--- OA_place: repository OA_type: green _id: '22052' abstract: - lang: eng text: 'We consider the focusing cubic nonlinear Schrödinger equation (NLS) in the exterior Ω of a smooth, compact, strictly convex obstacle in three dimensions. We prove that the threshold for global existence and scattering is the same as for the problem posed on Euclidean space. Specifically, we prove that if E(u0)M(u0)Applied Mathematics Research eXpress. 2016;2016(1):146-180. doi:10.1093/amrx/abv012 apa: Killip, R., Vişan, M., & Zhang, X. (2016). The focusing cubic NLS on exterior domains in three dimensions. Applied Mathematics Research EXpress. Oxford University Press. https://doi.org/10.1093/amrx/abv012 chicago: Killip, Rowan, Monica Vişan, and Xiaoyi Zhang. “The Focusing Cubic NLS on Exterior Domains in Three Dimensions.” Applied Mathematics Research EXpress. Oxford University Press, 2016. https://doi.org/10.1093/amrx/abv012. ieee: R. Killip, M. Vişan, and X. Zhang, “The focusing cubic NLS on exterior domains in three dimensions,” Applied Mathematics Research eXpress, vol. 2016, no. 1. Oxford University Press, pp. 146–180, 2016. ista: Killip R, Vişan M, Zhang X. 2016. The focusing cubic NLS on exterior domains in three dimensions. Applied Mathematics Research eXpress. 2016(1), 146–180. mla: Killip, Rowan, et al. “The Focusing Cubic NLS on Exterior Domains in Three Dimensions.” Applied Mathematics Research EXpress, vol. 2016, no. 1, Oxford University Press, 2016, pp. 146–80, doi:10.1093/amrx/abv012. short: R. Killip, M. Vişan, X. Zhang, Applied Mathematics Research EXpress 2016 (2016) 146–180. das_tickbox: '1' date_created: 2026-06-19T07:54:24Z date_published: 2016-01-01T00:00:00Z date_updated: 2026-06-25T08:30:19Z day: '01' doi: 10.1093/amrx/abv012 extern: '1' external_id: arxiv: - '1501.05062' intvolume: ' 2016' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1501.05062 month: '01' oa: 1 oa_version: Preprint page: 146-180 publication: Applied Mathematics Research eXpress publication_identifier: eissn: - 1687-1197 issn: - 1687-1200 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The focusing cubic NLS on exterior domains in three dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2016 year: '2016' ... --- OA_place: repository OA_type: green _id: '22073' abstract: - lang: eng text: We prove scale-invariant Strichartz inequalities for the Schrödinger equation on rectangular tori (rational or irrational) in all dimensions. We use these estimates to give a simpler treatment of local well-posedness of the energy-critical nonlinear Schrödinger equation in dimensions three and four. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Rowan full_name: Killip, Rowan last_name: Killip - first_name: Monica full_name: Visan, Monica id: 056daca0-b8d1-11f0-964f-f91054abf8ca last_name: Visan citation: ama: Killip R, Vişan M. Scale-invariant Strichartz estimates on tori and applications. Mathematical Research Letters. 2016;23(2):445-472. doi:10.4310/mrl.2016.v23.n2.a8 apa: Killip, R., & Vişan, M. (2016). Scale-invariant Strichartz estimates on tori and applications. Mathematical Research Letters. International Press. https://doi.org/10.4310/mrl.2016.v23.n2.a8 chicago: Killip, Rowan, and Monica Vişan. “Scale-Invariant Strichartz Estimates on Tori and Applications.” Mathematical Research Letters. International Press, 2016. https://doi.org/10.4310/mrl.2016.v23.n2.a8. ieee: R. Killip and M. Vişan, “Scale-invariant Strichartz estimates on tori and applications,” Mathematical Research Letters, vol. 23, no. 2. International Press, pp. 445–472, 2016. ista: Killip R, Vişan M. 2016. Scale-invariant Strichartz estimates on tori and applications. Mathematical Research Letters. 23(2), 445–472. mla: Killip, Rowan, and Monica Vişan. “Scale-Invariant Strichartz Estimates on Tori and Applications.” Mathematical Research Letters, vol. 23, no. 2, International Press, 2016, pp. 445–72, doi:10.4310/mrl.2016.v23.n2.a8. short: R. Killip, M. Vişan, Mathematical Research Letters 23 (2016) 445–472. das_tickbox: '1' date_created: 2026-06-19T08:22:27Z date_published: 2016-06-06T00:00:00Z date_updated: 2026-06-30T10:59:10Z day: '06' doi: 10.4310/mrl.2016.v23.n2.a8 extern: '1' external_id: arxiv: - '1409.3603' intvolume: ' 23' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.48550/arXiv.1409.3603 ' month: '06' oa: 1 oa_version: Preprint page: 445-472 publication: Mathematical Research Letters publication_identifier: eissn: - 1945-001X issn: - 1073-2780 publication_status: published publisher: International Press quality_controlled: '1' scopus_import: '1' status: public title: Scale-invariant Strichartz estimates on tori and applications type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2016' ... --- _id: '1223' abstract: - lang: eng text: We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder. article_processing_charge: No arxiv: 1 author: - first_name: Richard full_name: Froese, Richard last_name: Froese - first_name: Darrick full_name: Lee, Darrick last_name: Lee - first_name: Christian full_name: Sadel, Christian id: 4760E9F8-F248-11E8-B48F-1D18A9856A87 last_name: Sadel orcid: 0000-0001-8255-3968 - first_name: Wolfgang full_name: Spitzer, Wolfgang last_name: Spitzer - first_name: Günter full_name: Stolz, Günter last_name: Stolz citation: ama: Froese R, Lee D, Sadel C, Spitzer W, Stolz G. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 2016;6(3):557-600. doi:10.4171/JST/132 apa: Froese, R., Lee, D., Sadel, C., Spitzer, W., & Stolz, G. (2016). Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/132 chicago: Froese, Richard, Darrick Lee, Christian Sadel, Wolfgang Spitzer, and Günter Stolz. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory. EMS Press, 2016. https://doi.org/10.4171/JST/132. ieee: R. Froese, D. Lee, C. Sadel, W. Spitzer, and G. Stolz, “Localization for transversally periodic random potentials on binary trees,” Journal of Spectral Theory, vol. 6, no. 3. EMS Press, pp. 557–600, 2016. ista: Froese R, Lee D, Sadel C, Spitzer W, Stolz G. 2016. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 6(3), 557–600. mla: Froese, Richard, et al. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory, vol. 6, no. 3, EMS Press, 2016, pp. 557–600, doi:10.4171/JST/132. short: R. Froese, D. Lee, C. Sadel, W. Spitzer, G. Stolz, Journal of Spectral Theory 6 (2016) 557–600. das_tickbox: '1' date_created: 2018-12-11T11:50:48Z date_published: 2016-01-01T00:00:00Z date_updated: 2026-07-06T11:55:04Z day: '01' department: - _id: LaEr doi: 10.4171/JST/132 external_id: arxiv: - '1408.3961' isi: - '000388627000004' intvolume: ' 6' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.3961 month: '01' oa: 1 oa_version: Preprint page: 557 - 600 publication: Journal of Spectral Theory publication_status: published publisher: EMS Press publist_id: '6112' quality_controlled: '1' scopus_import: '1' status: public title: Localization for transversally periodic random potentials on binary trees type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2016' ... --- OA_place: repository OA_type: green _id: '1170' abstract: - lang: eng text: The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway. article_processing_charge: No article_type: original author: - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Jörg full_name: Stelling, Jörg last_name: Stelling citation: ama: Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X apa: Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/15M103306X chicago: Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics, 2016. https://doi.org/10.1137/15M103306X. ieee: M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics, pp. B988–B1008, 2016. ista: Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008. mla: Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics, 2016, pp. B988–1008, doi:10.1137/15M103306X. short: M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008. corr_author: '1' das_tickbox: '1' date_created: 2018-12-11T11:50:31Z date_published: 2016-11-15T00:00:00Z date_updated: 2026-07-06T14:00:20Z day: '15' ddc: - '003' - '518' - '570' - '621' department: - _id: CaGu - _id: GaTk doi: 10.1137/15M103306X external_id: isi: - '000391853100010' file: - access_level: open_access checksum: 781bc3ffd30b2dd65b7727c5a285fc78 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:41Z date_updated: 2025-06-25T11:26:45Z file_id: '5095' file_name: IST-2017-811-v1+1_modular_parameter_identification.pdf file_size: 871964 relation: main_file file_date_updated: 2025-06-25T11:26:45Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: B988 - B1008 publication: SIAM Journal on Scientific Computing publication_status: published publisher: Society for Industrial and Applied Mathematics publist_id: '6186' pubrep_id: '811' quality_controlled: '1' scopus_import: '1' status: public title: Modular parameter identification of biomolecular networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 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. article_processing_charge: No arxiv: 1 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. das_tickbox: '1' date_created: 2018-12-11T11:51:40Z date_published: 2016-05-03T00:00:00Z date_updated: 2026-07-06T13:59:54Z day: '03' department: - _id: VlKo doi: 10.1137/15M1010257 ec_funded: 1 external_id: arxiv: - '1502.07770' isi: - '000385275400005' intvolume: ' 9' isi: 1 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2016' ... --- _id: '1272' abstract: - lang: eng text: We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams. acknowledgement: 'This work was supported by Austrian Science Fund (FWF): P25816-N15.' article_processing_charge: No author: - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721. doi:10.1080/16864360.2016.1150718 apa: Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. Taylor & Francis. https://doi.org/10.1080/16864360.2016.1150718 chicago: Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications. Taylor & Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718. ieee: M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” Computer-Aided Design and Applications, vol. 13, no. 5. Taylor & Francis, pp. 712–721, 2016. ista: Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721. mla: Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications, vol. 13, no. 5, Taylor & Francis, 2016, pp. 712–21, doi:10.1080/16864360.2016.1150718. short: M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721. das_tickbox: '1' date_created: 2018-12-11T11:51:04Z date_published: 2016-09-02T00:00:00Z date_updated: 2026-07-07T05:34:31Z day: '02' ddc: - '004' - '516' department: - _id: HeEd doi: 10.1080/16864360.2016.1150718 file: - access_level: open_access checksum: c746f3a48edb62b588d92ea5d0fd2c0e content_type: application/pdf creator: system date_created: 2018-12-12T10:16:20Z date_updated: 2020-07-14T12:44:42Z file_id: '5206' file_name: IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf file_size: 1678369 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 13' issue: '5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 712 - 721 publication: Computer-Aided Design and Applications publication_status: published publisher: Taylor & Francis publist_id: '6048' pubrep_id: '694' quality_controlled: '1' scopus_import: '1' status: public title: Generalized offsetting of planar structures using skeletons tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2016' ... --- _id: '1254' abstract: - lang: eng text: We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/. acknowledgement: "AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics \ of Kyoto University for providing access\r\nto their server for conducting \ computations for this\r\nproject." article_processing_charge: No arxiv: 1 author: - first_name: Ali full_name: Golmakani, Ali last_name: Golmakani - first_name: Stefano full_name: Luzzatto, Stefano last_name: Luzzatto - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk citation: ama: Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124. doi:10.1080/10586458.2015.1048011 apa: Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2015.1048011 chicago: Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics. Taylor & Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011. ieee: A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” Experimental Mathematics, vol. 25, no. 2. Taylor & Francis, pp. 116–124, 2016. ista: Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124. mla: Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor & Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011. short: A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124. corr_author: '1' das_tickbox: '1' date_created: 2018-12-11T11:50:58Z date_published: 2016-04-02T00:00:00Z date_updated: 2026-07-07T05:34:16Z day: '02' department: - _id: HeEd doi: 10.1080/10586458.2015.1048011 ec_funded: 1 external_id: arxiv: - '1504.00116' isi: - '000372490500002' intvolume: ' 25' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.00116 month: '04' oa: 1 oa_version: Preprint page: 116 - 124 project: - _id: 255F06BE-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '622033' name: Persistent Homology - Images, Data and Maps publication: Experimental Mathematics publication_status: published publisher: Taylor & Francis publist_id: '6071' quality_controlled: '1' scopus_import: '1' status: public title: Uniform expansivity outside a critical neighborhood in the quadratic family type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2016' ... --- _id: '1188' abstract: - lang: eng text: "We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations." acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night. article_number: '123502' article_processing_charge: No arxiv: 1 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: Davide full_name: Masoero, Davide last_name: Masoero citation: ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f' apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/aa4e8f' chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.' ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOP Publishing, 2016.' ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.' mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:10.1088/1742-5468/aa4e8f.' short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).' das_tickbox: '1' date_created: 2018-12-11T11:50:37Z date_published: 2016-12-30T00:00:00Z date_updated: 2026-07-07T13:11:22Z day: '30' department: - _id: GaTk doi: 10.1088/1742-5468/aa4e8f ec_funded: 1 external_id: arxiv: - '1606.09048' isi: - '000391973900001' intvolume: ' 2016' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.09048 month: '12' 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: 'Journal of Statistical Mechanics: Theory and Experiment' publication_status: published publisher: IOP Publishing publist_id: '6165' quality_controlled: '1' scopus_import: '1' status: public title: Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2016 year: '2016' ... --- _id: '1441' abstract: - lang: eng text: 'Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.' acknowledgement: 'A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).' article_processing_charge: No author: - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Alexandra-Madelaine full_name: Tichy, Alexandra-Madelaine id: 29D8BB2C-F248-11E8-B48F-1D18A9856A87 last_name: Tichy - first_name: Catherine full_name: Mckenzie, Catherine id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87 last_name: Mckenzie - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. 2016;55(21):6339-6342. doi:10.1002/anie.201601736 apa: Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., & Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201601736 chicago: Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie International Edition. Wiley, 2016. https://doi.org/10.1002/anie.201601736. ieee: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” Angewandte Chemie International Edition, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016. ista: Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. 55(21), 6339–6342. mla: Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie International Edition, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:10.1002/anie.201601736. short: E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie International Edition 55 (2016) 6339–6342. corr_author: '1' das_tickbox: '1' date_created: 2018-12-11T11:52:02Z date_published: 2016-05-17T00:00:00Z date_updated: 2026-07-08T05:54:25Z day: '17' ddc: - '571' - '576' department: - _id: HaJa doi: 10.1002/anie.201601736 ec_funded: 1 external_id: isi: - '000377918400039' file: - access_level: open_access checksum: 26da07960e57ac4750b54179197ce57f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:03Z date_updated: 2020-07-14T12:44:55Z file_id: '5255' file_name: IST-2017-840-v1+1_reichhart.pdf file_size: 1268662 relation: main_file file_date_updated: 2020-07-14T12:44:55Z has_accepted_license: '1' intvolume: ' 55' isi: 1 issue: '21' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 6339 - 6342 project: - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology - _id: 255A6082-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Angewandte Chemie International Edition publication_status: published publisher: Wiley publist_id: '5755' pubrep_id: '840' quality_controlled: '1' related_material: record: - id: '418' relation: dissertation_contains status: public scopus_import: '1' status: public title: A phytochrome sensory domain permits receptor activation by red light type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2016' ... --- _id: '1339' abstract: - lang: eng text: "We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n" acknowledgement: We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140). article_number: '143507' article_processing_charge: No arxiv: 1 author: - first_name: Gerard full_name: Verbiest, Gerard last_name: Verbiest - first_name: Duo full_name: Xu, Duo id: 3454D55E-F248-11E8-B48F-1D18A9856A87 last_name: Xu - first_name: Matthias full_name: Goldsche, Matthias last_name: Goldsche - first_name: Timofiy full_name: Khodkov, Timofiy last_name: Khodkov - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Nils full_name: Von Den Driesch, Nils last_name: Von Den Driesch - first_name: Dan full_name: Buca, Dan last_name: Buca - first_name: Christoph full_name: Stampfer, Christoph last_name: Stampfer citation: ama: Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 2016;109. doi:10.1063/1.4964122 apa: Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122 chicago: Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter. American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122. ieee: G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical resonators,” Applied Physics Letter, vol. 109. American Institute of Physics, 2016. ista: Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 109, 143507. mla: Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter, vol. 109, 143507, American Institute of Physics, 2016, doi:10.1063/1.4964122. short: G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied Physics Letter 109 (2016). das_tickbox: '1' date_created: 2018-12-11T11:51:28Z date_published: 2016-10-04T00:00:00Z date_updated: 2026-07-08T06:31:59Z day: '04' department: - _id: JoFi doi: 10.1063/1.4964122 external_id: arxiv: - '1607.04406' isi: - '000386152800065' intvolume: ' 109' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.04406 month: '10' oa: 1 oa_version: Preprint publication: Applied Physics Letter publication_status: published publisher: American Institute of Physics publist_id: '5928' quality_controlled: '1' scopus_import: '1' status: public title: Tunable mechanical coupling between driven microelectromechanical resonators type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2016' ... --- OA_place: repository OA_type: green _id: '22171' abstract: - lang: eng text: 'We show that over the binary field [Formula: see text], the Bar-Natan perturbation of Khovanov homology splits as the direct sum of its two reduced theories, which we also prove are isomorphic. This extends Shumakovitch’s analogous result for ordinary Khovanov homology, without the perturbation. ' article_number: '1650014' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Yuval full_name: Wigderson, Yuval id: 2d0023a0-1567-11f0-833d-d5c1e476d4b5 last_name: Wigderson citation: ama: Wigderson Y. The Bar-Natan theory splits. Journal of Knot Theory and Its Ramifications. 2016;25(04). doi:10.1142/s0218216516500140 apa: Wigderson, Y. (2016). The Bar-Natan theory splits. Journal of Knot Theory and Its Ramifications. World Scientific Publishing. https://doi.org/10.1142/s0218216516500140 chicago: Wigderson, Yuval. “The Bar-Natan Theory Splits.” Journal of Knot Theory and Its Ramifications. World Scientific Publishing, 2016. https://doi.org/10.1142/s0218216516500140. ieee: Y. Wigderson, “The Bar-Natan theory splits,” Journal of Knot Theory and Its Ramifications, vol. 25, no. 04. World Scientific Publishing, 2016. ista: Wigderson Y. 2016. The Bar-Natan theory splits. Journal of Knot Theory and Its Ramifications. 25(04), 1650014. mla: Wigderson, Yuval. “The Bar-Natan Theory Splits.” Journal of Knot Theory and Its Ramifications, vol. 25, no. 04, 1650014, World Scientific Publishing, 2016, doi:10.1142/s0218216516500140. short: Y. Wigderson, Journal of Knot Theory and Its Ramifications 25 (2016). date_created: 2026-06-29T10:56:23Z date_published: 2016-04-01T00:00:00Z date_updated: 2026-07-14T08:48:58Z day: '01' doi: 10.1142/s0218216516500140 extern: '1' external_id: arxiv: - '1508.05982' intvolume: ' 25' issue: '04' keyword: - Khovanov homology - categorification - Bar-Natan theory - link homology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1508.05982 mathsc: - 57M25 - 57M27 month: '04' oa: 1 oa_version: Preprint publication: Journal of Knot Theory and Its Ramifications publication_identifier: eissn: - 1793-6527 issn: - 0218-2165 publication_status: published publisher: World Scientific Publishing quality_controlled: '1' scopus_import: '1' status: public title: The Bar-Natan theory splits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2016' ... --- OA_place: repository OA_type: green _id: '22202' abstract: - lang: eng text: We use modular symmetric designs to study the existence of Hadamard matrices modulo certain primes. We solve the 7-modular and 11-modular versions of the Hadamard conjecture for all but a finite number of cases. In doing so, we state a conjectural sufficient condition for the existence of a p-modular Hadamard matrix for all but finitely many cases. When 2 is a primitive root of a prime p, we conditionally solve this conjecture and therefore the p-modular version of the Hadamard conjecture for all but finitely many cases when p ≡ 3(mod 4), and prove a weaker result for p ≡ 1 (mod 4). Finally, we look at constraints on the existence of m-modular Hadamard matrices when the size of the matrix is small compared to m. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Vivian Zieve full_name: Kuperberg, Vivian Zieve id: c3bac823-112d-11f0-a3f5-c264f852e697 last_name: Kuperberg citation: ama: Kuperberg VZ. Hadamard matrices modulo p and small modular Hadamard matrices. Journal of Combinatorial Designs. 2016;24(9):393-405. doi:10.1002/jcd.21522 apa: Kuperberg, V. Z. (2016). Hadamard matrices modulo p and small modular Hadamard matrices. Journal of Combinatorial Designs. Wiley. https://doi.org/10.1002/jcd.21522 chicago: Kuperberg, Vivian Zieve. “Hadamard Matrices modulo p and Small Modular Hadamard Matrices.” Journal of Combinatorial Designs. Wiley, 2016. https://doi.org/10.1002/jcd.21522. ieee: V. Z. Kuperberg, “Hadamard matrices modulo p and small modular Hadamard matrices,” Journal of Combinatorial Designs, vol. 24, no. 9. Wiley, pp. 393–405, 2016. ista: Kuperberg VZ. 2016. Hadamard matrices modulo p and small modular Hadamard matrices. Journal of Combinatorial Designs. 24(9), 393–405. mla: Kuperberg, Vivian Zieve. “Hadamard Matrices modulo p and Small Modular Hadamard Matrices.” Journal of Combinatorial Designs, vol. 24, no. 9, Wiley, 2016, pp. 393–405, doi:10.1002/jcd.21522. short: V.Z. Kuperberg, Journal of Combinatorial Designs 24 (2016) 393–405. date_created: 2026-06-29T13:00:27Z date_published: 2016-09-01T00:00:00Z date_updated: 2026-07-14T11:35:58Z day: '01' doi: 10.1002/jcd.21522 extern: '1' external_id: arxiv: - '1409.0148' intvolume: ' 24' issue: '9' keyword: - modular hadamard matrices - modular symmetric designs language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1409.0148 month: '09' oa: 1 oa_version: Preprint page: 393-405 publication: Journal of Combinatorial Designs publication_identifier: eissn: - 1520-6610 issn: - 1063-8539 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Hadamard matrices modulo p and small modular Hadamard matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2016' ... --- _id: '1100' abstract: - lang: eng text: During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation. acknowledged_ssus: - _id: SSU acknowledgement: 'We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.' article_processing_charge: No author: - first_name: Keisuke full_name: Sako, Keisuke id: 3BED66BE-F248-11E8-B48F-1D18A9856A87 last_name: Sako orcid: 0000-0002-6453-8075 - first_name: Saurabh full_name: Pradhan, Saurabh last_name: Pradhan - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Patrick full_name: Mueller, Patrick last_name: Mueller - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Daniel full_name: Capek, Daniel id: 31C42484-F248-11E8-B48F-1D18A9856A87 last_name: Capek orcid: 0000-0001-5199-9940 - first_name: Sanjeev full_name: Galande, Sanjeev last_name: Galande - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 2016;16(3):866-877. doi:10.1016/j.celrep.2016.06.036 apa: Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.06.036 chicago: Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.06.036. ieee: K. Sako et al., “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” Cell Reports, vol. 16, no. 3. Cell Press, pp. 866–877, 2016. ista: Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877. mla: Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:10.1016/j.celrep.2016.06.036. short: K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877. date_created: 2018-12-11T11:50:08Z date_published: 2016-07-19T00:00:00Z date_updated: 2026-07-18T22:30:34Z day: '19' ddc: - '570' - '576' department: - _id: CaHe - _id: HaJa doi: 10.1016/j.celrep.2016.06.036 ec_funded: 1 external_id: isi: - '000380264200024' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:11:04Z date_updated: 2018-12-12T10:11:04Z file_id: '4857' file_name: IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf file_size: 3921947 relation: main_file file_date_updated: 2018-12-12T10:11:04Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 866 - 877 project: - _id: 2529486C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T 560-B17 name: Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation - _id: 2527D5CC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I812-B12 name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology publication: Cell Reports publication_status: published publisher: Cell Press publist_id: '6275' pubrep_id: '754' quality_controlled: '1' related_material: record: - id: '961' relation: dissertation_contains status: public - id: '50' relation: dissertation_contains status: public scopus_import: '1' status: public title: Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 16 year: '2016' ... --- _id: '1321' abstract: - lang: eng text: Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion. acknowledged_ssus: - _id: SSU acknowledgement: "This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support." article_processing_charge: No article_type: original author: - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Alexander full_name: Eichner, Alexander id: 4DFA52AE-F248-11E8-B48F-1D18A9856A87 last_name: Eichner - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: David full_name: De Gorter, David last_name: De Gorter - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Jonathan full_name: Bayerl, Jonathan last_name: Bayerl - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Frank full_name: Lai, Frank last_name: Lai - first_name: Markus full_name: Moser, Markus last_name: Moser - first_name: Dontscho full_name: Kerjaschki, Dontscho last_name: Kerjaschki - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Victor full_name: Small, Victor last_name: Small - first_name: Theresia full_name: Stradal, Theresia last_name: Stradal - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 2016;18:1253-1259. doi:10.1038/ncb3426 apa: Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3426 chicago: Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/ncb3426. ieee: A. F. Leithner et al., “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” Nature Cell Biology, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016. ista: Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259. mla: Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” Nature Cell Biology, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:10.1038/ncb3426. short: A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259. corr_author: '1' date_created: 2018-12-11T11:51:21Z date_published: 2016-10-24T00:00:00Z date_updated: 2026-07-18T22:30:53Z day: '24' ddc: - '570' department: - _id: MiSi - _id: NanoFab - _id: Bio doi: 10.1038/ncb3426 ec_funded: 1 external_id: isi: - '000387165600018' file: - access_level: open_access checksum: e1411cb7c99a2d9089c178a6abef25e7 content_type: application/pdf creator: dernst date_created: 2020-05-14T16:33:46Z date_updated: 2020-07-14T12:44:43Z file_id: '7844' file_name: 2018_NatureCell_Leithner.pdf file_size: 4433280 relation: main_file file_date_updated: 2020-07-14T12:44:43Z has_accepted_license: '1' intvolume: ' 18' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '10' oa: 1 oa_version: Submitted Version page: 1253 - 1259 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5949' quality_controlled: '1' related_material: record: - id: '323' relation: dissertation_contains status: public scopus_import: '1' status: public title: Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 18 year: '2016' ... --- _id: '1183' abstract: - lang: eng text: Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function. acknowledgement: "This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility" article_processing_charge: No article_type: original author: - first_name: Dora-Clara full_name: Tarlungeanu, Dora-Clara id: 2ABCE612-F248-11E8-B48F-1D18A9856A87 last_name: Tarlungeanu - first_name: Elena full_name: Deliu, Elena id: 37A40D7E-F248-11E8-B48F-1D18A9856A87 last_name: Deliu orcid: 0000-0002-7370-5293 - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter orcid: 0000-0002-9033-9096 - first_name: Majdi full_name: Kara, Majdi last_name: Kara - first_name: Philipp full_name: Janiesch, Philipp last_name: Janiesch - first_name: Mariafrancesca full_name: Scalise, Mariafrancesca last_name: Scalise - first_name: Michele full_name: Galluccio, Michele last_name: Galluccio - first_name: Mateja full_name: Tesulov, Mateja last_name: Tesulov - first_name: Emanuela full_name: Morelli, Emanuela id: 3F4D1282-F248-11E8-B48F-1D18A9856A87 last_name: Morelli - first_name: Fatma full_name: Sönmez, Fatma last_name: Sönmez - first_name: Kaya full_name: Bilgüvar, Kaya last_name: Bilgüvar - first_name: Ryuichi full_name: Ohgaki, Ryuichi last_name: Ohgaki - first_name: Yoshikatsu full_name: Kanai, Yoshikatsu last_name: Kanai - first_name: Anide full_name: Johansen, Anide last_name: Johansen - first_name: Seham full_name: Esharif, Seham last_name: Esharif - first_name: Tawfeg full_name: Ben Omran, Tawfeg last_name: Ben Omran - first_name: Meral full_name: Topcu, Meral last_name: Topcu - first_name: Avner full_name: Schlessinger, Avner last_name: Schlessinger - first_name: Cesare full_name: Indiveri, Cesare last_name: Indiveri - first_name: Kent full_name: Duncan, Kent last_name: Duncan - first_name: Ahmet full_name: Caglayan, Ahmet last_name: Caglayan - first_name: Murat full_name: Günel, Murat last_name: Günel - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 2016;167(6):1481-1494. doi:10.1016/j.cell.2016.11.013 apa: Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013 chicago: Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013. ieee: D.-C. Tarlungeanu et al., “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016. ista: Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494. mla: Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013. short: D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494. date_created: 2018-12-11T11:50:35Z date_published: 2016-12-01T00:00:00Z date_updated: 2026-07-18T22:30:52Z day: '01' ddc: - '576' - '616' department: - _id: GaNo doi: 10.1016/j.cell.2016.11.013 external_id: isi: - '000389470500012' file: - access_level: open_access checksum: 7fe01ab12a6610d3db421e0136db2f77 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:44Z date_updated: 2020-07-14T12:44:37Z file_id: '5030' file_name: IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf file_size: 73907957 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 167' isi: 1 issue: '6' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 1481 - 1494 project: - _id: 25473368-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F03523 name: Transmembrane Transporters in Health and Disease publication: Cell publication_status: published publisher: Cell Press publist_id: '6170' pubrep_id: '771' quality_controlled: '1' related_material: record: - id: '395' relation: dissertation_contains status: public scopus_import: '1' status: public title: Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 167 year: '2016' ... --- _id: '1437' abstract: - lang: eng text: We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks. alternative_title: - POPL arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir full_name: Goharshady, Amir id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:10.1145/2837614.2837624' apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837624' chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. https://doi.org/10.1145/2837614.2837624. ieee: 'K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.' ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.' mla: Chatterjee, Krishnendu, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. Vol. 20–22, ACM, 2016, pp. 733–47, doi:10.1145/2837614.2837624. short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747. conference: end_date: 2016-01-22 location: St. Petersburg, FL, USA name: 'POPL: Principles of Programming Languages' start_date: 2016-01-20 corr_author: '1' date_created: 2018-12-11T11:52:01Z date_published: 2016-01-11T00:00:00Z date_updated: 2026-07-18T22:31:08Z day: '11' department: - _id: KrCh doi: 10.1145/2837614.2837624 ec_funded: 1 external_id: arxiv: - '1510.07565' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.07565 month: '01' oa: 1 oa_version: Preprint page: 733 - 747 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' publication_status: published publisher: ACM publist_id: '5761' quality_controlled: '1' related_material: record: - id: '5441' relation: earlier_version status: public - id: '5442' relation: earlier_version status: public - id: '6009' relation: later_version status: public - id: '821' relation: dissertation_contains status: public - id: '8934' relation: dissertation_contains status: public scopus_import: 1 status: public title: Algorithms for algebraic path properties in concurrent systems of constant treewidth components type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20-22 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 article_processing_charge: No arxiv: 1 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 corr_author: '1' date_created: 2018-12-11T11:51:43Z date_published: 2016-07-01T00:00:00Z date_updated: 2026-07-18T22:31:09Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-319-41528-4_1 ec_funded: 1 external_id: arxiv: - '1604.07169' isi: - '000387731200001' intvolume: ' 9779' isi: 1 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 9779 year: '2016' ...