[{"quality_controlled":"1","date_created":"2020-09-17T10:42:42Z","article_processing_charge":"No","month":"12","page":"175-209","volume":167,"language":[{"iso":"eng"}],"publication_status":"published","extern":"1","publication_identifier":{"issn":["0012-7094"]},"oa":1,"title":"On the marked length spectrum of generic strictly convex billiard tables","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.08838"}],"doi":"10.1215/00127094-2017-0038","type":"journal_article","publication":"Duke Mathematical Journal","author":[{"full_name":"Huang, Guan","last_name":"Huang","first_name":"Guan"},{"first_name":"Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"},{"last_name":"Sorrentino","full_name":"Sorrentino, Alfonso","first_name":"Alfonso"}],"external_id":{"arxiv":["1603.08838"]},"issue":"1","intvolume":"       167","day":"08","arxiv":1,"year":"2017","citation":{"ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “On the marked length spectrum of generic strictly convex billiard tables,” <i>Duke Mathematical Journal</i>, vol. 167, no. 1. Duke University Press, pp. 175–209, 2017.","apa":"Huang, G., Kaloshin, V., &#38; Sorrentino, A. (2017). On the marked length spectrum of generic strictly convex billiard tables. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-2017-0038\">https://doi.org/10.1215/00127094-2017-0038</a>","ista":"Huang G, Kaloshin V, Sorrentino A. 2017. On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. 167(1), 175–209.","ama":"Huang G, Kaloshin V, Sorrentino A. On the marked length spectrum of generic strictly convex billiard tables. <i>Duke Mathematical Journal</i>. 2017;167(1):175-209. doi:<a href=\"https://doi.org/10.1215/00127094-2017-0038\">10.1215/00127094-2017-0038</a>","mla":"Huang, Guan, et al. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” <i>Duke Mathematical Journal</i>, vol. 167, no. 1, Duke University Press, 2017, pp. 175–209, doi:<a href=\"https://doi.org/10.1215/00127094-2017-0038\">10.1215/00127094-2017-0038</a>.","short":"G. Huang, V. Kaloshin, A. Sorrentino, Duke Mathematical Journal 167 (2017) 175–209.","chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” <i>Duke Mathematical Journal</i>. Duke University Press, 2017. <a href=\"https://doi.org/10.1215/00127094-2017-0038\">https://doi.org/10.1215/00127094-2017-0038</a>."},"publisher":"Duke University Press","status":"public","_id":"8423","oa_version":"Preprint","date_published":"2017-12-08T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1215/00127094-2017-0038","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In this paper we show that for a generic strictly convex domain, one can recover the eigendata corresponding to Aubry–Mather periodic orbits of the induced billiard map from the (maximal) marked length spectrum of the domain."}],"date_updated":"2021-01-12T08:19:11Z"},{"abstract":[{"text":"We show that any sufficiently (finitely) smooth ℤ₂-symmetric strictly convex domain sufficiently close to a circle is dynamically spectrally rigid; i.e., all deformations among domains in the same class that preserve the length of all periodic orbits of the associated billiard flow must necessarily be isometric deformations. This gives a partial answer to a question of P. Sarnak.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:12Z","article_type":"original","fulldoi":"https://doi.org/10.4007/annals.2017.186.1.7","date_published":"2017-07-01T00:00:00Z","publisher":"Annals of Mathematics","year":"2017","citation":{"ieee":"J. De Simoi, V. Kaloshin, and Q. Wei, “Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle,” <i>Annals of Mathematics</i>, vol. 186, no. 1. Annals of Mathematics, pp. 277–314, 2017.","apa":"De Simoi, J., Kaloshin, V., &#38; Wei, Q. (2017). Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. <i>Annals of Mathematics</i>. Annals of Mathematics. <a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">https://doi.org/10.4007/annals.2017.186.1.7</a>","ama":"De Simoi J, Kaloshin V, Wei Q. Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. <i>Annals of Mathematics</i>. 2017;186(1):277-314. doi:<a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">10.4007/annals.2017.186.1.7</a>","ista":"De Simoi J, Kaloshin V, Wei Q. 2017. Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics. 186(1), 277–314.","short":"J. De Simoi, V. Kaloshin, Q. Wei, Annals of Mathematics 186 (2017) 277–314.","mla":"De Simoi, Jacopo, et al. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” <i>Annals of Mathematics</i>, vol. 186, no. 1, Annals of Mathematics, 2017, pp. 277–314, doi:<a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">10.4007/annals.2017.186.1.7</a>.","chicago":"De Simoi, Jacopo, Vadim Kaloshin, and Qiaoling Wei. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” <i>Annals of Mathematics</i>. Annals of Mathematics, 2017. <a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">https://doi.org/10.4007/annals.2017.186.1.7</a>."},"day":"01","arxiv":1,"oa_version":"Preprint","_id":"8427","status":"public","intvolume":"       186","issue":"1","external_id":{"arxiv":["1606.00230"]},"author":[{"first_name":"Jacopo","last_name":"De Simoi","full_name":"De Simoi, Jacopo"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","first_name":"Vadim","orcid":"0000-0002-6051-2628"},{"first_name":"Qiaoling","full_name":"Wei, Qiaoling","last_name":"Wei"}],"publication":"Annals of Mathematics","extern":"1","type":"journal_article","doi":"10.4007/annals.2017.186.1.7","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.00230"}],"oa":1,"title":"Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle","publication_identifier":{"issn":["0003-486X"]},"month":"07","publication_status":"published","language":[{"iso":"eng"}],"volume":186,"page":"277-314","quality_controlled":"1","article_processing_charge":"No","date_created":"2020-09-17T10:46:42Z"},{"article_processing_charge":"No","date_created":"2020-09-18T10:05:54Z","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"volume":113,"page":"2311-2315","month":"12","type":"journal_article","doi":"10.1016/j.bpj.2017.09.019","title":"Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity","publication_identifier":{"issn":["0006-3495"]},"extern":"1","author":[{"first_name":"François","full_name":"Dehez, François","last_name":"Dehez"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"last_name":"King","full_name":"King, Martin S.","first_name":"Martin S."},{"last_name":"Kunji","full_name":"Kunji, Edmund R.S.","first_name":"Edmund R.S."},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"}],"publication":"Biophysical Journal","intvolume":"       113","issue":"11","oa_version":"None","status":"public","_id":"8444","publisher":"Elsevier","citation":{"ista":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical Journal. 113(11), 2311–2315.","ama":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. 2017;113(11):2311-2315. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>","apa":"Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., &#38; Chipot, C. (2017). Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>","ieee":"F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,” <i>Biophysical Journal</i>, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.","chicago":"Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>.","mla":"Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>, vol. 113, no. 11, Elsevier, 2017, pp. 2311–15, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>.","short":"F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal 113 (2017) 2311–2315."},"year":"2017","day":"05","keyword":["Biophysics"],"article_type":"original","fulldoi":"https://doi.org/10.1016/j.bpj.2017.09.019","date_published":"2017-12-05T00:00:00Z","date_updated":"2021-01-12T08:19:18Z","abstract":[{"lang":"eng","text":"Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":"         8","day":"27","citation":{"chicago":"Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel, Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” <i>Nature Communications</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00165-8\">https://doi.org/10.1038/s41467-017-00165-8</a>.","short":"V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse, A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 8 (2017).","mla":"Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” <i>Nature Communications</i>, vol. 8, 145, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00165-8\">10.1038/s41467-017-00165-8</a>.","ista":"Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications. 8, 145.","ama":"Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/s41467-017-00165-8\">10.1038/s41467-017-00165-8</a>","ieee":"V. Kurauskas <i>et al.</i>, “Slow conformational exchange and overall rocking motion in ubiquitin protein crystals,” <i>Nature Communications</i>, vol. 8. Springer Nature, 2017.","apa":"Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse, J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-017-00165-8\">https://doi.org/10.1038/s41467-017-00165-8</a>"},"year":"2017","publisher":"Springer Nature","_id":"8445","status":"public","oa_version":"Published Version","OA_place":"publisher","date_published":"2017-07-27T00:00:00Z","OA_type":"gold","article_type":"original","fulldoi":"https://doi.org/10.1038/s41467-017-00165-8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins."}],"date_updated":"2025-01-22T14:32:38Z","quality_controlled":"1","date_created":"2020-09-18T10:06:01Z","article_processing_charge":"Yes","month":"07","language":[{"iso":"eng"}],"volume":8,"publication_status":"published","article_number":"145","extern":"1","publication_identifier":{"issn":["2041-1723"]},"title":"Slow conformational exchange and overall rocking motion in ubiquitin protein crystals","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-017-00165-8"}],"doi":"10.1038/s41467-017-00165-8","type":"journal_article","publication":"Nature Communications","author":[{"last_name":"Kurauskas","full_name":"Kurauskas, Vilius","first_name":"Vilius"},{"last_name":"Izmailov","full_name":"Izmailov, Sergei A.","first_name":"Sergei A."},{"full_name":"Rogacheva, Olga N.","last_name":"Rogacheva","first_name":"Olga N."},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"full_name":"Woodhouse, Joyce","last_name":"Woodhouse","first_name":"Joyce"},{"first_name":"Anastasya","last_name":"Shilova","full_name":"Shilova, Anastasya"},{"first_name":"Yi","last_name":"Xue","full_name":"Xue, Yi"},{"first_name":"Tairan","full_name":"Yuwen, Tairan","last_name":"Yuwen"},{"last_name":"Coquelle","full_name":"Coquelle, Nicolas","first_name":"Nicolas"},{"first_name":"Jacques-Philippe","last_name":"Colletier","full_name":"Colletier, Jacques-Philippe"},{"first_name":"Nikolai R.","last_name":"Skrynnikov","full_name":"Skrynnikov, Nikolai R."},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"scopus_import":"1"},{"doi":"10.1002/cphc.201700572","type":"journal_article","publication_identifier":{"issn":["1439-4235","1439-7641"]},"title":"Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins","extern":"1","author":[{"first_name":"Hugo","last_name":"Fraga","full_name":"Fraga, Hugo"},{"first_name":"Charles‐Adrien","last_name":"Arnaud","full_name":"Arnaud, Charles‐Adrien"},{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"first_name":"Maxime","full_name":"Audin, Maxime","last_name":"Audin"},{"last_name":"Kurauskas","full_name":"Kurauskas, Vilius","first_name":"Vilius"},{"first_name":"Pavel","full_name":"Macek, Pavel","last_name":"Macek"},{"first_name":"Carsten","last_name":"Krichel","full_name":"Krichel, Carsten"},{"first_name":"Jia‐Ying","full_name":"Guan, Jia‐Ying","last_name":"Guan"},{"last_name":"Boisbouvier","full_name":"Boisbouvier, Jerome","first_name":"Jerome"},{"last_name":"Sprangers","full_name":"Sprangers, Remco","first_name":"Remco"},{"first_name":"Cécile","last_name":"Breyton","full_name":"Breyton, Cécile"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"publication":"ChemPhysChem","date_created":"2020-09-18T10:06:09Z","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"volume":18,"publication_status":"published","page":"2697-2703","month":"08","article_type":"original","fulldoi":"https://doi.org/10.1002/cphc.201700572","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"date_published":"2017-08-09T00:00:00Z","date_updated":"2021-01-12T08:19:19Z","abstract":[{"text":"Solid‐state NMR spectroscopy can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here the use of two sets of experiments is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross‐polarization for heteronuclear transfers. The utility of these experiments is exemplified with application to assemblies of deuterated, fully amide‐protonated proteins from approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies from approximately 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. The resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is compared to NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        18","issue":"19","oa_version":"None","_id":"8446","status":"public","citation":{"chicago":"Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” <i>ChemPhysChem</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/cphc.201700572\">https://doi.org/10.1002/cphc.201700572</a>.","short":"H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel, J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18 (2017) 2697–2703.","mla":"Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” <i>ChemPhysChem</i>, vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:<a href=\"https://doi.org/10.1002/cphc.201700572\">10.1002/cphc.201700572</a>.","ista":"Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. ChemPhysChem. 18(19), 2697–2703.","ama":"Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. <i>ChemPhysChem</i>. 2017;18(19):2697-2703. doi:<a href=\"https://doi.org/10.1002/cphc.201700572\">10.1002/cphc.201700572</a>","apa":"Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., … Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201700572\">https://doi.org/10.1002/cphc.201700572</a>","ieee":"H. Fraga <i>et al.</i>, “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins,” <i>ChemPhysChem</i>, vol. 18, no. 19. Wiley, pp. 2697–2703, 2017."},"year":"2017","publisher":"Wiley","day":"09"},{"issue":"10","intvolume":"        87","day":"01","year":"2017","citation":{"ista":"Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 87(10), 86–95.","ama":"Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. <i>Solid State Nuclear Magnetic Resonance</i>. 2017;87(10):86-95. doi:<a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">10.1016/j.ssnmr.2017.04.002</a>","apa":"Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., &#38; Schanda, P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. <i>Solid State Nuclear Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">https://doi.org/10.1016/j.ssnmr.2017.04.002</a>","ieee":"D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda, “Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals,” <i>Solid State Nuclear Magnetic Resonance</i>, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.","chicago":"Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser, and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” <i>Solid State Nuclear Magnetic Resonance</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">https://doi.org/10.1016/j.ssnmr.2017.04.002</a>.","mla":"Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” <i>Solid State Nuclear Magnetic Resonance</i>, vol. 87, no. 10, Elsevier, 2017, pp. 86–95, doi:<a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">10.1016/j.ssnmr.2017.04.002</a>.","short":"D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid State Nuclear Magnetic Resonance 87 (2017) 86–95."},"publisher":"Elsevier","_id":"8447","status":"public","oa_version":"None","date_published":"2017-10-01T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1016/j.ssnmr.2017.04.002","keyword":["Nuclear and High Energy Physics","Instrumentation","General Chemistry","Radiation"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility."}],"date_updated":"2021-01-12T08:19:20Z","quality_controlled":"1","date_created":"2020-09-18T10:06:18Z","article_processing_charge":"No","month":"10","page":"86-95","language":[{"iso":"eng"}],"volume":87,"publication_status":"published","extern":"1","publication_identifier":{"issn":["0926-2040"]},"title":"Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals","doi":"10.1016/j.ssnmr.2017.04.002","type":"journal_article","publication":"Solid State Nuclear Magnetic Resonance","author":[{"first_name":"Diego F.","full_name":"Gauto, Diego F.","last_name":"Gauto"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"full_name":"Rovó, Petra","last_name":"Rovó","first_name":"Petra"},{"first_name":"Vilius","last_name":"Kurauskas","full_name":"Kurauskas, Vilius"},{"last_name":"Linser","full_name":"Linser, Rasmus","first_name":"Rasmus"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}]},{"page":"125-129","volume":281,"language":[{"iso":"eng"}],"publication_status":"published","month":"08","date_created":"2020-09-18T10:06:27Z","article_processing_charge":"No","quality_controlled":"1","publication":"Journal of Magnetic Resonance","author":[{"last_name":"Franco","full_name":"Franco, Rémi","first_name":"Rémi"},{"full_name":"Favier, Adrien","last_name":"Favier","first_name":"Adrien"},{"first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"}],"publication_identifier":{"issn":["1090-7807"]},"title":"Optimized fast mixing device for real-time NMR applications","doi":"10.1016/j.jmr.2017.05.016","type":"journal_article","extern":"1","status":"public","_id":"8448","oa_version":"None","day":"01","citation":{"ama":"Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. 2017;281(8):125-129. doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>","ista":"Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129.","ieee":"R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing device for real-time NMR applications,” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8. Elsevier, pp. 125–129, 2017.","apa":"Franco, R., Favier, A., Schanda, P., &#38; Brutscher, B. (2017). Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>","chicago":"Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>.","mla":"Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8, Elsevier, 2017, pp. 125–29, doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>.","short":"R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 281 (2017) 125–129."},"year":"2017","publisher":"Elsevier","issue":"8","intvolume":"       281","date_updated":"2021-01-12T08:19:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present an improved fast mixing device based on the rapid mixing of two solutions inside the NMR probe, as originally proposed by Hore and coworkers (J. Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium studies of molecular kinetics by multidimensional real-time NMR spectrsocopy. The novelty of this device is that it allows removing the injector from the NMR detection volume after mixing, and thus provides good magnetic field homogeneity independently of the initial sample volume placed in the NMR probe. The apparatus is simple to build, inexpensive, and can be used without any hardware modification on any type of liquid-state NMR spectrometer. We demonstrate the performance of our fast mixing device in terms of improved magnetic field homogeneity, and show an application to the study of protein folding and the structural characterization of transiently populated folding intermediates.","lang":"eng"}],"date_published":"2017-08-01T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.jmr.2017.05.016","article_type":"original","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"]},{"author":[{"last_name":"Rennella","full_name":"Rennella, Enrico","first_name":"Enrico"},{"full_name":"Sára, Tomáš","last_name":"Sára","first_name":"Tomáš"},{"full_name":"Juen, Michael","last_name":"Juen","first_name":"Michael"},{"first_name":"Christoph","last_name":"Wunderlich","full_name":"Wunderlich, Christoph"},{"full_name":"Imbert, Lionel","last_name":"Imbert","first_name":"Lionel"},{"full_name":"Solyom, Zsofia","last_name":"Solyom","first_name":"Zsofia"},{"full_name":"Favier, Adrien","last_name":"Favier","first_name":"Adrien"},{"last_name":"Ayala","full_name":"Ayala, Isabel","first_name":"Isabel"},{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","full_name":"Schanda, Paul"},{"last_name":"Konrat","full_name":"Konrat, Robert","first_name":"Robert"},{"first_name":"Christoph","last_name":"Kreutz","full_name":"Kreutz, Christoph"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"}],"abstract":[{"lang":"eng","text":"Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein."}],"publication":"Nucleic Acids Research","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:20Z","extern":"1","doi":"10.1093/nar/gkx044","fulldoi":"https://doi.org/10.1093/nar/gkx044","article_type":"original","type":"journal_article","publication_identifier":{"issn":["0305-1048","1362-4962"]},"date_published":"2017-04-20T00:00:00Z","title":"RNA binding and chaperone activity of the E.coli cold-shock protein CspA","citation":{"ista":"Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research. 45(7), 4255–4268.","ama":"Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. <i>Nucleic Acids Research</i>. 2017;45(7):4255-4268. doi:<a href=\"https://doi.org/10.1093/nar/gkx044\">10.1093/nar/gkx044</a>","apa":"Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., … Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock protein CspA. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkx044\">https://doi.org/10.1093/nar/gkx044</a>","ieee":"E. Rennella <i>et al.</i>, “RNA binding and chaperone activity of the E.coli cold-shock protein CspA,” <i>Nucleic Acids Research</i>, vol. 45, no. 7. Oxford University Press, pp. 4255–4268, 2017.","chicago":"Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” <i>Nucleic Acids Research</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/nar/gkx044\">https://doi.org/10.1093/nar/gkx044</a>.","short":"E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier, I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic Acids Research 45 (2017) 4255–4268.","mla":"Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” <i>Nucleic Acids Research</i>, vol. 45, no. 7, Oxford University Press, 2017, pp. 4255–68, doi:<a href=\"https://doi.org/10.1093/nar/gkx044\">10.1093/nar/gkx044</a>."},"year":"2017","publisher":"Oxford University Press","day":"20","month":"04","language":[{"iso":"eng"}],"volume":45,"oa_version":"None","publication_status":"published","page":"4255-4268","_id":"8449","status":"public","quality_controlled":"1","intvolume":"        45","issue":"7","date_created":"2020-09-18T10:06:34Z","article_processing_charge":"No"},{"quality_controlled":"1","intvolume":"      1635","date_created":"2020-09-18T10:06:44Z","article_processing_charge":"No","day":"29","month":"07","year":"2017","citation":{"ista":"Kurauskas V, Schanda P, Sounier R. 2017.Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: Membrane protein structure and function characterization. Methods in Molecular Biology, vol. 1635, 109–123.","ama":"Kurauskas V, Schanda P, Sounier R. Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In: <i>Membrane Protein Structure and Function Characterization</i>. Vol 1635. Springer Nature; 2017:109-123. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">10.1007/978-1-4939-7151-0_6</a>","apa":"Kurauskas, V., Schanda, P., &#38; Sounier, R. (2017). Methyl-specific isotope labeling strategies for NMR studies of membrane proteins. In <i>Membrane protein structure and function characterization</i> (Vol. 1635, pp. 109–123). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">https://doi.org/10.1007/978-1-4939-7151-0_6</a>","ieee":"V. Kurauskas, P. Schanda, and R. Sounier, “Methyl-specific isotope labeling strategies for NMR studies of membrane proteins,” in <i>Membrane protein structure and function characterization</i>, vol. 1635, Springer Nature, 2017, pp. 109–123.","chicago":"Kurauskas, Vilius, Paul Schanda, and Remy Sounier. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” In <i>Membrane Protein Structure and Function Characterization</i>, 1635:109–23. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">https://doi.org/10.1007/978-1-4939-7151-0_6</a>.","mla":"Kurauskas, Vilius, et al. “Methyl-Specific Isotope Labeling Strategies for NMR Studies of Membrane Proteins.” <i>Membrane Protein Structure and Function Characterization</i>, vol. 1635, Springer Nature, 2017, pp. 109–23, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7151-0_6\">10.1007/978-1-4939-7151-0_6</a>.","short":"V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and Function Characterization, Springer Nature, 2017, pp. 109–123."},"publisher":"Springer Nature","status":"public","_id":"8450","page":"109-123","volume":1635,"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"None","extern":"1","publication_identifier":{"issn":["1064-3745","1940-6029"],"isbn":["9781493971497","9781493971510"]},"title":"Methyl-specific isotope labeling strategies for NMR studies of membrane proteins","date_published":"2017-07-29T00:00:00Z","doi":"10.1007/978-1-4939-7151-0_6","fulldoi":"https://doi.org/10.1007/978-1-4939-7151-0_6","type":"book_chapter","publication":"Membrane protein structure and function characterization","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Methyl groups are very useful probes of structure, dynamics, and interactions in protein NMR spectroscopy. In particular, methyl-directed experiments provide high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking environment. In this chapter, we discuss the approach for labeling methyl groups in E. coli-based protein expression, as exemplified with the mitochondrial carrier GGC.","lang":"eng"}],"author":[{"last_name":"Kurauskas","full_name":"Kurauskas, Vilius","first_name":"Vilius"},{"full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"first_name":"Remy","last_name":"Sounier","full_name":"Sounier, Remy"}],"alternative_title":["Methods in Molecular Biology"],"date_updated":"2022-08-26T09:14:20Z"},{"intvolume":"        56","quality_controlled":"1","issue":"9","article_processing_charge":"No","date_created":"2020-09-18T10:06:50Z","publisher":"Wiley","year":"2017","citation":{"ama":"Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. <i>Angewandte Chemie International Edition</i>. 2017;56(9):2508-2512. doi:<a href=\"https://doi.org/10.1002/anie.201610441\">10.1002/anie.201610441</a>","ista":"Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. 2017. Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. Angewandte Chemie International Edition. 56(9), 2508–2512.","ieee":"B. Bersch, J. M. Dörr, A. Hessel, J. A. Killian, and P. Schanda, “Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs,” <i>Angewandte Chemie International Edition</i>, vol. 56, no. 9. Wiley, pp. 2508–2512, 2017.","apa":"Bersch, B., Dörr, J. M., Hessel, A., Killian, J. A., &#38; Schanda, P. (2017). Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201610441\">https://doi.org/10.1002/anie.201610441</a>","chicago":"Bersch, Beate, Jonas M. Dörr, Audrey Hessel, J. Antoinette Killian, and Paul Schanda. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs.” <i>Angewandte Chemie International Edition</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/anie.201610441\">https://doi.org/10.1002/anie.201610441</a>.","mla":"Bersch, Beate, et al. “Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs.” <i>Angewandte Chemie International Edition</i>, vol. 56, no. 9, Wiley, 2017, pp. 2508–12, doi:<a href=\"https://doi.org/10.1002/anie.201610441\">10.1002/anie.201610441</a>.","short":"B. Bersch, J.M. Dörr, A. Hessel, J.A. Killian, P. Schanda, Angewandte Chemie International Edition 56 (2017) 2508–2512."},"month":"01","day":"27","oa_version":"None","publication_status":"published","language":[{"iso":"eng"}],"volume":56,"_id":"8451","page":"2508-2512","status":"public","extern":"1","type":"journal_article","article_type":"original","fulldoi":"https://doi.org/10.1002/anie.201610441","doi":"10.1002/anie.201610441","title":"Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs","date_published":"2017-01-27T00:00:00Z","publication_identifier":{"issn":["1433-7851"]},"abstract":[{"lang":"eng","text":"The structure, dynamics, and function of membrane proteins are intimately linked to the properties of the membrane environment in which the proteins are embedded. For structural and biophysical characterization, membrane proteins generally need to be extracted from the membrane and reconstituted in a suitable membrane‐mimicking environment. Ensuring functional and structural integrity in these environments is often a major concern. The styrene/maleic acid co‐polymer has recently been shown to be able to extract lipid/membrane protein patches directly from native membranes to form nanosize discoidal proteolipid particles, also referred to as native nanodiscs. In this work, we show that high‐resolution solid‐state NMR spectra can be obtained from an integral membrane protein in native nanodiscs, as exemplified by the 2×34 kDa bacterial cation diffusion facilitator CzcD."}],"author":[{"first_name":"Beate","full_name":"Bersch, Beate","last_name":"Bersch"},{"last_name":"Dörr","full_name":"Dörr, Jonas M.","first_name":"Jonas M."},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"last_name":"Killian","full_name":"Killian, J. Antoinette","first_name":"J. Antoinette"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Angewandte Chemie International Edition","date_updated":"2021-01-12T08:19:22Z"},{"author":[{"first_name":"Muhammad","orcid":"0000-0002-2111-4846","last_name":"Nauman","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad"},{"first_name":"Yunjeong","last_name":"Hong","full_name":"Hong, Yunjeong"},{"first_name":"Tayyaba","last_name":"Hussain","full_name":"Hussain, Tayyaba"},{"last_name":"Seo","full_name":"Seo, M. S.","first_name":"M. S."},{"first_name":"S. Y.","full_name":"Park, S. Y.","last_name":"Park"},{"first_name":"N.","full_name":"Lee, N.","last_name":"Lee"},{"first_name":"Y. J.","full_name":"Choi, Y. J.","last_name":"Choi"},{"first_name":"Woun","full_name":"Kang, Woun","last_name":"Kang"},{"first_name":"Younjung","full_name":"Jo, Younjung","last_name":"Jo"}],"abstract":[{"text":"Magnetic anisotropy in strontium iridate (Sr2IrO4) is found to be large because of the strong spin-orbit interactions. In our work, we studied the in-plane magnetic anisotropy of Sr2IrO4 and traced the anisotropic exchange interactions between the isospins in the crystal. The magnetic-field-dependent torque τ(H) showed a prominent transition from the canted antiferromagnetic state to the weak ferromagnetic (WFM) state. A comprehensive analysis was conducted to examine the isotropic and anisotropic regimes and probe the easy magnetization axis along the a b plane. The angle-dependent torque τ(θ) revealed a deviation from the sinusoidal behavior, and small differences in hysteresis were observed around 0° and 90° in the low-magnetic-field regime. This indicates that the orientation of the easy axis of the FM component is along the b axis, where the antiferromagnetic to WFM spin-flop transition occurs. We compared the coefficients of the magnetic susceptibility tensors and captured the anisotropy of the material. The in-plane τ(θ) revealed a tendency toward isotropic behavior for fields with values above the field value of the WFM transition.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Physical Review B","date_updated":"2021-02-03T12:53:00Z","extern":"1","article_number":"155102","type":"journal_article","fulldoi":"https://doi.org/10.1103/physrevb.96.155102","doi":"10.1103/physrevb.96.155102","article_type":"original","date_published":"2017-10-01T00:00:00Z","title":"In-plane magnetic anisotropy in strontium iridate Sr2IrO4","publication_identifier":{"issn":["2469-9950","2469-9969"]},"publisher":"American Physical Society","year":"2017","citation":{"ieee":"M. Nauman <i>et al.</i>, “In-plane magnetic anisotropy in strontium iridate Sr2IrO4,” <i>Physical Review B</i>, vol. 96, no. 15. American Physical Society, 2017.","apa":"Nauman, M., Hong, Y., Hussain, T., Seo, M. S., Park, S. Y., Lee, N., … Jo, Y. (2017). In-plane magnetic anisotropy in strontium iridate Sr2IrO4. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.96.155102\">https://doi.org/10.1103/physrevb.96.155102</a>","ista":"Nauman M, Hong Y, Hussain T, Seo MS, Park SY, Lee N, Choi YJ, Kang W, Jo Y. 2017. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. Physical Review B. 96(15), 155102.","ama":"Nauman M, Hong Y, Hussain T, et al. In-plane magnetic anisotropy in strontium iridate Sr2IrO4. <i>Physical Review B</i>. 2017;96(15). doi:<a href=\"https://doi.org/10.1103/physrevb.96.155102\">10.1103/physrevb.96.155102</a>","mla":"Nauman, Muhammad, et al. “In-Plane Magnetic Anisotropy in Strontium Iridate Sr2IrO4.” <i>Physical Review B</i>, vol. 96, no. 15, 155102, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/physrevb.96.155102\">10.1103/physrevb.96.155102</a>.","short":"M. Nauman, Y. Hong, T. Hussain, M.S. Seo, S.Y. Park, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Physical Review B 96 (2017).","chicago":"Nauman, Muhammad, Yunjeong Hong, Tayyaba Hussain, M. S. Seo, S. Y. Park, N. Lee, Y. J. Choi, Woun Kang, and Younjung Jo. “In-Plane Magnetic Anisotropy in Strontium Iridate Sr2IrO4.” <i>Physical Review B</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/physrevb.96.155102\">https://doi.org/10.1103/physrevb.96.155102</a>."},"month":"10","day":"01","publication_status":"published","oa_version":"None","volume":96,"language":[{"iso":"eng"}],"_id":"9065","status":"public","intvolume":"        96","quality_controlled":"1","issue":"15","article_processing_charge":"No","date_created":"2021-02-02T15:49:21Z"},{"author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","first_name":"Arseniy"},{"last_name":"Vysotsky","full_name":"Vysotsky, Vladislav","first_name":"Vladislav"}],"publication":"The American Mathematical Monthly","scopus_import":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07997"}],"doi":"10.4169/amer.math.monthly.124.7.588","title":"On the lengths of curves passing through boundary points of a planar convex shape","oa":1,"publication_identifier":{"issn":["0002-9890"]},"month":"01","publication_status":"published","department":[{"_id":"HeEd"}],"volume":124,"language":[{"iso":"eng"}],"page":"588 - 596","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"article_processing_charge":"No","date_created":"2018-12-11T11:49:09Z","abstract":[{"lang":"eng","text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor &amp;#xbd; cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape."}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6534","date_updated":"2025-07-10T12:01:35Z","article_type":"original","fulldoi":"https://doi.org/10.4169/amer.math.monthly.124.7.588","date_published":"2017-01-01T00:00:00Z","publisher":"Mathematical Association of America","year":"2017","citation":{"mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>. Mathematical Association of America, 2017. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>.","apa":"Akopyan, A., &#38; Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. Mathematical Association of America. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>","ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” <i>The American Mathematical Monthly</i>, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. 2017;124(7):588-596. doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>","ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596."},"isi":1,"day":"01","arxiv":1,"oa_version":"Submitted Version","status":"public","_id":"909","intvolume":"       124","issue":"7","external_id":{"isi":["000413947300002"],"arxiv":["1605.07997"]}},{"has_accepted_license":"1","date_published":"2017-10-01T00:00:00Z","ddc":["576"],"fulldoi":"https://doi.org/10.1534/genetics.117.300129","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6533","date_updated":"2025-04-15T08:22:21Z","issue":"2","external_id":{"isi":["000412232600019"]},"intvolume":"       207","file":[{"creator":"system","date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","access_level":"open_access","checksum":"f7c32dabf52e6d9e709d9203761e39fd","relation":"main_file","date_created":"2018-12-12T10:17:12Z","file_size":494268,"file_name":"IST-2018-974-v1+1_manuscript.pdf","file_id":"5264"}],"isi":1,"day":"01","publisher":"Genetics Society of America","citation":{"apa":"Novak, S., &#38; Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” <i>Genetics</i>, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. 2017;207(2):653-668. doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>.","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>."},"year":"2017","_id":"910","status":"public","oa_version":"Submitted Version","oa":1,"title":"When does frequency-independent selection maintain genetic variation?","type":"journal_article","doi":"10.1534/genetics.117.300129","publication":"Genetics","author":[{"first_name":"Sebastian","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"corr_author":"1","scopus_import":"1","project":[{"grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:49:09Z","month":"10","page":"653 - 668","publication_status":"published","pubrep_id":"974","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"volume":207},{"publist_id":"6532","date_updated":"2026-04-08T07:26:44Z","abstract":[{"text":"We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset.","lang":"eng"}],"ec_funded":1,"file_date_updated":"2020-08-10T07:14:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.5244/c.31.85","ddc":["000"],"date_published":"2017-09-01T00:00:00Z","has_accepted_license":"1","oa_version":"Published Version","status":"public","_id":"911","year":"2017","citation":{"mla":"Royer, Amélie, et al. <i>Probabilistic Image Colorization</i>. BMVA Press, 2017, p. 85.1-85.12, doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>.","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>.","apa":"Royer, A., Kolesnikov, A., &#38; Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.","ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>"},"publisher":"BMVA Press","day":"01","arxiv":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2020-08-10T07:14:33Z","creator":"dernst","success":1,"file_id":"8224","file_name":"2017_BMVC_Royer.pdf","file_size":1625363,"date_created":"2020-08-10T07:14:33Z"}],"external_id":{"arxiv":["1705.04258"]},"scopus_import":"1","corr_author":"1","conference":{"start_date":"2017-09-04","name":"BMVC: British Machine Vision Conference","end_date":"2017-09-07","location":"London, United Kingdom"},"author":[{"full_name":"Royer, Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","last_name":"Royer","first_name":"Amélie","orcid":"0000-0002-8407-0705"},{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"doi":"10.5244/c.31.85","type":"conference","publication_identifier":{"eisbn":["190172560X"]},"title":"Probabilistic image colorization","oa":1,"department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"85.1-85.12","month":"09","date_created":"2018-12-11T11:49:09Z","article_processing_charge":"No","quality_controlled":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"8390","status":"public"}]},"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"day":"14","citation":{"chicago":"Zuidema, Paquita, Giuseppe Torri, Caroline J Muller, and Arunchandra Chandra. “A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their Interactions with the Larger-Scale Environment.” <i>Surveys in Geophysics</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10712-017-9447-x\">https://doi.org/10.1007/s10712-017-9447-x</a>.","mla":"Zuidema, Paquita, et al. “A Survey of Precipitation-Induced Atmospheric Cold Pools over Oceans and Their Interactions with the Larger-Scale Environment.” <i>Surveys in Geophysics</i>, vol. 38, no. 6, Springer Nature, 2017, pp. 1283–305, doi:<a href=\"https://doi.org/10.1007/s10712-017-9447-x\">10.1007/s10712-017-9447-x</a>.","short":"P. Zuidema, G. Torri, C.J. Muller, A. Chandra, Surveys in Geophysics 38 (2017) 1283–1305.","ista":"Zuidema P, Torri G, Muller CJ, Chandra A. 2017. A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. Surveys in Geophysics. 38(6), 1283–1305.","ama":"Zuidema P, Torri G, Muller CJ, Chandra A. A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. <i>Surveys in Geophysics</i>. 2017;38(6):1283-1305. doi:<a href=\"https://doi.org/10.1007/s10712-017-9447-x\">10.1007/s10712-017-9447-x</a>","ieee":"P. Zuidema, G. Torri, C. J. Muller, and A. Chandra, “A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment,” <i>Surveys in Geophysics</i>, vol. 38, no. 6. Springer Nature, pp. 1283–1305, 2017.","apa":"Zuidema, P., Torri, G., Muller, C. J., &#38; Chandra, A. (2017). A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment. <i>Surveys in Geophysics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10712-017-9447-x\">https://doi.org/10.1007/s10712-017-9447-x</a>"},"year":"2017","publisher":"Springer Nature","_id":"9137","status":"public","oa_version":"Published Version","issue":"6","intvolume":"        38","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Pools of air cooled by partial rain evaporation span up to several hundreds of kilometers in nature and typically last less than 1 day, ultimately losing their identity to the large-scale flow. These fundamentally differ in character from the radiatively-driven dry pools defining convective aggregation. Advancement in remote sensing and in computer capabilities has promoted exploration of how precipitation-induced cold pool processes modify the convective spectrum and life cycle. This contribution surveys current understanding of such cold pools over the tropical and subtropical oceans. In shallow convection with low rain rates, the cold pools moisten, preserving the near-surface equivalent potential temperature or increasing it if the surface moisture fluxes cannot ventilate beyond the new surface layer; both conditions indicate downdraft origin air from within the boundary layer. When rain rates exceed ∼ 2 mm h−1, convective-scale downdrafts can bring down drier air of lower equivalent potential temperature from above the boundary layer. The resulting density currents facilitate the lifting of locally thermodynamically favorable air and can impose an arc-shaped mesoscale cloud organization. This organization allows clouds capable of reaching 4–5 km within otherwise dry environments. These are more commonly observed in the northern hemisphere trade wind regime, where the flow to the intertropical convergence zone is unimpeded by the equator. Their near-surface air properties share much with those shown from cold pools sampled in the equatorial Indian Ocean. Cold pools are most effective at influencing the mesoscale organization when the atmosphere is moist in the lower free troposphere and dry above, suggesting an optimal range of water vapor paths. Outstanding questions on the relationship between cold pools, their accompanying moisture distribution and cloud cover are detailed further. Near-surface water vapor rings are documented in one model inside but near the cold pool edge; these are not consistent with observations, but do improve with smaller horizontal grid spacings."}],"date_updated":"2022-01-24T12:41:45Z","date_published":"2017-11-14T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1007/s10712-017-9447-x","keyword":["Geochemistry and Petrology","Geophysics"],"month":"11","page":"1283-1305","volume":38,"language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","date_created":"2021-02-15T14:20:07Z","article_processing_charge":"No","publication":"Surveys in Geophysics","author":[{"first_name":"Paquita","last_name":"Zuidema","full_name":"Zuidema, Paquita"},{"first_name":"Giuseppe","full_name":"Torri, Giuseppe","last_name":"Torri"},{"last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","first_name":"Caroline J"},{"last_name":"Chandra","full_name":"Chandra, Arunchandra","first_name":"Arunchandra"}],"extern":"1","publication_identifier":{"issn":["0169-3298","1573-0956"]},"title":"A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment","oa":1,"doi":"10.1007/s10712-017-9447-x","main_file_link":[{"url":"https://doi.org/10.1007/s10712-017-9447-x","open_access":"1"}],"type":"journal_article"},{"day":"01","citation":{"mla":"Holloway, Christopher E., et al. “Observing Convective Aggregation.” <i>Surveys in Geophysics</i>, vol. 38, no. 6, Springer Nature, 2017, pp. 1199–236, doi:<a href=\"https://doi.org/10.1007/s10712-017-9419-1\">10.1007/s10712-017-9419-1</a>.","short":"C.E. Holloway, A.A. Wing, S. Bony, C.J. Muller, H. Masunaga, T.S. L’Ecuyer, D.D. Turner, P. Zuidema, Surveys in Geophysics 38 (2017) 1199–1236.","chicago":"Holloway, Christopher E., Allison A. Wing, Sandrine Bony, Caroline J Muller, Hirohiko Masunaga, Tristan S. L’Ecuyer, David D. Turner, and Paquita Zuidema. “Observing Convective Aggregation.” <i>Surveys in Geophysics</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10712-017-9419-1\">https://doi.org/10.1007/s10712-017-9419-1</a>.","ieee":"C. E. Holloway <i>et al.</i>, “Observing convective aggregation,” <i>Surveys in Geophysics</i>, vol. 38, no. 6. Springer Nature, pp. 1199–1236, 2017.","apa":"Holloway, C. E., Wing, A. A., Bony, S., Muller, C. J., Masunaga, H., L’Ecuyer, T. S., … Zuidema, P. (2017). Observing convective aggregation. <i>Surveys in Geophysics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10712-017-9419-1\">https://doi.org/10.1007/s10712-017-9419-1</a>","ista":"Holloway CE, Wing AA, Bony S, Muller CJ, Masunaga H, L’Ecuyer TS, Turner DD, Zuidema P. 2017. Observing convective aggregation. Surveys in Geophysics. 38(6), 1199–1236.","ama":"Holloway CE, Wing AA, Bony S, et al. Observing convective aggregation. <i>Surveys in Geophysics</i>. 2017;38(6):1199-1236. doi:<a href=\"https://doi.org/10.1007/s10712-017-9419-1\">10.1007/s10712-017-9419-1</a>"},"year":"2017","publisher":"Springer Nature","status":"public","_id":"9138","oa_version":"Published Version","issue":"6","intvolume":"        38","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network."}],"date_updated":"2022-01-24T12:43:13Z","date_published":"2017-11-01T00:00:00Z","fulldoi":"https://doi.org/10.1007/s10712-017-9419-1","article_type":"original","keyword":["Geochemistry and Petrology","Geophysics"],"month":"11","page":"1199-1236","language":[{"iso":"eng"}],"volume":38,"publication_status":"published","quality_controlled":"1","date_created":"2021-02-15T14:20:38Z","article_processing_charge":"No","publication":"Surveys in Geophysics","author":[{"first_name":"Christopher E.","last_name":"Holloway","full_name":"Holloway, Christopher E."},{"first_name":"Allison A.","last_name":"Wing","full_name":"Wing, Allison A."},{"first_name":"Sandrine","last_name":"Bony","full_name":"Bony, Sandrine"},{"orcid":"0000-0001-5836-5350","first_name":"Caroline J","full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"},{"full_name":"Masunaga, Hirohiko","last_name":"Masunaga","first_name":"Hirohiko"},{"full_name":"L’Ecuyer, Tristan S.","last_name":"L’Ecuyer","first_name":"Tristan S."},{"first_name":"David D.","full_name":"Turner, David D.","last_name":"Turner"},{"first_name":"Paquita","full_name":"Zuidema, Paquita","last_name":"Zuidema"}],"extern":"1","publication_identifier":{"issn":["0169-3298","1573-0956"]},"title":"Observing convective aggregation","oa":1,"doi":"10.1007/s10712-017-9419-1","main_file_link":[{"url":"https://doi.org/10.1007/s10712-017-9419-1","open_access":"1"}],"type":"journal_article"},{"issue":"6","intvolume":"        38","_id":"9139","status":"public","oa_version":"None","day":"01","citation":{"ama":"Wing AA, Emanuel K, Holloway CE, Muller CJ. Convective self-aggregation in numerical simulations: A review. <i>Surveys in Geophysics</i>. 2017;38(6):1173-1197. doi:<a href=\"https://doi.org/10.1007/s10712-017-9408-4\">10.1007/s10712-017-9408-4</a>","ista":"Wing AA, Emanuel K, Holloway CE, Muller CJ. 2017. Convective self-aggregation in numerical simulations: A review. Surveys in Geophysics. 38(6), 1173–1197.","ieee":"A. A. Wing, K. Emanuel, C. E. Holloway, and C. J. Muller, “Convective self-aggregation in numerical simulations: A review,” <i>Surveys in Geophysics</i>, vol. 38, no. 6. Springer Nature, pp. 1173–1197, 2017.","apa":"Wing, A. A., Emanuel, K., Holloway, C. E., &#38; Muller, C. J. (2017). Convective self-aggregation in numerical simulations: A review. <i>Surveys in Geophysics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10712-017-9408-4\">https://doi.org/10.1007/s10712-017-9408-4</a>","chicago":"Wing, Allison A., Kerry Emanuel, Christopher E. Holloway, and Caroline J Muller. “Convective Self-Aggregation in Numerical Simulations: A Review.” <i>Surveys in Geophysics</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10712-017-9408-4\">https://doi.org/10.1007/s10712-017-9408-4</a>.","mla":"Wing, Allison A., et al. “Convective Self-Aggregation in Numerical Simulations: A Review.” <i>Surveys in Geophysics</i>, vol. 38, no. 6, Springer Nature, 2017, pp. 1173–97, doi:<a href=\"https://doi.org/10.1007/s10712-017-9408-4\">10.1007/s10712-017-9408-4</a>.","short":"A.A. Wing, K. Emanuel, C.E. Holloway, C.J. Muller, Surveys in Geophysics 38 (2017) 1173–1197."},"year":"2017","publisher":"Springer Nature","date_published":"2017-11-01T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1007/s10712-017-9408-4","keyword":["Geochemistry and Petrology","Geophysics"],"date_updated":"2022-01-24T12:42:36Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Organized convection in the tropics occurs across a range of spatial and temporal scales and strongly influences cloud cover and humidity. One mode of organization found is “self-aggregation,” in which moist convection spontaneously organizes into one or several isolated clusters despite spatially homogeneous boundary conditions and forcing. Self-aggregation is driven by interactions between clouds, moisture, radiation, surface fluxes, and circulation, and occurs in a wide variety of idealized simulations of radiative–convective equilibrium. Here we provide a review of convective self-aggregation in numerical simulations, including its character, causes, and effects. We describe the evolution of self-aggregation including its time and length scales and the physical mechanisms leading to its triggering and maintenance, and we also discuss possible links to climate and climate change."}],"date_created":"2021-02-15T14:20:56Z","article_processing_charge":"No","quality_controlled":"1","page":"1173-1197","language":[{"iso":"eng"}],"volume":38,"publication_status":"published","month":"11","publication_identifier":{"issn":["0169-3298","1573-0956"]},"title":"Convective self-aggregation in numerical simulations: A review","doi":"10.1007/s10712-017-9408-4","type":"journal_article","extern":"1","publication":"Surveys in Geophysics","author":[{"full_name":"Wing, Allison A.","last_name":"Wing","first_name":"Allison A."},{"last_name":"Emanuel","full_name":"Emanuel, Kerry","first_name":"Kerry"},{"first_name":"Christopher E.","full_name":"Holloway, Christopher E.","last_name":"Holloway"},{"first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"}]},{"status":"public","_id":"915","oa_version":"Submitted Version","isi":1,"day":"01","publisher":"IEEE","citation":{"ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.530\">10.1109/CVPR.2017.530</a>","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.","apa":"Swoboda, P., &#38; Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.530\">https://doi.org/10.1109/CVPR.2017.530</a>","ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.","chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.530\">https://doi.org/10.1109/CVPR.2017.530</a>.","short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","mla":"Swoboda, Paul, and Bjoern Andres. <i>A Message Passing Algorithm for the Minimum Cost Multicut Problem</i>. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.530\">10.1109/CVPR.2017.530</a>."},"year":"2017","external_id":{"isi":["000418371405009"]},"intvolume":"      2017","file":[{"file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf","file_size":883264,"date_created":"2019-01-18T12:52:46Z","file_id":"5849","date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","checksum":"7e51dacefa693574581a32da3eff63dc","access_level":"open_access"}],"publist_id":"6526","date_updated":"2024-11-04T13:52:34Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes.  We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:15Z","ec_funded":1,"date_published":"2017-07-01T00:00:00Z","has_accepted_license":"1","ddc":["000"],"fulldoi":"https://doi.org/10.1109/CVPR.2017.530","page":"4990-4999","publication_status":"published","department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"volume":2017,"month":"07","article_processing_charge":"No","date_created":"2018-12-11T11:49:11Z","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160"}],"quality_controlled":"1","conference":{"start_date":"2017-07-21","location":"Honolulu, HA, United States","name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26"},"corr_author":"1","scopus_import":"1","author":[{"full_name":"Swoboda, Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"},{"full_name":"Andres, Bjoern","last_name":"Andres","first_name":"Bjoern"}],"title":"A message passing algorithm for the minimum cost multicut problem","oa":1,"publication_identifier":{"isbn":["978-153860457-1"]},"type":"conference","doi":"10.1109/CVPR.2017.530"},{"month":"06","volume":47,"language":[{"iso":"eng"}],"publication_status":"published","page":"1457-1472","quality_controlled":"1","date_created":"2021-02-15T15:11:04Z","article_processing_charge":"No","author":[{"first_name":"O.","last_name":"Richet","full_name":"Richet, O."},{"full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","orcid":"0000-0001-5836-5350"},{"last_name":"Chomaz","full_name":"Chomaz, J.-M.","first_name":"J.-M."}],"publication":"Journal of Physical Oceanography","extern":"1","doi":"10.1175/jpo-d-16-0197.1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1175/JPO-D-16-0197.1"}],"type":"journal_article","publication_identifier":{"issn":["0022-3670","1520-0485"]},"oa":1,"title":"Impact of a mean current on the internal tide energy dissipation at the critical latitude","citation":{"chicago":"Richet, O., Caroline J Muller, and J.-M. Chomaz. “Impact of a Mean Current on the Internal Tide Energy Dissipation at the Critical Latitude.” <i>Journal of Physical Oceanography</i>. American Meteorological Society, 2017. <a href=\"https://doi.org/10.1175/jpo-d-16-0197.1\">https://doi.org/10.1175/jpo-d-16-0197.1</a>.","mla":"Richet, O., et al. “Impact of a Mean Current on the Internal Tide Energy Dissipation at the Critical Latitude.” <i>Journal of Physical Oceanography</i>, vol. 47, no. 6, American Meteorological Society, 2017, pp. 1457–72, doi:<a href=\"https://doi.org/10.1175/jpo-d-16-0197.1\">10.1175/jpo-d-16-0197.1</a>.","short":"O. Richet, C.J. Muller, J.-M. Chomaz, Journal of Physical Oceanography 47 (2017) 1457–1472.","ama":"Richet O, Muller CJ, Chomaz J-M. Impact of a mean current on the internal tide energy dissipation at the critical latitude. <i>Journal of Physical Oceanography</i>. 2017;47(6):1457-1472. doi:<a href=\"https://doi.org/10.1175/jpo-d-16-0197.1\">10.1175/jpo-d-16-0197.1</a>","ista":"Richet O, Muller CJ, Chomaz J-M. 2017. Impact of a mean current on the internal tide energy dissipation at the critical latitude. Journal of Physical Oceanography. 47(6), 1457–1472.","apa":"Richet, O., Muller, C. J., &#38; Chomaz, J.-M. (2017). Impact of a mean current on the internal tide energy dissipation at the critical latitude. <i>Journal of Physical Oceanography</i>. American Meteorological Society. <a href=\"https://doi.org/10.1175/jpo-d-16-0197.1\">https://doi.org/10.1175/jpo-d-16-0197.1</a>","ieee":"O. Richet, C. J. Muller, and J.-M. Chomaz, “Impact of a mean current on the internal tide energy dissipation at the critical latitude,” <i>Journal of Physical Oceanography</i>, vol. 47, no. 6. American Meteorological Society, pp. 1457–1472, 2017."},"year":"2017","publisher":"American Meteorological Society","day":"01","oa_version":"Published Version","status":"public","_id":"9152","intvolume":"        47","issue":"6","abstract":[{"text":"Previous numerical studies of the dissipation of internal tides in idealized settings suggest the existence of a critical latitude (~29°) where dissipation is enhanced. But observations only indicate a modest enhancement at this latitude. To resolve this difference between observational and numerical results, the authors study the latitudinal dependence of internal tides’ dissipation in more realistic conditions. In particular, the ocean is not a quiescent medium; the presence of large-scale currents or mesoscale eddies can impact the propagation and dissipation of internal tides. This paper investigates the impact of a weak background mean current in numerical simulations. The authors focus on the local dissipation of high spatial mode internal waves near their generation site. The vertical profile of dissipation and its variation with latitude without the mean current are consistent with earlier studies. But adding a weak mean current has a major impact on the latitudinal distribution of dissipation. The peak at the critical latitude disappears, and the dissipation is closer to a constant, albeit with two weak peaks at ~25° and ~35° latitude. This disappearance results from the Doppler shift of the internal tides’ frequency, which hinders the nonlinear transfer of energy to small-scale secondary waves via the parametric subharmonic instability (PSI). The new two weak peaks correspond to the Doppler-shifted critical latitudes of the left- and right-propagating waves. The results are confirmed in simulations with simple sinusoidal topography. Thus, although nonlinear transfers via PSI are efficient at dissipating internal tides, the exact location of the dissipation is sensitive to large-scale oceanic conditions.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-24T13:36:31Z","fulldoi":"https://doi.org/10.1175/jpo-d-16-0197.1","article_type":"original","keyword":["Oceanography"],"date_published":"2017-06-01T00:00:00Z"},{"date_updated":"2024-11-04T13:52:34Z","publist_id":"6525","ec_funded":1,"abstract":[{"lang":"eng","text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each."}],"file_date_updated":"2020-07-14T12:48:15Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","fulldoi":"https://doi.org/10.1109/CVPR.2017.747","has_accepted_license":"1","date_published":"2017-01-01T00:00:00Z","ddc":["000"],"oa_version":"Submitted Version","status":"public","_id":"916","publisher":"IEEE","year":"2017","citation":{"ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.747\">10.1109/CVPR.2017.747</a>","ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., &#38; Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.747\">https://doi.org/10.1109/CVPR.2017.747</a>","ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071.","chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.747\">https://doi.org/10.1109/CVPR.2017.747</a>.","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","mla":"Swoboda, Paul, et al. <i>A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching</i>. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.747\">10.1109/CVPR.2017.747</a>."},"isi":1,"day":"01","intvolume":"      2017","file":[{"file_name":"2017_CVPR_Swoboda2.pdf","date_created":"2019-01-18T12:49:38Z","file_size":944332,"file_id":"5848","date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"e38a2740daad1ea178465843b5072906"}],"external_id":{"isi":["000418371407018"]},"scopus_import":"1","conference":{"end_date":"2017-07-26","name":"CVPR: Computer Vision and Pattern Recognition","location":"Honolulu, HA, United States","start_date":"2017-07-21"},"corr_author":"1","author":[{"full_name":"Swoboda, Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"},{"last_name":"Rother","full_name":"Rother, Carsten","first_name":"Carsten"},{"last_name":"Abu Alhaija","full_name":"Abu Alhaija, Carsten","first_name":"Carsten"},{"full_name":"Kainmueller, Dagmar","last_name":"Kainmueller","first_name":"Dagmar"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"type":"conference","doi":"10.1109/CVPR.2017.747","title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","oa":1,"publication_identifier":{"isbn":["978-153860457-1"]},"publication_status":"published","department":[{"_id":"VlKo"}],"volume":2017,"language":[{"iso":"eng"}],"page":"7062-7071","month":"01","article_processing_charge":"No","date_created":"2018-12-11T11:49:11Z","quality_controlled":"1","project":[{"grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}]}]