[{"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"FrLo"}],"author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"full_name":"Khanna, Rajiv","last_name":"Khanna","first_name":"Rajiv"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"full_name":"Jaggi, Martin","last_name":"Jaggi","first_name":"Martin"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","publisher":"ML Research Press","publication_status":"published","_id":"14205","quality_controlled":"1","citation":{"chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, 54:860–68. ML Research Press, 2017.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.","short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.","ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>. Vol 54. ML Research Press; 2017:860-868.","mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i>, vol. 54, ML Research Press, 2017, pp. 860–68.","apa":"Locatello, F., Khanna, R., Tschannen, M., &#38; Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In <i>Proceedings of the 20th International Conference on Artificial Intelligence and Statistics</i> (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press."},"extern":"1","arxiv":1,"abstract":[{"lang":"eng","text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions."}],"type":"conference","year":"2017","external_id":{"arxiv":["1702.06457"]},"page":"860-868","conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2017-04-20","end_date":"2017-04-22","location":"Fort Lauderdale, FL, United States"},"date_updated":"2023-09-13T09:49:10Z","oa":1,"date_published":"2017-02-21T00:00:00Z","intvolume":"        54","month":"02","oa_version":"Preprint","publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.06457"}],"date_created":"2023-08-22T14:17:19Z","status":"public","day":"21","volume":54},{"external_id":{"arxiv":["1705.11041"]},"article_processing_charge":"No","department":[{"_id":"FrLo"}],"conference":{"location":"Long Beach, CA, United States","start_date":"2017-12-04","end_date":"2017-12-09","name":"NeurIPS: Neural Information Processing Systems"},"language":[{"iso":"eng"}],"year":"2017","date_published":"2017-05-31T00:00:00Z","month":"05","date_updated":"2023-09-13T08:32:23Z","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Greedy algorithms for cone constrained optimization with convergence guarantees","oa":1,"publication":"Advances in Neural Information Processing Systems","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.11041"}],"oa_version":"Preprint","citation":{"apa":"Locatello, F., Tschannen, M., Rätsch, G., &#38; Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In <i>Advances in Neural Information Processing Systems</i>. Long Beach, CA, United States.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” <i>Advances in Neural Information Processing Systems</i>, 2017.","ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in <i>Advances in Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017.","ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: <i>Advances in Neural Information Processing Systems</i>. ; 2017.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In <i>Advances in Neural Information Processing Systems</i>, 2017."},"publication_identifier":{"isbn":["9781510860964"]},"extern":"1","arxiv":1,"abstract":[{"lang":"eng","text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings."}],"type":"conference","date_created":"2023-08-22T14:17:38Z","_id":"14206","quality_controlled":"1","status":"public","day":"31"},{"publication_status":"published","quality_controlled":"1","_id":"14286","scopus_import":"1","abstract":[{"lang":"eng","text":"The bacteriophage M13 has found frequent applications in nanobiotechnology due to its chemically and genetically tunable protein surface and its ability to self-assemble into colloidal membranes. Additionally, its single-stranded (ss) genome is commonly used as scaffold for DNA origami. Despite the manifold uses of M13, upstream production methods for phage and scaffold ssDNA are underexamined with respect to future industrial usage. Here, the high-cell-density phage production with Escherichia coli as host organism was studied in respect of medium composition, infection time, multiplicity of infection, and specific growth rate. The specific growth rate and the multiplicity of infection were identified as the crucial state variables that influence phage amplification rate on one hand and the concentration of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784."}],"type":"journal_article","publication_identifier":{"issn":["0006-3592"]},"extern":"1","citation":{"short":"B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology and Bioengineering 114 (2017) 777–784.","ista":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering. 114(4), 777–784.","ieee":"B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production,” <i>Biotechnology and Bioengineering</i>, vol. 114, no. 4. Wiley, pp. 777–784, 2017.","ama":"Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. <i>Biotechnology and Bioengineering</i>. 2017;114(4):777-784. doi:<a href=\"https://doi.org/10.1002/bit.26200\">10.1002/bit.26200</a>","chicago":"Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz, and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” <i>Biotechnology and Bioengineering</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/bit.26200\">https://doi.org/10.1002/bit.26200</a>.","apa":"Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., &#38; Weuster-Botz, D. (2017). Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production. <i>Biotechnology and Bioengineering</i>. Wiley. <a href=\"https://doi.org/10.1002/bit.26200\">https://doi.org/10.1002/bit.26200</a>","mla":"Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” <i>Biotechnology and Bioengineering</i>, vol. 114, no. 4, Wiley, 2017, pp. 777–84, doi:<a href=\"https://doi.org/10.1002/bit.26200\">10.1002/bit.26200</a>."},"article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Specific growth rate and multiplicity of infection affect high-cell-density fermentation with bacteriophage M13 for ssDNA production","author":[{"last_name":"Kick","first_name":"Benjamin","full_name":"Kick, Benjamin"},{"full_name":"Hensler, Samantha","first_name":"Samantha","last_name":"Hensler"},{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M"},{"last_name":"Dietz","first_name":"Hendrik","full_name":"Dietz, Hendrik"},{"full_name":"Weuster-Botz, Dirk","last_name":"Weuster-Botz","first_name":"Dirk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","oa_version":"None","publication":"Biotechnology and Bioengineering","doi":"10.1002/bit.26200","status":"public","day":"01","date_created":"2023-09-06T12:08:29Z","volume":114,"pmid":1,"year":"2017","external_id":{"pmid":["27748519"]},"page":"777-784","issue":"4","keyword":["Applied Microbiology and Biotechnology","Bioengineering","Biotechnology"],"date_updated":"2023-11-07T12:36:20Z","date_published":"2017-04-01T00:00:00Z","month":"04","intvolume":"       114"},{"year":"2017","external_id":{"pmid":["28336611"]},"date_updated":"2023-11-07T12:33:05Z","issue":"6331","month":"03","intvolume":"       355","date_published":"2017-03-24T00:00:00Z","article_number":"eaam5488","oa_version":"None","doi":"10.1126/science.aam5488","publication":"Science","date_created":"2023-09-06T12:08:55Z","status":"public","day":"24","pmid":1,"volume":355,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes","author":[{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M"},{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","_id":"14287","quality_controlled":"1","extern":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"citation":{"apa":"Praetorius, F. M., &#38; Dietz, H. (2017). Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aam5488\">https://doi.org/10.1126/science.aam5488</a>","mla":"Praetorius, Florian M., and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” <i>Science</i>, vol. 355, no. 6331, eaam5488, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/science.aam5488\">10.1126/science.aam5488</a>.","ama":"Praetorius FM, Dietz H. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. <i>Science</i>. 2017;355(6331). doi:<a href=\"https://doi.org/10.1126/science.aam5488\">10.1126/science.aam5488</a>","ieee":"F. M. Praetorius and H. Dietz, “Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes,” <i>Science</i>, vol. 355, no. 6331. American Association for the Advancement of Science, 2017.","ista":"Praetorius FM, Dietz H. 2017. Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes. Science. 355(6331), eaam5488.","short":"F.M. Praetorius, H. Dietz, Science 355 (2017).","chicago":"Praetorius, Florian M, and Hendrik Dietz. “Self-Assembly of Genetically Encoded DNA-Protein Hybrid Nanoscale Shapes.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aam5488\">https://doi.org/10.1126/science.aam5488</a>."},"type":"journal_article","abstract":[{"lang":"eng","text":"We describe an approach to bottom-up fabrication that allows integration of the functional diversity of proteins into designed three-dimensional structural frameworks. A set of custom staple proteins based on transcription activator–like effector proteins folds a double-stranded DNA template into a user-defined shape. Each staple protein is designed to recognize and closely link two distinct double-helical DNA sequences at separate positions on the template. We present design rules for constructing megadalton-scale DNA-protein hybrid shapes; introduce various structural motifs, such as custom curvature, corners, and vertices; and describe principles for creating multilayer DNA-protein objects with enhanced rigidity. We demonstrate self-assembly of our hybrid nanostructures in one-pot mixtures that include the genetic information for the designed proteins, the template DNA, RNA polymerase, ribosomes, and cofactors for transcription and translation."}],"scopus_import":"1"},{"pmid":1,"volume":552,"date_created":"2023-09-06T12:14:20Z","day":"07","status":"public","doi":"10.1038/nature24650","publication":"Nature","oa_version":"None","month":"12","intvolume":"       552","date_published":"2017-12-07T00:00:00Z","date_updated":"2023-11-07T12:24:49Z","issue":"7683","page":"84-87","external_id":{"pmid":["29219963"]},"year":"2017","citation":{"chicago":"Praetorius, Florian M, Benjamin Kick, Karl L. Behler, Maximilian N. Honemann, Dirk Weuster-Botz, and Hendrik Dietz. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>.","short":"F.M. Praetorius, B. Kick, K.L. Behler, M.N. Honemann, D. Weuster-Botz, H. Dietz, Nature 552 (2017) 84–87.","ieee":"F. M. Praetorius, B. Kick, K. L. Behler, M. N. Honemann, D. Weuster-Botz, and H. Dietz, “Biotechnological mass production of DNA origami,” <i>Nature</i>, vol. 552, no. 7683. Springer Nature, pp. 84–87, 2017.","ista":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. 2017. Biotechnological mass production of DNA origami. Nature. 552(7683), 84–87.","ama":"Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. Biotechnological mass production of DNA origami. <i>Nature</i>. 2017;552(7683):84-87. doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>","mla":"Praetorius, Florian M., et al. “Biotechnological Mass Production of DNA Origami.” <i>Nature</i>, vol. 552, no. 7683, Springer Nature, 2017, pp. 84–87, doi:<a href=\"https://doi.org/10.1038/nature24650\">10.1038/nature24650</a>.","apa":"Praetorius, F. M., Kick, B., Behler, K. L., Honemann, M. N., Weuster-Botz, D., &#38; Dietz, H. (2017). Biotechnological mass production of DNA origami. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature24650\">https://doi.org/10.1038/nature24650</a>"},"extern":"1","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12. These structures are customizable in that they can be site-specifically functionalized13 or constructed to exhibit machine-like14,15 or logic-gating behaviour16. Their use has been limited to applications that require only small amounts of material (of the order of micrograms), owing to the limitations of current production methods. But many proposed applications, for example as therapeutic agents or in complex materials3,16,17,18,19,20,21,22, could be realized if more material could be used. In DNA origami, a nanostructure is assembled from a very long single-stranded scaffold molecule held in place by many short single-stranded staple oligonucleotides. Only the bacteriophage-derived scaffold molecules are amenable to scalable and efficient mass production23; the shorter staple strands are obtained through costly solid-phase synthesis24 or enzymatic processes25. Here we show that single strands of DNA of virtually arbitrary length and with virtually arbitrary sequences can be produced in a scalable and cost-efficient manner by using bacteriophages to generate single-stranded precursor DNA that contains target strand sequences interleaved with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA for several DNA origami using shaker-flask cultures, and demonstrate end-to-end production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank bioreactor. Our method is compatible with existing DNA origami design frameworks and retains the modularity and addressability of DNA origami objects that are necessary for implementing custom modifications using functional groups. With all of the production and purification steps amenable to scaling, we expect that our method will expand the scope of DNA nanotechnology in many areas of science and technology."}],"_id":"14290","quality_controlled":"1","publication_status":"published","publisher":"Springer Nature","title":"Biotechnological mass production of DNA origami","author":[{"full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"full_name":"Kick, Benjamin","first_name":"Benjamin","last_name":"Kick"},{"full_name":"Behler, Karl L.","first_name":"Karl L.","last_name":"Behler"},{"last_name":"Honemann","first_name":"Maximilian N.","full_name":"Honemann, Maximilian N."},{"first_name":"Dirk","last_name":"Weuster-Botz","full_name":"Weuster-Botz, Dirk"},{"full_name":"Dietz, Hendrik","first_name":"Hendrik","last_name":"Dietz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","language":[{"iso":"eng"}],"article_type":"original"},{"day":"03","status":"public","date_created":"2023-09-06T13:19:10Z","volume":112,"oa_version":"None","publication":"Biophysical Journal","doi":"10.1016/j.bpj.2016.11.171","issue":"3","keyword":["Biophysics"],"date_updated":"2023-11-07T11:28:58Z","article_number":"25a","date_published":"2017-02-03T00:00:00Z","month":"02","intvolume":"       112","year":"2017","quality_controlled":"1","_id":"14308","scopus_import":"1","abstract":[{"text":"Here we describe an approach to bottom-up fabrication with nanometer-precision that allows integrating the functional diversity of proteins in designed three-dimensional structural frameworks. We reimagined the successful DNA origami design principle using a set of custom staple proteins to fold a double-stranded DNA template into a user-defined shape. Each staple protein recognizes two distinct double-helical DNA sequences and can carry additional functionalities. The staple proteins we present here are based on the transcription activator-like (TAL) effector proteins. Due to their repetitive structure these proteins offer a unique programmability that enables us to construct numerous staple proteins targeting any desired DNA sequence. Our approach is general, meaning that many different objects may be created using the same set of rules, and it is modular, because components can be modified or exchanged individually. We present rules for constructing megadalton-scale DNA-protein hybrid nanostructures; introduce important structural motifs, such as curvature, corners, and vertices; describe principles for creating multi-layer DNA-protein objects with enhanced rigidity; and demonstrate the possibility to combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since all components can be encoded genetically, our structures should be amenable to biotechnological mass-production. Moreover, since the target objects can self-assemble at room temperature in near-physiological buffer, our hybrid origami may also provide an attractive method to realize positioning and scaffolding tasks in vivo. We expect our method to find application both in scaffolding protein functionalities and in manipulating the spatial arrangement of genomic DNA.","lang":"eng"}],"type":"journal_article","extern":"1","publication_identifier":{"issn":["0006-3495"]},"citation":{"apa":"Praetorius, F. M., &#38; Dietz, H. (2017). Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>","mla":"Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>, vol. 112, no. 3, 25a, Elsevier, 2017, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>.","short":"F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).","ieee":"F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,” <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier, 2017.","ista":"Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 112(3), 25a.","ama":"Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. 2017;112(3). doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>","chicago":"Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>."},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Genetically encoded DNA-protein hybrid origami","author":[{"full_name":"Praetorius, Florian M","last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Dietz","first_name":"Hendrik","full_name":"Dietz, Hendrik"}],"publisher":"Elsevier","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"publisher":"Springer Nature","author":[{"full_name":"Siavashpouri, M","first_name":"M","last_name":"Siavashpouri"},{"first_name":"CH","last_name":"Wachauf","full_name":"Wachauf, CH"},{"full_name":"Zakhary, MJ","last_name":"Zakhary","first_name":"MJ"},{"full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","last_name":"Praetorius"},{"first_name":"H","last_name":"Dietz","full_name":"Dietz, H"},{"full_name":"Dogic, Z","last_name":"Dogic","first_name":"Z"}],"title":"Molecular engineering of chiral colloidal liquid crystals using DNA origami","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","arxiv":1,"abstract":[{"lang":"eng","text":"Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials."}],"publication_identifier":{"eissn":["1476-4660"],"issn":["1476-1122"]},"extern":"1","citation":{"ama":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular engineering of chiral colloidal liquid crystals using DNA origami. <i>Nature Materials</i>. 2017;16(8):849-856. doi:<a href=\"https://doi.org/10.1038/nmat4909\">10.1038/nmat4909</a>","ieee":"M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z. Dogic, “Molecular engineering of chiral colloidal liquid crystals using DNA origami,” <i>Nature Materials</i>, vol. 16, no. 8. Springer Nature, pp. 849–856, 2017.","short":"M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic, Nature Materials 16 (2017) 849–856.","ista":"Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017. Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials. 16(8), 849–856.","chicago":"Siavashpouri, M, CH Wachauf, MJ Zakhary, Florian M Praetorius, H Dietz, and Z Dogic. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” <i>Nature Materials</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nmat4909\">https://doi.org/10.1038/nmat4909</a>.","apa":"Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &#38; Dogic, Z. (2017). Molecular engineering of chiral colloidal liquid crystals using DNA origami. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nmat4909\">https://doi.org/10.1038/nmat4909</a>","mla":"Siavashpouri, M., et al. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using DNA Origami.” <i>Nature Materials</i>, vol. 16, no. 8, Springer Nature, 2017, pp. 849–56, doi:<a href=\"https://doi.org/10.1038/nmat4909\">10.1038/nmat4909</a>."},"quality_controlled":"1","_id":"14309","publication_status":"published","intvolume":"        16","month":"05","date_published":"2017-05-22T00:00:00Z","issue":"8","oa":1,"date_updated":"2023-11-07T11:40:00Z","external_id":{"arxiv":["1705.08944"],"pmid":["28530665"]},"page":"849-856","year":"2017","pmid":1,"volume":16,"status":"public","day":"22","date_created":"2023-09-06T13:37:27Z","doi":"10.1038/nmat4909","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1705.08944"}],"publication":"Nature Materials","oa_version":"Preprint"},{"article_processing_charge":"No","year":"2017","article_type":"original","language":[{"iso":"eng"}],"article_number":"155102","publisher":"American Physical Society","month":"10","intvolume":"        96","date_published":"2017-10-01T00:00:00Z","issue":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"In-plane magnetic anisotropy in strontium iridate Sr2IrO4","author":[{"full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846","last_name":"Nauman","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad"},{"first_name":"Yunjeong","last_name":"Hong","full_name":"Hong, Yunjeong"},{"last_name":"Hussain","first_name":"Tayyaba","full_name":"Hussain, Tayyaba"},{"first_name":"M. S.","last_name":"Seo","full_name":"Seo, M. S."},{"full_name":"Park, S. Y.","last_name":"Park","first_name":"S. Y."},{"full_name":"Lee, N.","last_name":"Lee","first_name":"N."},{"full_name":"Choi, Y. J.","last_name":"Choi","first_name":"Y. J."},{"full_name":"Kang, Woun","first_name":"Woun","last_name":"Kang"},{"full_name":"Jo, Younjung","first_name":"Younjung","last_name":"Jo"}],"date_updated":"2021-02-03T12:53:00Z","publication_status":"published","doi":"10.1103/physrevb.96.155102","publication":"Physical Review B","oa_version":"None","type":"journal_article","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_identifier":{"issn":["2469-9950","2469-9969"]},"extern":"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>.","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>.","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>","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.","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).","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."},"volume":96,"day":"01","status":"public","quality_controlled":"1","_id":"9065","date_created":"2021-02-02T15:49:21Z"},{"volume":124,"status":"public","day":"01","date_created":"2018-12-11T11:49:09Z","main_file_link":[{"url":"https://arxiv.org/abs/1605.07997","open_access":"1"}],"doi":"10.4169/amer.math.monthly.124.7.588","publication":"The American Mathematical Monthly","isi":1,"oa_version":"Submitted Version","ec_funded":1,"month":"01","intvolume":"       124","date_published":"2017-01-01T00:00:00Z","issue":"7","oa":1,"date_updated":"2023-10-17T11:24:57Z","page":"588 - 596","external_id":{"isi":["000413947300002"],"arxiv":["1605.07997"]},"year":"2017","type":"journal_article","scopus_import":"1","arxiv":1,"abstract":[{"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.","lang":"eng"}],"publication_identifier":{"issn":["00029890"]},"citation":{"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>.","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.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","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.","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>","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>.","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>"},"quality_controlled":"1","_id":"909","publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"publisher":"Mathematical Association of America","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","last_name":"Akopyan"},{"first_name":"Vladislav","last_name":"Vysotsky","full_name":"Vysotsky, Vladislav"}],"title":"On the lengths of curves passing through boundary points of a planar convex shape","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"publist_id":"6534","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}]},{"publisher":"Genetics Society of America","has_accepted_license":"1","file":[{"file_id":"5264","content_type":"application/pdf","file_size":494268,"creator":"system","relation":"main_file","checksum":"f7c32dabf52e6d9e709d9203761e39fd","access_level":"open_access","file_name":"IST-2018-974-v1+1_manuscript.pdf","date_created":"2018-12-12T10:17:12Z","date_updated":"2020-07-14T12:48:15Z"}],"author":[{"orcid":"0000-0002-2519-824X","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"}],"title":"When does frequency-independent selection maintain genetic variation?","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"publist_id":"6533","article_processing_charge":"No","pubrep_id":"974","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:15Z","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"}],"scopus_import":"1","citation":{"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.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","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>","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>.","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>"},"quality_controlled":"1","_id":"910","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"month":"10","intvolume":"       207","date_published":"2017-10-01T00:00:00Z","issue":"2","oa":1,"date_updated":"2023-09-26T15:49:15Z","external_id":{"isi":["000412232600019"]},"page":"653 - 668","year":"2017","volume":207,"status":"public","day":"01","date_created":"2018-12-11T11:49:09Z","ddc":["576"],"doi":"10.1534/genetics.117.300129","publication":"Genetics","isi":1,"ec_funded":1,"oa_version":"Submitted Version"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"ChLa"}],"publist_id":"6532","author":[{"full_name":"Royer, Amélie","orcid":"0000-0002-8407-0705","last_name":"Royer","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie"},{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"}],"title":"Probabilistic image colorization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","access_level":"open_access","file_size":1625363,"creator":"dernst","content_type":"application/pdf","file_id":"8224","date_created":"2020-08-10T07:14:33Z","date_updated":"2020-08-10T07:14:33Z","file_name":"2017_BMVC_Royer.pdf","success":1}],"has_accepted_license":"1","publisher":"BMVA Press","project":[{"grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"publication_status":"published","_id":"911","quality_controlled":"1","publication_identifier":{"eisbn":["190172560X"]},"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>.","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>","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>.","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","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>"},"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"}],"scopus_import":"1","arxiv":1,"file_date_updated":"2020-08-10T07:14:33Z","type":"conference","year":"2017","page":"85.1-85.12","external_id":{"arxiv":["1705.04258"]},"conference":{"location":"London, United Kingdom","name":"BMVC: British Machine Vision Conference","end_date":"2017-09-07","start_date":"2017-09-04"},"date_updated":"2023-10-16T10:04:02Z","oa":1,"date_published":"2017-09-01T00:00:00Z","month":"09","related_material":{"record":[{"id":"8390","relation":"dissertation_contains","status":"public"}]},"oa_version":"Published Version","ec_funded":1,"doi":"10.5244/c.31.85","date_created":"2018-12-11T11:49:09Z","ddc":["000"],"day":"01","status":"public"},{"publisher":"AIP Publishing","title":"A lower bound for the BCS functional with boundary conditions at infinity","author":[{"full_name":"Deuchert, Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0003-3146-6746","last_name":"Deuchert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"6531","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"citation":{"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>","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>.","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>","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity.  Journal of Mathematical Physics. 58(8), 081901.","short":"A. Deuchert,  Journal of Mathematical Physics 58 (2017).","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.","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>."},"publication_identifier":{"issn":["00222488"]},"abstract":[{"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","lang":"eng"}],"scopus_import":"1","type":"journal_article","_id":"912","quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","date_published":"2017-08-01T00:00:00Z","intvolume":"        58","month":"08","article_number":"081901","date_updated":"2024-02-28T13:07:56Z","oa":1,"issue":"8","external_id":{"isi":["000409197200015"]},"year":"2017","volume":58,"date_created":"2018-12-11T11:49:10Z","status":"public","day":"01","publication":" Journal of Mathematical Physics","doi":"10.1063/1.4996580","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.04616"}],"ec_funded":1,"oa_version":"Submitted Version","isi":1},{"year":"2017","page":"1283-1305","issue":"6","oa":1,"date_updated":"2022-01-24T12:41:45Z","keyword":["Geochemistry and Petrology","Geophysics"],"intvolume":"        38","month":"11","date_published":"2017-11-14T00:00:00Z","oa_version":"Published Version","doi":"10.1007/s10712-017-9447-x","main_file_link":[{"url":"https://doi.org/10.1007/s10712-017-9447-x","open_access":"1"}],"publication":"Surveys in Geophysics","status":"public","day":"14","date_created":"2021-02-15T14:20:07Z","volume":38,"article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Zuidema","first_name":"Paquita","full_name":"Zuidema, Paquita"},{"first_name":"Giuseppe","last_name":"Torri","full_name":"Torri, Giuseppe"},{"full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","orcid":"0000-0001-5836-5350"},{"full_name":"Chandra, Arunchandra","first_name":"Arunchandra","last_name":"Chandra"}],"publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","_id":"9137","type":"journal_article","abstract":[{"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.","lang":"eng"}],"extern":"1","publication_identifier":{"issn":["0169-3298","1573-0956"]},"citation":{"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>.","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>","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>.","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.","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.","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."}},{"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Observing convective aggregation","author":[{"last_name":"Holloway","first_name":"Christopher E.","full_name":"Holloway, Christopher E."},{"full_name":"Wing, Allison A.","last_name":"Wing","first_name":"Allison A."},{"first_name":"Sandrine","last_name":"Bony","full_name":"Bony, Sandrine"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"},{"full_name":"Masunaga, Hirohiko","last_name":"Masunaga","first_name":"Hirohiko"},{"full_name":"L’Ecuyer, Tristan S.","last_name":"L’Ecuyer","first_name":"Tristan S."},{"last_name":"Turner","first_name":"David D.","full_name":"Turner, David D."},{"full_name":"Zuidema, Paquita","last_name":"Zuidema","first_name":"Paquita"}],"publisher":"Springer Nature","publication_status":"published","_id":"9138","quality_controlled":"1","publication_identifier":{"issn":["0169-3298","1573-0956"]},"extern":"1","citation":{"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.","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.","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>","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>.","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>"},"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."}],"type":"journal_article","year":"2017","page":"1199-1236","keyword":["Geochemistry and Petrology","Geophysics"],"date_updated":"2022-01-24T12:43:13Z","oa":1,"issue":"6","date_published":"2017-11-01T00:00:00Z","intvolume":"        38","month":"11","oa_version":"Published Version","publication":"Surveys in Geophysics","doi":"10.1007/s10712-017-9419-1","main_file_link":[{"url":"https://doi.org/10.1007/s10712-017-9419-1","open_access":"1"}],"date_created":"2021-02-15T14:20:38Z","day":"01","status":"public","volume":38},{"article_processing_charge":"No","page":"1173-1197","article_type":"original","year":"2017","language":[{"iso":"eng"}],"publisher":"Springer Nature","date_published":"2017-11-01T00:00:00Z","intvolume":"        38","month":"11","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Convective self-aggregation in numerical simulations: A review","author":[{"full_name":"Wing, Allison A.","first_name":"Allison A.","last_name":"Wing"},{"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","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","last_name":"Muller","full_name":"Muller, Caroline J"}],"issue":"6","keyword":["Geochemistry and Petrology","Geophysics"],"date_updated":"2022-01-24T12:42:36Z","publication":"Surveys in Geophysics","doi":"10.1007/s10712-017-9408-4","publication_status":"published","oa_version":"None","abstract":[{"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.","lang":"eng"}],"type":"journal_article","volume":38,"citation":{"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.","short":"A.A. Wing, K. Emanuel, C.E. Holloway, C.J. Muller, Surveys in Geophysics 38 (2017) 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.","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>","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>","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>."},"publication_identifier":{"issn":["0169-3298","1573-0956"]},"extern":"1","quality_controlled":"1","day":"01","status":"public","_id":"9139","date_created":"2021-02-15T14:20:56Z"},{"article_number":"170547","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","intvolume":"         4","month":"07","date_published":"2017-07-05T00:00:00Z","issue":"7","oa":1,"date_updated":"2023-09-26T15:45:47Z","external_id":{"isi":["000406670000025"]},"year":"2017","volume":4,"day":"05","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:49:10Z","ddc":["576","592"],"doi":"10.1098/rsos.170547","publication":"Royal Society Open Science","isi":1,"oa_version":"Published Version","related_material":{"record":[{"id":"9853","relation":"research_data","status":"public"}]},"publisher":"Royal Society, The","has_accepted_license":"1","file":[{"access_level":"open_access","checksum":"351ae5e7a37e6e7d9295cd41146c4190","relation":"main_file","file_id":"4684","content_type":"application/pdf","creator":"system","file_size":530412,"date_created":"2018-12-12T10:08:24Z","date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf"}],"title":"Ant queens increase their reproductive efforts after pathogen infection","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Giehr, Julia","last_name":"Giehr","first_name":"Julia"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"last_name":"Schrempf","first_name":"Alexandra","full_name":"Schrempf, Alexandra"}],"publist_id":"6527","department":[{"_id":"SyCr"}],"article_processing_charge":"No","pubrep_id":"849","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:15Z","scopus_import":"1","abstract":[{"lang":"eng","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."}],"publication_identifier":{"issn":["20545703"]},"citation":{"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>.","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).","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.","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.","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>.","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>"},"quality_controlled":"1","_id":"914","publication_status":"published"},{"doi":"10.1109/CVPR.2017.530","ec_funded":1,"oa_version":"Submitted Version","isi":1,"volume":2017,"day":"01","status":"public","ddc":["000"],"date_created":"2018-12-11T11:49:11Z","conference":{"start_date":"2017-07-21","end_date":"2017-07-26","name":"CVPR: Computer Vision and Pattern Recognition","location":"Honolulu, HA, United States"},"external_id":{"isi":["000418371405009"]},"page":"4990-4999","year":"2017","date_published":"2017-07-01T00:00:00Z","month":"07","intvolume":"      2017","oa":1,"date_updated":"2023-09-26T15:43:27Z","publication_status":"published","project":[{"grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"abstract":[{"lang":"eng","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."}],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:15Z","type":"conference","publication_identifier":{"isbn":["978-153860457-1"]},"citation":{"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.","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.","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.","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>","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>.","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>"},"quality_controlled":"1","_id":"915","publist_id":"6526","department":[{"_id":"VlKo"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"IEEE","has_accepted_license":"1","title":"A message passing algorithm for the minimum cost multicut problem","author":[{"last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul"},{"full_name":"Andres, Bjoern","last_name":"Andres","first_name":"Bjoern"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"7e51dacefa693574581a32da3eff63dc","relation":"main_file","access_level":"open_access","file_size":883264,"creator":"dernst","file_id":"5849","content_type":"application/pdf","date_created":"2019-01-18T12:52:46Z","date_updated":"2020-07-14T12:48:15Z","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf"}]},{"publication_status":"published","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"}],"type":"journal_article","publication_identifier":{"issn":["0022-3670","1520-0485"]},"citation":{"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>","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>.","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.","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.","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>","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>."},"extern":"1","quality_controlled":"1","_id":"9152","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"American Meteorological Society","title":"Impact of a mean current on the internal tide energy dissipation at the critical latitude","author":[{"last_name":"Richet","first_name":"O.","full_name":"Richet, O."},{"full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350","last_name":"Muller"},{"full_name":"Chomaz, J.-M.","last_name":"Chomaz","first_name":"J.-M."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"Journal of Physical Oceanography","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"}],"oa_version":"Published Version","volume":47,"day":"01","status":"public","date_created":"2021-02-15T15:11:04Z","page":"1457-1472","year":"2017","date_published":"2017-06-01T00:00:00Z","intvolume":"        47","month":"06","oa":1,"issue":"6","keyword":["Oceanography"],"date_updated":"2022-01-24T13:36:31Z"},{"_id":"916","quality_controlled":"1","publication_identifier":{"isbn":["978-153860457-1"]},"citation":{"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>.","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>","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>.","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>","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.","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","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."},"type":"conference","file_date_updated":"2020-07-14T12:48:15Z","scopus_import":"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."}],"project":[{"call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","file":[{"creator":"dernst","file_size":944332,"file_id":"5848","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"e38a2740daad1ea178465843b5072906","file_name":"2017_CVPR_Swoboda2.pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-01-18T12:49:38Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","author":[{"full_name":"Swoboda, Paul","last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"first_name":"Carsten","last_name":"Abu Alhaija","full_name":"Abu Alhaija, Carsten"},{"full_name":"Kainmueller, Dagmar","last_name":"Kainmueller","first_name":"Dagmar"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"has_accepted_license":"1","publisher":"IEEE","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"VlKo"}],"publist_id":"6525","ddc":["000"],"date_created":"2018-12-11T11:49:11Z","status":"public","day":"01","volume":2017,"isi":1,"ec_funded":1,"oa_version":"Submitted Version","doi":"10.1109/CVPR.2017.747","date_updated":"2023-09-26T15:41:40Z","oa":1,"intvolume":"      2017","month":"01","date_published":"2017-01-01T00:00:00Z","year":"2017","external_id":{"isi":["000418371407018"]},"page":"7062-7071","conference":{"location":"Honolulu, HA, United States","end_date":"2017-07-26","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition"}},{"article_processing_charge":"No","page":"81-89","article_type":"original","year":"2017","language":[{"iso":"eng"}],"publisher":"Elsevier","date_published":"2017-07-01T00:00:00Z","month":"07","intvolume":"        30","title":"Eppur si muove, and yet it moves: Patchy (phoretic) swimmers","author":[{"full_name":"Aubret, A.","first_name":"A.","last_name":"Aubret"},{"last_name":"Ramananarivo","first_name":"S.","full_name":"Ramananarivo, S."},{"full_name":"Palacci, Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","date_updated":"2021-02-22T09:32:11Z","publication":"Current Opinion in Colloid & Interface Science","doi":"10.1016/j.cocis.2017.05.007","publication_status":"published","oa_version":"None","scopus_import":"1","abstract":[{"lang":"eng","text":"Advances in colloidal synthesis allow for the design of particles with controlled patches. This article reviews routes towards colloidal locomotion, where energy is consumed and converted into motion, and its implementation with active patchy particles. A special emphasis is given to phoretic swimmers, where the self-propulsion originates from an interfacial phenomenon, raising experimental challenges and opening up opportunities for particles with controlled anisotropic surface chemistry and novel behaviors."}],"type":"journal_article","volume":30,"extern":"1","publication_identifier":{"issn":["1359-0294"]},"citation":{"chicago":"Aubret, A., S. Ramananarivo, and Jérémie A Palacci. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.” <i>Current Opinion in Colloid &#38; Interface Science</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.cocis.2017.05.007\">https://doi.org/10.1016/j.cocis.2017.05.007</a>.","ista":"Aubret A, Ramananarivo S, Palacci JA. 2017. Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. Current Opinion in Colloid &#38; Interface Science. 30, 81–89.","short":"A. Aubret, S. Ramananarivo, J.A. Palacci, Current Opinion in Colloid &#38; Interface Science 30 (2017) 81–89.","ieee":"A. Aubret, S. Ramananarivo, and J. A. Palacci, “Eppur si muove, and yet it moves: Patchy (phoretic) swimmers,” <i>Current Opinion in Colloid &#38; Interface Science</i>, vol. 30. Elsevier, pp. 81–89, 2017.","ama":"Aubret A, Ramananarivo S, Palacci JA. Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. <i>Current Opinion in Colloid &#38; Interface Science</i>. 2017;30:81-89. doi:<a href=\"https://doi.org/10.1016/j.cocis.2017.05.007\">10.1016/j.cocis.2017.05.007</a>","mla":"Aubret, A., et al. “Eppur Si Muove, and yet It Moves: Patchy (Phoretic) Swimmers.” <i>Current Opinion in Colloid &#38; Interface Science</i>, vol. 30, Elsevier, 2017, pp. 81–89, doi:<a href=\"https://doi.org/10.1016/j.cocis.2017.05.007\">10.1016/j.cocis.2017.05.007</a>.","apa":"Aubret, A., Ramananarivo, S., &#38; Palacci, J. A. (2017). Eppur si muove, and yet it moves: Patchy (phoretic) swimmers. <i>Current Opinion in Colloid &#38; Interface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cocis.2017.05.007\">https://doi.org/10.1016/j.cocis.2017.05.007</a>"},"quality_controlled":"1","day":"01","status":"public","_id":"9165","date_created":"2021-02-18T14:29:42Z"}]