[{"publisher":"Springer Nature","day":"15","date_published":"2017-06-15T00:00:00Z","month":"06","article_number":"15651","title":"Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering","article_processing_charge":"No","intvolume":"         8","status":"public","doi":"10.1038/ncomms15651","publication_identifier":{"eissn":["2041-1723"]},"extern":"1","scopus_import":"1","year":"2017","_id":"14005","date_updated":"2023-08-22T08:26:06Z","oa":1,"publication":"Nature Communications","date_created":"2023-08-10T06:36:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"apa":"Walt, S. G., Bhargava Ram, N., Atala, M., Shvetsov-Shilovski, N. I., von Conta, A., Baykusheva, D. R., … Wörner, H. J. (2017). Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ncomms15651\">https://doi.org/10.1038/ncomms15651</a>","short":"S.G. Walt, N. Bhargava Ram, M. Atala, N.I. Shvetsov-Shilovski, A. von Conta, D.R. Baykusheva, M. Lein, H.J. Wörner, Nature Communications 8 (2017).","chicago":"Walt, Samuel G., Niraghatam Bhargava Ram, Marcos Atala, Nikolay I Shvetsov-Shilovski, Aaron von Conta, Denitsa Rangelova Baykusheva, Manfred Lein, and Hans Jakob Wörner. “Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography and Rescattering.” <i>Nature Communications</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/ncomms15651\">https://doi.org/10.1038/ncomms15651</a>.","ama":"Walt SG, Bhargava Ram N, Atala M, et al. Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15651\">10.1038/ncomms15651</a>","mla":"Walt, Samuel G., et al. “Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography and Rescattering.” <i>Nature Communications</i>, vol. 8, 15651, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15651\">10.1038/ncomms15651</a>.","ieee":"S. G. Walt <i>et al.</i>, “Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering,” <i>Nature Communications</i>, vol. 8. Springer Nature, 2017.","ista":"Walt SG, Bhargava Ram N, Atala M, Shvetsov-Shilovski NI, von Conta A, Baykusheva DR, Lein M, Wörner HJ. 2017. Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering. Nature Communications. 8, 15651."},"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"volume":8,"author":[{"first_name":"Samuel G.","last_name":"Walt","full_name":"Walt, Samuel G."},{"full_name":"Bhargava Ram, Niraghatam","last_name":"Bhargava Ram","first_name":"Niraghatam"},{"last_name":"Atala","full_name":"Atala, Marcos","first_name":"Marcos"},{"last_name":"Shvetsov-Shilovski","full_name":"Shvetsov-Shilovski, Nikolay I","first_name":"Nikolay I"},{"first_name":"Aaron","full_name":"von Conta, Aaron","last_name":"von Conta"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"full_name":"Lein, Manfred","last_name":"Lein","first_name":"Manfred"},{"last_name":"Wörner","full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob"}],"pmid":1,"external_id":{"pmid":["28643771"]},"quality_controlled":"1","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms15651"}],"abstract":[{"lang":"eng","text":"Strong-field photoelectron holography and laser-induced electron diffraction (LIED) are two powerful emerging methods for probing the ultrafast dynamics of molecules. However, both of them have remained restricted to static systems and to nuclear dynamics induced by strong-field ionization. Here we extend these promising methods to image purely electronic valence-shell dynamics in molecules using photoelectron holography. In the same experiment, we use LIED and photoelectron holography simultaneously, to observe coupled electronic-rotational dynamics taking place on similar timescales. These results offer perspectives for imaging ultrafast dynamics of molecules on femtosecond to attosecond timescales."}],"type":"journal_article"},{"article_type":"original","issue":"12","type":"journal_article","abstract":[{"lang":"eng","text":"We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N2O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H2O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology."}],"pmid":1,"author":[{"full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","first_name":"Denitsa Rangelova"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"volume":146,"quality_controlled":"1","external_id":{"pmid":["28388142"]},"date_created":"2023-08-10T06:36:19Z","publication":"The Journal of Chemical Physics","_id":"14006","date_updated":"2023-08-22T08:30:59Z","year":"2017","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"citation":{"mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond Delays in Molecular Photoionization.” <i>The Journal of Chemical Physics</i>, vol. 146, no. 12, 124306, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4977933\">10.1063/1.4977933</a>.","ieee":"D. R. Baykusheva and H. J. Wörner, “Theory of attosecond delays in molecular photoionization,” <i>The Journal of Chemical Physics</i>, vol. 146, no. 12. AIP Publishing, 2017.","short":"D.R. Baykusheva, H.J. Wörner, The Journal of Chemical Physics 146 (2017).","apa":"Baykusheva, D. R., &#38; Wörner, H. J. (2017). Theory of attosecond delays in molecular photoionization. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4977933\">https://doi.org/10.1063/1.4977933</a>","ama":"Baykusheva DR, Wörner HJ. Theory of attosecond delays in molecular photoionization. <i>The Journal of Chemical Physics</i>. 2017;146(12). doi:<a href=\"https://doi.org/10.1063/1.4977933\">10.1063/1.4977933</a>","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Theory of Attosecond Delays in Molecular Photoionization.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4977933\">https://doi.org/10.1063/1.4977933</a>.","ista":"Baykusheva DR, Wörner HJ. 2017. Theory of attosecond delays in molecular photoionization. The Journal of Chemical Physics. 146(12), 124306."},"oa_version":"None","language":[{"iso":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       146","article_processing_charge":"No","title":"Theory of attosecond delays in molecular photoionization","article_number":"124306","month":"03","date_published":"2017-03-28T00:00:00Z","day":"28","publisher":"AIP Publishing","scopus_import":"1","extern":"1","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"status":"public","doi":"10.1063/1.4977933"},{"citation":{"ista":"Baykusheva DR, Wörner HJ. 2017. Comment on ‘Time delays in molecular photoionization’. Journal of Physics B: Atomic, Molecular and Optical Physics. 50(7), 078002.","apa":"Baykusheva, D. R., &#38; Wörner, H. J. (2017). Comment on ‘Time delays in molecular photoionization.’ <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6455/aa62b5\">https://doi.org/10.1088/1361-6455/aa62b5</a>","short":"D.R. Baykusheva, H.J. Wörner, Journal of Physics B: Atomic, Molecular and Optical Physics 50 (2017).","ama":"Baykusheva DR, Wörner HJ. Comment on ‘Time delays in molecular photoionization.’ <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>. 2017;50(7). doi:<a href=\"https://doi.org/10.1088/1361-6455/aa62b5\">10.1088/1361-6455/aa62b5</a>","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time Delays in Molecular Photoionization.’” <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>. IOP Publishing, 2017. <a href=\"https://doi.org/10.1088/1361-6455/aa62b5\">https://doi.org/10.1088/1361-6455/aa62b5</a>.","mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Comment on ‘Time Delays in Molecular Photoionization.’” <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>, vol. 50, no. 7, 078002, IOP Publishing, 2017, doi:<a href=\"https://doi.org/10.1088/1361-6455/aa62b5\">10.1088/1361-6455/aa62b5</a>.","ieee":"D. R. Baykusheva and H. J. Wörner, “Comment on ‘Time delays in molecular photoionization,’” <i>Journal of Physics B: Atomic, Molecular and Optical Physics</i>, vol. 50, no. 7. IOP Publishing, 2017."},"keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"oa_version":"Preprint","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","arxiv":1,"date_created":"2023-08-10T06:36:29Z","oa":1,"publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","date_updated":"2023-08-22T08:32:43Z","_id":"14007","year":"2017","scopus_import":"1","publication_identifier":{"eissn":["1361-6455"],"issn":["0953-4075"]},"extern":"1","status":"public","doi":"10.1088/1361-6455/aa62b5","article_processing_charge":"No","title":"Comment on ‘Time delays in molecular photoionization’","intvolume":"        50","article_number":"078002","date_published":"2017-03-15T00:00:00Z","month":"03","publisher":"IOP Publishing","day":"15","issue":"7","type":"journal_article","abstract":[{"text":"In a recent article by Hockett et al (2016 J. Phys. B: At. Mol. Opt. Phys. 49 095602), time delays arising in the context of molecular single-photon ionization are investigated from a theoretical point of view. We argue that one of the central equations given in this article is incorrect and present a reformulation that is consistent with the established treatment of angle-dependent scattering delays (Eisenbud 1948 PhD Thesis Princeton University; Wigner 1955 Phys. Rev. 98 145–7; Smith 1960 Phys. Rev. 118 349–6; Nussenzveig 1972 Phys. Rev. D 6 1534–42).","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.09352"}],"article_type":"letter_note","quality_controlled":"1","external_id":{"arxiv":["1611.09352"]},"author":[{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Wörner","full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob"}],"volume":50},{"title":"Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source","article_processing_charge":"No","intvolume":"       355","month":"01","date_published":"2017-01-05T00:00:00Z","day":"05","publisher":"American Association for the Advancement of Science","scopus_import":"1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"extern":"1","status":"public","doi":"10.1126/science.aah6114","date_created":"2023-08-10T06:36:39Z","publication":"Science","year":"2017","_id":"14008","date_updated":"2023-08-22T08:34:38Z","citation":{"ista":"Pertot Y, Schmidt C, Matthews M, Chauvet A, Huppert M, Svoboda V, von Conta A, Tehlar A, Baykusheva DR, Wolf J-P, Wörner HJ. 2017. Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source. Science. 355(6322), 264–267.","short":"Y. Pertot, C. Schmidt, M. Matthews, A. Chauvet, M. Huppert, V. Svoboda, A. von Conta, A. Tehlar, D.R. Baykusheva, J.-P. Wolf, H.J. Wörner, Science 355 (2017) 264–267.","apa":"Pertot, Y., Schmidt, C., Matthews, M., Chauvet, A., Huppert, M., Svoboda, V., … Wörner, H. J. (2017). Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aah6114\">https://doi.org/10.1126/science.aah6114</a>","chicago":"Pertot, Yoann, Cédric Schmidt, Mary Matthews, Adrien Chauvet, Martin Huppert, Vit Svoboda, Aaron von Conta, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water Window High-Harmonic Source.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aah6114\">https://doi.org/10.1126/science.aah6114</a>.","ama":"Pertot Y, Schmidt C, Matthews M, et al. Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source. <i>Science</i>. 2017;355(6322):264-267. doi:<a href=\"https://doi.org/10.1126/science.aah6114\">10.1126/science.aah6114</a>","mla":"Pertot, Yoann, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water Window High-Harmonic Source.” <i>Science</i>, vol. 355, no. 6322, American Association for the Advancement of Science, 2017, pp. 264–67, doi:<a href=\"https://doi.org/10.1126/science.aah6114\">10.1126/science.aah6114</a>.","ieee":"Y. Pertot <i>et al.</i>, “Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source,” <i>Science</i>, vol. 355, no. 6322. American Association for the Advancement of Science, pp. 264–267, 2017."},"keyword":["Multidisciplinary"],"oa_version":"None","language":[{"iso":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"264-267","author":[{"first_name":"Yoann","last_name":"Pertot","full_name":"Pertot, Yoann"},{"first_name":"Cédric","full_name":"Schmidt, Cédric","last_name":"Schmidt"},{"last_name":"Matthews","full_name":"Matthews, Mary","first_name":"Mary"},{"first_name":"Adrien","last_name":"Chauvet","full_name":"Chauvet, Adrien"},{"full_name":"Huppert, Martin","last_name":"Huppert","first_name":"Martin"},{"last_name":"Svoboda","full_name":"Svoboda, Vit","first_name":"Vit"},{"first_name":"Aaron","last_name":"von Conta","full_name":"von Conta, Aaron"},{"full_name":"Tehlar, Andres","last_name":"Tehlar","first_name":"Andres"},{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"},{"first_name":"Jean-Pierre","full_name":"Wolf, Jean-Pierre","last_name":"Wolf"},{"first_name":"Hans Jakob","last_name":"Wörner","full_name":"Wörner, Hans Jakob"}],"pmid":1,"volume":355,"quality_controlled":"1","external_id":{"pmid":["28059713"]},"article_type":"original","issue":"6322","type":"journal_article","abstract":[{"text":"Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically been limited to large-scale facilities, to subpicosecond temporal resolution, and to the condensed phase. We report the realization of TR-XAS with a temporal resolution in the low femtosecond range by developing a tabletop high-harmonic source reaching up to 350 electron volts, thus partially covering the spectral region of 280 to 530 electron volts, where water is transmissive. We used this source to follow previously unexamined light-induced chemical reactions in the lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase. By probing element-specific core-to-valence transitions at the carbon K-edge or the sulfur L-edges, we characterized their reaction paths and observed the effect of symmetry breaking through the splitting of absorption bands and Rydberg-valence mixing induced by the geometry changes.","lang":"eng"}]},{"date_published":"2017-01-10T00:00:00Z","month":"01","day":"10","volume":95,"publisher":"American Physical Society","article_processing_charge":"No","title":"Spin-orbit delays in photoemission","intvolume":"        95","article_number":"013404","author":[{"last_name":"Jordan","full_name":"Jordan, I.","first_name":"I."},{"first_name":"M.","last_name":"Huppert","full_name":"Huppert, M."},{"first_name":"S.","full_name":"Pabst, S.","last_name":"Pabst"},{"last_name":"Kheifets","full_name":"Kheifets, A. S.","first_name":"A. S."},{"last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova"},{"first_name":"H. J.","last_name":"Wörner","full_name":"Wörner, H. J."}],"doi":"10.1103/physreva.95.013404","status":"public","scopus_import":"1","quality_controlled":"1","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"extern":"1","_id":"14009","date_updated":"2023-08-22T08:38:17Z","year":"2017","article_type":"original","date_created":"2023-08-10T06:36:58Z","publication":"Physical Review A","language":[{"iso":"eng"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Attosecond delays between photoelectron wave packets emitted from different electronic shells are now well established. Is there any delay between electrons originating from the same electronic shell but leaving the cation in different fine-structure states? This question is relevant for all attosecond photoemission studies involving heavy elements, be it atoms, molecules or solids. We answer this fundamental question by measuring energy-dependent delays between photoelectron wave packets associated with the 2P3/2 and 2P1/2 components of the electronic groundstates of Xe+ and Kr+. We observe delays reaching up to 33±6 as in the case of Xe. Our results are compared with two state-of-the-art theories. Whereas both theories quantitatively agree with the results obtained for Kr, neither of them fully reproduces the experimental results in Xe. Performing delay measurements very close to the ionization thresholds, we compare the agreement of several analytical formulas for the continuum-continuum delays with experimental data. Our results show an important influence of spin-orbit coupling on attosecond photoionization delays, highlight the requirement for additional theory development, and offer a precision benchmark for such work."}],"citation":{"ista":"Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. 2017. Spin-orbit delays in photoemission. Physical Review A. 95(1), 013404.","ieee":"I. Jordan, M. Huppert, S. Pabst, A. S. Kheifets, D. R. Baykusheva, and H. J. Wörner, “Spin-orbit delays in photoemission,” <i>Physical Review A</i>, vol. 95, no. 1. American Physical Society, 2017.","mla":"Jordan, I., et al. “Spin-Orbit Delays in Photoemission.” <i>Physical Review A</i>, vol. 95, no. 1, 013404, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/physreva.95.013404\">10.1103/physreva.95.013404</a>.","chicago":"Jordan, I., M. Huppert, S. Pabst, A. S. Kheifets, Denitsa Rangelova Baykusheva, and H. J. Wörner. “Spin-Orbit Delays in Photoemission.” <i>Physical Review A</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/physreva.95.013404\">https://doi.org/10.1103/physreva.95.013404</a>.","ama":"Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. Spin-orbit delays in photoemission. <i>Physical Review A</i>. 2017;95(1). doi:<a href=\"https://doi.org/10.1103/physreva.95.013404\">10.1103/physreva.95.013404</a>","apa":"Jordan, I., Huppert, M., Pabst, S., Kheifets, A. S., Baykusheva, D. R., &#38; Wörner, H. J. (2017). Spin-orbit delays in photoemission. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.95.013404\">https://doi.org/10.1103/physreva.95.013404</a>","short":"I. Jordan, M. Huppert, S. Pabst, A.S. Kheifets, D.R. Baykusheva, H.J. Wörner, Physical Review A 95 (2017)."},"issue":"1","oa_version":"None"},{"quality_controlled":"1","external_id":{"pmid":["29219334"],"arxiv":["1710.04474"]},"volume":119,"author":[{"first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"full_name":"Brennecke, Simon","last_name":"Brennecke","first_name":"Simon"},{"first_name":"Manfred","full_name":"Lein, Manfred","last_name":"Lein"},{"full_name":"Wörner, Hans Jakob","last_name":"Wörner","first_name":"Hans Jakob"}],"pmid":1,"type":"journal_article","abstract":[{"text":"High-harmonic spectroscopy driven by circularly polarized laser pulses and their counterrotating second harmonic is a new branch of attosecond science which currently lacks quantitative interpretations. We extend this technique to the midinfrared regime and record detailed high-harmonic spectra of several rare-gas atoms. These results are compared with the solution of the Schrödinger equation in three dimensions and calculations based on the strong-field approximation that incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit analysis of these results provides a transparent interpretation of the measured intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set of propensity rules related to the angular momentum of the atomic orbitals, (ii) atom-specific matrix elements related to their electronic structure, and (iii) the interference of the emissions associated with electrons in orbitals corotating or counterrotating with the laser fields. These results provide the foundation for a quantitative understanding of bicircular high-harmonic spectroscopy.","lang":"eng"}],"issue":"20","article_type":"original","main_file_link":[{"url":"https://arxiv.org/abs/1710.04474","open_access":"1"}],"status":"public","doi":"10.1103/physrevlett.119.203201","scopus_import":"1","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"extern":"1","date_published":"2017-11-17T00:00:00Z","month":"11","day":"17","publisher":"American Physical Society","title":"Signatures of electronic structure in bicircular high-harmonic spectroscopy","article_processing_charge":"No","intvolume":"       119","article_number":"203201","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","arxiv":1,"citation":{"ista":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20), 203201.","mla":"Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” <i>Physical Review Letters</i>, vol. 119, no. 20, 203201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/physrevlett.119.203201\">10.1103/physrevlett.119.203201</a>.","ieee":"D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of electronic structure in bicircular high-harmonic spectroscopy,” <i>Physical Review Letters</i>, vol. 119, no. 20. American Physical Society, 2017.","short":"D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters 119 (2017).","apa":"Baykusheva, D. R., Brennecke, S., Lein, M., &#38; Wörner, H. J. (2017). Signatures of electronic structure in bicircular high-harmonic spectroscopy. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.119.203201\">https://doi.org/10.1103/physrevlett.119.203201</a>","chicago":"Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic Spectroscopy.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/physrevlett.119.203201\">https://doi.org/10.1103/physrevlett.119.203201</a>.","ama":"Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure in bicircular high-harmonic spectroscopy. <i>Physical Review Letters</i>. 2017;119(20). doi:<a href=\"https://doi.org/10.1103/physrevlett.119.203201\">10.1103/physrevlett.119.203201</a>"},"keyword":["General Physics and Astronomy"],"oa_version":"Preprint","_id":"14031","date_updated":"2023-08-22T06:48:28Z","year":"2017","date_created":"2023-08-10T06:48:12Z","oa":1,"publication":"Physical Review Letters"},{"publication":"Nonlinear Analysis: Hybrid Systems","oa":1,"date_created":"2018-12-11T11:51:50Z","_id":"1407","date_updated":"2023-09-20T09:43:09Z","year":"2017","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"oa_version":"Preprint","citation":{"ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &#38; Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">https://doi.org/10.1016/j.nahs.2016.04.006</a>.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. <i>Nonlinear Analysis: Hybrid Systems</i>. 2017;23(2):230-253. doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.04.006\">10.1016/j.nahs.2016.04.006</a>.","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, no. 2. Elsevier, pp. 230–253, 2017."},"arxiv":1,"page":"230 - 253","related_material":{"record":[{"id":"1689","status":"public","relation":"earlier_version"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","language":[{"iso":"eng"}],"intvolume":"        23","publist_id":"5800","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","article_processing_charge":"No","day":"01","publisher":"Elsevier","date_published":"2017-02-01T00:00:00Z","month":"02","scopus_import":"1","doi":"10.1016/j.nahs.2016.04.006","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"issue":"2","abstract":[{"lang":"eng","text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study."}],"type":"journal_article","author":[{"first_name":"Mária","last_name":"Svoreňová","full_name":"Svoreňová, Mária"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan"},{"first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cěrná","full_name":"Cěrná, Ivana","first_name":"Ivana"},{"last_name":"Belta","full_name":"Belta, Cǎlin","first_name":"Cǎlin"}],"volume":23,"ec_funded":1,"external_id":{"arxiv":["1410.5387"],"isi":["000390637000014"]},"quality_controlled":"1","isi":1},{"date_published":"2017-02-21T00:00:00Z","month":"02","publisher":"ML Research Press","day":"21","article_processing_charge":"No","title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","intvolume":"        54","status":"public","extern":"1","department":[{"_id":"FrLo"}],"_id":"14205","year":"2017","date_updated":"2023-09-13T09:49:10Z","date_created":"2023-08-22T14:17:19Z","oa":1,"publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","page":"860-868","arxiv":1,"citation":{"ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>. Vol 54. ML Research Press; 2017:860-868.","chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, 54:860–68. ML Research Press, 2017.","apa":"Locatello, F., Khanna, R., Tschannen, M., &#38; Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i> (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.","short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.","mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, vol. 54, ML Research Press, 2017, pp. 860–68.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868."},"oa_version":"Preprint","volume":54,"author":[{"orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"last_name":"Khanna","full_name":"Khanna, Rajiv","first_name":"Rajiv"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"quality_controlled":"1","external_id":{"arxiv":["1702.06457"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.06457"}],"conference":{"location":"Fort Lauderdale, FL, United States","name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2017-04-20","end_date":"2017-04-22"},"type":"conference","abstract":[{"text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions.","lang":"eng"}]},{"date_published":"2017-05-31T00:00:00Z","month":"05","day":"31","article_processing_charge":"No","title":"Greedy algorithms for cone constrained optimization with convergence guarantees","author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello"},{"last_name":"Tschannen","full_name":"Tschannen, Michael","first_name":"Michael"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"full_name":"Jaggi, Martin","last_name":"Jaggi","first_name":"Martin"}],"status":"public","quality_controlled":"1","extern":"1","external_id":{"arxiv":["1705.11041"]},"publication_identifier":{"isbn":["9781510860964"]},"department":[{"_id":"FrLo"}],"_id":"14206","year":"2017","date_updated":"2023-09-13T08:32:23Z","date_created":"2023-08-22T14:17:38Z","publication":"Advances in Neural Information Processing Systems","conference":{"end_date":"2017-12-09","name":"NeurIPS: Neural Information Processing Systems","start_date":"2017-12-04","location":"Long Beach, CA, United States"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.11041"}],"language":[{"iso":"eng"}],"type":"conference","arxiv":1,"abstract":[{"lang":"eng","text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in <i>Advances in Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” <i>Advances in Neural Information Processing Systems</i>, 2017.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In <i>Advances in Neural Information Processing Systems</i>, 2017.","ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: <i>Advances in Neural Information Processing Systems</i>. ; 2017.","apa":"Locatello, F., Tschannen, M., Rätsch, G., &#38; Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In <i>Advances in Neural Information Processing Systems</i>. Long Beach, CA, United States.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017.","ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems."},"oa_version":"Preprint"},{"abstract":[{"text":"The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection, and specific growth rate. The specific growth rate and the multiplicity of infection were identified as the crucial state variables that influence phage amplification rate on one hand and the concentration of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784.","lang":"eng"}],"type":"journal_article","issue":"4","article_type":"original","external_id":{"pmid":["27748519"]},"quality_controlled":"1","volume":114,"author":[{"first_name":"Benjamin","full_name":"Kick, Benjamin","last_name":"Kick"},{"first_name":"Samantha","last_name":"Hensler","full_name":"Hensler, Samantha"},{"first_name":"Florian M","full_name":"Praetorius, Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"},{"first_name":"Dirk","full_name":"Weuster-Botz, Dirk","last_name":"Weuster-Botz"}],"pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"777-784","language":[{"iso":"eng"}],"oa_version":"None","citation":{"mla":"Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” <i>Biotechnology and Bioengineering</i>, vol. 114, no. 4, Wiley, 2017, pp. 777–84, doi:<a href=\"https://doi.org/10.1002/bit.26200\">10.1002/bit.26200</a>.","ieee":"B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production,” <i>Biotechnology and Bioengineering</i>, vol. 114, no. 4. Wiley, pp. 777–784, 2017.","apa":"Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., &#38; Weuster-Botz, D. (2017). Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. <i>Biotechnology and Bioengineering</i>. Wiley. <a href=\"https://doi.org/10.1002/bit.26200\">https://doi.org/10.1002/bit.26200</a>","short":"B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology and Bioengineering 114 (2017) 777–784.","ama":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. <i>Biotechnology and Bioengineering</i>. 2017;114(4):777-784. doi:<a href=\"https://doi.org/10.1002/bit.26200\">10.1002/bit.26200</a>","chicago":"Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz, and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” <i>Biotechnology and Bioengineering</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/bit.26200\">https://doi.org/10.1002/bit.26200</a>.","ista":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. 114(4), 777–784."},"keyword":["Applied Microbiology and Biotechnology","Bioengineering","Biotechnology"],"year":"2017","_id":"14286","date_updated":"2023-11-07T12:36:20Z","publication":"Biotechnology and Bioengineering","date_created":"2023-09-06T12:08:29Z","status":"public","doi":"10.1002/bit.26200","publication_identifier":{"issn":["0006-3592"]},"extern":"1","scopus_import":"1","day":"01","publisher":"Wiley","date_published":"2017-04-01T00:00:00Z","month":"04","title":"Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production","article_processing_charge":"No","intvolume":"       114"},{"external_id":{"pmid":["28336611"]},"quality_controlled":"1","author":[{"first_name":"Florian M","full_name":"Praetorius, Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Dietz","full_name":"Dietz, Hendrik","first_name":"Hendrik"}],"pmid":1,"volume":355,"issue":"6331","abstract":[{"text":"We describe an approach to bottom-up fabrication that allows integration of the functional diversity of proteins into designed three-dimensional structural frameworks. A set of custom staple proteins based on transcription activator–like effector proteins folds a double-stranded DNA template into a user-defined shape. Each staple protein is designed to recognize and closely link two distinct double-helical DNA sequences at separate positions on the template. We present design rules for constructing megadalton-scale DNA-protein hybrid shapes; introduce various structural motifs, such as custom curvature, corners, and vertices; and describe principles for creating multilayer DNA-protein objects with enhanced rigidity. We demonstrate self-assembly of our hybrid nanostructures in one-pot mixtures that include the genetic information for the designed proteins, the template DNA, RNA polymerase, ribosomes, and cofactors for transcription and translation.","lang":"eng"}],"type":"journal_article","article_type":"original","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"extern":"1","scopus_import":"1","doi":"10.1126/science.aam5488","status":"public","article_number":"eaam5488","title":"Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes","article_processing_charge":"No","intvolume":"       355","publisher":"American Association for the Advancement of Science","day":"24","date_published":"2017-03-24T00:00:00Z","month":"03","oa_version":"None","citation":{"chicago":"Praetorius, Florian M, and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aam5488\">https://doi.org/10.1126/science.aam5488</a>.","ama":"Praetorius FM, Dietz H. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. <i>Science</i>. 2017;355(6331). doi:<a href=\"https://doi.org/10.1126/science.aam5488\">10.1126/science.aam5488</a>","short":"F.M. Praetorius, H. Dietz, Science 355 (2017).","apa":"Praetorius, F. M., &#38; Dietz, H. (2017). Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aam5488\">https://doi.org/10.1126/science.aam5488</a>","ieee":"F. M. Praetorius and H. Dietz, “Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes,” <i>Science</i>, vol. 355, no. 6331. American Association for the Advancement of Science, 2017.","mla":"Praetorius, Florian M., and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” <i>Science</i>, vol. 355, no. 6331, eaam5488, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/science.aam5488\">10.1126/science.aam5488</a>.","ista":"Praetorius FM, Dietz H. 2017. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Science. 355(6331), eaam5488."},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Science","date_created":"2023-09-06T12:08:55Z","_id":"14287","date_updated":"2023-11-07T12:33:05Z","year":"2017"},{"abstract":[{"lang":"eng","text":"DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12. These structures are customizable in that they can be site-specifically functionalized13 or constructed to exhibit machine-like14,15 or logic-gating behaviour16. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials3,16,17,18,19,20,21,22, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production23; the shorter staple strands are obtained through costly solid-phase synthesis24 or enzymatic processes25. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in many areas of science and technology."}],"type":"journal_article","issue":"7683","article_type":"original","external_id":{"pmid":["29219963"]},"quality_controlled":"1","volume":552,"pmid":1,"author":[{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M"},{"first_name":"Benjamin","full_name":"Kick, Benjamin","last_name":"Kick"},{"full_name":"Behler, Karl L.","last_name":"Behler","first_name":"Karl L."},{"full_name":"Honemann, Maximilian N.","last_name":"Honemann","first_name":"Maximilian N."},{"first_name":"Dirk","full_name":"Weuster-Botz, Dirk","last_name":"Weuster-Botz"},{"first_name":"Hendrik","last_name":"Dietz","full_name":"Dietz, Hendrik"}],"page":"84-87","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"oa_version":"None","citation":{"ista":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. 2017. Biotechnological mass production of DNA origami. Nature. 552(7683), 84–87.","mla":"Praetorius, Florian M., et al. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>, vol. 552, no. 7683, Springer Nature, 2017, pp. 84–87, doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>.","ieee":"F. M. Praetorius, B. Kick, K. L. Behler, M. N. Honemann, D. Weuster-Botz, and H. Dietz, “Biotechnological mass production of DNA origami,” <i>Nature</i>, vol. 552, no. 7683. Springer Nature, pp. 84–87, 2017.","apa":"Praetorius, F. M., Kick, B., Behler, K. L., Honemann, M. N., Weuster-Botz, D., &#38; Dietz, H. (2017). Biotechnological mass production of DNA origami. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>","short":"F.M. Praetorius, B. Kick, K.L. Behler, M.N. Honemann, D. Weuster-Botz, H. Dietz, Nature 552 (2017) 84–87.","ama":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. Biotechnological mass production of DNA origami. <i>Nature</i>. 2017;552(7683):84-87. doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>","chicago":"Praetorius, Florian M, Benjamin Kick, Karl L. Behler, Maximilian N. Honemann, Dirk Weuster-Botz, and Hendrik Dietz. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>."},"_id":"14290","date_updated":"2023-11-07T12:24:49Z","year":"2017","publication":"Nature","date_created":"2023-09-06T12:14:20Z","status":"public","doi":"10.1038/nature24650","extern":"1","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"scopus_import":"1","day":"07","publisher":"Springer Nature","date_published":"2017-12-07T00:00:00Z","month":"12","intvolume":"       552","article_processing_charge":"No","title":"Biotechnological mass production of DNA origami"},{"type":"journal_article","abstract":[{"text":"Here we describe an approach to bottom-up fabrication with nanometer-precision that allows integrating the functional diversity of proteins in designed three-dimensional structural frameworks. We reimagined the successful DNA origami design principle using a set of custom staple proteins to fold a double-stranded DNA template into a user-defined shape. Each staple protein recognizes two distinct double-helical DNA sequences and can carry additional functionalities. The staple proteins we present here are based on the transcription activator-like (TAL) effector proteins. Due to their repetitive structure these proteins offer a unique programmability that enables us to construct numerous staple proteins targeting any desired DNA sequence. Our approach is general, meaning that many different objects may be created using the same set of rules, and it is modular, because components can be modified or exchanged individually. We present rules for constructing megadalton-scale DNA-protein hybrid nanostructures; introduce important structural motifs, such as curvature, corners, and vertices; describe principles for creating multi-layer DNA-protein objects with enhanced rigidity; and demonstrate the possibility to combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since all components can be encoded genetically, our structures should be amenable to biotechnological mass-production. Moreover, since the target objects can self-assemble at room temperature in near-physiological buffer, our hybrid origami may also provide an attractive method to realize positioning and scaffolding tasks in vivo. We expect our method to find application both in scaffolding protein functionalities and in manipulating the spatial arrangement of genomic DNA.","lang":"eng"}],"issue":"3","article_type":"original","quality_controlled":"1","volume":112,"author":[{"last_name":"Praetorius","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"},{"last_name":"Dietz","full_name":"Dietz, Hendrik","first_name":"Hendrik"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"ista":"Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 112(3), 25a.","mla":"Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>, vol. 112, no. 3, 25a, Elsevier, 2017, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>.","ieee":"F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,” <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier, 2017.","apa":"Praetorius, F. M., &#38; Dietz, H. (2017). Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>","short":"F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).","ama":"Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. 2017;112(3). doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>","chicago":"Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>."},"keyword":["Biophysics"],"oa_version":"None","date_updated":"2023-11-07T11:28:58Z","_id":"14308","year":"2017","date_created":"2023-09-06T13:19:10Z","publication":"Biophysical Journal","status":"public","doi":"10.1016/j.bpj.2016.11.171","scopus_import":"1","publication_identifier":{"issn":["0006-3495"]},"extern":"1","date_published":"2017-02-03T00:00:00Z","month":"02","day":"03","publisher":"Elsevier","article_processing_charge":"No","title":"Genetically encoded DNA-protein hybrid origami","intvolume":"       112","article_number":"25a"},{"volume":16,"pmid":1,"author":[{"first_name":"M","last_name":"Siavashpouri","full_name":"Siavashpouri, M"},{"first_name":"CH","last_name":"Wachauf","full_name":"Wachauf, CH"},{"last_name":"Zakhary","full_name":"Zakhary, MJ","first_name":"MJ"},{"last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","first_name":"Florian M"},{"first_name":"H","full_name":"Dietz, H","last_name":"Dietz"},{"last_name":"Dogic","full_name":"Dogic, Z","first_name":"Z"}],"external_id":{"pmid":["28530665"],"arxiv":["1705.08944"]},"quality_controlled":"1","article_type":"original","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1705.08944","open_access":"1"}],"abstract":[{"lang":"eng","text":"Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials."}],"type":"journal_article","issue":"8","day":"22","publisher":"Springer Nature","month":"05","date_published":"2017-05-22T00:00:00Z","intvolume":"        16","article_processing_charge":"No","title":"Molecular engineering of chiral colloidal liquid crystals using DNA origami","doi":"10.1038/nmat4909","status":"public","extern":"1","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"scopus_import":"1","_id":"14309","date_updated":"2023-11-07T11:40:00Z","year":"2017","publication":"Nature Materials","oa":1,"date_created":"2023-09-06T13:37:27Z","page":"849-856","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","language":[{"iso":"eng"}],"oa_version":"Preprint","citation":{"short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, Nature Materials 16 (2017) 849–856.","apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &#38; Dogic, Z. (2017). Molecular engineering of chiral colloidal liquid crystals using DNA origami. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nmat4909\">https://doi.org/10.1038/nmat4909</a>","ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of chiral colloidal liquid crystals using DNA origami. <i>Nature Materials</i>. 2017;16(8):849-856. doi:<a href=\"https://doi.org/10.1038/nmat4909\">10.1038/nmat4909</a>","chicago":"Siavashpouri, M, CH Wachauf, MJ Zakhary, Florian M Praetorius, H Dietz, and Z Dogic. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” <i>Nature Materials</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nmat4909\">https://doi.org/10.1038/nmat4909</a>.","mla":"Siavashpouri, M., et al. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” <i>Nature Materials</i>, vol. 16, no. 8, Springer Nature, 2017, pp. 849–56, doi:<a href=\"https://doi.org/10.1038/nmat4909\">10.1038/nmat4909</a>.","ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of chiral colloidal liquid crystals using DNA origami,” <i>Nature Materials</i>, vol. 16, no. 8. Springer Nature, pp. 849–856, 2017.","ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. 16(8), 849–856."}},{"_id":"9065","year":"2017","date_updated":"2021-02-03T12:53:00Z","article_type":"original","date_created":"2021-02-02T15:49:21Z","publication":"Physical Review B","type":"journal_article","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Magnetic anisotropy in strontium iridate (Sr2IrO4) is found to be large because of the strong spin-orbit interactions. In our work, we studied the in-plane magnetic anisotropy of Sr2IrO4 and traced the anisotropic exchange interactions between the isospins in the crystal. The magnetic-field-dependent torque τ(H) showed a prominent transition from the canted antiferromagnetic state to the weak ferromagnetic (WFM) state. A comprehensive analysis was conducted to examine the isotropic and anisotropic regimes and probe the easy magnetization axis along the a b plane. The angle-dependent torque τ(θ) revealed a deviation from the sinusoidal behavior, and small differences in hysteresis were observed around 0° and 90° in the low-magnetic-field regime. This indicates that the orientation of the easy axis of the FM component is along the b axis, where the antiferromagnetic to WFM spin-flop transition occurs. We compared the coefficients of the magnetic susceptibility tensors and captured the anisotropy of the material. The in-plane τ(θ) revealed a tendency toward isotropic behavior for fields with values above the field value of the WFM transition.","lang":"eng"}],"citation":{"ista":"Nauman M, Hong Y, Hussain T, Seo MS, Park SY, Lee N, Choi YJ, Kang W, Jo Y. 2017. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical Review B. 96(15), 155102.","mla":"Nauman, Muhammad, et al. “In-Plane Magnetic Anisotropy in Strontium Iridate Sr2IrO4.” <i>Physical Review B</i>, vol. 96, no. 15, 155102, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/physrevb.96.155102\">10.1103/physrevb.96.155102</a>.","ieee":"M. Nauman <i>et al.</i>, “In-plane magnetic anisotropy in strontium iridate Sr2IrO4,” <i>Physical Review B</i>, vol. 96, no. 15. American Physical Society, 2017.","apa":"Nauman, M., Hong, Y., Hussain, T., Seo, M. S., Park, S. Y., Lee, N., … Jo, Y. (2017). In-plane magnetic anisotropy in strontium iridate Sr2IrO4. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.96.155102\">https://doi.org/10.1103/physrevb.96.155102</a>","short":"M. Nauman, Y. Hong, T. Hussain, M.S. Seo, S.Y. Park, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Physical Review B 96 (2017).","chicago":"Nauman, Muhammad, Yunjeong Hong, Tayyaba Hussain, M. S. Seo, S. Y. Park, N. Lee, Y. J. Choi, Woun Kang, and Younjung Jo. “In-Plane Magnetic Anisotropy in Strontium Iridate Sr2IrO4.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/physrevb.96.155102\">https://doi.org/10.1103/physrevb.96.155102</a>.","ama":"Nauman M, Hong Y, Hussain T, et al. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. <i>Physical Review B</i>. 2017;96(15). doi:<a href=\"https://doi.org/10.1103/physrevb.96.155102\">10.1103/physrevb.96.155102</a>"},"oa_version":"None","issue":"15","date_published":"2017-10-01T00:00:00Z","month":"10","day":"01","volume":96,"publisher":"American Physical Society","title":"In-plane magnetic anisotropy in strontium iridate Sr2IrO4","article_processing_charge":"No","intvolume":"        96","article_number":"155102","author":[{"full_name":"Nauman, Muhammad","last_name":"Nauman","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad","orcid":"0000-0002-2111-4846"},{"full_name":"Hong, Yunjeong","last_name":"Hong","first_name":"Yunjeong"},{"full_name":"Hussain, Tayyaba","last_name":"Hussain","first_name":"Tayyaba"},{"first_name":"M. S.","last_name":"Seo","full_name":"Seo, M. S."},{"first_name":"S. Y.","last_name":"Park","full_name":"Park, S. Y."},{"last_name":"Lee","full_name":"Lee, N.","first_name":"N."},{"last_name":"Choi","full_name":"Choi, Y. J.","first_name":"Y. J."},{"full_name":"Kang, Woun","last_name":"Kang","first_name":"Woun"},{"last_name":"Jo","full_name":"Jo, Younjung","first_name":"Younjung"}],"status":"public","doi":"10.1103/physrevb.96.155102","quality_controlled":"1","publication_identifier":{"issn":["2469-9950","2469-9969"]},"extern":"1"},{"citation":{"ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.","ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. 2017;124(7):588-596. doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>","chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>. Mathematical Association of America, 2017. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","apa":"Akopyan, A., &#38; Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. Mathematical Association of America. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>","ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” <i>The American Mathematical Monthly</i>, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>."},"oa_version":"Submitted Version","language":[{"iso":"eng"}],"arxiv":1,"page":"588 - 596","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-11T11:49:09Z","publication":"The American Mathematical Monthly","oa":1,"department":[{"_id":"HeEd"}],"date_updated":"2023-10-17T11:24:57Z","_id":"909","year":"2017","scopus_import":"1","publication_identifier":{"issn":["00029890"]},"doi":"10.4169/amer.math.monthly.124.7.588","status":"public","intvolume":"       124","publist_id":"6534","title":"On the lengths of curves passing through boundary points of a planar convex shape","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","date_published":"2017-01-01T00:00:00Z","month":"01","publisher":"Mathematical Association of America","day":"01","issue":"7","type":"journal_article","abstract":[{"text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor &amp;#xbd; cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1605.07997","open_access":"1"}],"article_type":"original","quality_controlled":"1","external_id":{"isi":["000413947300002"],"arxiv":["1605.07997"]},"isi":1,"author":[{"first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan"},{"first_name":"Vladislav","last_name":"Vysotsky","full_name":"Vysotsky, Vladislav"}],"ec_funded":1,"volume":124},{"day":"01","publisher":"Genetics Society of America","date_published":"2017-10-01T00:00:00Z","month":"10","file":[{"file_size":494268,"file_name":"IST-2018-974-v1+1_manuscript.pdf","date_updated":"2020-07-14T12:48:15Z","access_level":"open_access","date_created":"2018-12-12T10:17:12Z","content_type":"application/pdf","file_id":"5264","checksum":"f7c32dabf52e6d9e709d9203761e39fd","creator":"system","relation":"main_file"}],"publist_id":"6533","intvolume":"       207","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"title":"When does frequency-independent selection maintain genetic variation?","article_processing_charge":"No","ddc":["576"],"status":"public","doi":"10.1534/genetics.117.300129","scopus_import":"1","_id":"910","year":"2017","date_updated":"2023-09-26T15:49:15Z","department":[{"_id":"NiBa"}],"publication":"Genetics","oa":1,"date_created":"2018-12-11T11:49:09Z","page":"653 - 668","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pubrep_id":"974","language":[{"iso":"eng"}],"oa_version":"Submitted Version","citation":{"apa":"Novak, S., &#38; Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. 2017;207(2):653-668. doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” <i>Genetics</i>, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668."},"volume":207,"ec_funded":1,"author":[{"first_name":"Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","last_name":"Novak"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"isi":1,"external_id":{"isi":["000412232600019"]},"quality_controlled":"1","abstract":[{"text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:15Z","type":"journal_article","issue":"2","has_accepted_license":"1"},{"has_accepted_license":"1","abstract":[{"text":"We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset.","lang":"eng"}],"type":"conference","file_date_updated":"2020-08-10T07:14:33Z","conference":{"end_date":"2017-09-07","name":"BMVC: British Machine Vision Conference","start_date":"2017-09-04","location":"London, United Kingdom"},"external_id":{"arxiv":["1705.04258"]},"quality_controlled":"1","author":[{"full_name":"Royer, Amélie","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","orcid":"0000-0002-8407-0705"},{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","first_name":"Alexander"},{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"ec_funded":1,"oa_version":"Published Version","citation":{"ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","mla":"Royer, Amélie, et al. <i>Probabilistic Image Colorization</i>. BMVA Press, 2017, p. 85.1-85.12, doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>.","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.","apa":"Royer, A., Kolesnikov, A., &#38; Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>.","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>"},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"page":"85.1-85.12","related_material":{"record":[{"id":"8390","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:49:09Z","date_updated":"2023-10-16T10:04:02Z","_id":"911","year":"2017","department":[{"_id":"ChLa"}],"publication_identifier":{"eisbn":["190172560X"]},"scopus_import":"1","status":"public","ddc":["000"],"doi":"10.5244/c.31.85","project":[{"grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","title":"Probabilistic image colorization","publist_id":"6532","file":[{"access_level":"open_access","date_updated":"2020-08-10T07:14:33Z","file_size":1625363,"file_name":"2017_BMVC_Royer.pdf","content_type":"application/pdf","file_id":"8224","date_created":"2020-08-10T07:14:33Z","creator":"dernst","relation":"main_file","success":1}],"day":"01","publisher":"BMVA Press","date_published":"2017-09-01T00:00:00Z","month":"09"},{"isi":1,"quality_controlled":"1","external_id":{"isi":["000409197200015"]},"ec_funded":1,"volume":58,"author":[{"full_name":"Deuchert, Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746","first_name":"Andreas"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n"}],"issue":"8","main_file_link":[{"url":"https://arxiv.org/abs/1703.04616","open_access":"1"}],"doi":"10.1063/1.4996580","status":"public","scopus_import":"1","publication_identifier":{"issn":["00222488"]},"date_published":"2017-08-01T00:00:00Z","month":"08","publisher":"AIP Publishing","day":"01","intvolume":"        58","publist_id":"6531","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020"}],"title":"A lower bound for the BCS functional with boundary conditions at infinity","article_processing_charge":"No","article_number":"081901","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8. AIP Publishing, 2017.","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>.","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. 2017;58(8). doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>.","short":"A. Deuchert,  Journal of Mathematical Physics 58 (2017).","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity.  Journal of Mathematical Physics. 58(8), 081901."},"oa_version":"Submitted Version","department":[{"_id":"RoSe"}],"_id":"912","date_updated":"2024-02-28T13:07:56Z","year":"2017","date_created":"2018-12-11T11:49:10Z","publication":" Journal of Mathematical Physics","oa":1},{"date_created":"2021-02-15T14:20:07Z","publication":"Surveys in Geophysics","oa":1,"date_updated":"2022-01-24T12:41:45Z","_id":"9137","year":"2017","keyword":["Geochemistry and Petrology","Geophysics"],"citation":{"mla":"Zuidema, Paquita, et al. “A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their Interactions with the Larger-Scale Environment.” <i>Surveys in Geophysics</i>, vol. 38, no. 6, Springer Nature, 2017, pp. 1283–305, doi:<a href=\"https://doi.org/10.1007/s10712-017-9447-x\">10.1007/s10712-017-9447-x</a>.","ieee":"P. Zuidema, G. Torri, C. J. Muller, and A. Chandra, “A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment,” <i>Surveys in Geophysics</i>, vol. 38, no. 6. Springer Nature, pp. 1283–1305, 2017.","short":"P. Zuidema, G. Torri, C.J. Muller, A. Chandra, Surveys in Geophysics 38 (2017) 1283–1305.","apa":"Zuidema, P., Torri, G., Muller, C. J., &#38; Chandra, A. (2017). A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. <i>Surveys in Geophysics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10712-017-9447-x\">https://doi.org/10.1007/s10712-017-9447-x</a>","ama":"Zuidema P, Torri G, Muller CJ, Chandra A. A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. <i>Surveys in Geophysics</i>. 2017;38(6):1283-1305. doi:<a href=\"https://doi.org/10.1007/s10712-017-9447-x\">10.1007/s10712-017-9447-x</a>","chicago":"Zuidema, Paquita, Giuseppe Torri, Caroline J Muller, and Arunchandra Chandra. “A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their Interactions with the Larger-Scale Environment.” <i>Surveys in Geophysics</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10712-017-9447-x\">https://doi.org/10.1007/s10712-017-9447-x</a>.","ista":"Zuidema P, Torri G, Muller CJ, Chandra A. 2017. A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. Surveys in Geophysics. 38(6), 1283–1305."},"oa_version":"Published Version","language":[{"iso":"eng"}],"page":"1283-1305","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","intvolume":"        38","title":"A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment","article_processing_charge":"No","month":"11","date_published":"2017-11-14T00:00:00Z","day":"14","publisher":"Springer Nature","extern":"1","publication_identifier":{"issn":["0169-3298","1573-0956"]},"status":"public","doi":"10.1007/s10712-017-9447-x","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s10712-017-9447-x"}],"article_type":"original","issue":"6","type":"journal_article","abstract":[{"lang":"eng","text":"Pools of air cooled by partial rain evaporation span up to several hundreds of kilometers in nature and typically last less than 1 day, ultimately losing their identity to the large-scale flow. These fundamentally differ in character from the radiatively-driven dry pools defining convective aggregation. Advancement in remote sensing and in computer capabilities has promoted exploration of how precipitation-induced cold pool processes modify the convective spectrum and life cycle. This contribution surveys current understanding of such cold pools over the tropical and subtropical oceans. In shallow convection with low rain rates, the cold pools moisten, preserving the near-surface equivalent potential temperature or increasing it if the surface moisture fluxes cannot ventilate beyond the new surface layer; both conditions indicate downdraft origin air from within the boundary layer. When rain rates exceed ∼ 2 mm h−1, convective-scale downdrafts can bring down drier air of lower equivalent potential temperature from above the boundary layer. The resulting density currents facilitate the lifting of locally thermodynamically favorable air and can impose an arc-shaped mesoscale cloud organization. This organization allows clouds capable of reaching 4–5 km within otherwise dry environments. These are more commonly observed in the northern hemisphere trade wind regime, where the flow to the intertropical convergence zone is unimpeded by the equator. Their near-surface air properties share much with those shown from cold pools sampled in the equatorial Indian Ocean. Cold pools are most effective at influencing the mesoscale organization when the atmosphere is moist in the lower free troposphere and dry above, suggesting an optimal range of water vapor paths. Outstanding questions on the relationship between cold pools, their accompanying moisture distribution and cloud cover are detailed further. Near-surface water vapor rings are documented in one model inside but near the cold pool edge; these are not consistent with observations, but do improve with smaller horizontal grid spacings."}],"author":[{"first_name":"Paquita","full_name":"Zuidema, Paquita","last_name":"Zuidema"},{"first_name":"Giuseppe","full_name":"Torri, Giuseppe","last_name":"Torri"},{"orcid":"0000-0001-5836-5350","first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller"},{"full_name":"Chandra, Arunchandra","last_name":"Chandra","first_name":"Arunchandra"}],"volume":38,"quality_controlled":"1"}]