--- _id: '1408' abstract: - lang: eng text: 'The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status.' acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). ' article_processing_charge: Yes (via OA deal) author: - first_name: Peter full_name: Franek, Peter id: 473294AE-F248-11E8-B48F-1D18A9856A87 last_name: Franek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál citation: ama: Franek P, Krcál M. On computability and triviality of well groups. Discrete & Computational Geometry. 2016;56(1):126-164. doi:10.1007/s00454-016-9794-2 apa: Franek, P., & Krcál, M. (2016). On computability and triviality of well groups. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9794-2 chicago: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry. Springer, 2016. https://doi.org/10.1007/s00454-016-9794-2. ieee: P. Franek and M. Krcál, “On computability and triviality of well groups,” Discrete & Computational Geometry, vol. 56, no. 1. Springer, pp. 126–164, 2016. ista: Franek P, Krcál M. 2016. On computability and triviality of well groups. Discrete & Computational Geometry. 56(1), 126–164. mla: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry, vol. 56, no. 1, Springer, 2016, pp. 126–64, doi:10.1007/s00454-016-9794-2. short: P. Franek, M. Krcál, Discrete & Computational Geometry 56 (2016) 126–164. date_created: 2018-12-11T11:51:51Z date_published: 2016-07-01T00:00:00Z date_updated: 2023-02-23T10:02:11Z day: '01' ddc: - '510' department: - _id: UlWa - _id: HeEd doi: 10.1007/s00454-016-9794-2 ec_funded: 1 file: - access_level: open_access checksum: e0da023abf6b72abd8c6a8c76740d53c content_type: application/pdf creator: system date_created: 2018-12-12T10:10:55Z date_updated: 2020-07-14T12:44:53Z file_id: '4846' file_name: IST-2016-614-v1+1_s00454-016-9794-2.pdf file_size: 905303 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 56' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 126 - 164 project: - _id: 25F8B9BC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M01980 name: Robust invariants of Nonlinear Systems - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5799' pubrep_id: '614' quality_controlled: '1' related_material: record: - id: '1510' relation: earlier_version status: public scopus_import: 1 status: public title: On computability and triviality of well groups 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: 56 year: '2016' ... --- _id: '1409' author: - first_name: Richard full_name: Abbott, Richard last_name: Abbott - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jeffrey full_name: Good, Jeffrey last_name: Good citation: ama: Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685 apa: Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.13685 chicago: Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell, 2016. https://doi.org/10.1111/mec.13685. ieee: R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016. ista: Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332. mla: Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:10.1111/mec.13685. short: R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332. date_created: 2018-12-11T11:51:51Z date_published: 2016-06-08T00:00:00Z date_updated: 2021-01-12T06:50:33Z day: '08' ddc: - '576' department: - _id: NiBa doi: 10.1111/mec.13685 file: - access_level: open_access checksum: ede7d0b8a471754f71f17e2b20f3135b content_type: application/pdf creator: system date_created: 2018-12-12T10:10:12Z date_updated: 2020-07-14T12:44:53Z file_id: '4797' file_name: IST-2017-772-v1+1_AbbotEtAl2016-3.pdf file_size: 226137 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 25' issue: '11' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 2325 - 2332 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '5798' pubrep_id: '772' quality_controlled: '1' scopus_import: 1 status: public title: Genomics of hybridization and its evolutionary consequences type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2016' ... --- _id: '1410' abstract: - lang: eng text: The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis. acknowledgement: the Odysseus Program of the Research Foundation-Flanders [G091608] to JF. author: - first_name: José full_name: Ugalde, José last_name: Ugalde - first_name: Cecilia full_name: Rodríguez Furlán, Cecilia last_name: Rodríguez Furlán - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Lorena full_name: Norambuena, Lorena last_name: Norambuena - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Gabriel full_name: León, Gabriel last_name: León - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos citation: ama: Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014 apa: Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014 chicago: Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014. ieee: J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016. ista: Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19. mla: Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014. short: J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19. date_created: 2018-12-11T11:51:51Z date_published: 2016-09-01T00:00:00Z date_updated: 2021-01-12T06:50:33Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1016/j.plantsci.2016.05.014 external_id: pmid: - '27457979' file: - access_level: open_access checksum: ca08de036e6ddc81e6f760e0ccdebd3f content_type: application/pdf creator: dernst date_created: 2019-04-17T07:41:57Z date_updated: 2020-07-14T12:44:53Z file_id: '6331' file_name: 2016_PlantScience_Ugalde.pdf file_size: 4338545 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 250' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 10 - 19 pmid: 1 publication: Plant Science publication_status: published publisher: Elsevier publist_id: '5797' pubrep_id: '1005' quality_controlled: '1' scopus_import: 1 status: public title: Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 250 year: '2016' ... --- _id: '1411' abstract: - lang: eng text: We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn on a compact two-dimensional surface M with boundary. Each αi and each βj is either an arc meeting the boundary of M at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise such that the total number of crossings of the ai with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. The proofs rely, among other things, on a result concerning simultaneous planar drawings of graphs by Erten and Kobourov. acknowledgement: 'Supported by the ERC Adv anced Grant No. 267165. ' author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Eric full_name: Sedgwick, Eric last_name: Sedgwick - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 2016;212(1):37-79. doi:10.1007/s11856-016-1294-9 apa: Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2016). Untangling two systems of noncrossing curves. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1294-9 chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1294-9. ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems of noncrossing curves,” Israel Journal of Mathematics, vol. 212, no. 1. Springer, pp. 37–79, 2016. ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2016. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 212(1), 37–79. mla: Matoušek, Jiří, et al. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics, vol. 212, no. 1, Springer, 2016, pp. 37–79, doi:10.1007/s11856-016-1294-9. short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Israel Journal of Mathematics 212 (2016) 37–79. date_created: 2018-12-11T11:51:52Z date_published: 2016-05-01T00:00:00Z date_updated: 2023-02-23T10:34:31Z day: '01' department: - _id: UlWa doi: 10.1007/s11856-016-1294-9 intvolume: ' 212' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1302.6475 month: '05' oa: 1 oa_version: Preprint page: 37 - 79 project: - _id: 25FA3206-B435-11E9-9278-68D0E5697425 grant_number: PP00P2_138948 name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics' publication: Israel Journal of Mathematics publication_status: published publisher: Springer publist_id: '5796' quality_controlled: '1' related_material: record: - id: '2244' relation: earlier_version status: public scopus_import: 1 status: public title: Untangling two systems of noncrossing curves type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 212 year: '2016' ... --- _id: '1412' abstract: - lang: eng text: Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods. acknowledgement: 'This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ' author: - first_name: Ryan full_name: Goldade, Ryan last_name: Goldade - first_name: Christopher full_name: Batty, Christopher last_name: Batty - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826 apa: Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826 chicago: Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826. ieee: R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 233–242, 2016. ista: Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242. mla: Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 233–42, doi:10.1111/cgf.12826. short: R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242. date_created: 2018-12-11T11:51:52Z date_published: 2016-05-27T00:00:00Z date_updated: 2023-02-21T10:38:30Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12826 ec_funded: 1 file: - access_level: open_access checksum: 8e61387ee2e3bd0e776fbe301629bfd9 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:18Z date_updated: 2020-07-14T12:44:53Z file_id: '5000' file_name: IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf file_size: 15873858 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: 233 - 242 project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5795' pubrep_id: '612' quality_controlled: '1' scopus_import: 1 status: public title: A practical method for high-resolution embedded liquid surfaces type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1413' abstract: - lang: eng text: This paper generalizes the well-known Diffusion Curves Images (DCI), which are composed of a set of Bezier curves with colors specified on either side. These colors are diffused as Laplace functions over the image domain, which results in smooth color gradients interrupted by the Bezier curves. Our new formulation allows for more color control away from the boundary, providing a similar expressive power as recent Bilaplace image models without introducing associated issues and computational costs. The new model is based on a special Laplace function blending and a new edge blur formulation. We demonstrate that given some user-defined boundary curves over an input raster image, fitting colors and edge blur from the image to the new model and subsequent editing and animation is equally convenient as with DCIs. Numerous examples and comparisons to DCIs are presented. author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke citation: ama: 'Jeschke S. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 2016;35(2):71-79. doi:10.1111/cgf.12812' apa: 'Jeschke, S. (2016). Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12812' chicago: 'Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12812.' ieee: 'S. Jeschke, “Generalized diffusion curves: An improved vector representation for smooth-shaded images,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 71–79, 2016.' ista: 'Jeschke S. 2016. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 35(2), 71–79.' mla: 'Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 71–79, doi:10.1111/cgf.12812.' short: S. Jeschke, Computer Graphics Forum 35 (2016) 71–79. date_created: 2018-12-11T11:51:53Z date_published: 2016-05-01T00:00:00Z date_updated: 2021-01-12T06:50:34Z day: '01' department: - _id: ChWo doi: 10.1111/cgf.12812 intvolume: ' 35' issue: '2' language: - iso: eng month: '05' oa_version: None page: 71 - 79 project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5794' quality_controlled: '1' scopus_import: 1 status: public title: 'Generalized diffusion curves: An improved vector representation for smooth-shaded images' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _id: '1414' abstract: - lang: eng text: In this paper, we present a method to model hyperelasticity that is well suited for representing the nonlinearity of real-world objects, as well as for estimating it from deformation examples. Previous approaches suffer several limitations, such as lack of integrability of elastic forces, failure to enforce energy convexity, lack of robustness of parameter estimation, or difficulty to model cross-modal effects. Our method avoids these problems by relying on a general energy-based definition of elastic properties. The accuracy of the resulting elastic model is maximized by defining an additive model of separable energy terms, which allow progressive parameter estimation. In addition, our method supports efficient modeling of extreme nonlinearities thanks to energy-limiting constraints. We combine our energy-based model with an optimization method to estimate model parameters from force-deformation examples, and we show successful modeling of diverse deformable objects, including cloth, human finger skin, and internal human anatomy in a medical imaging application. acknowledgement: This work was funded in part by grants from the Spanish Ministry of Economy (TIN2012-35840), the European Research Council (ERC Starting Grant no. 280135 Animetrics), and the EU FP7 (project no. 601165 WEARHAP). author: - first_name: Eder full_name: Miguel Villalba, Eder id: 3FB91342-F248-11E8-B48F-1D18A9856A87 last_name: Miguel Villalba - first_name: David full_name: Miraut, David last_name: Miraut - first_name: Miguel full_name: Otaduy, Miguel last_name: Otaduy citation: ama: Miguel Villalba E, Miraut D, Otaduy M. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 2016;35(2):385-396. doi:10.1111/cgf.12840 apa: Miguel Villalba, E., Miraut, D., & Otaduy, M. (2016). Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12840 chicago: Miguel Villalba, Eder, David Miraut, and Miguel Otaduy. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12840. ieee: E. Miguel Villalba, D. Miraut, and M. Otaduy, “Modeling and estimation of energy-based hyperelastic objects,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 385–396, 2016. ista: Miguel Villalba E, Miraut D, Otaduy M. 2016. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 35(2), 385–396. mla: Miguel Villalba, Eder, et al. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 385–96, doi:10.1111/cgf.12840. short: E. Miguel Villalba, D. Miraut, M. Otaduy, Computer Graphics Forum 35 (2016) 385–396. date_created: 2018-12-11T11:51:53Z date_published: 2016-05-01T00:00:00Z date_updated: 2021-01-12T06:50:35Z day: '01' department: - _id: BeBi doi: 10.1111/cgf.12840 intvolume: ' 35' issue: '2' language: - iso: eng month: '05' oa_version: None page: 385 - 396 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5792' quality_controlled: '1' scopus_import: 1 status: public title: Modeling and estimation of energy-based hyperelastic objects type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2016' ... --- _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' ...