[{"author":[{"last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","first_name":"Timothy D","orcid":"0000-0002-8314-0177"},{"full_name":"Prendiville, Sean","last_name":"Prendiville","first_name":"Sean"}],"day":"01","title":"A transference approach to a Roth-type theorem in the squares","oa_version":"Preprint","volume":2017,"article_type":"original","date_created":"2018-12-11T11:45:31Z","abstract":[{"lang":"eng","text":"We show that any subset of the squares of positive relative upper density contains nontrivial solutions to a translation-invariant linear equation in five or more variables, with explicit quantitative bounds. As a consequence, we establish the partition regularity of any diagonal quadric in five or more variables whose coefficients sum to zero. Unlike previous approaches, which are limited to equations in seven or more variables, we employ transference technology of Green to import bounds from the linear setting."}],"intvolume":"      2017","publication_identifier":{"issn":["1073-7928"]},"publication_status":"published","month":"04","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"issue":"7","citation":{"short":"T.D. Browning, S. Prendiville, International Mathematics Research Notices 2017 (2017) 2219–2248.","ieee":"T. D. Browning and S. Prendiville, “A transference approach to a Roth-type theorem in the squares,” <i>International Mathematics Research Notices</i>, vol. 2017, no. 7. Oxford University Press, pp. 2219–2248, 2017.","ama":"Browning TD, Prendiville S. A transference approach to a Roth-type theorem in the squares. <i>International Mathematics Research Notices</i>. 2017;2017(7):2219-2248. doi:<a href=\"https://doi.org/10.1093/imrn/rnw096\">10.1093/imrn/rnw096</a>","mla":"Browning, Timothy D., and Sean Prendiville. “A Transference Approach to a Roth-Type Theorem in the Squares.” <i>International Mathematics Research Notices</i>, vol. 2017, no. 7, Oxford University Press, 2017, pp. 2219–48, doi:<a href=\"https://doi.org/10.1093/imrn/rnw096\">10.1093/imrn/rnw096</a>.","apa":"Browning, T. D., &#38; Prendiville, S. (2017). A transference approach to a Roth-type theorem in the squares. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnw096\">https://doi.org/10.1093/imrn/rnw096</a>","chicago":"Browning, Timothy D, and Sean Prendiville. “A Transference Approach to a Roth-Type Theorem in the Squares.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/imrn/rnw096\">https://doi.org/10.1093/imrn/rnw096</a>.","ista":"Browning TD, Prendiville S. 2017. A transference approach to a Roth-type theorem in the squares. International Mathematics Research Notices. 2017(7), 2219–2248."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1093/imrn/rnw096","article_processing_charge":"No","publisher":"Oxford University Press","date_updated":"2024-03-05T11:52:36Z","_id":"268","type":"journal_article","page":"2219 - 2248","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.00136"}],"quality_controlled":"1","year":"2017","external_id":{"arxiv":["1510.00136"]},"publist_id":"7634","publication":"International Mathematics Research Notices","status":"public","extern":"1","date_published":"2017-04-01T00:00:00Z","acknowledgement":"Whilst working on this paper the authors were supported by ERC grant 306457."},{"page":"1249 - 1267","main_file_link":[{"url":"https://arxiv.org/abs/1311.5755","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/s00209-016-1746-2","article_processing_charge":"No","publisher":"Springer","date_updated":"2024-03-05T11:56:29Z","_id":"269","type":"journal_article","extern":"1","publication":"Mathematische Zeitschrift","status":"public","date_published":"2017-04-01T00:00:00Z","year":"2017","external_id":{"arxiv":["1311.5755"]},"publist_id":"7633","abstract":[{"text":"We investigate Fano varieties defined over a number field that contain subvarieties whose number of rational points of bounded height is comparable to the total number on the variety.","lang":"eng"}],"intvolume":"       285","publication_status":"published","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177"},{"full_name":"Loughran, Daniel","last_name":"Loughran","first_name":"Daniel"}],"day":"01","oa_version":"Preprint","title":"Varieties with too many rational points","volume":285,"article_type":"original","date_created":"2018-12-11T11:45:32Z","oa":1,"language":[{"iso":"eng"}],"issue":"3-4","citation":{"ista":"Browning TD, Loughran D. 2017. Varieties with too many rational points. Mathematische Zeitschrift. 285(3–4), 1249–1267.","chicago":"Browning, Timothy D, and Daniel Loughran. “Varieties with Too Many Rational Points.” <i>Mathematische Zeitschrift</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00209-016-1746-2\">https://doi.org/10.1007/s00209-016-1746-2</a>.","mla":"Browning, Timothy D., and Daniel Loughran. “Varieties with Too Many Rational Points.” <i>Mathematische Zeitschrift</i>, vol. 285, no. 3–4, Springer, 2017, pp. 1249–67, doi:<a href=\"https://doi.org/10.1007/s00209-016-1746-2\">10.1007/s00209-016-1746-2</a>.","apa":"Browning, T. D., &#38; Loughran, D. (2017). Varieties with too many rational points. <i>Mathematische Zeitschrift</i>. Springer. <a href=\"https://doi.org/10.1007/s00209-016-1746-2\">https://doi.org/10.1007/s00209-016-1746-2</a>","ama":"Browning TD, Loughran D. Varieties with too many rational points. <i>Mathematische Zeitschrift</i>. 2017;285(3-4):1249-1267. doi:<a href=\"https://doi.org/10.1007/s00209-016-1746-2\">10.1007/s00209-016-1746-2</a>","short":"T.D. Browning, D. Loughran, Mathematische Zeitschrift 285 (2017) 1249–1267.","ieee":"T. D. Browning and D. Loughran, “Varieties with too many rational points,” <i>Mathematische Zeitschrift</i>, vol. 285, no. 3–4. Springer, pp. 1249–1267, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"month":"04"},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.06342"}],"page":"1044 - 1080","type":"journal_article","_id":"270","date_updated":"2024-03-05T11:58:25Z","publisher":"Wiley","article_processing_charge":"No","doi":"10.1112/plms.12030","date_published":"2017-06-01T00:00:00Z","acknowledgement":"While working on this paper the authors were supported by ERC grants 306457 and 239606, respectively.","publication":"Proceedings of the London Mathematical Society","status":"public","extern":"1","publist_id":"7632","external_id":{"arxiv":["1606.06342"]},"year":"2017","publication_status":"published","publication_identifier":{"issn":["0024-6115"]},"intvolume":"       114","abstract":[{"lang":"eng","text":"Given a symmetric variety Y defined over Q and a non-zero polynomial with integer coefficients, we use techniques from homogeneous dynamics to establish conditions under which the polynomial can be made r-free for a Zariski dense set of integral points on Y . We also establish an asymptotic counting formula for this set. In the special case that Y is a quadric hypersurface, we give explicit bounds on the size of r by combining the argument with a uniform upper bound for the density of integral points on general affine quadrics defined over Q."}],"date_created":"2018-12-11T11:45:32Z","article_type":"original","volume":114,"oa_version":"Preprint","title":"Power-free values of polynomials on symmetric varieties","day":"01","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177"},{"first_name":"Alexander","full_name":"Gorodnik, Alexander","last_name":"Gorodnik"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Browning, Timothy D, and Alexander Gorodnik. “Power-Free Values of Polynomials on Symmetric Varieties.” <i>Proceedings of the London Mathematical Society</i>. Wiley, 2017. <a href=\"https://doi.org/10.1112/plms.12030\">https://doi.org/10.1112/plms.12030</a>.","ista":"Browning TD, Gorodnik A. 2017. Power-free values of polynomials on symmetric varieties. Proceedings of the London Mathematical Society. 114(6), 1044–1080.","apa":"Browning, T. D., &#38; Gorodnik, A. (2017). Power-free values of polynomials on symmetric varieties. <i>Proceedings of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/plms.12030\">https://doi.org/10.1112/plms.12030</a>","mla":"Browning, Timothy D., and Alexander Gorodnik. “Power-Free Values of Polynomials on Symmetric Varieties.” <i>Proceedings of the London Mathematical Society</i>, vol. 114, no. 6, Wiley, 2017, pp. 1044–80, doi:<a href=\"https://doi.org/10.1112/plms.12030\">10.1112/plms.12030</a>.","ama":"Browning TD, Gorodnik A. Power-free values of polynomials on symmetric varieties. <i>Proceedings of the London Mathematical Society</i>. 2017;114(6):1044-1080. doi:<a href=\"https://doi.org/10.1112/plms.12030\">10.1112/plms.12030</a>","ieee":"T. D. Browning and A. Gorodnik, “Power-free values of polynomials on symmetric varieties,” <i>Proceedings of the London Mathematical Society</i>, vol. 114, no. 6. Wiley, pp. 1044–1080, 2017.","short":"T.D. Browning, A. Gorodnik, Proceedings of the London Mathematical Society 114 (2017) 1044–1080."},"issue":"6","language":[{"iso":"eng"}],"oa":1,"month":"06","arxiv":1},{"author":[{"full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177"},{"full_name":"Matthiesen, Lilian","last_name":"Matthiesen","first_name":"Lilian"}],"day":"01","oa_version":"Submitted Version","title":"Norm forms for arbitrary number fields as products of linear polynomials","volume":50,"article_type":"original","date_created":"2018-12-11T11:45:32Z","intvolume":"        50","abstract":[{"lang":"eng","text":"Given a number field K/Q and a polynomial P ε Q [t], all of whose roots are Q, let X be the variety defined by the equation NK (x) = P (t). Combining additive combinatiorics with descent we show that the Brauer-Manin obstruction is the only obstruction to the Hesse principle and weak approximation on any smooth and projective model of X."}],"publication_status":"published","month":"12","oa":1,"language":[{"iso":"eng"}],"issue":"6","citation":{"chicago":"Browning, Timothy D, and Lilian Matthiesen. “Norm Forms for Arbitrary Number Fields as Products of Linear Polynomials.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Societe Mathematique de France, 2017. <a href=\"https://doi.org/10.24033/asens.2348\">https://doi.org/10.24033/asens.2348</a>.","ista":"Browning TD, Matthiesen L. 2017. Norm forms for arbitrary number fields as products of linear polynomials. Annales Scientifiques de l’Ecole Normale Superieure. 50(6), 1383–1446.","mla":"Browning, Timothy D., and Lilian Matthiesen. “Norm Forms for Arbitrary Number Fields as Products of Linear Polynomials.” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 50, no. 6, Societe Mathematique de France, 2017, pp. 1383–446, doi:<a href=\"https://doi.org/10.24033/asens.2348\">10.24033/asens.2348</a>.","apa":"Browning, T. D., &#38; Matthiesen, L. (2017). Norm forms for arbitrary number fields as products of linear polynomials. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. Societe Mathematique de France. <a href=\"https://doi.org/10.24033/asens.2348\">https://doi.org/10.24033/asens.2348</a>","ama":"Browning TD, Matthiesen L. Norm forms for arbitrary number fields as products of linear polynomials. <i>Annales Scientifiques de l’Ecole Normale Superieure</i>. 2017;50(6):1383-1446. doi:<a href=\"https://doi.org/10.24033/asens.2348\">10.24033/asens.2348</a>","short":"T.D. Browning, L. Matthiesen, Annales Scientifiques de l’Ecole Normale Superieure 50 (2017) 1383–1446.","ieee":"T. D. Browning and L. Matthiesen, “Norm forms for arbitrary number fields as products of linear polynomials,” <i>Annales Scientifiques de l’Ecole Normale Superieure</i>, vol. 50, no. 6. Societe Mathematique de France, pp. 1383–1446, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.24033/asens.2348","article_processing_charge":"No","publisher":"Societe Mathematique de France","date_updated":"2024-03-05T12:13:35Z","_id":"272","type":"journal_article","page":"1383 - 1446","main_file_link":[{"url":"https://research-information.bristol.ac.uk/en/publications/norm-forms-for-arbitrary-number-fields-as-products-of-linear-polynomials(f79a584b-ec58-47c8-aa97-8c5505e3f751).html","open_access":"1"}],"quality_controlled":"1","year":"2017","publist_id":"7630","status":"public","extern":"1","publication":"Annales Scientifiques de l'Ecole Normale Superieure","date_published":"2017-12-01T00:00:00Z","acknowledgement":"While working on this paper the first author was supported by ERC grant 306457 and the second author was supported by EPSRC grant EP/E053262/1 and by ERC grant 208091. Some of this work was carried out during the programme “Arithmetic and geometry” in 2013 at the Hausdorff Institute in Bonn."},{"file":[{"file_id":"7820","date_created":"2020-05-12T09:23:27Z","file_size":408974,"creator":"dernst","date_updated":"2020-07-14T12:45:45Z","relation":"main_file","checksum":"89db06a0e8083524449cb59b56bf4e5b","file_name":"2018_PMLR_Kolmogorov.pdf","content_type":"application/pdf","access_level":"open_access"}],"department":[{"_id":"VlKo"}],"arxiv":1,"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In <i>Proceedings of the 31st Conference On Learning Theory</i>, 75:228–49. ML Research Press, 2017.","ista":"Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory  vol. 75, 228–249.","apa":"Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In <i>Proceedings of the 31st Conference On Learning Theory</i> (Vol. 75, pp. 228–249). ML Research Press.","mla":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” <i>Proceedings of the 31st Conference On Learning Theory</i>, vol. 75, ML Research Press, 2017, pp. 228–49.","ama":"Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: <i>Proceedings of the 31st Conference On Learning Theory</i>. Vol 75. ML Research Press; 2017:228-249.","ieee":"V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in <i>Proceedings of the 31st Conference On Learning Theory</i>, 2017, vol. 75, pp. 228–249.","short":"V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:45:33Z","volume":75,"oa_version":"Published Version","title":"A faster approximation algorithm for the Gibbs partition function","author":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"day":"27","publication_status":"published","file_date_updated":"2020-07-14T12:45:45Z","abstract":[{"lang":"eng","text":"We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        75","has_accepted_license":"1","publist_id":"7628","external_id":{"arxiv":["1608.04223"]},"year":"2017","conference":{"end_date":"2018-07-09","start_date":"2018-07-06","name":"COLT: Annual Conference on Learning Theory "},"date_published":"2017-12-27T00:00:00Z","ec_funded":1,"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Proceedings of the 31st Conference On Learning Theory","type":"conference","date_updated":"2023-10-17T12:32:13Z","_id":"274","publisher":"ML Research Press","article_processing_charge":"No","quality_controlled":"1","ddc":["510"],"page":"228-249"},{"quality_controlled":"1","ddc":["530"],"date_updated":"2023-02-23T12:36:07Z","_id":"313","type":"conference","doi":"10.1088/1742-6596/999/1/012004","alternative_title":["Journal of Physics: Conference Series"],"publisher":"American Physical Society","conference":{"name":"Annual International Laser Physics Workshop LPHYS","end_date":"2017-08-21","start_date":"2017-08-17","location":"Kazan, Russian Federation"},"date_published":"2017-07-14T00:00:00Z","status":"public","publist_id":"7552","year":"2017","external_id":{"arxiv":["1611.03701"]},"related_material":{"record":[{"relation":"later_version","status":"public","id":"6013"}]},"publication_identifier":{"issn":["17426588"]},"publication_status":"published","file_date_updated":"2020-07-14T12:46:00Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.","lang":"eng"}],"intvolume":"       999","volume":999,"date_created":"2018-12-11T11:45:46Z","author":[{"first_name":"Nicolas","full_name":"Camus, Nicolas","last_name":"Camus"},{"first_name":"Enderalp","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu"},{"full_name":"Fechner, Lutz","last_name":"Fechner","first_name":"Lutz"},{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"last_name":"Laux","full_name":"Laux, Martin","first_name":"Martin"},{"first_name":"Yonghao","last_name":"Mi","full_name":"Mi, Yonghao"},{"first_name":"Karen","last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen"},{"last_name":"Pfeifer","full_name":"Pfeifer, Thomas","first_name":"Thomas"},{"last_name":"Keitel","full_name":"Keitel, Cristoph","first_name":"Cristoph"},{"first_name":"Robert","full_name":"Moshammer, Robert","last_name":"Moshammer"}],"scopus_import":1,"day":"14","title":"Experimental evidence for Wigner's tunneling time","oa_version":"Published Version","issue":"1","citation":{"ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>","ieee":"N. Camus <i>et al.</i>, “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>.","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. <a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">https://doi.org/10.1088/1742-6596/999/1/012004</a>","mla":"Camus, Nicolas, et al. <i>Experimental Evidence for Wigner’s Tunneling Time</i>. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1088/1742-6596/999/1/012004\">10.1088/1742-6596/999/1/012004</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"article_number":"012004","file":[{"file_id":"5871","file_size":949321,"date_created":"2019-01-22T08:34:10Z","creator":"dernst","date_updated":"2020-07-14T12:46:00Z","relation":"main_file","checksum":"6e70b525a84f6d5fb175c48e9f5cb59a","file_name":"2017_Physics_Camus.pdf","content_type":"application/pdf","access_level":"open_access"}],"arxiv":1,"month":"07"},{"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"2","citation":{"mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2017). Quantitative fair simulation games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">https://doi.org/10.1016/j.ic.2016.10.006</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” <i>Information and Computation</i>, vol. 254, no. 2. Elsevier, pp. 143–166, 2017.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. <i>Information and Computation</i>. 2017;254(2):143-166. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.006\">10.1016/j.ic.2016.10.006</a>"},"month":"06","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms."}],"intvolume":"       254","publication_status":"published","oa_version":"None","title":"Quantitative fair simulation games","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"day":"01","scopus_import":"1","date_created":"2018-12-11T11:49:58Z","volume":254,"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Information and Computation","date_published":"2017-06-01T00:00:00Z","ec_funded":1,"external_id":{"isi":["000402025600002"]},"related_material":{"record":[{"id":"5428","status":"public","relation":"earlier_version"}]},"year":"2017","isi":1,"publist_id":"6322","page":"143 - 166","quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.ic.2016.10.006","article_processing_charge":"No","type":"journal_article","date_updated":"2023-09-20T12:07:48Z","_id":"1066"},{"citation":{"ama":"Polshyn H. Magnetic force microscopy studies of mesoscopic superconducting structures. 2017.","ieee":"H. Polshyn, “Magnetic force microscopy studies of mesoscopic superconducting structures,” University of Illinois at Urbana-Champaign, 2017.","short":"H. Polshyn, Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures, University of Illinois at Urbana-Champaign, 2017.","chicago":"Polshyn, Hryhoriy. “Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures.” University of Illinois at Urbana-Champaign, 2017.","ista":"Polshyn H. 2017. Magnetic force microscopy studies of mesoscopic superconducting structures. University of Illinois at Urbana-Champaign.","apa":"Polshyn, H. (2017). <i>Magnetic force microscopy studies of mesoscopic superconducting structures</i>. University of Illinois at Urbana-Champaign.","mla":"Polshyn, Hryhoriy. <i>Magnetic Force Microscopy Studies of Mesoscopic Superconducting Structures</i>. University of Illinois at Urbana-Champaign, 2017."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2017-09-18T00:00:00Z","oa":1,"degree_awarded":"PhD","status":"public","extern":"1","language":[{"iso":"eng"}],"keyword":["physics","superconductivity","magnetic force microscopy","phase slips"],"year":"2017","supervisor":[{"first_name":"Raffi","last_name":"Budakian","full_name":"Budakian, Raffi"}],"month":"09","main_file_link":[{"url":"http://hdl.handle.net/2142/99178","open_access":"1"}],"publication_status":"published","page":"103","abstract":[{"lang":"eng","text":"The superconducting state of matter enables one to observe quantum effects on the macroscopic scale and hosts many fascinating phenomena. Topological defects of the superconducting order parameter, such as vortices and fluxoid states in multiply connected structures, are often the key ingredients of these phenomena. This dissertation describes a new mode of magnetic force microscopy (Φ0-MFM) for investigating vortex and fluxoid sates in mesoscopic superconducting (SC) structures. The technique relies on the magneto-mechanical coupling of a MFM cantilever to the motion of fluxons. The novelty of the technique is that a magnetic particle attached to the cantilever is used not only to sense the state of a SC structure, but also as a primary source of the inhomogeneous magnetic field which induces that state. Φ0-MFM enables us to map the transitions between tip-induced states during a scan: at the positions of the tip, where the two lowest energy states become degenerate, small oscillations of the tip drive the transitions between these states, which causes a significant shift in the resonant frequency and dissipation of the cantilever. For narrow-wall aluminum rings, the mapped fluxoid transitions form concentric contours on a scan. We show that the changes in the cantilever resonant frequency and dissipation are well-described by a stochastic resonance (SR) of cantilever-driven thermally activated phase slips (TAPS). The SR model allows us to experimentally determine the rate of TAPS and compare it to the Langer-Ambegaokar-McCumber-Halperin (LAMH) theory for TAPS in 1D superconducting structures. Further, we use the SR model to qualitatively study the effects of a locally applied magnetic field on the phase slip rate in rings containing constrictions. The states with multiple vortices or winding numbers could be useful for the development of novel superconducting devices, or the study of vortex interactions and interference effects. Using Φ0-MFM allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. We show that Φ0-MFM images of the fluxoid transitions allow us to identify the underlying states and to investigate their energetics and dynamics even in complicated structures."}],"_id":"10663","date_updated":"2022-01-25T15:00:26Z","date_created":"2022-01-25T14:54:14Z","type":"dissertation","alternative_title":["Graduate Dissertations and Theses at Illinois"],"article_processing_charge":"No","day":"18","author":[{"orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"}],"publisher":"University of Illinois at Urbana-Champaign","title":"Magnetic force microscopy studies of mesoscopic superconducting structures","oa_version":"Published Version"},{"quality_controlled":"1","page":"354 - 366","ddc":["572","597"],"date_updated":"2023-09-20T12:06:27Z","_id":"1067","type":"journal_article","doi":"10.1016/j.devcel.2017.01.010","article_processing_charge":"No","publisher":"Cell Press","ec_funded":1,"date_published":"2017-02-27T00:00:00Z","project":[{"call_identifier":"FP7","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","grant_number":"201439","_id":"2524F500-B435-11E9-9278-68D0E5697425"}],"publication":"Developmental Cell","status":"public","publist_id":"6320","isi":1,"year":"2017","external_id":{"isi":["000395368300007"]},"publication_status":"published","publication_identifier":{"issn":["15345807"]},"file_date_updated":"2018-12-12T10:10:57Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"intvolume":"        40","acknowledged_ssus":[{"_id":"PreCl"}],"volume":40,"date_created":"2018-12-11T11:49:58Z","author":[{"first_name":"Hitoshi","last_name":"Morita","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"first_name":"Martin","last_name":"Bock","full_name":"Bock, Martin"},{"orcid":"0000-0003-4761-5996","first_name":"Gabriel","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"scopus_import":"1","day":"27","title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","oa_version":"Published Version","issue":"4","citation":{"apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., &#38; Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>.","chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">https://doi.org/10.1016/j.devcel.2017.01.010</a>.","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” <i>Developmental Cell</i>, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. <i>Developmental Cell</i>. 2017;40(4):354-366. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.01.010\">10.1016/j.devcel.2017.01.010</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"pubrep_id":"869","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","relation":"main_file","date_updated":"2018-12-12T10:10:57Z","creator":"system","file_size":6866187,"date_created":"2018-12-12T10:10:57Z","file_id":"4849"}],"month":"02"},{"year":"2017","isi":1,"external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"publist_id":"6311","publication":"Transactions of the American Mathematical Society","status":"public","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"ec_funded":1,"date_published":"2017-05-01T00:00:00Z","acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”.","article_processing_charge":"No","doi":"10.1090/tran/6991","publisher":"American Mathematical Society","_id":"1072","date_updated":"2023-09-20T12:05:56Z","type":"journal_article","page":"3741 - 3762","main_file_link":[{"url":"https://arxiv.org/abs/1312.1231","open_access":"1"}],"quality_controlled":"1","month":"05","arxiv":1,"department":[{"_id":"HeEd"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. 2017;369(5):3741-3762. doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” <i>Transactions of the American Mathematical Society</i>, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:<a href=\"https://doi.org/10.1090/tran/6991\">10.1090/tran/6991</a>.","apa":"Bauer, U., &#38; Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6991\">https://doi.org/10.1090/tran/6991</a>"},"issue":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","scopus_import":"1","author":[{"last_name":"Bauer","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","orcid":"0000-0002-9683-0724"},{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"}],"title":"The Morse theory of Čech and delaunay complexes","oa_version":"Preprint","volume":369,"date_created":"2018-12-11T11:49:59Z","article_type":"original","abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field."}],"intvolume":"       369","publication_status":"published"},{"volume":54,"date_created":"2018-12-11T11:50:00Z","scopus_import":"1","day":"01","author":[{"first_name":"Martin","full_name":"Čadek, Martin","last_name":"Čadek"},{"first_name":"Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"},{"first_name":"Lukáš","full_name":"Vokřínek, Lukáš","last_name":"Vokřínek"}],"title":"Algorithmic solvability of the lifting extension problem","oa_version":"Submitted Version","publication_status":"published","publication_identifier":{"issn":["01795376"]},"abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}],"intvolume":"        54","department":[{"_id":"UlWa"}],"month":"06","citation":{"short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete &#38; Computational Geometry 54 (2017) 915–965.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4. Springer, pp. 915–965, 2017.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. 2017;54(4):915-965. doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:<a href=\"https://doi.org/10.1007/s00454-016-9855-6\">10.1007/s00454-016-9855-6</a>.","apa":"Čadek, M., Krcál, M., &#38; Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete &#38; Computational Geometry. 54(4), 915–965.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00454-016-9855-6\">https://doi.org/10.1007/s00454-016-9855-6</a>."},"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"_id":"1073","date_updated":"2023-09-20T12:01:28Z","type":"journal_article","article_processing_charge":"No","doi":"10.1007/s00454-016-9855-6","publisher":"Springer","main_file_link":[{"url":"https://arxiv.org/abs/1307.6444","open_access":"1"}],"quality_controlled":"1","page":"915 - 965","publist_id":"6309","year":"2017","isi":1,"external_id":{"isi":["000400072700008"]},"date_published":"2017-06-01T00:00:00Z","publication":"Discrete & Computational Geometry","status":"public"},{"oa":1,"language":[{"iso":"eng"}],"citation":{"chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>.","ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","apa":"Ringbauer, H., Coop, G., &#38; Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.116.196220\">https://doi.org/10.1534/genetics.116.196220</a>","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” <i>Genetics</i>, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. <i>Genetics</i>. 2017;205(3):1335-1351. doi:<a href=\"https://doi.org/10.1534/genetics.116.196220\">10.1534/genetics.116.196220</a>","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” <i>Genetics</i>, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351."},"issue":"3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"03","department":[{"_id":"NiBa"}],"intvolume":"       205","abstract":[{"lang":"eng","text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance."}],"publication_identifier":{"issn":["00166731"]},"publication_status":"published","day":"01","scopus_import":"1","author":[{"full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald","orcid":"0000-0002-4884-9682"},{"first_name":"Graham","full_name":"Coop, Graham","last_name":"Coop"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"}],"title":"Inferring recent demography from isolation by distance of long shared sequence blocks","oa_version":"Preprint","volume":205,"date_created":"2018-12-11T11:50:00Z","publication":"Genetics","status":"public","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"date_published":"2017-03-01T00:00:00Z","year":"2017","isi":1,"related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"external_id":{"isi":["000395807200023"]},"publist_id":"6307","page":"1335 - 1351","main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1534/genetics.116.196220","publisher":"Genetics Society of America","_id":"1074","date_updated":"2025-05-28T11:42:51Z","type":"journal_article"},{"year":"2017","date_published":"2017-03-01T00:00:00Z","conference":{"start_date":"2017-03-13","end_date":"2017-03-17","name":"APS: American Physical Society","location":"New Orleans, LA, United States"},"status":"public","extern":"1","publication":"APS March Meeting 2017","date_updated":"2022-02-08T10:44:35Z","_id":"10745","type":"conference","article_processing_charge":"No","alternative_title":["Bulletin of the American Physical Society"],"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR17/Session/P39.11"}],"quality_controlled":"1","article_number":"P39.00011","month":"03","issue":"4","citation":{"ama":"Polshyn H, Naibert T, Budakian R.  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In: <i>APS March Meeting 2017</i>. Vol 62. American Physical Society; 2017.","ieee":"H. Polshyn, T. Naibert, and R. Budakian, “ Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures,” in <i>APS March Meeting 2017</i>, New Orleans, LA, United States, 2017, vol. 62, no. 4.","short":"H. Polshyn, T. Naibert, R. Budakian, in:, APS March Meeting 2017, American Physical Society, 2017.","ista":"Polshyn H, Naibert T, Budakian R. 2017.  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. APS March Meeting 2017. APS: American Physical Society, Bulletin of the American Physical Society, vol. 62, P39.00011.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, and Raffi Budakian. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” In <i>APS March Meeting 2017</i>, Vol. 62. American Physical Society, 2017.","apa":"Polshyn, H., Naibert, T., &#38; Budakian, R. (2017).  Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures. In <i>APS March Meeting 2017</i> (Vol. 62). New Orleans, LA, United States: American Physical Society.","mla":"Polshyn, Hryhoriy, et al. “ Probing and Controlling Fluxoid States in Multiply-Connected Mesoscopic Superconducting Structures.” <i>APS March Meeting 2017</i>, vol. 62, no. 4, P39.00011, American Physical Society, 2017."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"language":[{"iso":"eng"}],"volume":62,"date_created":"2022-02-08T09:49:17Z","author":[{"orcid":"0000-0001-8223-8896","first_name":"Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","full_name":"Polshyn, Hryhoriy"},{"first_name":"Tyler","last_name":"Naibert","full_name":"Naibert, Tyler"},{"first_name":"Raffi","full_name":"Budakian, Raffi","last_name":"Budakian"}],"day":"01","oa_version":"Published Version","title":" Probing and controlling fluxoid states in multiply-connected mesoscopic superconducting structures","publication_identifier":{"issn":["0003-0503"]},"publication_status":"published","intvolume":"        62","abstract":[{"lang":"eng","text":"New ways to investigate and manipulate fluxoid and vortex states of mesoscopic superconducting structures are of great interest. The states with multiple vortices or winding numbers could be useful for the study of vortex interactions and interference effects, the braiding of Majorana bound states by winding vortices, and the development of novel superconducting devices. We demonstrate a methodology based on magnetic force microscopy that allows us to induce, probe and control fluxoid states in thin wall structures comprised of multiple loops. By using micro-magnet as a source of inhomogeneous magnetic field, we can efficiently explore the configuration space of fluxoid states. Scanning over the structure reveals the energy crossing points of the lowest laying fluxoid states. This is due the strong interaction of cantilever with thermally activated fluxoid transitions at points of degeneracy. We show that measured patterns of fluxoid transitions allow to identify the states, investigate their energetics, and manipulate them. Further, we show that the dynamics of driven fluxoid transitions can be described by stochastic resonance model, which provides a unique way of measuring fluxoid transition rate and related energy barrier for chosen transitions even in complicated structures"}]},{"publist_id":"6306","year":"2017","date_published":"2017-02-01T00:00:00Z","extern":"1","status":"public","publication":"Austria and America: 20th-Century Cross-Cultural Encounters","_id":"1075","date_updated":"2021-01-12T06:48:06Z","type":"book_chapter","alternative_title":["American Studies in Austria"],"publisher":"LIT Verlag Berlin-Münster-Wien-Zürich-London","editor":[{"full_name":"Parker, Joshua","last_name":"Parker","first_name":"Joshua"},{"full_name":"Poole, Ralph","last_name":"Poole","first_name":"Ralph"}],"page":"73 - 80","ddc":["001"],"file":[{"file_id":"4666","creator":"system","date_updated":"2018-12-12T10:08:06Z","file_size":380624,"date_created":"2018-12-12T10:08:06Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-732-v1+1_Austria_and_America_Cross-Cultural_Encounters.pdf"}],"month":"02","citation":{"ama":"Wenzl B. An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In: Parker J, Poole R, eds. <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>. Vol 15. LIT Verlag Berlin-Münster-Wien-Zürich-London; 2017:73-80.","ieee":"B. Wenzl, “An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;,” in <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, vol. 15, J. Parker and R. Poole, Eds. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","short":"B. Wenzl, in:, J. Parker, R. Poole (Eds.), Austria and America: 20th-Century Cross-Cultural Encounters, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80.","ista":"Wenzl B. 2017.An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In: Austria and America: 20th-Century Cross-Cultural Encounters. American Studies in Austria, vol. 15, 73–80.","chicago":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” In <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, 15:73–80. LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017.","apa":"Wenzl, B. (2017). An American in Allied-occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot; In J. Parker &#38; R. Poole (Eds.), <i>Austria and America: 20th-Century Cross-Cultural Encounters</i> (Vol. 15, pp. 73–80). LIT Verlag Berlin-Münster-Wien-Zürich-London.","mla":"Wenzl, Bernhard. “An American in Allied-Occupied Austria: John Dos Passos Reports on &#38;quot;The Vienna Frontier&#38;quot;” <i>Austria and America: 20th-Century Cross-Cultural Encounters</i>, edited by Joshua Parker and Ralph Poole, vol. 15, LIT Verlag Berlin-Münster-Wien-Zürich-London, 2017, pp. 73–80."},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":15,"date_created":"2018-12-11T11:50:00Z","day":"01","author":[{"last_name":"Wenzl","full_name":"Wenzl, Bernhard","id":"479E9046-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"}],"oa_version":"None","title":"An American in Allied-occupied Austria: John Dos Passos Reports on &quot;The Vienna Frontier&quot;","file_date_updated":"2018-12-12T10:08:06Z","publication_identifier":{"isbn":["978-3643908124"]},"publication_status":"published","has_accepted_license":"1","intvolume":"        15"},{"author":[{"first_name":"Michael","full_name":"Klaiber, Michael","last_name":"Klaiber"},{"first_name":"Jiří","full_name":"Daněk, Jiří","last_name":"Daněk"},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp","orcid":"0000-0001-5973-0874"},{"first_name":"Karen","last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen"},{"first_name":"Christoph","full_name":"Keitel, Christoph","last_name":"Keitel"}],"scopus_import":"1","day":"01","title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","oa_version":"Submitted Version","volume":95,"date_created":"2018-12-11T11:50:01Z","intvolume":"        95","abstract":[{"lang":"eng","text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed."}],"publication_identifier":{"issn":["24699926"]},"publication_status":"published","month":"02","department":[{"_id":"MiLe"}],"article_number":"023403","oa":1,"language":[{"iso":"eng"}],"issue":"2","citation":{"chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>.","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation.  Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>.","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., &#38; Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">https://doi.org/10.1103/PhysRevA.95.023403</a>","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2017;95(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.95.023403\">10.1103/PhysRevA.95.023403</a>","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel,  Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 95, no. 2. American Physical Society, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1103/PhysRevA.95.023403","article_processing_charge":"No","publisher":"American Physical Society","date_updated":"2023-09-20T11:57:23Z","_id":"1076","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.07018"}],"quality_controlled":"1","isi":1,"year":"2017","external_id":{"isi":["000400571700011"]},"publist_id":"6305","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","ec_funded":1,"date_published":"2017-02-01T00:00:00Z"},{"ddc":["570"],"quality_controlled":"1","publisher":"Royal Society of London","article_processing_charge":"Yes (in subscription journal)","doi":"10.1098/rsif.2016.0139","type":"journal_article","_id":"1077","date_updated":"2025-05-28T11:42:51Z","status":"public","publication":"Journal of the Royal Society Interface","project":[{"call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"date_published":"2017-01-04T00:00:00Z","ec_funded":1,"related_material":{"record":[{"id":"9864","status":"public","relation":"research_data"}]},"external_id":{"isi":["000393380400001"]},"year":"2017","isi":1,"publist_id":"6303","intvolume":"        14","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2019-01-18T09:14:02Z","publication_status":"published","publication_identifier":{"issn":["17425689"]},"oa_version":"Published Version","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","scopus_import":"1","day":"04","author":[{"first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","last_name":"Vladar","first_name":"Harold","orcid":"0000-0002-5985-7653"},{"first_name":"Tomasz","last_name":"Włodarski","full_name":"Włodarski, Tomasz"},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:50:01Z","volume":14,"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>.","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsif.2016.0139\">https://doi.org/10.1098/rsif.2016.0139</a>","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. <i>Journal of the Royal Society Interface</i>. 2017;14(126). doi:<a href=\"https://doi.org/10.1098/rsif.2016.0139\">10.1098/rsif.2016.0139</a>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” <i>Journal of the Royal Society Interface</i>, vol. 14, no. 126. Royal Society of London, 2017."},"issue":"126","month":"01","article_number":"20160139","file":[{"file_id":"5843","creator":"dernst","date_updated":"2019-01-18T09:14:02Z","date_created":"2019-01-18T09:14:02Z","file_size":1092015,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2017_JRSI_Redondo.pdf"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}]},{"author":[{"orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"day":"18","scopus_import":"1","oa_version":"Published Version","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","volume":2017,"date_created":"2018-12-11T11:50:01Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. "}],"intvolume":"      2017","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"publication_status":"published","file_date_updated":"2018-12-12T10:16:32Z","month":"01","department":[{"_id":"JiFr"},{"_id":"Bio"}],"article_number":"e55044","file":[{"file_id":"5219","creator":"system","date_updated":"2018-12-12T10:16:31Z","date_created":"2018-12-12T10:16:31Z","file_size":57678,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf"},{"file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:32Z","file_size":1317820,"date_updated":"2018-12-12T10:16:32Z","creator":"system","file_id":"5220"}],"oa":1,"pubrep_id":"808","language":[{"iso":"eng"}],"issue":"119","citation":{"ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments, 2017. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>.","apa":"von Wangenheim, D., Hauschild, R., &#38; Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of Visualized Experiments JoVE</i>. Journal of Visualized Experiments. <a href=\"https://doi.org/10.3791/55044\">https://doi.org/10.3791/55044</a>","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” <i>Journal of Visualized Experiments JoVE</i>, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. <i>Journal of visualized experiments JoVE</i>. 2017;2017(119). doi:<a href=\"https://doi.org/10.3791/55044\">10.3791/55044</a>","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” <i>Journal of visualized experiments JoVE</i>, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.3791/55044","article_processing_charge":"No","publisher":"Journal of Visualized Experiments","date_updated":"2025-05-07T11:12:33Z","_id":"1078","type":"journal_article","ddc":["580"],"year":"2017","isi":1,"external_id":{"isi":["000397847200041"]},"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5565"}]},"publist_id":"6302","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Journal of visualized experiments JoVE","ec_funded":1,"date_published":"2017-01-18T00:00:00Z"},{"publication_status":"published","publication_identifier":{"issn":["13850172"]},"intvolume":"        20","abstract":[{"text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers.","lang":"eng"}],"volume":20,"date_created":"2018-12-11T11:50:02Z","day":"01","scopus_import":"1","author":[{"first_name":"Phan","full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam"},{"first_name":"Hanne","last_name":"Van Den Bosch","full_name":"Van Den Bosch, Hanne"}],"title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","oa_version":"Submitted Version","citation":{"short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2. Springer, 2017.","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. 2017;20(2). doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>","mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 20, no. 2, 6, Springer, 2017, doi:<a href=\"https://doi.org/10.1007/s11040-017-9238-0\">10.1007/s11040-017-9238-0</a>.","apa":"Nam, P., &#38; Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11040-017-9238-0\">https://doi.org/10.1007/s11040-017-9238-0</a>.","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6."},"issue":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"article_number":"6","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.07368"}],"quality_controlled":"1","_id":"1079","date_updated":"2023-09-20T11:53:35Z","type":"journal_article","article_processing_charge":"No","doi":"10.1007/s11040-017-9238-0","publisher":"Springer","date_published":"2017-06-01T00:00:00Z","status":"public","publication":"Mathematical Physics, Analysis and Geometry","project":[{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"publist_id":"6300","year":"2017","isi":1,"external_id":{"isi":["000401270000004"]}},{"publist_id":"6301","year":"2017","isi":1,"external_id":{"isi":["000393096600001"]},"ec_funded":1,"date_published":"2017-01-31T00:00:00Z","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"publication":"Nature Communications","status":"public","date_updated":"2023-09-20T11:55:31Z","_id":"1080","type":"journal_article","doi":"10.1038/ncomms14114","article_processing_charge":"No","publisher":"Nature Publishing Group","quality_controlled":"1","ddc":["004","006"],"department":[{"_id":"KrCh"}],"file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-786-v1+1_ncomms14114.pdf","file_id":"5133","date_updated":"2018-12-12T10:15:15Z","creator":"system","file_size":897050,"date_created":"2018-12-12T10:15:15Z"}],"article_number":"14114","month":"01","citation":{"apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>, vol. 8, 14114, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>.","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14114\">https://doi.org/10.1038/ncomms14114</a>.","ieee":"J. Reiter <i>et al.</i>, “Reconstructing metastatic seeding patterns of human cancers,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14114\">10.1038/ncomms14114</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"pubrep_id":"786","language":[{"iso":"eng"}],"volume":8,"date_created":"2018-12-11T11:50:02Z","author":[{"last_name":"Reiter","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","first_name":"Johannes"},{"first_name":"Alvin","last_name":"Makohon Moore","full_name":"Makohon Moore, Alvin"},{"first_name":"Jeffrey","full_name":"Gerold, Jeffrey","last_name":"Gerold"},{"last_name":"Božić","full_name":"Božić, Ivana","first_name":"Ivana"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Iacobuzio Donahue, Christine","last_name":"Iacobuzio Donahue","first_name":"Christine"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"day":"31","scopus_import":"1","oa_version":"Published Version","title":"Reconstructing metastatic seeding patterns of human cancers","publication_identifier":{"issn":["20411723"]},"publication_status":"published","file_date_updated":"2018-12-12T10:15:15Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods.","lang":"eng"}],"intvolume":"         8"},{"article_processing_charge":"No","doi":"10.1111/mmi.13597","publisher":"Wiley-Blackwell","_id":"1084","date_updated":"2023-09-20T11:48:43Z","type":"journal_article","page":"16 - 31","quality_controlled":"1","isi":1,"year":"2017","external_id":{"isi":["000398059200002"]},"publist_id":"6294","publication":"Molecular Microbiology","status":"public","date_published":"2017-04-01T00:00:00Z","day":"01","scopus_import":"1","author":[{"first_name":"Chong","full_name":"Fang, Chong","last_name":"Fang"},{"last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A","first_name":"Anna A","orcid":"0000-0002-1391-8377"},{"full_name":"Grafe, Martin","last_name":"Grafe","first_name":"Martin"},{"first_name":"Ralf","full_name":"Heermann, Ralf","last_name":"Heermann"},{"last_name":"Jung","full_name":"Jung, Kirsten","first_name":"Kirsten"},{"first_name":"Susanne","last_name":"Gebhard","full_name":"Gebhard, Susanne"},{"last_name":"Mascher","full_name":"Mascher, Thorsten","first_name":"Thorsten"}],"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","oa_version":"None","volume":104,"date_created":"2018-12-11T11:50:03Z","abstract":[{"lang":"eng","text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities."}],"intvolume":"       104","publication_identifier":{"issn":[" 0950382X"]},"publication_status":"published","month":"04","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"citation":{"ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., &#38; Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mmi.13597\">https://doi.org/10.1111/mmi.13597</a>","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” <i>Molecular Microbiology</i>, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>.","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. <i>Molecular Microbiology</i>. 2017;104(1):16-31. doi:<a href=\"https://doi.org/10.1111/mmi.13597\">10.1111/mmi.13597</a>","ieee":"C. Fang <i>et al.</i>, “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” <i>Molecular Microbiology</i>, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31."},"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"}]