--- _id: '1415' abstract: - lang: eng 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. author: - first_name: Florian full_name: Ferstl, Florian last_name: Ferstl - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Rüdiger full_name: Westermann, Rüdiger last_name: Westermann - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey citation: 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 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 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. 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. 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. 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. short: F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232. date_created: 2018-12-11T11:51:53Z date_published: 2016-05-01T00:00:00Z date_updated: 2023-02-21T10:38:38Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12825 file: - access_level: open_access checksum: 984afbe510ed48019025dff1dcc7baad content_type: application/pdf creator: system date_created: 2018-12-12T10:12:22Z date_updated: 2020-07-14T12:44:53Z file_id: '4940' file_name: IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf file_size: 5938324 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 35' issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 225 - 232 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5793' pubrep_id: '611' quality_controlled: '1' scopus_import: 1 status: public title: Narrow band FLIP for liquid simulations type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1416' abstract: - lang: eng 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. article_number: '195145' author: - first_name: Erik full_name: Van Loon, Erik last_name: Van Loon - first_name: Mikhail full_name: Katsnelson, Mikhail last_name: Katsnelson - first_name: Lauriane full_name: Chomaz, Lauriane last_name: Chomaz - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: 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 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 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. 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. 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. short: E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 93 (2016). date_created: 2018-12-11T11:51:54Z date_published: 2016-05-15T00:00:00Z date_updated: 2021-01-12T06:50:36Z day: '15' department: - _id: MiLe doi: 10.1103/PhysRevB.93.195145 intvolume: ' 93' issue: '19' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1603.09358 month: '05' oa: 1 oa_version: Preprint publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '5791' quality_controlled: '1' scopus_import: 1 status: public title: Interaction-driven Lifshitz transition with dipolar fermions in optical lattices type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2016' ... --- _id: '1417' abstract: - lang: eng 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. 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.) author: - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Petr full_name: Skůpa, Petr last_name: Skůpa - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Petr full_name: Klíma, Petr last_name: Klíma - first_name: Mária full_name: Čarná, Mária last_name: Čarná - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Ignacio full_name: Moreno, Ignacio last_name: Moreno - first_name: Petre full_name: Dobrev, Petre last_name: Dobrev - first_name: Ariel full_name: Orellana, Ariel last_name: Orellana - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 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 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 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. 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. date_created: 2018-12-11T11:51:54Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:36Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1111/nph.14019 file: - access_level: open_access checksum: 23522ced3508ffe7a4f247c4230e6493 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:32Z date_updated: 2020-07-14T12:44:53Z file_id: '5016' file_name: IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf file_size: 3828383 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 211' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 65 - 74 publication: New Phytologist publication_status: published publisher: Wiley-Blackwell publist_id: '5790' pubrep_id: '1004' quality_controlled: '1' scopus_import: 1 status: public title: PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 211 year: '2016' ... --- _id: '1419' abstract: - lang: eng 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. article_number: '175701' author: - first_name: Andrzej full_name: Tomski, Andrzej last_name: Tomski - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 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' 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' 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.' 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.' short: 'A. Tomski, J. Kaczmarczyk, Journal of Physics: Condensed Matter 28 (2016).' date_created: 2018-12-11T11:51:55Z date_published: 2016-03-29T00:00:00Z date_updated: 2021-01-12T06:50:36Z day: '29' department: - _id: MiLe doi: 10.1088/0953-8984/28/17/175701 ec_funded: 1 intvolume: ' 28' issue: '17' language: - iso: eng month: '03' oa_version: None project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Journal of Physics: Condensed Matter' publication_status: published publisher: IOP Publishing Ltd. publist_id: '5788' quality_controlled: '1' scopus_import: 1 status: public title: 'Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2016' ... --- _id: '1420' 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. ' article_processing_charge: No arxiv: 1 author: - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: 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 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 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. 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. ista: Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548. 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. short: K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548. date_created: 2018-12-11T11:51:55Z date_published: 2016-04-06T00:00:00Z date_updated: 2025-05-28T11:42:47Z day: '06' department: - _id: GaTk - _id: NiBa doi: 10.1534/genetics.115.184127 ec_funded: 1 external_id: arxiv: - '1510.08344' intvolume: ' 202' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.08344 month: '04' oa: 1 oa_version: Preprint page: 1523 - 1548 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 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5787' quality_controlled: '1' scopus_import: '1' status: public title: A general approximation for the dynamics of quantitative traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1421' abstract: - lang: eng 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.' author: - first_name: Stanley full_name: Bak, Stanley last_name: Bak - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Taylor full_name: Johnson, Taylor last_name: Johnson - first_name: Pradyot full_name: Prakash, Pradyot last_name: Prakash citation: 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' 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' 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. 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.' 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.' mla: Bak, Stanley, et al. Scalable Static Hybridization Methods for Analysis of Nonlinear Systems. Springer, 2016, pp. 155–64, doi:10.1145/2883817.2883837. short: S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164. conference: end_date: 2016-04-14 location: Vienna, Austria name: 'HSCC 2016: International Conference on Hybrid Systems: Computation and Control' start_date: 2016-04-12 date_created: 2018-12-11T11:51:55Z date_published: 2016-04-11T00:00:00Z date_updated: 2021-01-12T06:50:37Z day: '11' department: - _id: ToHe doi: 10.1145/2883817.2883837 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 155 - 164 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5786' quality_controlled: '1' scopus_import: 1 status: public title: Scalable static hybridization methods for analysis of nonlinear systems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1422' 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. acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). ' article_processing_charge: Yes (via OA deal) author: - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: 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 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. 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. 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. 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. short: R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923. date_created: 2018-12-11T11:51:56Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:38Z day: '01' ddc: - '510' - '530' department: - _id: RoSe doi: 10.1007/s11005-016-0847-5 file: - access_level: open_access checksum: fb404923d8ca9a1faeb949561f26cbea content_type: application/pdf creator: system date_created: 2018-12-12T10:15:57Z date_updated: 2020-07-14T12:44:53Z file_id: '5181' file_name: IST-2016-591-v1+1_s11005-016-0847-5.pdf file_size: 458968 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 106' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 913 - 923 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 - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '5785' pubrep_id: '591' quality_controlled: '1' scopus_import: 1 status: public title: Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 106 year: '2016' ... --- _id: '1423' 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.' acknowledgement: C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475. article_number: '25676' author: - first_name: Seung full_name: Baek, Seung last_name: Baek - first_name: Hyeongchai full_name: Jeong, Hyeongchai last_name: Jeong - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: 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 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 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. 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. ista: Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676. 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. short: S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016). date_created: 2018-12-11T11:51:56Z date_published: 2016-05-10T00:00:00Z date_updated: 2021-01-12T06:50:38Z day: '10' ddc: - '000' department: - _id: KrCh doi: 10.1038/srep25676 file: - access_level: open_access checksum: ee17c482370d2e1b3add393710d3c696 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:08Z date_updated: 2020-07-14T12:44:53Z file_id: '5327' file_name: IST-2016-590-v1+1_srep25676.pdf file_size: 1349915 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '5784' pubrep_id: '590' quality_controlled: '1' scopus_import: 1 status: public title: Comparing reactive and memory-one strategies of direct reciprocity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2016' ... --- _id: '1426' 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.' acknowledgement: C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475. article_number: '160036' author: - first_name: Maria full_name: Chakra, Maria last_name: Chakra - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Arne full_name: Traulsen, Arne last_name: Traulsen citation: 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 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 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. 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. 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. 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. short: M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016). date_created: 2018-12-11T11:51:57Z date_published: 2016-05-01T00:00:00Z date_updated: 2021-01-12T06:50:39Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1098/rsos.160036 file: - access_level: open_access checksum: bf84211b31fe87451e738ba301d729c3 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:49Z date_updated: 2020-07-14T12:44:53Z file_id: '5104' file_name: IST-2016-589-v1+1_160036.full.pdf file_size: 937002 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 3' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Royal Society Open Science publication_status: published publisher: Royal Society, The publist_id: '5776' pubrep_id: '589' quality_controlled: '1' scopus_import: 1 status: public title: Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2016' ... --- _id: '1427' abstract: - lang: eng 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. author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Anaisa full_name: Moreno, Anaisa last_name: Moreno - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: 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 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 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. 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. 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. 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. short: M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769. date_created: 2018-12-11T11:51:57Z date_published: 2016-03-01T00:00:00Z date_updated: 2021-01-12T06:50:39Z day: '01' ddc: - '570' - '576' department: - _id: CaGu - _id: JoBo doi: 10.1093/molbev/msv269 ec_funded: 1 file: - access_level: open_access checksum: 1f456ce1d2aa2f67176a1709f9702ecf content_type: application/pdf creator: system date_created: 2018-12-12T10:09:27Z date_updated: 2020-07-14T12:44:53Z file_id: '4751' file_name: IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf file_size: 648115 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 33' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 761 - 769 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5772' pubrep_id: '588' quality_controlled: '1' scopus_import: 1 status: public title: Epistatic interactions in the arabinose cis-regulatory element tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2016' ... --- _id: '1428' 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. article_number: '012016' author: - first_name: Martin full_name: Könenberg, Martin last_name: Könenberg - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason 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' 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' 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.' 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.' short: 'M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing Ltd., 2016.' conference: end_date: 2015-08-25 location: Shanghai, China name: 24th International Laser Physics Workshop (LPHYS'15) start_date: 2015-08-21 date_created: 2018-12-11T11:51:58Z date_published: 2016-03-07T00:00:00Z date_updated: 2021-01-12T06:50:40Z day: '07' ddc: - '510' - '530' department: - _id: RoSe doi: 10.1088/1742-6596/691/1/012016 file: - access_level: open_access checksum: 109db801749072c3f6c8f1a1848700fa content_type: application/pdf creator: system date_created: 2018-12-12T10:10:55Z date_updated: 2020-07-14T12:44:53Z file_id: '4847' file_name: IST-2016-585-v1+1_JPCS_691_1_012016.pdf file_size: 1434688 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 691' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version 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 publication: 'Journal of Physics: Conference Series' publication_status: published publisher: IOP Publishing Ltd. publist_id: '5770' pubrep_id: '585' quality_controlled: '1' scopus_import: 1 status: public title: Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 691 year: '2016' ... --- _id: '1429' 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. 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. article_number: 11332 (2016) author: - first_name: Chad full_name: Husko, Chad last_name: Husko - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Simon full_name: Lefrançois, Simon last_name: Lefrançois - first_name: Sylvain full_name: Combrié, Sylvain last_name: Combrié - first_name: Gaëlle full_name: Lehoucq, Gaëlle last_name: Lehoucq - first_name: Alfredo full_name: De Rossi, Alfredo last_name: De Rossi - first_name: Benjamin full_name: Eggleton, Benjamin last_name: Eggleton - first_name: Laurens full_name: Kuipers, Laurens last_name: Kuipers citation: 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 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 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. 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. 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. short: C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:58Z date_published: 2016-04-15T00:00:00Z date_updated: 2021-01-12T06:50:40Z day: '15' ddc: - '530' department: - _id: JoFi doi: 10.1038/ncomms11332 file: - access_level: open_access checksum: 6484fa81a2e52e4fdd7935e1ae6091d4 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:53Z date_updated: 2020-07-14T12:44:53Z file_id: '5177' file_name: IST-2016-583-v1+1_ncomms11332.pdf file_size: 965176 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5769' pubrep_id: '583' quality_controlled: '1' scopus_import: 1 status: public title: Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '14302' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Evi full_name: Stahl, Evi last_name: Stahl - first_name: Florian M full_name: Praetorius, Florian M id: dfec9381-4341-11ee-8fd8-faa02bba7d62 last_name: Praetorius - first_name: Carina C. full_name: de Oliveira Mann, Carina C. last_name: de Oliveira Mann - first_name: Karl-Peter full_name: Hopfner, Karl-Peter last_name: Hopfner - first_name: Hendrik full_name: Dietz, Hendrik last_name: Dietz citation: 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 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 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. short: E. Stahl, F.M. Praetorius, C.C. de Oliveira Mann, K.-P. Hopfner, H. Dietz, ACS Nano 10 (2016) 9156–9164. date_created: 2023-09-06T12:52:00Z date_published: 2016-09-01T00:00:00Z date_updated: 2023-11-07T12:08:46Z day: '01' doi: 10.1021/acsnano.6b04787 extern: '1' external_id: pmid: - '27583560' intvolume: ' 10' issue: '10' language: - iso: eng month: '09' oa_version: None page: 9156-9164 pmid: 1 publication: ACS Nano publication_identifier: eissn: - 1936-086X issn: - 1936-0851 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Impact of heterogeneity and lattice bond strength on DNA triangle crystal growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2016' ... --- _id: '14304' 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. article_processing_charge: No article_type: original author: - first_name: Thomas G. full_name: Martin, Thomas G. last_name: Martin - first_name: Tanmay A. M. full_name: Bharat, Tanmay A. M. last_name: Bharat - first_name: Andreas C. full_name: Joerger, Andreas C. last_name: Joerger - first_name: Xiao-chen full_name: Bai, Xiao-chen last_name: Bai - first_name: Florian M full_name: Praetorius, Florian M id: dfec9381-4341-11ee-8fd8-faa02bba7d62 last_name: Praetorius - first_name: Alan R. full_name: Fersht, 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 citation: 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 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 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. 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. 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. 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. 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. date_created: 2023-09-06T12:53:48Z date_published: 2016-10-13T00:00:00Z date_updated: 2023-11-07T11:53:06Z day: '13' doi: 10.1073/pnas.1612720113 extern: '1' external_id: pmid: - '27821763' intvolume: ' 113' issue: '47' language: - iso: eng month: '10' oa_version: Published Version page: E7456-E7463 pmid: 1 publication: PNAS publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Design of a molecular support for cryo-EM structure determination type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2016' ... --- _id: '9019' abstract: - lang: eng 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: fre 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. article_processing_charge: No article_type: original author: - first_name: May M full_name: Bakail, May M id: FB3C3F8E-522F-11EA-B186-22963DDC885E last_name: Bakail orcid: 0000-0002-9592-1587 - first_name: Francoise full_name: Ochsenbein, Francoise last_name: Ochsenbein citation: 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 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. 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. 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. 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. short: M.M. Bakail, F. Ochsenbein, Comptes Rendus Chimie 19 (2016) 19–27. date_created: 2021-01-19T11:11:54Z date_published: 2016-02-06T00:00:00Z date_updated: 2023-02-23T13:46:55Z day: '06' ddc: - '570' doi: 10.1016/j.crci.2015.12.004 extern: '1' file: - access_level: open_access checksum: c262814ffdbfe95900256ab9ff42cdf5 content_type: application/pdf creator: dernst date_created: 2021-01-22T12:36:52Z date_updated: 2021-01-22T12:36:52Z file_id: '9035' file_name: 2016_ComptesRendueChimie_Bakail.pdf file_size: 2045260 relation: main_file success: 1 file_date_updated: 2021-01-22T12:36:52Z has_accepted_license: '1' intvolume: ' 19' issue: 1-2 keyword: - General Chemistry - General Chemical Engineering language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 19-27 publication: Comptes Rendus Chimie publication_identifier: issn: - 1631-0748 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Targeting protein–protein interactions, a wide open field for drug design tmp: image: /images/cc_by_nc_nd.png 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) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2016' ... --- _id: '9051' abstract: - lang: eng 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.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Megan S. full_name: Davies Wykes, Megan S. last_name: Davies Wykes - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Takuji full_name: Adachi, Takuji last_name: Adachi - first_name: Leif full_name: Ristroph, Leif last_name: Ristroph - first_name: Xiao full_name: Zhong, Xiao last_name: Zhong - first_name: Michael D. full_name: Ward, Michael D. last_name: Ward - first_name: Jun full_name: Zhang, Jun last_name: Zhang - first_name: Michael J. full_name: Shelley, Michael J. last_name: Shelley citation: 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 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 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. 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. 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. date_created: 2021-02-01T13:44:00Z date_published: 2016-05-28T00:00:00Z date_updated: 2023-02-23T13:47:38Z day: '28' doi: 10.1039/c5sm03127c extern: '1' external_id: arxiv: - '1509.06330' pmid: - '27121100' intvolume: ' 12' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.06330 month: '05' oa: 1 oa_version: Preprint page: 4584-4589 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Dynamic self-assembly of microscale rotors and swimmers type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 12 year: '2016' ... --- _id: '9052' 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. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Henrique full_name: Moyses, Henrique last_name: Moyses - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 - first_name: Stefano full_name: Sacanna, Stefano last_name: Sacanna - first_name: David G. full_name: Grier, David G. last_name: Grier citation: 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 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 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. 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. 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. 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. short: H. Moyses, J.A. Palacci, S. Sacanna, D.G. Grier, Soft Matter 12 (2016) 6357–6364. date_created: 2021-02-01T13:44:15Z date_published: 2016-08-14T00:00:00Z date_updated: 2023-02-23T13:47:40Z day: '14' doi: 10.1039/c6sm01163b extern: '1' external_id: arxiv: - '1609.01497' pmid: - '27338294' intvolume: ' 12' issue: '30' keyword: - General Chemistry - Condensed Matter Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1609.01497 month: '08' oa: 1 oa_version: Preprint page: 6357-6364 pmid: 1 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' scopus_import: '1' status: public title: Trochoidal trajectories of self-propelled Janus particles in a diverging laser beam type: journal_article user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 12 year: '2016' ... --- _id: '9140' abstract: - lang: eng 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.' article_processing_charge: No article_type: original author: - first_name: P. full_name: Drobinski, P. last_name: Drobinski - first_name: B. full_name: Alonzo, B. last_name: Alonzo - first_name: S. full_name: Bastin, S. last_name: Bastin - first_name: N. Da full_name: Silva, N. Da last_name: Silva - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 citation: 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' 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' 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.' 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.' 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.' 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.' short: 'P. Drobinski, B. Alonzo, S. Bastin, N.D. Silva, C.J. Muller, Journal of Geophysical Research: Atmospheres 121 (2016) 3100–3119.' date_created: 2021-02-15T14:21:16Z date_published: 2016-03-16T00:00:00Z date_updated: 2022-01-24T13:41:02Z day: '16' doi: 10.1002/2015jd023497 extern: '1' intvolume: ' 121' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/2015JD023497 month: '03' oa: 1 oa_version: Published Version page: 3100-3119 publication: 'Journal of Geophysical Research: Atmospheres' publication_identifier: issn: - 2169-897X - 2169-8996 publication_status: published publisher: American Geophysical Union quality_controlled: '1' status: public title: 'Scaling of precipitation extremes with temperature in the French Mediterranean region: What explains the hook shape?' type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 121 year: '2016' ... --- _id: '92' 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.' 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. author: - first_name: Jaqueline full_name: Cole, Jaqueline last_name: Cole - first_name: Tzechia full_name: Lin, Tzechia last_name: Lin - first_name: Christopher full_name: Ashcroft, Christopher last_name: Ashcroft - first_name: Javier full_name: Pérez Moreno, Javier last_name: Pérez Moreno - first_name: Yizhou full_name: Tan, Yizhou last_name: Tan - first_name: Perumal full_name: Venkatesan, Perumal last_name: Venkatesan - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Philip full_name: Pattison, Philip last_name: Pattison - first_name: Alison full_name: Edwards, Alison last_name: Edwards - first_name: Ross full_name: Piltz, Ross last_name: Piltz - first_name: Koen full_name: Clays, Koen last_name: Clays - first_name: Andivelu full_name: Ilangovan, Andivelu last_name: Ilangovan citation: 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 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 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. 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. 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. 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. 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. date_created: 2018-12-11T11:44:35Z date_published: 2016-12-05T00:00:00Z date_updated: 2021-01-12T08:21:55Z day: '05' doi: 10.1021/acs.jpcc.6b10724 extern: '1' intvolume: ' 120' issue: '51' language: - iso: eng month: '12' oa_version: None page: 29439 - 29448 publication: Journal of Physical Chemistry C publication_status: published publisher: American Chemical Society publist_id: '7962' quality_controlled: '1' status: public title: Relating the structure of geminal Amido Esters to their molecular hyperpolarizability type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 120 year: '2016' ... --- _id: '930' abstract: - lang: eng 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. 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. article_processing_charge: No author: - first_name: Adriana full_name: Sánchez Danés, Adriana last_name: Sánchez Danés - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Jean full_name: Larsimont, Jean last_name: Larsimont - first_name: Mélanie full_name: Liagre, Mélanie last_name: Liagre - first_name: Khalil full_name: Youssef, Khalil last_name: Youssef - first_name: Benjamin full_name: Simons, Benjamin last_name: Simons - first_name: Cédric full_name: Blanpain, Cédric last_name: Blanpain citation: 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 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 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. 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. 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. 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. short: A. Sánchez Danés, E.B. Hannezo, J. Larsimont, M. Liagre, K. Youssef, B. Simons, C. Blanpain, Nature 536 (2016) 298–303. date_created: 2018-12-11T11:49:15Z date_published: 2016-07-08T00:00:00Z date_updated: 2021-01-12T08:21:59Z day: '08' doi: 10.1038/nature19069 extern: '1' intvolume: ' 536' issue: '7616' language: - iso: eng month: '07' oa_version: None page: 298 - 303 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '6508' status: public title: Defining the clonal dynamics leading to mouse skin tumour initiation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 536 year: '2016' ...