[{"oa":1,"quality_controlled":"1","_id":"14004","type":"journal_article","day":"17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-10T06:35:51Z","keyword":["General Physics and Astronomy"],"month":"11","main_file_link":[{"url":"https://arxiv.org/abs/1710.04474","open_access":"1"}],"intvolume":"       119","arxiv":1,"abstract":[{"lang":"eng","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."}],"status":"public","publication_status":"published","date_published":"2017-11-17T00:00:00Z","article_processing_charge":"No","oa_version":"Preprint","extern":"1","article_number":"203201","language":[{"iso":"eng"}],"article_type":"original","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova"},{"last_name":"Brennecke","first_name":"Simon","full_name":"Brennecke, Simon"},{"last_name":"Lein","first_name":"Manfred","full_name":"Lein, Manfred"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"publication":"Physical Review Letters","fulldoi":"https://doi.org/10.1103/physrevlett.119.203201","title":"Signatures of electronic structure in bicircular high-harmonic spectroscopy","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"issue":"20","scopus_import":"1","date_updated":"2023-08-22T08:21:10Z","doi":"10.1103/physrevlett.119.203201","external_id":{"arxiv":["1710.04474"]},"volume":119,"publisher":"American Physical Society","citation":{"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.","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>","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.","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>.","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>","short":"D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters 119 (2017).","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>."},"year":"2017"},{"publication_identifier":{"eissn":["2041-1723"]},"title":"Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering","publication":"Nature Communications","author":[{"full_name":"Walt, Samuel G.","first_name":"Samuel G.","last_name":"Walt"},{"first_name":"Niraghatam","full_name":"Bhargava Ram, Niraghatam","last_name":"Bhargava Ram"},{"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","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva"},{"full_name":"Lein, Manfred","first_name":"Manfred","last_name":"Lein"},{"last_name":"Wörner","full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob"}],"fulldoi":"https://doi.org/10.1038/ncomms15651","publisher":"Springer Nature","volume":8,"citation":{"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).","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>","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.","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>","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.","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>."},"year":"2017","scopus_import":"1","external_id":{"pmid":["28643771"]},"pmid":1,"doi":"10.1038/ncomms15651","date_updated":"2023-08-22T08:26:06Z","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_created":"2023-08-10T06:36:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         8","month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms15651"}],"quality_controlled":"1","type":"journal_article","_id":"14005","day":"15","oa":1,"article_number":"15651","language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","extern":"1","date_published":"2017-06-15T00:00:00Z","status":"public","publication_status":"published","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No"},{"pmid":1,"external_id":{"pmid":["28388142"]},"doi":"10.1063/1.4977933","date_updated":"2023-08-22T08:30:59Z","scopus_import":"1","year":"2017","citation":{"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.","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.","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>","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>.","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>"},"volume":146,"publisher":"AIP Publishing","title":"Theory of attosecond delays in molecular photoionization","fulldoi":"https://doi.org/10.1063/1.4977933","author":[{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"publication":"The Journal of Chemical Physics","issue":"12","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"extern":"1","oa_version":"None","article_processing_charge":"No","date_published":"2017-03-28T00:00:00Z","abstract":[{"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.","lang":"eng"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"article_type":"original","article_number":"124306","type":"journal_article","_id":"14006","day":"28","quality_controlled":"1","intvolume":"       146","month":"03","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-10T06:36:19Z"},{"article_number":"078002","article_type":"letter_note","language":[{"iso":"eng"}],"publication_status":"published","status":"public","abstract":[{"lang":"eng","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)."}],"date_published":"2017-03-15T00:00:00Z","article_processing_charge":"No","oa_version":"Preprint","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-10T06:36:29Z","keyword":["Condensed Matter Physics","Atomic and Molecular Physics","and Optics"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.09352"}],"month":"03","intvolume":"        50","arxiv":1,"oa":1,"quality_controlled":"1","day":"15","_id":"14007","type":"journal_article","volume":50,"publisher":"IOP Publishing","year":"2017","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.","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>.","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.","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).","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>."},"scopus_import":"1","date_updated":"2023-08-22T08:32:43Z","doi":"10.1088/1361-6455/aa62b5","external_id":{"arxiv":["1611.09352"]},"publication_identifier":{"eissn":["1361-6455"],"issn":["0953-4075"]},"issue":"7","author":[{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva"},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"}],"publication":"Journal of Physics B: Atomic, Molecular and Optical Physics","fulldoi":"https://doi.org/10.1088/1361-6455/aa62b5","title":"Comment on ‘Time delays in molecular photoionization’"},{"quality_controlled":"1","day":"05","_id":"14008","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-10T06:36:39Z","keyword":["Multidisciplinary"],"month":"01","intvolume":"       355","oa_version":"None","extern":"1","status":"public","abstract":[{"lang":"eng","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."}],"publication_status":"published","date_published":"2017-01-05T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original","title":"Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source","page":"264-267","author":[{"last_name":"Pertot","first_name":"Yoann","full_name":"Pertot, Yoann"},{"last_name":"Schmidt","first_name":"Cédric","full_name":"Schmidt, Cédric"},{"last_name":"Matthews","full_name":"Matthews, Mary","first_name":"Mary"},{"last_name":"Chauvet","first_name":"Adrien","full_name":"Chauvet, Adrien"},{"last_name":"Huppert","full_name":"Huppert, Martin","first_name":"Martin"},{"full_name":"Svoboda, Vit","first_name":"Vit","last_name":"Svoboda"},{"first_name":"Aaron","full_name":"von Conta, Aaron","last_name":"von Conta"},{"first_name":"Andres","full_name":"Tehlar, Andres","last_name":"Tehlar"},{"last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova"},{"first_name":"Jean-Pierre","full_name":"Wolf, Jean-Pierre","last_name":"Wolf"},{"last_name":"Wörner","first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob"}],"publication":"Science","fulldoi":"https://doi.org/10.1126/science.aah6114","issue":"6322","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"scopus_import":"1","doi":"10.1126/science.aah6114","date_updated":"2023-08-22T08:34:38Z","pmid":1,"external_id":{"pmid":["28059713"]},"volume":355,"publisher":"American Association for the Advancement of Science","citation":{"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>","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.","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>","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.","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>."},"year":"2017"},{"article_number":"013404","language":[{"iso":"eng"}],"article_type":"original","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."}],"publication_status":"published","status":"public","date_published":"2017-01-10T00:00:00Z","article_processing_charge":"No","oa_version":"None","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-10T06:36:58Z","month":"01","intvolume":"        95","quality_controlled":"1","_id":"14009","type":"journal_article","day":"10","volume":95,"publisher":"American Physical Society","year":"2017","citation":{"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>.","short":"I. Jordan, M. Huppert, S. Pabst, A.S. Kheifets, D.R. Baykusheva, H.J. Wörner, Physical Review A 95 (2017).","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>","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>","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."},"scopus_import":"1","date_updated":"2023-08-22T08:38:17Z","doi":"10.1103/physreva.95.013404","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"issue":"1","author":[{"first_name":"I.","full_name":"Jordan, I.","last_name":"Jordan"},{"first_name":"M.","full_name":"Huppert, M.","last_name":"Huppert"},{"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.","full_name":"Wörner, H. J.","last_name":"Wörner"}],"publication":"Physical Review A","fulldoi":"https://doi.org/10.1103/physreva.95.013404","title":"Spin-orbit delays in photoemission"},{"volume":119,"publisher":"American Physical Society","year":"2017","citation":{"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>","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.","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.","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>","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>."},"scopus_import":"1","external_id":{"arxiv":["1710.04474"],"pmid":["29219334"]},"pmid":1,"date_updated":"2023-08-22T06:48:28Z","doi":"10.1103/physrevlett.119.203201","issue":"20","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"title":"Signatures of electronic structure in bicircular high-harmonic spectroscopy","author":[{"full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"first_name":"Simon","full_name":"Brennecke, Simon","last_name":"Brennecke"},{"last_name":"Lein","full_name":"Lein, Manfred","first_name":"Manfred"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"publication":"Physical Review Letters","fulldoi":"https://doi.org/10.1103/physrevlett.119.203201","article_number":"203201","language":[{"iso":"eng"}],"article_type":"original","oa_version":"Preprint","extern":"1","date_published":"2017-11-17T00:00:00Z","publication_status":"published","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"}],"status":"public","article_processing_charge":"No","arxiv":1,"keyword":["General Physics and Astronomy"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-10T06:48:12Z","intvolume":"       119","month":"11","main_file_link":[{"url":"https://arxiv.org/abs/1710.04474","open_access":"1"}],"quality_controlled":"1","_id":"14031","type":"journal_article","day":"17","oa":1},{"year":"2017","citation":{"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.","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.","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>","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>.","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.","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>."},"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Elsevier","volume":23,"external_id":{"arxiv":["1410.5387"],"isi":["000390637000014"]},"date_updated":"2025-06-11T06:33:00Z","doi":"10.1016/j.nahs.2016.04.006","scopus_import":"1","ec_funded":1,"issue":"2","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1689"}]},"page":"230 - 253","title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1016/j.nahs.2016.04.006","author":[{"last_name":"Svoreňová","full_name":"Svoreňová, Mária","first_name":"Mária"},{"last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Cěrná","first_name":"Ivana","full_name":"Cěrná, Ivana"},{"full_name":"Belta, Cǎlin","first_name":"Cǎlin","last_name":"Belta"}],"publication":"Nonlinear Analysis: Hybrid Systems","language":[{"iso":"eng"}],"publist_id":"5800","oa_version":"Preprint","isi":1,"article_processing_charge":"No","date_published":"2017-02-01T00:00:00Z","publication_status":"published","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."}],"status":"public","arxiv":1,"intvolume":"        23","main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"month":"02","date_created":"2018-12-11T11:51:50Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1407","type":"journal_article","day":"01","quality_controlled":"1","oa":1},{"article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","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."}],"status":"public","date_published":"2017-02-21T00:00:00Z","extern":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"oa":1,"_id":"14205","type":"conference","day":"21","quality_controlled":"1","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.06457"}],"intvolume":"        54","date_created":"2023-08-22T14:17:19Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"date_updated":"2023-09-13T09:49:10Z","external_id":{"arxiv":["1702.06457"]},"department":[{"_id":"FrLo"}],"year":"2017","citation":{"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.","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.","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.","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.","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.","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."},"volume":54,"publisher":"ML Research Press","conference":{"end_date":"2017-04-22","name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2017-04-20","location":"Fort Lauderdale, FL, United States"},"publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"full_name":"Khanna, Rajiv","first_name":"Rajiv","last_name":"Khanna"},{"full_name":"Tschannen, Michael","first_name":"Michael","last_name":"Tschannen"},{"full_name":"Jaggi, Martin","first_name":"Martin","last_name":"Jaggi"}],"title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","page":"860-868"},{"_id":"14206","day":"31","type":"conference","quality_controlled":"1","title":"Greedy algorithms for cone constrained optimization with convergence guarantees","conference":{"location":"Long Beach, CA, United States","name":"NeurIPS: Neural Information Processing Systems","end_date":"2017-12-09","start_date":"2017-12-04"},"oa":1,"author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"full_name":"Jaggi, Martin","first_name":"Martin","last_name":"Jaggi"}],"publication":"Advances in Neural Information Processing Systems","arxiv":1,"publication_identifier":{"isbn":["9781510860964"]},"month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1705.11041","open_access":"1"}],"date_created":"2023-08-22T14:17:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1705.11041"]},"extern":"1","date_updated":"2024-10-14T12:29:50Z","oa_version":"Preprint","article_processing_charge":"No","date_published":"2017-05-31T00:00:00Z","abstract":[{"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.","lang":"eng"}],"status":"public","publication_status":"published","language":[{"iso":"eng"}],"citation":{"mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” <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.","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.","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.","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.","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."},"year":"2017","department":[{"_id":"FrLo"}]},{"intvolume":"       114","month":"04","keyword":["Applied Microbiology and Biotechnology","Bioengineering","Biotechnology"],"date_created":"2023-09-06T12:08:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","_id":"14286","type":"journal_article","quality_controlled":"1","article_type":"original","language":[{"iso":"eng"}],"extern":"1","oa_version":"None","article_processing_charge":"No","date_published":"2017-04-01T00:00:00Z","status":"public","publication_status":"published","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"}],"issue":"4","publication_identifier":{"issn":["0006-3592"]},"page":"777-784","title":"Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production","fulldoi":"https://doi.org/10.1002/bit.26200","publication":"Biotechnology and Bioengineering","author":[{"first_name":"Benjamin","full_name":"Kick, Benjamin","last_name":"Kick"},{"last_name":"Hensler","full_name":"Hensler, Samantha","first_name":"Samantha"},{"last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","full_name":"Praetorius, Florian M"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"},{"last_name":"Weuster-Botz","full_name":"Weuster-Botz, Dirk","first_name":"Dirk"}],"year":"2017","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>.","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.","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.","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>.","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>","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."},"publisher":"Wiley","volume":114,"external_id":{"pmid":["27748519"]},"pmid":1,"doi":"10.1002/bit.26200","date_updated":"2023-11-07T12:36:20Z","scopus_import":"1"},{"month":"03","intvolume":"       355","date_created":"2023-09-06T12:08:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"24","_id":"14287","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"original","article_number":"eaam5488","extern":"1","oa_version":"None","article_processing_charge":"No","status":"public","publication_status":"published","abstract":[{"lang":"eng","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."}],"date_published":"2017-03-24T00:00:00Z","issue":"6331","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"title":"Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes","fulldoi":"https://doi.org/10.1126/science.aam5488","author":[{"last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M","first_name":"Florian M"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"}],"publication":"Science","citation":{"ista":"Praetorius FM, Dietz H. 2017. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Science. 355(6331), eaam5488.","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>","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>.","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.","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>","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>."},"year":"2017","volume":355,"publisher":"American Association for the Advancement of Science","date_updated":"2023-11-07T12:33:05Z","doi":"10.1126/science.aam5488","external_id":{"pmid":["28336611"]},"pmid":1,"scopus_import":"1"},{"page":"84-87","title":"Biotechnological mass production of DNA origami","author":[{"full_name":"Praetorius, Florian M","first_name":"Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Kick","full_name":"Kick, Benjamin","first_name":"Benjamin"},{"full_name":"Behler, Karl L.","first_name":"Karl L.","last_name":"Behler"},{"full_name":"Honemann, Maximilian N.","first_name":"Maximilian N.","last_name":"Honemann"},{"first_name":"Dirk","full_name":"Weuster-Botz, Dirk","last_name":"Weuster-Botz"},{"last_name":"Dietz","first_name":"Hendrik","full_name":"Dietz, Hendrik"}],"publication":"Nature","fulldoi":"https://doi.org/10.1038/nature24650","issue":"7683","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"scopus_import":"1","external_id":{"pmid":["29219963"]},"pmid":1,"doi":"10.1038/nature24650","date_updated":"2023-11-07T12:24:49Z","volume":552,"publisher":"Springer Nature","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.","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>.","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.","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>."},"year":"2017","quality_controlled":"1","_id":"14290","type":"journal_article","day":"07","date_created":"2023-09-06T12:14:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       552","month":"12","oa_version":"None","extern":"1","date_published":"2017-12-07T00:00:00Z","publication_status":"published","status":"public","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."}],"article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original"},{"quality_controlled":"1","type":"journal_article","_id":"14308","day":"03","keyword":["Biophysics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-06T13:19:10Z","intvolume":"       112","month":"02","oa_version":"None","extern":"1","date_published":"2017-02-03T00:00:00Z","publication_status":"published","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"}],"status":"public","article_processing_charge":"No","article_number":"25a","article_type":"original","language":[{"iso":"eng"}],"title":"Genetically encoded DNA-protein hybrid origami","author":[{"first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"last_name":"Dietz","full_name":"Dietz, Hendrik","first_name":"Hendrik"}],"publication":"Biophysical Journal","fulldoi":"https://doi.org/10.1016/j.bpj.2016.11.171","issue":"3","publication_identifier":{"issn":["0006-3495"]},"scopus_import":"1","doi":"10.1016/j.bpj.2016.11.171","date_updated":"2024-10-14T12:31:35Z","volume":112,"publisher":"Elsevier","year":"2017","citation":{"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>","ista":"Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 112(3), 25a.","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>.","ieee":"F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,” <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier, 2017.","short":"F.M. Praetorius, H. Dietz, Biophysical Journal 112 (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>","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>."}},{"arxiv":1,"intvolume":"        16","month":"05","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1705.08944","open_access":"1"}],"date_created":"2023-09-06T13:37:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","_id":"14309","type":"journal_article","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"article_type":"original","extern":"1","oa_version":"Preprint","article_processing_charge":"No","date_published":"2017-05-22T00:00:00Z","publication_status":"published","status":"public","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."}],"issue":"8","publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"page":"849-856","title":"Molecular engineering of chiral colloidal liquid crystals using DNA origami","fulldoi":"https://doi.org/10.1038/nmat4909","author":[{"last_name":"Siavashpouri","full_name":"Siavashpouri, M","first_name":"M"},{"last_name":"Wachauf","full_name":"Wachauf, CH","first_name":"CH"},{"last_name":"Zakhary","full_name":"Zakhary, MJ","first_name":"MJ"},{"full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"full_name":"Dietz, H","first_name":"H","last_name":"Dietz"},{"last_name":"Dogic","full_name":"Dogic, Z","first_name":"Z"}],"publication":"Nature Materials","year":"2017","citation":{"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>.","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>","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, Nature Materials 16 (2017) 849–856.","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.","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>.","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.","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>"},"volume":16,"publisher":"Springer Nature","external_id":{"pmid":["28530665"],"arxiv":["1705.08944"]},"pmid":1,"doi":"10.1038/nmat4909","date_updated":"2023-11-07T11:40:00Z","scopus_import":"1"},{"author":[{"full_name":"Siavashpouri, Mahsa","first_name":"Mahsa","last_name":"Siavashpouri"},{"last_name":"Wachauf","first_name":"Christian","full_name":"Wachauf, Christian"},{"last_name":"Zakhary","full_name":"Zakhary, Mark","first_name":"Mark"},{"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"},{"last_name":"Dogic","full_name":"Dogic, Zvonimir","first_name":"Zvonimir"}],"publication":"APS March Meeting 2017","quality_controlled":"1","title":"Molecular engineering of colloidal liquid crystals using DNA origami","_id":"14310","type":"conference_abstract","day":"01","date_created":"2023-09-06T13:40:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","date_published":"2017-03-01T00:00:00Z","publication_status":"published","status":"public","article_processing_charge":"No","oa_version":"None","date_updated":"2023-11-07T11:36:15Z","extern":"1","publisher":"APS","citation":{"mla":"Siavashpouri, Mahsa, et al. “Molecular Engineering of Colloidal Liquid Crystals Using DNA Origami.” <i>APS March Meeting 2017</i>, APS, 2017.","apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &#38; Dogic, Z. (2017). Molecular engineering of colloidal liquid crystals using DNA origami. In <i>APS March Meeting 2017</i>. APS.","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, in:, APS March Meeting 2017, APS, 2017.","ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of colloidal liquid crystals using DNA origami,” in <i>APS March Meeting 2017</i>, 2017.","chicago":"Siavashpouri, Mahsa, Christian Wachauf, Mark Zakhary, Florian M Praetorius, Hendrik Dietz, and Zvonimir Dogic. “Molecular Engineering of Colloidal Liquid Crystals Using DNA Origami.” In <i>APS March Meeting 2017</i>. APS, 2017.","ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of colloidal liquid crystals using DNA origami. In: <i>APS March Meeting 2017</i>. APS; 2017.","ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of colloidal liquid crystals using DNA origami. APS March Meeting 2017. ."},"year":"2017","language":[{"iso":"eng"}]},{"OA_type":"free access","intvolume":"        78","month":"01","main_file_link":[{"url":"https://doi.org/10.1016/j.jsc.2016.03.008","open_access":"1"}],"date_created":"2018-12-11T11:51:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"1433","day":"01","corr_author":"1","quality_controlled":"1","oa":1,"article_type":"original","language":[{"iso":"eng"}],"publist_id":"5765","oa_version":"Published Version","isi":1,"article_processing_charge":"No","date_published":"2017-01-01T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology.","lang":"eng"}],"ddc":["500"],"acknowledgement":"Michael Kerber acknowledges support by the Max Planck Center for Visual Computing and Communications (FKZ-01IMC01 and FKZ-01IM10001). Ulrich Bauer, Jan Reininghaus, and Hubert Wagner acknowledge support by the EU Project TOPOSYS (FP7-ICT-318493-STREP).","publication_identifier":{"issn":[" 0747-7171"]},"related_material":{"record":[{"relation":"earlier_version","id":"10894","status":"public"}]},"page":"76 - 90","title":"Phat - Persistent homology algorithms toolbox","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"fulldoi":"https://doi.org/10.1016/j.jsc.2016.03.008","publication":"Journal of Symbolic Computation","author":[{"last_name":"Bauer","first_name":"Ulrich","full_name":"Bauer, Ulrich"},{"last_name":"Kerber","full_name":"Kerber, Michael","first_name":"Michael"},{"full_name":"Reininghaus, Jan","first_name":"Jan","last_name":"Reininghaus"},{"orcid":"0009-0009-9111-8429","first_name":"Hubert","full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner"}],"year":"2017","citation":{"ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” <i>Journal of Symbolic Computation</i>, vol. 78. Academic Press, pp. 76–90, 2017.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. 2017;78:76-90. doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>","mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>, vol. 78, Academic Press, 2017, pp. 76–90, doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90.","apa":"Bauer, U., Kerber, M., Reininghaus, J., &#38; Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>"},"department":[{"_id":"HeEd"}],"publisher":"Academic Press","volume":78,"external_id":{"isi":["000384396000005"]},"date_updated":"2026-06-18T17:35:16Z","doi":"10.1016/j.jsc.2016.03.008","scopus_import":"1","ec_funded":1},{"publication_identifier":{"issn":["2050-084X"]},"fulldoi":"https://doi.org/10.7554/elife.26163","author":[{"first_name":"Jiunn CN","full_name":"Fong, Jiunn CN","last_name":"Fong"},{"full_name":"Rogers, Andrew","first_name":"Andrew","last_name":"Rogers"},{"id":"6437c950-2a03-11ee-914d-d6476dd7b75c","last_name":"Michael","first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen"},{"first_name":"Nicole C","full_name":"Parsley, Nicole C","last_name":"Parsley"},{"last_name":"Cornell","first_name":"William-Cole","full_name":"Cornell, William-Cole"},{"full_name":"Lin, Yu-Cheng","first_name":"Yu-Cheng","last_name":"Lin"},{"full_name":"Singh, Praveen K","first_name":"Praveen K","last_name":"Singh"},{"full_name":"Hartmann, Raimo","first_name":"Raimo","last_name":"Hartmann"},{"last_name":"Drescher","first_name":"Knut","full_name":"Drescher, Knut"},{"first_name":"Evgeny","full_name":"Vinogradov, Evgeny","last_name":"Vinogradov"},{"full_name":"Dietrich, Lars EP","first_name":"Lars EP","last_name":"Dietrich"},{"first_name":"Carrie L","full_name":"Partch, Carrie L","last_name":"Partch"},{"first_name":"Fitnat H","full_name":"Yildiz, Fitnat H","last_name":"Yildiz"}],"publication":"eLife","title":"Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms","citation":{"ama":"Fong JC, Rogers A, Michael AK, et al. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.26163\">10.7554/elife.26163</a>","ista":"Fong JC, Rogers A, Michael AK, Parsley NC, Cornell W-C, Lin Y-C, Singh PK, Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH. 2017. Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife. 6, 26163.","chicago":"Fong, Jiunn CN, Andrew Rogers, Alicia K. Michael, Nicole C Parsley, William-Cole Cornell, Yu-Cheng Lin, Praveen K Singh, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio Cholerae Biofilms.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/elife.26163\">https://doi.org/10.7554/elife.26163</a>.","ieee":"J. C. Fong <i>et al.</i>, “Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","short":"J.C. Fong, A. Rogers, A.K. Michael, N.C. Parsley, W.-C. Cornell, Y.-C. Lin, P.K. Singh, R. Hartmann, K. Drescher, E. Vinogradov, L.E. Dietrich, C.L. Partch, F.H. Yildiz, ELife 6 (2017).","apa":"Fong, J. C., Rogers, A., Michael, A. K., Parsley, N. C., Cornell, W.-C., Lin, Y.-C., … Yildiz, F. H. (2017). Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.26163\">https://doi.org/10.7554/elife.26163</a>","mla":"Fong, Jiunn CN, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio Cholerae Biofilms.” <i>ELife</i>, vol. 6, 26163, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/elife.26163\">10.7554/elife.26163</a>."},"year":"2017","volume":6,"publisher":"eLife Sciences Publications","date_updated":"2024-03-25T12:22:54Z","doi":"10.7554/elife.26163","pmid":1,"external_id":{"pmid":["28762945"]},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.26163"}],"month":"08","intvolume":"         6","date_created":"2024-03-21T07:55:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"oa":1,"type":"journal_article","_id":"15154","day":"01","quality_controlled":"1","language":[{"iso":"eng"}],"article_type":"original","article_number":"26163","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Biofilm formation is critical for the infection cycle of Vibrio cholerae. Vibrio exopolysaccharides (VPS) and the matrix proteins RbmA, Bap1 and RbmC are required for the development of biofilm architecture. We demonstrate that RbmA binds VPS directly and uses a binary structural switch within its first fibronectin type III (FnIII-1) domain to control RbmA structural dynamics and the formation of VPS-dependent higher-order structures. The structural switch in FnIII-1 regulates interactions in trans with the FnIII-2 domain, leading to open (monomeric) or closed (dimeric) interfaces. The ability of RbmA to switch between open and closed states is important for V. cholerae biofilm formation, as RbmA variants with switches that are locked in either of the two states lead to biofilms with altered architecture and structural integrity."}],"status":"public","publication_status":"published","date_published":"2017-08-01T00:00:00Z","extern":"1","oa_version":"Published Version"},{"oa_version":"Published Version","extern":"1","status":"public","abstract":[{"lang":"eng","text":"The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination."}],"publication_status":"published","date_published":"2017-05-18T00:00:00Z","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"quality_controlled":"1","_id":"15155","day":"18","type":"journal_article","oa":1,"date_created":"2024-03-21T07:56:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Cell Biology","Molecular Biology"],"month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.molcel.2017.04.011"}],"intvolume":"        66","scopus_import":"1","doi":"10.1016/j.molcel.2017.04.011","date_updated":"2024-03-25T12:19:20Z","publisher":"Elsevier","volume":66,"citation":{"mla":"Gustafson, Chelsea L., et al. “A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.” <i>Molecular Cell</i>, vol. 66, no. 4, Elsevier, 2017, p. 447–457.e7, doi:<a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">10.1016/j.molcel.2017.04.011</a>.","short":"C.L. Gustafson, N.C. Parsley, H. Asimgil, H.-W. Lee, C. Ahlbach, A.K. Michael, H. Xu, O.L. Williams, T.L. Davis, A.C. Liu, C.L. Partch, Molecular Cell 66 (2017) 447–457.e7.","apa":"Gustafson, C. L., Parsley, N. C., Asimgil, H., Lee, H.-W., Ahlbach, C., Michael, A. K., … Partch, C. L. (2017). A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. <i>Molecular Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">https://doi.org/10.1016/j.molcel.2017.04.011</a>","ieee":"C. L. Gustafson <i>et al.</i>, “A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms,” <i>Molecular Cell</i>, vol. 66, no. 4. Elsevier, p. 447–457.e7, 2017.","chicago":"Gustafson, Chelsea L., Nicole C. Parsley, Hande Asimgil, Hsiau-Wei Lee, Christopher Ahlbach, Alicia K. Michael, Haiyan Xu, et al. “A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.” <i>Molecular Cell</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">https://doi.org/10.1016/j.molcel.2017.04.011</a>.","ista":"Gustafson CL, Parsley NC, Asimgil H, Lee H-W, Ahlbach C, Michael AK, Xu H, Williams OL, Davis TL, Liu AC, Partch CL. 2017. A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell. 66(4), 447–457.e7.","ama":"Gustafson CL, Parsley NC, Asimgil H, et al. A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. <i>Molecular Cell</i>. 2017;66(4):447-457.e7. doi:<a href=\"https://doi.org/10.1016/j.molcel.2017.04.011\">10.1016/j.molcel.2017.04.011</a>"},"year":"2017","title":"A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms","page":"447-457.e7","publication":"Molecular Cell","author":[{"first_name":"Chelsea L.","full_name":"Gustafson, Chelsea L.","last_name":"Gustafson"},{"first_name":"Nicole C.","full_name":"Parsley, Nicole C.","last_name":"Parsley"},{"last_name":"Asimgil","first_name":"Hande","full_name":"Asimgil, Hande"},{"full_name":"Lee, Hsiau-Wei","first_name":"Hsiau-Wei","last_name":"Lee"},{"full_name":"Ahlbach, Christopher","first_name":"Christopher","last_name":"Ahlbach"},{"first_name":"Alicia Kathleen","full_name":"Michael, Alicia Kathleen","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"first_name":"Haiyan","full_name":"Xu, Haiyan","last_name":"Xu"},{"full_name":"Williams, Owen L.","first_name":"Owen L.","last_name":"Williams"},{"last_name":"Davis","full_name":"Davis, Tara L.","first_name":"Tara L."},{"last_name":"Liu","full_name":"Liu, Andrew C.","first_name":"Andrew C."},{"last_name":"Partch","full_name":"Partch, Carrie L.","first_name":"Carrie L."}],"fulldoi":"https://doi.org/10.1016/j.molcel.2017.04.011","issue":"4","publication_identifier":{"issn":["1097-2765"]}},{"quality_controlled":"1","day":"17","_id":"15156","type":"journal_article","keyword":["Multidisciplinary"],"date_created":"2024-03-21T07:56:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       355","month":"03","oa_version":"None","extern":"1","date_published":"2017-03-17T00:00:00Z","publication_status":"published","abstract":[{"text":"Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post–adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA.","lang":"eng"}],"status":"public","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"page":"1174-1180","title":"Structural basis of the day-night transition in a bacterial circadian clock","author":[{"last_name":"Tseng","first_name":"Roger","full_name":"Tseng, Roger"},{"last_name":"Goularte","full_name":"Goularte, Nicolette F.","first_name":"Nicolette F."},{"last_name":"Chavan","first_name":"Archana","full_name":"Chavan, Archana"},{"first_name":"Jansen","full_name":"Luu, Jansen","last_name":"Luu"},{"first_name":"Susan E.","full_name":"Cohen, Susan E.","last_name":"Cohen"},{"first_name":"Yong-Gang","full_name":"Chang, Yong-Gang","last_name":"Chang"},{"first_name":"Joel","full_name":"Heisler, Joel","last_name":"Heisler"},{"first_name":"Sheng","full_name":"Li, Sheng","last_name":"Li"},{"full_name":"Michael, Alicia Kathleen","first_name":"Alicia Kathleen","last_name":"Michael","id":"6437c950-2a03-11ee-914d-d6476dd7b75c"},{"full_name":"Tripathi, Sarvind","first_name":"Sarvind","last_name":"Tripathi"},{"full_name":"Golden, Susan S.","first_name":"Susan S.","last_name":"Golden"},{"first_name":"Andy","full_name":"LiWang, Andy","last_name":"LiWang"},{"first_name":"Carrie L.","full_name":"Partch, Carrie L.","last_name":"Partch"}],"publication":"Science","fulldoi":"https://doi.org/10.1126/science.aag2516","issue":"6330","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"scopus_import":"1","date_updated":"2024-03-25T12:16:44Z","doi":"10.1126/science.aag2516","publisher":"American Association for the Advancement of Science","volume":355,"year":"2017","citation":{"ieee":"R. Tseng <i>et al.</i>, “Structural basis of the day-night transition in a bacterial circadian clock,” <i>Science</i>, vol. 355, no. 6330. American Association for the Advancement of Science, pp. 1174–1180, 2017.","chicago":"Tseng, Roger, Nicolette F. Goularte, Archana Chavan, Jansen Luu, Susan E. Cohen, Yong-Gang Chang, Joel Heisler, et al. “Structural Basis of the Day-Night Transition in a Bacterial Circadian Clock.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aag2516\">https://doi.org/10.1126/science.aag2516</a>.","ista":"Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang Y-G, Heisler J, Li S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. 2017. Structural basis of the day-night transition in a bacterial circadian clock. Science. 355(6330), 1174–1180.","ama":"Tseng R, Goularte NF, Chavan A, et al. Structural basis of the day-night transition in a bacterial circadian clock. <i>Science</i>. 2017;355(6330):1174-1180. doi:<a href=\"https://doi.org/10.1126/science.aag2516\">10.1126/science.aag2516</a>","mla":"Tseng, Roger, et al. “Structural Basis of the Day-Night Transition in a Bacterial Circadian Clock.” <i>Science</i>, vol. 355, no. 6330, American Association for the Advancement of Science, 2017, pp. 1174–80, doi:<a href=\"https://doi.org/10.1126/science.aag2516\">10.1126/science.aag2516</a>.","short":"R. Tseng, N.F. Goularte, A. Chavan, J. Luu, S.E. Cohen, Y.-G. Chang, J. Heisler, S. Li, A.K. Michael, S. Tripathi, S.S. Golden, A. LiWang, C.L. Partch, Science 355 (2017) 1174–1180.","apa":"Tseng, R., Goularte, N. F., Chavan, A., Luu, J., Cohen, S. E., Chang, Y.-G., … Partch, C. L. (2017). Structural basis of the day-night transition in a bacterial circadian clock. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aag2516\">https://doi.org/10.1126/science.aag2516</a>"}}]