[{"oa":1,"abstract":[{"lang":"eng","text":"For any strictly convex planar domain Ω ⊂ R2 with a C∞ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi–Merlose [5]. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine Ω up to isometry. In this paper we give a counterexample, namely, we present two nonisometric domains Ω and Ω¯ with the same collection of Marvizi–Melrose invariants. Moreover, each domain has countably many periodic orbits {Sn}n≥1 (resp. {S¯n}n⩾1) of period going to infinity such that Sn and S¯n have the same period and perimeter for each n."}],"publisher":"Springer Nature","date_created":"2020-09-17T10:43:21Z","publication":"Regular and Chaotic Dynamics","title":"Nonisometric domains with the same Marvizi-Melrose invariants","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:11Z","main_file_link":[{"url":"https://arxiv.org/abs/1801.00952","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1801.00952"]},"status":"public","extern":"1","publication_status":"published","date_published":"2018-02-05T00:00:00Z","year":"2018","citation":{"short":"L. Buhovsky, V. Kaloshin, Regular and Chaotic Dynamics 23 (2018) 54–59.","chicago":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” <i>Regular and Chaotic Dynamics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1134/s1560354718010057\">https://doi.org/10.1134/s1560354718010057</a>.","ista":"Buhovsky L, Kaloshin V. 2018. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 23, 54–59.","ama":"Buhovsky L, Kaloshin V. Nonisometric domains with the same Marvizi-Melrose invariants. <i>Regular and Chaotic Dynamics</i>. 2018;23:54-59. doi:<a href=\"https://doi.org/10.1134/s1560354718010057\">10.1134/s1560354718010057</a>","ieee":"L. Buhovsky and V. Kaloshin, “Nonisometric domains with the same Marvizi-Melrose invariants,” <i>Regular and Chaotic Dynamics</i>, vol. 23. Springer Nature, pp. 54–59, 2018.","apa":"Buhovsky, L., &#38; Kaloshin, V. (2018). Nonisometric domains with the same Marvizi-Melrose invariants. <i>Regular and Chaotic Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1134/s1560354718010057\">https://doi.org/10.1134/s1560354718010057</a>","mla":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” <i>Regular and Chaotic Dynamics</i>, vol. 23, Springer Nature, 2018, pp. 54–59, doi:<a href=\"https://doi.org/10.1134/s1560354718010057\">10.1134/s1560354718010057</a>."},"intvolume":"        23","author":[{"last_name":"Buhovsky","full_name":"Buhovsky, Lev","first_name":"Lev"},{"first_name":"Vadim","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"}],"page":"54-59","article_processing_charge":"No","oa_version":"Preprint","month":"02","type":"journal_article","publication_identifier":{"issn":["1560-3547","1468-4845"]},"day":"05","doi":"10.1134/s1560354718010057","volume":23,"_id":"8426","article_type":"original"},{"citation":{"mla":"Weinhäupl, Katharina, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” <i>Cell</i>, vol. 175, no. 5, Elsevier, 2018, p. 1365–1379.e25, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.10.039\">10.1016/j.cell.2018.10.039</a>.","ieee":"K. Weinhäupl <i>et al.</i>, “Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space,” <i>Cell</i>, vol. 175, no. 5. Elsevier, p. 1365–1379.e25, 2018.","ama":"Weinhäupl K, Lindau C, Hessel A, et al. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. <i>Cell</i>. 2018;175(5):1365-1379.e25. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.10.039\">10.1016/j.cell.2018.10.039</a>","apa":"Weinhäupl, K., Lindau, C., Hessel, A., Wang, Y., Schütze, C., Jores, T., … Schanda, P. (2018). Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2018.10.039\">https://doi.org/10.1016/j.cell.2018.10.039</a>","ista":"Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P. 2018. Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space. Cell. 175(5), 1365–1379.e25.","chicago":"Weinhäupl, Katharina, Caroline Lindau, Audrey Hessel, Yong Wang, Conny Schütze, Tobias Jores, Laura Melchionda, et al. “Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space.” <i>Cell</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.10.039\">https://doi.org/10.1016/j.cell.2018.10.039</a>.","short":"K. Weinhäupl, C. Lindau, A. Hessel, Y. Wang, C. Schütze, T. Jores, L. Melchionda, B. Schönfisch, H. Kalbacher, B. Bersch, D. Rapaport, M. Brennich, K. Lindorff-Larsen, N. Wiedemann, P. Schanda, Cell 175 (2018) 1365–1379.e25."},"date_published":"2018-11-15T00:00:00Z","_id":"8436","year":"2018","publication_status":"published","volume":175,"extern":"1","status":"public","day":"15","doi":"10.1016/j.cell.2018.10.039","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0092-8674"]},"author":[{"first_name":"Katharina","full_name":"Weinhäupl, Katharina","last_name":"Weinhäupl"},{"first_name":"Caroline","full_name":"Lindau, Caroline","last_name":"Lindau"},{"last_name":"Hessel","full_name":"Hessel, Audrey","first_name":"Audrey"},{"first_name":"Yong","full_name":"Wang, Yong","last_name":"Wang"},{"last_name":"Schütze","full_name":"Schütze, Conny","first_name":"Conny"},{"first_name":"Tobias","full_name":"Jores, Tobias","last_name":"Jores"},{"first_name":"Laura","full_name":"Melchionda, Laura","last_name":"Melchionda"},{"last_name":"Schönfisch","full_name":"Schönfisch, Birgit","first_name":"Birgit"},{"full_name":"Kalbacher, Hubert","first_name":"Hubert","last_name":"Kalbacher"},{"first_name":"Beate","full_name":"Bersch, Beate","last_name":"Bersch"},{"last_name":"Rapaport","full_name":"Rapaport, Doron","first_name":"Doron"},{"full_name":"Brennich, Martha","first_name":"Martha","last_name":"Brennich"},{"first_name":"Kresten","full_name":"Lindorff-Larsen, Kresten","last_name":"Lindorff-Larsen"},{"first_name":"Nils","full_name":"Wiedemann, Nils","last_name":"Wiedemann"},{"first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"}],"intvolume":"       175","issue":"5","article_type":"original","publisher":"Elsevier","article_processing_charge":"No","abstract":[{"text":"The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial “transfer-chaperone” system is able to guide α-helical and β-barrel membrane proteins in a “nascent chain-like” conformation through a ribosome-free compartment.","lang":"eng"}],"page":"1365-1379.e25","date_updated":"2021-01-12T08:19:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space","type":"journal_article","keyword":["General Biochemistry","Genetics and Molecular Biology"],"publication":"Cell","month":"11","date_created":"2020-09-18T10:04:39Z","oa_version":"None"},{"publication":"Science Advances","month":"09","title":"Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle","type":"journal_article","date_created":"2020-09-18T10:04:51Z","oa_version":"None","date_updated":"2022-08-26T09:11:06Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Chaperonins are ubiquitous protein assemblies present in bacteria, eukaryota, and archaea, facilitating the folding of proteins, preventing protein aggregation, and thus participating in maintaining protein homeostasis in the cell. During their functional cycle, they bind unfolded client proteins inside their double ring structure and promote protein folding by closing the ring chamber in an adenosine 5′-triphosphate (ATP)–dependent manner. Although the static structures of fully open and closed forms of chaperonins were solved by x-ray crystallography or electron microscopy, elucidating the mechanisms of such ATP-driven molecular events requires studying the proteins at the structural level under working conditions. We introduce an approach that combines site-specific nuclear magnetic resonance observation of very large proteins, enabled by advanced isotope labeling methods, with an in situ ATP regeneration system. Using this method, we provide functional insight into the 1-MDa large hsp60 chaperonin while processing client proteins and reveal how nucleotide binding, hydrolysis, and release control switching between closed and open states. While the open conformation stabilizes the unfolded state of client proteins, the internalization of the client protein inside the chaperonin cavity speeds up its functional cycle. This approach opens new perspectives to study structures and mechanisms of various ATP-driven biological machineries in the heat of action.","lang":"eng"}],"publisher":"American Association for the Advancement of Science","article_processing_charge":"No","article_type":"original","author":[{"last_name":"Mas","first_name":"Guillaume","full_name":"Mas, Guillaume"},{"last_name":"Guan","full_name":"Guan, Jia-Ying","first_name":"Jia-Ying"},{"last_name":"Crublet","first_name":"Elodie","full_name":"Crublet, Elodie"},{"last_name":"Debled","full_name":"Debled, Elisa Colas","first_name":"Elisa Colas"},{"full_name":"Moriscot, Christine","first_name":"Christine","last_name":"Moriscot"},{"first_name":"Pierre","full_name":"Gans, Pierre","last_name":"Gans"},{"full_name":"Schoehn, Guy","first_name":"Guy","last_name":"Schoehn"},{"full_name":"Macek, Pavel","first_name":"Pavel","last_name":"Macek"},{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"last_name":"Boisbouvier","first_name":"Jerome","full_name":"Boisbouvier, Jerome"}],"issue":"9","intvolume":"         4","article_number":"eaau4196","language":[{"iso":"eng"}],"day":"19","doi":"10.1126/sciadv.aau4196","publication_identifier":{"issn":["2375-2548"]},"quality_controlled":"1","citation":{"short":"G. Mas, J.-Y. Guan, E. Crublet, E.C. Debled, C. Moriscot, P. Gans, G. Schoehn, P. Macek, P. Schanda, J. Boisbouvier, Science Advances 4 (2018).","chicago":"Mas, Guillaume, Jia-Ying Guan, Elodie Crublet, Elisa Colas Debled, Christine Moriscot, Pierre Gans, Guy Schoehn, Pavel Macek, Paul Schanda, and Jerome Boisbouvier. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” <i>Science Advances</i>. American Association for the Advancement of Science, 2018. <a href=\"https://doi.org/10.1126/sciadv.aau4196\">https://doi.org/10.1126/sciadv.aau4196</a>.","ieee":"G. Mas <i>et al.</i>, “Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle,” <i>Science Advances</i>, vol. 4, no. 9. American Association for the Advancement of Science, 2018.","ama":"Mas G, Guan J-Y, Crublet E, et al. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. <i>Science Advances</i>. 2018;4(9). doi:<a href=\"https://doi.org/10.1126/sciadv.aau4196\">10.1126/sciadv.aau4196</a>","apa":"Mas, G., Guan, J.-Y., Crublet, E., Debled, E. C., Moriscot, C., Gans, P., … Boisbouvier, J. (2018). Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.aau4196\">https://doi.org/10.1126/sciadv.aau4196</a>","ista":"Mas G, Guan J-Y, Crublet E, Debled EC, Moriscot C, Gans P, Schoehn G, Macek P, Schanda P, Boisbouvier J. 2018. Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle. Science Advances. 4(9), eaau4196.","mla":"Mas, Guillaume, et al. “Structural Investigation of a Chaperonin in Action Reveals How Nucleotide Binding Regulates the Functional Cycle.” <i>Science Advances</i>, vol. 4, no. 9, eaau4196, American Association for the Advancement of Science, 2018, doi:<a href=\"https://doi.org/10.1126/sciadv.aau4196\">10.1126/sciadv.aau4196</a>."},"volume":4,"extern":"1","publication_status":"published","status":"public","year":"2018","_id":"8437","date_published":"2018-09-19T00:00:00Z"},{"title":"Dynamics and interactions of AAC3 in DPC are not functionally relevant","type":"journal_article","publication":"Nature Structural & Molecular Biology","keyword":["Molecular Biology","Structural Biology"],"month":"09","oa_version":"None","date_created":"2020-09-18T10:04:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:16Z","page":"745-747","publisher":"Springer Nature","article_processing_charge":"No","article_type":"letter_note","author":[{"first_name":"Vilius","full_name":"Kurauskas, Vilius","last_name":"Kurauskas"},{"full_name":"Hessel, Audrey","first_name":"Audrey","last_name":"Hessel"},{"last_name":"Dehez","full_name":"Dehez, François","first_name":"François"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"first_name":"Beate","full_name":"Bersch, Beate","last_name":"Bersch"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"}],"intvolume":"        25","issue":"9","day":"03","doi":"10.1038/s41594-018-0127-4","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["1545-9993","1545-9985"]},"citation":{"chicago":"Kurauskas, Vilius, Audrey Hessel, François Dehez, Christophe Chipot, Beate Bersch, and Paul Schanda. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41594-018-0127-4\">https://doi.org/10.1038/s41594-018-0127-4</a>.","short":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, P. Schanda, Nature Structural &#38; Molecular Biology 25 (2018) 745–747.","mla":"Kurauskas, Vilius, et al. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 25, no. 9, Springer Nature, 2018, pp. 745–47, doi:<a href=\"https://doi.org/10.1038/s41594-018-0127-4\">10.1038/s41594-018-0127-4</a>.","ama":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. Dynamics and interactions of AAC3 in DPC are not functionally relevant. <i>Nature Structural &#38; Molecular Biology</i>. 2018;25(9):745-747. doi:<a href=\"https://doi.org/10.1038/s41594-018-0127-4\">10.1038/s41594-018-0127-4</a>","ieee":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, and P. Schanda, “Dynamics and interactions of AAC3 in DPC are not functionally relevant,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 25, no. 9. Springer Nature, pp. 745–747, 2018.","apa":"Kurauskas, V., Hessel, A., Dehez, F., Chipot, C., Bersch, B., &#38; Schanda, P. (2018). Dynamics and interactions of AAC3 in DPC are not functionally relevant. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-018-0127-4\">https://doi.org/10.1038/s41594-018-0127-4</a>","ista":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. 2018. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural &#38; Molecular Biology. 25(9), 745–747."},"date_published":"2018-09-03T00:00:00Z","_id":"8438","year":"2018","publication_status":"published","extern":"1","status":"public","volume":25},{"article_processing_charge":"No","publisher":"American Chemical Society","abstract":[{"text":"Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly hampers their structural study in an environment similar to the bacterial surface. We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long O-antigen polysaccharides assembled in solution as vesicles or elongated micelles. Solid-state NMR with magic-angle spinning permitted the identification of NMR signals arising from regions with different flexibilities in the LPS, from the lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa LPS, for which we could confirm that a specific oligosaccharide is involved in the antibiotic binding. The possibility to study LPS alone and bound to a ligand when it is assembled in membrane-like structures opens great prospects for the investigation of proteins and antibiotics that specifically target such an important molecule at the surface of Gram-negative bacteria.","lang":"eng"}],"page":"2106-2113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:16Z","oa_version":"None","date_created":"2020-09-18T10:05:09Z","type":"journal_article","title":"Solid state NMR studies of intact lipopolysaccharide endotoxin","publication":"ACS Chemical Biology","keyword":["Molecular Medicine","Biochemistry","General Medicine"],"month":"07","date_published":"2018-07-02T00:00:00Z","_id":"8439","year":"2018","publication_status":"published","volume":13,"extern":"1","status":"public","citation":{"ista":"Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin. ACS Chemical Biology. 13(8), 2106–2113.","ama":"Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact lipopolysaccharide endotoxin. <i>ACS Chemical Biology</i>. 2018;13(8):2106-2113. doi:<a href=\"https://doi.org/10.1021/acschembio.8b00271\">10.1021/acschembio.8b00271</a>","apa":"Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi, A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide endotoxin. <i>ACS Chemical Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acschembio.8b00271\">https://doi.org/10.1021/acschembio.8b00271</a>","ieee":"C. Laguri <i>et al.</i>, “Solid state NMR studies of intact lipopolysaccharide endotoxin,” <i>ACS Chemical Biology</i>, vol. 13, no. 8. American Chemical Society, pp. 2106–2113, 2018.","mla":"Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” <i>ACS Chemical Biology</i>, vol. 13, no. 8, American Chemical Society, 2018, pp. 2106–13, doi:<a href=\"https://doi.org/10.1021/acschembio.8b00271\">10.1021/acschembio.8b00271</a>.","short":"C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi, A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113.","chicago":"Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid State NMR Studies of Intact Lipopolysaccharide Endotoxin.” <i>ACS Chemical Biology</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acschembio.8b00271\">https://doi.org/10.1021/acschembio.8b00271</a>."},"quality_controlled":"1","publication_identifier":{"issn":["1554-8929","1554-8937"]},"doi":"10.1021/acschembio.8b00271","day":"02","language":[{"iso":"eng"}],"intvolume":"        13","issue":"8","author":[{"first_name":"Cedric","full_name":"Laguri, Cedric","last_name":"Laguri"},{"last_name":"Silipo","full_name":"Silipo, Alba","first_name":"Alba"},{"first_name":"Alessandra M.","full_name":"Martorana, Alessandra M.","last_name":"Martorana"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"},{"last_name":"Marchetti","full_name":"Marchetti, Roberta","first_name":"Roberta"},{"first_name":"Alessandra","full_name":"Polissi, Alessandra","last_name":"Polissi"},{"full_name":"Molinaro, Antonio","first_name":"Antonio","last_name":"Molinaro"},{"last_name":"Simorre","full_name":"Simorre, Jean-Pierre","first_name":"Jean-Pierre"}],"article_type":"original"},{"article_processing_charge":"No","publisher":"American Society for Biochemistry & Molecular Biology","abstract":[{"lang":"eng","text":"Mycobacterium tuberculosis can remain dormant in the host, an ability that explains the failure of many current tuberculosis treatments. Recently, the natural products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein substrates, such as proteins containing phosphorylated arginine residues, to the ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these dynamics are caused by conformational changes and do not result from unfolding or oligomerization of this domain. Cyclomarin binding to this domain specifically blocked these N-terminal dynamics. On the basis of these results, we propose a mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics, which modulates the chaperone enzymatic activity leading eventually to cell death."}],"page":"8379-8393","date_updated":"2021-01-12T08:19:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2020-09-18T10:05:18Z","title":"The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis","type":"journal_article","keyword":["Cell Biology","Biochemistry","Molecular Biology"],"publication":"Journal of Biological Chemistry","month":"06","date_published":"2018-06-01T00:00:00Z","_id":"8440","year":"2018","volume":293,"publication_status":"published","status":"public","extern":"1","citation":{"mla":"Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” <i>Journal of Biological Chemistry</i>, vol. 293, no. 22, American Society for Biochemistry &#38; Molecular Biology, 2018, pp. 8379–93, doi:<a href=\"https://doi.org/10.1074/jbc.ra118.002251\">10.1074/jbc.ra118.002251</a>.","ieee":"K. Weinhäupl <i>et al.</i>, “The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,” <i>Journal of Biological Chemistry</i>, vol. 293, no. 22. American Society for Biochemistry &#38; Molecular Biology, pp. 8379–8393, 2018.","ama":"Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. <i>Journal of Biological Chemistry</i>. 2018;293(22):8379-8393. doi:<a href=\"https://doi.org/10.1074/jbc.ra118.002251\">10.1074/jbc.ra118.002251</a>","apa":"Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg, A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.ra118.002251\">https://doi.org/10.1074/jbc.ra118.002251</a>","ista":"Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis. Journal of Biological Chemistry. 293(22), 8379–8393.","chicago":"Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2018. <a href=\"https://doi.org/10.1074/jbc.ra118.002251\">https://doi.org/10.1074/jbc.ra118.002251</a>.","short":"K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg, P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393."},"quality_controlled":"1","publication_identifier":{"issn":["0021-9258","1083-351X"]},"day":"01","doi":"10.1074/jbc.ra118.002251","language":[{"iso":"eng"}],"intvolume":"       293","issue":"22","author":[{"last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina","first_name":"Katharina"},{"last_name":"Brennich","first_name":"Martha","full_name":"Brennich, Martha"},{"last_name":"Kazmaier","first_name":"Uli","full_name":"Kazmaier, Uli"},{"last_name":"Lelievre","full_name":"Lelievre, Joel","first_name":"Joel"},{"full_name":"Ballell, Lluis","first_name":"Lluis","last_name":"Ballell"},{"last_name":"Goldberg","first_name":"Alfred","full_name":"Goldberg, Alfred"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"},{"first_name":"Hugo","full_name":"Fraga, Hugo","last_name":"Fraga"}],"article_type":"original"},{"date_updated":"2021-01-12T08:19:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals","type":"journal_article","month":"05","publication":"Journal of Biomolecular NMR","oa_version":"Published Version","date_created":"2020-09-18T10:05:28Z","publisher":"Springer Nature","article_processing_charge":"No","abstract":[{"text":"Solid-state near-rotary-resonance measurements of the spin–lattice relaxation rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1ρ data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, “dead time” in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1ρ measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30–50 μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process.","lang":"eng"}],"page":"53-67","author":[{"full_name":"Krushelnitsky, Alexey","first_name":"Alexey","last_name":"Krushelnitsky"},{"last_name":"Gauto","full_name":"Gauto, Diego","first_name":"Diego"},{"last_name":"Rodriguez Camargo","first_name":"Diana C.","full_name":"Rodriguez Camargo, Diana C."},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"},{"full_name":"Saalwächter, Kay","first_name":"Kay","last_name":"Saalwächter"}],"intvolume":"        71","issue":"1","article_type":"original","citation":{"apa":"Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., &#38; Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-018-0191-4\">https://doi.org/10.1007/s10858-018-0191-4</a>","ieee":"A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter, “Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals,” <i>Journal of Biomolecular NMR</i>, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.","ama":"Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. <i>Journal of Biomolecular NMR</i>. 2018;71(1):53-67. doi:<a href=\"https://doi.org/10.1007/s10858-018-0191-4\">10.1007/s10858-018-0191-4</a>","ista":"Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K. 2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals. Journal of Biomolecular NMR. 71(1), 53–67.","mla":"Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” <i>Journal of Biomolecular NMR</i>, vol. 71, no. 1, Springer Nature, 2018, pp. 53–67, doi:<a href=\"https://doi.org/10.1007/s10858-018-0191-4\">10.1007/s10858-018-0191-4</a>.","short":"A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter, Journal of Biomolecular NMR 71 (2018) 53–67.","chicago":"Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda, and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s10858-018-0191-4\">https://doi.org/10.1007/s10858-018-0191-4</a>."},"year":"2018","_id":"8441","date_published":"2018-05-30T00:00:00Z","extern":"1","publication_status":"published","status":"public","volume":71,"doi":"10.1007/s10858-018-0191-4","day":"30","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0925-2738","1573-5001"]}},{"article_processing_charge":"No","publisher":"American Chemical Society","page":"3559-3607","abstract":[{"lang":"eng","text":"Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:18Z","date_created":"2020-09-18T10:05:35Z","oa_version":"None","publication":"Chemical Reviews","month":"02","keyword":["General Chemistry"],"type":"journal_article","title":"Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies","volume":118,"status":"public","publication_status":"published","extern":"1","year":"2018","_id":"8442","date_published":"2018-02-28T00:00:00Z","citation":{"mla":"Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” <i>Chemical Reviews</i>, vol. 118, no. 7, American Chemical Society, 2018, pp. 3559–607, doi:<a href=\"https://doi.org/10.1021/acs.chemrev.7b00570\">10.1021/acs.chemrev.7b00570</a>.","ieee":"C. Chipot <i>et al.</i>, “Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies,” <i>Chemical Reviews</i>, vol. 118, no. 7. American Chemical Society, pp. 3559–3607, 2018.","apa":"Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire, L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. <i>Chemical Reviews</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.chemrev.7b00570\">https://doi.org/10.1021/acs.chemrev.7b00570</a>","ama":"Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. <i>Chemical Reviews</i>. 2018;118(7):3559-3607. doi:<a href=\"https://doi.org/10.1021/acs.chemrev.7b00570\">10.1021/acs.chemrev.7b00570</a>","ista":"Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ, Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607.","chicago":"Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann, Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies.” <i>Chemical Reviews</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.chemrev.7b00570\">https://doi.org/10.1021/acs.chemrev.7b00570</a>.","short":"C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire, B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118 (2018) 3559–3607."},"publication_identifier":{"issn":["0009-2665","1520-6890"]},"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1021/acs.chemrev.7b00570","day":"28","issue":"7","intvolume":"       118","author":[{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"},{"last_name":"Dehez","full_name":"Dehez, François","first_name":"François"},{"last_name":"Schnell","full_name":"Schnell, Jason R.","first_name":"Jason R."},{"full_name":"Zitzmann, Nicole","first_name":"Nicole","last_name":"Zitzmann"},{"last_name":"Pebay-Peyroula","full_name":"Pebay-Peyroula, Eva","first_name":"Eva"},{"first_name":"Laurent J.","full_name":"Catoire, Laurent J.","last_name":"Catoire"},{"last_name":"Miroux","first_name":"Bruno","full_name":"Miroux, Bruno"},{"full_name":"Kunji, Edmund R. S.","first_name":"Edmund R. S.","last_name":"Kunji"},{"first_name":"Gianluigi","full_name":"Veglia, Gianluigi","last_name":"Veglia"},{"first_name":"Timothy A.","full_name":"Cross, Timothy A.","last_name":"Cross"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda"}],"article_type":"original"},{"page":"933-938","abstract":[{"text":"Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers differ markedly and could alter the structural organization of MPs, albeit without general rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure determination by NMR, but the physiological relevance of several prominent structures has been questioned, though indirectly, by other biophysical techniques, e.g., functional/thermostability assay (TSA) and molecular dynamics (MD) simulations. Here, we resolve unambiguously this controversy by probing the functional relevance of three different mitochondrial carriers (MCs) in DPC at the atomic level, using an exhaustive set of solution-NMR experiments, complemented by functional/TSA and MD data. Our results provide atomic-level insight into the structure, substrate interaction and dynamics of the detergent–membrane protein complexes and demonstrates cogently that, while high-resolution NMR signals can be obtained for MCs in DPC, they systematically correspond to nonfunctional states.","lang":"eng"}],"article_processing_charge":"No","publisher":"American Chemical Society","date_created":"2020-09-18T10:05:45Z","oa_version":"None","keyword":["General Materials Science"],"publication":"The Journal of Physical Chemistry Letters","month":"02","title":"How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine","type":"journal_article","date_updated":"2021-01-12T08:19:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1948-7185"]},"quality_controlled":"1","language":[{"iso":"eng"}],"day":"03","doi":"10.1021/acs.jpclett.8b00269","publication_status":"published","volume":9,"status":"public","extern":"1","date_published":"2018-02-03T00:00:00Z","_id":"8443","year":"2018","citation":{"chicago":"Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.jpclett.8b00269\">https://doi.org/10.1021/acs.jpclett.8b00269</a>.","short":"V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher, M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez, B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938.","mla":"Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.” <i>The Journal of Physical Chemistry Letters</i>, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.8b00269\">10.1021/acs.jpclett.8b00269</a>.","ista":"Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry Letters. 9(5), 933–938.","ieee":"V. Kurauskas <i>et al.</i>, “How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine,” <i>The Journal of Physical Chemistry Letters</i>, vol. 9, no. 5. American Chemical Society, pp. 933–938, 2018.","apa":"Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L., … Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.8b00269\">https://doi.org/10.1021/acs.jpclett.8b00269</a>","ama":"Kurauskas V, Hessel A, Ma P, et al. How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine. <i>The Journal of Physical Chemistry Letters</i>. 2018;9(5):933-938. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.8b00269\">10.1021/acs.jpclett.8b00269</a>"},"article_type":"original","issue":"5","intvolume":"         9","author":[{"first_name":"Vilius","full_name":"Kurauskas, Vilius","last_name":"Kurauskas"},{"full_name":"Hessel, Audrey","first_name":"Audrey","last_name":"Hessel"},{"last_name":"Ma","full_name":"Ma, Peixiang","first_name":"Peixiang"},{"last_name":"Lunetti","first_name":"Paola","full_name":"Lunetti, Paola"},{"first_name":"Katharina","full_name":"Weinhäupl, Katharina","last_name":"Weinhäupl"},{"last_name":"Imbert","first_name":"Lionel","full_name":"Imbert, Lionel"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"},{"last_name":"King","first_name":"Martin S.","full_name":"King, Martin S."},{"full_name":"Sounier, Rémy","first_name":"Rémy","last_name":"Sounier"},{"last_name":"Dolce","first_name":"Vincenza","full_name":"Dolce, Vincenza"},{"last_name":"Kunji","first_name":"Edmund R. S.","full_name":"Kunji, Edmund R. S."},{"last_name":"Capobianco","first_name":"Loredana","full_name":"Capobianco, Loredana"},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"},{"last_name":"Dehez","full_name":"Dehez, François","first_name":"François"},{"last_name":"Bersch","full_name":"Bersch, Beate","first_name":"Beate"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"}]},{"doi":"10.1101/494088","day":"13","language":[{"iso":"eng"}],"_id":"8547","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416","call_identifier":"FWF"}],"year":"2018","date_published":"2018-12-13T00:00:00Z","status":"public","publication_status":"submitted","citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, <a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>","ieee":"A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"author":[{"last_name":"Llorca","full_name":"Llorca, Alfredo","first_name":"Alfredo"},{"last_name":"Ciceri","full_name":"Ciceri, Gabriele","first_name":"Gabriele"},{"first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie"},{"full_name":"Wong, Fong K.","first_name":"Fong K.","last_name":"Wong"},{"last_name":"Diana","full_name":"Diana, Giovanni","first_name":"Giovanni"},{"last_name":"Serafeimidou","first_name":"Eleni","full_name":"Serafeimidou, Eleni"},{"first_name":"Marian","full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero"},{"last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arnold, Sebastian J.","first_name":"Sebastian J.","last_name":"Arnold"},{"last_name":"Meyer","full_name":"Meyer, Martin","first_name":"Martin"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"last_name":"Maravall","first_name":"Miguel","full_name":"Maravall, Miguel"},{"last_name":"Marín","first_name":"Oscar","full_name":"Marín, Oscar"}],"oa":1,"abstract":[{"text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.","lang":"eng"}],"department":[{"_id":"SiHi"}],"ec_funded":1,"article_processing_charge":"No","publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","date_created":"2020-09-21T12:01:50Z","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","type":"preprint","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","publication":"bioRxiv","month":"12","main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"date_updated":"2024-10-22T10:46:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Submitted Version","type":"book_chapter","month":"07","scopus_import":1,"ddc":["000"],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"page":"143 - 161","editor":[{"first_name":"Marten","full_name":"Lohstroh, Marten","last_name":"Lohstroh"},{"first_name":"Patricia","full_name":"Derler, Patricia","last_name":"Derler"},{"last_name":"Sirjani","full_name":"Sirjani, Marjan","first_name":"Marjan"}],"publist_id":"7968","doi":"10.1007/978-3-319-95246-8_9","day":"20","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"_id":"86","volume":10760,"date_created":"2018-12-11T11:44:33Z","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","title":"Computing average response time","publication":"Principles of Modeling","date_updated":"2025-04-15T06:26:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"9995c6ce6957333baf616fc4f20be597","creator":"dernst","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","file_size":516307,"file_id":"7053","date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z","access_level":"open_access"}],"ec_funded":1,"publisher":"Springer","has_accepted_license":"1","intvolume":"     10760","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2018-07-20T00:00:00Z","year":"2018","publication_status":"published","status":"public","alternative_title":["LNCS"],"file_date_updated":"2020-07-14T12:48:14Z","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In <i>Principles of Modeling</i>, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” <i>Principles of Modeling</i>, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, &#38; M. Sirjani (Eds.), <i>Principles of Modeling</i> (Vol. 10760, pp. 143–161). Springer. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in <i>Principles of Modeling</i>, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. <i>Principles of Modeling</i>. Vol 10760. Springer; 2018:143-161. doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161."}},{"oa_version":"Published Version","type":"journal_article","month":"02","article_processing_charge":"No","scopus_import":"1","ddc":["570"],"isi":1,"department":[{"_id":"JoDa"}],"article_number":"2724","article_type":"original","_id":"8618","volume":8,"publication_identifier":{"issn":["2045-2322"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"doi":"10.1038/s41598-018-19947-1","day":"09","date_updated":"2024-10-21T06:02:43Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"date_created":"2020-10-06T16:33:37Z","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","keyword":["Multidisciplinary"],"publication":"Scientific Reports","publisher":"Springer Nature","oa":1,"abstract":[{"lang":"eng","text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting."}],"file":[{"checksum":"e642080fcbde9584c63544f587c74f03","relation":"main_file","content_type":"application/pdf","file_name":"2018_ScientificReports_Gregor.pdf","file_size":2818077,"creator":"dernst","success":1,"date_created":"2020-10-06T16:35:16Z","file_id":"8619","date_updated":"2020-10-06T16:35:16Z","access_level":"open_access"}],"intvolume":"         8","author":[{"last_name":"Gregor","full_name":"Gregor, Carola","first_name":"Carola"},{"last_name":"Sidenstein","first_name":"Sven C.","full_name":"Sidenstein, Sven C."},{"last_name":"Andresen","full_name":"Andresen, Martin","first_name":"Martin"},{"last_name":"Sahl","full_name":"Sahl, Steffen J.","first_name":"Steffen J."},{"last_name":"Danzl","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G"},{"last_name":"Hell","first_name":"Stefan W.","full_name":"Hell, Stefan W."}],"has_accepted_license":"1","year":"2018","date_published":"2018-02-09T00:00:00Z","publication_status":"published","status":"public","file_date_updated":"2020-10-06T16:35:16Z","citation":{"short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>.","ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>, vol. 8. Springer Nature, 2018.","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38; Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000424630400037"],"pmid":["29426833"]}},{"article_processing_charge":"No","scopus_import":"1","page":"9577-9588","oa_version":"Preprint","type":"journal_article","month":"12","_id":"9053","volume":14,"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"doi":"10.1039/c8sm01760c","day":"21","article_type":"original","publisher":"Royal Society of Chemistry ","oa":1,"abstract":[{"lang":"eng","text":"The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We recently demonstrated the hierarchical self-assembly of phoretic microswimmers into self-spinning microgears and their synchronization by diffusiophoretic interactions [Aubret et al., Nat. Phys., 2018]. In this paper, we adopt a pedagogical approach and expose our strategy to control self-assembly and build machines using phoretic phenomena. We notably introduce Highly Inclined Laminated Optical sheets microscopy (HILO) to image and characterize anisotropic and dynamic diffusiophoretic interactions, which cannot be performed by conventional fluorescence microscopy. The dynamics of a (haematite) photocatalytic material immersed in (hydrogen peroxide) fuel under various illumination patterns is first described and quantitatively rationalized by a model of diffusiophoresis, the migration of a colloidal particle in a concentration gradient. It is further exploited to design phototactic microswimmers that direct towards the high intensity of light, as a result of the reorientation of the haematite in a light gradient. We finally show the assembly of self-spinning microgears from colloidal microswimmers and carefully characterize the interactions using HILO techniques. The results are compared with analytical and numerical predictions and agree quantitatively, stressing the important role played by concentration gradients induced by chemical activity to control and design interactions. Because the approach described hereby is generic, this works paves the way for the rational design of machines by controlling phoretic phenomena."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.11121"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","arxiv":1,"pmid":1,"date_updated":"2023-02-23T13:47:43Z","date_created":"2021-02-01T13:44:41Z","title":"Diffusiophoretic design of self-spinning microgears from colloidal microswimmers","publication":"Soft Matter","keyword":["General Chemistry","Condensed Matter Physics"],"year":"2018","date_published":"2018-12-21T00:00:00Z","publication_status":"published","extern":"1","status":"public","citation":{"ista":"Aubret A, Palacci JA. 2018. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 14(47), 9577–9588.","apa":"Aubret, A., &#38; Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>","ama":"Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. 2018;14(47):9577-9588. doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>","ieee":"A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” <i>Soft Matter</i>, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018.","mla":"Aubret, Antoine, and Jérémie A. Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” <i>Soft Matter</i>, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>.","short":"A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588.","chicago":"Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” <i>Soft Matter</i>. Royal Society of Chemistry , 2018. <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["30456407"],"arxiv":["1909.11121"]},"intvolume":"        14","issue":"47","author":[{"first_name":"Antoine","full_name":"Aubret, Antoine","last_name":"Aubret"},{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci"}]},{"_id":"9062","volume":14,"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"day":"01","doi":"10.1038/s41567-018-0227-4","article_type":"original","article_processing_charge":"No","scopus_import":"1","page":"1114-1118","oa_version":"Preprint","type":"journal_article","month":"11","date_published":"2018-11-01T00:00:00Z","year":"2018","publication_status":"published","extern":"1","status":"public","citation":{"chicago":"Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” <i>Nature Physics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41567-018-0227-4\">https://doi.org/10.1038/s41567-018-0227-4</a>.","short":"A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118.","mla":"Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” <i>Nature Physics</i>, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:<a href=\"https://doi.org/10.1038/s41567-018-0227-4\">10.1038/s41567-018-0227-4</a>.","ista":"Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118.","ama":"Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. <i>Nature Physics</i>. 2018;14(11):1114-1118. doi:<a href=\"https://doi.org/10.1038/s41567-018-0227-4\">10.1038/s41567-018-0227-4</a>","ieee":"A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” <i>Nature Physics</i>, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018.","apa":"Aubret, A., Youssef, M., Sacanna, S., &#38; Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-018-0227-4\">https://doi.org/10.1038/s41567-018-0227-4</a>"},"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1810.01033"]},"intvolume":"        14","issue":"11","author":[{"full_name":"Aubret, Antoine","first_name":"Antoine","last_name":"Aubret"},{"last_name":"Youssef","first_name":"Mena","full_name":"Youssef, Mena"},{"full_name":"Sacanna, Stefano","first_name":"Stefano","last_name":"Sacanna"},{"first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","last_name":"Palacci"}],"publisher":"Springer Nature","oa":1,"abstract":[{"lang":"eng","text":"Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery."}],"date_updated":"2023-02-23T13:48:02Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1810.01033","open_access":"1"}],"date_created":"2021-02-02T13:52:49Z","title":"Targeted assembly and synchronization of self-spinning microgears","publication":"Nature Physics"},{"article_type":"original","article_number":"1805564","doi":"10.1002/adma.201805564","day":"29","publication_identifier":{"issn":["0935-9648","1521-4095"]},"_id":"9066","volume":30,"type":"journal_article","month":"10","oa_version":"Preprint","article_processing_charge":"No","author":[{"last_name":"Lee","first_name":"Nara","full_name":"Lee, Nara"},{"first_name":"Eunjung","full_name":"Ko, Eunjung","last_name":"Ko"},{"last_name":"Choi","full_name":"Choi, Hwan Young","first_name":"Hwan Young"},{"first_name":"Yun Jeong","full_name":"Hong, Yun Jeong","last_name":"Hong"},{"first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","last_name":"Nauman"},{"first_name":"Woun","full_name":"Kang, Woun","last_name":"Kang"},{"first_name":"Hyoung Joon","full_name":"Choi, Hyoung Joon","last_name":"Choi"},{"full_name":"Choi, Young Jai","first_name":"Young Jai","last_name":"Choi"},{"last_name":"Jo","first_name":"Younjung","full_name":"Jo, Younjung"}],"intvolume":"        30","issue":"52","language":[{"iso":"eng"}],"external_id":{"arxiv":["1811.04562"]},"quality_controlled":"1","citation":{"chicago":"Lee, Nara, Eunjung Ko, Hwan Young Choi, Yun Jeong Hong, Muhammad Nauman, Woun Kang, Hyoung Joon Choi, Young Jai Choi, and Younjung Jo. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” <i>Advanced Materials</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/adma.201805564\">https://doi.org/10.1002/adma.201805564</a>.","short":"N. Lee, E. Ko, H.Y. Choi, Y.J. Hong, M. Nauman, W. Kang, H.J. Choi, Y.J. Choi, Y. Jo, Advanced Materials 30 (2018).","mla":"Lee, Nara, et al. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” <i>Advanced Materials</i>, vol. 30, no. 52, 1805564, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/adma.201805564\">10.1002/adma.201805564</a>.","apa":"Lee, N., Ko, E., Choi, H. Y., Hong, Y. J., Nauman, M., Kang, W., … Jo, Y. (2018). Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201805564\">https://doi.org/10.1002/adma.201805564</a>","ieee":"N. Lee <i>et al.</i>, “Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate,” <i>Advanced Materials</i>, vol. 30, no. 52. Wiley, 2018.","ama":"Lee N, Ko E, Choi HY, et al. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. <i>Advanced Materials</i>. 2018;30(52). doi:<a href=\"https://doi.org/10.1002/adma.201805564\">10.1002/adma.201805564</a>","ista":"Lee N, Ko E, Choi HY, Hong YJ, Nauman M, Kang W, Choi HJ, Choi YJ, Jo Y. 2018. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. 30(52), 1805564."},"date_published":"2018-10-29T00:00:00Z","year":"2018","extern":"1","publication_status":"published","status":"public","title":"Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate","publication":"Advanced Materials","keyword":["Mechanical Engineering","General Materials Science","Mechanics of Materials"],"date_created":"2021-02-02T15:50:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"date_updated":"2021-02-03T13:58:39Z","abstract":[{"text":"The novel electronic state of the canted antiferromagnetic (AFM) insulator, strontium iridate (Sr2IrO4) has been well described by the spin-orbit-entangled isospin Jeff = 1/2, but the role of isospin in transport phenomena remains poorly understood. In this study, antiferromagnet-based spintronic functionality is demonstrated by combining unique characteristics of the isospin state in Sr2IrO4. Based on magnetic and transport measurements, large and highly anisotropic magnetoresistance (AMR) is obtained by manipulating the antiferromagnetic isospin domains. First-principles calculations suggest that electrons whose isospin directions are strongly coupled to in-plane net magnetic moment encounter the isospin mismatch when moving across antiferromagnetic domain boundaries, which generates a high resistance state. By rotating a magnetic field that aligns in-plane net moments and removes domain boundaries, the macroscopically-ordered isospins govern dynamic transport through the system, which leads to the extremely angle-sensitive AMR. As with this work that establishes a link between isospins and magnetotransport in strongly spin-orbit-coupled AFM Sr2IrO4, the peculiar AMR effect provides a beneficial foundation for fundamental and applied research on AFM spintronics.","lang":"eng"}],"publisher":"Wiley"},{"month":"05","publication":"Physica B: Condensed Matter","title":"Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se","type":"journal_article","date_created":"2021-02-02T15:52:43Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-02-04T07:18:57Z","page":"235-238","abstract":[{"text":"We report the temperature-dependent resistivity ρ(T) of chalcogenide NiS2-xSex (x = 0.1) using hydrostatic pressure as a control parameter in the temperature range of 4–300 K. The insulating behavior of ρ(T) survives at low temperatures in the pressure regime below 7.5 kbar, whereas a clear insulator-to-metallic transition is observed above 7.5 kbar. Two types of magnetic transitions, from the paramagnetic (PM) to the antiferromagnetic (AFM) state and from the AFM state to the weak ferromagnetic (WF) state, were evaluated and confirmed by magnetization measurement. According to the temperature–pressure phase diagram, the WF phase survives up to 7.5 kbar, and the transition temperature of the WF transition decreases as the pressure increases, whereas the metal–insulator transition temperature increases up to 9.4 kbar. We analyzed the metallic behavior and proposed Fermi-liquid behavior of NiS1.9Se0.1.","lang":"eng"}],"publisher":"Elsevier","article_processing_charge":"No","article_type":"original","author":[{"full_name":"Hussain, Tayyaba","first_name":"Tayyaba","last_name":"Hussain"},{"last_name":"Oh","full_name":"Oh, Myeong-jun","first_name":"Myeong-jun"},{"last_name":"Nauman","first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846"},{"full_name":"Jo, Younjung","first_name":"Younjung","last_name":"Jo"},{"first_name":"Garam","full_name":"Han, Garam","last_name":"Han"},{"first_name":"Changyoung","full_name":"Kim, Changyoung","last_name":"Kim"},{"full_name":"Kang, Woun","first_name":"Woun","last_name":"Kang"}],"intvolume":"       536","language":[{"iso":"eng"}],"doi":"10.1016/j.physb.2017.11.032","day":"01","publication_identifier":{"issn":["0921-4526"]},"quality_controlled":"1","citation":{"ista":"Hussain T, Oh M, Nauman M, Jo Y, Han G, Kim C, Kang W. 2018. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. 536, 235–238.","ama":"Hussain T, Oh M, Nauman M, et al. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. <i>Physica B: Condensed Matter</i>. 2018;536:235-238. doi:<a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">10.1016/j.physb.2017.11.032</a>","ieee":"T. Hussain <i>et al.</i>, “Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se,” <i>Physica B: Condensed Matter</i>, vol. 536. Elsevier, pp. 235–238, 2018.","apa":"Hussain, T., Oh, M., Nauman, M., Jo, Y., Han, G., Kim, C., &#38; Kang, W. (2018). Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. <i>Physica B: Condensed Matter</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">https://doi.org/10.1016/j.physb.2017.11.032</a>","mla":"Hussain, Tayyaba, et al. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” <i>Physica B: Condensed Matter</i>, vol. 536, Elsevier, 2018, pp. 235–38, doi:<a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">10.1016/j.physb.2017.11.032</a>.","short":"T. Hussain, M. Oh, M. Nauman, Y. Jo, G. Han, C. Kim, W. Kang, Physica B: Condensed Matter 536 (2018) 235–238.","chicago":"Hussain, Tayyaba, Myeong-jun Oh, Muhammad Nauman, Younjung Jo, Garam Han, Changyoung Kim, and Woun Kang. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” <i>Physica B: Condensed Matter</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">https://doi.org/10.1016/j.physb.2017.11.032</a>."},"status":"public","volume":536,"extern":"1","publication_status":"published","date_published":"2018-05-01T00:00:00Z","_id":"9068","year":"2018"},{"article_number":"jcs.204198","publist_id":"6530","volume":131,"_id":"913","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"publication_identifier":{"issn":["0021-9533"]},"doi":"10.1242/jcs.204198","day":"29","pubrep_id":"988","oa_version":"Published Version","month":"01","type":"journal_article","article_processing_charge":"No","isi":1,"ddc":["581"],"scopus_import":"1","department":[{"_id":"JiFr"}],"issue":"2","intvolume":"       131","author":[{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"first_name":"Cecilia","full_name":"Rodríguez Furlán, Cecilia","last_name":"Rodríguez Furlán"},{"last_name":"Adamowski","first_name":"Maciek","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"full_name":"Norambuena, Lorena","first_name":"Lorena","last_name":"Norambuena"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"has_accepted_license":"1","publication_status":"published","status":"public","year":"2018","date_published":"2018-01-29T00:00:00Z","citation":{"short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018).","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. Company of Biologists, 2018. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>.","ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2018;131(2). doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 131, no. 2. Company of Biologists, 2018.","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., &#38; Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>","ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>."},"corr_author":"1","file_date_updated":"2020-07-14T12:48:15Z","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000424842400019"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T12:01:38Z","date_created":"2018-12-11T11:49:10Z","publication":"Journal of Cell Science","title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","ec_funded":1,"publisher":"Company of Biologists","oa":1,"file":[{"creator":"dernst","file_name":"2017_adamowski_PATELLINS_are.pdf","file_size":14925985,"relation":"main_file","content_type":"application/pdf","checksum":"bf156c20a4f117b4b932370d54cbac8c","date_updated":"2020-07-14T12:48:15Z","access_level":"open_access","file_id":"6299","date_created":"2019-04-12T08:46:32Z"}],"abstract":[{"text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis.","lang":"eng"}]},{"article_processing_charge":"No","page":"6136-6155","oa_version":"Published Version","month":"09","type":"journal_article","volume":123,"_id":"9134","publication_identifier":{"issn":["2169-9275"]},"doi":"10.1029/2017jc013591","day":"01","article_type":"original","publisher":"American Geophysical Union","oa":1,"abstract":[{"lang":"eng","text":"Several studies have shown the existence of a critical latitude where the dissipation of internal tides is strongly enhanced. Internal tides are internal waves generated by barotropic tidal currents impinging rough topography at the seafloor. Their dissipation and concomitant diapycnal mixing are believed to be important for water masses and the large‐scale ocean circulation. The purpose of this study is to clarify the physical processes at the origin of this strong latitudinal dependence of tidal energy dissipation. We find that different mechanisms are involved equatorward and poleward of the critical latitude. Triadic resonant instabilities are responsible for the dissipation of internal tides equatorward of the critical latitude. In particular, a dominant triad involving the primary internal tide and near‐inertial waves is key. At the critical latitude, the peak of energy dissipation is explained by both increased instability growth rates, and smaller scales of secondary waves thus more prone to break and dissipate their energy. Surprisingly, poleward of the critical latitude, the generation of evanescent waves appears to be crucial. Triadic instabilities have been widely studied, but the transfer of energy to evanescent waves has received comparatively little attention. Our work suggests that the nonlinear transfer of energy from the internal tide to evanescent waves (corresponding to the 2f‐pump mechanism described by Young et al., 2008, https://doi.org/10.1017/S0022112008001742) is an efficient mechanism to dissipate internal tide energy near and poleward of the critical latitude. The theoretical results are confirmed in idealized high‐resolution numerical simulations of a barotropic M2 tide impinging sinusoidal topography in a linearly stratified fluid."}],"date_updated":"2022-01-24T12:39:03Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2017JC013591"}],"date_created":"2021-02-15T14:17:25Z","publication":"Journal of Geophysical Research: Oceans","title":"Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude","publication_status":"published","extern":"1","status":"public","date_published":"2018-09-01T00:00:00Z","year":"2018","citation":{"short":"O. Richet, J.-M. Chomaz, C.J. Muller, Journal of Geophysical Research: Oceans 123 (2018) 6136–6155.","chicago":"Richet, O., J.-M. Chomaz, and Caroline J Muller. “Internal Tide Dissipation at Topography: Triadic Resonant Instability Equatorward and Evanescent Waves Poleward of the Critical Latitude.” <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union, 2018. <a href=\"https://doi.org/10.1029/2017jc013591\">https://doi.org/10.1029/2017jc013591</a>.","ista":"Richet O, Chomaz J-M, Muller CJ. 2018. Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. Journal of Geophysical Research: Oceans. 123(9), 6136–6155.","ama":"Richet O, Chomaz J-M, Muller CJ. Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. <i>Journal of Geophysical Research: Oceans</i>. 2018;123(9):6136-6155. doi:<a href=\"https://doi.org/10.1029/2017jc013591\">10.1029/2017jc013591</a>","apa":"Richet, O., Chomaz, J.-M., &#38; Muller, C. J. (2018). Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2017jc013591\">https://doi.org/10.1029/2017jc013591</a>","ieee":"O. Richet, J.-M. Chomaz, and C. J. Muller, “Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude,” <i>Journal of Geophysical Research: Oceans</i>, vol. 123, no. 9. American Geophysical Union, pp. 6136–6155, 2018.","mla":"Richet, O., et al. “Internal Tide Dissipation at Topography: Triadic Resonant Instability Equatorward and Evanescent Waves Poleward of the Critical Latitude.” <i>Journal of Geophysical Research: Oceans</i>, vol. 123, no. 9, American Geophysical Union, 2018, pp. 6136–55, doi:<a href=\"https://doi.org/10.1029/2017jc013591\">10.1029/2017jc013591</a>."},"quality_controlled":"1","language":[{"iso":"eng"}],"issue":"9","intvolume":"       123","author":[{"first_name":"O.","full_name":"Richet, O.","last_name":"Richet"},{"last_name":"Chomaz","first_name":"J.-M.","full_name":"Chomaz, J.-M."},{"last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}]},{"article_type":"original","doi":"10.1073/pnas.1719967115","day":"20","publication_identifier":{"issn":["0027-8424","1091-6490"]},"volume":115,"_id":"9135","month":"03","type":"journal_article","oa_version":"Published Version","page":"2930-2935","article_processing_charge":"No","author":[{"first_name":"Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","last_name":"Muller"},{"last_name":"Romps","full_name":"Romps, David M.","first_name":"David M."}],"issue":"12","intvolume":"       115","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"chicago":"Muller, Caroline J, and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1719967115\">https://doi.org/10.1073/pnas.1719967115</a>.","short":"C.J. Muller, D.M. Romps, Proceedings of the National Academy of Sciences 115 (2018) 2930–2935.","mla":"Muller, Caroline J., and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 12, Proceedings of the National Academy of Sciences, 2018, pp. 2930–35, doi:<a href=\"https://doi.org/10.1073/pnas.1719967115\">10.1073/pnas.1719967115</a>.","ista":"Muller CJ, Romps DM. 2018. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. Proceedings of the National Academy of Sciences. 115(12), 2930–2935.","ieee":"C. J. Muller and D. M. Romps, “Acceleration of tropical cyclogenesis by self-aggregation feedbacks,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 12. Proceedings of the National Academy of Sciences, pp. 2930–2935, 2018.","apa":"Muller, C. J., &#38; Romps, D. M. (2018). Acceleration of tropical cyclogenesis by self-aggregation feedbacks. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1719967115\">https://doi.org/10.1073/pnas.1719967115</a>","ama":"Muller CJ, Romps DM. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(12):2930-2935. doi:<a href=\"https://doi.org/10.1073/pnas.1719967115\">10.1073/pnas.1719967115</a>"},"status":"public","extern":"1","publication_status":"published","year":"2018","date_published":"2018-03-20T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","keyword":["Multidisciplinary"],"title":"Acceleration of tropical cyclogenesis by self-aggregation feedbacks","date_created":"2021-02-15T14:18:16Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-24T12:39:49Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1719967115","open_access":"1"}],"abstract":[{"lang":"eng","text":"Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone."}],"oa":1,"publisher":"Proceedings of the National Academy of Sciences"},{"title":"Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios","keyword":["Atmospheric Science"],"publication":"Climate Dynamics","date_created":"2021-02-15T14:18:53Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00382-016-3083-x"}],"date_updated":"2022-01-24T12:40:40Z","abstract":[{"lang":"eng","text":"In this study we investigate the scaling of precipitation extremes with temperature in the Mediterranean region by assessing against observations the present day and future regional climate simulations performed in the frame of the HyMeX and MED-CORDEX programs. Over the 1979–2008 period, despite differences in quantitative precipitation simulation across the various models, the change in precipitation extremes with respect to temperature is robust and consistent. The spatial variability of the temperature–precipitation extremes relationship displays a hook shape across the Mediterranean, with negative slope at high temperatures and a slope following Clausius–Clapeyron (CC)-scaling at low temperatures. The temperature at which the slope of the temperature–precipitation extreme relation sharply changes (or temperature break), ranges from about 20 °C in the western Mediterranean to <10 °C in Greece. In addition, this slope is always negative in the arid regions of the Mediterranean. The scaling of the simulated precipitation extremes is insensitive to ocean–atmosphere coupling, while it depends very weakly on the resolution at high temperatures for short precipitation accumulation times. In future climate scenario simulations covering the 2070–2100 period, the temperature break shifts to higher temperatures by a value which is on average the mean regional temperature change due to global warming. The slope of the simulated future temperature–precipitation extremes relationship is close to CC-scaling at temperatures below the temperature break, while at high temperatures, the negative slope is close, but somewhat flatter or steeper, than in the current climate depending on the model. Overall, models predict more intense precipitation extremes in the future. Adjusting the temperature–precipitation extremes relationship in the present climate using the CC law and the temperature shift in the future allows the recovery of the temperature–precipitation extremes relationship in the future climate. This implies negligible regional changes of relative humidity in the future despite the large warming and drying over the Mediterranean. This suggests that the Mediterranean Sea is the primary source of moisture which counteracts the drying and warming impacts on relative humidity in parts of the Mediterranean region."}],"oa":1,"publisher":"Springer Nature","author":[{"full_name":"Drobinski, Philippe","first_name":"Philippe","last_name":"Drobinski"},{"last_name":"Silva","first_name":"Nicolas Da","full_name":"Silva, Nicolas Da"},{"last_name":"Panthou","full_name":"Panthou, Gérémy","first_name":"Gérémy"},{"last_name":"Bastin","first_name":"Sophie","full_name":"Bastin, Sophie"},{"first_name":"Caroline J","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","last_name":"Muller"},{"first_name":"Bodo","full_name":"Ahrens, Bodo","last_name":"Ahrens"},{"first_name":"Marco","full_name":"Borga, Marco","last_name":"Borga"},{"first_name":"Dario","full_name":"Conte, Dario","last_name":"Conte"},{"last_name":"Fosser","first_name":"Giorgia","full_name":"Fosser, Giorgia"},{"full_name":"Giorgi, Filippo","first_name":"Filippo","last_name":"Giorgi"},{"last_name":"Güttler","first_name":"Ivan","full_name":"Güttler, Ivan"},{"full_name":"Kotroni, Vassiliki","first_name":"Vassiliki","last_name":"Kotroni"},{"first_name":"Laurent","full_name":"Li, Laurent","last_name":"Li"},{"full_name":"Morin, Efrat","first_name":"Efrat","last_name":"Morin"},{"last_name":"Önol","first_name":"Bariş","full_name":"Önol, Bariş"},{"last_name":"Quintana-Segui","full_name":"Quintana-Segui, Pere","first_name":"Pere"},{"full_name":"Romera, Raquel","first_name":"Raquel","last_name":"Romera"},{"full_name":"Torma, Csaba Zsolt","first_name":"Csaba Zsolt","last_name":"Torma"}],"intvolume":"        51","issue":"3","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"chicago":"Drobinski, Philippe, Nicolas Da Silva, Gérémy Panthou, Sophie Bastin, Caroline J Muller, Bodo Ahrens, Marco Borga, et al. “Scaling Precipitation Extremes with Temperature in the Mediterranean: Past Climate Assessment and Projection in Anthropogenic Scenarios.” <i>Climate Dynamics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00382-016-3083-x\">https://doi.org/10.1007/s00382-016-3083-x</a>.","short":"P. Drobinski, N.D. Silva, G. Panthou, S. Bastin, C.J. Muller, B. Ahrens, M. Borga, D. Conte, G. Fosser, F. Giorgi, I. Güttler, V. Kotroni, L. Li, E. Morin, B. Önol, P. Quintana-Segui, R. Romera, C.Z. Torma, Climate Dynamics 51 (2018) 1237–1257.","mla":"Drobinski, Philippe, et al. “Scaling Precipitation Extremes with Temperature in the Mediterranean: Past Climate Assessment and Projection in Anthropogenic Scenarios.” <i>Climate Dynamics</i>, vol. 51, no. 3, Springer Nature, 2018, pp. 1237–57, doi:<a href=\"https://doi.org/10.1007/s00382-016-3083-x\">10.1007/s00382-016-3083-x</a>.","ieee":"P. Drobinski <i>et al.</i>, “Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios,” <i>Climate Dynamics</i>, vol. 51, no. 3. Springer Nature, pp. 1237–1257, 2018.","apa":"Drobinski, P., Silva, N. D., Panthou, G., Bastin, S., Muller, C. J., Ahrens, B., … Torma, C. Z. (2018). Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. <i>Climate Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00382-016-3083-x\">https://doi.org/10.1007/s00382-016-3083-x</a>","ama":"Drobinski P, Silva ND, Panthou G, et al. Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. <i>Climate Dynamics</i>. 2018;51(3):1237-1257. doi:<a href=\"https://doi.org/10.1007/s00382-016-3083-x\">10.1007/s00382-016-3083-x</a>","ista":"Drobinski P, Silva ND, Panthou G, Bastin S, Muller CJ, Ahrens B, Borga M, Conte D, Fosser G, Giorgi F, Güttler I, Kotroni V, Li L, Morin E, Önol B, Quintana-Segui P, Romera R, Torma CZ. 2018. Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. Climate Dynamics. 51(3), 1237–1257."},"year":"2018","date_published":"2018-08-01T00:00:00Z","status":"public","publication_status":"published","extern":"1","type":"journal_article","month":"08","oa_version":"Published Version","page":"1237-1257","article_processing_charge":"No","article_type":"original","day":"01","doi":"10.1007/s00382-016-3083-x","publication_identifier":{"issn":["0930-7575","1432-0894"]},"_id":"9136","volume":51}]