--- _id: '1371' abstract: - lang: eng text: Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure. acknowledgement: 'MZ has been supported by Polish National Science Centre Grant No. DEC-2012/07/N/NZ2/00107 and by Foundation of Polish Science award START. ' author: - first_name: Olivier full_name: Martin, Olivier last_name: Martin - first_name: André full_name: Krzywicki, André last_name: Krzywicki - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 citation: ama: 'Martin O, Krzywicki A, Zagórski MP. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 2016;17:124-158. doi:10.1016/j.plrev.2016.06.002' apa: 'Martin, O., Krzywicki, A., & Zagórski, M. P. (2016). Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.002' chicago: 'Martin, Olivier, André Krzywicki, and Marcin P Zagórski. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.002.' ieee: 'O. Martin, A. Krzywicki, and M. P. Zagórski, “Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function,” Physics of Life Reviews, vol. 17. Elsevier, pp. 124–158, 2016.' ista: 'Martin O, Krzywicki A, Zagórski MP. 2016. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 17, 124–158.' mla: 'Martin, Olivier, et al. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 124–58, doi:10.1016/j.plrev.2016.06.002.' short: O. Martin, A. Krzywicki, M.P. Zagórski, Physics of Life Reviews 17 (2016) 124–158. date_created: 2018-12-11T11:51:38Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:50:13Z day: '01' department: - _id: AnKi doi: 10.1016/j.plrev.2016.06.002 ec_funded: 1 intvolume: ' 17' language: - iso: eng month: '07' oa_version: None page: 124 - 158 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physics of Life Reviews publication_status: published publisher: Elsevier publist_id: '5840' quality_controlled: '1' scopus_import: 1 status: public title: 'Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2016' ... --- _id: '1372' abstract: - lang: eng text: Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism. acknowledgement: 'Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P' author: - first_name: Markéta full_name: Pernisová, Markéta last_name: Pernisová - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Danka full_name: Haruštiaková, Danka last_name: Haruštiaková - first_name: Martina full_name: Matonohova, Martina last_name: Matonohova - first_name: Lukáš full_name: Spíchal, Lukáš last_name: Spíchal - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko citation: ama: Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049 apa: Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049 chicago: Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14049. ieee: M. Pernisová et al., “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” New Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016. ista: Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509. mla: Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049. short: M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509. date_created: 2018-12-11T11:51:38Z date_published: 2016-10-01T00:00:00Z date_updated: 2021-01-12T06:50:13Z day: '01' ddc: - '581' department: - _id: JiFr doi: 10.1111/nph.14049 file: - access_level: open_access checksum: 27fd841ceaf0403559d7048ef51500f9 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:53Z date_updated: 2020-07-14T12:44:47Z file_id: '5108' file_name: IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf file_size: 972763 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 212' issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 497 - 509 publication: New Phytologist publication_status: published publisher: Wiley-Blackwell publist_id: '5839' pubrep_id: '1006' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 212 year: '2016' ... --- _id: '1373' article_processing_charge: No author: - first_name: Olivier full_name: Martin, Olivier last_name: Martin - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 citation: ama: 'Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 2016;17:168-171. doi:10.1016/j.plrev.2016.06.006' apa: 'Martin, O., & Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.006' chicago: 'Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.006.' ieee: 'O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function",” Physics of Life Reviews, vol. 17. Elsevier, pp. 168–171, 2016.' ista: 'Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 17, 168–171.' mla: 'Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 168–71, doi:10.1016/j.plrev.2016.06.006.' short: O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171. date_created: 2018-12-11T11:51:39Z date_published: 2016-07-01T00:00:00Z date_updated: 2022-08-26T09:39:27Z day: '01' department: - _id: AnKi doi: 10.1016/j.plrev.2016.06.006 intvolume: ' 17' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01531698 month: '07' oa: 1 oa_version: Preprint page: 168 - 171 publication: Physics of Life Reviews publication_status: published publisher: Elsevier publist_id: '5838' quality_controlled: '1' scopus_import: '1' status: public title: 'Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2016' ... --- _id: '1377' abstract: - lang: eng text: We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Thomas full_name: Pock, Thomas last_name: Pock - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257 apa: Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M1010257 chicago: Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M1010257. ieee: V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016. ista: Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636. mla: Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:10.1137/15M1010257. short: V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636. date_created: 2018-12-11T11:51:40Z date_published: 2016-05-03T00:00:00Z date_updated: 2021-01-12T06:50:15Z day: '03' department: - _id: VlKo doi: 10.1137/15M1010257 ec_funded: 1 intvolume: ' 9' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.07770 month: '05' oa: 1 oa_version: Preprint page: 605 - 636 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: SIAM Journal on Imaging Sciences publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '5834' quality_controlled: '1' scopus_import: 1 status: public title: Total variation on a tree type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2016' ... --- _id: '1378' abstract: - lang: eng text: 'We give a detailed and easily accessible proof of Gromov''s Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M.' alternative_title: - LIPIcs author: - first_name: Dominic full_name: Dotterrer, Dominic last_name: Dotterrer - first_name: Tali full_name: Kaufman, Tali last_name: Kaufman - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:35.1-35.10. doi:10.4230/LIPIcs.SoCG.2016.35' apa: 'Dotterrer, D., Kaufman, T., & Wagner, U. (2016). On expansion and topological overlap (Vol. 51, p. 35.1-35.10). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.35' chicago: Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological Overlap,” 51:35.1-35.10. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.35. ieee: 'D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 35.1-35.10.' ista: 'Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.' mla: Dotterrer, Dominic, et al. On Expansion and Topological Overlap. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10, doi:10.4230/LIPIcs.SoCG.2016.35. short: D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10. conference: end_date: 2016-06-17 location: Medford, MA, USA name: 'SoCG: Symposium on Computational Geometry' start_date: 2016-06-14 date_created: 2018-12-11T11:51:41Z date_published: 2016-06-01T00:00:00Z date_updated: 2023-09-27T12:29:56Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2016.35 file: - access_level: open_access checksum: cee65b0e722d50f9d1cc70c90ec1d59b content_type: application/pdf creator: system date_created: 2018-12-12T10:08:38Z date_updated: 2020-07-14T12:44:47Z file_id: '4699' file_name: IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf file_size: 536923 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 51' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 35.1 - 35.10 project: - _id: 25FA3206-B435-11E9-9278-68D0E5697425 grant_number: PP00P2_138948 name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics' publication_status: published publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing publist_id: '5833' pubrep_id: '623' quality_controlled: '1' related_material: record: - id: '742' relation: later_version status: public scopus_import: 1 status: public title: On expansion and topological overlap 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: 51 year: '2016' ... --- _id: '1379' abstract: - lang: eng text: We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case. alternative_title: - LIPIcs author: - first_name: Benjamin full_name: Burton, Benjamin last_name: Burton - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:24.1-24.15. doi:10.4230/LIPIcs.SoCG.2016.24' apa: 'Burton, B., de Mesmay, A. N., & Wagner, U. (2016). Finding non-orientable surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.24' chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.24. ieee: 'B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 24.1-24.15.' ista: 'Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15.' mla: Burton, Benjamin, et al. Finding Non-Orientable Surfaces in 3-Manifolds. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15, doi:10.4230/LIPIcs.SoCG.2016.24. short: B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15. conference: end_date: 2016-06-17 location: Medford, MA, USA name: 'SoCG: Symposium on Computational Geometry' start_date: 2016-06-14 date_created: 2018-12-11T11:51:41Z date_published: 2016-06-01T00:00:00Z date_updated: 2023-02-23T12:23:20Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2016.24 file: - access_level: open_access checksum: f04248a61c24297cfabd30c5f8e0deb9 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:12Z date_updated: 2020-07-14T12:44:47Z file_id: '4930' file_name: IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf file_size: 574770 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 51' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 24.1 - 24.15 publication_status: published publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing publist_id: '5832' pubrep_id: '622' quality_controlled: '1' related_material: record: - id: '534' relation: later_version status: public scopus_import: 1 status: public title: Finding non-orientable surfaces in 3-manifolds 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: 51 year: '2016' ... --- _id: '1380' abstract: - lang: eng text: We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP. article_number: '23' author: - first_name: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev - first_name: Joël full_name: Ouaknine, Joël last_name: Ouaknine - first_name: James full_name: Worrell, James last_name: Worrell citation: ama: Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. Journal of the ACM. 2016;63(3). doi:10.1145/2857050 apa: Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the complexity of the orbit problem. Journal of the ACM. ACM. https://doi.org/10.1145/2857050 chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2857050. ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” Journal of the ACM, vol. 63, no. 3. ACM, 2016. ista: Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23. mla: Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” Journal of the ACM, vol. 63, no. 3, 23, ACM, 2016, doi:10.1145/2857050. short: V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016). date_created: 2018-12-11T11:51:41Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:50:17Z day: '01' department: - _id: KrCh doi: 10.1145/2857050 intvolume: ' 63' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.2981 month: '06' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '5831' quality_controlled: '1' scopus_import: 1 status: public title: On the complexity of the orbit problem type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2016' ... --- _id: '1381' abstract: - lang: eng text: 'Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.' alternative_title: - LIPIcs author: - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:10.4230/LIPIcs.SoCG.2016.51' apa: 'Mabillard, I., & Wagner, U. (2016). Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. https://doi.org/10.4230/LIPIcs.SoCG.2016.51' chicago: Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.51. ieee: 'I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 51.1-51.12.' ista: 'Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.' mla: Mabillard, Isaac, and Uli Wagner. Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:10.4230/LIPIcs.SoCG.2016.51. short: I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12. conference: end_date: 2016-06-17 location: Medford, MA, USA name: 'SoCG: Symposium on Computational Geometry' start_date: 2016-06-14 date_created: 2018-12-11T11:51:41Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:50:17Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2016.51 file: - access_level: open_access checksum: 92c0c3735fe908f8ded6e484005cb3b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:06Z date_updated: 2020-07-14T12:44:47Z file_id: '4791' file_name: IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf file_size: 622969 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 51' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 51.1 - 51.12 project: - _id: 25FA3206-B435-11E9-9278-68D0E5697425 grant_number: PP00P2_138948 name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics' publication_status: published publisher: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH publist_id: '5830' pubrep_id: '621' quality_controlled: '1' scopus_import: 1 status: public title: Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range 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: 51 year: '2016' ... --- _id: '1382' abstract: - lang: eng text: Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales. acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for her efforts in tracking down the more obscure references. author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 citation: ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140. doi:10.1093/aob/mcw043 apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcw043 chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany. Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043. ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” Annals of Botany, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016. ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140. mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043. short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140. date_created: 2018-12-11T11:51:42Z date_published: 2016-06-01T00:00:00Z date_updated: 2024-02-21T13:49:53Z day: '1' department: - _id: NiBa doi: 10.1093/aob/mcw043 intvolume: ' 117' issue: '7' language: - iso: eng month: '06' oa_version: None page: 1133 - 1140 publication: Annals of Botany publication_status: published publisher: Oxford University Press publist_id: '5828' quality_controlled: '1' related_material: record: - id: '5550' relation: popular_science status: public scopus_import: 1 status: public title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2016' ... --- _id: '1386' abstract: - lang: eng text: We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 citation: ama: 'Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:10.1007/978-3-319-41528-4_1' apa: 'Chatterjee, K., Fu, H., & Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41528-4_1' chicago: Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. https://doi.org/10.1007/978-3-319-41528-4_1. ieee: 'K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.' ista: 'Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22.' mla: Chatterjee, Krishnendu, et al. Termination Analysis of Probabilistic Programs through Positivstellensatz’s. Vol. 9779, Springer, 2016, pp. 3–22, doi:10.1007/978-3-319-41528-4_1. short: K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22. conference: end_date: 2016-07-23 location: Toronto, Canada name: 'CAV: Computer Aided Verification' start_date: 2016-07-17 date_created: 2018-12-11T11:51:43Z date_published: 2016-07-01T00:00:00Z date_updated: 2024-03-25T23:30:18Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-319-41528-4_1 ec_funded: 1 intvolume: ' 9779' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1604.07169 month: '07' oa: 1 oa_version: Preprint page: 3 - 22 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '5824' quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: 1 status: public title: Termination analysis of probabilistic programs through Positivstellensatz's type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9779 year: '2016' ... --- _id: '1389' abstract: - lang: eng text: "The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear\r\ndifferential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision." author: - first_name: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev - first_name: Joël full_name: Ouaknine, Joël last_name: Ouaknine - first_name: James full_name: Worrell, James last_name: Worrell citation: ama: 'Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous linear dynamical systems. In: LICS ’16. IEEE; 2016:515-524. doi:10.1145/2933575.2934548' apa: 'Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On recurrent reachability for continuous linear dynamical systems. In LICS ’16 (pp. 515–524). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934548' chicago: Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” In LICS ’16, 515–24. IEEE, 2016. https://doi.org/10.1145/2933575.2934548. ieee: V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for continuous linear dynamical systems,” in LICS ’16, New York, NY, USA, 2016, pp. 515–524. ista: 'Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.' mla: Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” LICS ’16, IEEE, 2016, pp. 515–24, doi:10.1145/2933575.2934548. short: V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524. conference: end_date: 2018-07-08 location: New York, NY, USA name: 'LICS: Logic in Computer Science' start_date: 2018-07-05 date_created: 2018-12-11T11:51:44Z date_published: 2016-07-05T00:00:00Z date_updated: 2021-01-12T06:50:20Z day: '05' department: - _id: KrCh doi: 10.1145/2933575.2934548 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.03632 month: '07' oa: 1 oa_version: Preprint page: 515 - 524 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: LICS '16 publication_status: published publisher: IEEE publist_id: '5820' quality_controlled: '1' scopus_import: 1 status: public title: On recurrent reachability for continuous linear dynamical systems type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1390' abstract: - lang: eng text: "The goal of automatic program repair is to identify a set of syntactic changes that can turn a program that is incorrect with respect\r\nto a given specification into a correct one. Existing program repair techniques typically aim to find any program that meets the given specification. Such “best-effort” strategies can end up generating a program that is quite different from the original one. Novel techniques have been proposed to compute syntactically minimal program fixes, but the smallest syntactic fix to a program can still significantly alter the original program’s behaviour. We propose a new approach to program repair based on program distances, which can quantify changes not only to the program syntax but also to the program semantics. We call this the quantitative program repair problem where the “optimal” repair is derived using multiple distances. We implement a solution to the quantitative repair\r\nproblem in a prototype tool called Qlose\r\n(Quantitatively close), using the program synthesizer Sketch. We evaluate the effectiveness of different distances in obtaining desirable repairs by evaluating\r\nQlose on programs taken from educational tools such as CodeHunt and edX." alternative_title: - LNCS author: - first_name: Loris full_name: D'Antoni, Loris last_name: D'Antoni - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Rishabh full_name: Singh, Rishabh last_name: Singh citation: ama: 'D’Antoni L, Samanta R, Singh R. QLOSE: Program repair with quantitative objectives. In: Vol 9780. Springer; 2016:383-401. doi:10.1007/978-3-319-41540-6_21' apa: 'D’Antoni, L., Samanta, R., & Singh, R. (2016). QLOSE: Program repair with quantitative objectives (Vol. 9780, pp. 383–401). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_21' chicago: 'D’Antoni, Loris, Roopsha Samanta, and Rishabh Singh. “QLOSE: Program Repair with Quantitative Objectives,” 9780:383–401. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_21.' ieee: 'L. D’Antoni, R. Samanta, and R. Singh, “QLOSE: Program repair with quantitative objectives,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 383–401.' ista: 'D’Antoni L, Samanta R, Singh R. 2016. QLOSE: Program repair with quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 9780, 383–401.' mla: 'D’Antoni, Loris, et al. QLOSE: Program Repair with Quantitative Objectives. Vol. 9780, Springer, 2016, pp. 383–401, doi:10.1007/978-3-319-41540-6_21.' short: L. D’Antoni, R. Samanta, R. Singh, in:, Springer, 2016, pp. 383–401. conference: end_date: 2016-07-23 location: Toronto, Canada name: 'CAV: Computer Aided Verification' start_date: 2016-07-17 date_created: 2018-12-11T11:51:45Z date_published: 2016-07-13T00:00:00Z date_updated: 2021-01-12T06:50:21Z day: '13' department: - _id: ToHe doi: 10.1007/978-3-319-41540-6_21 ec_funded: 1 intvolume: ' 9780' language: - iso: eng month: '07' oa_version: None page: 383 - 401 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '5819' quality_controlled: '1' scopus_import: 1 status: public title: 'QLOSE: Program repair with quantitative objectives' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9780 year: '2016' ... --- _id: '1391' abstract: - lang: eng text: "We present an extension to the quantifier-free theory of integer arrays which allows us to express counting. The properties expressible in Array Folds Logic (AFL) include statements such as "the first array cell contains the array length," and "the array contains equally many minimal and maximal elements." These properties cannot be expressed in quantified fragments of the theory of arrays, nor in the theory of concatenation. Using reduction to counter machines, we show that the satisfiability problem of AFL is PSPACE-complete, and with a natural restriction the complexity decreases to NP. We also show that adding either universal quantifiers or concatenation leads to undecidability.\r\nAFL contains terms that fold a function over an array. We demonstrate that folding, a well-known concept from functional languages, allows us to concisely summarize loops that count over arrays, which occurs frequently in real-life programs. We provide a tool that can discharge proof obligations in AFL, and we demonstrate on practical examples that our decision procedure can solve a broad range of problems in symbolic testing and program verification." alternative_title: - LNCS author: - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - 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: Andrey full_name: Kupriyanov, Andrey id: 2C311BF8-F248-11E8-B48F-1D18A9856A87 last_name: Kupriyanov citation: ama: 'Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer; 2016:230-248. doi:10.1007/978-3-319-41540-6_13' apa: 'Daca, P., Henzinger, T. A., & Kupriyanov, A. (2016). Array folds logic (Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_13' chicago: Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds Logic,” 9780:230–48. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_13. ieee: 'P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 230–248.' ista: 'Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer Aided Verification, LNCS, vol. 9780, 230–248.' mla: Daca, Przemyslaw, et al. Array Folds Logic. Vol. 9780, Springer, 2016, pp. 230–48, doi:10.1007/978-3-319-41540-6_13. short: P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248. conference: end_date: 2016-07-23 location: Toronto, Canada name: 'CAV: Computer Aided Verification' start_date: 2016-07-17 date_created: 2018-12-11T11:51:45Z date_published: 2016-07-13T00:00:00Z date_updated: 2023-09-07T11:58:33Z day: '13' department: - _id: ToHe doi: 10.1007/978-3-319-41540-6_13 ec_funded: 1 intvolume: ' 9780' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1603.06850 month: '07' oa: 1 oa_version: Preprint page: 230 - 248 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '5818' quality_controlled: '1' related_material: record: - id: '1155' relation: dissertation_contains status: public scopus_import: 1 status: public title: Array folds logic type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9780 year: '2016' ... --- _id: '1394' abstract: - lang: eng text: "The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity." acknowledgement: "The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038." article_number: '036005' author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Fabrizio full_name: Capuani, Fabrizio last_name: Capuani - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino citation: ama: 'De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005' apa: 'De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005' chicago: 'De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005.' ieee: 'D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.' ista: 'De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.' mla: 'De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.' short: D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016). date_created: 2018-12-11T11:51:46Z date_published: 2016-05-27T00:00:00Z date_updated: 2021-01-12T06:50:23Z day: '27' department: - _id: GaTk doi: 10.1088/1478-3975/13/3/036005 ec_funded: 1 intvolume: ' 13' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1601.03243 month: '05' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Biology publication_status: published publisher: IOP Publishing Ltd. publist_id: '5815' quality_controlled: '1' scopus_import: 1 status: public title: 'Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2016' ... --- _id: '1396' abstract: - lang: eng text: CA3 pyramidal neurons are thought to pay a key role in memory storage and pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent excitatory synapses. To examine the induction rules of synaptic plasticity at CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute to LTP induction without requirement of a somatic action potential (AP). We next examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3 synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was symmetric and broad, with a half-width of ~150 ms. Consistent with these specific STDP induction properties, post-presynaptic sequences led to a supralinear summation of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage and recall was substantially more robust with symmetric than with asymmetric STDP rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral synapses with distinct induction rules. LTP induced by HFS may be associated with dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic activity induced LTP only if EPSP-AP were temporally very close. Together, these induction mechanisms of synaptiic plasticity may contribute to memory storage in the CA3-CA3 microcircuit at different ranges of activity. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Rajiv Kumar full_name: Mishra, Rajiv Kumar id: 46CB58F2-F248-11E8-B48F-1D18A9856A87 last_name: Mishra citation: ama: Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016. apa: Mishra, R. K. (2016). Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria. chicago: Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus.” Institute of Science and Technology Austria, 2016. ieee: R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus,” Institute of Science and Technology Austria, 2016. ista: Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria. mla: Mishra, Rajiv Kumar. Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus. Institute of Science and Technology Austria, 2016. short: R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:51:46Z date_published: 2016-03-01T00:00:00Z date_updated: 2023-09-07T11:55:26Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: PeJo file: - access_level: closed checksum: 5a010a838faf040f7064f3cfb802f743 content_type: application/pdf creator: dernst date_created: 2019-08-09T12:14:46Z date_updated: 2020-07-14T12:44:48Z file_id: '6782' file_name: Thesis_Mishra_Rajiv (Final).pdf file_size: 2407572 relation: main_file - access_level: open_access checksum: 81b26d9ede92c99f1d8cc6fa1d04cbbb content_type: application/pdf creator: dernst date_created: 2021-02-22T11:48:44Z date_updated: 2021-02-22T11:48:44Z file_id: '9183' file_name: 2016_RajivMishra_Thesis.pdf file_size: 2407572 relation: main_file success: 1 file_date_updated: 2021-02-22T11:48:44Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '83' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5811' related_material: record: - id: '1432' relation: part_of_dissertation status: public status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 title: Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '1397' abstract: - lang: eng text: 'We study partially observable Markov decision processes (POMDPs) with objectives used in verification and artificial intelligence. The qualitative analysis problem given a POMDP and an objective asks whether there is a strategy (policy) to ensure that the objective is satisfied almost surely (with probability 1), resp. with positive probability (with probability greater than 0). For POMDPs with limit-average payoff, where a reward value in the interval [0,1] is associated to every transition, and the payoff of an infinite path is the long-run average of the rewards, we consider two types of path constraints: (i) a quantitative limit-average constraint defines the set of paths where the payoff is at least a given threshold L1 = 1. Our main results for qualitative limit-average constraint under almost-sure winning are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative limit-average constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We present a prototype implementation of our EXPTIME algorithm. For POMDPs with w-regular conditions specified as parity objectives, while the qualitative analysis problems are known to be undecidable even for very special case of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. Based on our theoretical algorithms we also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of well-known POMDP examples for robotics applications. For POMDPs with a set of target states and an integer cost associated with every transition, we study the optimization objective that asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely. We show that for general integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double and exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms that extend existing algorithms for POMDPs with finite-horizon objectives. We show experimentally that it performs well in many examples of interest. We study more deeply the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a strategy to ensure that the target set is reached almost surely. While in general the problem EXPTIME-complete, in many practical cases strategies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. We first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. In this work we consider Goal DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. In the end we present a short summary of a few other results related to verification of MDPs and POMDPs.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik citation: ama: Chmelik M. Algorithms for partially observable markov decision processes. 2016. apa: Chmelik, M. (2016). Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria. chicago: Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.” Institute of Science and Technology Austria, 2016. ieee: M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016. ista: Chmelik M. 2016. Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria. mla: Chmelik, Martin. Algorithms for Partially Observable Markov Decision Processes. Institute of Science and Technology Austria, 2016. short: M. Chmelik, Algorithms for Partially Observable Markov Decision Processes, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:51:47Z date_published: 2016-02-01T00:00:00Z date_updated: 2023-09-07T11:54:58Z day: '01' degree_awarded: PhD department: - _id: KrCh language: - iso: eng month: '02' oa_version: None page: '232' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5810' status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Algorithms for partially observable markov decision processes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '1398' abstract: - lang: eng text: Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum. acknowledgement: "I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Thomas full_name: Ellis, Thomas id: 3153D6D4-F248-11E8-B48F-1D18A9856A87 last_name: Ellis orcid: 0000-0002-8511-0254 citation: ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526 apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526 chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 . ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016. ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria. mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 . short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:51:47Z date_published: 2016-02-18T00:00:00Z date_updated: 2024-02-21T13:51:39Z day: '18' ddc: - '576' degree_awarded: PhD department: - _id: NiBa doi: '10.15479/AT:ISTA:TH_526 ' file: - access_level: open_access checksum: a89b17ff27cf92c9a15f6b3d46bd7e53 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:51Z date_updated: 2020-07-14T12:44:48Z file_id: '5106' file_name: IST-2016-526-v1+1_Ellis_signed_thesis.pdf file_size: 11928241 relation: main_file file_date_updated: 2020-07-14T12:44:48Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '130' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5809' pubrep_id: '526' related_material: record: - id: '5553' relation: popular_science status: public - id: '5551' relation: popular_science status: public - id: '5552' relation: popular_science status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '14010' abstract: - lang: eng text: We report measurements of energy-dependent attosecond photoionization delays between the two outer-most valence shells of N2O and H2O. The combination of single-shot signal referencing with the use of different metal foils to filter the attosecond pulse train enables us to extract delays from congested spectra. Remarkably large delays up to 160 as are observed in N2O, whereas the delays in H2O are all smaller than 50 as in the photon-energy range of 20-40 eV. These results are interpreted by developing a theory of molecular photoionization delays. The long delays measured in N2O are shown to reflect the population of molecular shape resonances that trap the photoelectron for a duration of up to ∼110 as. The unstructured continua of H2O result in much smaller delays at the same photon energies. Our experimental and theoretical methods make the study of molecular attosecond photoionization dynamics accessible. article_number: '093001' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Martin full_name: Huppert, Martin last_name: Huppert - first_name: Inga full_name: Jordan, Inga last_name: Jordan - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Aaron full_name: von Conta, Aaron last_name: von Conta - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Huppert M, Jordan I, Baykusheva DR, von Conta A, Wörner HJ. Attosecond delays in molecular photoionization. Physical Review Letters. 2016;117(9). doi:10.1103/physrevlett.117.093001 apa: Huppert, M., Jordan, I., Baykusheva, D. R., von Conta, A., & Wörner, H. J. (2016). Attosecond delays in molecular photoionization. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.117.093001 chicago: Huppert, Martin, Inga Jordan, Denitsa Rangelova Baykusheva, Aaron von Conta, and Hans Jakob Wörner. “Attosecond Delays in Molecular Photoionization.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/physrevlett.117.093001. ieee: M. Huppert, I. Jordan, D. R. Baykusheva, A. von Conta, and H. J. Wörner, “Attosecond delays in molecular photoionization,” Physical Review Letters, vol. 117, no. 9. American Physical Society, 2016. ista: Huppert M, Jordan I, Baykusheva DR, von Conta A, Wörner HJ. 2016. Attosecond delays in molecular photoionization. Physical Review Letters. 117(9), 093001. mla: Huppert, Martin, et al. “Attosecond Delays in Molecular Photoionization.” Physical Review Letters, vol. 117, no. 9, 093001, American Physical Society, 2016, doi:10.1103/physrevlett.117.093001. short: M. Huppert, I. Jordan, D.R. Baykusheva, A. von Conta, H.J. Wörner, Physical Review Letters 117 (2016). date_created: 2023-08-10T06:37:07Z date_published: 2016-08-26T00:00:00Z date_updated: 2023-08-22T08:42:50Z day: '26' doi: 10.1103/physrevlett.117.093001 extern: '1' external_id: arxiv: - '1607.07435' pmid: - '27610849' intvolume: ' 117' issue: '9' keyword: - General Physics and Astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.07435 month: '08' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Attosecond delays in molecular photoionization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2016' ... --- _id: '14011' abstract: - lang: eng text: We introduce bicircular high-harmonic spectroscopy as a new method to probe dynamical symmetries of atoms and molecules and their evolution in time. Our approach is based on combining a circularly polarized femtosecond fundamental field of frequency ω with its counterrotating second harmonic 2ω. We demonstrate the ability of bicircular high-harmonic spectroscopy to characterize the orbital angular momentum symmetry of atomic orbitals. We further show that breaking the threefold rotational symmetry of the generating medium-at the level of either the ensemble or that of a single molecule-results in the emission of the otherwise parity-forbidden frequencies 3qω  (q∈N), which provide a background-free probe of dynamical molecular symmetries. article_number: '123001' article_processing_charge: No article_type: original author: - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: Md Sabbir full_name: Ahsan, Md Sabbir last_name: Ahsan - first_name: 'Nan' full_name: Lin, Nan last_name: Lin - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: Baykusheva DR, Ahsan MS, Lin N, Wörner HJ. Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules. Physical Review Letters. 2016;116(12). doi:10.1103/physrevlett.116.123001 apa: Baykusheva, D. R., Ahsan, M. S., Lin, N., & Wörner, H. J. (2016). Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.116.123001 chicago: Baykusheva, Denitsa Rangelova, Md Sabbir Ahsan, Nan Lin, and Hans Jakob Wörner. “Bicircular High-Harmonic Spectroscopy Reveals Dynamical Symmetries of Atoms and Molecules.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/physrevlett.116.123001. ieee: D. R. Baykusheva, M. S. Ahsan, N. Lin, and H. J. Wörner, “Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules,” Physical Review Letters, vol. 116, no. 12. American Physical Society, 2016. ista: Baykusheva DR, Ahsan MS, Lin N, Wörner HJ. 2016. Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules. Physical Review Letters. 116(12), 123001. mla: Baykusheva, Denitsa Rangelova, et al. “Bicircular High-Harmonic Spectroscopy Reveals Dynamical Symmetries of Atoms and Molecules.” Physical Review Letters, vol. 116, no. 12, 123001, American Physical Society, 2016, doi:10.1103/physrevlett.116.123001. short: D.R. Baykusheva, M.S. Ahsan, N. Lin, H.J. Wörner, Physical Review Letters 116 (2016). date_created: 2023-08-10T06:37:16Z date_published: 2016-03-25T00:00:00Z date_updated: 2023-08-22T08:44:10Z day: '25' doi: 10.1103/physrevlett.116.123001 extern: '1' external_id: pmid: - '27058077' intvolume: ' 116' issue: '12' keyword: - General Physics and Astronomy language: - iso: eng month: '03' oa_version: None pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Bicircular high-harmonic spectroscopy reveals dynamical symmetries of atoms and molecules type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 116 year: '2016' ... --- _id: '14012' abstract: - lang: eng text: Monochromatization of high-harmonic sources has opened fascinating perspectives regarding time-resolved photoemission from all phases of matter. Such studies have invariably involved the use of spectral filters or spectrally dispersive optical components that are inherently lossy and technically complex. Here we present a new technique for the spectral selection of near-threshold harmonics and their spatial separation from the driving beams without any optical elements. We discover the existence of a narrow phase-matching gate resulting from the combination of the non-collinear generation geometry in an extended medium, atomic resonances and absorption. Our technique offers a filter contrast of up to 104 for the selected harmonics against the adjacent ones and offers multiple temporally synchronized beamlets in a single unified scheme. We demonstrate the selective generation of 133, 80 or 56 nm femtosecond pulses from a 400-nm driver, which is specific to the target gas. These results open new pathways towards phase-sensitive multi-pulse spectroscopy in the vacuum- and extreme-ultraviolet, and frequency-selective output coupling from enhancement cavities. article_processing_charge: No article_type: original author: - first_name: Rajendran full_name: Rajeev, Rajendran last_name: Rajeev - first_name: Johannes full_name: Hellwagner, Johannes last_name: Hellwagner - first_name: Anne full_name: Schumacher, Anne last_name: Schumacher - first_name: Inga full_name: Jordan, Inga last_name: Jordan - first_name: Martin full_name: Huppert, Martin last_name: Huppert - first_name: Andres full_name: Tehlar, Andres last_name: Tehlar - first_name: Bhargava Ram full_name: Niraghatam, Bhargava Ram last_name: Niraghatam - first_name: Denitsa Rangelova full_name: Baykusheva, Denitsa Rangelova id: 71b4d059-2a03-11ee-914d-dfa3beed6530 last_name: Baykusheva - first_name: 'Nan' full_name: Lin, Nan last_name: Lin - first_name: Aaron full_name: von Conta, Aaron last_name: von Conta - first_name: Hans Jakob full_name: Wörner, Hans Jakob last_name: Wörner citation: ama: 'Rajeev R, Hellwagner J, Schumacher A, et al. In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses. Light: Science & Applications. 2016;5(11):e16170-e16170. doi:10.1038/lsa.2016.170' apa: 'Rajeev, R., Hellwagner, J., Schumacher, A., Jordan, I., Huppert, M., Tehlar, A., … Wörner, H. J. (2016). In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses. Light: Science & Applications. Springer Nature. https://doi.org/10.1038/lsa.2016.170' chicago: 'Rajeev, Rajendran, Johannes Hellwagner, Anne Schumacher, Inga Jordan, Martin Huppert, Andres Tehlar, Bhargava Ram Niraghatam, et al. “In Situ Frequency Gating and Beam Splitting of Vacuum- and Extreme-Ultraviolet Pulses.” Light: Science & Applications. Springer Nature, 2016. https://doi.org/10.1038/lsa.2016.170.' ieee: 'R. Rajeev et al., “In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses,” Light: Science & Applications, vol. 5, no. 11. Springer Nature, pp. e16170–e16170, 2016.' ista: 'Rajeev R, Hellwagner J, Schumacher A, Jordan I, Huppert M, Tehlar A, Niraghatam BR, Baykusheva DR, Lin N, von Conta A, Wörner HJ. 2016. In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses. Light: Science & Applications. 5(11), e16170–e16170.' mla: 'Rajeev, Rajendran, et al. “In Situ Frequency Gating and Beam Splitting of Vacuum- and Extreme-Ultraviolet Pulses.” Light: Science & Applications, vol. 5, no. 11, Springer Nature, 2016, pp. e16170–e16170, doi:10.1038/lsa.2016.170.' short: 'R. Rajeev, J. Hellwagner, A. Schumacher, I. Jordan, M. Huppert, A. Tehlar, B.R. Niraghatam, D.R. Baykusheva, N. Lin, A. von Conta, H.J. Wörner, Light: Science & Applications 5 (2016) e16170–e16170.' date_created: 2023-08-10T06:37:25Z date_published: 2016-11-01T00:00:00Z date_updated: 2023-08-22T08:46:05Z day: '01' doi: 10.1038/lsa.2016.170 extern: '1' external_id: pmid: - '30167130' intvolume: ' 5' issue: '11' keyword: - Atomic and Molecular Physics - and Optics - Electronic - Optical and Magnetic Materials language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/lsa.2016.170 month: '11' oa: 1 oa_version: Published Version page: e16170-e16170 pmid: 1 publication: 'Light: Science & Applications' publication_identifier: eissn: - 2047-7538 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: In situ frequency gating and beam splitting of vacuum- and extreme-ultraviolet pulses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2016' ...