee":"M. M. Bakail and F. Ochsenbein, “Targeting protein–protein interactions, a wide open field for drug design,” Comptes Rendus Chimie, vol. 19, no. 1–2. Elsevier, pp. 19–27, 2016.","chicago":"Bakail, May M, and Francoise Ochsenbein. “Targeting Protein–Protein Interactions, a Wide Open Field for Drug Design.” Comptes Rendus Chimie. Elsevier, 2016. https://doi.org/10.1016/j.crci.2015.12.004.","short":"M.M. Bakail, F. Ochsenbein, Comptes Rendus Chimie 19 (2016) 19–27.","ama":"Bakail MM, Ochsenbein F. Targeting protein–protein interactions, a wide open field for drug design. Comptes Rendus Chimie. 2016;19(1-2):19-27. doi:10.1016/j.crci.2015.12.004","apa":"Bakail, M. M., & Ochsenbein, F. (2016). Targeting protein–protein interactions, a wide open field for drug design. Comptes Rendus Chimie. Elsevier. https://doi.org/10.1016/j.crci.2015.12.004","mla":"Bakail, May M., and Francoise Ochsenbein. “Targeting Protein–Protein Interactions, a Wide Open Field for Drug Design.” Comptes Rendus Chimie, vol. 19, no. 1–2, Elsevier, 2016, pp. 19–27, doi:10.1016/j.crci.2015.12.004.","ista":"Bakail MM, Ochsenbein F. 2016. Targeting protein–protein interactions, a wide open field for drug design. Comptes Rendus Chimie. 19(1–2), 19–27."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","author":[{"full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M","orcid":"0000-0002-9592-1587","last_name":"Bakail"},{"first_name":"Francoise","full_name":"Ochsenbein, Francoise","last_name":"Ochsenbein"}],"oa":1,"_id":"9019","file_date_updated":"2021-01-22T12:36:52Z","ddc":["570"],"date_created":"2021-01-19T11:11:54Z","year":"2016","publication":"Comptes Rendus Chimie","volume":19,"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_published":"2016-02-06T00:00:00Z","title":"Targeting protein–protein interactions, a wide open field for drug design","keyword":["General Chemistry","General Chemical Engineering"],"quality_controlled":"1"},{"date_created":"2021-02-01T13:44:00Z","volume":12,"article_processing_charge":"No","publication":"Soft Matter","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.06330"}],"year":"2016","quality_controlled":"1","title":"Dynamic self-assembly of microscale rotors and swimmers","date_published":"2016-05-28T00:00:00Z","type":"journal_article","author":[{"first_name":"Megan S.","full_name":"Davies Wykes, Megan S.","last_name":"Davies Wykes"},{"orcid":"0000-0002-7253-9465","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","last_name":"Palacci"},{"first_name":"Takuji","full_name":"Adachi, Takuji","last_name":"Adachi"},{"full_name":"Ristroph, Leif","first_name":"Leif","last_name":"Ristroph"},{"full_name":"Zhong, Xiao","first_name":"Xiao","last_name":"Zhong"},{"full_name":"Ward, Michael D.","first_name":"Michael D.","last_name":"Ward"},{"last_name":"Zhang","full_name":"Zhang, Jun","first_name":"Jun"},{"first_name":"Michael J.","full_name":"Shelley, Michael J.","last_name":"Shelley"}],"oa":1,"citation":{"ista":"Davies Wykes MS, Palacci JA, Adachi T, Ristroph L, Zhong X, Ward MD, Zhang J, Shelley MJ. 2016. Dynamic self-assembly of microscale rotors and swimmers. Soft Matter. 12(20), 4584–4589.","mla":"Davies Wykes, Megan S., et al. “Dynamic Self-Assembly of Microscale Rotors and Swimmers.” Soft Matter, vol. 12, no. 20, Royal Society of Chemistry, 2016, pp. 4584–89, doi:10.1039/c5sm03127c.","apa":"Davies Wykes, M. S., Palacci, J. A., Adachi, T., Ristroph, L., Zhong, X., Ward, M. D., … Shelley, M. J. (2016). Dynamic self-assembly of microscale rotors and swimmers. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c5sm03127c","ama":"Davies Wykes MS, Palacci JA, Adachi T, et al. Dynamic self-assembly of microscale rotors and swimmers. Soft Matter. 2016;12(20):4584-4589. doi:10.1039/c5sm03127c","short":"M.S. Davies Wykes, J.A. Palacci, T. Adachi, L. Ristroph, X. Zhong, M.D. Ward, J. Zhang, M.J. Shelley, Soft Matter 12 (2016) 4584–4589.","chicago":"Davies Wykes, Megan S., Jérémie A Palacci, Takuji Adachi, Leif Ristroph, Xiao Zhong, Michael D. Ward, Jun Zhang, and Michael J. Shelley. “Dynamic Self-Assembly of Microscale Rotors and Swimmers.” Soft Matter. Royal Society of Chemistry, 2016. https://doi.org/10.1039/c5sm03127c.","ieee":"M. S. Davies Wykes et al., “Dynamic self-assembly of microscale rotors and swimmers,” Soft Matter, vol. 12, no. 20. Royal Society of Chemistry, pp. 4584–4589, 2016."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2023-02-23T13:47:38Z","oa_version":"Preprint","_id":"9051","scopus_import":"1","external_id":{"pmid":["27121100"],"arxiv":["1509.06330"]},"article_type":"original","page":"4584-4589","intvolume":" 12","arxiv":1,"language":[{"iso":"eng"}],"publisher":"Royal Society of Chemistry","month":"05","extern":"1","day":"28","publication_status":"published","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"pmid":1,"status":"public","abstract":[{"text":"Biological systems often involve the self-assembly of basic components into complex and functioning structures. Artificial systems that mimic such processes can provide a well-controlled setting to explore the principles involved and also synthesize useful micromachines. Our experiments show that immotile, but active, components self-assemble into two types of structure that exhibit the fundamental forms of motility: translation and rotation. Specifically, micron-scale metallic rods are designed to induce extensile surface flows in the presence of a chemical fuel; these rods interact with each other and pair up to form either a swimmer or a rotor. Such pairs can transition reversibly between these two configurations, leading to kinetics reminiscent of bacterial run-and-tumble motion.","lang":"eng"}],"doi":"10.1039/c5sm03127c","issue":"20"},{"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"pmid":1,"status":"public","abstract":[{"lang":"eng","text":"We describe colloidal Janus particles with metallic and dielectric faces that swim vigorously when illuminated by defocused optical tweezers without consuming any chemical fuel. Rather than wandering randomly, these optically-activated colloidal swimmers circulate back and forth through the beam of light, tracing out sinuous rosette patterns. We propose a model for this mode of light-activated transport that accounts for the observed behavior through a combination of self-thermophoresis and optically-induced torque. In the deterministic limit, this model yields trajectories that resemble rosette curves known as hypotrochoids."}],"doi":"10.1039/c6sm01163b","issue":"30","month":"08","day":"14","extern":"1","publication_status":"published","publisher":"Royal Society of Chemistry ","article_type":"original","page":"6357-6364","intvolume":" 12","arxiv":1,"language":[{"iso":"eng"}],"_id":"9052","scopus_import":"1","external_id":{"pmid":["27338294"],"arxiv":["1609.01497"]},"type":"journal_article","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ista":"Moyses H, Palacci JA, Sacanna S, Grier DG. 2016. Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. Soft Matter. 12(30), 6357–6364.","apa":"Moyses, H., Palacci, J. A., Sacanna, S., & Grier, D. G. (2016). Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c6sm01163b","mla":"Moyses, Henrique, et al. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” Soft Matter, vol. 12, no. 30, Royal Society of Chemistry , 2016, pp. 6357–64, doi:10.1039/c6sm01163b.","ieee":"H. Moyses, J. A. Palacci, S. Sacanna, and D. G. Grier, “Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam,” Soft Matter, vol. 12, no. 30. Royal Society of Chemistry , pp. 6357–6364, 2016.","ama":"Moyses H, Palacci JA, Sacanna S, Grier DG. Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam. Soft Matter. 2016;12(30):6357-6364. doi:10.1039/c6sm01163b","short":"H. Moyses, J.A. Palacci, S. Sacanna, D.G. Grier, Soft Matter 12 (2016) 6357–6364.","chicago":"Moyses, Henrique, Jérémie A Palacci, Stefano Sacanna, and David G. Grier. “Trochoidal Trajectories of Self-Propelled Janus Particles in a Diverging Laser Beam.” Soft Matter. Royal Society of Chemistry , 2016. https://doi.org/10.1039/c6sm01163b."},"oa":1,"author":[{"full_name":"Moyses, Henrique","first_name":"Henrique","last_name":"Moyses"},{"last_name":"Palacci","first_name":"Jérémie A","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"},{"last_name":"Sacanna","full_name":"Sacanna, Stefano","first_name":"Stefano"},{"first_name":"David G.","full_name":"Grier, David G.","last_name":"Grier"}],"date_updated":"2023-02-23T13:47:40Z","oa_version":"Preprint","quality_controlled":"1","title":"Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam","date_published":"2016-08-14T00:00:00Z","keyword":["General Chemistry","Condensed Matter Physics"],"date_created":"2021-02-01T13:44:15Z","publication":"Soft Matter","article_processing_charge":"No","volume":12,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.01497"}],"year":"2016"},{"status":"public","publication_identifier":{"issn":["2169-897X","2169-8996"]},"issue":"7","doi":"10.1002/2015jd023497","abstract":[{"text":"Expected changes to future extreme precipitation remain a key uncertainty associated with anthropogenic climate change. Extreme precipitation has been proposed to scale with the precipitable water content in the atmosphere. Assuming constant relative humidity, this implies an increase of precipitation extremes at a rate of about 7% °C−1 globally as indicated by the Clausius‐Clapeyron relationship. Increases faster and slower than Clausius‐Clapeyron have also been reported. In this work, we examine the scaling between precipitation extremes and temperature in the present climate using simulations and measurements from surface weather stations collected in the frame of the HyMeX and MED‐CORDEX programs in Southern France. Of particular interest are departures from the Clausius‐Clapeyron thermodynamic expectation, their spatial and temporal distribution, and their origin. Looking at the scaling of precipitation extreme with temperature, two regimes emerge which form a hook shape: one at low temperatures (cooler than around 15°C) with rates of increase close to the Clausius‐Clapeyron rate and one at high temperatures (warmer than about 15°C) with sub‐Clausius‐Clapeyron rates and most often negative rates. On average, the region of focus does not seem to exhibit super Clausius‐Clapeyron behavior except at some stations, in contrast to earlier studies. Many factors can contribute to departure from Clausius‐Clapeyron scaling: time and spatial averaging, choice of scaling temperature (surface versus condensation level), and precipitation efficiency and vertical velocity in updrafts that are not necessarily constant with temperature. But most importantly, the dynamical contribution of orography to precipitation in the fall over this area during the so‐called “Cevenoles” events, explains the hook shape of the scaling of precipitation extremes.","lang":"eng"}],"month":"03","publication_status":"published","extern":"1","day":"16","publisher":"American Geophysical Union","intvolume":" 121","page":"3100-3119","article_type":"original","language":[{"iso":"eng"}],"_id":"9140","type":"journal_article","date_updated":"2022-01-24T13:41:02Z","oa_version":"Published Version","oa":1,"author":[{"first_name":"P.","full_name":"Drobinski, P.","last_name":"Drobinski"},{"first_name":"B.","full_name":"Alonzo, B.","last_name":"Alonzo"},{"full_name":"Bastin, S.","first_name":"S.","last_name":"Bastin"},{"full_name":"Silva, N. Da","first_name":"N. Da","last_name":"Silva"},{"last_name":"Muller","full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"P. Drobinski, B. Alonzo, S. Bastin, N. D. Silva, and C. J. Muller, “Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape?,” Journal of Geophysical Research: Atmospheres, vol. 121, no. 7. American Geophysical Union, pp. 3100–3119, 2016.","chicago":"Drobinski, P., B. Alonzo, S. Bastin, N. Da Silva, and Caroline J Muller. “Scaling of Precipitation Extremes with Temperature in the French Mediterranean Region: What Explains the Hook Shape?” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2016. https://doi.org/10.1002/2015jd023497.","ama":"Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape? Journal of Geophysical Research: Atmospheres. 2016;121(7):3100-3119. doi:10.1002/2015jd023497","short":"P. Drobinski, B. Alonzo, S. Bastin, N.D. Silva, C.J. Muller, Journal of Geophysical Research: Atmospheres 121 (2016) 3100–3119.","apa":"Drobinski, P., Alonzo, B., Bastin, S., Silva, N. D., & Muller, C. J. (2016). Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape? Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1002/2015jd023497","mla":"Drobinski, P., et al. “Scaling of Precipitation Extremes with Temperature in the French Mediterranean Region: What Explains the Hook Shape?” Journal of Geophysical Research: Atmospheres, vol. 121, no. 7, American Geophysical Union, 2016, pp. 3100–19, doi:10.1002/2015jd023497.","ista":"Drobinski P, Alonzo B, Bastin S, Silva ND, Muller CJ. 2016. Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape? Journal of Geophysical Research: Atmospheres. 121(7), 3100–3119."},"title":"Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape?","date_published":"2016-03-16T00:00:00Z","quality_controlled":"1","date_created":"2021-02-15T14:21:16Z","year":"2016","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/2015JD023497"}],"volume":121,"article_processing_charge":"No","publication":"Journal of Geophysical Research: Atmospheres"},{"month":"12","type":"journal_article","extern":"1","author":[{"first_name":"Jaqueline","full_name":"Cole, Jaqueline","last_name":"Cole"},{"last_name":"Lin","first_name":"Tzechia","full_name":"Lin, Tzechia"},{"last_name":"Ashcroft","full_name":"Ashcroft, Christopher","first_name":"Christopher"},{"first_name":"Javier","full_name":"Pérez Moreno, Javier","last_name":"Pérez Moreno"},{"full_name":"Tan, Yizhou","first_name":"Yizhou","last_name":"Tan"},{"first_name":"Perumal","full_name":"Venkatesan, Perumal","last_name":"Venkatesan"},{"last_name":"Higginbotham","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363"},{"full_name":"Pattison, Philip","first_name":"Philip","last_name":"Pattison"},{"last_name":"Edwards","first_name":"Alison","full_name":"Edwards, Alison"},{"last_name":"Piltz","first_name":"Ross","full_name":"Piltz, Ross"},{"last_name":"Clays","first_name":"Koen","full_name":"Clays, Koen"},{"first_name":"Andivelu","full_name":"Ilangovan, Andivelu","last_name":"Ilangovan"}],"day":"05","citation":{"chicago":"Cole, Jaqueline, Tzechia Lin, Christopher Ashcroft, Javier Pérez Moreno, Yizhou Tan, Perumal Venkatesan, Andrew P Higginbotham, et al. “Relating the Structure of Geminal Amido Esters to Their Molecular Hyperpolarizability.” Journal of Physical Chemistry C. American Chemical Society, 2016. https://doi.org/10.1021/acs.jpcc.6b10724.","ama":"Cole J, Lin T, Ashcroft C, et al. Relating the structure of geminal Amido Esters to their molecular hyperpolarizability. Journal of Physical Chemistry C. 2016;120(51):29439-29448. doi:10.1021/acs.jpcc.6b10724","short":"J. Cole, T. Lin, C. Ashcroft, J. Pérez Moreno, Y. Tan, P. Venkatesan, A.P. Higginbotham, P. Pattison, A. Edwards, R. Piltz, K. Clays, A. Ilangovan, Journal of Physical Chemistry C 120 (2016) 29439–29448.","ieee":"J. Cole et al., “Relating the structure of geminal Amido Esters to their molecular hyperpolarizability,” Journal of Physical Chemistry C, vol. 120, no. 51. American Chemical Society, pp. 29439–29448, 2016.","mla":"Cole, Jaqueline, et al. “Relating the Structure of Geminal Amido Esters to Their Molecular Hyperpolarizability.” Journal of Physical Chemistry C, vol. 120, no. 51, American Chemical Society, 2016, pp. 29439–48, doi:10.1021/acs.jpcc.6b10724.","apa":"Cole, J., Lin, T., Ashcroft, C., Pérez Moreno, J., Tan, Y., Venkatesan, P., … Ilangovan, A. (2016). Relating the structure of geminal Amido Esters to their molecular hyperpolarizability. Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/acs.jpcc.6b10724","ista":"Cole J, Lin T, Ashcroft C, Pérez Moreno J, Tan Y, Venkatesan P, Higginbotham AP, Pattison P, Edwards A, Piltz R, Clays K, Ilangovan A. 2016. Relating the structure of geminal Amido Esters to their molecular hyperpolarizability. Journal of Physical Chemistry C. 120(51), 29439–29448."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"J.M.C. thanks the 1851 Royal Commission of the Great Exhibition for a Design Fellowship, hosted by Argonne National Laboratory where work done was supported by the DOE Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. T.-C.L acknowledges the Taiwanese Government for a Studying Abroad Scholarship. C.M.A is indebted to the EPSRC UK for a DTA Ph.D. studentship (Grants EP/J500380/1 and EP/L504920/1). Y.T. is grateful for a Cavendish-NUDT Scholarship. The Swiss-Norwegian Collaborative Research Group at the ESRF, Grenoble, France, is thanked for access to synchrotron facilities. The OPAL reactor, ANSTO, Australia, is acknowledged for access to neutron scattering facilities via a program proposal, ID 1236. J.P-M. is grateful to Skidmore College for supporting this work via a full-year sabbatical with enhancement. All authors thank the EPSRC UK National Service for Computational Chemistry Software (NSCCS) and acknowledge contributions from its staff in supporting this work.","oa_version":"None","publication_status":"published","date_updated":"2021-01-12T08:21:55Z","_id":"92","status":"public","publist_id":"7962","abstract":[{"lang":"eng","text":"Advanced organic nonlinear optical (NLO) materials have attracted increasing attention due to their multitude of applications in modern telecommunication devices. Arguably the most important advantage of organic NLO materials, relative to traditionally used inorganic NLO materials, is their short optical response time. Geminal amido esters with their donor-π-acceptor (D-π-A) architecture exhibit high levels of electron delocalization and substantial intramolecular charge transfer, which should endow these materials with short optical response times and large molecular (hyper)polarizabilities. In order to test this hypothesis, the linear and second-order nonlinear optical properties of five geminal amido esters, (E)-ethyl 3-(X-phenylamino)-2-(Y-phenylcarbamoyl)acrylate (1, X = 4-H, Y = 4-H; 2, X = 4-CH3, Y = 4-CH3; 3, X = 4-NO2, Y = 2,5-OCH3; 4, X = 2-Cl, Y = 2-Cl; 5, X = 4-Cl, Y = 4-Cl) were synthesized and characterized, whereby NLO structure-function relationships were established including intramolecular charge transfer characteristics, crystal field effects, and molecular first hyperpolarizabilities (β). Given the typically large errors (10-30%) associated with the determination of β coefficients, three independent methods were used: (i) density functional theory, (ii) hyper-Rayleigh scattering, and (iii) high-resolution X-ray diffraction data analysis based on multipolar modeling of electron densities at each atom. These three methods delivered consistent values of β, and based on these results, 3 should hold the most promise for NLO applications. The correlation between the molecular structure of these geminal amido esters and their linear and nonlinear optical properties thus provide molecular design guidelines for organic NLO materials; this leads to the ultimate goal of generating bespoke organic molecules to suit a given NLO device application."}],"doi":"10.1021/acs.jpcc.6b10724","issue":"51","page":"29439 - 29448","date_created":"2018-12-11T11:44:35Z","intvolume":" 120","language":[{"iso":"eng"}],"volume":120,"publication":"Journal of Physical Chemistry C","year":"2016","publisher":"American Chemical Society","quality_controlled":"1","date_published":"2016-12-05T00:00:00Z","title":"Relating the structure of geminal Amido Esters to their molecular hyperpolarizability"},{"month":"07","type":"journal_article","author":[{"last_name":"Sánchez Danés","first_name":"Adriana","full_name":"Sánchez Danés, Adriana"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"full_name":"Larsimont, Jean","first_name":"Jean","last_name":"Larsimont"},{"last_name":"Liagre","full_name":"Liagre, Mélanie","first_name":"Mélanie"},{"first_name":"Khalil","full_name":"Youssef, Khalil","last_name":"Youssef"},{"last_name":"Simons","first_name":"Benjamin","full_name":"Simons, Benjamin"},{"first_name":"Cédric","full_name":"Blanpain, Cédric","last_name":"Blanpain"}],"extern":"1","citation":{"mla":"Sánchez Danés, Adriana, et al. “Defining the Clonal Dynamics Leading to Mouse Skin Tumour Initiation.” Nature, vol. 536, no. 7616, Nature Publishing Group, 2016, pp. 298–303, doi:10.1038/nature19069.","apa":"Sánchez Danés, A., Hannezo, E. B., Larsimont, J., Liagre, M., Youssef, K., Simons, B., & Blanpain, C. (2016). Defining the clonal dynamics leading to mouse skin tumour initiation. Nature. Nature Publishing Group. https://doi.org/10.1038/nature19069","ista":"Sánchez Danés A, Hannezo EB, Larsimont J, Liagre M, Youssef K, Simons B, Blanpain C. 2016. Defining the clonal dynamics leading to mouse skin tumour initiation. Nature. 536(7616), 298–303.","chicago":"Sánchez Danés, Adriana, Edouard B Hannezo, Jean Larsimont, Mélanie Liagre, Khalil Youssef, Benjamin Simons, and Cédric Blanpain. “Defining the Clonal Dynamics Leading to Mouse Skin Tumour Initiation.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature19069.","short":"A. Sánchez Danés, E.B. Hannezo, J. Larsimont, M. Liagre, K. Youssef, B. Simons, C. Blanpain, Nature 536 (2016) 298–303.","ama":"Sánchez Danés A, Hannezo EB, Larsimont J, et al. Defining the clonal dynamics leading to mouse skin tumour initiation. Nature. 2016;536(7616):298-303. doi:10.1038/nature19069","ieee":"A. Sánchez Danés et al., “Defining the clonal dynamics leading to mouse skin tumour initiation,” Nature, vol. 536, no. 7616. Nature Publishing Group, pp. 298–303, 2016."},"day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:21:59Z","acknowledgement":"We would like to thank J.-M. Vanderwinden and the LiMiF for the help with confocal microscopy. C.B. is an investigator of WELBIO. A.S.-D. and J.C.L. are supported by a fellowship of the FNRS and FRIA respectively. B.D.S. and E.H. are supported by the Wellcome Trust (grant numbers 098357/Z/12/Z and 110326/Z/15/Z). E.H. is supported by a fellowship from Trinity College, Cambridge. This work was supported by the FNRS, the IUAP program, the Fondation contre le Cancer, the ULB fondation, the foundation Bettencourt Schueller, the foundation Baillet Latour, a consolidator grant of the European Research Council.","oa_version":"None","publication_status":"published","_id":"930","status":"public","publist_id":"6508","abstract":[{"text":"The changes in cell dynamics after oncogenic mutation that lead to the development of tumours are currently unknown. Here, using skin epidermis as a model, we assessed the effect of oncogenic hedgehog signalling in distinct cell populations and their capacity to induce basal cell carcinoma, the most frequent cancer in humans. We found that only stem cells, and not progenitors, initiated tumour formation upon oncogenic hedgehog signalling. This difference was due to the hierarchical organization of tumour growth in oncogene-targeted stem cells, characterized by an increase in symmetric self-renewing divisions and a higher p53-dependent resistance to apoptosis, leading to rapid clonal expansion and progression into invasive tumours. Our work reveals that the capacity of oncogene-targeted cells to induce tumour formation is dependent not only on their long-term survival and expansion, but also on the specific clonal dynamics of the cancer cell of origin.","lang":"eng"}],"doi":"10.1038/nature19069","issue":"7616","page":"298 - 303","intvolume":" 536","date_created":"2018-12-11T11:49:15Z","language":[{"iso":"eng"}],"volume":536,"article_processing_charge":"No","publication":"Nature","year":"2016","publisher":"Nature Publishing Group","title":"Defining the clonal dynamics leading to mouse skin tumour initiation","date_published":"2016-07-08T00:00:00Z"}]