[{"date_updated":"2023-10-16T11:15:22Z","publication":"Handbook of Discrete and Computational Geometry, Third Edition","abstract":[{"lang":"eng","text":"The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"book_chapter","scopus_import":"1","title":"Computational topology for structural molecular biology","quality_controlled":"1","oa_version":"None","citation":{"apa":"Edelsbrunner, H., &#38; Koehl, P. (2017). Computational topology for structural molecular biology. In C. Toth, J. O’Rourke, &#38; J. Goodman (Eds.), <i>Handbook of Discrete and Computational Geometry, Third Edition</i> (pp. 1709–1735). Taylor &#38; Francis. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>","ieee":"H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular biology,” in <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor &#38; Francis, 2017, pp. 1709–1735.","chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” In <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis, 2017. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>.","ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735.","mla":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth et al., Taylor &#38; Francis, 2017, pp. 1709–35, doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>.","short":"H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition, Taylor &#38; Francis, 2017, pp. 1709–1735.","ama":"Edelsbrunner H, Koehl P. Computational topology for structural molecular biology. In: Toth C, O’Rourke J, Goodman J, eds. <i>Handbook of Discrete and Computational Geometry, Third Edition</i>. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis; 2017:1709-1735. doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>"},"doi":"10.1201/9781315119601","date_created":"2018-12-11T11:44:32Z","day":"09","publisher":"Taylor & Francis","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koehl, Patrice","first_name":"Patrice","last_name":"Koehl"}],"publication_identifier":{"eisbn":["9781498711425"]},"publist_id":"7970","year":"2017","status":"public","month":"11","_id":"84","series_title":"Handbook of Discrete and Computational Geometry","date_published":"2017-11-09T00:00:00Z","publication_status":"published","page":"1709 - 1735","editor":[{"last_name":"Toth","first_name":"Csaba","full_name":"Toth, Csaba"},{"last_name":"O'Rourke","first_name":"Joseph","full_name":"O'Rourke, Joseph"},{"last_name":"Goodman","first_name":"Jacob","full_name":"Goodman, Jacob"}],"department":[{"_id":"HeEd"}]},{"article_type":"original","_id":"8423","day":"08","publisher":"Duke University Press","extern":"1","page":"175-209","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"journal_article","volume":167,"date_updated":"2021-01-12T08:19:11Z","language":[{"iso":"eng"}],"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."}],"citation":{"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>","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.","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>.","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.","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.","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>"},"issue":"1","year":"2017","month":"12","status":"public","arxiv":1,"date_created":"2020-09-17T10:42:42Z","publication_identifier":{"issn":["0012-7094"]},"intvolume":"       167","author":[{"full_name":"Huang, Guan","first_name":"Guan","last_name":"Huang"},{"first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"full_name":"Sorrentino, Alfonso","first_name":"Alfonso","last_name":"Sorrentino"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.08838"}],"date_published":"2017-12-08T00:00:00Z","article_processing_charge":"No","publication":"Duke Mathematical Journal","doi":"10.1215/00127094-2017-0038","external_id":{"arxiv":["1603.08838"]},"oa_version":"Preprint","quality_controlled":"1","title":"On the marked length spectrum of generic strictly convex billiard tables"},{"article_processing_charge":"No","publication":"Annals of Mathematics","oa_version":"Preprint","external_id":{"arxiv":["1606.00230"]},"doi":"10.4007/annals.2017.186.1.7","title":"Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle","quality_controlled":"1","year":"2017","status":"public","month":"07","date_created":"2020-09-17T10:46:42Z","arxiv":1,"author":[{"full_name":"De Simoi, Jacopo","first_name":"Jacopo","last_name":"De Simoi"},{"first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Wei","first_name":"Qiaoling","full_name":"Wei, Qiaoling"}],"publication_identifier":{"issn":["0003-486X"]},"intvolume":"       186","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1606.00230","open_access":"1"}],"date_published":"2017-07-01T00:00:00Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":186,"type":"journal_article","date_updated":"2021-01-12T08:19:12Z","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"citation":{"short":"J. De Simoi, V. Kaloshin, Q. Wei, Annals of Mathematics 186 (2017) 277–314.","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>","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>.","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.","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>","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.","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>."},"issue":"1","article_type":"original","_id":"8427","publisher":"Annals of Mathematics","day":"01","extern":"1","page":"277-314"},{"year":"2017","status":"public","month":"12","_id":"8444","article_type":"original","date_created":"2020-09-18T10:05:54Z","publisher":"Elsevier","day":"05","extern":"1","author":[{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"},{"full_name":"King, Martin S.","first_name":"Martin S.","last_name":"King"},{"last_name":"Kunji","first_name":"Edmund R.S.","full_name":"Kunji, Edmund R.S."},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"}],"intvolume":"       113","publication_identifier":{"issn":["0006-3495"]},"publication_status":"published","page":"2311-2315","date_published":"2017-12-05T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Biophysics"],"article_processing_charge":"No","volume":113,"type":"journal_article","date_updated":"2021-01-12T08:19:18Z","publication":"Biophysical Journal","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."}],"language":[{"iso":"eng"}],"oa_version":"None","doi":"10.1016/j.bpj.2017.09.019","citation":{"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>.","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>","short":"F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal 113 (2017) 2311–2315.","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>.","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>","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."},"issue":"11","title":"Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity","quality_controlled":"1"},{"volume":8,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"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","citation":{"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>.","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>","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).","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>.","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>","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."},"article_number":"145","_id":"8445","article_type":"original","extern":"1","publisher":"Springer Nature","day":"27","OA_type":"gold","article_processing_charge":"Yes","publication":"Nature Communications","doi":"10.1038/s41467-017-00165-8","oa_version":"Published Version","OA_place":"publisher","quality_controlled":"1","title":"Slow conformational exchange and overall rocking motion in ubiquitin protein crystals","scopus_import":"1","month":"07","status":"public","year":"2017","publication_identifier":{"issn":["2041-1723"]},"intvolume":"         8","author":[{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"full_name":"Izmailov, Sergei A.","first_name":"Sergei A.","last_name":"Izmailov"},{"last_name":"Rogacheva","first_name":"Olga N.","full_name":"Rogacheva, Olga N."},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"last_name":"Woodhouse","first_name":"Joyce","full_name":"Woodhouse, Joyce"},{"last_name":"Shilova","first_name":"Anastasya","full_name":"Shilova, Anastasya"},{"full_name":"Xue, Yi","first_name":"Yi","last_name":"Xue"},{"last_name":"Yuwen","first_name":"Tairan","full_name":"Yuwen, Tairan"},{"full_name":"Coquelle, Nicolas","first_name":"Nicolas","last_name":"Coquelle"},{"last_name":"Colletier","first_name":"Jacques-Philippe","full_name":"Colletier, Jacques-Philippe"},{"full_name":"Skrynnikov, Nikolai R.","first_name":"Nikolai R.","last_name":"Skrynnikov"},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"date_created":"2020-09-18T10:06:01Z","publication_status":"published","date_published":"2017-07-27T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-017-00165-8"}]},{"date_created":"2020-09-18T10:06:09Z","day":"09","publisher":"Wiley","extern":"1","author":[{"full_name":"Fraga, Hugo","first_name":"Hugo","last_name":"Fraga"},{"last_name":"Arnaud","first_name":"Charles‐Adrien","full_name":"Arnaud, Charles‐Adrien"},{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"last_name":"Audin","first_name":"Maxime","full_name":"Audin, Maxime"},{"full_name":"Kurauskas, Vilius","first_name":"Vilius","last_name":"Kurauskas"},{"full_name":"Macek, Pavel","first_name":"Pavel","last_name":"Macek"},{"full_name":"Krichel, Carsten","first_name":"Carsten","last_name":"Krichel"},{"first_name":"Jia‐Ying","last_name":"Guan","full_name":"Guan, Jia‐Ying"},{"full_name":"Boisbouvier, Jerome","first_name":"Jerome","last_name":"Boisbouvier"},{"full_name":"Sprangers, Remco","first_name":"Remco","last_name":"Sprangers"},{"full_name":"Breyton, Cécile","first_name":"Cécile","last_name":"Breyton"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"}],"publication_identifier":{"issn":["1439-4235","1439-7641"]},"intvolume":"        18","year":"2017","status":"public","_id":"8446","month":"08","article_type":"original","date_published":"2017-08-09T00:00:00Z","page":"2697-2703","publication_status":"published","date_updated":"2021-01-12T08:19:19Z","publication":"ChemPhysChem","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"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"type":"journal_article","volume":18,"article_processing_charge":"No","issue":"19","title":"Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins","quality_controlled":"1","oa_version":"None","citation":{"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.","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.","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>.","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>","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>","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>."},"doi":"10.1002/cphc.201700572"},{"doi":"10.1016/j.ssnmr.2017.04.002","citation":{"short":"D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid State Nuclear Magnetic Resonance 87 (2017) 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>","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>.","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.","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>."},"oa_version":"None","issue":"10","title":"Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Nuclear and High Energy Physics","Instrumentation","General Chemistry","Radiation"],"volume":87,"type":"journal_article","article_processing_charge":"No","date_updated":"2021-01-12T08:19:20Z","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."}],"publication":"Solid State Nuclear Magnetic Resonance","language":[{"iso":"eng"}],"publication_status":"published","page":"86-95","date_published":"2017-10-01T00:00:00Z","year":"2017","status":"public","article_type":"original","_id":"8447","month":"10","date_created":"2020-09-18T10:06:18Z","day":"01","publisher":"Elsevier","extern":"1","author":[{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"last_name":"Hessel","first_name":"Audrey","full_name":"Hessel, Audrey"},{"first_name":"Petra","last_name":"Rovó","full_name":"Rovó, Petra"},{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"full_name":"Linser, Rasmus","first_name":"Rasmus","last_name":"Linser"},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"intvolume":"        87","publication_identifier":{"issn":["0926-2040"]}},{"issue":"8","quality_controlled":"1","title":"Optimized fast mixing device for real-time NMR applications","doi":"10.1016/j.jmr.2017.05.016","oa_version":"None","citation":{"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.","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>","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.","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>.","short":"R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 281 (2017) 125–129.","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>","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>."},"date_updated":"2021-01-12T08:19:20Z","language":[{"iso":"eng"}],"publication":"Journal of Magnetic Resonance","abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","volume":281,"type":"journal_article","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"date_published":"2017-08-01T00:00:00Z","publication_status":"published","page":"125-129","day":"01","publisher":"Elsevier","date_created":"2020-09-18T10:06:27Z","publication_identifier":{"issn":["1090-7807"]},"intvolume":"       281","extern":"1","author":[{"full_name":"Franco, Rémi","first_name":"Rémi","last_name":"Franco"},{"last_name":"Favier","first_name":"Adrien","full_name":"Favier, Adrien"},{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"}],"year":"2017","month":"08","_id":"8448","article_type":"original","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","article_processing_charge":"No","volume":45,"date_updated":"2021-01-12T08:19:20Z","language":[{"iso":"eng"}],"publication":"Nucleic Acids Research","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."}],"doi":"10.1093/nar/gkx044","citation":{"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>.","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.","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>.","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.","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>"},"oa_version":"None","issue":"7","quality_controlled":"1","title":"RNA binding and chaperone activity of the E.coli cold-shock protein CspA","year":"2017","month":"04","_id":"8449","article_type":"original","status":"public","day":"20","publisher":"Oxford University Press","date_created":"2020-09-18T10:06:34Z","intvolume":"        45","publication_identifier":{"issn":["0305-1048","1362-4962"]},"extern":"1","author":[{"first_name":"Enrico","last_name":"Rennella","full_name":"Rennella, Enrico"},{"full_name":"Sára, Tomáš","last_name":"Sára","first_name":"Tomáš"},{"full_name":"Juen, Michael","first_name":"Michael","last_name":"Juen"},{"full_name":"Wunderlich, Christoph","last_name":"Wunderlich","first_name":"Christoph"},{"full_name":"Imbert, Lionel","last_name":"Imbert","first_name":"Lionel"},{"full_name":"Solyom, Zsofia","first_name":"Zsofia","last_name":"Solyom"},{"full_name":"Favier, Adrien","first_name":"Adrien","last_name":"Favier"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"full_name":"Weinhäupl, Katharina","first_name":"Katharina","last_name":"Weinhäupl"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda"},{"full_name":"Konrat, Robert","first_name":"Robert","last_name":"Konrat"},{"first_name":"Christoph","last_name":"Kreutz","full_name":"Kreutz, Christoph"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"}],"publication_status":"published","page":"4255-4268","date_published":"2017-04-20T00:00:00Z"},{"title":"Methyl-specific isotope labeling strategies for NMR studies of membrane proteins","quality_controlled":"1","alternative_title":["Methods in Molecular Biology"],"citation":{"short":"V. Kurauskas, P. Schanda, R. Sounier, in:, Membrane Protein Structure and Function Characterization, Springer Nature, 2017, pp. 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>","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>.","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.","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>."},"doi":"10.1007/978-1-4939-7151-0_6","oa_version":"None","abstract":[{"lang":"eng","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."}],"publication":"Membrane protein structure and function characterization","language":[{"iso":"eng"}],"date_updated":"2022-08-26T09:14:20Z","volume":1635,"type":"book_chapter","article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2017-07-29T00:00:00Z","publication_status":"published","page":"109-123","extern":"1","author":[{"full_name":"Kurauskas, Vilius","first_name":"Vilius","last_name":"Kurauskas"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"},{"last_name":"Sounier","first_name":"Remy","full_name":"Sounier, Remy"}],"intvolume":"      1635","publication_identifier":{"issn":["1064-3745","1940-6029"],"isbn":["9781493971497","9781493971510"]},"date_created":"2020-09-18T10:06:44Z","day":"29","publisher":"Springer Nature","status":"public","_id":"8450","month":"07","year":"2017"},{"date_created":"2020-09-18T10:06:50Z","publisher":"Wiley","day":"27","extern":"1","author":[{"full_name":"Bersch, Beate","first_name":"Beate","last_name":"Bersch"},{"last_name":"Dörr","first_name":"Jonas M.","full_name":"Dörr, Jonas M."},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"full_name":"Killian, J. Antoinette","first_name":"J. Antoinette","last_name":"Killian"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"}],"intvolume":"        56","publication_identifier":{"issn":["1433-7851"]},"year":"2017","status":"public","_id":"8451","month":"01","article_type":"original","date_published":"2017-01-27T00:00:00Z","page":"2508-2512","publication_status":"published","date_updated":"2021-01-12T08:19:22Z","abstract":[{"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.","lang":"eng"}],"publication":"Angewandte Chemie International Edition","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":56,"article_processing_charge":"No","issue":"9","title":"Proton-detected solid-state NMR spectroscopy of a Zinc diffusion facilitator protein in native nanodiscs","quality_controlled":"1","oa_version":"None","citation":{"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.","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>","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>.","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.","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."},"doi":"10.1002/anie.201610441"},{"date_published":"2017-10-01T00:00:00Z","publication_status":"published","date_created":"2021-02-02T15:49:21Z","publisher":"American Physical Society","day":"01","extern":"1","author":[{"last_name":"Nauman","first_name":"Muhammad","full_name":"Nauman, Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","orcid":"0000-0002-2111-4846"},{"first_name":"Yunjeong","last_name":"Hong","full_name":"Hong, Yunjeong"},{"first_name":"Tayyaba","last_name":"Hussain","full_name":"Hussain, Tayyaba"},{"first_name":"M. S.","last_name":"Seo","full_name":"Seo, M. S."},{"first_name":"S. Y.","last_name":"Park","full_name":"Park, S. Y."},{"full_name":"Lee, N.","last_name":"Lee","first_name":"N."},{"full_name":"Choi, Y. J.","last_name":"Choi","first_name":"Y. J."},{"first_name":"Woun","last_name":"Kang","full_name":"Kang, Woun"},{"first_name":"Younjung","last_name":"Jo","full_name":"Jo, Younjung"}],"intvolume":"        96","publication_identifier":{"issn":["2469-9950","2469-9969"]},"year":"2017","status":"public","article_type":"original","_id":"9065","month":"10","issue":"15","article_number":"155102","title":"In-plane magnetic anisotropy in strontium iridate Sr2IrO4","quality_controlled":"1","citation":{"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).","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>","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>","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>.","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.","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."},"oa_version":"None","doi":"10.1103/physrevb.96.155102","date_updated":"2021-02-03T12:53:00Z","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"}],"publication":"Physical Review B","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":96,"article_processing_charge":"No","type":"journal_article"},{"doi":"10.4169/amer.math.monthly.124.7.588","oa_version":"Submitted Version","external_id":{"arxiv":["1605.07997"],"isi":["000413947300002"]},"title":"On the lengths of curves passing through boundary points of a planar convex shape","quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","publication":"The American Mathematical Monthly","department":[{"_id":"HeEd"}],"publication_status":"published","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07997"}],"date_published":"2017-01-01T00:00:00Z","status":"public","month":"01","year":"2017","author":[{"first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vysotsky, Vladislav","last_name":"Vysotsky","first_name":"Vladislav"}],"publist_id":"6534","publication_identifier":{"issn":["0002-9890"]},"intvolume":"       124","isi":1,"date_created":"2018-12-11T11:49:09Z","arxiv":1,"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.","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>","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.","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>.","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."},"issue":"7","type":"journal_article","volume":124,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"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."}],"language":[{"iso":"eng"}],"date_updated":"2025-07-10T12:01:35Z","page":"588 - 596","_id":"909","article_type":"original","publisher":"Mathematical Association of America","day":"01"},{"page":"653 - 668","_id":"910","day":"01","publisher":"Genetics Society of America","citation":{"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>.","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.","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>.","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.","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>","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668."},"issue":"2","has_accepted_license":"1","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"type":"journal_article","volume":207,"date_updated":"2025-04-15T08:22:21Z","language":[{"iso":"eng"}],"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"}],"publication_status":"published","department":[{"_id":"NiBa"}],"pubrep_id":"974","corr_author":"1","date_published":"2017-10-01T00:00:00Z","ec_funded":1,"year":"2017","month":"10","status":"public","date_created":"2018-12-11T11:49:09Z","isi":1,"publist_id":"6533","intvolume":"       207","author":[{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"file":[{"file_name":"IST-2018-974-v1+1_manuscript.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-12T10:17:12Z","content_type":"application/pdf","file_id":"5264","creator":"system","file_size":494268,"checksum":"f7c32dabf52e6d9e709d9203761e39fd","relation":"main_file"}],"ddc":["576"],"doi":"10.1534/genetics.117.300129","external_id":{"isi":["000412232600019"]},"file_date_updated":"2020-07-14T12:48:15Z","oa_version":"Submitted Version","scopus_import":"1","quality_controlled":"1","title":"When does frequency-independent selection maintain genetic variation?","article_processing_charge":"No","publication":"Genetics"},{"corr_author":"1","date_published":"2017-08-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.04616"}],"ec_funded":1,"publication_status":"published","department":[{"_id":"RoSe"}],"arxiv":1,"date_created":"2018-12-11T11:49:10Z","isi":1,"intvolume":"        58","publication_identifier":{"issn":["0022-2488"]},"publist_id":"6531","author":[{"orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","full_name":"Deuchert, Andreas","first_name":"Andreas","last_name":"Deuchert"}],"year":"2017","month":"08","status":"public","scopus_import":"1","quality_controlled":"1","title":"A lower bound for the BCS functional with boundary conditions at infinity","external_id":{"isi":["000409197200015"],"arxiv":["1703.04616"]},"oa_version":"Submitted Version","doi":"10.1063/1.4996580","publication":" Journal of Mathematical Physics","article_processing_charge":"No","publisher":"AIP Publishing","day":"01","_id":"912","article_number":"081901","issue":"8","citation":{"short":"A. Deuchert,  Journal of Mathematical Physics 58 (2017).","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. 2017;58(8). doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>.","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity.  Journal of Mathematical Physics. 58(8), 081901.","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>.","ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8. AIP Publishing, 2017."},"date_updated":"2025-06-04T08:19:58Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n"}],"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"journal_article","volume":58},{"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1007/s10712-017-9447-x","open_access":"1"}],"date_published":"2017-11-14T00:00:00Z","year":"2017","status":"public","month":"11","date_created":"2021-02-15T14:20:07Z","author":[{"last_name":"Zuidema","first_name":"Paquita","full_name":"Zuidema, Paquita"},{"full_name":"Torri, Giuseppe","last_name":"Torri","first_name":"Giuseppe"},{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","last_name":"Muller"},{"full_name":"Chandra, Arunchandra","first_name":"Arunchandra","last_name":"Chandra"}],"intvolume":"        38","publication_identifier":{"issn":["0169-3298","1573-0956"]},"doi":"10.1007/s10712-017-9447-x","oa_version":"Published Version","title":"A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment","quality_controlled":"1","article_processing_charge":"No","publication":"Surveys in Geophysics","page":"1283-1305","article_type":"original","_id":"9137","publisher":"Springer Nature","day":"14","extern":"1","citation":{"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>","short":"P. Zuidema, G. Torri, C.J. Muller, A. Chandra, Surveys in Geophysics 38 (2017) 1283–1305.","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>.","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.","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>.","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>"},"issue":"6","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","keyword":["Geochemistry and Petrology","Geophysics"],"type":"journal_article","volume":38,"date_updated":"2022-01-24T12:41:45Z","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."}],"language":[{"iso":"eng"}]},{"publication":"Surveys in Geophysics","article_processing_charge":"No","quality_controlled":"1","title":"Observing convective aggregation","doi":"10.1007/s10712-017-9419-1","oa_version":"Published Version","date_created":"2021-02-15T14:20:38Z","publication_identifier":{"issn":["0169-3298","1573-0956"]},"intvolume":"        38","author":[{"full_name":"Holloway, Christopher E.","last_name":"Holloway","first_name":"Christopher E."},{"last_name":"Wing","first_name":"Allison A.","full_name":"Wing, Allison A."},{"last_name":"Bony","first_name":"Sandrine","full_name":"Bony, Sandrine"},{"first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","full_name":"Muller, Caroline J"},{"full_name":"Masunaga, Hirohiko","first_name":"Hirohiko","last_name":"Masunaga"},{"first_name":"Tristan S.","last_name":"L’Ecuyer","full_name":"L’Ecuyer, Tristan S."},{"full_name":"Turner, David D.","last_name":"Turner","first_name":"David D."},{"first_name":"Paquita","last_name":"Zuidema","full_name":"Zuidema, Paquita"}],"year":"2017","month":"11","status":"public","date_published":"2017-11-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1007/s10712-017-9419-1","open_access":"1"}],"publication_status":"published","date_updated":"2022-01-24T12:43:13Z","language":[{"iso":"eng"}],"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."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"type":"journal_article","volume":38,"keyword":["Geochemistry and Petrology","Geophysics"],"issue":"6","citation":{"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>","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.","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>.","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.","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>"},"publisher":"Springer Nature","day":"01","extern":"1","article_type":"original","_id":"9138","page":"1199-1236"},{"year":"2017","month":"11","_id":"9139","article_type":"original","status":"public","day":"01","publisher":"Springer Nature","date_created":"2021-02-15T14:20:56Z","publication_identifier":{"issn":["0169-3298","1573-0956"]},"intvolume":"        38","extern":"1","author":[{"last_name":"Wing","first_name":"Allison A.","full_name":"Wing, Allison A."},{"full_name":"Emanuel, Kerry","first_name":"Kerry","last_name":"Emanuel"},{"last_name":"Holloway","first_name":"Christopher E.","full_name":"Holloway, Christopher E."},{"first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"page":"1173-1197","publication_status":"published","date_published":"2017-11-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":38,"article_processing_charge":"No","keyword":["Geochemistry and Petrology","Geophysics"],"date_updated":"2022-01-24T12:42:36Z","language":[{"iso":"eng"}],"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."}],"publication":"Surveys in Geophysics","citation":{"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.","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>.","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>","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.","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>.","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>","short":"A.A. Wing, K. Emanuel, C.E. Holloway, C.J. Muller, Surveys in Geophysics 38 (2017) 1173–1197."},"doi":"10.1007/s10712-017-9408-4","oa_version":"None","issue":"6","quality_controlled":"1","title":"Convective self-aggregation in numerical simulations: A review"},{"type":"journal_article","volume":4,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.","lang":"eng"}],"language":[{"iso":"eng"}],"date_updated":"2025-07-10T12:01:39Z","citation":{"mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>.","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. 2017;4(7). doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017).","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>. Royal Society, The, 2017. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>.","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” <i>Royal Society Open Science</i>, vol. 4, no. 7. Royal Society, The, 2017.","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., &#38; Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547."},"has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"issue":"7","article_number":"170547","_id":"914","related_material":{"record":[{"relation":"research_data","id":"9853","status":"public"}]},"day":"05","publisher":"Royal Society, The","article_processing_charge":"No","publication":"Royal Society Open Science","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","oa_version":"Published Version","doi":"10.1098/rsos.170547","external_id":{"isi":["000406670000025"]},"file_date_updated":"2020-07-14T12:48:15Z","ddc":["576","592"],"file":[{"file_id":"4684","creator":"system","content_type":"application/pdf","file_size":530412,"checksum":"351ae5e7a37e6e7d9295cd41146c4190","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:24Z","date_updated":"2020-07-14T12:48:15Z","relation":"main_file"}],"title":"Ant queens increase their reproductive efforts after pathogen infection","quality_controlled":"1","scopus_import":"1","status":"public","month":"07","year":"2017","author":[{"full_name":"Giehr, Julia","last_name":"Giehr","first_name":"Julia"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V"},{"first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"last_name":"Schrempf","first_name":"Alexandra","full_name":"Schrempf, Alexandra"}],"intvolume":"         4","publication_identifier":{"issn":["2054-5703"]},"publist_id":"6527","date_created":"2018-12-11T11:49:10Z","isi":1,"pubrep_id":"849","department":[{"_id":"SyCr"}],"publication_status":"published","date_published":"2017-07-05T00:00:00Z"},{"type":"conference","volume":2017,"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"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"}],"language":[{"iso":"eng"}],"date_updated":"2024-11-04T13:52:34Z","citation":{"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>.","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>","short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","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>.","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>","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."},"has_accepted_license":"1","conference":{"end_date":"2017-07-26","name":"CVPR: Computer Vision and Pattern Recognition","location":"Honolulu, HA, United States","start_date":"2017-07-21"},"_id":"915","publisher":"IEEE","day":"01","page":"4990-4999","article_processing_charge":"No","oa_version":"Submitted Version","external_id":{"isi":["000418371405009"]},"file_date_updated":"2020-07-14T12:48:15Z","doi":"10.1109/CVPR.2017.530","ddc":["000"],"file":[{"relation":"main_file","checksum":"7e51dacefa693574581a32da3eff63dc","file_size":883264,"content_type":"application/pdf","creator":"dernst","file_id":"5849","date_created":"2019-01-18T12:52:46Z","date_updated":"2020-07-14T12:48:15Z","access_level":"open_access","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf"}],"title":"A message passing algorithm for the minimum cost multicut problem","quality_controlled":"1","scopus_import":"1","status":"public","month":"07","year":"2017","author":[{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda"},{"full_name":"Andres, Bjoern","first_name":"Bjoern","last_name":"Andres"}],"publist_id":"6526","publication_identifier":{"isbn":["978-153860457-1"]},"intvolume":"      2017","isi":1,"date_created":"2018-12-11T11:49:11Z","department":[{"_id":"VlKo"}],"publication_status":"published","ec_funded":1,"date_published":"2017-07-01T00:00:00Z","corr_author":"1"}]