[{"publication_status":"published","date_published":"2015-10-22T00:00:00Z","status":"public","external_id":{"pmid":["26494175"]},"citation":{"ama":"Kraus PM, Mignolet B, Baykusheva DR, et al. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. <i>Science</i>. 2015;350(6262):790-795. doi:<a href=\"https://doi.org/10.1126/science.aab2160\">10.1126/science.aab2160</a>","apa":"Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Measurement and laser control of attosecond charge migration in ionized iodoacetylene. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aab2160\">https://doi.org/10.1126/science.aab2160</a>","mla":"Kraus, P. M., et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” <i>Science</i>, vol. 350, no. 6262, American Association for the Advancement of Science, 2015, pp. 790–95, doi:<a href=\"https://doi.org/10.1126/science.aab2160\">10.1126/science.aab2160</a>.","ista":"Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Grassi G, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Measurement and laser control of attosecond charge migration in ionized iodoacetylene. Science. 350(6262), 790–795.","chicago":"Kraus, P. M., B. Mignolet, Denitsa Rangelova Baykusheva, A. Rupenyan, L. Horný, E. F. Penka, G. Grassi, et al. “Measurement and Laser Control of Attosecond Charge Migration in Ionized Iodoacetylene.” <i>Science</i>. American Association for the Advancement of Science, 2015. <a href=\"https://doi.org/10.1126/science.aab2160\">https://doi.org/10.1126/science.aab2160</a>.","ieee":"P. M. Kraus <i>et al.</i>, “Measurement and laser control of attosecond charge migration in ionized iodoacetylene,” <i>Science</i>, vol. 350, no. 6262. American Association for the Advancement of Science, pp. 790–795, 2015.","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, G. Grassi, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Science 350 (2015) 790–795."},"extern":"1","intvolume":"       350","abstract":[{"lang":"eng","text":"The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes."}],"date_updated":"2023-08-22T08:47:39Z","type":"journal_article","month":"10","oa_version":"None","page":"790-795","date_created":"2023-08-10T06:37:35Z","volume":350,"year":"2015","_id":"14013","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"quality_controlled":"1","doi":"10.1126/science.aab2160","language":[{"iso":"eng"}],"issue":"6262","keyword":["Multidisciplinary"],"day":"22","author":[{"last_name":"Kraus","first_name":"P. M.","full_name":"Kraus, P. M."},{"last_name":"Mignolet","first_name":"B.","full_name":"Mignolet, B."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Rupenyan","first_name":"A.","full_name":"Rupenyan, A."},{"last_name":"Horný","first_name":"L.","full_name":"Horný, L."},{"last_name":"Penka","first_name":"E. F.","full_name":"Penka, E. F."},{"full_name":"Grassi, G.","last_name":"Grassi","first_name":"G."},{"full_name":"Tolstikhin, O. I.","first_name":"O. I.","last_name":"Tolstikhin"},{"last_name":"Schneider","first_name":"J.","full_name":"Schneider, J."},{"last_name":"Jensen","first_name":"F.","full_name":"Jensen, F."},{"full_name":"Madsen, L. B.","last_name":"Madsen","first_name":"L. B."},{"last_name":"Bandrauk","first_name":"A. D.","full_name":"Bandrauk, A. D."},{"last_name":"Remacle","first_name":"F.","full_name":"Remacle, F."},{"last_name":"Wörner","first_name":"H. J.","full_name":"Wörner, H. J."}],"title":"Measurement and laser control of attosecond charge migration in ionized iodoacetylene","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Association for the Advancement of Science","scopus_import":"1","article_processing_charge":"No","article_type":"original","publication":"Science"},{"publication":"Journal of Physics: Conference Series","article_type":"original","scopus_import":"1","article_processing_charge":"No","publisher":"IOP Publishing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"112135","title":"Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography","author":[{"full_name":"Walt, Samuel G","first_name":"Samuel G","last_name":"Walt"},{"full_name":"Ram, N Bhargava","last_name":"Ram","first_name":"N Bhargava"},{"last_name":"von Conta","first_name":"Aaron","full_name":"von Conta, Aaron"},{"full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","last_name":"Baykusheva","first_name":"Denitsa Rangelova"},{"first_name":"Marcos","last_name":"Atala","full_name":"Atala, Marcos"},{"last_name":"Wörner","first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob"}],"day":"01","keyword":["General Physics and Astronomy"],"issue":"11","language":[{"iso":"eng"}],"doi":"10.1088/1742-6596/635/11/112135","quality_controlled":"1","publication_identifier":{"issn":["1742-6588"],"eissn":["1742-6596"]},"_id":"14014","year":"2015","volume":635,"date_created":"2023-08-10T06:37:44Z","oa_version":"Published Version","type":"journal_article","month":"11","date_updated":"2023-08-22T08:51:33Z","abstract":[{"text":"We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons.","lang":"eng"}],"intvolume":"       635","extern":"1","citation":{"short":"S.G. Walt, N.B. Ram, A. von Conta, D.R. Baykusheva, M. Atala, H.J. Wörner, Journal of Physics: Conference Series 635 (2015).","ieee":"S. G. Walt, N. B. Ram, A. von Conta, D. R. Baykusheva, M. Atala, and H. J. Wörner, “Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography,” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11. IOP Publishing, 2015.","chicago":"Walt, Samuel G, N Bhargava Ram, Aaron von Conta, Denitsa Rangelova Baykusheva, Marcos Atala, and Hans Jakob Wörner. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” <i>Journal of Physics: Conference Series</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">https://doi.org/10.1088/1742-6596/635/11/112135</a>.","mla":"Walt, Samuel G., et al. “Resolving the Dynamics of Valence-Shell Electrons and Nuclei through Laser-Induced Diffraction and Holography.” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11, 112135, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">10.1088/1742-6596/635/11/112135</a>.","ista":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. 2015. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. Journal of Physics: Conference Series. 635(11), 112135.","apa":"Walt, S. G., Ram, N. B., von Conta, A., Baykusheva, D. R., Atala, M., &#38; Wörner, H. J. (2015). Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. <i>Journal of Physics: Conference Series</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">https://doi.org/10.1088/1742-6596/635/11/112135</a>","ama":"Walt SG, Ram NB, von Conta A, Baykusheva DR, Atala M, Wörner HJ. Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography. <i>Journal of Physics: Conference Series</i>. 2015;635(11). doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112135\">10.1088/1742-6596/635/11/112135</a>"},"status":"public","date_published":"2015-11-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1088/1742-6596/635/11/112135","open_access":"1"}],"publication_status":"published","oa":1},{"keyword":["General Physics and Astronomy"],"language":[{"iso":"eng"}],"issue":"11","doi":"10.1088/1742-6596/635/11/112136","quality_controlled":"1","publication_identifier":{"eissn":["1742-6596"],"issn":["1742-6588"]},"publication":"Journal of Physics: Conference Series","article_processing_charge":"No","scopus_import":"1","article_type":"original","publisher":"IOP Publishing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Attosecond charge migration and its laser control","article_number":"112136","author":[{"full_name":"Kraus, P M","last_name":"Kraus","first_name":"P M"},{"last_name":"Mignolet","first_name":"B","full_name":"Mignolet, B"},{"first_name":"Denitsa Rangelova","last_name":"Baykusheva","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova"},{"full_name":"Rupenyan, A","last_name":"Rupenyan","first_name":"A"},{"last_name":"Horný","first_name":"L","full_name":"Horný, L"},{"first_name":"E F","last_name":"Penka","full_name":"Penka, E F"},{"last_name":"Tolstikhin","first_name":"O I","full_name":"Tolstikhin, O I"},{"last_name":"Schneider","first_name":"J","full_name":"Schneider, J"},{"first_name":"F","last_name":"Jensen","full_name":"Jensen, F"},{"full_name":"Madsen, L B","last_name":"Madsen","first_name":"L B"},{"first_name":"A D","last_name":"Bandrauk","full_name":"Bandrauk, A D"},{"full_name":"Remacle, F","last_name":"Remacle","first_name":"F"},{"full_name":"Wörner, H J","first_name":"H J","last_name":"Wörner"}],"day":"01","intvolume":"       635","extern":"1","citation":{"ama":"Kraus PM, Mignolet B, Baykusheva DR, et al. Attosecond charge migration and its laser control. <i>Journal of Physics: Conference Series</i>. 2015;635(11). doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">10.1088/1742-6596/635/11/112136</a>","ista":"Kraus PM, Mignolet B, Baykusheva DR, Rupenyan A, Horný L, Penka EF, Tolstikhin OI, Schneider J, Jensen F, Madsen LB, Bandrauk AD, Remacle F, Wörner HJ. 2015. Attosecond charge migration and its laser control. Journal of Physics: Conference Series. 635(11), 112136.","mla":"Kraus, P. M., et al. “Attosecond Charge Migration and Its Laser Control.” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11, 112136, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">10.1088/1742-6596/635/11/112136</a>.","apa":"Kraus, P. M., Mignolet, B., Baykusheva, D. R., Rupenyan, A., Horný, L., Penka, E. F., … Wörner, H. J. (2015). Attosecond charge migration and its laser control. <i>Journal of Physics: Conference Series</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">https://doi.org/10.1088/1742-6596/635/11/112136</a>","ieee":"P. M. Kraus <i>et al.</i>, “Attosecond charge migration and its laser control,” <i>Journal of Physics: Conference Series</i>, vol. 635, no. 11. IOP Publishing, 2015.","chicago":"Kraus, P M, B Mignolet, Denitsa Rangelova Baykusheva, A Rupenyan, L Horný, E F Penka, O I Tolstikhin, et al. “Attosecond Charge Migration and Its Laser Control.” <i>Journal of Physics: Conference Series</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1742-6596/635/11/112136\">https://doi.org/10.1088/1742-6596/635/11/112136</a>.","short":"P.M. Kraus, B. Mignolet, D.R. Baykusheva, A. Rupenyan, L. Horný, E.F. Penka, O.I. Tolstikhin, J. Schneider, F. Jensen, L.B. Madsen, A.D. Bandrauk, F. Remacle, H.J. Wörner, Journal of Physics: Conference Series 635 (2015)."},"status":"public","date_published":"2015-07-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1742-6596/635/11/112136"}],"publication_status":"published","oa":1,"_id":"14015","year":"2015","volume":635,"date_created":"2023-08-10T06:37:53Z","date_updated":"2023-08-22T08:49:14Z","abstract":[{"text":"We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes.","lang":"eng"}],"type":"journal_article","month":"07","oa_version":"Published Version"},{"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms8039"}],"date_published":"2015-05-05T00:00:00Z","external_id":{"pmid":["25940229"]},"status":"public","citation":{"short":"P.M. Kraus, O.I. Tolstikhin, D.R. Baykusheva, A. Rupenyan, J. Schneider, C.Z. Bisgaard, T. Morishita, F. Jensen, L.B. Madsen, H.J. Wörner, Nature Communications 6 (2015).","ieee":"P. M. Kraus <i>et al.</i>, “Observation of laser-induced electronic structure in oriented polyatomic molecules,” <i>Nature Communications</i>, vol. 6. Springer Nature, 2015.","chicago":"Kraus, P. M., O. I. Tolstikhin, Denitsa Rangelova Baykusheva, A. Rupenyan, J. Schneider, C. Z. Bisgaard, T. Morishita, F. Jensen, L. B. Madsen, and H. J. Wörner. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” <i>Nature Communications</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/ncomms8039\">https://doi.org/10.1038/ncomms8039</a>.","mla":"Kraus, P. M., et al. “Observation of Laser-Induced Electronic Structure in Oriented Polyatomic Molecules.” <i>Nature Communications</i>, vol. 6, 7039, Springer Nature, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms8039\">10.1038/ncomms8039</a>.","ista":"Kraus PM, Tolstikhin OI, Baykusheva DR, Rupenyan A, Schneider J, Bisgaard CZ, Morishita T, Jensen F, Madsen LB, Wörner HJ. 2015. Observation of laser-induced electronic structure in oriented polyatomic molecules. Nature Communications. 6, 7039.","apa":"Kraus, P. M., Tolstikhin, O. I., Baykusheva, D. R., Rupenyan, A., Schneider, J., Bisgaard, C. Z., … Wörner, H. J. (2015). Observation of laser-induced electronic structure in oriented polyatomic molecules. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/ncomms8039\">https://doi.org/10.1038/ncomms8039</a>","ama":"Kraus PM, Tolstikhin OI, Baykusheva DR, et al. Observation of laser-induced electronic structure in oriented polyatomic molecules. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms8039\">10.1038/ncomms8039</a>"},"intvolume":"         6","extern":"1","oa_version":"Published Version","type":"journal_article","month":"05","abstract":[{"lang":"eng","text":"All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies."}],"date_updated":"2023-08-22T08:52:56Z","date_created":"2023-08-10T06:38:01Z","volume":6,"year":"2015","_id":"14016","publication_identifier":{"eissn":["2041-1723"]},"quality_controlled":"1","doi":"10.1038/ncomms8039","language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"day":"05","author":[{"full_name":"Kraus, P. M.","first_name":"P. M.","last_name":"Kraus"},{"last_name":"Tolstikhin","first_name":"O. I.","full_name":"Tolstikhin, O. I."},{"id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","last_name":"Baykusheva"},{"last_name":"Rupenyan","first_name":"A.","full_name":"Rupenyan, A."},{"first_name":"J.","last_name":"Schneider","full_name":"Schneider, J."},{"first_name":"C. Z.","last_name":"Bisgaard","full_name":"Bisgaard, C. Z."},{"first_name":"T.","last_name":"Morishita","full_name":"Morishita, T."},{"full_name":"Jensen, F.","last_name":"Jensen","first_name":"F."},{"full_name":"Madsen, L. B.","last_name":"Madsen","first_name":"L. B."},{"last_name":"Wörner","first_name":"H. J.","full_name":"Wörner, H. J."}],"article_number":"7039","title":"Observation of laser-induced electronic structure in oriented polyatomic molecules","pmid":1,"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Nature Communications"},{"date_created":"2023-08-10T06:38:10Z","volume":91,"month":"02","type":"journal_article","oa_version":"Preprint","date_updated":"2023-08-22T08:56:34Z","abstract":[{"text":"The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results.","lang":"eng"}],"_id":"14017","year":"2015","main_file_link":[{"url":"https://arxiv.org/abs/1504.03933","open_access":"1"}],"date_published":"2015-02-19T00:00:00Z","oa":1,"publication_status":"published","citation":{"chicago":"Zhang, Song Bin, Denitsa Rangelova Baykusheva, Peter M. Kraus, Hans Jakob Wörner, and Nina Rohringer. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” <i>Physical Review A</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/physreva.91.023421\">https://doi.org/10.1103/physreva.91.023421</a>.","ieee":"S. B. Zhang, D. R. Baykusheva, P. M. Kraus, H. J. Wörner, and N. Rohringer, “Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation,” <i>Physical Review A</i>, vol. 91, no. 2. American Physical Society, 2015.","short":"S.B. Zhang, D.R. Baykusheva, P.M. Kraus, H.J. Wörner, N. Rohringer, Physical Review A 91 (2015).","ama":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. <i>Physical Review A</i>. 2015;91(2). doi:<a href=\"https://doi.org/10.1103/physreva.91.023421\">10.1103/physreva.91.023421</a>","apa":"Zhang, S. B., Baykusheva, D. R., Kraus, P. M., Wörner, H. J., &#38; Rohringer, N. (2015). Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.91.023421\">https://doi.org/10.1103/physreva.91.023421</a>","ista":"Zhang SB, Baykusheva DR, Kraus PM, Wörner HJ, Rohringer N. 2015. Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation. Physical Review A. 91(2), 023421.","mla":"Zhang, Song Bin, et al. “Theoretical Study of Molecular Electronic and Rotational Coherences by High-Order-Harmonic Generation.” <i>Physical Review A</i>, vol. 91, no. 2, 023421, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/physreva.91.023421\">10.1103/physreva.91.023421</a>."},"intvolume":"        91","extern":"1","external_id":{"arxiv":["1504.03933"]},"status":"public","article_number":"023421","arxiv":1,"title":"Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation","day":"19","author":[{"full_name":"Zhang, Song Bin","last_name":"Zhang","first_name":"Song Bin"},{"last_name":"Baykusheva","first_name":"Denitsa Rangelova","full_name":"Baykusheva, Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"last_name":"Kraus","first_name":"Peter M.","full_name":"Kraus, Peter M."},{"full_name":"Wörner, Hans Jakob","first_name":"Hans Jakob","last_name":"Wörner"},{"last_name":"Rohringer","first_name":"Nina","full_name":"Rohringer, Nina"}],"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Physical Review A","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1103/physreva.91.023421","publication_identifier":{"eissn":["1094-1622"],"issn":["1050-2947"]},"issue":"2","language":[{"iso":"eng"}],"keyword":["Atomic and Molecular Physics","and Optics"]},{"_id":"1424","year":"2015","department":[{"_id":"HeEd"}],"acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems","date_created":"2018-12-11T11:51:56Z","publist_id":"5782","volume":28,"title":"Statistical topological data analysis-A kernel perspective","oa_version":"Submitted Version","month":"12","type":"conference","date_updated":"2021-01-12T06:50:38Z","abstract":[{"lang":"eng","text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data."}],"day":"01","author":[{"full_name":"Kwitt, Roland","first_name":"Roland","last_name":"Kwitt"},{"first_name":"Stefan","last_name":"Huber","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Niethammer, Marc","first_name":"Marc","last_name":"Niethammer"},{"full_name":"Lin, Weili","first_name":"Weili","last_name":"Lin"},{"orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich","first_name":"Ulrich","last_name":"Bauer"}],"page":"3070 - 3078","language":[{"iso":"eng"}],"citation":{"chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.","short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078.","ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., &#38; Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","mla":"Kwitt, Roland, et al. <i>Statistical Topological Data Analysis-A Kernel Perspective</i>. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78."},"conference":{"end_date":"2015-12-12","name":"NIPS: Neural Information Processing Systems","location":"Montreal, Canada","start_date":"2015-12-07"},"intvolume":"        28","status":"public","alternative_title":["Advances in Neural Information Processing Systems"],"quality_controlled":"1","main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}],"date_published":"2015-12-01T00:00:00Z","publication_status":"published","oa":1},{"scopus_import":1,"ec_funded":1,"department":[{"_id":"ChLa"}],"publisher":"Neural Information Processing Systems","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5781","title":"Lifelong learning with non-i.i.d. tasks","day":"01","author":[{"first_name":"Anastasia","last_name":"Pentina","full_name":"Pentina, Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2015-12-12","start_date":"2015-12-07","location":"Montreal, Canada","name":"NIPS: Neural Information Processing Systems"},"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","_id":"1425","year":"2015","date_created":"2018-12-11T11:51:57Z","volume":2015,"oa_version":"None","month":"01","type":"conference","abstract":[{"lang":"eng","text":"In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm."}],"date_updated":"2021-01-12T06:50:39Z","page":"1540 - 1548","citation":{"short":"A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015, pp. 1540–1548.","ieee":"A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.","chicago":"Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.","mla":"Pentina, Anastasia, and Christoph Lampert. <i>Lifelong Learning with Non-i.i.d. Tasks</i>. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.","ista":"Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548.","apa":"Pentina, A., &#38; Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ama":"Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems; 2015:1540-1548."},"intvolume":"      2015","status":"public","alternative_title":["Advances in Neural Information Processing Systems"],"main_file_link":[{"url":"http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks","open_access":"1"}],"date_published":"2015-01-01T00:00:00Z","publication_status":"published","oa":1},{"language":[{"iso":"eng"}],"citation":{"ama":"Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>. ACM; 2015:1455-1462. doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>","ista":"Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.","mla":"Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, ACM, 2015, pp. 1455–62, doi:<a href=\"https://doi.org/10.1145/2739480.2754758\">10.1145/2739480.2754758</a>.","apa":"Paixao, T., Sudholt, D., Heredia, J., &#38; Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i> (pp. 1455–1462). Madrid, Spain: ACM. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>","ieee":"T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, Madrid, Spain, 2015, pp. 1455–1462.","chicago":"Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In <i>Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation</i>, 1455–62. ACM, 2015. <a href=\"https://doi.org/10.1145/2739480.2754758\">https://doi.org/10.1145/2739480.2754758</a>.","short":"T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462."},"conference":{"start_date":"2015-07-11","location":"Madrid, Spain","name":"GECCO: Genetic and evolutionary computation conference","end_date":"2015-07-15"},"status":"public","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.06260"}],"date_published":"2015-07-11T00:00:00Z","doi":"10.1145/2739480.2754758","publication_status":"published","oa":1,"ec_funded":1,"scopus_import":1,"_id":"1430","publication":"Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","date_created":"2018-12-11T11:51:58Z","publist_id":"5768","title":"First steps towards a runtime comparison of natural and artificial evolution","oa_version":"Preprint","type":"conference","month":"07","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"date_updated":"2021-01-12T06:50:41Z","day":"11","author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"last_name":"Heredia","first_name":"Jorge","full_name":"Heredia, Jorge"},{"last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"}],"page":"1455 - 1462"},{"year":"2015","_id":"14303","oa_version":"Published Version","month":"06","type":"journal_article","abstract":[{"lang":"eng","text":"Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale."}],"date_updated":"2023-11-07T11:56:32Z","page":"4672-4676","date_created":"2023-09-06T12:52:47Z","volume":15,"external_id":{"pmid":["26028443"]},"status":"public","citation":{"apa":"Kick, B., Praetorius, F. M., Dietz, H., &#38; Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. <i>Nano Letters</i>. ACS Publications. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">https://doi.org/10.1021/acs.nanolett.5b01461</a>","mla":"Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” <i>Nano Letters</i>, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">10.1021/acs.nanolett.5b01461</a>.","ista":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676.","ama":"Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. <i>Nano Letters</i>. 2015;15(7):4672-4676. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">10.1021/acs.nanolett.5b01461</a>","short":"B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676.","chicago":"Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” <i>Nano Letters</i>. ACS Publications, 2015. <a href=\"https://doi.org/10.1021/acs.nanolett.5b01461\">https://doi.org/10.1021/acs.nanolett.5b01461</a>.","ieee":"B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” <i>Nano Letters</i>, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015."},"extern":"1","intvolume":"        15","publication_status":"published","oa":1,"main_file_link":[{"url":"https://doi.org/10.1021/acs.nanolett.5b01461","open_access":"1"}],"date_published":"2015-06-01T00:00:00Z","pmid":1,"publisher":"ACS Publications","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"letter_note","article_processing_charge":"No","publication":"Nano Letters","day":"01","author":[{"full_name":"Kick, B","first_name":"B","last_name":"Kick"},{"full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius","first_name":"Florian M"},{"full_name":"Dietz, H","first_name":"H","last_name":"Dietz"},{"full_name":"Weuster-Botz, D","last_name":"Weuster-Botz","first_name":"D"}],"title":"Efficient production of single-stranded phage DNA as scaffolds for DNA origami","issue":"7","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"quality_controlled":"1","doi":"10.1021/acs.nanolett.5b01461"},{"pmid":1,"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","article_processing_charge":"No","publication":"Nucleic Acids Research","day":"18","author":[{"first_name":"Nicolas","last_name":"Richet","full_name":"Richet, Nicolas"},{"full_name":"Liu, Danni","last_name":"Liu","first_name":"Danni"},{"full_name":"Legrand, Pierre","first_name":"Pierre","last_name":"Legrand"},{"full_name":"Velours, Christophe","first_name":"Christophe","last_name":"Velours"},{"full_name":"Corpet, Armelle","first_name":"Armelle","last_name":"Corpet"},{"full_name":"Gaubert, Albane","last_name":"Gaubert","first_name":"Albane"},{"last_name":"Bakail","first_name":"May M","full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587"},{"first_name":"Gwenaelle","last_name":"Moal-Raisin","full_name":"Moal-Raisin, Gwenaelle"},{"full_name":"Guerois, Raphael","last_name":"Guerois","first_name":"Raphael"},{"full_name":"Compper, Christel","last_name":"Compper","first_name":"Christel"},{"full_name":"Besle, Arthur","first_name":"Arthur","last_name":"Besle"},{"full_name":"Guichard, Berengère","last_name":"Guichard","first_name":"Berengère"},{"last_name":"Almouzni","first_name":"Genevieve","full_name":"Almouzni, Genevieve"},{"full_name":"Ochsenbein, Françoise","first_name":"Françoise","last_name":"Ochsenbein"}],"title":"Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork","issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1362-4962","0305-1048"]},"quality_controlled":"1","doi":"10.1093/nar/gkv021","year":"2015","_id":"9017","month":"02","oa_version":"Published Version","type":"journal_article","date_updated":"2023-02-23T13:46:50Z","abstract":[{"lang":"eng","text":"MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway."}],"page":"1905-1917","date_created":"2021-01-19T11:01:01Z","volume":43,"external_id":{"pmid":["25618846"]},"status":"public","citation":{"apa":"Richet, N., Liu, D., Legrand, P., Velours, C., Corpet, A., Gaubert, A., … Ochsenbein, F. (2015). Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkv021\">https://doi.org/10.1093/nar/gkv021</a>","ista":"Richet N, Liu D, Legrand P, Velours C, Corpet A, Gaubert A, Bakail MM, Moal-Raisin G, Guerois R, Compper C, Besle A, Guichard B, Almouzni G, Ochsenbein F. 2015. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. Nucleic Acids Research. 43(3), 1905–1917.","mla":"Richet, Nicolas, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” <i>Nucleic Acids Research</i>, vol. 43, no. 3, Oxford University Press, 2015, pp. 1905–17, doi:<a href=\"https://doi.org/10.1093/nar/gkv021\">10.1093/nar/gkv021</a>.","ama":"Richet N, Liu D, Legrand P, et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork. <i>Nucleic Acids Research</i>. 2015;43(3):1905-1917. doi:<a href=\"https://doi.org/10.1093/nar/gkv021\">10.1093/nar/gkv021</a>","short":"N. Richet, D. Liu, P. Legrand, C. Velours, A. Corpet, A. Gaubert, M.M. Bakail, G. Moal-Raisin, R. Guerois, C. Compper, A. Besle, B. Guichard, G. Almouzni, F. Ochsenbein, Nucleic Acids Research 43 (2015) 1905–1917.","chicago":"Richet, Nicolas, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May M Bakail, et al. “Structural Insight into How the Human Helicase Subunit MCM2 May Act as a Histone Chaperone Together with ASF1 at the Replication Fork.” <i>Nucleic Acids Research</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/nar/gkv021\">https://doi.org/10.1093/nar/gkv021</a>.","ieee":"N. Richet <i>et al.</i>, “Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork,” <i>Nucleic Acids Research</i>, vol. 43, no. 3. Oxford University Press, pp. 1905–1917, 2015."},"intvolume":"        43","extern":"1","publication_status":"published","date_published":"2015-02-18T00:00:00Z"},{"file":[{"creator":"cziletti","relation":"main_file","content_type":"application/pdf","file_size":2416780,"success":1,"file_name":"2015_ScienceAdvances_Palacci.pdf","access_level":"open_access","date_created":"2021-02-02T13:22:19Z","checksum":"b97d62433581875c1b85210c5f6ae370","date_updated":"2021-02-02T13:22:19Z","file_id":"9058"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","day":"01","author":[{"first_name":"Jérémie A","last_name":"Palacci","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465"},{"first_name":"Stefano","last_name":"Sacanna","full_name":"Sacanna, Stefano"},{"first_name":"Anaïs","last_name":"Abramian","full_name":"Abramian, Anaïs"},{"full_name":"Barral, Jérémie","first_name":"Jérémie","last_name":"Barral"},{"first_name":"Kasey","last_name":"Hanson","full_name":"Hanson, Kasey"},{"full_name":"Grosberg, Alexander Y.","first_name":"Alexander Y.","last_name":"Grosberg"},{"last_name":"Pine","first_name":"David J.","full_name":"Pine, David J."},{"first_name":"Paul M.","last_name":"Chaikin","full_name":"Chaikin, Paul M."}],"article_number":"e1400214","title":"Artificial rheotaxis","arxiv":1,"pmid":1,"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"American Association for the Advancement of Science ","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Science Advances","publication_identifier":{"issn":["2375-2548"]},"quality_controlled":"1","doi":"10.1126/sciadv.1400214","issue":"4","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"journal_article","month":"05","abstract":[{"text":"Motility is a basic feature of living microorganisms, and how it works is often determined by environmental cues. Recent efforts have focused on developing artificial systems that can mimic microorganisms, in particular their self-propulsion. We report on the design and characterization of synthetic self-propelled particles that migrate upstream, known as positive rheotaxis. This phenomenon results from a purely physical mechanism involving the interplay between the polarity of the particles and their alignment by a viscous torque. We show quantitative agreement between experimental data and a simple model of an overdamped Brownian pendulum. The model notably predicts the existence of a stagnation point in a diverging flow. We take advantage of this property to demonstrate that our active particles can sense and predictably organize in an imposed flow. Our colloidal system represents an important step toward the realization of biomimetic microsystems with the ability to sense and respond to environmental changes.","lang":"eng"}],"date_updated":"2023-02-23T13:47:52Z","file_date_updated":"2021-02-02T13:22:19Z","date_created":"2021-02-02T13:15:02Z","volume":1,"year":"2015","_id":"9057","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["530"],"date_published":"2015-05-01T00:00:00Z","external_id":{"pmid":["26601175"],"arxiv":["1505.05111"]},"status":"public","citation":{"ama":"Palacci JA, Sacanna S, Abramian A, et al. Artificial rheotaxis. <i>Science Advances</i>. 2015;1(4). doi:<a href=\"https://doi.org/10.1126/sciadv.1400214\">10.1126/sciadv.1400214</a>","mla":"Palacci, Jérémie A., et al. “Artificial Rheotaxis.” <i>Science Advances</i>, vol. 1, no. 4, e1400214, American Association for the Advancement of Science , 2015, doi:<a href=\"https://doi.org/10.1126/sciadv.1400214\">10.1126/sciadv.1400214</a>.","ista":"Palacci JA, Sacanna S, Abramian A, Barral J, Hanson K, Grosberg AY, Pine DJ, Chaikin PM. 2015. Artificial rheotaxis. Science Advances. 1(4), e1400214.","apa":"Palacci, J. A., Sacanna, S., Abramian, A., Barral, J., Hanson, K., Grosberg, A. Y., … Chaikin, P. M. (2015). Artificial rheotaxis. <i>Science Advances</i>. American Association for the Advancement of Science . <a href=\"https://doi.org/10.1126/sciadv.1400214\">https://doi.org/10.1126/sciadv.1400214</a>","ieee":"J. A. Palacci <i>et al.</i>, “Artificial rheotaxis,” <i>Science Advances</i>, vol. 1, no. 4. American Association for the Advancement of Science , 2015.","chicago":"Palacci, Jérémie A, Stefano Sacanna, Anaïs Abramian, Jérémie Barral, Kasey Hanson, Alexander Y. Grosberg, David J. Pine, and Paul M. Chaikin. “Artificial Rheotaxis.” <i>Science Advances</i>. American Association for the Advancement of Science , 2015. <a href=\"https://doi.org/10.1126/sciadv.1400214\">https://doi.org/10.1126/sciadv.1400214</a>.","short":"J.A. Palacci, S. Sacanna, A. Abramian, J. Barral, K. Hanson, A.Y. Grosberg, D.J. Pine, P.M. Chaikin, Science Advances 1 (2015)."},"intvolume":"         1","extern":"1"},{"status":"public","citation":{"mla":"Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0125888\">10.1371/journal.pone.0125888</a>.","ista":"Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V, Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).","apa":"Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko, V., &#38; Kondrashov, F. (2015). Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0125888\">https://doi.org/10.1371/journal.pone.0125888</a>","ama":"Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0125888\">10.1371/journal.pone.0125888</a>","short":"O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko, F. Kondrashov, PLoS One 10 (2015).","ieee":"O. Arkhipova <i>et al.</i>, “Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","chicago":"Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova, Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0125888\">https://doi.org/10.1371/journal.pone.0125888</a>."},"issue":"5","extern":1,"intvolume":"        10","publication_status":"published","quality_controlled":0,"doi":"10.1371/journal.pone.0125888","date_published":"2015-05-11T00:00:00Z","year":"2015","publisher":"Public Library of Science","acknowledgement":"Funding: The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, \"Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)\" and (BFU2012-31329), the European Union and the European Research Council under grant agreement 335980_EinME. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Our author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher until last days. A number of his work remains unfinished. We mourn premature care of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for the sequencing.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"PLoS One","_id":"906","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2021-01-12T08:21:48Z","day":"11","abstract":[{"lang":"eng","text":"The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1."}],"month":"05","type":"journal_article","author":[{"first_name":"Oksana","last_name":"Arkhipova","full_name":"Arkhipova, Oksana V"},{"full_name":"Meer, Margarita V","last_name":"Meer","first_name":"Margarita"},{"full_name":"Mikoulinskaia, Galina V","first_name":"Galina","last_name":"Mikoulinskaia"},{"last_name":"Zakharova","first_name":"Marina","full_name":"Zakharova, Marina V"},{"first_name":"Alexander","last_name":"Galushko","full_name":"Galushko, Alexander S"},{"full_name":"Akimenko, Vasilii K","last_name":"Akimenko","first_name":"Vasilii"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor"}],"publist_id":"6742","date_created":"2018-12-11T11:49:08Z","title":"Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer","volume":10},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"American Geophysical Union","article_processing_charge":"No","article_type":"original","publication":"Journal of Geophysical Research: Oceans","day":"08","author":[{"full_name":"Lefauve, Adrien","first_name":"Adrien","last_name":"Lefauve"},{"first_name":"Caroline J","last_name":"Muller","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350"},{"first_name":"Angélique","last_name":"Melet","full_name":"Melet, Angélique"}],"title":"A three-dimensional map of tidal dissipation over abyssal hills","language":[{"iso":"eng"}],"issue":"7","publication_identifier":{"issn":["2169-9275"]},"quality_controlled":"1","doi":"10.1002/2014jc010598","year":"2015","_id":"9141","date_updated":"2022-01-24T13:45:41Z","abstract":[{"lang":"eng","text":"The breaking of internal tides is believed to provide a large part of the power needed to mix the abyssal ocean and sustain the meridional overturning circulation. Both the fraction of internal tide energy that is dissipated locally and the resulting vertical mixing distribution are crucial for the ocean state, but remain poorly quantified. Here we present a first worldwide estimate of mixing due to internal tides generated at small‐scale abyssal hills. Our estimate is based on linear wave theory, a nonlinear parameterization for wave breaking and uses quasi‐global small‐scale abyssal hill bathymetry, stratification, and tidal data. We show that a large fraction of abyssal‐hill generated internal tide energy is locally dissipated over mid‐ocean ridges in the Southern Hemisphere. Significant dissipation occurs above ridge crests, and, upon rescaling by the local stratification, follows a monotonic exponential decay with height off the bottom, with a nonuniform decay scale. We however show that a substantial part of the dissipation occurs over the smoother flanks of mid‐ocean ridges, and exhibits a middepth maximum due to the interplay of wave amplitude with stratification. We link the three‐dimensional map of dissipation to abyssal hills characteristics, ocean stratification, and tidal forcing, and discuss its potential implementation in time‐evolving parameterizations for global climate models. Current tidal parameterizations only account for waves generated at large‐scale satellite‐resolved bathymetry. Our results suggest that the presence of small‐scale, mostly unresolved abyssal hills could significantly enhance the spatial inhomogeneity of tidal mixing, particularly above mid‐ocean ridges in the Southern Hemisphere."}],"type":"journal_article","month":"06","oa_version":"Published Version","page":"4760-4777","date_created":"2021-02-15T14:21:49Z","volume":120,"status":"public","citation":{"ama":"Lefauve A, Muller CJ, Melet A. A three-dimensional map of tidal dissipation over abyssal hills. <i>Journal of Geophysical Research: Oceans</i>. 2015;120(7):4760-4777. doi:<a href=\"https://doi.org/10.1002/2014jc010598\">10.1002/2014jc010598</a>","mla":"Lefauve, Adrien, et al. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” <i>Journal of Geophysical Research: Oceans</i>, vol. 120, no. 7, American Geophysical Union, 2015, pp. 4760–77, doi:<a href=\"https://doi.org/10.1002/2014jc010598\">10.1002/2014jc010598</a>.","ista":"Lefauve A, Muller CJ, Melet A. 2015. A three-dimensional map of tidal dissipation over abyssal hills. Journal of Geophysical Research: Oceans. 120(7), 4760–4777.","apa":"Lefauve, A., Muller, C. J., &#38; Melet, A. (2015). A three-dimensional map of tidal dissipation over abyssal hills. <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2014jc010598\">https://doi.org/10.1002/2014jc010598</a>","ieee":"A. Lefauve, C. J. Muller, and A. Melet, “A three-dimensional map of tidal dissipation over abyssal hills,” <i>Journal of Geophysical Research: Oceans</i>, vol. 120, no. 7. American Geophysical Union, pp. 4760–4777, 2015.","chicago":"Lefauve, Adrien, Caroline J Muller, and Angélique Melet. “A Three-Dimensional Map of Tidal Dissipation over Abyssal Hills.” <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union, 2015. <a href=\"https://doi.org/10.1002/2014jc010598\">https://doi.org/10.1002/2014jc010598</a>.","short":"A. Lefauve, C.J. Muller, A. Melet, Journal of Geophysical Research: Oceans 120 (2015) 4760–4777."},"extern":"1","intvolume":"       120","publication_status":"published","oa":1,"main_file_link":[{"url":"https://doi.org/10.1002/2014JC010598","open_access":"1"}],"date_published":"2015-06-08T00:00:00Z"},{"title":"Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop","volume":76,"date_created":"2018-12-11T11:49:13Z","publist_id":"6514","page":"1 - 8","author":[{"last_name":"Boubaker","first_name":"Riadh","full_name":"Boubaker, Riadh"},{"full_name":"Platel, Vincent","first_name":"Vincent","last_name":"Platel"},{"full_name":"Bergès, Alexis","last_name":"Bergès","first_name":"Alexis"},{"full_name":"Bancelin, Mathieu","first_name":"Mathieu","last_name":"Bancelin"},{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"oa_version":"None","month":"02","type":"journal_article","abstract":[{"text":"This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper.","lang":"eng"}],"date_updated":"2021-01-12T08:21:56Z","day":"05","_id":"924","publication":"Applied Thermal Engineering","article_processing_charge":"No","acknowledgement":"The work presented in this paper is supported by Alstom Transport, site de Tarbes (Contract number is 11099).","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","doi":"10.1016/j.applthermaleng.2014.10.009","date_published":"2015-02-05T00:00:00Z","publication_status":"published","extern":"1","intvolume":"        76","citation":{"chicago":"Boubaker, Riadh, Vincent Platel, Alexis Bergès, Mathieu Bancelin, and Edouard B Hannezo. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” <i>Applied Thermal Engineering</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">https://doi.org/10.1016/j.applthermaleng.2014.10.009</a>.","ieee":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, and E. B. Hannezo, “Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop,” <i>Applied Thermal Engineering</i>, vol. 76. Elsevier, pp. 1–8, 2015.","short":"R. Boubaker, V. Platel, A. Bergès, M. Bancelin, E.B. Hannezo, Applied Thermal Engineering 76 (2015) 1–8.","ama":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. <i>Applied Thermal Engineering</i>. 2015;76:1-8. doi:<a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">10.1016/j.applthermaleng.2014.10.009</a>","apa":"Boubaker, R., Platel, V., Bergès, A., Bancelin, M., &#38; Hannezo, E. B. (2015). Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. <i>Applied Thermal Engineering</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">https://doi.org/10.1016/j.applthermaleng.2014.10.009</a>","ista":"Boubaker R, Platel V, Bergès A, Bancelin M, Hannezo EB. 2015. Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop. Applied Thermal Engineering. 76, 1–8.","mla":"Boubaker, Riadh, et al. “Dynamic Model of Heat and Mass Transfer in an Unsaturated Porous Wick of Capillary Pumped Loop.” <i>Applied Thermal Engineering</i>, vol. 76, Elsevier, 2015, pp. 1–8, doi:<a href=\"https://doi.org/10.1016/j.applthermaleng.2014.10.009\">10.1016/j.applthermaleng.2014.10.009</a>."},"language":[{"iso":"eng"}],"status":"public"},{"language":[{"iso":"eng"}],"doi":"10.7554/eLife.09206","quality_controlled":"1","publication":"eLife","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"eLife Sciences Publications","article_number":"e09206","title":"Assembly and positioning of actomyosin rings by contractility and planar cell polarity","publist_id":"6512","author":[{"full_name":"Sehring, Ivonne","first_name":"Ivonne","last_name":"Sehring"},{"full_name":"Recho, Pierre","first_name":"Pierre","last_name":"Recho"},{"last_name":"Denker","first_name":"Elsa","full_name":"Denker, Elsa"},{"full_name":"Kourakis, Matthew","last_name":"Kourakis","first_name":"Matthew"},{"full_name":"Mathiesen, Birthe","last_name":"Mathiesen","first_name":"Birthe"},{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Bo","last_name":"Dong","full_name":"Dong, Bo"},{"full_name":"Jiang, Di","last_name":"Jiang","first_name":"Di"}],"day":"21","file":[{"creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":7202224,"file_name":"2015_eLife_Sehring.pdf","access_level":"open_access","date_created":"2018-12-20T15:50:56Z","checksum":"1e4024b3161adcae4a53a0b3dc8a946e","date_updated":"2020-07-14T12:48:15Z","file_id":"5769"}],"intvolume":"         4","extern":"1","citation":{"short":"I. Sehring, P. Recho, E. Denker, M. Kourakis, B. Mathiesen, E.B. Hannezo, B. Dong, D. Jiang, ELife 4 (2015).","chicago":"Sehring, Ivonne, Pierre Recho, Elsa Denker, Matthew Kourakis, Birthe Mathiesen, Edouard B Hannezo, Bo Dong, and Di Jiang. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” <i>ELife</i>. eLife Sciences Publications, 2015. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>.","ieee":"I. Sehring <i>et al.</i>, “Assembly and positioning of actomyosin rings by contractility and planar cell polarity,” <i>eLife</i>, vol. 4. eLife Sciences Publications, 2015.","apa":"Sehring, I., Recho, P., Denker, E., Kourakis, M., Mathiesen, B., Hannezo, E. B., … Jiang, D. (2015). Assembly and positioning of actomyosin rings by contractility and planar cell polarity. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.09206\">https://doi.org/10.7554/eLife.09206</a>","mla":"Sehring, Ivonne, et al. “Assembly and Positioning of Actomyosin Rings by Contractility and Planar Cell Polarity.” <i>ELife</i>, vol. 4, e09206, eLife Sciences Publications, 2015, doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>.","ista":"Sehring I, Recho P, Denker E, Kourakis M, Mathiesen B, Hannezo EB, Dong B, Jiang D. 2015. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. eLife. 4, e09206.","ama":"Sehring I, Recho P, Denker E, et al. Assembly and positioning of actomyosin rings by contractility and planar cell polarity. <i>eLife</i>. 2015;4. doi:<a href=\"https://doi.org/10.7554/eLife.09206\">10.7554/eLife.09206</a>"},"status":"public","date_published":"2015-10-21T00:00:00Z","ddc":["539","570"],"oa":1,"publication_status":"published","has_accepted_license":"1","_id":"928","year":"2015","volume":4,"date_created":"2018-12-11T11:49:15Z","file_date_updated":"2020-07-14T12:48:15Z","type":"journal_article","month":"10","oa_version":"Published Version","date_updated":"2021-01-12T08:21:58Z","abstract":[{"text":"The actomyosin cytoskeleton is a primary force-generating mechanism in morphogenesis, thus a robust spatial control of cytoskeletal positioning is essential. In this report, we demonstrate that actomyosin contractility and planar cell polarity (PCP) interact in post-mitotic Ciona notochord cells to self-assemble and reposition actomyosin rings, which play an essential role for cell elongation. Intriguingly, rings always form at the cells′ anterior edge before migrating towards the center as contractility increases, reflecting a novel dynamical property of the cortex. Our drug and genetic manipulations uncover a tug-of-war between contractility, which localizes cortical flows toward the equator and PCP, which tries to reposition them. We develop a simple model of the physical forces underlying this tug-of-war, which quantitatively reproduces our results. We thus propose a quantitative framework for dissecting the relative contribution of contractility and PCP to the self-assembly and repositioning of cytoskeletal structures, which should be applicable to other morphogenetic events.","lang":"eng"}]},{"oa_version":"None","type":"journal_article","month":"07","abstract":[{"lang":"eng","text":"An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. "}],"date_updated":"2021-01-12T08:21:59Z","day":"14","author":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Dong","first_name":"Bo","full_name":"Dong, Bo"},{"last_name":"Recho","first_name":"Pierre","full_name":"Recho, Pierre"},{"last_name":"Joanny","first_name":"Jean","full_name":"Joanny, Jean"},{"full_name":"Hayashi, Shigeo","last_name":"Hayashi","first_name":"Shigeo"}],"page":"8620 - 8625","publist_id":"6513","date_created":"2018-12-11T11:49:15Z","title":"Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes","volume":112,"year":"2015","acknowledgement":"We thank H. Oda, R. E. Ward, K. Saigo, T. Nishimura, D. Pinheiro, Y. Bellaiche, the Bloomington Stock Center, Drosophila Genetic Resource Center (Kyoto), and the Developmental Studies Hybridoma Bank for generously providing antibodies and fly stocks; A. Hayashi for sharing phalloidin staining samples; Y. H. Zhang for plasmid and protocol for CBP preparation; and T. Kondo and J. Prost for suggestions and discussion. This work was supported by the Taishan Scholar Program of Shandong and the Fundamental Research Funds for the Central Universities in China (3005000-841412019) (to B.D.) and a Grant-in-Aid for Scientific Research on Innovative Areas from Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.H.). E.H. acknowledges support from the Young Researcher Prize of the Bettencourt-Schueller Foundation.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","article_processing_charge":"No","_id":"929","publication":"PNAS","publication_status":"published","doi":"10.1073/pnas.1504762112","date_published":"2015-07-14T00:00:00Z","status":"public","issue":"28","language":[{"iso":"eng"}],"citation":{"apa":"Hannezo, E. B., Dong, B., Recho, P., Joanny, J., &#38; Hayashi, S. (2015). Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1504762112\">https://doi.org/10.1073/pnas.1504762112</a>","ista":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. 2015. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. PNAS. 112(28), 8620–8625.","mla":"Hannezo, Edouard B., et al. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” <i>PNAS</i>, vol. 112, no. 28, National Academy of Sciences, 2015, pp. 8620–25, doi:<a href=\"https://doi.org/10.1073/pnas.1504762112\">10.1073/pnas.1504762112</a>.","ama":"Hannezo EB, Dong B, Recho P, Joanny J, Hayashi S. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes. <i>PNAS</i>. 2015;112(28):8620-8625. doi:<a href=\"https://doi.org/10.1073/pnas.1504762112\">10.1073/pnas.1504762112</a>","short":"E.B. Hannezo, B. Dong, P. Recho, J. Joanny, S. Hayashi, PNAS 112 (2015) 8620–8625.","chicago":"Hannezo, Edouard B, Bo Dong, Pierre Recho, Jean Joanny, and Shigeo Hayashi. “Cortical Instability Drives Periodic Supracellular Actin Pattern Formation in Epithelial Tubes.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1504762112\">https://doi.org/10.1073/pnas.1504762112</a>.","ieee":"E. B. Hannezo, B. Dong, P. Recho, J. Joanny, and S. Hayashi, “Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes,” <i>PNAS</i>, vol. 112, no. 28. National Academy of Sciences, pp. 8620–8625, 2015."},"intvolume":"       112","extern":"1"},{"page":"15314 - 15319","abstract":[{"text":"Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data.","lang":"eng"}],"date_updated":"2021-01-12T08:22:01Z","type":"journal_article","month":"12","oa_version":"None","volume":112,"date_created":"2018-12-11T11:49:16Z","year":"2015","_id":"933","publication_status":"published","oa":1,"date_published":"2015-12-15T00:00:00Z","main_file_link":[{"url":"https://www.pnas.org/content/pnas/112/50/15314.full.pdf","open_access":"1"}],"status":"public","external_id":{"pmid":["26627719"]},"extern":"1","intvolume":"       112","citation":{"mla":"García, Simón, et al. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>, vol. 112, no. 50, National Academy of Sciences, 2015, pp. 15314–19, doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>.","ista":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. 2015. Physics of active jamming during collective cellular motion in a monolayer. PNAS. 112(50), 15314–15319.","apa":"García, S., Hannezo, E. B., Elgeti, J., Joanny, J., Silberzan, P., &#38; Gov, N. (2015). Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>","ama":"García S, Hannezo EB, Elgeti J, Joanny J, Silberzan P, Gov N. Physics of active jamming during collective cellular motion in a monolayer. <i>PNAS</i>. 2015;112(50):15314-15319. doi:<a href=\"https://doi.org/10.1073/pnas.1510973112\">10.1073/pnas.1510973112</a>","short":"S. García, E.B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, N. Gov, PNAS 112 (2015) 15314–15319.","ieee":"S. García, E. B. Hannezo, J. Elgeti, J. Joanny, P. Silberzan, and N. Gov, “Physics of active jamming during collective cellular motion in a monolayer,” <i>PNAS</i>, vol. 112, no. 50. National Academy of Sciences, pp. 15314–15319, 2015.","chicago":"García, Simón, Edouard B Hannezo, Jens Elgeti, Jean Joanny, Pascal Silberzan, and Nir Gov. “Physics of Active Jamming during Collective Cellular Motion in a Monolayer.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1510973112\">https://doi.org/10.1073/pnas.1510973112</a>."},"author":[{"last_name":"García","first_name":"Simón","full_name":"García, Simón"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"},{"first_name":"Jean","last_name":"Joanny","full_name":"Joanny, Jean"},{"full_name":"Silberzan, Pascal","last_name":"Silberzan","first_name":"Pascal"},{"first_name":"Nir","last_name":"Gov","full_name":"Gov, Nir"}],"day":"15","title":"Physics of active jamming during collective cellular motion in a monolayer","publist_id":"6511","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication":"PNAS","doi":"10.1073/pnas.1510973112","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"50"},{"issue":"24","language":[{"iso":"eng"}],"doi":"10.1101/gad.269902.115","quality_controlled":"1","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"publication":"Genes and Development","article_type":"review","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_processing_charge":"No","scopus_import":"1","publisher":"Cold Spring Harbor Laboratory Press","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"pmid":1,"title":"Evolution and function of genomic imprinting in plants","author":[{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"day":"15","file":[{"file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","success":1,"file_size":1116846,"content_type":"application/pdf","relation":"main_file","creator":"asandaue","file_id":"9533","date_updated":"2021-06-08T09:55:10Z","checksum":"086a88cfca4677646da26ed960cb02e9","date_created":"2021-06-08T09:55:10Z","access_level":"open_access"}],"extern":"1","intvolume":"        29","citation":{"short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>.","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>"},"status":"public","external_id":{"pmid":["26680300"]},"date_published":"2015-12-15T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","_id":"9532","year":"2015","volume":29,"file_date_updated":"2021-06-08T09:55:10Z","date_created":"2021-06-08T09:56:24Z","page":"2517–2531","type":"journal_article","month":"12","oa_version":"Published Version","date_updated":"2021-12-14T07:58:15Z","abstract":[{"lang":"eng","text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings."}]},{"day":"01","author":[{"full_name":"Krivelevich, Michael","first_name":"Michael","last_name":"Krivelevich"},{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","first_name":"Benny","last_name":"Sudakov"}],"arxiv":1,"title":"Cycles and matchings in randomly perturbed digraphs and hypergraphs","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Elsevier","scopus_import":"1","article_processing_charge":"No","article_type":"original","publication":"Electronic Notes in Discrete Mathematics","publication_identifier":{"issn":["1571-0653"]},"quality_controlled":"1","doi":"10.1016/j.endm.2015.06.027","language":[{"iso":"eng"}],"date_updated":"2023-02-23T14:01:28Z","abstract":[{"text":"We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.","lang":"eng"}],"oa_version":"Preprint","type":"journal_article","month":"11","page":"181-187","date_created":"2021-06-21T06:40:34Z","volume":49,"year":"2015","_id":"9575","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1501.04816"}],"date_published":"2015-11-01T00:00:00Z","external_id":{"arxiv":["1501.04816"]},"status":"public","citation":{"short":"M. Krivelevich, M.A. Kwan, B. Sudakov, Electronic Notes in Discrete Mathematics 49 (2015) 181–187.","ieee":"M. Krivelevich, M. A. Kwan, and B. Sudakov, “Cycles and matchings in randomly perturbed digraphs and hypergraphs,” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49. Elsevier, pp. 181–187, 2015.","chicago":"Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>.","ista":"Krivelevich M, Kwan MA, Sudakov B. 2015. Cycles and matchings in randomly perturbed digraphs and hypergraphs. Electronic Notes in Discrete Mathematics. 49, 181–187.","mla":"Krivelevich, Michael, et al. “Cycles and Matchings in Randomly Perturbed Digraphs and Hypergraphs.” <i>Electronic Notes in Discrete Mathematics</i>, vol. 49, Elsevier, 2015, pp. 181–87, doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>.","apa":"Krivelevich, M., Kwan, M. A., &#38; Sudakov, B. (2015). Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">https://doi.org/10.1016/j.endm.2015.06.027</a>","ama":"Krivelevich M, Kwan MA, Sudakov B. Cycles and matchings in randomly perturbed digraphs and hypergraphs. <i>Electronic Notes in Discrete Mathematics</i>. 2015;49:181-187. doi:<a href=\"https://doi.org/10.1016/j.endm.2015.06.027\">10.1016/j.endm.2015.06.027</a>"},"intvolume":"        49","extern":"1"},{"publication":"International Journal of Plasticity","_id":"9673","article_processing_charge":"No","scopus_import":"1","article_type":"original","publisher":"Elsevier","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","title":"A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions","volume":67,"date_created":"2021-07-15T14:09:32Z","author":[{"last_name":"Leung","first_name":"H.S.","full_name":"Leung, H.S."},{"full_name":"Leung, P.S.S.","first_name":"P.S.S.","last_name":"Leung"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng"},{"first_name":"A.H.W.","last_name":"Ngan","full_name":"Ngan, A.H.W."}],"page":"1-25","day":"01","abstract":[{"lang":"eng","text":"Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation."}],"date_updated":"2023-02-23T14:04:28Z","oa_version":"None","month":"04","type":"journal_article","intvolume":"        67","extern":"1","language":[{"iso":"eng"}],"citation":{"short":"H.S. Leung, P.S.S. Leung, B. Cheng, A.H.W. Ngan, International Journal of Plasticity 67 (2015) 1–25.","chicago":"Leung, H.S., P.S.S. Leung, Bingqing Cheng, and A.H.W. Ngan. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” <i>International Journal of Plasticity</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>.","ieee":"H. S. Leung, P. S. S. Leung, B. Cheng, and A. H. W. Ngan, “A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions,” <i>International Journal of Plasticity</i>, vol. 67. Elsevier, pp. 1–25, 2015.","apa":"Leung, H. S., Leung, P. S. S., Cheng, B., &#38; Ngan, A. H. W. (2015). A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. <i>International Journal of Plasticity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">https://doi.org/10.1016/j.ijplas.2014.09.009</a>","mla":"Leung, H. S., et al. “A New Dislocation-Density-Function Dynamics Scheme for Computational Crystal Plasticity by Explicit Consideration of Dislocation Elastic Interactions.” <i>International Journal of Plasticity</i>, vol. 67, Elsevier, 2015, pp. 1–25, doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>.","ista":"Leung HS, Leung PSS, Cheng B, Ngan AHW. 2015. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. International Journal of Plasticity. 67, 1–25.","ama":"Leung HS, Leung PSS, Cheng B, Ngan AHW. A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions. <i>International Journal of Plasticity</i>. 2015;67:1-25. doi:<a href=\"https://doi.org/10.1016/j.ijplas.2014.09.009\">10.1016/j.ijplas.2014.09.009</a>"},"status":"public","doi":"10.1016/j.ijplas.2014.09.009","date_published":"2015-04-01T00:00:00Z","publication_status":"published","publication_identifier":{"issn":["0749-6419"]}}]